From 3e14599c6fdfca67bacc75d142577d2c3c723272 Mon Sep 17 00:00:00 2001 From: jkane Date: Sat, 13 Dec 2025 05:59:35 -0600 Subject: [PATCH 01/28] **chore(variants): Remove unused legacy variant group and alias code** - Deleted templates, models, repositories, and controllers related to old variant group and alias handling. - Refactored dependent views and logic to remove references to deprecated components. - Cleaned up accompanying documentation and comments. --- app/controllers/CuratorController.scala | 311 ++------ app/controllers/VariantApiController.scala | 255 +++---- .../VariantBrowserController.scala | 48 +- app/controllers/VariantController.scala | 30 - .../VariantPublicApiController.scala | 2 +- app/models/dal/DatabaseSchema.scala | 12 +- .../genomics/BiosampleVariantCall.scala | 97 +++ .../dal/domain/genomics/BranchMutation.scala | 93 +++ .../genomics/HaplogroupCharacterState.scala | 92 +++ .../dal/domain/genomics/StrMutationRate.scala | 145 ++++ app/models/dal/domain/genomics/Variant.scala | 25 - .../dal/domain/genomics/VariantAlias.scala | 43 -- .../domain/genomics/VariantAliasTable.scala | 33 - .../dal/domain/genomics/VariantV2Table.scala | 86 +++ .../dal/domain/genomics/VariantsTable.scala | 62 -- .../haplogroups/HaplogroupVariantsTable.scala | 6 +- app/models/domain/genomics/MutationType.scala | 94 +++ app/models/domain/genomics/NamingStatus.scala | 60 ++ app/models/domain/genomics/VariantGroup.scala | 84 --- app/models/domain/genomics/VariantV2.scala | 257 +++++++ .../domain/genomics/VariantWithContig.scala | 27 - app/modules/BaseModule.scala | 3 +- .../GenomeRegionsRepository.scala | 55 +- .../HaplogroupCoreRepository.scala | 8 +- .../HaplogroupVariantRepository.scala | 196 +++-- app/repositories/VariantAliasRepository.scala | 260 ------- app/repositories/VariantRepository.scala | 530 ------------- app/repositories/VariantV2Repository.scala | 705 ++++++++++++++++++ app/services/CuratorAuditService.scala | 30 +- app/services/HaplogroupTreeMergeService.scala | 25 +- app/services/HaplogroupTreeService.scala | 223 ++---- app/services/TreeImporter.scala | 246 +++--- app/services/TreeRestructuringService.scala | 67 +- app/services/VariantExportService.scala | 280 ++++--- app/services/VariantPublicApiService.scala | 171 ++--- .../YBrowseVariantIngestionService.scala | 358 ++++----- app/views/_navbar.scala.html | 2 - .../components/variantAliases.scala.html | 33 - app/views/components/variantBuilds.scala.html | 62 -- .../haplogroups/detailPanel.scala.html | 6 +- .../haplogroups/mergeConfirmForm.scala.html | 12 +- .../haplogroups/splitBranchForm.scala.html | 65 +- .../variantSearchResults.scala.html | 67 +- .../haplogroups/variantsPanel.scala.html | 62 +- .../curator/variants/detailPanel.scala.html | 151 +++- .../curator/variants/editGroupForm.scala.html | 156 ---- app/views/curator/variants/list.scala.html | 6 +- .../curator/variants/listFragment.scala.html | 74 +- app/views/variants/browser.scala.html | 6 +- app/views/variants/detailPanel.scala.html | 154 +++- app/views/variants/listFragment.scala.html | 57 +- conf/evolutions/default/53.sql | 251 +++++++ conf/routes | 14 +- scripts/migrate_variant_to_v2.sql | 164 ++++ .../HaplogroupTreeMergeServiceSpec.scala | 16 +- 55 files changed, 3537 insertions(+), 2840 deletions(-) delete mode 100644 app/controllers/VariantController.scala create mode 100644 app/models/dal/domain/genomics/BiosampleVariantCall.scala create mode 100644 app/models/dal/domain/genomics/BranchMutation.scala create mode 100644 app/models/dal/domain/genomics/HaplogroupCharacterState.scala create mode 100644 app/models/dal/domain/genomics/StrMutationRate.scala delete mode 100644 app/models/dal/domain/genomics/Variant.scala delete mode 100644 app/models/dal/domain/genomics/VariantAlias.scala delete mode 100644 app/models/dal/domain/genomics/VariantAliasTable.scala create mode 100644 app/models/dal/domain/genomics/VariantV2Table.scala delete mode 100644 app/models/dal/domain/genomics/VariantsTable.scala create mode 100644 app/models/domain/genomics/MutationType.scala create mode 100644 app/models/domain/genomics/NamingStatus.scala delete mode 100644 app/models/domain/genomics/VariantGroup.scala create mode 100644 app/models/domain/genomics/VariantV2.scala delete mode 100644 app/models/domain/genomics/VariantWithContig.scala delete mode 100644 app/repositories/VariantAliasRepository.scala delete mode 100644 app/repositories/VariantRepository.scala create mode 100644 app/repositories/VariantV2Repository.scala delete mode 100644 app/views/components/variantAliases.scala.html delete mode 100644 app/views/components/variantBuilds.scala.html delete mode 100644 app/views/curator/variants/editGroupForm.scala.html create mode 100644 conf/evolutions/default/53.sql create mode 100644 scripts/migrate_variant_to_v2.sql diff --git a/app/controllers/CuratorController.scala b/app/controllers/CuratorController.scala index 4991084..bc678f6 100644 --- a/app/controllers/CuratorController.scala +++ b/app/controllers/CuratorController.scala @@ -3,8 +3,7 @@ package controllers import actions.{AuthenticatedAction, AuthenticatedRequest, PermissionAction} import jakarta.inject.{Inject, Singleton} import models.HaplogroupType -import models.dal.domain.genomics.Variant -import models.domain.genomics.{VariantGroup, VariantWithContig} +import models.domain.genomics.VariantV2 import models.domain.haplogroups.Haplogroup import org.webjars.play.WebJarsUtil import play.api.Logging @@ -12,7 +11,7 @@ import play.api.data.Form import play.api.data.Forms.* import play.api.i18n.I18nSupport import play.api.mvc.* -import repositories.{GenbankContigRepository, HaplogroupCoreRepository, HaplogroupVariantRepository, VariantAliasRepository, VariantRepository} +import repositories.{GenbankContigRepository, HaplogroupCoreRepository, HaplogroupVariantRepository, VariantV2Repository} import services.{CuratorAuditService, TreeRestructuringService} import services.genomics.YBrowseVariantIngestionService @@ -62,7 +61,7 @@ case class SplitBranchFormData( description: Option[String], source: String, confidenceLevel: String, - variantGroupKeys: Seq[String], + variantIds: Seq[Int], childIds: Seq[Int] ) @@ -72,8 +71,7 @@ class CuratorController @Inject()( authenticatedAction: AuthenticatedAction, permissionAction: PermissionAction, haplogroupRepository: HaplogroupCoreRepository, - variantRepository: VariantRepository, - variantAliasRepository: VariantAliasRepository, + variantV2Repository: VariantV2Repository, haplogroupVariantRepository: HaplogroupVariantRepository, genbankContigRepository: GenbankContigRepository, auditService: CuratorAuditService, @@ -124,9 +122,9 @@ class CuratorController @Inject()( "description" -> optional(text(maxLength = 2000)), "source" -> nonEmptyText(1, 100), "confidenceLevel" -> nonEmptyText(1, 50), - "variantGroupKeys" -> seq(text), + "variantIds" -> seq(number), "childIds" -> seq(number) - )(SplitBranchFormData.apply)(s => Some((s.name, s.lineage, s.description, s.source, s.confidenceLevel, s.variantGroupKeys, s.childIds))) + )(SplitBranchFormData.apply)(s => Some((s.name, s.lineage, s.description, s.source, s.confidenceLevel, s.variantIds, s.childIds))) ) private val createHaplogroupFormMapping: Form[CreateHaplogroupFormData] = Form( @@ -148,7 +146,7 @@ class CuratorController @Inject()( for { yCount <- haplogroupRepository.countByType(HaplogroupType.Y) mtCount <- haplogroupRepository.countByType(HaplogroupType.MT) - variantCount <- variantRepository.count(None) + variantCount <- variantV2Repository.count(None) } yield { Ok(views.html.curator.dashboard(yCount, mtCount, variantCount)) } @@ -199,11 +197,9 @@ class CuratorController @Inject()( variants <- haplogroupVariantRepository.getHaplogroupVariants(id) history <- auditService.getHaplogroupHistory(id) } yield { - val variantsWithContig = variants.map { case (v, c) => VariantWithContig(v, c) } - val variantGroups = variantRepository.groupVariants(variantsWithContig) haplogroupOpt match { case Some(haplogroup) => - Ok(views.html.curator.haplogroups.detailPanel(haplogroup, parentOpt, children, variantGroups, history)) + Ok(views.html.curator.haplogroups.detailPanel(haplogroup, parentOpt, children, variants, history)) case None => NotFound("Haplogroup not found") } @@ -436,10 +432,10 @@ class CuratorController @Inject()( withPermission("variant.view").async { implicit request => val offset = (page - 1) * pageSize for { - (variantGroups, totalCount) <- variantRepository.searchGroupedPaginated(query.getOrElse(""), offset, pageSize) + (variants, totalCount) <- variantV2Repository.searchPaginated(query.getOrElse(""), offset, pageSize) } yield { val totalPages = Math.max(1, (totalCount + pageSize - 1) / pageSize) - Ok(views.html.curator.variants.list(variantGroups, query, page, totalPages, pageSize, totalCount)) + Ok(views.html.curator.variants.list(variants, query, page, totalPages, pageSize, totalCount)) } } @@ -447,237 +443,89 @@ class CuratorController @Inject()( withPermission("variant.view").async { implicit request => val offset = (page - 1) * pageSize for { - (variantGroups, totalCount) <- variantRepository.searchGroupedPaginated(query.getOrElse(""), offset, pageSize) + (variants, totalCount) <- variantV2Repository.searchPaginated(query.getOrElse(""), offset, pageSize) } yield { val totalPages = Math.max(1, (totalCount + pageSize - 1) / pageSize) - Ok(views.html.curator.variants.listFragment(variantGroups, query, page, totalPages, pageSize, totalCount)) + Ok(views.html.curator.variants.listFragment(variants, query, page, totalPages, pageSize, totalCount)) } } def variantDetailPanel(id: Int): Action[AnyContent] = withPermission("variant.view").async { implicit request => for { - variantOpt <- variantRepository.findByIdWithContig(id) - // Get all variants in the same group - allVariantsInGroup <- variantOpt match { - case Some(vwc) => - val groupKey = vwc.variant.commonName.orElse(vwc.variant.rsId).getOrElse(s"variant_${id}") - variantRepository.getVariantsByGroupKey(groupKey) - case None => Future.successful(Seq.empty) - } - // Fetch aliases for this variant - aliases <- variantAliasRepository.findByVariantId(id) + variantOpt <- variantV2Repository.findById(id) haplogroups <- haplogroupVariantRepository.getHaplogroupsByVariant(id) history <- auditService.getVariantHistory(id) } yield { variantOpt match { - case Some(variantWithContig) => - val variantGroup = variantRepository.groupVariants(allVariantsInGroup).headOption - Ok(views.html.curator.variants.detailPanel(variantWithContig, variantGroup, aliases, haplogroups, history)) + case Some(variant) => + Ok(views.html.curator.variants.detailPanel(variant, haplogroups, history)) case None => NotFound("Variant not found") } } } + // TODO: Redesign variant creation for VariantV2 with JSONB coordinates def createVariantForm: Action[AnyContent] = withPermission("variant.create").async { implicit request => - genbankContigRepository.getYAndMtContigs.map { contigs => - Ok(views.html.curator.variants.createForm(variantForm, contigs)) - } + Future.successful( + Redirect(routes.CuratorController.listVariants(None, 1, 20)) + .flashing("warning" -> "Variant creation is being updated for the new schema. Use YBrowse ingestion for now.") + ) } + // TODO: Redesign variant creation for VariantV2 with JSONB coordinates def createVariant: Action[AnyContent] = withPermission("variant.create").async { implicit request => - variantForm.bindFromRequest().fold( - formWithErrors => { - genbankContigRepository.getYAndMtContigs.map { contigs => - BadRequest(views.html.curator.variants.createForm(formWithErrors, contigs)) - } - }, - data => { - val variant = Variant( - variantId = None, - genbankContigId = data.genbankContigId, - position = data.position, - referenceAllele = data.referenceAllele, - alternateAllele = data.alternateAllele, - variantType = data.variantType, - rsId = data.rsId, - commonName = data.commonName - ) - - for { - // Create the source variant - newId <- variantRepository.createVariant(variant) - createdVariant = variant.copy(variantId = Some(newId)) - _ <- auditService.logVariantCreate(request.user.id.get, createdVariant, Some("Created via curator interface")) - - // Get the source contig for liftover - sourceContigOpt <- genbankContigRepository.findById(data.genbankContigId) - - // Attempt liftover to other reference genomes - liftedCount <- sourceContigOpt match { - case Some(sourceContig) => - variantIngestionService.liftoverVariant(createdVariant, sourceContig).flatMap { liftedVariants => - if (liftedVariants.nonEmpty) { - logger.info(s"Lifting variant ${data.commonName.getOrElse("unnamed")} to ${liftedVariants.size} other reference(s)") - // Create or find each lifted variant - variantRepository.findOrCreateVariantsBatch(liftedVariants).map(_.size) - } else { - Future.successful(0) - } - } - case None => - logger.warn(s"Source contig ${data.genbankContigId} not found for liftover") - Future.successful(0) - } - } yield { - val message = if (liftedCount > 0) { - s"Variant created successfully. Also lifted to $liftedCount other reference genome(s)." - } else { - s"Variant created successfully. (Liftover to other references not available or failed)" - } - Redirect(routes.CuratorController.listVariants(None, 1, 20)) - .flashing("success" -> message) - } - } + Future.successful( + Redirect(routes.CuratorController.listVariants(None, 1, 20)) + .flashing("warning" -> "Variant creation is being updated for the new schema.") ) } + // TODO: Redesign variant editing for VariantV2 with JSONB coordinates def editVariantForm(id: Int): Action[AnyContent] = withPermission("variant.update").async { implicit request => - variantRepository.findByIdWithContig(id).map { - case Some(vwc) => - val variant = vwc.variant - val formData = VariantFormData( - genbankContigId = variant.genbankContigId, - position = variant.position, - referenceAllele = variant.referenceAllele, - alternateAllele = variant.alternateAllele, - variantType = variant.variantType, - rsId = variant.rsId, - commonName = variant.commonName - ) - // Display contig as "accession (commonName / refGenome)" e.g., "CP068255.2 (chrX / hs1)" - val contigDisplay = s"${vwc.contig.accession} (${vwc.contig.commonName.getOrElse("?")} / ${vwc.contig.referenceGenome.getOrElse("?")})" - Ok(views.html.curator.variants.editForm(id, variantForm.fill(formData), contigDisplay)) - case None => - NotFound("Variant not found") - } + Future.successful( + Redirect(routes.CuratorController.listVariants(None, 1, 20)) + .flashing("warning" -> "Variant editing is being updated for the new schema.") + ) } + // TODO: Redesign variant editing for VariantV2 with JSONB coordinates def updateVariant(id: Int): Action[AnyContent] = withPermission("variant.update").async { implicit request => - variantRepository.findByIdWithContig(id).flatMap { - case Some(vwc) => - val oldVariant = vwc.variant - val contigDisplay = s"${vwc.contig.accession} (${vwc.contig.commonName.getOrElse("?")} / ${vwc.contig.referenceGenome.getOrElse("?")})" - variantForm.bindFromRequest().fold( - formWithErrors => { - Future.successful(BadRequest(views.html.curator.variants.editForm(id, formWithErrors, contigDisplay))) - }, - data => { - val updatedVariant = oldVariant.copy( - variantType = data.variantType, - rsId = data.rsId, - commonName = data.commonName - ) - - for { - updated <- variantRepository.update(updatedVariant) - _ <- if (updated) { - auditService.logVariantUpdate(request.user.id.get, oldVariant, updatedVariant, Some("Updated via curator interface")) - } else { - Future.successful(()) - } - } yield { - if (updated) { - Redirect(routes.CuratorController.listVariants(None, 1, 20)) - .flashing("success" -> "Variant updated successfully") - } else { - BadRequest("Failed to update variant") - } - } - } - ) - case None => - Future.successful(NotFound("Variant not found")) - } + Future.successful( + Redirect(routes.CuratorController.listVariants(None, 1, 20)) + .flashing("warning" -> "Variant editing is being updated for the new schema.") + ) } + // TODO: Remove variant group concept - VariantV2 is already consolidated def editVariantGroupForm(groupKey: String): Action[AnyContent] = withPermission("variant.update").async { implicit request => - variantRepository.getVariantsByGroupKey(groupKey).map { variants => - if (variants.isEmpty) { - NotFound("Variant group not found") - } else { - val variantGroup = variantRepository.groupVariants(variants).head - // Use shared values from group for form - val formData = VariantFormData( - genbankContigId = variants.head.variant.genbankContigId, - position = variants.head.variant.position, - referenceAllele = variants.head.variant.referenceAllele, - alternateAllele = variants.head.variant.alternateAllele, - variantType = variants.head.variant.variantType, - rsId = variantGroup.rsId, - commonName = variantGroup.commonName - ) - Ok(views.html.curator.variants.editGroupForm(groupKey, variantGroup, variantForm.fill(formData))) - } - } + Future.successful( + Redirect(routes.CuratorController.listVariants(None, 1, 20)) + .flashing("warning" -> "Variant group editing is being updated for the new schema.") + ) } + // TODO: Remove variant group concept - VariantV2 is already consolidated def updateVariantGroup(groupKey: String): Action[AnyContent] = withPermission("variant.update").async { implicit request => - variantRepository.getVariantsByGroupKey(groupKey).flatMap { variants => - if (variants.isEmpty) { - Future.successful(NotFound("Variant group not found")) - } else { - val variantGroup = variantRepository.groupVariants(variants).head - variantForm.bindFromRequest().fold( - formWithErrors => { - Future.successful(BadRequest(views.html.curator.variants.editGroupForm(groupKey, variantGroup, formWithErrors))) - }, - data => { - // Update all variants in the group with the shared fields - val updateFutures = variants.map { vwc => - val oldVariant = vwc.variant - val updatedVariant = oldVariant.copy( - variantType = data.variantType, - rsId = data.rsId, - commonName = data.commonName - ) - for { - updated <- variantRepository.update(updatedVariant) - _ <- if (updated) { - auditService.logVariantUpdate(request.user.id.get, oldVariant, updatedVariant, Some(s"Updated via group edit ($groupKey)")) - } else { - Future.successful(()) - } - } yield updated - } - - Future.sequence(updateFutures).map { results => - if (results.forall(identity)) { - Redirect(routes.CuratorController.listVariants(None, 1, 20)) - .flashing("success" -> s"Updated ${results.size} variants in group $groupKey") - } else { - BadRequest(s"Failed to update some variants in group") - } - } - } - ) - } - } + Future.successful( + Redirect(routes.CuratorController.listVariants(None, 1, 20)) + .flashing("warning" -> "Variant group editing is being updated for the new schema.") + ) } def deleteVariant(id: Int): Action[AnyContent] = withPermission("variant.delete").async { implicit request => - variantRepository.findById(id).flatMap { + variantV2Repository.findById(id).flatMap { case Some(variant) => for { - deleted <- variantRepository.delete(id) + deleted <- variantV2Repository.delete(id) _ <- if (deleted) { auditService.logVariantDelete(request.user.id.get, variant, Some("Deleted via curator interface")) } else { @@ -716,76 +564,53 @@ class CuratorController @Inject()( withPermission("haplogroup.view").async { implicit request => for { haplogroupOpt <- haplogroupRepository.findById(haplogroupId) - variantGroups <- query match { - case Some(q) if q.nonEmpty => variantRepository.searchGrouped(q, 20) + variants <- query match { + case Some(q) if q.nonEmpty => variantV2Repository.searchByName(q) case _ => Future.successful(Seq.empty) } existingVariantIds <- haplogroupVariantRepository.getVariantsByHaplogroup(haplogroupId).map(_.flatMap(_.variantId).toSet) } yield { - // Filter out groups where ALL variants are already associated - val availableGroups = variantGroups.filterNot { group => - group.variantIds.forall(existingVariantIds.contains) - } + // Filter out variants that are already associated + val availableVariants = variants.filterNot(v => v.variantId.exists(existingVariantIds.contains)) haplogroupOpt match { case Some(haplogroup) => - Ok(views.html.curator.haplogroups.variantSearchResults(haplogroupId, haplogroup.name, query, availableGroups)) + Ok(views.html.curator.haplogroups.variantSearchResults(haplogroupId, haplogroup.name, query, availableVariants)) case None => NotFound("Haplogroup not found") } } } - def addVariantGroupToHaplogroup(haplogroupId: Int, groupKey: String): Action[AnyContent] = + def addVariantToHaplogroup(haplogroupId: Int, variantId: Int): Action[AnyContent] = withPermission("haplogroup.update").async { implicit request => for { - // Get all variants in the group - variantsInGroup <- variantRepository.getVariantsByGroupKey(groupKey) - existingVariantIds <- haplogroupVariantRepository.getVariantsByHaplogroup(haplogroupId).map(_.flatMap(_.variantId).toSet) - - // Add each variant that isn't already associated - addedIds <- Future.traverse(variantsInGroup.filterNot(v => existingVariantIds.contains(v.variant.variantId.getOrElse(-1)))) { vwc => - for { - hvId <- haplogroupVariantRepository.addVariantToHaplogroup(haplogroupId, vwc.variant.variantId.get) - _ <- auditService.logVariantAddedToHaplogroup( - request.user.email.getOrElse(request.user.id.map(_.toString).getOrElse("unknown")), - hvId, - Some(s"Added variant ${vwc.variant.variantId.get} (${groupKey}) to haplogroup $haplogroupId") - ) - } yield hvId - } - + hvId <- haplogroupVariantRepository.addVariantToHaplogroup(haplogroupId, variantId) + _ <- auditService.logVariantAddedToHaplogroup( + request.user.email.getOrElse(request.user.id.map(_.toString).getOrElse("unknown")), + hvId, + Some(s"Added variant $variantId to haplogroup $haplogroupId") + ) // Fetch updated variants for display variants <- haplogroupVariantRepository.getHaplogroupVariants(haplogroupId) - variantsWithContig = variants.map { case (v, c) => VariantWithContig(v, c) } - variantGroups = variantRepository.groupVariants(variantsWithContig) } yield { - Ok(views.html.curator.haplogroups.variantsPanel(haplogroupId, variantGroups)) + Ok(views.html.curator.haplogroups.variantsPanel(haplogroupId, variants)) .withHeaders("HX-Trigger" -> "variantAdded") } } - def removeVariantGroupFromHaplogroup(haplogroupId: Int, groupKey: String): Action[AnyContent] = + def removeVariantFromHaplogroup(haplogroupId: Int, variantId: Int): Action[AnyContent] = withPermission("haplogroup.update").async { implicit request => for { - // Get all variants in the group - variantsInGroup <- variantRepository.getVariantsByGroupKey(groupKey) - - // Remove each variant - removed <- Future.traverse(variantsInGroup.flatMap(_.variant.variantId)) { variantId => - haplogroupVariantRepository.removeVariantFromHaplogroup(haplogroupId, variantId) - } - + removed <- haplogroupVariantRepository.removeVariantFromHaplogroup(haplogroupId, variantId) // Fetch updated variants for display variants <- haplogroupVariantRepository.getHaplogroupVariants(haplogroupId) - variantsWithContig = variants.map { case (v, c) => VariantWithContig(v, c) } - variantGroups = variantRepository.groupVariants(variantsWithContig) } yield { - if (removed.sum > 0) { - Ok(views.html.curator.haplogroups.variantsPanel(haplogroupId, variantGroups)) + if (removed > 0) { + Ok(views.html.curator.haplogroups.variantsPanel(haplogroupId, variants)) .withHeaders("HX-Trigger" -> "variantRemoved") } else { - BadRequest("Failed to remove variant group") + BadRequest("Failed to remove variant") } } } @@ -802,7 +627,7 @@ class CuratorController @Inject()( def splitBranchForm(parentId: Int): Action[AnyContent] = withPermission("haplogroup.update").async { implicit request => treeRestructuringService.getSplitPreview(parentId).map { preview => - Ok(views.html.curator.haplogroups.splitBranchForm(preview.parent, preview.variantGroups, preview.children, splitBranchForm)) + Ok(views.html.curator.haplogroups.splitBranchForm(preview.parent, preview.variants, preview.children, splitBranchForm)) }.recover { case e: IllegalArgumentException => NotFound(e.getMessage) @@ -815,7 +640,7 @@ class CuratorController @Inject()( splitBranchForm.bindFromRequest().fold( formWithErrors => { Future.successful(BadRequest(views.html.curator.haplogroups.splitBranchForm( - preview.parent, preview.variantGroups, preview.children, formWithErrors + preview.parent, preview.variants, preview.children, formWithErrors ))) }, data => { @@ -835,7 +660,7 @@ class CuratorController @Inject()( treeRestructuringService.splitBranch( parentId, newHaplogroup, - data.variantGroupKeys, + data.variantIds, data.childIds, request.user.id.get ).map { newId => @@ -844,7 +669,7 @@ class CuratorController @Inject()( }.recover { case e: IllegalArgumentException => BadRequest(views.html.curator.haplogroups.splitBranchForm( - preview.parent, preview.variantGroups, preview.children, + preview.parent, preview.variants, preview.children, splitBranchForm.fill(data).withGlobalError(e.getMessage) )) } diff --git a/app/controllers/VariantApiController.scala b/app/controllers/VariantApiController.scala index daa910b..f0460db 100644 --- a/app/controllers/VariantApiController.scala +++ b/app/controllers/VariantApiController.scala @@ -3,11 +3,11 @@ package controllers import actions.ApiSecurityAction import jakarta.inject.{Inject, Singleton} import models.api.* -import models.dal.domain.genomics.Variant +import models.domain.genomics.VariantV2 import play.api.Logger -import play.api.libs.json.Json +import play.api.libs.json.{JsObject, Json} import play.api.mvc.{Action, AnyContent, BaseController, ControllerComponents} -import repositories.{GenbankContigRepository, VariantAliasRepository, VariantRepository} +import repositories.VariantV2Repository import scala.concurrent.{ExecutionContext, Future} @@ -15,82 +15,53 @@ import scala.concurrent.{ExecutionContext, Future} * Private API controller for bulk variant operations. * Secured with X-API-Key authentication. * - * Endpoints are unlisted and intended for system integration. + * Updated for VariantV2 schema with JSONB coordinates and aliases. */ @Singleton class VariantApiController @Inject()( - val controllerComponents: ControllerComponents, - secureApi: ApiSecurityAction, - variantRepository: VariantRepository, - variantAliasRepository: VariantAliasRepository, - genbankContigRepository: GenbankContigRepository - )(implicit ec: ExecutionContext) extends BaseController { + val controllerComponents: ControllerComponents, + secureApi: ApiSecurityAction, + variantRepository: VariantV2Repository +)(implicit ec: ExecutionContext) extends BaseController { private val logger = Logger(this.getClass) /** - * Bulk add reference builds to existing variants. - * Matches variants by name or rsId, then creates new variant records - * for the specified reference genome if they don't exist. + * Bulk add reference builds (coordinates) to existing variants. + * Matches variants by name or rsId, then adds coordinates for the specified reference genome. */ def bulkAddBuilds(): Action[BulkAddVariantBuildsRequest] = secureApi.jsonAction[BulkAddVariantBuildsRequest].async { request => val requests = request.body.variants logger.info(s"Bulk add builds request for ${requests.size} variants") - // Collect all unique contig+genome combinations needed - val contigGenomePairs = requests.map(r => (r.contig, r.refGenome)).distinct + val resultFutures = requests.map(processAddBuildRequest) - // Resolve all contigs - genbankContigRepository.findByCommonNames(contigGenomePairs.map(_._1).distinct).flatMap { contigs => - // Build lookup map: (commonName, refGenome) -> contigId - val contigMap = contigs.flatMap { c => - for { - cn <- c.commonName - rg <- c.referenceGenome - } yield (cn, rg) -> c.id.get - }.toMap - - // Also try without 'chr' prefix - val contigMapWithFallback = contigMap ++ contigs.flatMap { c => - for { - cn <- c.commonName - rg <- c.referenceGenome - } yield (cn.stripPrefix("chr"), rg) -> c.id.get - }.toMap - - // Process each request - val resultFutures = requests.map { req => - processAddBuildRequest(req, contigMapWithFallback) - } - - Future.sequence(resultFutures).map { results => - val succeeded = results.count(_.status == "success") - val failed = results.count(_.status != "success") + Future.sequence(resultFutures).map { results => + val succeeded = results.count(_.status == "success") + val failed = results.count(_.status != "success") - logger.info(s"Bulk add builds completed: $succeeded succeeded, $failed failed") + logger.info(s"Bulk add builds completed: $succeeded succeeded, $failed failed") - Ok(Json.toJson(BulkVariantOperationResponse( - total = results.size, - succeeded = succeeded, - failed = failed, - results = results - ))) - } + Ok(Json.toJson(BulkVariantOperationResponse( + total = results.size, + succeeded = succeeded, + failed = failed, + results = results + ))) } } /** * Bulk update rsIds for variants matched by name. + * Adds rsId as an alias to the variant's aliases JSONB. */ def bulkUpdateRsIds(): Action[BulkUpdateRsIdsRequest] = secureApi.jsonAction[BulkUpdateRsIdsRequest].async { request => val requests = request.body.variants logger.info(s"Bulk update rsIds request for ${requests.size} variants") - val resultFutures = requests.map { req => - processUpdateRsIdRequest(req) - } + val resultFutures = requests.map(processUpdateRsIdRequest) Future.sequence(resultFutures).map { results => val succeeded = results.count(_.status == "success") @@ -107,107 +78,116 @@ class VariantApiController @Inject()( } } - private def processAddBuildRequest( - req: AddVariantBuildRequest, - contigMap: Map[(String, String), Int] - ): Future[VariantOperationResult] = { + private def processAddBuildRequest(req: AddVariantBuildRequest): Future[VariantOperationResult] = { val identifier = req.name.orElse(req.rsId) - // Resolve contig ID - val contigIdOpt = contigMap.get((req.contig, req.refGenome)) - .orElse(contigMap.get((req.contig.stripPrefix("chr"), req.refGenome))) - .orElse(contigMap.get(("chr" + req.contig.stripPrefix("chr"), req.refGenome))) - - contigIdOpt match { + identifier match { case None => Future.successful(VariantOperationResult( name = req.name, rsId = req.rsId, status = "error", - message = Some(s"Contig '${req.contig}' not found for reference genome '${req.refGenome}'") + message = Some("Either name or rsId must be provided") )) - case Some(contigId) => - // Check if this exact build already exists - variantRepository.findVariant(contigId, req.position, req.refAllele, req.altAllele).flatMap { - case Some(existing) => - // Build already exists + case Some(id) => + // Find variant by name or alias + val findFuture = req.name match { + case Some(name) => variantRepository.findByCanonicalName(name) + case None => variantRepository.findByAlias(req.rsId.get).map(_.headOption) + } + + findFuture.flatMap { + case None => Future.successful(VariantOperationResult( name = req.name, rsId = req.rsId, - status = "skipped", - message = Some("Build already exists"), - variantId = existing.variantId + status = "error", + message = Some(s"Variant not found with identifier '$id'") )) - case None => - // Create new variant record for this build - val newVariant = Variant( - genbankContigId = contigId, - position = req.position, - referenceAllele = req.refAllele, - alternateAllele = req.altAllele, - variantType = req.variantType, - rsId = req.rsId, - commonName = req.name - ) - - variantRepository.createVariant(newVariant).map { newId => - VariantOperationResult( - name = req.name, - rsId = req.rsId, - status = "success", - message = Some(s"Created build for ${req.refGenome}"), - variantId = Some(newId) - ) - }.recover { case e: Exception => - logger.error(s"Failed to create variant build: ${e.getMessage}", e) - VariantOperationResult( + case Some(variant) => + // Check if this build already exists + val existingCoords = variant.coordinates.asOpt[Map[String, JsObject]].getOrElse(Map.empty) + if (existingCoords.contains(req.refGenome)) { + Future.successful(VariantOperationResult( name = req.name, rsId = req.rsId, - status = "error", - message = Some(s"Database error: ${e.getMessage}") + status = "skipped", + message = Some(s"Build ${req.refGenome} already exists"), + variantId = variant.variantId + )) + } else { + // Add the new coordinates + val newCoords = Json.obj( + "contig" -> req.contig, + "position" -> req.position, + "ref" -> req.refAllele, + "alt" -> req.altAllele ) + + variantRepository.addCoordinates(variant.variantId.get, req.refGenome, newCoords).map { _ => + VariantOperationResult( + name = req.name, + rsId = req.rsId, + status = "success", + message = Some(s"Added coordinates for ${req.refGenome}"), + variantId = variant.variantId + ) + }.recover { case e: Exception => + logger.error(s"Failed to add coordinates: ${e.getMessage}", e) + VariantOperationResult( + name = req.name, + rsId = req.rsId, + status = "error", + message = Some(s"Database error: ${e.getMessage}") + ) + } } } } } private def processUpdateRsIdRequest(req: UpdateVariantRsIdRequest): Future[VariantOperationResult] = { - // Find all variants with this name - variantRepository.searchByName(req.name).flatMap { variants => - if (variants.isEmpty) { - Future.successful(VariantOperationResult( - name = Some(req.name), - rsId = Some(req.rsId), - status = "error", - message = Some(s"No variant found with name '${req.name}'") - )) - } else { - // Update rsId on all matching variants (all builds of this variant) - val updateFutures = variants.map { v => - variantRepository.update(v.copy(rsId = Some(req.rsId))) + variantRepository.findByCanonicalName(req.name).flatMap { + case None => + // Try finding by alias + variantRepository.findByAlias(req.name).flatMap { variants => + if (variants.isEmpty) { + Future.successful(VariantOperationResult( + name = Some(req.name), + rsId = Some(req.rsId), + status = "error", + message = Some(s"No variant found with name '${req.name}'") + )) + } else { + updateVariantRsId(variants.head, req) + } } - Future.sequence(updateFutures).map { results => - val updatedCount = results.count(_ == true) - VariantOperationResult( - name = Some(req.name), - rsId = Some(req.rsId), - status = "success", - message = Some(s"Updated rsId on $updatedCount variant record(s)"), - variantId = variants.headOption.flatMap(_.variantId) - ) - }.recover { case e: Exception => - logger.error(s"Failed to update rsId: ${e.getMessage}", e) - VariantOperationResult( - name = Some(req.name), - rsId = Some(req.rsId), - status = "error", - message = Some(s"Database error: ${e.getMessage}") - ) - } - } + case Some(variant) => + updateVariantRsId(variant, req) + } + } + + private def updateVariantRsId(variant: VariantV2, req: UpdateVariantRsIdRequest): Future[VariantOperationResult] = { + // Add rsId as an alias + variantRepository.addAlias(variant.variantId.get, "rs_id", req.rsId, Some("bulk_update")).map { _ => + VariantOperationResult( + name = Some(req.name), + rsId = Some(req.rsId), + status = "success", + message = Some("Added rsId as alias"), + variantId = variant.variantId + ) + }.recover { case e: Exception => + logger.error(s"Failed to update rsId: ${e.getMessage}", e) + VariantOperationResult( + name = Some(req.name), + rsId = Some(req.rsId), + status = "error", + message = Some(s"Database error: ${e.getMessage}") + ) } } @@ -217,7 +197,7 @@ class VariantApiController @Inject()( /** * Bulk update alias sources by prefix pattern. - * Example: Update all "FGC*" aliases from source "migration" to source "FGC". + * Updates the source field in aliases JSONB for matching alias values. */ def bulkUpdateAliasSources(): Action[BulkUpdateAliasSourcesRequest] = secureApi.jsonAction[BulkUpdateAliasSourcesRequest].async { request => @@ -225,7 +205,7 @@ class VariantApiController @Inject()( logger.info(s"Bulk update alias sources request for ${updates.size} prefix patterns") val resultFutures = updates.map { req => - variantAliasRepository.bulkUpdateSourceByPrefix(req.aliasPrefix, req.newSource, req.oldSource).map { count => + variantRepository.bulkUpdateAliasSource(req.aliasPrefix, req.newSource, req.oldSource).map { count => AliasSourceUpdateResult( aliasPrefix = req.aliasPrefix, newSource = req.newSource, @@ -259,18 +239,12 @@ class VariantApiController @Inject()( /** * Get statistics about alias sources in the database. - * Useful for planning source cleanup operations. */ def getAliasSourceStats(): Action[AnyContent] = secureApi.async { _ => - for { - sources <- variantAliasRepository.getDistinctSources() - counts <- Future.traverse(sources)(source => - variantAliasRepository.countBySource(source).map(count => AliasSourceSummary(source, count)) - ) - } yield { - val totalAliases = counts.map(_.count).sum + variantRepository.getAliasSourceStats().map { stats => + val totalAliases = stats.map(_._2).sum Ok(Json.toJson(AliasSourceStatsResponse( - sources = counts.sortBy(-_.count), + sources = stats.map { case (source, count) => AliasSourceSummary(source, count) }, totalAliases = totalAliases ))) } @@ -278,10 +252,9 @@ class VariantApiController @Inject()( /** * Preview how many aliases would be affected by a source update. - * Useful for dry-run before actual update. */ def previewAliasSourceUpdate(aliasPrefix: String, currentSource: String): Action[AnyContent] = secureApi.async { _ => - variantAliasRepository.countByPrefixAndSource(aliasPrefix, currentSource).map { count => + variantRepository.countAliasesByPrefixAndSource(aliasPrefix, Some(currentSource)).map { count => Ok(Json.obj( "aliasPrefix" -> aliasPrefix, "currentSource" -> currentSource, diff --git a/app/controllers/VariantBrowserController.scala b/app/controllers/VariantBrowserController.scala index c17992f..e519718 100644 --- a/app/controllers/VariantBrowserController.scala +++ b/app/controllers/VariantBrowserController.scala @@ -1,12 +1,13 @@ package controllers import jakarta.inject.{Inject, Singleton} -import models.domain.genomics.VariantGroup +import models.domain.genomics.VariantV2 +import models.domain.haplogroups.Haplogroup import org.webjars.play.WebJarsUtil import play.api.cache.AsyncCacheApi import play.api.i18n.I18nSupport import play.api.mvc.* -import repositories.{HaplogroupVariantRepository, VariantAliasRepository, VariantRepository} +import repositories.{HaplogroupVariantRepository, VariantV2Repository} import scala.concurrent.duration.* import scala.concurrent.{ExecutionContext, Future} @@ -18,12 +19,11 @@ import scala.concurrent.{ExecutionContext, Future} */ @Singleton class VariantBrowserController @Inject()( - val controllerComponents: ControllerComponents, - variantRepository: VariantRepository, - variantAliasRepository: VariantAliasRepository, - haplogroupVariantRepository: HaplogroupVariantRepository, - cache: AsyncCacheApi - )(using webJarsUtil: WebJarsUtil, ec: ExecutionContext) + val controllerComponents: ControllerComponents, + variantRepository: VariantV2Repository, + haplogroupVariantRepository: HaplogroupVariantRepository, + cache: AsyncCacheApi +)(using webJarsUtil: WebJarsUtil, ec: ExecutionContext) extends BaseController with I18nSupport { private val DefaultPageSize = 25 @@ -31,7 +31,6 @@ class VariantBrowserController @Inject()( // Cache durations - public view can be stale private val SearchCacheDuration = 15.minutes private val DetailCacheDuration = 1.hour - private val TotalCountCacheDuration = 30.minutes /** * Main variant browser page with search functionality. @@ -40,10 +39,10 @@ class VariantBrowserController @Inject()( implicit request: Request[AnyContent] => val offset = (page - 1) * pageSize for { - (variantGroups, totalCount) <- getCachedSearchResults(query.getOrElse(""), offset, pageSize) + (variants, totalCount) <- getCachedSearchResults(query.getOrElse(""), offset, pageSize) } yield { val totalPages = Math.max(1, (totalCount + pageSize - 1) / pageSize) - Ok(views.html.variants.browser(variantGroups, query, page, totalPages, pageSize, totalCount)) + Ok(views.html.variants.browser(variants, query, page, totalPages, pageSize, totalCount)) } } @@ -54,10 +53,10 @@ class VariantBrowserController @Inject()( implicit request: Request[AnyContent] => val offset = (page - 1) * pageSize for { - (variantGroups, totalCount) <- getCachedSearchResults(query.getOrElse(""), offset, pageSize) + (variants, totalCount) <- getCachedSearchResults(query.getOrElse(""), offset, pageSize) } yield { val totalPages = Math.max(1, (totalCount + pageSize - 1) / pageSize) - Ok(views.html.variants.listFragment(variantGroups, query, page, totalPages, pageSize, totalCount)) + Ok(views.html.variants.listFragment(variants, query, page, totalPages, pageSize, totalCount)) } } @@ -72,12 +71,11 @@ class VariantBrowserController @Inject()( /** * Get cached search results or fetch from database. - * Cache key includes query, offset, and limit for proper pagination caching. */ - private def getCachedSearchResults(query: String, offset: Int, limit: Int): Future[(Seq[VariantGroup], Int)] = { - val cacheKey = s"variant-search:${query.toLowerCase.trim}:$offset:$limit" + private def getCachedSearchResults(query: String, offset: Int, limit: Int): Future[(Seq[VariantV2], Int)] = { + val cacheKey = s"variant-browser:${query.toLowerCase.trim}:$offset:$limit" cache.getOrElseUpdate(cacheKey, SearchCacheDuration) { - variantRepository.searchGroupedPaginated(query, offset, limit) + variantRepository.searchPaginated(query, offset, limit) } } @@ -85,23 +83,15 @@ class VariantBrowserController @Inject()( * Get cached detail panel or fetch from database. */ private def getCachedDetailPanel(id: Int)(implicit request: Request[AnyContent]): Future[Result] = { - val cacheKey = s"variant-detail:$id" + val cacheKey = s"variant-browser-detail:$id" cache.getOrElseUpdate(cacheKey, DetailCacheDuration) { for { - variantOpt <- variantRepository.findByIdWithContig(id) - allVariantsInGroup <- variantOpt match { - case Some(vwc) => - val groupKey = vwc.variant.commonName.orElse(vwc.variant.rsId).getOrElse(s"variant_${id}") - variantRepository.getVariantsByGroupKey(groupKey) - case None => Future.successful(Seq.empty) - } - aliases <- variantAliasRepository.findByVariantId(id) + variantOpt <- variantRepository.findById(id) haplogroups <- haplogroupVariantRepository.getHaplogroupsByVariant(id) } yield { variantOpt match { - case Some(variantWithContig) => - val variantGroup = variantRepository.groupVariants(allVariantsInGroup).headOption - Ok(views.html.variants.detailPanel(variantWithContig, variantGroup, aliases, haplogroups)) + case Some(variant) => + Ok(views.html.variants.detailPanel(variant, haplogroups)) case None => NotFound("Variant not found") } diff --git a/app/controllers/VariantController.scala b/app/controllers/VariantController.scala deleted file mode 100644 index cc03b4e..0000000 --- a/app/controllers/VariantController.scala +++ /dev/null @@ -1,30 +0,0 @@ -package controllers - -import jakarta.inject.{Inject, Singleton} -import models.dal.domain.genomics.Variant -import play.api.libs.json.{Json, OFormat} -import play.api.mvc.{Action, AnyContent, BaseController, ControllerComponents} -import repositories.VariantRepository - -import scala.concurrent.ExecutionContext - -@Singleton -class VariantController @Inject()( - val controllerComponents: ControllerComponents, - variantRepository: VariantRepository - )(implicit ec: ExecutionContext) extends BaseController { - - implicit val variantFormat: OFormat[Variant] = Json.format[Variant] - - /** - * Searches for variants by name (rsId or commonName). - * - * @param name The name to search for (e.g., "rs123" or "M269"). - * @return A JSON array of matching variants. - */ - def search(name: String): Action[AnyContent] = Action.async { implicit request => - variantRepository.searchByName(name).map { variants => - Ok(Json.toJson(variants)) - } - } -} diff --git a/app/controllers/VariantPublicApiController.scala b/app/controllers/VariantPublicApiController.scala index d97709f..9e4178f 100644 --- a/app/controllers/VariantPublicApiController.scala +++ b/app/controllers/VariantPublicApiController.scala @@ -88,7 +88,7 @@ class VariantPublicApiController @Inject()( ).withHeaders( "Content-Type" -> "application/gzip", "X-Variant-Count" -> metadata.map(_.variantCount.toString).getOrElse("unknown"), - "X-Generated-At" -> metadata.map(_.generatedAt).getOrElse("unknown") + "X-Generated-At" -> metadata.map(_.generatedAt.toString).getOrElse("unknown") ) } else { NotFound(Json.obj( diff --git a/app/models/dal/DatabaseSchema.scala b/app/models/dal/DatabaseSchema.scala index 766d4b4..0a9d06e 100644 --- a/app/models/dal/DatabaseSchema.scala +++ b/app/models/dal/DatabaseSchema.scala @@ -70,17 +70,22 @@ object DatabaseSchema { val genbankContigs = TableQuery[GenbankContigsTable] val geneAnnotations = TableQuery[GeneAnnotationsTable] val populations = TableQuery[PopulationsTable] - val sequenceFiles = TableQuery[SequenceFilesTable] // Added back + val sequenceFiles = TableQuery[SequenceFilesTable] val sequenceLibraries = TableQuery[SequenceLibrariesTable] val sequencingLabs = TableQuery[SequencingLabsTable] val sequencerInstruments = TableQuery[SequencerInstrumentsTable] val specimenDonors = TableQuery[SpecimenDonorsTable] val validationServices = TableQuery[ValidationServicesTable] - val variants = TableQuery[VariantsTable] - val variantAliases = TableQuery[VariantAliasTable] val testTypeDefinition = TableQuery[TestTypeTable] + // Consolidated variant schema (replaces variant + variant_alias) + val variantsV2 = TableQuery[VariantV2Table] + val haplogroupCharacterStates = TableQuery[HaplogroupCharacterStateTable] + val branchMutations = TableQuery[BranchMutationTable] + val biosampleVariantCalls = TableQuery[BiosampleVariantCallTable] + val strMutationRates = TableQuery[StrMutationRateTable] + // New tables for Atmosphere Lexicon sync val populationBreakdowns = TableQuery[PopulationBreakdownTable] val populationComponents = TableQuery[PopulationComponentTable] @@ -92,7 +97,6 @@ object DatabaseSchema { val genomeRegions = TableQuery[GenomeRegionTable] val genomeRegionVersions = TableQuery[GenomeRegionVersionTable] val cytobands = TableQuery[CytobandTable] - val strMarkers = TableQuery[StrMarkerTable] } object haplogroups { diff --git a/app/models/dal/domain/genomics/BiosampleVariantCall.scala b/app/models/dal/domain/genomics/BiosampleVariantCall.scala new file mode 100644 index 0000000..643886b --- /dev/null +++ b/app/models/dal/domain/genomics/BiosampleVariantCall.scala @@ -0,0 +1,97 @@ +package models.dal.domain.genomics + +import models.dal.MyPostgresProfile.api.* +import play.api.libs.json.{Json, OFormat} + +import java.time.Instant + +/** + * Represents an observed variant call from a biosample. + * + * This is the input data for ASR - the actual observed states + * from sequenced samples. + * + * @param id Auto-generated primary key + * @param biosampleId FK to the biosample + * @param variantId FK to the variant + * @param observedState The observed state (allele, repeat count, "present"/"absent") + * @param qualityScore Phred-scale quality score + * @param readDepth Number of reads supporting the call + * @param confidence Confidence level: "high", "medium", "low" + * @param source Data source: "ftdna", "yfull", "user_upload", etc. + * @param createdAt When the call was recorded + */ +case class BiosampleVariantCall( + id: Option[Int] = None, + biosampleId: Int, + variantId: Int, + observedState: String, + qualityScore: Option[Int] = None, + readDepth: Option[Int] = None, + confidence: Option[String] = None, + source: Option[String] = None, + createdAt: Instant = Instant.now() +) + +object BiosampleVariantCall { + implicit val format: OFormat[BiosampleVariantCall] = Json.format[BiosampleVariantCall] + + object Confidence { + val HIGH = "high" + val MEDIUM = "medium" + val LOW = "low" + } +} + +/** + * Slick table definition for biosample_variant_call. + */ +class BiosampleVariantCallTable(tag: Tag) + extends Table[BiosampleVariantCall](tag, Some("public"), "biosample_variant_call") { + + def id = column[Int]("id", O.PrimaryKey, O.AutoInc) + + def biosampleId = column[Int]("biosample_id") + + def variantId = column[Int]("variant_id") + + def observedState = column[String]("observed_state") + + def qualityScore = column[Option[Int]]("quality_score") + + def readDepth = column[Option[Int]]("read_depth") + + def confidence = column[Option[String]]("confidence") + + def source = column[Option[String]]("source") + + def createdAt = column[Instant]("created_at") + + def * = ( + id.?, + biosampleId, + variantId, + observedState, + qualityScore, + readDepth, + confidence, + source, + createdAt + ).mapTo[BiosampleVariantCall] + + // Note: biosample FK references public.biosample table + // We don't define the FK here to avoid circular dependencies + // The DB-level FK constraint handles referential integrity + + def variantFK = foreignKey( + "biosample_variant_call_variant_fk", + variantId, + TableQuery[VariantV2Table] + )(_.variantId, onDelete = ForeignKeyAction.Cascade) + + def uniqueBiosampleVariant = index( + "idx_biosample_variant_call_unique", + (biosampleId, variantId), + unique = true + ) +} diff --git a/app/models/dal/domain/genomics/BranchMutation.scala b/app/models/dal/domain/genomics/BranchMutation.scala new file mode 100644 index 0000000..ad345a4 --- /dev/null +++ b/app/models/dal/domain/genomics/BranchMutation.scala @@ -0,0 +1,93 @@ +package models.dal.domain.genomics + +import models.dal.MyPostgresProfile.api.* +import models.dal.domain.haplogroups.HaplogroupsTable +import play.api.libs.json.{Json, OFormat} + +/** + * Represents a state transition along a tree branch. + * + * Records where mutations occurred in the phylogenetic tree, + * tracking the change from parent to child haplogroup state. + * + * @param id Auto-generated primary key + * @param variantId FK to the variant that changed + * @param parentHaplogroupId FK to parent haplogroup node + * @param childHaplogroupId FK to child haplogroup node + * @param fromState State at parent node (e.g., "G", "15") + * @param toState State at child node (e.g., "A", "16") + * @param stepDirection For STRs: +1 = expansion, -1 = contraction; NULL for SNPs + * @param confidence Confidence from ASR algorithm + */ +case class BranchMutation( + id: Option[Int] = None, + variantId: Int, + parentHaplogroupId: Int, + childHaplogroupId: Int, + fromState: String, + toState: String, + stepDirection: Option[Int] = None, + confidence: Option[BigDecimal] = None +) + +object BranchMutation { + implicit val format: OFormat[BranchMutation] = Json.format[BranchMutation] +} + +/** + * Slick table definition for branch_mutation. + */ +class BranchMutationTable(tag: Tag) + extends Table[BranchMutation](tag, Some("public"), "branch_mutation") { + + def id = column[Int]("id", O.PrimaryKey, O.AutoInc) + + def variantId = column[Int]("variant_id") + + def parentHaplogroupId = column[Int]("parent_haplogroup_id") + + def childHaplogroupId = column[Int]("child_haplogroup_id") + + def fromState = column[String]("from_state") + + def toState = column[String]("to_state") + + def stepDirection = column[Option[Int]]("step_direction") + + def confidence = column[Option[BigDecimal]]("confidence") + + def * = ( + id.?, + variantId, + parentHaplogroupId, + childHaplogroupId, + fromState, + toState, + stepDirection, + confidence + ).mapTo[BranchMutation] + + def variantFK = foreignKey( + "branch_mutation_variant_fk", + variantId, + TableQuery[VariantV2Table] + )(_.variantId, onDelete = ForeignKeyAction.Cascade) + + def parentHaplogroupFK = foreignKey( + "branch_mutation_parent_haplogroup_fk", + parentHaplogroupId, + TableQuery[HaplogroupsTable] + )(_.haplogroupId, onDelete = ForeignKeyAction.Cascade) + + def childHaplogroupFK = foreignKey( + "branch_mutation_child_haplogroup_fk", + childHaplogroupId, + TableQuery[HaplogroupsTable] + )(_.haplogroupId, onDelete = ForeignKeyAction.Cascade) + + def uniqueBranchVariant = index( + "idx_branch_mutation_unique", + (variantId, parentHaplogroupId, childHaplogroupId), + unique = true + ) +} diff --git a/app/models/dal/domain/genomics/HaplogroupCharacterState.scala b/app/models/dal/domain/genomics/HaplogroupCharacterState.scala new file mode 100644 index 0000000..19bf668 --- /dev/null +++ b/app/models/dal/domain/genomics/HaplogroupCharacterState.scala @@ -0,0 +1,92 @@ +package models.dal.domain.genomics + +import models.dal.MyPostgresProfile.api.* +import models.dal.domain.haplogroups.HaplogroupsTable +import play.api.libs.json.{JsValue, Json, OFormat} + +import java.time.Instant + +/** + * Represents an ASR-reconstructed character state at a haplogroup node. + * + * This table stores the inferred ancestral state for each variant at each + * haplogroup in the tree. Used for: + * - SNPs: ancestral vs derived allele + * - STRs: inferred repeat count (modal haplotype) + * - SVs: presence/absence, orientation, copy number + * + * @param id Auto-generated primary key + * @param haplogroupId FK to the haplogroup node + * @param variantId FK to the variant + * @param inferredState The reconstructed state (allele, count, "present"/"absent", etc.) + * @param confidence Confidence score from ASR algorithm (0.0-1.0) + * @param stateProbabilities JSONB probability distribution for uncertain reconstructions + * @param algorithm ASR method used: "parsimony", "ml", "bayesian" + * @param reconstructedAt Timestamp of reconstruction + */ +case class HaplogroupCharacterState( + id: Option[Int] = None, + haplogroupId: Int, + variantId: Int, + inferredState: String, + confidence: Option[BigDecimal] = None, + stateProbabilities: Option[JsValue] = None, + algorithm: Option[String] = None, + reconstructedAt: Instant = Instant.now() +) + +object HaplogroupCharacterState { + implicit val format: OFormat[HaplogroupCharacterState] = Json.format[HaplogroupCharacterState] +} + +/** + * Slick table definition for haplogroup_character_state. + */ +class HaplogroupCharacterStateTable(tag: Tag) + extends Table[HaplogroupCharacterState](tag, Some("public"), "haplogroup_character_state") { + + def id = column[Int]("id", O.PrimaryKey, O.AutoInc) + + def haplogroupId = column[Int]("haplogroup_id") + + def variantId = column[Int]("variant_id") + + def inferredState = column[String]("inferred_state") + + def confidence = column[Option[BigDecimal]]("confidence") + + def stateProbabilities = column[Option[JsValue]]("state_probabilities") + + def algorithm = column[Option[String]]("algorithm") + + def reconstructedAt = column[Instant]("reconstructed_at") + + def * = ( + id.?, + haplogroupId, + variantId, + inferredState, + confidence, + stateProbabilities, + algorithm, + reconstructedAt + ).mapTo[HaplogroupCharacterState] + + def haplogroupFK = foreignKey( + "haplogroup_character_state_haplogroup_fk", + haplogroupId, + TableQuery[HaplogroupsTable] + )(_.haplogroupId, onDelete = ForeignKeyAction.Cascade) + + def variantFK = foreignKey( + "haplogroup_character_state_variant_fk", + variantId, + TableQuery[VariantV2Table] + )(_.variantId, onDelete = ForeignKeyAction.Cascade) + + def uniqueHaplogroupVariant = index( + "idx_character_state_unique", + (haplogroupId, variantId), + unique = true + ) +} diff --git a/app/models/dal/domain/genomics/StrMutationRate.scala b/app/models/dal/domain/genomics/StrMutationRate.scala new file mode 100644 index 0000000..b8d920a --- /dev/null +++ b/app/models/dal/domain/genomics/StrMutationRate.scala @@ -0,0 +1,145 @@ +package models.dal.domain.genomics + +import models.dal.MyPostgresProfile.api.* +import play.api.libs.json.{Json, OFormat} + +import java.time.Instant + +/** + * Per-marker STR mutation rates for ASR and age estimation. + * + * Sources include Ballantyne 2010, Willems 2016, and other published studies. + * These rates are critical for accurate branch age estimation using the + * stepwise mutation model. + * + * @param id Auto-generated primary key + * @param markerName STR marker name (e.g., DYS456, DYS389I) + * @param panelNames Panels containing this marker (PowerPlex, YHRD, BigY, etc.) + * @param mutationRate Mutations per generation + * @param mutationRateLower 95% CI lower bound + * @param mutationRateUpper 95% CI upper bound + * @param omegaPlus Probability of expansion (default 0.5) + * @param omegaMinus Probability of contraction (default 0.5) + * @param multiStepRate Combined rate for multi-step mutations (omega_2 + omega_3 + ...) + * @param source Publication source (e.g., "Ballantyne 2010") + * @param createdAt When the rate was recorded + */ +case class StrMutationRate( + id: Option[Int] = None, + markerName: String, + panelNames: Option[List[String]] = None, + mutationRate: BigDecimal, + mutationRateLower: Option[BigDecimal] = None, + mutationRateUpper: Option[BigDecimal] = None, + omegaPlus: Option[BigDecimal] = Some(BigDecimal("0.5")), + omegaMinus: Option[BigDecimal] = Some(BigDecimal("0.5")), + multiStepRate: Option[BigDecimal] = None, + source: Option[String] = None, + createdAt: Instant = Instant.now() +) { + + /** + * Check if mutation is biased toward expansion. + */ + def isExpansionBiased: Boolean = + omegaPlus.getOrElse(BigDecimal("0.5")) > BigDecimal("0.5") + + /** + * Check if mutation is biased toward contraction. + */ + def isContractionBiased: Boolean = + omegaMinus.getOrElse(BigDecimal("0.5")) > BigDecimal("0.5") + + /** + * Get the symmetry of mutation direction (1.0 = perfectly symmetric). + * Values < 1.0 indicate directional bias. + */ + def directionalSymmetry: BigDecimal = { + val plus = omegaPlus.getOrElse(BigDecimal("0.5")) + val minus = omegaMinus.getOrElse(BigDecimal("0.5")) + if (plus >= minus) minus / plus else plus / minus + } +} + +object StrMutationRate { + implicit val format: OFormat[StrMutationRate] = Json.format[StrMutationRate] + + /** + * Create a rate entry with symmetric mutation probability. + */ + def symmetric( + markerName: String, + rate: BigDecimal, + source: String + ): StrMutationRate = StrMutationRate( + markerName = markerName, + mutationRate = rate, + source = Some(source) + ) + + /** + * Create a rate entry with directional bias. + */ + def withBias( + markerName: String, + rate: BigDecimal, + omegaPlus: BigDecimal, + omegaMinus: BigDecimal, + source: String + ): StrMutationRate = StrMutationRate( + markerName = markerName, + mutationRate = rate, + omegaPlus = Some(omegaPlus), + omegaMinus = Some(omegaMinus), + source = Some(source) + ) +} + +/** + * Slick table definition for str_mutation_rate. + */ +class StrMutationRateTable(tag: Tag) + extends Table[StrMutationRate](tag, Some("public"), "str_mutation_rate") { + + def id = column[Int]("id", O.PrimaryKey, O.AutoInc) + + def markerName = column[String]("marker_name") + + def panelNames = column[Option[List[String]]]("panel_names") + + def mutationRate = column[BigDecimal]("mutation_rate") + + def mutationRateLower = column[Option[BigDecimal]]("mutation_rate_lower") + + def mutationRateUpper = column[Option[BigDecimal]]("mutation_rate_upper") + + def omegaPlus = column[Option[BigDecimal]]("omega_plus") + + def omegaMinus = column[Option[BigDecimal]]("omega_minus") + + def multiStepRate = column[Option[BigDecimal]]("multi_step_rate") + + def source = column[Option[String]]("source") + + def createdAt = column[Instant]("created_at") + + def * = ( + id.?, + markerName, + panelNames, + mutationRate, + mutationRateLower, + mutationRateUpper, + omegaPlus, + omegaMinus, + multiStepRate, + source, + createdAt + ).mapTo[StrMutationRate] + + def uniqueMarkerName = index( + "idx_str_mutation_rate_marker_unique", + markerName, + unique = true + ) +} diff --git a/app/models/dal/domain/genomics/Variant.scala b/app/models/dal/domain/genomics/Variant.scala deleted file mode 100644 index da10b4b..0000000 --- a/app/models/dal/domain/genomics/Variant.scala +++ /dev/null @@ -1,25 +0,0 @@ -package models.dal.domain.genomics - -/** - * Represents a genetic variant with detailed information about its genomic location, reference allele, - * alternate allele, variant type, and optional metadata such as identifiers and common names. - * - * @param variantId An optional unique identifier for the variant, used internally for tracking purposes. - * @param genbankContigId The unique identifier for the genomic contig in GenBank where this variant is located. - * @param position The position of the variant on the genomic contig. - * @param referenceAllele The reference allele at the specific genomic position. - * @param alternateAllele The alternate allele representing the variant at the specific position. - * @param variantType The type of the variant (e.g., SNP, insertion, deletion). - * @param rsId An optional rs identifier (dbSNP ID) associated with this variant, if available. - * @param commonName An optional common name or description for the variant. - */ -case class Variant( - variantId: Option[Int] = None, - genbankContigId: Int, - position: Int, - referenceAllele: String, - alternateAllele: String, - variantType: String, - rsId: Option[String], - commonName: Option[String] - ) diff --git a/app/models/dal/domain/genomics/VariantAlias.scala b/app/models/dal/domain/genomics/VariantAlias.scala deleted file mode 100644 index 0f6deec..0000000 --- a/app/models/dal/domain/genomics/VariantAlias.scala +++ /dev/null @@ -1,43 +0,0 @@ -package models.dal.domain.genomics - -import java.time.LocalDateTime - -/** - * Represents an alternative name (alias) for a variant. - * - * Variants are often known by multiple names across different research groups and databases: - * - ISOGG names (e.g., M269, P312) - * - YFull names (e.g., BY12345) - * - FTDNA names - * - dbSNP rsIDs (e.g., rs9786076) - * - Publication-specific identifiers - * - * This model allows tracking all known names for a variant while maintaining - * a primary display name. - * - * @param id Unique identifier for this alias record - * @param variantId The variant this alias belongs to - * @param aliasType Type of alias: 'common_name', 'rs_id', 'isogg', 'yfull', 'ftdna', etc. - * @param aliasValue The actual alias value (e.g., "M269", "rs9786076") - * @param source Where this alias came from: 'ybrowse', 'isogg', 'curator', 'migration', etc. - * @param isPrimary Whether this is the primary alias for its type (used for display) - * @param createdAt When this alias was recorded - */ -case class VariantAlias( - id: Option[Int] = None, - variantId: Int, - aliasType: String, - aliasValue: String, - source: Option[String] = None, - isPrimary: Boolean = false, - createdAt: LocalDateTime = LocalDateTime.now() -) - -object VariantAliasType { - val CommonName = "common_name" - val RsId = "rs_id" - val Isogg = "isogg" - val YFull = "yfull" - val Ftdna = "ftdna" - val Publication = "publication" -} diff --git a/app/models/dal/domain/genomics/VariantAliasTable.scala b/app/models/dal/domain/genomics/VariantAliasTable.scala deleted file mode 100644 index fa43291..0000000 --- a/app/models/dal/domain/genomics/VariantAliasTable.scala +++ /dev/null @@ -1,33 +0,0 @@ -package models.dal.domain.genomics - -import models.dal.MyPostgresProfile.api.* - -import java.time.LocalDateTime - -/** - * Represents the `variant_alias` table in the database, which stores alternative names - * for genetic variants from different sources (YBrowse, ISOGG, YFull, publications, etc.). - * - * @param tag A Slick `Tag` object used to scope and reference the table within a database schema. - */ -class VariantAliasTable(tag: Tag) extends Table[VariantAlias](tag, Some("public"), "variant_alias") { - def id = column[Int]("id", O.PrimaryKey, O.AutoInc) - - def variantId = column[Int]("variant_id") - - def aliasType = column[String]("alias_type") - - def aliasValue = column[String]("alias_value") - - def source = column[Option[String]]("source") - - def isPrimary = column[Boolean]("is_primary") - - def createdAt = column[LocalDateTime]("created_at") - - def * = (id.?, variantId, aliasType, aliasValue, source, isPrimary, createdAt).mapTo[VariantAlias] - - def variantFK = foreignKey("variant_alias_variant_fk", variantId, TableQuery[VariantsTable])(_.variantId, onDelete = ForeignKeyAction.Cascade) - - def uniqueAlias = index("variant_alias_unique", (variantId, aliasType, aliasValue), unique = true) -} diff --git a/app/models/dal/domain/genomics/VariantV2Table.scala b/app/models/dal/domain/genomics/VariantV2Table.scala new file mode 100644 index 0000000..5ab31f8 --- /dev/null +++ b/app/models/dal/domain/genomics/VariantV2Table.scala @@ -0,0 +1,86 @@ +package models.dal.domain.genomics + +import models.dal.MyPostgresProfile.api.* +import models.dal.domain.haplogroups.HaplogroupsTable +import models.domain.genomics.{MutationType, NamingStatus, VariantV2} +import play.api.libs.json.JsValue +import slick.ast.BaseTypedType +import slick.jdbc.JdbcType + +import java.time.Instant + +/** + * Slick table definition for the `variant_v2` table. + * + * This table stores consolidated variants with JSONB columns for coordinates + * (supporting multiple reference genomes) and aliases (supporting multiple + * naming sources). + * + * Schema: + * - One row per logical variant (not per reference genome) + * - JSONB `coordinates` contains position + alleles per assembly + * - JSONB `aliases` contains all known names grouped by source + * - `defining_haplogroup_id` distinguishes parallel mutations + */ +class VariantV2Table(tag: Tag) extends Table[VariantV2](tag, Some("public"), "variant_v2") { + + // MappedColumnType for MutationType enum + implicit val mutationTypeMapper: JdbcType[MutationType] with BaseTypedType[MutationType] = + MappedColumnType.base[MutationType, String]( + _.dbValue, + MutationType.fromStringOrDefault(_) + ) + + // MappedColumnType for NamingStatus enum + implicit val namingStatusMapper: JdbcType[NamingStatus] with BaseTypedType[NamingStatus] = + MappedColumnType.base[NamingStatus, String]( + _.dbValue, + NamingStatus.fromStringOrDefault(_) + ) + + def variantId = column[Int]("variant_id", O.PrimaryKey, O.AutoInc) + + def canonicalName = column[Option[String]]("canonical_name") + + def mutationType = column[MutationType]("mutation_type") + + def namingStatus = column[NamingStatus]("naming_status") + + def aliases = column[JsValue]("aliases") + + def coordinates = column[JsValue]("coordinates") + + def definingHaplogroupId = column[Option[Int]]("defining_haplogroup_id") + + def evidence = column[JsValue]("evidence") + + def primers = column[JsValue]("primers") + + def notes = column[Option[String]]("notes") + + def createdAt = column[Instant]("created_at") + + def updatedAt = column[Instant]("updated_at") + + def * = ( + variantId.?, + canonicalName, + mutationType, + namingStatus, + aliases, + coordinates, + definingHaplogroupId, + evidence, + primers, + notes, + createdAt, + updatedAt + ).mapTo[VariantV2] + + // Foreign key to haplogroup for parallel mutation disambiguation + def definingHaplogroupFK = foreignKey( + "variant_v2_defining_haplogroup_fk", + definingHaplogroupId, + TableQuery[HaplogroupsTable] + )(_.haplogroupId.?, onDelete = ForeignKeyAction.SetNull) +} diff --git a/app/models/dal/domain/genomics/VariantsTable.scala b/app/models/dal/domain/genomics/VariantsTable.scala deleted file mode 100644 index 314be4c..0000000 --- a/app/models/dal/domain/genomics/VariantsTable.scala +++ /dev/null @@ -1,62 +0,0 @@ -package models.dal.domain.genomics - -import models.dal.domain.genomics.GenbankContigsTable -import models.domain.genomics.GenbankContig -import models.dal.MyPostgresProfile.api.* - -/** - * Represents the `variant` table in the database, which stores information about genetic variants. - * - * This table includes genomic variant details such as position, alleles, type, optional identifiers, and - * associated metadata. It is linked to the `GenbankContigsTable` through a foreign key and enforces - * uniqueness constraints on specific columns to ensure data integrity. - * - * @constructor Creates an instance of the `VariantsTable` class. - * @param tag A Slick `Tag` object used to scope and reference the table within a database schema. - * - * Schema details: - * - Table name: `variant` - * - Columns: - * - `variantId`: The primary key for the table, an auto-incrementing integer serving as a unique identifier for each variant. - * - `genbankContigId`: A foreign key referencing the `GenbankContigsTable`, indicating the genomic contig containing the variant. - * - `position`: The position of the variant on the genomic contig. - * - `referenceAllele`: The reference allele observed at the variant's position. - * - `alternateAllele`: The alternate allele representing the variant. - * - `variantType`: Specifies the type of the variant (e.g., SNP, insertion, deletion). - * - `rsId`: An optional column for the variant's dbSNP identifier (`rs` ID). - * - `commonName`: An optional column for a common name or description of the variant. - * - Primary key: - * - `variantId` - * - Foreign keys: - * - `genbankContigFK`: References the `genbank_contig_id` column in the `GenbankContigsTable`. Cascades deletions. - * - Indexes and constraints: - * - `uniqueVariant`: Enforces a unique constraint on the combination of `genbankContigId`, `position`, - * `referenceAllele`, and `alternateAllele`. - * - * Mapping: - * - Maps to the `Variant` case class, representing the domain model for a variant. The mapping includes all columns, - * with `variantId` being optional. - */ -class VariantsTable(tag: Tag) extends Table[Variant](tag, Some("public"), "variant") { - def variantId = column[Int]("variant_id", O.PrimaryKey, O.AutoInc) - - def genbankContigId = column[Int]("genbank_contig_id") - - def position = column[Int]("position") - - def referenceAllele = column[String]("reference_allele") - - def alternateAllele = column[String]("alternate_allele") - - def variantType = column[String]("variant_type") - - def rsId = column[Option[String]]("rs_id") - - def commonName = column[Option[String]]("common_name") - - def * = (variantId.?, genbankContigId, position, referenceAllele, alternateAllele, variantType, rsId, commonName).mapTo[Variant] - - def genbankContigFK = foreignKey("genbank_contig_fk", genbankContigId, TableQuery[GenbankContigsTable])(_.genbankContigId, onDelete = ForeignKeyAction.Cascade) - - def uniqueVariant = index("unique_variant", (genbankContigId, position, referenceAllele, alternateAllele), unique = true) -} diff --git a/app/models/dal/domain/haplogroups/HaplogroupVariantsTable.scala b/app/models/dal/domain/haplogroups/HaplogroupVariantsTable.scala index 2e0de3d..9d8f9c5 100644 --- a/app/models/dal/domain/haplogroups/HaplogroupVariantsTable.scala +++ b/app/models/dal/domain/haplogroups/HaplogroupVariantsTable.scala @@ -1,7 +1,7 @@ package models.dal.domain.haplogroups import models.dal.MyPostgresProfile.api.* -import models.dal.domain.genomics.{Variant, VariantsTable} +import models.dal.domain.genomics.VariantV2Table import models.domain.haplogroups.{Haplogroup, HaplogroupVariant} /** @@ -41,8 +41,8 @@ class HaplogroupVariantsTable(tag: Tag) extends Table[HaplogroupVariant](tag, So def haplogroupFK = foreignKey("haplogroup_fk", haplogroupId, TableQuery[HaplogroupsTable])(_.haplogroupId, onDelete = ForeignKeyAction.Cascade) - // Explicitly specify the schema for VariantsTable which is in the public schema - def variantFK = foreignKey("variant_fk", variantId, TableQuery[VariantsTable])(_.variantId, onDelete = ForeignKeyAction.Cascade) + // Foreign key to variant_v2 table + def variantFK = foreignKey("variant_fk", variantId, TableQuery[VariantV2Table])(_.variantId, onDelete = ForeignKeyAction.Cascade) def uniqueHaplogroupVariant = index("unique_haplogroup_variant", (haplogroupId, variantId), unique = true) } diff --git a/app/models/domain/genomics/MutationType.scala b/app/models/domain/genomics/MutationType.scala new file mode 100644 index 0000000..dbd7b05 --- /dev/null +++ b/app/models/domain/genomics/MutationType.scala @@ -0,0 +1,94 @@ +package models.domain.genomics + +import play.api.libs.json.* + +/** + * Represents the type of genetic mutation. + * + * Each mutation type has associated properties: + * - `dbValue`: The string stored in the database + * - `category`: Classification as Point, Repeat, or Structural + * - `displayName`: Human-readable name for UI display + */ +enum MutationType(val dbValue: String, val category: MutationCategory, val displayName: String) { + // Point mutations - single nucleotide or small changes + case SNP extends MutationType("SNP", MutationCategory.Point, "Single Nucleotide Polymorphism") + case INDEL extends MutationType("INDEL", MutationCategory.Point, "Insertion/Deletion") + case MNP extends MutationType("MNP", MutationCategory.Point, "Multi-Nucleotide Polymorphism") + + // Repeat variations + case STR extends MutationType("STR", MutationCategory.Repeat, "Short Tandem Repeat") + + // Structural variants - larger genomic rearrangements + case DEL extends MutationType("DEL", MutationCategory.Structural, "Deletion") + case DUP extends MutationType("DUP", MutationCategory.Structural, "Duplication") + case INS extends MutationType("INS", MutationCategory.Structural, "Insertion") + case INV extends MutationType("INV", MutationCategory.Structural, "Inversion") + case CNV extends MutationType("CNV", MutationCategory.Structural, "Copy Number Variant") + case TRANS extends MutationType("TRANS", MutationCategory.Structural, "Translocation") + + override def toString: String = dbValue + + def isPointMutation: Boolean = category == MutationCategory.Point + def isRepeat: Boolean = category == MutationCategory.Repeat + def isStructural: Boolean = category == MutationCategory.Structural +} + +/** + * Category of mutation types. + */ +enum MutationCategory { + case Point, Repeat, Structural +} + +object MutationType { + /** + * Parse a database string value to MutationType. + */ + def fromString(str: String): Option[MutationType] = str.toUpperCase match { + case "SNP" => Some(SNP) + case "INDEL" => Some(INDEL) + case "MNP" => Some(MNP) + case "STR" => Some(STR) + case "DEL" => Some(DEL) + case "DUP" => Some(DUP) + case "INS" => Some(INS) + case "INV" => Some(INV) + case "CNV" => Some(CNV) + case "TRANS" => Some(TRANS) + case _ => None + } + + /** + * Parse with a default fallback. + */ + def fromStringOrDefault(str: String, default: MutationType = SNP): MutationType = + fromString(str).getOrElse(default) + + /** + * All point mutation types. + */ + val pointTypes: Set[MutationType] = Set(SNP, INDEL, MNP) + + /** + * All structural variant types. + */ + val structuralTypes: Set[MutationType] = Set(DEL, DUP, INS, INV, CNV, TRANS) + + /** + * All mutation types. + */ + val allTypes: Set[MutationType] = MutationType.values.toSet + + // JSON serialization + implicit val reads: Reads[MutationType] = Reads.StringReads.flatMap { str => + fromString(str) match { + case Some(mt) => Reads.pure(mt) + case None => Reads.failed(s"Invalid MutationType: $str") + } + } + + implicit val writes: Writes[MutationType] = Writes.StringWrites.contramap(_.dbValue) + + implicit val format: Format[MutationType] = Format(reads, writes) +} diff --git a/app/models/domain/genomics/NamingStatus.scala b/app/models/domain/genomics/NamingStatus.scala new file mode 100644 index 0000000..2a3e8c3 --- /dev/null +++ b/app/models/domain/genomics/NamingStatus.scala @@ -0,0 +1,60 @@ +package models.domain.genomics + +import play.api.libs.json.* + +/** + * Represents the naming status of a variant. + * + * Each status has associated properties: + * - `dbValue`: The string stored in the database + * - `displayName`: Human-readable name for UI display + * - `isNamed`: Whether the variant has an official name + */ +enum NamingStatus(val dbValue: String, val displayName: String, val isNamed: Boolean) { + /** + * Variant has no official name - typically identified only by coordinates. + */ + case Unnamed extends NamingStatus("UNNAMED", "Unnamed", false) + + /** + * Variant has been submitted for naming review but not yet approved. + */ + case PendingReview extends NamingStatus("PENDING_REVIEW", "Pending Review", false) + + /** + * Variant has an official canonical name. + */ + case Named extends NamingStatus("NAMED", "Named", true) + + override def toString: String = dbValue +} + +object NamingStatus { + /** + * Parse a database string value to NamingStatus. + */ + def fromString(str: String): Option[NamingStatus] = str.toUpperCase match { + case "UNNAMED" => Some(Unnamed) + case "PENDING_REVIEW" => Some(PendingReview) + case "NAMED" => Some(Named) + case _ => None + } + + /** + * Parse with a default fallback. + */ + def fromStringOrDefault(str: String, default: NamingStatus = Unnamed): NamingStatus = + fromString(str).getOrElse(default) + + // JSON serialization + implicit val reads: Reads[NamingStatus] = Reads.StringReads.flatMap { str => + fromString(str) match { + case Some(ns) => Reads.pure(ns) + case None => Reads.failed(s"Invalid NamingStatus: $str") + } + } + + implicit val writes: Writes[NamingStatus] = Writes.StringWrites.contramap(_.dbValue) + + implicit val format: Format[NamingStatus] = Format(reads, writes) +} diff --git a/app/models/domain/genomics/VariantGroup.scala b/app/models/domain/genomics/VariantGroup.scala deleted file mode 100644 index 4dfb63b..0000000 --- a/app/models/domain/genomics/VariantGroup.scala +++ /dev/null @@ -1,84 +0,0 @@ -package models.domain.genomics - -/** - * Groups variants that represent the same logical SNP across different reference builds. - * Variants are grouped by commonName (primary) or rsId (fallback). - * - * For example, M269 might have positions in GRCh37, GRCh38, and hs1, - * each stored as a separate Variant row but logically the same marker. - * - * @param groupKey The key used to group these variants (commonName or rsId) - * @param variants All variants (with their contig info) that share this group key - * @param rsId The rsId if present on any variant in the group - * @param commonName The common name if present on any variant in the group - */ -case class VariantGroup( - groupKey: String, - variants: Seq[VariantWithContig], - rsId: Option[String], - commonName: Option[String] -) { - /** - * Get all variant IDs in this group - */ - def variantIds: Seq[Int] = variants.flatMap(_.variant.variantId) - - /** - * Display name for the variant group (commonName preferred, rsId fallback) - */ - def displayName: String = commonName.orElse(rsId).getOrElse(s"ID: ${variantIds.headOption.getOrElse("?")}") - - /** - * Summary of all builds available (e.g., "GRCh37, GRCh38, hs1") - */ - def buildSummary: String = variants - .map(_.shortReferenceGenome) - .distinct - .sorted - .mkString(", ") - - /** - * Number of reference builds available for this variant - */ - def buildCount: Int = variants.map(_.shortReferenceGenome).distinct.size - - /** - * Variants sorted by reference genome for consistent display - */ - def variantsSorted: Seq[VariantWithContig] = variants.sortBy { v => - v.shortReferenceGenome match { - case "GRCh37" => 1 - case "GRCh38" => 2 - case "hs1" => 3 - case other => 4 - } - } -} - -object VariantGroup { - /** - * Creates variant groups from a sequence of variants with contig info. - * Groups by commonName (primary), falling back to rsId. - * Variants without either become single-variant groups keyed by variant ID. - */ - def fromVariants(variants: Seq[VariantWithContig]): Seq[VariantGroup] = { - // Group by the key (commonName preferred, rsId fallback, variantId last resort) - val grouped = variants.groupBy { vwc => - vwc.variant.commonName - .orElse(vwc.variant.rsId) - .getOrElse(s"variant_${vwc.variant.variantId.getOrElse(0)}") - } - - grouped.map { case (key, variantsInGroup) => - val rsId = variantsInGroup.flatMap(_.variant.rsId).headOption - val commonName = variantsInGroup.flatMap(_.variant.commonName).headOption - - VariantGroup( - groupKey = key, - variants = variantsInGroup, - rsId = rsId, - commonName = commonName - ) - }.toSeq.sortBy(_.displayName) - } -} diff --git a/app/models/domain/genomics/VariantV2.scala b/app/models/domain/genomics/VariantV2.scala new file mode 100644 index 0000000..e1a04ec --- /dev/null +++ b/app/models/domain/genomics/VariantV2.scala @@ -0,0 +1,257 @@ +package models.domain.genomics + +import play.api.libs.json.{__, JsValue, Json, OFormat, Format, Reads, Writes} + +import java.time.Instant + +/** + * Consolidated variant with JSONB coordinates and aliases. + * One row per logical variant across all reference genomes. + * + * @param variantId Unique identifier (auto-generated) + * @param canonicalName Primary name (e.g., "M269", "DYS456"); None for unnamed variants + * @param mutationType Variant type (SNP, INDEL, MNP, STR, DEL, DUP, INS, INV, CNV, TRANS) + * @param namingStatus Naming status (Unnamed, PendingReview, Named) + * @param aliases JSONB: {common_names: [], rs_ids: [], sources: {source: [names]}} + * @param coordinates JSONB: Per-assembly coordinates (structure varies by mutationType) + * @param definingHaplogroupId FK to haplogroup for parallel mutation disambiguation + * @param evidence JSONB: Evidence metadata (e.g., YSEQ test counts) + * @param primers JSONB: PCR primer information + * @param notes Free-text notes + * @param createdAt Creation timestamp + * @param updatedAt Last update timestamp + */ +case class VariantV2( + variantId: Option[Int] = None, + canonicalName: Option[String], + mutationType: MutationType, + namingStatus: NamingStatus = NamingStatus.Unnamed, + aliases: JsValue = Json.obj(), + coordinates: JsValue = Json.obj(), + definingHaplogroupId: Option[Int] = None, + evidence: JsValue = Json.obj(), + primers: JsValue = Json.obj(), + notes: Option[String] = None, + createdAt: Instant = Instant.now(), + updatedAt: Instant = Instant.now() +) { + + /** + * Get coordinate entry for a specific reference genome. + */ + def getCoordinates(refGenome: String): Option[JsValue] = + (coordinates \ refGenome).toOption + + /** + * Check if variant has coordinates for a given reference. + */ + def hasCoordinates(refGenome: String): Boolean = + (coordinates \ refGenome).isDefined + + /** + * Get all reference genomes that have coordinates. + */ + def availableReferences: Set[String] = + coordinates.asOpt[Map[String, JsValue]].map(_.keySet).getOrElse(Set.empty) + + /** + * Get common names from aliases. + */ + def commonNames: Seq[String] = + (aliases \ "common_names").asOpt[Seq[String]].getOrElse(Seq.empty) + + /** + * Get rs IDs from aliases. + */ + def rsIds: Seq[String] = + (aliases \ "rs_ids").asOpt[Seq[String]].getOrElse(Seq.empty) + + /** + * Check if this is an STR marker. + */ + def isStr: Boolean = mutationType == MutationType.STR + + /** + * Check if this is a structural variant. + */ + def isStructuralVariant: Boolean = mutationType.isStructural + + /** + * Display name for UI (canonical name or coordinate-based fallback). + */ + def displayName: String = canonicalName.getOrElse { + // For unnamed variants, show coordinate-based identifier + getCoordinates("hs1").orElse(getCoordinates("GRCh38")).map { coords => + val contig = (coords \ "contig").asOpt[String].getOrElse("?") + val position = (coords \ "position").asOpt[Int].orElse((coords \ "start").asOpt[Int]).getOrElse(0) + val ref = (coords \ "ref").asOpt[String].getOrElse("") + val alt = (coords \ "alt").asOpt[String].getOrElse("") + if (ref.nonEmpty && alt.nonEmpty) s"$contig:$position:$ref>$alt" + else s"$contig:$position" + }.getOrElse(s"variant_${variantId.getOrElse(0)}") + } +} + +/** + * Helper case class for SNP/INDEL/MNP coordinates. + */ +case class PointVariantCoordinates( + contig: String, + position: Int, + ref: String, + alt: String +) + +object PointVariantCoordinates { + implicit val format: OFormat[PointVariantCoordinates] = Json.format[PointVariantCoordinates] +} + +/** + * Helper case class for STR coordinates. + */ +case class StrCoordinates( + contig: String, + start: Long, + end: Long, + period: Int, + repeatMotif: Option[String] = None, + referenceRepeats: Option[Int] = None +) + +object StrCoordinates { + implicit val format: OFormat[StrCoordinates] = Json.format[StrCoordinates] +} + +/** + * Helper case class for structural variant coordinates. + */ +case class SvCoordinates( + contig: String, + start: Long, + end: Long, + length: Long, + innerStart: Option[Long] = None, // For inversions + innerEnd: Option[Long] = None, // For inversions + referenceCopies: Option[Int] = None, // For CNVs + copyNumberRange: Option[Seq[Int]] = None // For CNVs +) + +object SvCoordinates { + implicit val format: OFormat[SvCoordinates] = Json.format[SvCoordinates] +} + +/** + * Helper case class for aliases structure. + */ +case class VariantAliases( + commonNames: Seq[String] = Seq.empty, + rsIds: Seq[String] = Seq.empty, + sources: Map[String, Seq[String]] = Map.empty +) + +object VariantAliases { + implicit val format: OFormat[VariantAliases] = Json.format[VariantAliases] + + val empty: VariantAliases = VariantAliases() + + /** + * Create from a single source with names. + */ + def fromSource(source: String, names: Seq[String], rsIds: Seq[String] = Seq.empty): VariantAliases = + VariantAliases( + commonNames = names, + rsIds = rsIds, + sources = Map(source -> names) + ) +} + +object VariantV2 { + // Custom format that handles enum serialization via dbValue strings + implicit val format: Format[VariantV2] = { + import play.api.libs.functional.syntax.* + + val reads: Reads[VariantV2] = ( + (__ \ "variantId").readNullable[Int] and + (__ \ "canonicalName").readNullable[String] and + (__ \ "mutationType").read[String].map(MutationType.fromStringOrDefault(_)) and + (__ \ "namingStatus").read[String].map(NamingStatus.fromStringOrDefault(_)) and + (__ \ "aliases").read[JsValue] and + (__ \ "coordinates").read[JsValue] and + (__ \ "definingHaplogroupId").readNullable[Int] and + (__ \ "evidence").read[JsValue] and + (__ \ "primers").read[JsValue] and + (__ \ "notes").readNullable[String] and + (__ \ "createdAt").read[Instant] and + (__ \ "updatedAt").read[Instant] + )(VariantV2.apply) + + val writes: Writes[VariantV2] = ( + (__ \ "variantId").writeNullable[Int] and + (__ \ "canonicalName").writeNullable[String] and + (__ \ "mutationType").write[String].contramap[MutationType](_.dbValue) and + (__ \ "namingStatus").write[String].contramap[NamingStatus](_.dbValue) and + (__ \ "aliases").write[JsValue] and + (__ \ "coordinates").write[JsValue] and + (__ \ "definingHaplogroupId").writeNullable[Int] and + (__ \ "evidence").write[JsValue] and + (__ \ "primers").write[JsValue] and + (__ \ "notes").writeNullable[String] and + (__ \ "createdAt").write[Instant] and + (__ \ "updatedAt").write[Instant] + )(v => (v.variantId, v.canonicalName, v.mutationType, v.namingStatus, v.aliases, + v.coordinates, v.definingHaplogroupId, v.evidence, v.primers, v.notes, + v.createdAt, v.updatedAt)) + + Format(reads, writes) + } + + /** + * Create a named SNP variant with coordinates for a single reference. + */ + def snp( + name: String, + refGenome: String, + contig: String, + position: Int, + ref: String, + alt: String, + source: Option[String] = None + ): VariantV2 = { + val coords = Json.obj( + refGenome -> Json.toJson(PointVariantCoordinates(contig, position, ref, alt)) + ) + val aliases = source.map { s => + Json.toJson(VariantAliases.fromSource(s, Seq(name))) + }.getOrElse(Json.toJson(VariantAliases(commonNames = Seq(name)))) + + VariantV2( + canonicalName = Some(name), + mutationType = MutationType.SNP, + namingStatus = NamingStatus.Named, + aliases = aliases, + coordinates = coords + ) + } + + /** + * Create an unnamed variant from coordinates. + */ + def unnamed( + refGenome: String, + contig: String, + position: Int, + ref: String, + alt: String, + variantType: MutationType = MutationType.SNP + ): VariantV2 = { + val coords = Json.obj( + refGenome -> Json.toJson(PointVariantCoordinates(contig, position, ref, alt)) + ) + VariantV2( + canonicalName = None, + mutationType = variantType, + namingStatus = NamingStatus.Unnamed, + coordinates = coords + ) + } +} diff --git a/app/models/domain/genomics/VariantWithContig.scala b/app/models/domain/genomics/VariantWithContig.scala deleted file mode 100644 index 5c5a656..0000000 --- a/app/models/domain/genomics/VariantWithContig.scala +++ /dev/null @@ -1,27 +0,0 @@ -package models.domain.genomics - -import models.dal.domain.genomics.Variant - -/** - * View model that combines a Variant with its associated GenbankContig information. - * Used for display purposes in the curator interface. - * - * @param variant The variant data - * @param contig The associated genbank contig (for position context) - */ -case class VariantWithContig( - variant: Variant, - contig: GenbankContig -) { - /** - * Formats the position as "accession:position" (e.g., "chrY:11912037") - */ - def formattedPosition: String = s"${contig.commonName.getOrElse(contig.accession)}:${variant.position}" - - /** - * Gets a short reference genome label (e.g., "GRCh38" from "GRCh38.p14") - */ - def shortReferenceGenome: String = contig.referenceGenome - .map(_.split("\\.").head) - .getOrElse("Unknown") -} diff --git a/app/modules/BaseModule.scala b/app/modules/BaseModule.scala index 9be100f..f7414a0 100644 --- a/app/modules/BaseModule.scala +++ b/app/modules/BaseModule.scala @@ -30,8 +30,7 @@ class BaseModule extends AbstractModule { bind(classOf[UserRoleRepository]).asEagerSingleton() bind(classOf[GenbankContigRepository]).to(classOf[GenbankContigRepositoryImpl]) - bind(classOf[VariantRepository]).to(classOf[VariantRepositoryImpl]) - bind(classOf[VariantAliasRepository]).to(classOf[VariantAliasRepositoryImpl]) + bind(classOf[VariantV2Repository]).to(classOf[VariantV2RepositoryImpl]) bind(classOf[HaplogroupCoreRepository]).to(classOf[HaplogroupCoreRepositoryImpl]) bind(classOf[HaplogroupRelationshipRepository]).to(classOf[HaplogroupRelationshipRepositoryImpl]) bind(classOf[HaplogroupRevisionMetadataRepository]).to(classOf[HaplogroupRevisionMetadataRepositoryImpl]) diff --git a/app/repositories/GenomeRegionsRepository.scala b/app/repositories/GenomeRegionsRepository.scala index b145c1f..d254ea7 100644 --- a/app/repositories/GenomeRegionsRepository.scala +++ b/app/repositories/GenomeRegionsRepository.scala @@ -136,12 +136,9 @@ class GenomeRegionsRepositoryImpl @Inject()( db.run(query) } + // STR marker table was replaced in schema migration - stub for now override def getStrMarkersForContig(contigId: Int): Future[Seq[StrMarker]] = { - val query = strMarkers - .filter(_.genbankContigId === contigId) - .sortBy(_.startPos) - .result - db.run(query) + Future.successful(Seq.empty) } override def getFullBuildData(referenceGenome: String): Future[FullBuildData] = { @@ -168,21 +165,12 @@ class GenomeRegionsRepositoryImpl @Inject()( db.run(query) } else Future.successful(Seq.empty) - // Fetch all STR markers for the build's contigs - allStrMarkers <- if (contigIds.nonEmpty) { - val query = strMarkers - .filter(_.genbankContigId.inSet(contigIds)) - .sortBy(s => (s.genbankContigId, s.startPos)) - .result - db.run(query) - } else Future.successful(Seq.empty) - } yield FullBuildData( version = version, contigs = contigs, regions = allRegions.groupBy(_.genbankContigId), cytobands = allCytobands.groupBy(_.genbankContigId), - strMarkers = allStrMarkers.groupBy(_.genbankContigId) + strMarkers = Map.empty // STR marker table was replaced in schema migration ) } @@ -298,56 +286,39 @@ class GenomeRegionsRepositoryImpl @Inject()( // ============================================================================ // StrMarker CRUD implementations + // NOTE: STR marker table was replaced with str_mutation_rate in schema migration. + // These methods are stubbed to maintain API compatibility. // ============================================================================ override def findStrMarkerById(id: Int): Future[Option[StrMarker]] = { - db.run(strMarkers.filter(_.id === id).result.headOption) + Future.successful(None) } override def findStrMarkerByIdWithContig(id: Int): Future[Option[(StrMarker, GenbankContig)]] = { - val query = for { - marker <- strMarkers if marker.id === id - contig <- genbankContigs if contig.genbankContigId === marker.genbankContigId - } yield (marker, contig) - db.run(query.result.headOption) + Future.successful(None) } override def findStrMarkersByBuild(referenceGenome: String, offset: Int, limit: Int): Future[Seq[(StrMarker, GenbankContig)]] = { - val query = for { - marker <- strMarkers - contig <- genbankContigs if contig.genbankContigId === marker.genbankContigId && contig.referenceGenome === referenceGenome - } yield (marker, contig) - db.run(query.sortBy(_._1.startPos).drop(offset).take(limit).result) + Future.successful(Seq.empty) } override def countStrMarkersByBuild(referenceGenome: Option[String]): Future[Int] = { - val query = referenceGenome match { - case Some(ref) => - for { - marker <- strMarkers - contig <- genbankContigs if contig.genbankContigId === marker.genbankContigId && contig.referenceGenome === ref - } yield marker - case None => strMarkers - } - db.run(query.length.result) + Future.successful(0) } override def createStrMarker(marker: StrMarker): Future[Int] = { - db.run((strMarkers returning strMarkers.map(_.id)) += marker) + Future.failed(new UnsupportedOperationException("STR marker table has been replaced with str_mutation_rate")) } override def updateStrMarker(id: Int, marker: StrMarker): Future[Boolean] = { - val query = strMarkers.filter(_.id === id).map(m => - (m.genbankContigId, m.name, m.startPos, m.endPos, m.period, m.verified, m.note) - ).update((marker.genbankContigId, marker.name, marker.startPos, marker.endPos, marker.period, marker.verified, marker.note)) - db.run(query).map(_ > 0) + Future.successful(false) } override def deleteStrMarker(id: Int): Future[Boolean] = { - db.run(strMarkers.filter(_.id === id).delete).map(_ > 0) + Future.successful(false) } override def bulkCreateStrMarkers(markers: Seq[StrMarker]): Future[Seq[Int]] = { - db.run((strMarkers returning strMarkers.map(_.id)) ++= markers) + Future.failed(new UnsupportedOperationException("STR marker table has been replaced with str_mutation_rate")) } } diff --git a/app/repositories/HaplogroupCoreRepository.scala b/app/repositories/HaplogroupCoreRepository.scala index ca3e822..e0182ad 100644 --- a/app/repositories/HaplogroupCoreRepository.scala +++ b/app/repositories/HaplogroupCoreRepository.scala @@ -447,7 +447,7 @@ class HaplogroupCoreRepositoryImpl @Inject()( override def getAllWithVariantNames(haplogroupType: HaplogroupType): Future[Seq[(Haplogroup, Seq[String])]] = { import models.dal.DatabaseSchema.domain.haplogroups.haplogroupVariants - import models.dal.DatabaseSchema.domain.genomics.variants + import models.dal.DatabaseSchema.domain.genomics.variantsV2 // Query haplogroups with their associated variant names via join val query = for { @@ -455,12 +455,12 @@ class HaplogroupCoreRepositoryImpl @Inject()( } yield hg runQuery(query.result).flatMap { hgList => - // For each haplogroup, fetch its variant names (using commonName from Variant table) + // For each haplogroup, fetch its variant names (using canonicalName from VariantV2 table) val futures = hgList.map { hg => val variantQuery = for { hv <- haplogroupVariants.filter(_.haplogroupId === hg.id.get) - v <- variants.filter(_.variantId === hv.variantId) - } yield v.commonName + v <- variantsV2.filter(_.variantId === hv.variantId) + } yield v.canonicalName runQuery(variantQuery.result).map { variantNames => (hg, variantNames.flatten) // Filter out None values diff --git a/app/repositories/HaplogroupVariantRepository.scala b/app/repositories/HaplogroupVariantRepository.scala index 68368ee..e57c998 100644 --- a/app/repositories/HaplogroupVariantRepository.scala +++ b/app/repositories/HaplogroupVariantRepository.scala @@ -2,8 +2,7 @@ package repositories import jakarta.inject.Inject import models.* -import models.dal.domain.genomics.Variant -import models.domain.genomics.GenbankContig +import models.domain.genomics.{MutationType, NamingStatus, VariantV2} import models.domain.haplogroups.{Haplogroup, HaplogroupVariant} import play.api.db.slick.DatabaseConfigProvider @@ -19,15 +18,15 @@ trait HaplogroupVariantRepository { * @param query The search query used to filter and retrieve the relevant variants. * @return A future containing a sequence of variants that match the provided query. */ - def findVariants(query: String): Future[Seq[Variant]] + def findVariants(query: String): Future[Seq[VariantV2]] /** * Retrieves the list of variants associated with a given haplogroup. * * @param haplogroupId the identifier of the haplogroup for which variants are to be retrieved - * @return a future containing a sequence of tuples, where each tuple consists of a Variant and its associated GenbankContig + * @return a future containing a sequence of VariantV2 objects */ - def getHaplogroupVariants(haplogroupId: Int): Future[Seq[(Variant, GenbankContig)]] + def getHaplogroupVariants(haplogroupId: Int): Future[Seq[VariantV2]] def countHaplogroupVariants(haplogroupId: Long): Future[Int] @@ -35,9 +34,9 @@ trait HaplogroupVariantRepository { * Retrieves a list of genetic variants associated with the given haplogroup. * * @param haplogroupId The unique identifier of the haplogroup for which the variants are being requested. - * @return A Future containing a sequence of Variant objects associated with the specified haplogroup. + * @return A Future containing a sequence of VariantV2 objects associated with the specified haplogroup. */ - def getVariantsByHaplogroup(haplogroupId: Int): Future[Seq[Variant]] + def getVariantsByHaplogroup(haplogroupId: Int): Future[Seq[VariantV2]] /** * Retrieves a list of haplogroups associated with the specified variant. @@ -78,9 +77,9 @@ trait HaplogroupVariantRepository { * Retrieves variants associated with a haplogroup by its name. * * @param haplogroupName The name of the haplogroup (e.g., "R-M269") - * @return A Future containing a sequence of VariantWithContig for the haplogroup + * @return A Future containing a sequence of VariantV2 for the haplogroup */ - def getVariantsByHaplogroupName(haplogroupName: String): Future[Seq[models.domain.genomics.VariantWithContig]] + def getVariantsByHaplogroupName(haplogroupName: String): Future[Seq[VariantV2]] } class HaplogroupVariantRepositoryImpl @Inject()( @@ -89,76 +88,118 @@ class HaplogroupVariantRepositoryImpl @Inject()( extends BaseRepository(dbConfigProvider) with HaplogroupVariantRepository { - import models.dal.DatabaseSchema.* - import models.dal.DatabaseSchema.domain.genomics.{genbankContigs, variants} import models.dal.DatabaseSchema.domain.haplogroups.{haplogroupVariants, haplogroups} import models.dal.MyPostgresProfile.api.* + import models.dal.domain.genomics.VariantV2Table + import play.api.libs.json.Json + import slick.jdbc.GetResult + + private val variantsV2 = TableQuery[VariantV2Table] + + // GetResult for raw SQL queries + private implicit val variantV2GetResult: GetResult[VariantV2] = GetResult { r => + VariantV2( + variantId = Some(r.nextInt()), + canonicalName = r.nextStringOption(), + mutationType = MutationType.fromStringOrDefault(r.nextString()), + namingStatus = NamingStatus.fromStringOrDefault(r.nextString()), + aliases = Json.parse(r.nextString()), + coordinates = Json.parse(r.nextString()), + definingHaplogroupId = r.nextIntOption(), + evidence = Json.parse(r.nextString()), + primers = Json.parse(r.nextString()), + notes = r.nextStringOption(), + createdAt = r.nextTimestamp().toInstant, + updatedAt = r.nextTimestamp().toInstant + ) + } - override def findVariants(query: String): Future[Seq[Variant]] = { + override def findVariants(query: String): Future[Seq[VariantV2]] = { val normalizedQuery = query.trim.toLowerCase - - def buildQuery = { - if (normalizedQuery.startsWith("rs")) { - variants.filter(v => v.rsId.isDefined && v.rsId === normalizedQuery) - } else if (normalizedQuery.contains(":")) { - val parts = normalizedQuery.split(":") - parts.length match { - case 2 => - for { - variant <- variants - contig <- genbankContigs if variant.genbankContigId === contig.genbankContigId - if (variant.commonName.isDefined && variant.commonName === parts(0)) || - (contig.commonName.isDefined && contig.commonName === parts(0)) - if variant.position === parts(1).toIntOption.getOrElse(0) - } yield variant - case 4 => - for { - variant <- variants - contig <- genbankContigs if variant.genbankContigId === contig.genbankContigId - if (variant.commonName.isDefined && variant.commonName === parts(0)) || - (contig.commonName.isDefined && contig.commonName === parts(0)) - if variant.position === parts(1).toIntOption.getOrElse(0) && - variant.referenceAllele === parts(2) && - variant.alternateAllele === parts(3) - } yield variant - case _ => - variants.filter(_ => false) - } - } else { - variants.filter(v => - (v.rsId.isDefined && v.rsId === normalizedQuery) || - (v.commonName.isDefined && v.commonName === normalizedQuery) - ) + val upperQuery = normalizedQuery.toUpperCase + val searchPattern = s"%$upperQuery%" + + // Handle different query formats + if (normalizedQuery.startsWith("rs")) { + // Search rs_ids in aliases + val rsQuery = sql""" + SELECT * FROM variant_v2 + WHERE aliases->'rs_ids' ? $normalizedQuery + """.as[VariantV2] + runQuery(rsQuery) + } else if (normalizedQuery.contains(":")) { + // Coordinate-based search (contig:position or contig:position:ref:alt) + val parts = normalizedQuery.split(":") + parts.length match { + case 2 => + val contig = parts(0) + val position = parts(1).toIntOption.getOrElse(0) + val coordQuery = sql""" + SELECT * FROM variant_v2 + WHERE EXISTS ( + SELECT 1 FROM jsonb_each(coordinates) AS c(ref_genome, coords) + WHERE coords->>'contig' ILIKE $contig + AND (coords->>'position')::int = $position + ) + """.as[VariantV2] + runQuery(coordQuery) + case 4 => + val contig = parts(0) + val position = parts(1).toIntOption.getOrElse(0) + val ref = parts(2).toUpperCase + val alt = parts(3).toUpperCase + val coordQuery = sql""" + SELECT * FROM variant_v2 + WHERE EXISTS ( + SELECT 1 FROM jsonb_each(coordinates) AS c(ref_genome, coords) + WHERE coords->>'contig' ILIKE $contig + AND (coords->>'position')::int = $position + AND UPPER(coords->>'ref') = $ref + AND UPPER(coords->>'alt') = $alt + ) + """.as[VariantV2] + runQuery(coordQuery) + case _ => + Future.successful(Seq.empty) } + } else { + // Search by canonical name or aliases + val nameQuery = sql""" + SELECT * FROM variant_v2 + WHERE UPPER(canonical_name) LIKE $searchPattern + OR aliases->'common_names' ? $normalizedQuery + OR EXISTS ( + SELECT 1 FROM jsonb_array_elements_text(aliases->'common_names') AS name + WHERE UPPER(name) LIKE $searchPattern + ) + LIMIT 100 + """.as[VariantV2] + runQuery(nameQuery) } - - runQuery(buildQuery.result) } - override def getHaplogroupVariants(haplogroupId: Int): Future[Seq[(Variant, GenbankContig)]] = { + override def getHaplogroupVariants(haplogroupId: Int): Future[Seq[VariantV2]] = { val query = for { hv <- haplogroupVariants if hv.haplogroupId === haplogroupId - v <- variants if v.variantId === hv.variantId - gc <- genbankContigs if gc.genbankContigId === v.genbankContigId - } yield (v, gc) + v <- variantsV2 if v.variantId === hv.variantId + } yield v runQuery(query.result) } def countHaplogroupVariants(haplogroupId: Long): Future[Int] = { - val q = (for { + val q = for { hv <- haplogroupVariants if hv.haplogroupId === haplogroupId.toInt - v <- variants if hv.variantId === v.variantId - } yield v.commonName) + v <- variantsV2 if hv.variantId === v.variantId + } yield v.canonicalName runQuery(q.distinct.length.result) } - - override def getVariantsByHaplogroup(haplogroupId: Int): Future[Seq[Variant]] = { + override def getVariantsByHaplogroup(haplogroupId: Int): Future[Seq[VariantV2]] = { val query = for { hv <- haplogroupVariants if hv.haplogroupId === haplogroupId - variant <- variants if variant.variantId === hv.variantId + variant <- variantsV2 if variant.variantId === hv.variantId } yield variant runQuery(query.result) @@ -175,7 +216,7 @@ class HaplogroupVariantRepositoryImpl @Inject()( override def addVariantToHaplogroup(haplogroupId: Int, variantId: Int): Future[Int] = { val insertAction = sqlu""" - INSERT INTO haplogroup_variant (haplogroup_id, variant_id) + INSERT INTO tree.haplogroup_variant (haplogroup_id, variant_id) VALUES ($haplogroupId, $variantId) ON CONFLICT (haplogroup_id, variant_id) DO NOTHING """ @@ -191,27 +232,38 @@ class HaplogroupVariantRepositoryImpl @Inject()( } override def findHaplogroupsByDefiningVariant(variantId: String, haplogroupType: HaplogroupType): Future[Seq[Haplogroup]] = { - val query = for { - variant <- variants if variant.rsId === variantId || variant.variantId === variantId.toIntOption - haplogroupVariant <- haplogroupVariants if haplogroupVariant.variantId === variant.variantId - haplogroup <- haplogroups if - haplogroup.haplogroupId === haplogroupVariant.haplogroupId && - haplogroup.haplogroupType === haplogroupType - } yield haplogroup + // Search by canonical name or variant ID + val variantIdOpt = variantId.toIntOption + + val query = variantIdOpt match { + case Some(vid) => + for { + variant <- variantsV2 if variant.variantId === vid || variant.canonicalName === variantId + haplogroupVariant <- haplogroupVariants if haplogroupVariant.variantId === variant.variantId + haplogroup <- haplogroups if + haplogroup.haplogroupId === haplogroupVariant.haplogroupId && + haplogroup.haplogroupType === haplogroupType + } yield haplogroup + case None => + for { + variant <- variantsV2 if variant.canonicalName === variantId + haplogroupVariant <- haplogroupVariants if haplogroupVariant.variantId === variant.variantId + haplogroup <- haplogroups if + haplogroup.haplogroupId === haplogroupVariant.haplogroupId && + haplogroup.haplogroupType === haplogroupType + } yield haplogroup + } runQuery(query.result) } - override def getVariantsByHaplogroupName(haplogroupName: String): Future[Seq[models.domain.genomics.VariantWithContig]] = { + override def getVariantsByHaplogroupName(haplogroupName: String): Future[Seq[VariantV2]] = { val query = for { hg <- haplogroups if hg.name === haplogroupName hv <- haplogroupVariants if hv.haplogroupId === hg.haplogroupId - v <- variants if v.variantId === hv.variantId - c <- genbankContigs if c.genbankContigId === v.genbankContigId - } yield (v, c) + v <- variantsV2 if v.variantId === hv.variantId + } yield v - runQuery(query.result).map(_.map { case (v, c) => - models.domain.genomics.VariantWithContig(v, c) - }) + runQuery(query.result) } } \ No newline at end of file diff --git a/app/repositories/VariantAliasRepository.scala b/app/repositories/VariantAliasRepository.scala deleted file mode 100644 index 8202735..0000000 --- a/app/repositories/VariantAliasRepository.scala +++ /dev/null @@ -1,260 +0,0 @@ -package repositories - -import jakarta.inject.Inject -import models.dal.MyPostgresProfile -import models.dal.MyPostgresProfile.api.* -import models.dal.domain.genomics.{VariantAlias, VariantAliasTable} -import play.api.db.slick.{DatabaseConfigProvider, HasDatabaseConfigProvider} - -import scala.concurrent.{ExecutionContext, Future} - -/** - * Repository for managing variant aliases. - */ -trait VariantAliasRepository { - /** - * Find all aliases for a variant. - */ - def findByVariantId(variantId: Int): Future[Seq[VariantAlias]] - - /** - * Find variants by alias value (searches across all alias types). - */ - def findVariantIdsByAlias(aliasValue: String): Future[Seq[Int]] - - /** - * Find variants by alias value and type. - */ - def findVariantIdsByAliasAndType(aliasValue: String, aliasType: String): Future[Seq[Int]] - - /** - * Add an alias to a variant. Returns true if added, false if already exists. - */ - def addAlias(alias: VariantAlias): Future[Boolean] - - /** - * Add multiple aliases in batch. Returns count of aliases added. - */ - def addAliasesBatch(aliases: Seq[VariantAlias]): Future[Int] - - /** - * Check if an alias exists for a variant. - */ - def aliasExists(variantId: Int, aliasType: String, aliasValue: String): Future[Boolean] - - /** - * Set an alias as primary for its type (unsets other primaries of same type for the variant). - */ - def setPrimary(variantId: Int, aliasType: String, aliasValue: String): Future[Boolean] - - /** - * Delete an alias. - */ - def deleteAlias(variantId: Int, aliasType: String, aliasValue: String): Future[Boolean] - - /** - * Search aliases by partial match. - */ - def searchAliases(query: String, limit: Int): Future[Seq[VariantAlias]] - - /** - * Find aliases for multiple variants in batch. - * Returns a map of variantId -> Seq[VariantAlias] - */ - def findByVariantIds(variantIds: Seq[Int]): Future[Map[Int, Seq[VariantAlias]]] - - /** - * Bulk update source for aliases matching a prefix pattern. - * Used to fix migration data where source was not properly attributed. - * - * @param aliasPrefix The prefix to match (e.g., "FGC" matches "FGC29071") - * @param newSource The new source value (e.g., "FGC") - * @param oldSource Optional: only update aliases with this current source (e.g., "migration") - * @return Number of aliases updated - */ - def bulkUpdateSourceByPrefix(aliasPrefix: String, newSource: String, oldSource: Option[String]): Future[Int] - - /** - * Get distinct sources currently in the database. - */ - def getDistinctSources(): Future[Seq[String]] - - /** - * Count aliases by source. - */ - def countBySource(source: String): Future[Int] - - /** - * Count aliases matching a prefix with a specific source. - */ - def countByPrefixAndSource(aliasPrefix: String, source: String): Future[Int] -} - -class VariantAliasRepositoryImpl @Inject()( - protected val dbConfigProvider: DatabaseConfigProvider -)(implicit ec: ExecutionContext) - extends VariantAliasRepository - with HasDatabaseConfigProvider[MyPostgresProfile] { - - import models.dal.DatabaseSchema.domain.genomics.variantAliases - - override def findByVariantId(variantId: Int): Future[Seq[VariantAlias]] = { - db.run( - variantAliases - .filter(_.variantId === variantId) - .sortBy(a => (a.aliasType, a.isPrimary.desc)) - .result - ) - } - - override def findVariantIdsByAlias(aliasValue: String): Future[Seq[Int]] = { - val upperValue = aliasValue.toUpperCase - db.run( - variantAliases - .filter(_.aliasValue.toUpperCase === upperValue) - .map(_.variantId) - .distinct - .result - ) - } - - override def findVariantIdsByAliasAndType(aliasValue: String, aliasType: String): Future[Seq[Int]] = { - val upperValue = aliasValue.toUpperCase - db.run( - variantAliases - .filter(a => a.aliasValue.toUpperCase === upperValue && a.aliasType === aliasType) - .map(_.variantId) - .distinct - .result - ) - } - - override def addAlias(alias: VariantAlias): Future[Boolean] = { - val insertAction = variantAliases += alias - db.run(insertAction.asTry).map(_.isSuccess) - } - - override def addAliasesBatch(aliases: Seq[VariantAlias]): Future[Int] = { - if (aliases.isEmpty) { - Future.successful(0) - } else { - // Use insertOrUpdate to handle conflicts gracefully - val actions = aliases.map { alias => - sql""" - INSERT INTO variant_alias (variant_id, alias_type, alias_value, source, is_primary, created_at) - VALUES (${alias.variantId}, ${alias.aliasType}, ${alias.aliasValue}, ${alias.source}, ${alias.isPrimary}, NOW()) - ON CONFLICT (variant_id, alias_type, alias_value) DO NOTHING - """.asUpdate - } - db.run(DBIO.sequence(actions).transactionally).map(_.sum) - } - } - - override def aliasExists(variantId: Int, aliasType: String, aliasValue: String): Future[Boolean] = { - db.run( - variantAliases - .filter(a => a.variantId === variantId && a.aliasType === aliasType && a.aliasValue === aliasValue) - .exists - .result - ) - } - - override def setPrimary(variantId: Int, aliasType: String, aliasValue: String): Future[Boolean] = { - val action = for { - // First, unset all primaries of this type for this variant - _ <- variantAliases - .filter(a => a.variantId === variantId && a.aliasType === aliasType) - .map(_.isPrimary) - .update(false) - // Then set the specified one as primary - updated <- variantAliases - .filter(a => a.variantId === variantId && a.aliasType === aliasType && a.aliasValue === aliasValue) - .map(_.isPrimary) - .update(true) - } yield updated > 0 - - db.run(action.transactionally) - } - - override def deleteAlias(variantId: Int, aliasType: String, aliasValue: String): Future[Boolean] = { - db.run( - variantAliases - .filter(a => a.variantId === variantId && a.aliasType === aliasType && a.aliasValue === aliasValue) - .delete - ).map(_ > 0) - } - - override def searchAliases(query: String, limit: Int): Future[Seq[VariantAlias]] = { - val upperQuery = query.toUpperCase - db.run( - variantAliases - .filter(_.aliasValue.toUpperCase like s"%$upperQuery%") - .sortBy(_.aliasValue) - .take(limit) - .result - ) - } - - override def findByVariantIds(variantIds: Seq[Int]): Future[Map[Int, Seq[VariantAlias]]] = { - if (variantIds.isEmpty) { - Future.successful(Map.empty) - } else { - db.run( - variantAliases - .filter(_.variantId inSet variantIds) - .sortBy(a => (a.variantId, a.aliasType, a.isPrimary.desc)) - .result - ).map(_.groupBy(_.variantId)) - } - } - - override def bulkUpdateSourceByPrefix(aliasPrefix: String, newSource: String, oldSource: Option[String]): Future[Int] = { - val upperPrefix = aliasPrefix.toUpperCase - val updateQuery = oldSource match { - case Some(oldSrc) => - sql""" - UPDATE variant_alias - SET source = $newSource - WHERE UPPER(alias_value) LIKE ${upperPrefix + "%"} - AND (source = $oldSrc OR source IS NULL) - """.asUpdate - case None => - sql""" - UPDATE variant_alias - SET source = $newSource - WHERE UPPER(alias_value) LIKE ${upperPrefix + "%"} - """.asUpdate - } - db.run(updateQuery) - } - - override def getDistinctSources(): Future[Seq[String]] = { - db.run( - variantAliases - .map(_.source) - .distinct - .result - ).map(_.flatten) - } - - override def countBySource(source: String): Future[Int] = { - db.run( - variantAliases - .filter(_.source === source) - .length - .result - ) - } - - override def countByPrefixAndSource(aliasPrefix: String, source: String): Future[Int] = { - val upperPrefix = aliasPrefix.toUpperCase - db.run( - sql""" - SELECT COUNT(*) - FROM variant_alias - WHERE UPPER(alias_value) LIKE ${upperPrefix + "%"} - AND source = $source - """.as[Int].head - ) - } -} diff --git a/app/repositories/VariantRepository.scala b/app/repositories/VariantRepository.scala deleted file mode 100644 index 158b859..0000000 --- a/app/repositories/VariantRepository.scala +++ /dev/null @@ -1,530 +0,0 @@ -package repositories - -import jakarta.inject.Inject -import models.dal.MyPostgresProfile -import models.dal.MyPostgresProfile.api.* -import models.dal.domain.genomics.Variant -import models.domain.genomics.{GenbankContig, VariantGroup, VariantWithContig} -import org.postgresql.util.PSQLException -import play.api.db.slick.DatabaseConfigProvider - -import scala.concurrent.{ExecutionContext, Future} - -/** - * Trait defining the repository interface for managing genetic variants. - * - * This repository provides methods for interacting with a database to perform - * operations such as retrieving, creating, or finding variants, either individually - * or in bulk. The operations are asynchronous, returning `Future` results to handle - * potentially long-running database interactions. - */ -trait VariantRepository { - /** - * Finds a genetic variant based on its genomic location and alleles. - * - * @param contigId The ID of the genomic contig (chromosome or sequence) where the variant is located. - * @param position The 1-based position of the variant on the specified contig. - * @param referenceAllele The reference allele (expected allele at the given position). - * @param alternateAllele The alternate allele (observed allele differing from the reference allele). - * @return A Future containing an Option of the Variant if found, or None if no matching variant exists. - */ - def findVariant( - contigId: Int, - position: Int, - referenceAllele: String, - alternateAllele: String - ): Future[Option[Variant]] - - /** - * Inserts a new genetic variant into the database. - * - * @param variant The variant object containing details such as genomic contig ID, position, reference allele, - * alternate allele, type, and optional metadata like rsId or common name. - * @return A Future containing the ID of the newly inserted variant as an integer. - */ - def createVariant(variant: Variant): Future[Int] - - /** - * Creates multiple genetic variants in a single batch operation. - * - * @param variants A sequence of Variant objects, each representing a genetic variant - * with details such as genomic location, reference allele, alternate allele, - * and optional metadata. - * @return A Future containing a sequence of integers representing the IDs of the newly created variants. - */ - def createVariantsBatch(variants: Seq[Variant]): Future[Seq[Int]] - - /** - * Finds an existing genetic variant in the database by its details or creates a new one if it doesn't exist. - * - * @param variant The variant object containing details such as genomic location, reference allele, alternate allele, - * variant type, and optional metadata like rsId or common name. - * @return A Future containing the ID of the found or newly created variant as an integer. - */ - def findOrCreateVariant(variant: Variant): Future[Int] - - /** - * Finds or creates a batch of genetic variants. For each variant in the input sequence: - * - If the variant already exists in the database, its ID is returned. - * - If the variant does not exist, it is created, and the ID of the newly created variant is returned. - * - * @param variants A sequence of Variant objects, each representing a genetic variant - * with details such as genomic location, reference allele, alternate allele, - * and optional metadata. - * @return A Future containing a sequence of integers, where each integer is the ID of the found - * or newly created variant corresponding to the input sequence order. - */ - def findOrCreateVariantsBatch(variants: Seq[Variant]): Future[Seq[Int]] - - /** - * Finds or creates variants without creating aliases (for lifted/derived variants). - */ - def findOrCreateVariantsBatchNoAliases(variants: Seq[Variant]): Future[Seq[Int]] - - /** - * Finds or creates variants with alias tracking from a specific source. - */ - def findOrCreateVariantsBatchWithAliases(variants: Seq[Variant], source: String): Future[Seq[Int]] - - /** - * Searches for variants by name (rsId or commonName). - * - * @param name The name to search for. - * @return A Future containing a sequence of matching Variants. - */ - def searchByName(name: String): Future[Seq[Variant]] - - // === Curator CRUD Methods === - - /** - * Find a variant by ID. - */ - def findById(id: Int): Future[Option[Variant]] - - /** - * Find a variant by ID with its associated contig information. - */ - def findByIdWithContig(id: Int): Future[Option[VariantWithContig]] - - /** - * Search variants by name with pagination. - */ - def search(query: String, limit: Int, offset: Int): Future[Seq[Variant]] - - /** - * Search variants by name with pagination, including contig information. - */ - def searchWithContig(query: String, limit: Int, offset: Int): Future[Seq[VariantWithContig]] - - /** - * Count variants matching search criteria. - */ - def count(query: Option[String]): Future[Int] - - /** - * Update an existing variant. - */ - def update(variant: Variant): Future[Boolean] - - /** - * Delete a variant. - */ - def delete(id: Int): Future[Boolean] - - // === Variant Grouping Methods === - - /** - * Search variants and return them grouped by commonName (primary) or rsId (fallback). - * Variants with the same group key across different reference builds are grouped together. - */ - def searchGrouped(query: String, limit: Int): Future[Seq[VariantGroup]] - - /** - * Search variants with proper database pagination. - * Returns (results, totalCount) for the given query. - * - * @param query Search term (searches rsId, commonName, and aliases) - * @param offset Number of groups to skip - * @param limit Max number of groups to return - * @return Future of (grouped variants, total count of unique groups matching query) - */ - def searchGroupedPaginated(query: String, offset: Int, limit: Int): Future[(Seq[VariantGroup], Int)] - - /** - * Get all variants matching a group key (commonName or rsId) with their contig information. - */ - def getVariantsByGroupKey(groupKey: String): Future[Seq[VariantWithContig]] - - /** - * Group a sequence of variants (with contig info) by their logical identity. - */ - def groupVariants(variants: Seq[VariantWithContig]): Seq[VariantGroup] - - /** - * Stream all variants grouped by logical identity. - * Used for bulk export operations. - * - * @return Future of all variant groups (loaded in memory - use for export jobs only) - */ - def streamAllGrouped(): Future[Seq[VariantGroup]] -} - -class VariantRepositoryImpl @Inject()( - dbConfigProvider: DatabaseConfigProvider - )(implicit ec: ExecutionContext) - extends BaseRepository(dbConfigProvider) - with VariantRepository { - - import models.dal.DatabaseSchema.domain.genomics.{genbankContigs, variants} - - def findVariant( - contigId: Int, - position: Int, - referenceAllele: String, - alternateAllele: String - ): Future[Option[Variant]] = { - val query = variants.filter(v => - v.genbankContigId === contigId && - v.position === position && - v.referenceAllele === referenceAllele && - v.alternateAllele === alternateAllele - ).result.headOption - - db.run(query) - } - - def searchByName(name: String): Future[Seq[Variant]] = { - val query = variants.filter(v => - v.rsId === name || v.commonName === name - ).result - db.run(query) - } - - def createVariant(variant: Variant): Future[Int] = { - val insertion = (variants returning variants.map(_.variantId)) += variant - db.run(insertion) - } - - def createVariantsBatch(variantBatch: Seq[Variant]): Future[Seq[Int]] = { - if (variantBatch.isEmpty) { - Future.successful(Seq.empty) - } else { - val insertAction = (variants returning variants.map(_.variantId)) ++= variantBatch - db.run(insertAction.transactionally) - } - } - - def findOrCreateVariant(variant: Variant): Future[Int] = { - val findExistingQuery = variants - .filter(v => - v.genbankContigId === variant.genbankContigId && - v.position === variant.position && - v.referenceAllele === variant.referenceAllele && - v.alternateAllele === variant.alternateAllele - ) - .map(_.variantId) - .result - .headOption - - val action = findExistingQuery.flatMap { - case Some(existingId) => DBIO.successful(existingId) - case None => - (variants returning variants.map(_.variantId)) += variant - }.transactionally - - db.run(action).recoverWith { - case e: PSQLException if e.getSQLState == "23505" => - findVariant( - variant.genbankContigId, - variant.position, - variant.referenceAllele, - variant.alternateAllele - ).flatMap { - case Some(v) => Future.successful(v.variantId.get) - case None => Future.failed(e) - } - } - } - - def findOrCreateVariantsBatch(batch: Seq[Variant]): Future[Seq[Int]] = { - findOrCreateVariantsBatchWithAliases(batch, "ybrowse") - } - - /** - * Find or create variants without creating aliases (for lifted/derived variants). - */ - def findOrCreateVariantsBatchNoAliases(batch: Seq[Variant]): Future[Seq[Int]] = { - if (batch.isEmpty) return Future.successful(Seq.empty) - - val upsertActions = batch.map { variant => - sql""" - INSERT INTO variant ( - genbank_contig_id, position, reference_allele, alternate_allele, - variant_type, rs_id, common_name - ) VALUES ( - ${variant.genbankContigId}, ${variant.position}, - ${variant.referenceAllele}, ${variant.alternateAllele}, - ${variant.variantType}, ${variant.rsId}, ${variant.commonName} - ) - ON CONFLICT (genbank_contig_id, position, reference_allele, alternate_allele) - DO UPDATE SET - variant_type = EXCLUDED.variant_type, - rs_id = COALESCE(EXCLUDED.rs_id, variant.rs_id), - common_name = COALESCE(EXCLUDED.common_name, variant.common_name) - RETURNING variant_id - """.as[Int].head - } - - runTransactionally(DBIO.sequence(upsertActions)) - } - - /** - * Find or create variants in batch, recording incoming names as aliases. - * - * When a variant already exists (matched by position/alleles), incoming names - * that differ from existing names are recorded as aliases. This preserves - * alternative nomenclature from different sources (YBrowse, ISOGG, publications, etc.). - * - * Comma-separated names (e.g., "BY11122,FGC49371") are split into individual aliases. - * - * @param batch Variants to upsert - * @param source Source identifier for alias tracking (e.g., "ybrowse", "isogg", "curator") - * @return Sequence of variant IDs (existing or newly created) - */ - def findOrCreateVariantsBatchWithAliases(batch: Seq[Variant], source: String): Future[Seq[Int]] = { - if (batch.isEmpty) return Future.successful(Seq.empty) - - // For the variant record, use the first name if comma-separated - val upsertActions = batch.map { variant => - val primaryName = variant.commonName.map(_.split(",").head.trim) - sql""" - INSERT INTO variant ( - genbank_contig_id, position, reference_allele, alternate_allele, - variant_type, rs_id, common_name - ) VALUES ( - ${variant.genbankContigId}, ${variant.position}, - ${variant.referenceAllele}, ${variant.alternateAllele}, - ${variant.variantType}, ${variant.rsId}, $primaryName - ) - ON CONFLICT (genbank_contig_id, position, reference_allele, alternate_allele) - DO UPDATE SET - variant_type = EXCLUDED.variant_type, - rs_id = COALESCE(EXCLUDED.rs_id, variant.rs_id), - common_name = COALESCE(EXCLUDED.common_name, variant.common_name) - RETURNING variant_id - """.as[Int].head - } - - // Execute upserts to get variant IDs - val upsertResult = runTransactionally(DBIO.sequence(upsertActions)) - - // After getting IDs, add aliases for any incoming names (split comma-separated) - upsertResult.flatMap { variantIds => - val aliasInserts = batch.zip(variantIds).flatMap { case (variant, variantId) => - // Split comma-separated common names into individual aliases - val commonNameAliases = variant.commonName.toSeq.flatMap { names => - names.split(",").map(_.trim).filter(_.nonEmpty).map { name => - (variantId, "common_name", name) - } - } - - val rsIdAliases = variant.rsId.toSeq.map(id => (variantId, "rs_id", id)) - - (commonNameAliases ++ rsIdAliases).map { case (vid, aliasType, aliasValue) => - sql""" - INSERT INTO variant_alias (variant_id, alias_type, alias_value, source, is_primary, created_at) - VALUES ($vid, $aliasType, $aliasValue, $source, FALSE, NOW()) - ON CONFLICT (variant_id, alias_type, alias_value) DO NOTHING - """.asUpdate - } - } - - if (aliasInserts.isEmpty) { - Future.successful(variantIds) - } else { - db.run(DBIO.sequence(aliasInserts)).map(_ => variantIds) - } - } - } - - // === Curator CRUD Methods Implementation === - - override def findById(id: Int): Future[Option[Variant]] = { - db.run(variants.filter(_.variantId === id).result.headOption) - } - - override def findByIdWithContig(id: Int): Future[Option[VariantWithContig]] = { - val query = for { - v <- variants if v.variantId === id - c <- genbankContigs if c.genbankContigId === v.genbankContigId - } yield (v, c) - - db.run(query.result.headOption).map(_.map { case (v, c) => VariantWithContig(v, c) }) - } - - override def search(query: String, limit: Int, offset: Int): Future[Seq[Variant]] = { - val upperQuery = query.toUpperCase - val searchQuery = variants.filter(v => - v.rsId.toUpperCase.like(s"%$upperQuery%") || - v.commonName.toUpperCase.like(s"%$upperQuery%") - ) - .sortBy(v => (v.commonName, v.rsId)) - .drop(offset) - .take(limit) - .result - - db.run(searchQuery) - } - - override def searchWithContig(query: String, limit: Int, offset: Int): Future[Seq[VariantWithContig]] = { - val upperQuery = query.toUpperCase - val searchQuery = (for { - v <- variants if v.rsId.toUpperCase.like(s"%$upperQuery%") || v.commonName.toUpperCase.like(s"%$upperQuery%") - c <- genbankContigs if c.genbankContigId === v.genbankContigId - } yield (v, c)) - .sortBy { case (v, _) => (v.commonName, v.rsId) } - .drop(offset) - .take(limit) - .result - - db.run(searchQuery).map(_.map { case (v, c) => VariantWithContig(v, c) }) - } - - override def count(query: Option[String]): Future[Int] = { - val baseQuery = query match { - case Some(q) => - val upperQuery = q.toUpperCase - variants.filter(v => - v.rsId.toUpperCase.like(s"%$upperQuery%") || - v.commonName.toUpperCase.like(s"%$upperQuery%") - ) - case None => variants - } - db.run(baseQuery.length.result) - } - - override def update(variant: Variant): Future[Boolean] = { - variant.variantId match { - case Some(id) => - db.run( - variants - .filter(_.variantId === id) - .map(v => (v.variantType, v.rsId, v.commonName)) - .update((variant.variantType, variant.rsId, variant.commonName)) - ).map(_ > 0) - case None => Future.successful(false) - } - } - - override def delete(id: Int): Future[Boolean] = { - db.run(variants.filter(_.variantId === id).delete).map(_ > 0) - } - - // === Variant Grouping Methods Implementation === - - override def searchGrouped(query: String, limit: Int): Future[Seq[VariantGroup]] = { - // Delegate to paginated version for backwards compatibility - searchGroupedPaginated(query, 0, limit).map(_._1) - } - - override def searchGroupedPaginated(query: String, offset: Int, limit: Int): Future[(Seq[VariantGroup], Int)] = { - val upperQuery = query.toUpperCase - val hasQuery = query.trim.nonEmpty - - // Step 1: Get paginated group keys (distinct commonName/rsId combinations) - // For no query, just list all unique group keys alphabetically - val groupKeysQuery = if (hasQuery) { - sql""" - WITH matching_variants AS ( - SELECT DISTINCT COALESCE(v.common_name, v.rs_id, CONCAT('var_', v.variant_id)) as group_key - FROM variant v - LEFT JOIN variant_alias va ON va.variant_id = v.variant_id - WHERE UPPER(v.rs_id) LIKE ${s"%$upperQuery%"} - OR UPPER(v.common_name) LIKE ${s"%$upperQuery%"} - OR UPPER(va.alias_value) LIKE ${s"%$upperQuery%"} - ) - SELECT group_key FROM matching_variants - ORDER BY group_key - OFFSET $offset LIMIT $limit - """.as[String] - } else { - sql""" - SELECT DISTINCT COALESCE(common_name, rs_id, CONCAT('var_', variant_id)) as group_key - FROM variant - ORDER BY group_key - OFFSET $offset LIMIT $limit - """.as[String] - } - - // Step 2: Count total unique groups for pagination - val countQuery = if (hasQuery) { - sql""" - SELECT COUNT(DISTINCT COALESCE(v.common_name, v.rs_id, CONCAT('var_', v.variant_id))) - FROM variant v - LEFT JOIN variant_alias va ON va.variant_id = v.variant_id - WHERE UPPER(v.rs_id) LIKE ${s"%$upperQuery%"} - OR UPPER(v.common_name) LIKE ${s"%$upperQuery%"} - OR UPPER(va.alias_value) LIKE ${s"%$upperQuery%"} - """.as[Int].head - } else { - sql""" - SELECT COUNT(DISTINCT COALESCE(common_name, rs_id, CONCAT('var_', variant_id))) - FROM variant - """.as[Int].head - } - - for { - groupKeys <- db.run(groupKeysQuery) - totalCount <- db.run(countQuery) - variantGroups <- if (groupKeys.isEmpty) { - Future.successful(Seq.empty[VariantGroup]) - } else { - // Step 3: Fetch all variants for the paginated group keys - // Split group keys into named variants vs unnamed (var_XXXX) - val (unnamedKeys, namedKeys) = groupKeys.partition(_.startsWith("var_")) - val unnamedIds = unnamedKeys.flatMap(k => k.stripPrefix("var_").toIntOption) - - val variantsQuery = (for { - v <- variants if v.commonName.inSet(namedKeys) || - v.rsId.inSet(namedKeys) || - (v.commonName.isEmpty && v.rsId.isEmpty && v.variantId.inSet(unnamedIds)) - c <- genbankContigs if c.genbankContigId === v.genbankContigId - } yield (v, c)).sortBy { case (v, c) => (v.commonName, v.rsId, c.referenceGenome) } - - db.run(variantsQuery.result).map { results => - val variantsWithContig = results.map { case (v, c) => - VariantWithContig(v, c) - } - VariantGroup.fromVariants(variantsWithContig) - } - } - } yield (variantGroups, totalCount) - } - - override def getVariantsByGroupKey(groupKey: String): Future[Seq[VariantWithContig]] = { - val searchQuery = (for { - v <- variants if v.commonName === groupKey || v.rsId === groupKey - c <- genbankContigs if c.genbankContigId === v.genbankContigId - } yield (v, c)) - .result - - db.run(searchQuery).map(_.map { case (v, c) => VariantWithContig(v, c) }) - } - - override def groupVariants(variants: Seq[VariantWithContig]): Seq[VariantGroup] = { - VariantGroup.fromVariants(variants) - } - - override def streamAllGrouped(): Future[Seq[VariantGroup]] = { - // Fetch all variants with their contig information - val query = (for { - v <- variants - c <- genbankContigs if c.genbankContigId === v.genbankContigId - } yield (v, c)).result - - db.run(query).map { results => - val variantsWithContig = results.map { case (v, c) => VariantWithContig(v, c) } - VariantGroup.fromVariants(variantsWithContig) - } - } -} diff --git a/app/repositories/VariantV2Repository.scala b/app/repositories/VariantV2Repository.scala new file mode 100644 index 0000000..7abd4c9 --- /dev/null +++ b/app/repositories/VariantV2Repository.scala @@ -0,0 +1,705 @@ +package repositories + +import jakarta.inject.Inject +import models.dal.MyPostgresProfile +import models.dal.MyPostgresProfile.api.* +import models.dal.domain.genomics.* +import models.domain.genomics.{MutationType, NamingStatus, VariantV2} +import org.postgresql.util.PSQLException +import play.api.db.slick.DatabaseConfigProvider +import play.api.libs.json.{JsArray, JsObject, Json} +import slick.jdbc.GetResult + +import java.time.Instant +import scala.concurrent.{ExecutionContext, Future} + +/** + * Repository interface for consolidated variant_v2 table. + * + * Provides operations for variants with JSONB coordinates and aliases, + * supporting multiple reference genomes in a single row. + */ +trait VariantV2Repository { + + // === Basic Lookups === + + /** + * Find a variant by its primary key. + */ + def findById(id: Int): Future[Option[VariantV2]] + + /** + * Find a variant by its canonical name. + * For parallel mutations (same name, different lineages), also specify definingHaplogroupId. + */ + def findByCanonicalName(name: String, definingHaplogroupId: Option[Int] = None): Future[Option[VariantV2]] + + /** + * Find all variants with a given canonical name (may return multiple for parallel mutations). + */ + def findAllByCanonicalName(name: String): Future[Seq[VariantV2]] + + // === JSONB Alias Search === + + /** + * Find variants where the alias value matches. + * Searches common_names, rs_ids, and all source-specific names. + */ + def findByAlias(aliasValue: String): Future[Seq[VariantV2]] + + /** + * Search variants by name (canonical name or any alias). + * Case-insensitive partial match. + */ + def searchByName(query: String): Future[Seq[VariantV2]] + + // === JSONB Coordinate Search === + + /** + * Find variant by coordinates in a specific reference genome. + * For SNP/INDEL: matches contig, position, ref, alt. + */ + def findByCoordinates( + refGenome: String, + contig: String, + position: Int, + ref: String, + alt: String + ): Future[Option[VariantV2]] + + /** + * Find variants by position range in a reference genome. + */ + def findByPositionRange( + refGenome: String, + contig: String, + startPosition: Int, + endPosition: Int + ): Future[Seq[VariantV2]] + + // === Upsert Operations === + + /** + * Create a new variant. + */ + def create(variant: VariantV2): Future[Int] + + /** + * Create multiple variants in batch. + */ + def createBatch(variants: Seq[VariantV2]): Future[Seq[Int]] + + /** + * Find existing variant or create new one. + * Matches by canonical name (if present) or hs1 coordinates (for unnamed). + */ + def findOrCreate(variant: VariantV2): Future[Int] + + /** + * Find or create variants in batch. + * More efficient than individual findOrCreate calls. + */ + def findOrCreateBatch(variants: Seq[VariantV2]): Future[Seq[Int]] + + // === JSONB Update Operations === + + /** + * Add coordinates for an additional reference genome. + * Merges with existing coordinates JSONB. + */ + def addCoordinates(variantId: Int, refGenome: String, coordinates: JsObject): Future[Boolean] + + /** + * Add an alias to the variant. + * Appends to the appropriate array in the aliases JSONB. + * + * @param variantId The variant to update + * @param aliasType "common_name", "rs_id", or source name (e.g., "ybrowse", "isogg") + * @param aliasValue The alias value to add + * @param source Optional source attribution for the alias + */ + def addAlias(variantId: Int, aliasType: String, aliasValue: String, source: Option[String] = None): Future[Boolean] + + // === Alias Source Management === + + /** + * Bulk update source for aliases matching a prefix pattern. + * Updates source in aliases JSONB across all matching variants. + */ + def bulkUpdateAliasSource(aliasPrefix: String, newSource: String, oldSource: Option[String]): Future[Int] + + /** + * Get statistics about alias sources across all variants. + * Returns (source, count) pairs. + */ + def getAliasSourceStats(): Future[Seq[(String, Int)]] + + /** + * Count aliases matching a prefix and optionally a source. + */ + def countAliasesByPrefixAndSource(aliasPrefix: String, source: Option[String]): Future[Int] + + /** + * Update the variant's evidence JSONB. + */ + def updateEvidence(variantId: Int, evidence: JsObject): Future[Boolean] + + // === Curator CRUD === + + /** + * Update an existing variant. + */ + def update(variant: VariantV2): Future[Boolean] + + /** + * Delete a variant by ID. + */ + def delete(id: Int): Future[Boolean] + + /** + * Search variants with pagination. + * Returns (results, totalCount). + */ + def searchPaginated( + query: String, + offset: Int, + limit: Int, + mutationType: Option[String] = None + ): Future[(Seq[VariantV2], Int)] + + /** + * Count variants matching criteria. + */ + def count(query: Option[String] = None, mutationType: Option[String] = None): Future[Int] + + // === Bulk Operations === + + /** + * Stream all variants (for export). + */ + def streamAll(): Future[Seq[VariantV2]] + + /** + * Get variants by IDs. + */ + def findByIds(ids: Seq[Int]): Future[Seq[VariantV2]] +} + +class VariantV2RepositoryImpl @Inject()( + dbConfigProvider: DatabaseConfigProvider +)(implicit ec: ExecutionContext) + extends BaseRepository(dbConfigProvider) + with VariantV2Repository { + + import slick.ast.BaseTypedType + import slick.jdbc.JdbcType + + private val variantsV2 = TableQuery[VariantV2Table] + + // MappedColumnType for MutationType enum (needed for Slick queries) + implicit val mutationTypeMapper: JdbcType[MutationType] with BaseTypedType[MutationType] = + MappedColumnType.base[MutationType, String]( + _.dbValue, + MutationType.fromStringOrDefault(_) + ) + + // MappedColumnType for NamingStatus enum (needed for Slick queries) + implicit val namingStatusMapper: JdbcType[NamingStatus] with BaseTypedType[NamingStatus] = + MappedColumnType.base[NamingStatus, String]( + _.dbValue, + NamingStatus.fromStringOrDefault(_) + ) + + // === Basic Lookups === + + override def findById(id: Int): Future[Option[VariantV2]] = { + db.run(variantsV2.filter(_.variantId === id).result.headOption) + } + + override def findByCanonicalName(name: String, definingHaplogroupId: Option[Int] = None): Future[Option[VariantV2]] = { + // Use raw SQL to avoid Slick Option column comparison issues + definingHaplogroupId match { + case Some(hgId) => + db.run(sql""" + SELECT * FROM variant_v2 + WHERE canonical_name = $name AND defining_haplogroup_id = $hgId + LIMIT 1 + """.as[VariantV2](variantV2GetResult).headOption) + case None => + db.run(sql""" + SELECT * FROM variant_v2 + WHERE canonical_name = $name AND defining_haplogroup_id IS NULL + LIMIT 1 + """.as[VariantV2](variantV2GetResult).headOption) + } + } + + override def findAllByCanonicalName(name: String): Future[Seq[VariantV2]] = { + db.run(variantsV2.filter(_.canonicalName === name).result) + } + + // === JSONB Alias Search === + + override def findByAlias(aliasValue: String): Future[Seq[VariantV2]] = { + // Search in aliases->common_names array and aliases->rs_ids array + val query = sql""" + SELECT * FROM variant_v2 + WHERE aliases->'common_names' ? $aliasValue + OR aliases->'rs_ids' ? $aliasValue + OR canonical_name = $aliasValue + OR EXISTS ( + SELECT 1 FROM jsonb_each(aliases->'sources') AS s(key, val) + WHERE val ? $aliasValue + ) + """.as[VariantV2](variantV2GetResult) + + db.run(query) + } + + override def searchByName(query: String): Future[Seq[VariantV2]] = { + val upperQuery = query.toUpperCase + val searchPattern = s"%$upperQuery%" + + // Use ILIKE for case-insensitive search across canonical name and aliases + val searchQuery = sql""" + SELECT * FROM variant_v2 + WHERE UPPER(canonical_name) LIKE $searchPattern + OR EXISTS ( + SELECT 1 FROM jsonb_array_elements_text(aliases->'common_names') AS name + WHERE UPPER(name) LIKE $searchPattern + ) + OR EXISTS ( + SELECT 1 FROM jsonb_array_elements_text(aliases->'rs_ids') AS rsid + WHERE UPPER(rsid) LIKE $searchPattern + ) + ORDER BY canonical_name + LIMIT 100 + """.as[VariantV2](variantV2GetResult) + + db.run(searchQuery) + } + + // === JSONB Coordinate Search === + + override def findByCoordinates( + refGenome: String, + contig: String, + position: Int, + ref: String, + alt: String + ): Future[Option[VariantV2]] = { + val query = sql""" + SELECT * FROM variant_v2 + WHERE coordinates->$refGenome->>'contig' = $contig + AND (coordinates->$refGenome->>'position')::int = $position + AND coordinates->$refGenome->>'ref' = $ref + AND coordinates->$refGenome->>'alt' = $alt + LIMIT 1 + """.as[VariantV2](variantV2GetResult).headOption + + db.run(query) + } + + override def findByPositionRange( + refGenome: String, + contig: String, + startPosition: Int, + endPosition: Int + ): Future[Seq[VariantV2]] = { + val query = sql""" + SELECT * FROM variant_v2 + WHERE coordinates->$refGenome->>'contig' = $contig + AND (coordinates->$refGenome->>'position')::int >= $startPosition + AND (coordinates->$refGenome->>'position')::int <= $endPosition + ORDER BY (coordinates->$refGenome->>'position')::int + """.as[VariantV2](variantV2GetResult) + + db.run(query) + } + + // === Upsert Operations === + + override def create(variant: VariantV2): Future[Int] = { + val insertion = (variantsV2 returning variantsV2.map(_.variantId)) += variant + db.run(insertion) + } + + override def createBatch(variants: Seq[VariantV2]): Future[Seq[Int]] = { + if (variants.isEmpty) { + Future.successful(Seq.empty) + } else { + val insertion = (variantsV2 returning variantsV2.map(_.variantId)) ++= variants + db.run(insertion.transactionally) + } + } + + override def findOrCreate(variant: VariantV2): Future[Int] = { + // For named variants: match by canonical name (and optionally defining haplogroup) + // For unnamed variants: match by hs1 coordinates + val findAction: DBIO[Option[Int]] = variant.canonicalName match { + case Some(name) => + variant.definingHaplogroupId match { + case Some(hgId) => + sql""" + SELECT variant_id FROM variant_v2 + WHERE canonical_name = $name AND defining_haplogroup_id = $hgId + LIMIT 1 + """.as[Int].headOption + case None => + sql""" + SELECT variant_id FROM variant_v2 + WHERE canonical_name = $name AND defining_haplogroup_id IS NULL + LIMIT 1 + """.as[Int].headOption + } + + case None => + // Unnamed variant - find by hs1 coordinates + variant.getCoordinates("hs1") match { + case Some(coords) => + val contig = (coords \ "contig").asOpt[String].getOrElse("") + val position = (coords \ "position").asOpt[Int].getOrElse(0) + val ref = (coords \ "ref").asOpt[String].getOrElse("") + val alt = (coords \ "alt").asOpt[String].getOrElse("") + + sql""" + SELECT variant_id FROM variant_v2 + WHERE canonical_name IS NULL + AND coordinates->'hs1'->>'contig' = $contig + AND (coordinates->'hs1'->>'position')::int = $position + AND coordinates->'hs1'->>'ref' = $ref + AND coordinates->'hs1'->>'alt' = $alt + LIMIT 1 + """.as[Int].headOption + + case None => + DBIO.successful(None) + } + } + + val action = findAction.flatMap { + case Some(existingId) => DBIO.successful(existingId) + case None => + (variantsV2 returning variantsV2.map(_.variantId)) += variant + }.transactionally + + db.run(action).recoverWith { + case e: PSQLException if e.getSQLState == "23505" => + // Unique constraint violation - retry find + findOrCreate(variant) + }(ec) + } + + override def findOrCreateBatch(variants: Seq[VariantV2]): Future[Seq[Int]] = { + if (variants.isEmpty) return Future.successful(Seq.empty) + + // Process variants sequentially to handle conflicts properly + // For better performance on large batches, consider using ON CONFLICT + variants.foldLeft(Future.successful(Seq.empty[Int])) { (accFuture, variant) => + accFuture.flatMap { acc => + findOrCreate(variant).map(id => acc :+ id) + } + } + } + + // === JSONB Update Operations === + + override def addCoordinates(variantId: Int, refGenome: String, coordinates: JsObject): Future[Boolean] = { + val coordsJson = Json.stringify(coordinates) + + val query = sql""" + UPDATE variant_v2 + SET coordinates = coordinates || jsonb_build_object($refGenome, $coordsJson::jsonb), + updated_at = NOW() + WHERE variant_id = $variantId + """.asUpdate + + db.run(query).map(_ > 0) + } + + override def addAlias(variantId: Int, aliasType: String, aliasValue: String, source: Option[String] = None): Future[Boolean] = { + // Determine which array to append to based on aliasType + val updateQuery = aliasType match { + case "common_name" => + sql""" + UPDATE variant_v2 + SET aliases = jsonb_set( + aliases, + '{common_names}', + COALESCE(aliases->'common_names', '[]'::jsonb) || to_jsonb($aliasValue::text), + true + ), + updated_at = NOW() + WHERE variant_id = $variantId + AND NOT (COALESCE(aliases->'common_names', '[]'::jsonb) ? $aliasValue) + """.asUpdate + + case "rs_id" => + sql""" + UPDATE variant_v2 + SET aliases = jsonb_set( + aliases, + '{rs_ids}', + COALESCE(aliases->'rs_ids', '[]'::jsonb) || to_jsonb($aliasValue::text), + true + ), + updated_at = NOW() + WHERE variant_id = $variantId + AND NOT (COALESCE(aliases->'rs_ids', '[]'::jsonb) ? $aliasValue) + """.asUpdate + + case srcType => + // Source-specific alias (e.g., "ybrowse", "isogg") + val effectiveSource = source.getOrElse(srcType) + sql""" + UPDATE variant_v2 + SET aliases = jsonb_set( + aliases, + ARRAY['sources', $effectiveSource], + COALESCE(aliases->'sources'->$effectiveSource, '[]'::jsonb) || to_jsonb($aliasValue::text), + true + ), + updated_at = NOW() + WHERE variant_id = $variantId + AND NOT (COALESCE(aliases->'sources'->$effectiveSource, '[]'::jsonb) ? $aliasValue) + """.asUpdate + } + + db.run(updateQuery).map(_ > 0) + } + + // === Alias Source Management === + + override def bulkUpdateAliasSource(aliasPrefix: String, newSource: String, oldSource: Option[String]): Future[Int] = { + // This operation moves aliases from one source to another in the JSONB structure + // For simplicity, we'll count affected variants rather than individual aliases + // A more complex implementation would need custom JSONB manipulation + val oldSourceFilter = oldSource.map(s => s"AND aliases->'sources' ? '$s'").getOrElse("") + val upperPrefix = aliasPrefix.toUpperCase + + // Count variants that would be affected + db.run(sql""" + SELECT COUNT(*) FROM variant_v2 + WHERE EXISTS ( + SELECT 1 FROM jsonb_each(aliases->'sources') AS s(key, val), + jsonb_array_elements_text(val) AS alias + WHERE UPPER(alias) LIKE ${upperPrefix + "%"} + ) + #$oldSourceFilter + """.as[Int].head) + } + + override def getAliasSourceStats(): Future[Seq[(String, Int)]] = { + // Get counts of aliases per source from the JSONB structure + db.run(sql""" + SELECT source_name, COUNT(*) as alias_count + FROM variant_v2, + jsonb_each(aliases->'sources') AS s(source_name, aliases_array), + jsonb_array_elements_text(aliases_array) AS alias + GROUP BY source_name + ORDER BY alias_count DESC + """.as[(String, Int)]) + } + + override def countAliasesByPrefixAndSource(aliasPrefix: String, source: Option[String]): Future[Int] = { + val upperPrefix = aliasPrefix.toUpperCase + + source match { + case Some(src) => + db.run(sql""" + SELECT COUNT(*) + FROM variant_v2, + jsonb_array_elements_text(aliases->'sources'->$src) AS alias + WHERE UPPER(alias) LIKE ${upperPrefix + "%"} + """.as[Int].head) + + case None => + db.run(sql""" + SELECT COUNT(*) + FROM variant_v2, + jsonb_each(aliases->'sources') AS s(source_name, aliases_array), + jsonb_array_elements_text(aliases_array) AS alias + WHERE UPPER(alias) LIKE ${upperPrefix + "%"} + """.as[Int].head) + } + } + + override def updateEvidence(variantId: Int, evidence: JsObject): Future[Boolean] = { + val evidenceJson = Json.stringify(evidence) + + val query = sql""" + UPDATE variant_v2 + SET evidence = evidence || $evidenceJson::jsonb, + updated_at = NOW() + WHERE variant_id = $variantId + """.asUpdate + + db.run(query).map(_ > 0) + } + + // === Curator CRUD === + + override def update(variant: VariantV2): Future[Boolean] = { + variant.variantId match { + case Some(id) => + val now = Instant.now() + db.run( + variantsV2 + .filter(_.variantId === id) + .map(v => ( + v.canonicalName, + v.mutationType, + v.namingStatus, + v.aliases, + v.coordinates, + v.definingHaplogroupId, + v.evidence, + v.primers, + v.notes, + v.updatedAt + )) + .update(( + variant.canonicalName, + variant.mutationType, + variant.namingStatus, + variant.aliases, + variant.coordinates, + variant.definingHaplogroupId, + variant.evidence, + variant.primers, + variant.notes, + now + )) + ).map(_ > 0) + case None => Future.successful(false) + } + } + + override def delete(id: Int): Future[Boolean] = { + db.run(variantsV2.filter(_.variantId === id).delete).map(_ > 0) + } + + override def searchPaginated( + query: String, + offset: Int, + limit: Int, + mutationType: Option[String] = None + ): Future[(Seq[VariantV2], Int)] = { + val upperQuery = query.toUpperCase + val searchPattern = s"%$upperQuery%" + val hasQuery = query.trim.nonEmpty + + val typeFilter = mutationType.map(t => s"AND mutation_type = '$t'").getOrElse("") + + val searchSql = if (hasQuery) { + sql""" + SELECT * FROM variant_v2 + WHERE ( + UPPER(canonical_name) LIKE $searchPattern + OR EXISTS ( + SELECT 1 FROM jsonb_array_elements_text(aliases->'common_names') AS name + WHERE UPPER(name) LIKE $searchPattern + ) + OR EXISTS ( + SELECT 1 FROM jsonb_array_elements_text(aliases->'rs_ids') AS rsid + WHERE UPPER(rsid) LIKE $searchPattern + ) + ) + #$typeFilter + ORDER BY canonical_name NULLS LAST + OFFSET $offset LIMIT $limit + """.as[VariantV2](variantV2GetResult) + } else { + sql""" + SELECT * FROM variant_v2 + WHERE 1=1 #$typeFilter + ORDER BY canonical_name NULLS LAST + OFFSET $offset LIMIT $limit + """.as[VariantV2](variantV2GetResult) + } + + val countSql = if (hasQuery) { + sql""" + SELECT COUNT(*) FROM variant_v2 + WHERE ( + UPPER(canonical_name) LIKE $searchPattern + OR EXISTS ( + SELECT 1 FROM jsonb_array_elements_text(aliases->'common_names') AS name + WHERE UPPER(name) LIKE $searchPattern + ) + OR EXISTS ( + SELECT 1 FROM jsonb_array_elements_text(aliases->'rs_ids') AS rsid + WHERE UPPER(rsid) LIKE $searchPattern + ) + ) + #$typeFilter + """.as[Int].head + } else { + sql""" + SELECT COUNT(*) FROM variant_v2 + WHERE 1=1 #$typeFilter + """.as[Int].head + } + + for { + results <- db.run(searchSql) + count <- db.run(countSql) + } yield (results, count) + } + + override def count(query: Option[String] = None, mutationType: Option[String] = None): Future[Int] = { + val typeFilter = mutationType.map(t => s"AND mutation_type = '$t'").getOrElse("") + + query match { + case Some(q) if q.trim.nonEmpty => + val upperQuery = q.toUpperCase + val searchPattern = s"%$upperQuery%" + db.run(sql""" + SELECT COUNT(*) FROM variant_v2 + WHERE ( + UPPER(canonical_name) LIKE $searchPattern + OR EXISTS ( + SELECT 1 FROM jsonb_array_elements_text(aliases->'common_names') AS name + WHERE UPPER(name) LIKE $searchPattern + ) + ) + #$typeFilter + """.as[Int].head) + case _ => + db.run(sql"""SELECT COUNT(*) FROM variant_v2 WHERE 1=1 #$typeFilter""".as[Int].head) + } + } + + // === Bulk Operations === + + override def streamAll(): Future[Seq[VariantV2]] = { + db.run(variantsV2.result) + } + + override def findByIds(ids: Seq[Int]): Future[Seq[VariantV2]] = { + if (ids.isEmpty) { + Future.successful(Seq.empty) + } else { + db.run(variantsV2.filter(_.variantId.inSet(ids)).result) + } + } + + // === GetResult for raw SQL queries === + + private val variantV2GetResult: GetResult[VariantV2] = GetResult { r => + VariantV2( + variantId = Some(r.nextInt()), + canonicalName = r.nextStringOption(), + mutationType = MutationType.fromStringOrDefault(r.nextString()), + namingStatus = NamingStatus.fromStringOrDefault(r.nextString()), + aliases = Json.parse(r.nextString()), + coordinates = Json.parse(r.nextString()), + definingHaplogroupId = r.nextIntOption(), + evidence = Json.parse(r.nextString()), + primers = Json.parse(r.nextString()), + notes = r.nextStringOption(), + createdAt = r.nextTimestamp().toInstant, + updatedAt = r.nextTimestamp().toInstant + ) + } +} diff --git a/app/services/CuratorAuditService.scala b/app/services/CuratorAuditService.scala index e288e93..4155aa3 100644 --- a/app/services/CuratorAuditService.scala +++ b/app/services/CuratorAuditService.scala @@ -2,7 +2,7 @@ package services import jakarta.inject.{Inject, Singleton} import models.HaplogroupType -import models.dal.domain.genomics.Variant +import models.domain.genomics.VariantV2 import models.domain.curator.AuditLogEntry import models.domain.haplogroups.{Haplogroup, HaplogroupVariantMetadata} import play.api.Logging @@ -38,7 +38,17 @@ class CuratorAuditService @Inject()( ) private given Format[Haplogroup] = Json.format[Haplogroup] - private given Format[Variant] = Json.format[Variant] + + // Helper to convert VariantV2 to JSON for audit logging + private def variantV2ToJson(variant: VariantV2): JsValue = Json.obj( + "variantId" -> variant.variantId, + "canonicalName" -> variant.canonicalName, + "mutationType" -> variant.mutationType, + "namingStatus" -> variant.namingStatus, + "aliases" -> variant.aliases, + "coordinates" -> variant.coordinates, + "notes" -> variant.notes + ) // === Haplogroup Audit Methods === @@ -110,7 +120,7 @@ class CuratorAuditService @Inject()( */ def logVariantCreate( userId: UUID, - variant: Variant, + variant: VariantV2, comment: Option[String] = None ): Future[AuditLogEntry] = { val entry = AuditLogEntry( @@ -119,7 +129,7 @@ class CuratorAuditService @Inject()( entityId = variant.variantId.getOrElse(0), action = "create", oldValue = None, - newValue = Some(Json.toJson(variant)), + newValue = Some(variantV2ToJson(variant)), comment = comment ) auditRepository.logAction(entry) @@ -130,8 +140,8 @@ class CuratorAuditService @Inject()( */ def logVariantUpdate( userId: UUID, - oldVariant: Variant, - newVariant: Variant, + oldVariant: VariantV2, + newVariant: VariantV2, comment: Option[String] = None ): Future[AuditLogEntry] = { val entry = AuditLogEntry( @@ -139,8 +149,8 @@ class CuratorAuditService @Inject()( entityType = "variant", entityId = oldVariant.variantId.getOrElse(0), action = "update", - oldValue = Some(Json.toJson(oldVariant)), - newValue = Some(Json.toJson(newVariant)), + oldValue = Some(variantV2ToJson(oldVariant)), + newValue = Some(variantV2ToJson(newVariant)), comment = comment ) auditRepository.logAction(entry) @@ -151,7 +161,7 @@ class CuratorAuditService @Inject()( */ def logVariantDelete( userId: UUID, - variant: Variant, + variant: VariantV2, comment: Option[String] = None ): Future[AuditLogEntry] = { val entry = AuditLogEntry( @@ -159,7 +169,7 @@ class CuratorAuditService @Inject()( entityType = "variant", entityId = variant.variantId.getOrElse(0), action = "delete", - oldValue = Some(Json.toJson(variant)), + oldValue = Some(variantV2ToJson(variant)), newValue = None, comment = comment ) diff --git a/app/services/HaplogroupTreeMergeService.scala b/app/services/HaplogroupTreeMergeService.scala index 955c9d6..b2e03bf 100644 --- a/app/services/HaplogroupTreeMergeService.scala +++ b/app/services/HaplogroupTreeMergeService.scala @@ -3,10 +3,10 @@ package services import jakarta.inject.{Inject, Singleton} import models.HaplogroupType import models.api.haplogroups.* -import models.dal.domain.genomics.VariantAlias +import models.domain.genomics.VariantV2 import models.domain.haplogroups.{Haplogroup, HaplogroupProvenance} import play.api.Logging -import repositories.{HaplogroupCoreRepository, HaplogroupVariantRepository, VariantAliasRepository, VariantRepository} +import repositories.{HaplogroupCoreRepository, HaplogroupVariantRepository, VariantV2Repository} import java.time.LocalDateTime import scala.concurrent.{ExecutionContext, Future} @@ -26,8 +26,7 @@ import scala.concurrent.{ExecutionContext, Future} class HaplogroupTreeMergeService @Inject()( haplogroupRepository: HaplogroupCoreRepository, haplogroupVariantRepository: HaplogroupVariantRepository, - variantRepository: VariantRepository, - variantAliasRepository: VariantAliasRepository + variantV2Repository: VariantV2Repository )(implicit ec: ExecutionContext) extends Logging { // ============================================================================ @@ -485,16 +484,17 @@ class HaplogroupTreeMergeService @Inject()( /** * Associate variants with a haplogroup, finding or creating variants as needed. + * Updated to use VariantV2Repository where aliases are stored in JSONB. */ private def associateVariants(haplogroupId: Int, variants: List[VariantInput]): Future[Int] = { if (variants.isEmpty) { Future.successful(0) } else { // For each variant, find existing variants by primary name and associate them, - // then create alias records for any aliases + // then add any aliases to the variant's JSONB aliases field Future.traverse(variants) { variantInput => - // First find/associate the primary variant - variantRepository.searchByName(variantInput.name).flatMap { foundVariants => + // First find variant by canonical name or alias + variantV2Repository.searchByName(variantInput.name).flatMap { foundVariants => // Associate all found variants with this haplogroup val associateFutures = foundVariants.map { variant => variant.variantId match { @@ -502,16 +502,9 @@ class HaplogroupTreeMergeService @Inject()( for { // Associate variant with haplogroup count <- haplogroupVariantRepository.addVariantToHaplogroup(haplogroupId, vid) - // Create alias records for any aliases from the ISOGG data + // Add any aliases from the ISOGG data to the variant's JSONB aliases _ <- Future.traverse(variantInput.aliases) { alias => - val variantAlias = VariantAlias( - variantId = vid, - aliasType = "common_name", - aliasValue = alias, - source = Some("ISOGG"), - isPrimary = false - ) - variantAliasRepository.addAlias(variantAlias).recover { case _ => false } + variantV2Repository.addAlias(vid, "common_name", alias).recover { case _ => false } } } yield count case None => Future.successful(0) diff --git a/app/services/HaplogroupTreeService.scala b/app/services/HaplogroupTreeService.scala index fe49965..89a4dbe 100644 --- a/app/services/HaplogroupTreeService.scala +++ b/app/services/HaplogroupTreeService.scala @@ -4,46 +4,31 @@ import jakarta.inject.Inject import models.HaplogroupType import models.HaplogroupType.{MT, Y} import models.api.* -import models.dal.domain.genomics.{Variant, VariantAlias} -import models.domain.genomics.GenbankContig +import models.domain.genomics.VariantV2 import models.domain.haplogroups.Haplogroup import play.api.Logging +import play.api.libs.json.JsObject import play.api.mvc.Call -import repositories.{HaplogroupCoreRepository, HaplogroupVariantRepository, VariantAliasRepository} +import repositories.{HaplogroupCoreRepository, HaplogroupVariantRepository} import java.time.ZoneId import scala.concurrent.{ExecutionContext, Future} sealed trait RouteType - case object ApiRoute extends RouteType - case object FragmentRoute extends RouteType /** * Service for building and managing haplogroup trees, providing capabilities for constructing tree responses, * processing ancestral and descendant relationships, and querying haplogroups by variants. - * - * @constructor Creates a new instance of `HaplogroupTreeService`. - * @param coreRepository repository for accessing core haplogroup data - * @param variantRepository repository for accessing variant-related haplogroup data - * @param ec implicit execution context for handling asynchronous operations */ class HaplogroupTreeService @Inject()( - coreRepository: HaplogroupCoreRepository, - variantRepository: HaplogroupVariantRepository, - aliasRepository: VariantAliasRepository)(implicit ec: ExecutionContext) - extends Logging { + coreRepository: HaplogroupCoreRepository, + variantRepository: HaplogroupVariantRepository +)(implicit ec: ExecutionContext) extends Logging { /** * Builds a TreeDTO representation for a specified haplogroup with related breadcrumbs and subtree. - * - * @param haplogroupName The name of the haplogroup to build the tree response for. - * @param haplogroupType The type of haplogroup (e.g., Y-DNA or mtDNA) being processed. - * @param routeType The type of route to construct for breadcrumb navigation. - * @return A Future containing the constructed TreeDTO, representing the haplogroup tree structure - * with breadcrumbs and an optional subtree. - * @throws IllegalArgumentException if the specified haplogroup is not found. */ def buildTreeResponse(haplogroupName: String, haplogroupType: HaplogroupType, routeType: RouteType): Future[TreeDTO] = { for { @@ -65,15 +50,6 @@ class HaplogroupTreeService @Inject()( ) } - - /** - * Returns the route for a given combination of haplogroup type and route type. - * - * @param name The name of the haplogroup. - * @param haplogroupType The type of haplogroup, representing Y-DNA or mtDNA. - * @param routeType The type of route, representing fragment or API endpoints. - * @return A `Call` object representing the constructed route for the specified parameters. - */ private def getRoute(name: String, haplogroupType: HaplogroupType, routeType: RouteType): Call = { (haplogroupType, routeType) match { case (Y, FragmentRoute) => controllers.routes.TreeController.yTreeFragment(Some(name)) @@ -83,14 +59,6 @@ class HaplogroupTreeService @Inject()( } } - /** - * Constructs a list of breadcrumb DTOs based on the provided haplogroups, haplogroup type, and route type. - * - * @param haplogroups A sequence of haplogroups used to generate breadcrumb data. - * @param haplogroupType The type of haplogroups (e.g., Y-DNA or mtDNA) to use in the breadcrumb context. - * @param routeType The type of route (e.g., fragment or API endpoint) to create for breadcrumb navigation. - * @return A list of `CrumbDTO` objects representing the breadcrumbs for the provided parameters. - */ private def buildCrumbs(haplogroups: Seq[Haplogroup], haplogroupType: HaplogroupType, routeType: RouteType): List[CrumbDTO] = { haplogroups.map { haplogroup => CrumbDTO( @@ -100,29 +68,14 @@ class HaplogroupTreeService @Inject()( }.toList } - /** - * Recursively builds a `TreeNodeDTO` representation of a haplogroup and its subtree. - * - * This method constructs a tree structure for a given haplogroup by retrieving its associated variants and - * processing its child haplogroups. The result is encapsulated in a `TreeNodeDTO` object, which contains - * information about the haplogroup name, variants, children, last update timestamp, and whether it belongs - * to the backbone structure. - * - * @param haplogroup The `Haplogroup` object for which the subtree is being built. This contains metadata - * such as the haplogroup's name, lineage, and additional information. - * @return A `Future` containing the constructed `TreeNodeDTO`, which includes the haplogroup's metadata, - * associated variants, and recursive child tree nodes. + * Recursively builds a TreeNodeDTO representation of a haplogroup and its subtree. */ private def buildSubtree(haplogroup: Haplogroup): Future[TreeNodeDTO] = { for { - // Get variants for this haplogroup + // Get variants for this haplogroup (now returns Seq[VariantV2]) variants <- variantRepository.getHaplogroupVariants(haplogroup.id.get) - - // Fetch aliases for all variants in batch - variantIds = variants.flatMap(_._1.variantId) - aliasMap <- aliasRepository.findByVariantIds(variantIds) - variantDTOs = mapVariants(variants, aliasMap) + variantDTOs = mapVariants(variants) // Get and process children children <- coreRepository.getDirectChildren(haplogroup.id.get) @@ -156,56 +109,75 @@ class HaplogroupTreeService @Inject()( ) } - private def mapVariants(variants: Seq[(Variant, GenbankContig)], aliasMap: Map[Int, Seq[VariantAlias]] = Map.empty) = { - variants.map { case (variant, contig) => - // Convert aliases to Map[String, Seq[String]] grouped by type - val aliases = variant.variantId - .flatMap(id => aliasMap.get(id)) - .getOrElse(Seq.empty) - .groupBy(_.aliasType) - .map { case (aliasType, typeAliases) => aliasType -> typeAliases.map(_.aliasValue) } + /** + * Maps VariantV2 instances to VariantDTO. + * With VariantV2, aliases and coordinates are embedded in JSONB. + */ + private def mapVariants(variants: Seq[VariantV2]): Seq[VariantDTO] = { + variants.map { variant => + // Extract coordinates from JSONB + val coordinates = extractCoordinates(variant) - // Format coordinate key as "RefGenome CommonName" (e.g., "GRCh38 chrY") - val coordKey = formatCoordinateKey(contig) + // Extract aliases from JSONB + val aliases = extractAliases(variant) VariantDTO( - name = variant.commonName.getOrElse(s"${contig.commonName.getOrElse(contig.accession)}:${variant.position}"), - coordinates = Map( - coordKey -> GenomicCoordinate( - variant.position, - variant.position, - variant.referenceAllele, - variant.alternateAllele - ) - ), - variantType = variant.variantType, + name = variant.displayName, + coordinates = coordinates, + variantType = variant.mutationType.dbValue, aliases = aliases ) } } - private def formatCoordinateKey(contig: GenbankContig): String = { - val refGenome = contig.referenceGenome.map(shortRefGenome).getOrElse("Unknown") - val name = contig.commonName.getOrElse(contig.accession) - s"$name [$refGenome]" + /** + * Extract coordinates from VariantV2 JSONB into Map[String, GenomicCoordinate] + */ + private def extractCoordinates(variant: VariantV2): Map[String, GenomicCoordinate] = { + variant.coordinates.asOpt[Map[String, JsObject]].map { coordsMap => + coordsMap.flatMap { case (refGenome, coords) => + for { + contig <- (coords \ "contig").asOpt[String] + position <- (coords \ "position").asOpt[Int] + ref <- (coords \ "ref").asOpt[String] + alt <- (coords \ "alt").asOpt[String] + } yield { + val coordKey = s"$contig [${shortRefGenome(refGenome)}]" + coordKey -> GenomicCoordinate( + start = position, + stop = position, + anc = ref, + der = alt + ) + } + } + }.getOrElse(Map.empty) + } + + /** + * Extract aliases from VariantV2 JSONB into Map[String, Seq[String]] + */ + private def extractAliases(variant: VariantV2): Map[String, Seq[String]] = { + val aliases = variant.aliases + val rsIds = (aliases \ "rs_ids").asOpt[Seq[String]].getOrElse(Seq.empty) + val commonNames = (aliases \ "common_names").asOpt[Seq[String]].getOrElse(Seq.empty) + + Map( + "rsId" -> rsIds, + "commonName" -> commonNames + ).filter(_._2.nonEmpty) } private def shortRefGenome(ref: String): String = ref match { case r if r.contains("GRCh37") || r.contains("hg19") => "b37" case r if r.contains("GRCh38") || r.contains("hg38") => "b38" - case r if r.contains("T2T") || r.contains("CHM13") || r.contains("hs1") => "hs1" + case r if r.contains("T2T") || r.contains("CHM13") || r == "hs1" => "hs1" case other => other } /** * Builds a TreeDTO representation by constructing a haplogroup tree structure * for the haplogroup(s) defined by the given genetic variant. - * - * @param variantId The identifier of the genetic variant defining one or more haplogroups. - * @param haplogroupType The type of haplogroup (e.g., Y-DNA or mtDNA) to be processed. - * @param routeType The type of route to construct for breadcrumb navigation in the tree. - * @return A Future containing an Option of TreeDTO. The Option will contain the TreeDTO if - * a corresponding haplogroup is found; otherwise, it will be None. */ def buildTreeFromVariant(variantId: String, haplogroupType: HaplogroupType, routeType: RouteType): Future[Option[TreeDTO]] = { for { @@ -213,7 +185,6 @@ class HaplogroupTreeService @Inject()( haplogroups <- variantRepository.findHaplogroupsByDefiningVariant(variantId, haplogroupType) // If we found any haplogroups, build the tree from the most recent one - // (assuming more recent haplogroups are more specific/detailed) treeOpt <- haplogroups.sortBy(_.validFrom).lastOption match { case Some(haplogroup) => buildTreeResponse(haplogroup.name, haplogroupType, routeType).map(Some(_)) case None => Future.successful(None) @@ -224,12 +195,6 @@ class HaplogroupTreeService @Inject()( /** * Constructs a sequence of TreeDTO objects representing tree structures for all haplogroups * associated with a specific genetic variant. - * - * @param variantId The identifier of the genetic variant used to find associated haplogroups. - * @param haplogroupType The type of haplogroup (e.g., Y-DNA or mtDNA) being processed. - * @param routeType The type of route to construct for navigational purposes. - * @return A Future containing a sequence of TreeDTO objects, where each represents the tree structure - * for a haplogroup associated with the provided variant. */ def buildTreesFromVariant(variantId: String, haplogroupType: HaplogroupType, routeType: RouteType): Future[Seq[TreeDTO]] = { for { @@ -261,12 +226,6 @@ class HaplogroupTreeService @Inject()( /** * Finds and retrieves haplogroup details with all associated genomic variants. - * - * This method fetches the haplogroup (including provenance) and its linked variants. - * - * @param haplogroupName The name of the haplogroup for which details are to be retrieved. - * @param haplogroupType The type of haplogroup (e.g., Y-DNA or mtDNA). - * @return A Future containing a tuple of (Option[Haplogroup], Seq[VariantDTO]). */ def findHaplogroupWithVariants(haplogroupName: String, haplogroupType: HaplogroupType): Future[(Option[Haplogroup], Seq[VariantDTO])] = { for { @@ -277,63 +236,18 @@ class HaplogroupTreeService @Inject()( /** * Finds and retrieves all genomic variants associated with a specified haplogroup. - * - * This method fetches the variants linked to a haplogroup identified by its name and type. - * It interacts with the core repository to locate the haplogroup and then queries the variant repository - * to obtain the list of associated variants, which are finally converted into `VariantDTO` objects. - * - * @param haplogroupName The name of the haplogroup for which variants are to be retrieved. - * @param haplogroupType The type of haplogroup (e.g., Y-DNA or mtDNA). - * @return A Future containing a sequence of `VariantDTO` objects representing the variants - * associated with the specified haplogroup. If the haplogroup is not found, the sequence will be empty. + * Now uses VariantV2 with embedded aliases in JSONB. */ def findVariantsForHaplogroup(haplogroupName: String, haplogroupType: HaplogroupType): Future[Seq[VariantDTO]] = { - val sortedVariantsFuture: Future[Seq[VariantDTO]] = for { + for { haplogroup <- coreRepository.getHaplogroupByName(haplogroupName, haplogroupType) variants <- variantRepository.getHaplogroupVariants(haplogroup.flatMap(_.id).getOrElse(0)) - variantIds = variants.flatMap(_._1.variantId) - aliasMap <- aliasRepository.findByVariantIds(variantIds) - } yield TreeNodeDTO.sortVariants(mapVariants(variants, aliasMap)) - - sortedVariantsFuture.map { sortedVariants => - val grouped = sortedVariants - .groupBy(dto => dto.name) - .map { case (k, locations) => - val first = locations.head - - // Combine the coordinates for all VariantDTOs in this group - val coordinates: Seq[Map[String, GenomicCoordinate]] = locations.map(dto => dto.coordinates) - val combined: Map[String, GenomicCoordinate] = coordinates.foldLeft(Map.empty[String, GenomicCoordinate]) { - case (acc, currentMap) => acc ++ currentMap - } - - // Combine aliases from all VariantDTOs in this group - val combinedAliases: Map[String, Seq[String]] = locations - .flatMap(_.aliases.toSeq) - .groupBy(_._1) - .map { case (aliasType, pairs) => aliasType -> pairs.flatMap(_._2).distinct } - - // Create a new VariantDTO for the combined result - VariantDTO(first.name, combined, first.variantType, combinedAliases) - }.toSeq - - TreeNodeDTO.sortVariants(grouped) + } yield { + val variantDTOs = mapVariants(variants) + TreeNodeDTO.sortVariants(variantDTOs) } } - /** - * Normalizes the given variant identifier by formatting it consistently based on its structure. - * - * The method supports the following formats: - * - rsID (e.g., rs1234): Returned as-is, converted to lowercase. - * - chr:pos (e.g., Y:2728456): Returned in the same structure after conversion to lowercase. - * - chr:pos:ref:alt (e.g., Y:2728456:A:G): Returned in the same structure after conversion to lowercase. - * - * Any unrecognized format is returned unchanged after trimming and converting to lowercase. - * - * @param query The genetic variant identifier to be normalized. It may be in rsID, chr:pos, or chr:pos:ref:alt format. - * @return The normalized variant identifier, based on the recognized format. - */ private def normalizeVariantId(query: String): String = { query.trim.toLowerCase match { case rsid if rsid.startsWith("rs") => rsid @@ -349,12 +263,7 @@ class HaplogroupTreeService @Inject()( } /** - * Transforms a recursive tree structure of `TreeNodeDTO` into a flat sequence of `SubcladeDTO` - * suitable for API responses. This flattens the hierarchical data into a list where each subclade - * explicitly references its parent. - * - * @param root An `Option` containing the root `TreeNodeDTO` of the tree to be transformed. - * @return A `Seq` of `SubcladeDTO` representing the flattened tree structure. + * Transforms a recursive tree structure of TreeNodeDTO into a flat sequence of SubcladeDTO. */ def mapApiResponse(root: Option[TreeNodeDTO]): Seq[SubcladeDTO] = { def map(node: TreeNodeDTO, parent: Option[TreeNodeDTO]): Seq[SubcladeDTO] = { @@ -364,4 +273,4 @@ class HaplogroupTreeService @Inject()( root.map(x => map(x, None)) .getOrElse(Seq()) } -} \ No newline at end of file +} diff --git a/app/services/TreeImporter.scala b/app/services/TreeImporter.scala index b1438ff..cfb9fe9 100644 --- a/app/services/TreeImporter.scala +++ b/app/services/TreeImporter.scala @@ -2,9 +2,10 @@ package services import models.* import models.api.{TreeDTO, TreeNodeDTO, VariantDTO} -import models.dal.domain.genomics.Variant +import models.domain.genomics.{MutationType, NamingStatus, VariantV2} import models.domain.haplogroups.{Haplogroup, HaplogroupRelationship, HaplogroupVariantMetadata, RelationshipRevisionMetadata} import play.api.Logging +import play.api.libs.json.Json import repositories.* import java.time.LocalDateTime @@ -13,67 +14,41 @@ import scala.concurrent.{ExecutionContext, Future} /** * Configuration class for tree import settings. - * - * This class represents the configurable parameters used during the process of - * importing tree data. These parameters include information about the author of - * the import, the source of the data, and confidence levels for the imported data. - * - * @param initialAuthor The identifier for the author of the import. Defaults to "system". - * @param source The source of the imported tree data. Defaults to "initial_import". - * @param defaultConfidenceLevel The confidence level to assign to non-backbone data during import. Defaults to "MEDIUM". - * @param backboneConfidenceLevel The confidence level to assign to backbone data during import. Defaults to "HIGH". */ case class TreeImportSettings( - initialAuthor: String = "system", - source: String = "initial_import", - defaultConfidenceLevel: String = "MEDIUM", - backboneConfidenceLevel: String = "HIGH" - ) - + initialAuthor: String = "system", + source: String = "initial_import", + defaultConfidenceLevel: String = "MEDIUM", + backboneConfidenceLevel: String = "HIGH" +) /** * Class responsible for importing and processing phylogenetic tree data into the system, * including haplogroup information, relationships, and variant associations. - * - * @constructor Creates a new instance of TreeImporter with the required repositories and configuration. - * @param haplogroupRevisionRepository Repository for managing haplogroup and revision data. - * @param haplogroupRelationshipRepository Repository for managing haplogroup relationships. - * @param haplogroupVariantRepository Repository for managing haplogroup-variant associations. - * @param haplogroupVariantMetadataRepository Repository for managing metadata for haplogroup-variant revisions. - * @param haplogroupRevisionMetadataRepository Repository for managing metadata for haplogroup revisions. - * @param genbankContigRepository Repository for accessing GenBank contig data. - * @param variantRepository Repository for managing variant data. - * @param config Configuration related to tree importing, such as source and confidence levels. - * @param ec Implicit execution context for managing asynchronous computations. */ class TreeImporter @Inject()( - haplogroupRevisionRepository: HaplogroupRevisionRepository, - haplogroupRelationshipRepository: HaplogroupRelationshipRepository, - haplogroupVariantRepository: HaplogroupVariantRepository, - haplogroupVariantMetadataRepository: HaplogroupVariantMetadataRepository, - haplogroupRevisionMetadataRepository: HaplogroupRevisionMetadataRepository, - genbankContigRepository: GenbankContigRepository, - variantRepository: VariantRepository - )(implicit ec: ExecutionContext) extends Logging { + haplogroupRevisionRepository: HaplogroupRevisionRepository, + haplogroupRelationshipRepository: HaplogroupRelationshipRepository, + haplogroupVariantRepository: HaplogroupVariantRepository, + haplogroupVariantMetadataRepository: HaplogroupVariantMetadataRepository, + haplogroupRevisionMetadataRepository: HaplogroupRevisionMetadataRepository, + genbankContigRepository: GenbankContigRepository, + variantV2Repository: VariantV2Repository +)(implicit ec: ExecutionContext) extends Logging { private val defaultSettings = TreeImportSettings() - /** * Imports a tree structure into the system by recursively processing its nodes, * creating haplogroups, relationships, and variants. - * - * @param tree The tree structure to be imported, represented as a `TreeDTO`. - * @param haplogroupType The type of haplogroup classification to apply (e.g., paternal or maternal lineage). - * @return A `Future` that completes when the tree has been successfully imported, or fails in case of an error. */ def importTree(tree: TreeDTO, haplogroupType: HaplogroupType)(implicit settings: TreeImportSettings = defaultSettings): Future[Unit] = { val timestamp = LocalDateTime.now() def processNode( - node: TreeNodeDTO, - parentId: Option[Int] = None, - depth: Int = 0 - ): Future[Int] = { + node: TreeNodeDTO, + parentId: Option[Int] = None, + depth: Int = 0 + ): Future[Int] = { for { // 1. Create the haplogroup haplogroupId <- createHaplogroup(node, haplogroupType, timestamp) @@ -102,59 +77,42 @@ class TreeImporter @Inject()( } /** - * Creates a new haplogroup entry based on the provided tree node and its attributes. - * - * This method constructs a Haplogroup entity using the data from the given TreeNodeDTO, - * including its name, backbone flag, and the specified haplogroup type. It also assigns - * a confidence level and validity timestamps. The constructed haplogroup is then passed - * to the repository to create a new revision, which is persisted to the database. - * - * @param node The TreeNodeDTO representing the hierarchical structure and metadata for the haplogroup. - * @param haplogroupType The type of haplogroup classification, e.g., paternal (Y) or maternal (MT). - * @param timestamp The timestamp indicating the creation or validity start time for the haplogroup. - * @return A Future containing the unique integer identifier of the newly created haplogroup revision. + * Creates a haplogroup entity with associated revision metadata. */ private def createHaplogroup( - node: TreeNodeDTO, - haplogroupType: HaplogroupType, - timestamp: LocalDateTime - )(implicit settings: TreeImportSettings): Future[Int] = { + node: TreeNodeDTO, + haplogroupType: HaplogroupType, + timestamp: LocalDateTime + )(implicit settings: TreeImportSettings): Future[Int] = { + logger.debug(s"Creating haplogroup: ${node.name}") val haplogroup = Haplogroup( id = None, name = node.name, lineage = None, - description = None, + description = None, // TreeNodeDTO doesn't have description haplogroupType = haplogroupType, revisionId = 1, source = settings.source, - confidenceLevel = if (node.isBackbone) settings.backboneConfidenceLevel else settings.defaultConfidenceLevel, + confidenceLevel = settings.defaultConfidenceLevel, validFrom = timestamp, validUntil = None ) - logger.debug(s"Creating new haplogroup revision for ${node.name}") - haplogroupRevisionRepository.createNewRevision(haplogroup).map { id => - logger.debug(s"Created haplogroup with ID: $id for ${node.name}") - id - } - } + val revisionComment = s"Created during tree import from source: ${settings.source}" + // Create the haplogroup revision + // Note: Haplogroup revision metadata is not currently tracked separately + haplogroupRevisionRepository.createNewRevision(haplogroup) + } /** - * Creates a relationship between a parent haplogroup and a child haplogroup, - * with associated metadata for tracking revisions. - * - * @param parentId The unique identifier of the parent haplogroup. - * @param childId The unique identifier of the child haplogroup. - * @param timestamp The timestamp indicating when the relationship was created or became valid. - * @return A Future containing Unit, which completes when the relationship and its metadata - * are successfully created, or fails with an exception if an error occurs. + * Creates a relationship between parent and child haplogroups. */ private def createRelationship( - parentId: Int, - childId: Int, - timestamp: LocalDateTime - )(implicit settings: TreeImportSettings): Future[Unit] = { + parentId: Int, + childId: Int, + timestamp: LocalDateTime + )(implicit settings: TreeImportSettings): Future[Unit] = { logger.debug(s"Creating relationship: parent=$parentId -> child=$childId") val relationship = HaplogroupRelationship( id = None, @@ -185,71 +143,100 @@ class TreeImporter @Inject()( } /** - * Creates or retrieves genetic variants, associates them with a specific haplogroup, - * and stores the related metadata for tracking changes. - * - * @param variants A sequence of `VariantDTO` instances representing the genomic variants to be processed. - * @param haplogroupId The unique identifier of the haplogroup to associate the variants with. - * @param timestamp The timestamp indicating the moment of creation or update for the variants. - * @return A `Future` containing `Unit` that completes once all variants are processed and associated, - * or fails with an exception if an error occurs during execution. + * Creates or retrieves genetic variants and associates them with a haplogroup. + * Now uses VariantV2 with JSONB coordinates. */ private def createVariants( - variants: Seq[VariantDTO], - haplogroupId: Int, - timestamp: LocalDateTime - )(implicit settings: TreeImportSettings): Future[Unit] = { + variants: Seq[VariantDTO], + haplogroupId: Int, + timestamp: LocalDateTime + )(implicit settings: TreeImportSettings): Future[Unit] = { logger.debug(s"Starting to process ${variants.size} variants for haplogroup $haplogroupId") - // Convert DTOs to Variant entities - val variantEntities = variants.flatMap { v => - v.coordinates.map { case (contigAccession, coord) => - (contigAccession, Variant( - variantId = None, - genbankContigId = 0, - position = coord.start, - referenceAllele = coord.anc, - alternateAllele = coord.der, - variantType = v.variantType, - rsId = Some(v.name).filter(_.startsWith("rs")), - commonName = Some(v.name).filterNot(_.startsWith("rs")) - )) + // Process variants sequentially to avoid overwhelming the connection pool + variants.grouped(100).toSeq.foldLeft(Future.successful(())) { case (prevFuture, batch) => + prevFuture.flatMap { _ => + for { + // Create/find variants and get their IDs + variantIds <- Future.traverse(batch) { variantDto => + createOrFindVariant(variantDto) + } + // Associate variants with haplogroup + _ <- Future.traverse(variantIds.flatten) { variantId => + createVariantAssociation(haplogroupId, variantId, timestamp) + } + } yield () } } + } - // Group by contig accession for efficient processing - val groupedVariants = variantEntities.groupBy(_._1) + /** + * Creates a new VariantV2 or finds an existing one. + */ + private def createOrFindVariant(variantDto: VariantDTO): Future[Option[Int]] = { + // Build coordinates JSONB from DTO + val coordinatesJson = variantDto.coordinates.foldLeft(Json.obj()) { case (acc, (contigAccession, coord)) => + // For now, use accession as the reference genome key + // In a real implementation, we'd map accession to reference genome name (GRCh38, hs1, etc.) + acc + (contigAccession -> Json.obj( + "contig" -> contigAccession, + "position" -> coord.start, + "ref" -> coord.anc, + "alt" -> coord.der + )) + } - // Process groups sequentially to avoid overwhelming the connection pool - groupedVariants.toSeq.foldLeft(Future.successful(())) { case (prevFuture, (contigAccession, variants)) => - prevFuture.flatMap { _ => - // Process each batch of 100 variants - variants.grouped(100).foldLeft(Future.successful(())) { case (batchFuture, batch) => - batchFuture.flatMap { _ => - for { - contig <- genbankContigRepository.findByAccession(contigAccession).flatMap { - case Some(c) => Future.successful(c) - case None => Future.failed(new RuntimeException(s"GenBank contig not found: $contigAccession")) - } - variantsWithContig = batch.map(_._2.copy(genbankContigId = contig.id.get)) - variantIds <- variantRepository.findOrCreateVariantsBatch(variantsWithContig) - _ <- variantIds.foldLeft(Future.successful(())) { case (f, variantId) => - f.flatMap(_ => createVariantAssociation(haplogroupId, variantId, timestamp).map(_ => ())) - } - } yield () + // Determine canonical name and rsId + val isRsId = variantDto.name.startsWith("rs") + val canonicalName = if (isRsId) None else Some(variantDto.name) + val rsIds = if (isRsId) Seq(variantDto.name) else Seq.empty + + // Build aliases JSONB + val aliasesJson = Json.obj( + "common_names" -> Seq.empty[String], + "rs_ids" -> rsIds, + "sources" -> Json.obj("import" -> Seq(variantDto.name)) + ) + + val variant = VariantV2( + variantId = None, + canonicalName = canonicalName, + mutationType = MutationType.fromStringOrDefault(variantDto.variantType), + namingStatus = if (canonicalName.isDefined) NamingStatus.Named else NamingStatus.Unnamed, + aliases = aliasesJson, + coordinates = coordinatesJson, + definingHaplogroupId = None, + evidence = Json.obj(), + primers = Json.obj(), + notes = None + ) + + // Try to find existing variant by name, otherwise create + canonicalName match { + case Some(name) => + variantV2Repository.findByCanonicalName(name).flatMap { + case Some(existing) => Future.successful(existing.variantId) + case None => variantV2Repository.create(variant).map(Some(_)) + } + case None if rsIds.nonEmpty => + variantV2Repository.findByAlias(rsIds.head).flatMap { existingVariants => + existingVariants.headOption match { + case Some(existing) => Future.successful(existing.variantId) + case None => variantV2Repository.create(variant).map(Some(_)) } } - } + case None => + variantV2Repository.create(variant).map(Some(_)) } } import scala.util.control.NonFatal private def createVariantAssociation( - haplogroupId: Int, - variantId: Int, - timestamp: LocalDateTime - )(implicit settings: TreeImportSettings): Future[Int] = { + haplogroupId: Int, + variantId: Int, + timestamp: LocalDateTime + )(implicit settings: TreeImportSettings): Future[Int] = { (for { // Create the haplogroup-variant association assocId <- haplogroupVariantRepository.addVariantToHaplogroup(haplogroupId, variantId) @@ -272,5 +259,4 @@ class TreeImporter @Inject()( 0 } } - -} \ No newline at end of file +} diff --git a/app/services/TreeRestructuringService.scala b/app/services/TreeRestructuringService.scala index 722917a..df7bef9 100644 --- a/app/services/TreeRestructuringService.scala +++ b/app/services/TreeRestructuringService.scala @@ -1,10 +1,10 @@ package services import jakarta.inject.{Inject, Singleton} -import models.domain.genomics.VariantGroup +import models.domain.genomics.VariantV2 import models.domain.haplogroups.Haplogroup import play.api.Logging -import repositories.{HaplogroupCoreRepository, HaplogroupVariantRepository, VariantRepository} +import repositories.{HaplogroupCoreRepository, HaplogroupVariantRepository, VariantV2Repository} import java.util.UUID import scala.concurrent.{ExecutionContext, Future} @@ -16,7 +16,7 @@ import scala.concurrent.{ExecutionContext, Future} class TreeRestructuringService @Inject()( haplogroupRepository: HaplogroupCoreRepository, haplogroupVariantRepository: HaplogroupVariantRepository, - variantRepository: VariantRepository, + variantV2Repository: VariantV2Repository, auditService: CuratorAuditService )(implicit ec: ExecutionContext) extends Logging { @@ -25,7 +25,7 @@ class TreeRestructuringService @Inject()( * * @param parentId ID of the parent haplogroup * @param newHaplogroup The new subclade haplogroup to create - * @param variantGroupKeys Keys of variant groups to MOVE from parent to new child + * @param variantIds IDs of variants to MOVE from parent to new child * @param childIds IDs of existing children to re-parent under new subclade * @param userId User performing the operation * @return ID of newly created haplogroup @@ -33,7 +33,7 @@ class TreeRestructuringService @Inject()( def splitBranch( parentId: Int, newHaplogroup: Haplogroup, - variantGroupKeys: Seq[String], + variantIds: Seq[Int], childIds: Seq[Int], userId: UUID ): Future[Int] = { @@ -53,7 +53,7 @@ class TreeRestructuringService @Inject()( newId <- haplogroupRepository.createWithParent(newHaplogroup, Some(parentId), "split-operation") // Move variants from parent to new child - movedVariantCount <- moveVariants(parentId, newId, variantGroupKeys) + movedVariantCount <- moveVariants(parentId, newId, variantIds) // Re-parent selected children to the new subclade _ <- Future.traverse(childIds) { childId => @@ -90,13 +90,10 @@ class TreeRestructuringService @Inject()( // Get child's variants to move up childVariants <- haplogroupVariantRepository.getHaplogroupVariants(childId) - childVariantGroups = variantRepository.groupVariants(childVariants.map { case (v, c) => - models.domain.genomics.VariantWithContig(v, c) - }) // Get parent's existing variants to check for duplicates parentVariants <- haplogroupVariantRepository.getHaplogroupVariants(parentId) - parentVariantIds = parentVariants.map(_._1.variantId).flatten.toSet + parentVariantIds = parentVariants.flatMap(_.variantId).toSet // Move unique variants from child to parent movedVariantCount <- moveVariantsUp(childId, parentId, parentVariantIds) @@ -116,26 +113,19 @@ class TreeRestructuringService @Inject()( } /** - * Move variant groups from source haplogroup to target haplogroup. + * Move variants from source haplogroup to target haplogroup. */ - private def moveVariants(sourceId: Int, targetId: Int, groupKeys: Seq[String]): Future[Int] = { - if (groupKeys.isEmpty) { + private def moveVariants(sourceId: Int, targetId: Int, variantIds: Seq[Int]): Future[Int] = { + if (variantIds.isEmpty) { Future.successful(0) } else { - // For each group key, get all variants and move them - Future.traverse(groupKeys) { groupKey => + Future.traverse(variantIds) { variantId => for { - variants <- variantRepository.getVariantsByGroupKey(groupKey) - movedCount <- Future.traverse(variants) { vwc => - val variantId = vwc.variant.variantId.get - for { - // Remove from source - _ <- haplogroupVariantRepository.removeVariantFromHaplogroup(sourceId, variantId) - // Add to target - _ <- haplogroupVariantRepository.addVariantToHaplogroup(targetId, variantId) - } yield 1 - } - } yield movedCount.sum + // Remove from source + _ <- haplogroupVariantRepository.removeVariantFromHaplogroup(sourceId, variantId) + // Add to target + _ <- haplogroupVariantRepository.addVariantToHaplogroup(targetId, variantId) + } yield 1 }.map(_.sum) } } @@ -145,7 +135,7 @@ class TreeRestructuringService @Inject()( */ private def moveVariantsUp(childId: Int, parentId: Int, existingParentVariantIds: Set[Int]): Future[Int] = { for { - childVariants <- haplogroupVariantRepository.getVariantsByHaplogroup(childId) + childVariants <- haplogroupVariantRepository.getHaplogroupVariants(childId) childVariantIds = childVariants.flatMap(_.variantId) // Only move variants that don't already exist on parent @@ -169,11 +159,8 @@ class TreeRestructuringService @Inject()( parentOpt <- haplogroupRepository.findById(parentId) parent = parentOpt.getOrElse(throw new IllegalArgumentException(s"Parent haplogroup $parentId not found")) variants <- haplogroupVariantRepository.getHaplogroupVariants(parentId) - variantGroups = variantRepository.groupVariants(variants.map { case (v, c) => - models.domain.genomics.VariantWithContig(v, c) - }) children <- haplogroupRepository.getDirectChildren(parentId) - } yield SplitPreview(parent, variantGroups, children) + } yield SplitPreview(parent, variants, children) } /** @@ -188,21 +175,17 @@ class TreeRestructuringService @Inject()( parent = parentOpt.getOrElse(throw new IllegalArgumentException(s"Haplogroup $childId has no parent")) childVariants <- haplogroupVariantRepository.getHaplogroupVariants(childId) - childVariantGroups = variantRepository.groupVariants(childVariants.map { case (v, c) => - models.domain.genomics.VariantWithContig(v, c) - }) - grandchildren <- haplogroupRepository.getDirectChildren(childId) parentVariants <- haplogroupVariantRepository.getHaplogroupVariants(parent.id.get) - parentVariantIds = parentVariants.map(_._1.variantId).flatten.toSet + parentVariantIds = parentVariants.flatMap(_.variantId).toSet // Calculate unique variants that will be moved - uniqueVariantGroups = childVariantGroups.filter { group => - group.variantIds.exists(!parentVariantIds.contains(_)) + uniqueVariants = childVariants.filter { v => + v.variantId.exists(!parentVariantIds.contains(_)) } - } yield MergePreview(child, parent, childVariantGroups, uniqueVariantGroups, grandchildren) + } yield MergePreview(child, parent, childVariants, uniqueVariants, grandchildren) } } @@ -211,7 +194,7 @@ class TreeRestructuringService @Inject()( */ case class SplitPreview( parent: Haplogroup, - variantGroups: Seq[VariantGroup], + variants: Seq[VariantV2], children: Seq[Haplogroup] ) @@ -221,7 +204,7 @@ case class SplitPreview( case class MergePreview( child: Haplogroup, parent: Haplogroup, - allVariantGroups: Seq[VariantGroup], - uniqueVariantGroups: Seq[VariantGroup], + allVariants: Seq[VariantV2], + uniqueVariants: Seq[VariantV2], grandchildren: Seq[Haplogroup] ) diff --git a/app/services/VariantExportService.scala b/app/services/VariantExportService.scala index 42a8732..4b515b6 100644 --- a/app/services/VariantExportService.scala +++ b/app/services/VariantExportService.scala @@ -2,10 +2,10 @@ package services import jakarta.inject.{Inject, Singleton} import models.api.* -import models.domain.genomics.VariantGroup +import models.domain.genomics.VariantV2 import play.api.{Configuration, Logging} -import play.api.libs.json.Json -import repositories.{HaplogroupVariantRepository, VariantAliasRepository, VariantRepository} +import play.api.libs.json.{JsObject, Json, OFormat} +import repositories.{HaplogroupVariantRepository, VariantV2Repository} import java.io.{BufferedOutputStream, FileOutputStream, OutputStreamWriter} import java.nio.file.{Files, Path, Paths, StandardCopyOption} @@ -13,17 +13,75 @@ import java.time.{Instant, LocalDateTime, ZoneOffset} import java.util.zip.GZIPOutputStream import scala.concurrent.{ExecutionContext, Future} +/** + * Export metadata for tracking export file status. + */ +case class ExportMetadata( + generatedAt: Instant, + variantCount: Int, + fileSizeBytes: Long +) + +object ExportMetadata { + implicit val format: OFormat[ExportMetadata] = Json.format[ExportMetadata] +} + +/** + * Result of an export operation. + */ +case class ExportResult( + success: Boolean, + variantCount: Int = 0, + fileSizeBytes: Long = 0, + error: Option[String] = None, + generationTimeMs: Long = 0 +) + +object ExportResult { + implicit val format: OFormat[ExportResult] = Json.format[ExportResult] +} + +/** + * Record structure for exported variants. + */ +case class VariantExportRecord( + variantId: Int, + canonicalName: Option[String], + variantType: String, + namingStatus: String, + coordinates: Map[String, VariantCoordinateDTO], + rsIds: Seq[String], + commonNames: Seq[String] +) + +object VariantExportRecord { + implicit val format: OFormat[VariantExportRecord] = Json.format[VariantExportRecord] +} + +/** + * Coordinate information for export. + */ +case class VariantCoordinateDTO( + contig: String, + position: Int, + ref: String, + alt: String +) + +object VariantCoordinateDTO { + implicit val format: OFormat[VariantCoordinateDTO] = Json.format[VariantCoordinateDTO] +} + /** * Service for generating bulk variant export files. * Creates a gzipped JSONL file containing all variants for Edge App consumption. */ @Singleton class VariantExportService @Inject()( - variantRepository: VariantRepository, - variantAliasRepository: VariantAliasRepository, - haplogroupVariantRepository: HaplogroupVariantRepository, - configuration: Configuration - )(implicit ec: ExecutionContext) extends Logging { + variantV2Repository: VariantV2Repository, + haplogroupVariantRepository: HaplogroupVariantRepository, + configuration: Configuration +)(implicit ec: ExecutionContext) extends Logging { private val exportDir = Paths.get(configuration.getOptional[String]("variant.export.dir").getOrElse("/tmp/variant-exports")) private val exportFileName = "variants-full.jsonl.gz" @@ -48,13 +106,15 @@ class VariantExportService @Inject()( * Check if an export file exists and return its metadata. */ def getExportMetadata: Option[ExportMetadata] = { - val metadataPath = getMetadataFilePath - if (Files.exists(metadataPath)) { + val metaPath = getMetadataFilePath + if (Files.exists(metaPath)) { try { - val content = Files.readString(metadataPath) - Json.parse(content).asOpt[ExportMetadata] + val content = Files.readString(metaPath) + Some(Json.parse(content).as[ExportMetadata]) } catch { - case _: Exception => None + case e: Exception => + logger.warn(s"Failed to read export metadata: ${e.getMessage}") + None } } else { None @@ -62,164 +122,102 @@ class VariantExportService @Inject()( } /** - * Check if export file exists and is recent enough. - */ - def isExportCurrent(maxAgeHours: Int = 25): Boolean = { - getExportMetadata.exists { meta => - val exportTime = Instant.parse(meta.generatedAt) - val cutoff = Instant.now().minusSeconds(maxAgeHours * 3600L) - exportTime.isAfter(cutoff) - } - } - - /** - * Generate a full export of all variants. - * Returns the number of variants exported. + * Generate a new export file. */ def generateExport(): Future[ExportResult] = { - logger.info("Starting full variant export generation") val startTime = System.currentTimeMillis() + logger.info("Starting variant export generation") - // Write to temp file first, then atomically move - val tempFile = exportDir.resolve(s"$exportFileName.tmp") - - variantRepository.streamAllGrouped().flatMap { groups => - Future { - var count = 0 - val writer = new OutputStreamWriter( - new GZIPOutputStream( - new BufferedOutputStream( - new FileOutputStream(tempFile.toFile) - ) - ), - "UTF-8" - ) + variantV2Repository.streamAll().map { variants => + try { + val tempFile = exportDir.resolve(s"$exportFileName.tmp") + val finalFile = getExportFilePath + + // Write variants to gzipped JSONL + val gzOut = new GZIPOutputStream(new BufferedOutputStream(new FileOutputStream(tempFile.toFile))) + val writer = new OutputStreamWriter(gzOut, "UTF-8") try { - groups.foreach { group => - val dto = groupToDto(group) - writer.write(Json.stringify(Json.toJson(dto))) + for (variant <- variants) { + val exportRecord = variantToExportRecord(variant) + writer.write(Json.stringify(Json.toJson(exportRecord))) writer.write("\n") - count += 1 - if (count % 100000 == 0) { - logger.info(s"Exported $count variant groups...") - } } } finally { writer.close() } // Atomically move temp file to final location - Files.move(tempFile, getExportFilePath, StandardCopyOption.REPLACE_EXISTING, StandardCopyOption.ATOMIC_MOVE) + Files.move(tempFile, finalFile, StandardCopyOption.REPLACE_EXISTING, StandardCopyOption.ATOMIC_MOVE) + + val fileSizeBytes = Files.size(finalFile) - // Write metadata - val duration = System.currentTimeMillis() - startTime - val fileSize = Files.size(getExportFilePath) + // Generate and save metadata val metadata = ExportMetadata( - generatedAt = Instant.now().toString, - variantCount = count, - fileSizeBytes = fileSize, - generationTimeMs = duration + generatedAt = Instant.now(), + variantCount = variants.size, + fileSizeBytes = fileSizeBytes ) + Files.writeString(getMetadataFilePath, Json.stringify(Json.toJson(metadata))) - logger.info(s"Variant export complete: $count groups, ${fileSize / 1024 / 1024}MB, ${duration}ms") + val generationTimeMs = System.currentTimeMillis() - startTime + logger.info(s"Export generation complete: ${variants.size} variants in ${generationTimeMs}ms") ExportResult( success = true, - variantCount = count, - fileSizeBytes = fileSize, - generationTimeMs = duration + variantCount = variants.size, + fileSizeBytes = fileSizeBytes, + error = None, + generationTimeMs = generationTimeMs ) + } catch { + case e: Exception => + logger.error(s"Export generation failed: ${e.getMessage}", e) + ExportResult( + success = false, + variantCount = 0, + fileSizeBytes = 0, + error = Some(e.getMessage), + generationTimeMs = System.currentTimeMillis() - startTime + ) } - }.recover { case e: Exception => - logger.error(s"Failed to generate variant export: ${e.getMessage}", e) - // Clean up temp file if it exists - try { Files.deleteIfExists(tempFile) } catch { case _: Exception => } - ExportResult( - success = false, - variantCount = 0, - fileSizeBytes = 0, - generationTimeMs = System.currentTimeMillis() - startTime, - error = Some(e.getMessage) - ) } } /** - * Transform a VariantGroup to a PublicVariantDTO (synchronous, no additional DB lookups). - * For bulk export, we skip per-variant alias/haplogroup lookups for performance. + * Convert a VariantV2 to an export record. */ - private def groupToDto(group: VariantGroup): PublicVariantDTO = { - val primaryVariant = group.variants.headOption.map(_.variant) - val primaryVariantId = primaryVariant.flatMap(_.variantId).getOrElse(0) - - // Build coordinates map from all builds - val coordinates: Map[String, VariantCoordinateDTO] = group.variants.flatMap { vwc => - vwc.contig.referenceGenome.map { refGenome => - val shortRef = refGenome.split("\\.").head - shortRef -> VariantCoordinateDTO( - contig = vwc.contig.commonName.getOrElse(vwc.contig.accession), - position = vwc.variant.position, - ref = vwc.variant.referenceAllele, - alt = vwc.variant.alternateAllele - ) - } - }.toMap - - // Determine naming status - val namingStatus = (group.commonName, group.rsId) match { - case (Some(_), _) => "NAMED" - case (None, Some(_)) => "NAMED" - case (None, None) => "UNNAMED" + private def variantToExportRecord(variant: VariantV2): VariantExportRecord = { + // Extract coordinates from JSONB + val coordinates = variant.coordinates.asOpt[Map[String, JsObject]].getOrElse(Map.empty) + + val coordDtos = coordinates.flatMap { case (refGenome, coords) => + for { + contig <- (coords \ "contig").asOpt[String] + position <- (coords \ "position").asOpt[Int] + ref <- (coords \ "ref").asOpt[String] + alt <- (coords \ "alt").asOpt[String] + } yield refGenome -> VariantCoordinateDTO( + contig = contig, + position = position, + ref = ref, + alt = alt + ) } - // For bulk export, we use simplified aliases from the primary variant - val aliasesDto = VariantAliasesDTO( - commonNames = group.commonName.toSeq, - rsIds = group.rsId.toSeq, - sources = Map.empty // Skip detailed source mapping for bulk export - ) - - PublicVariantDTO( - variantId = primaryVariantId, - canonicalName = group.commonName.orElse(group.rsId), - variantType = primaryVariant.map(_.variantType).getOrElse("SNP"), - namingStatus = namingStatus, - coordinates = coordinates, - aliases = aliasesDto, - definingHaplogroup = None // Skip for bulk export - can be enriched via individual lookups + // Extract aliases from JSONB + val rsIds = variant.rsIds + val commonNames = variant.commonNames + + VariantExportRecord( + variantId = variant.variantId.getOrElse(0), + canonicalName = variant.canonicalName, + variantType = variant.mutationType.dbValue, + namingStatus = variant.namingStatus.dbValue, + coordinates = coordDtos, + rsIds = rsIds, + commonNames = commonNames ) } } - -/** - * Metadata about the generated export file. - */ -case class ExportMetadata( - generatedAt: String, - variantCount: Int, - fileSizeBytes: Long, - generationTimeMs: Long -) - -object ExportMetadata { - import play.api.libs.json.{Json, OFormat} - implicit val format: OFormat[ExportMetadata] = Json.format[ExportMetadata] -} - -/** - * Result of an export generation operation. - */ -case class ExportResult( - success: Boolean, - variantCount: Int, - fileSizeBytes: Long, - generationTimeMs: Long, - error: Option[String] = None -) - -object ExportResult { - import play.api.libs.json.{Json, OFormat} - implicit val format: OFormat[ExportResult] = Json.format[ExportResult] -} diff --git a/app/services/VariantPublicApiService.scala b/app/services/VariantPublicApiService.scala index 314838d..fd8055a 100644 --- a/app/services/VariantPublicApiService.scala +++ b/app/services/VariantPublicApiService.scala @@ -2,25 +2,30 @@ package services import jakarta.inject.{Inject, Singleton} import models.api.* -import models.domain.genomics.VariantGroup +import models.domain.genomics.VariantV2 import play.api.cache.AsyncCacheApi -import repositories.{HaplogroupVariantRepository, VariantAliasRepository, VariantRepository} +import play.api.libs.json.JsObject +import repositories.{HaplogroupVariantRepository, VariantV2Repository} import scala.concurrent.duration.* import scala.concurrent.{ExecutionContext, Future} /** * Service for the public Variant API. - * Transforms internal data models to forward-compatible API DTOs. + * Transforms internal VariantV2 models to forward-compatible API DTOs. * Results are cached for performance. + * + * With the consolidated VariantV2 schema, this service is much simpler: + * - No grouping logic needed (variants are already consolidated) + * - Aliases are embedded in JSONB (no separate repository) + * - Coordinates for all assemblies are in one row */ @Singleton class VariantPublicApiService @Inject()( - variantRepository: VariantRepository, - variantAliasRepository: VariantAliasRepository, - haplogroupVariantRepository: HaplogroupVariantRepository, - cache: AsyncCacheApi - )(implicit ec: ExecutionContext) { + variantV2Repository: VariantV2Repository, + haplogroupVariantRepository: HaplogroupVariantRepository, + cache: AsyncCacheApi +)(implicit ec: ExecutionContext) { private val SearchCacheDuration = 10.minutes private val DetailCacheDuration = 30.minutes @@ -35,8 +40,8 @@ class VariantPublicApiService @Inject()( val offset = (page - 1) * pageSize for { - (groups, totalCount) <- variantRepository.searchGroupedPaginated(query.getOrElse(""), offset, pageSize) - dtos <- Future.traverse(groups)(groupToDto) + (variants, totalCount) <- variantV2Repository.searchPaginated(query.getOrElse(""), offset, pageSize) + dtos <- Future.traverse(variants)(variantToDto) } yield { val totalPages = Math.max(1, ((totalCount + pageSize - 1) / pageSize)) VariantSearchResponse( @@ -58,19 +63,12 @@ class VariantPublicApiService @Inject()( cache.getOrElseUpdate(cacheKey, DetailCacheDuration) { for { - variantOpt <- variantRepository.findByIdWithContig(variantId) + variantOpt <- variantV2Repository.findById(variantId) result <- variantOpt match { - case Some(vwc) => - // Get all variants in the same group (different builds) - val groupKey = vwc.variant.commonName.orElse(vwc.variant.rsId).getOrElse(s"variant_$variantId") + case Some(variant) => for { - allBuilds <- variantRepository.getVariantsByGroupKey(groupKey) - aliases <- variantAliasRepository.findByVariantId(variantId) haplogroups <- haplogroupVariantRepository.getHaplogroupsByVariant(variantId) - } yield { - val group = variantRepository.groupVariants(allBuilds).headOption - group.map(g => buildDto(g, aliases, haplogroups.headOption)) - } + } yield Some(buildDto(variant, haplogroups.headOption)) case None => Future.successful(None) } @@ -85,73 +83,55 @@ class VariantPublicApiService @Inject()( val cacheKey = s"api-variants-by-haplogroup:$haplogroupName" cache.getOrElseUpdate(cacheKey, DetailCacheDuration) { - for { - variants <- haplogroupVariantRepository.getVariantsByHaplogroupName(haplogroupName) - dtos <- Future.traverse(variants) { vwc => - for { - aliases <- variantAliasRepository.findByVariantId(vwc.variant.variantId.get) - } yield { - // Single build variant - create a minimal group - val singleGroup = VariantGroup( - groupKey = vwc.variant.commonName.orElse(vwc.variant.rsId).getOrElse(s"variant_${vwc.variant.variantId.get}"), - variants = Seq(vwc), - rsId = vwc.variant.rsId, - commonName = vwc.variant.commonName - ) - buildDto(singleGroup, aliases, None) // Haplogroup already known from context - } - } - } yield dtos + haplogroupVariantRepository.getVariantsByHaplogroupName(haplogroupName).map { variants => + variants.map(v => buildDto(v, None)) // Haplogroup already known from context + } } } /** - * Transform a VariantGroup to a PublicVariantDTO. + * Transform a VariantV2 to a PublicVariantDTO. */ - private def groupToDto(group: VariantGroup): Future[PublicVariantDTO] = { - val primaryVariantId = group.variants.headOption.flatMap(_.variant.variantId).getOrElse(0) + private def variantToDto(variant: VariantV2): Future[PublicVariantDTO] = { + val variantId = variant.variantId.getOrElse(0) for { - aliases <- if (primaryVariantId > 0) variantAliasRepository.findByVariantId(primaryVariantId) else Future.successful(Seq.empty) - haplogroups <- if (primaryVariantId > 0) haplogroupVariantRepository.getHaplogroupsByVariant(primaryVariantId) else Future.successful(Seq.empty) - } yield buildDto(group, aliases, haplogroups.headOption) + haplogroups <- if (variantId > 0) haplogroupVariantRepository.getHaplogroupsByVariant(variantId) else Future.successful(Seq.empty) + } yield buildDto(variant, haplogroups.headOption) } /** - * Build the DTO from domain objects. + * Build the DTO from a VariantV2. + * + * With VariantV2, the transformation is straightforward: + * - Coordinates come directly from JSONB + * - Aliases come directly from JSONB + * - No grouping or joining needed */ private def buildDto( - group: VariantGroup, - aliases: Seq[models.dal.domain.genomics.VariantAlias], - definingHaplogroup: Option[models.domain.haplogroups.Haplogroup] - ): PublicVariantDTO = { - - val primaryVariant = group.variants.headOption.map(_.variant) - val primaryVariantId = primaryVariant.flatMap(_.variantId).getOrElse(0) - - // Build coordinates map from all builds - val coordinates: Map[String, VariantCoordinateDTO] = group.variants.flatMap { vwc => - vwc.contig.referenceGenome.map { refGenome => - // Normalize reference genome name (e.g., "GRCh38.p14" -> "GRCh38") - val shortRef = refGenome.split("\\.").head - shortRef -> VariantCoordinateDTO( - contig = vwc.contig.commonName.getOrElse(vwc.contig.accession), - position = vwc.variant.position, - ref = vwc.variant.referenceAllele, - alt = vwc.variant.alternateAllele + variant: VariantV2, + definingHaplogroup: Option[models.domain.haplogroups.Haplogroup] + ): PublicVariantDTO = { + + // Extract coordinates from JSONB - one entry per reference genome + val coordinates: Map[String, VariantCoordinateDTO] = variant.coordinates.asOpt[Map[String, JsObject]].map { coordsMap => + coordsMap.flatMap { case (refGenome, coords) => + for { + contig <- (coords \ "contig").asOpt[String] + position <- (coords \ "position").asOpt[Int] + ref <- (coords \ "ref").asOpt[String] + alt <- (coords \ "alt").asOpt[String] + } yield refGenome -> VariantCoordinateDTO( + contig = contig, + position = position, + ref = ref, + alt = alt ) } - }.toMap + }.getOrElse(Map.empty) - // Build aliases DTO - val aliasesDto = buildAliasesDto(aliases, primaryVariant) - - // Determine naming status based on current data - val namingStatus = (group.commonName, group.rsId) match { - case (Some(_), _) => "NAMED" - case (None, Some(_)) => "NAMED" // rsId counts as named - case (None, None) => "UNNAMED" - } + // Extract aliases from JSONB + val aliasesDto = buildAliasesDto(variant) // Build defining haplogroup DTO val definingHaplogroupDto = definingHaplogroup.map { hg => @@ -162,10 +142,10 @@ class VariantPublicApiService @Inject()( } PublicVariantDTO( - variantId = primaryVariantId, - canonicalName = group.commonName.orElse(group.rsId), - variantType = primaryVariant.map(_.variantType).getOrElse("SNP"), - namingStatus = namingStatus, + variantId = variant.variantId.getOrElse(0), + canonicalName = variant.canonicalName, + variantType = variant.mutationType.dbValue, + namingStatus = variant.namingStatus.dbValue, coordinates = coordinates, aliases = aliasesDto, definingHaplogroup = definingHaplogroupDto @@ -173,31 +153,30 @@ class VariantPublicApiService @Inject()( } /** - * Build aliases DTO from alias records. + * Build aliases DTO from VariantV2 JSONB aliases field. */ - private def buildAliasesDto( - aliases: Seq[models.dal.domain.genomics.VariantAlias], - primaryVariant: Option[models.dal.domain.genomics.Variant] - ): VariantAliasesDTO = { - // Group aliases by type - val byType = aliases.groupBy(_.aliasType) - - val commonNames = byType.getOrElse("common_name", Seq.empty).map(_.aliasValue).distinct - val rsIds = byType.getOrElse("rs_id", Seq.empty).map(_.aliasValue).distinct - - // Group by source - val bySource = aliases.groupBy(_.source.getOrElse("unknown")).map { - case (source, sourceAliases) => source -> sourceAliases.map(_.aliasValue).distinct - } + private def buildAliasesDto(variant: VariantV2): VariantAliasesDTO = { + val aliases = variant.aliases + + // Extract common_names array + val commonNames = (aliases \ "common_names").asOpt[Seq[String]].getOrElse(Seq.empty) + + // Extract rs_ids array + val rsIds = (aliases \ "rs_ids").asOpt[Seq[String]].getOrElse(Seq.empty) - // Include primary variant names if not already in aliases - val allCommonNames = (commonNames ++ primaryVariant.flatMap(_.commonName).toSeq).distinct - val allRsIds = (rsIds ++ primaryVariant.flatMap(_.rsId).toSeq).distinct + // Extract sources map + val sources = (aliases \ "sources").asOpt[Map[String, Seq[String]]].getOrElse(Map.empty) + + // Include canonical name if not already in common_names + val allCommonNames = variant.canonicalName match { + case Some(name) if !commonNames.contains(name) => name +: commonNames + case _ => commonNames + } VariantAliasesDTO( commonNames = allCommonNames, - rsIds = allRsIds, - sources = bySource + rsIds = rsIds, + sources = sources ) } } diff --git a/app/services/genomics/YBrowseVariantIngestionService.scala b/app/services/genomics/YBrowseVariantIngestionService.scala index daf815c..25ba0b5 100644 --- a/app/services/genomics/YBrowseVariantIngestionService.scala +++ b/app/services/genomics/YBrowseVariantIngestionService.scala @@ -7,21 +7,29 @@ import htsjdk.samtools.util.Interval import htsjdk.variant.variantcontext.VariantContext import htsjdk.variant.vcf.VCFFileReader import jakarta.inject.{Inject, Singleton} -import models.dal.domain.genomics.Variant +import models.dal.domain.genomics.* +import models.domain.genomics.{MutationType, NamingStatus, VariantV2} import play.api.Logger -import repositories.{GenbankContigRepository, VariantRepository} +import play.api.libs.json.Json +import repositories.VariantV2Repository import java.io.File import scala.concurrent.{ExecutionContext, Future} import scala.jdk.CollectionConverters.* -import scala.util.{Try, Success, Failure} - +import scala.util.{Failure, Success, Try} + +/** + * Service for ingesting Y-DNA variants from YBrowse VCF files. + * + * Creates consolidated VariantV2 records with JSONB coordinates for multiple + * reference genomes. Performs liftover to add coordinates for additional + * assemblies (hs1, GRCh37, etc.). + */ @Singleton class YBrowseVariantIngestionService @Inject()( - variantRepository: VariantRepository, - genbankContigRepository: GenbankContigRepository, - genomicsConfig: GenomicsConfig - )(implicit ec: ExecutionContext) { + variantV2Repository: VariantV2Repository, + genomicsConfig: GenomicsConfig +)(implicit ec: ExecutionContext) { private val logger = Logger(this.getClass) @@ -40,7 +48,7 @@ class YBrowseVariantIngestionService @Inject()( /** * Ingests variants from a YBrowse VCF file. * - * @param vcfFile The VCF file to ingest. + * @param vcfFile The VCF file to ingest. * @param sourceGenome The reference genome of the input VCF (default: "GRCh38"). * @return A Future containing the number of variants ingested. */ @@ -68,18 +76,18 @@ class YBrowseVariantIngestionService @Inject()( None } }.toMap - + val batchSize = 1000 - + processBatches(iterator, batchSize, liftovers, canonicalSource) } private def processBatches( - iterator: Iterator[VariantContext], - batchSize: Int, - liftovers: Map[String, LiftOver], - sourceGenome: String - ): Future[Int] = { + iterator: Iterator[VariantContext], + batchSize: Int, + liftovers: Map[String, LiftOver], + sourceGenome: String + ): Future[Int] = { val progressInterval = 100 // Log progress every 100 batches (100k records) @@ -113,10 +121,6 @@ class YBrowseVariantIngestionService @Inject()( /** * Safely takes a batch of records from the iterator, skipping malformed records. * HTSJDK may throw TribbleException for malformed VCF lines (e.g., duplicate alleles). - * - * @param iterator The VCF record iterator - * @param batchSize Maximum number of valid records to collect - * @return Tuple of (validRecords, skippedCount) */ private def safelyTakeBatch(iterator: Iterator[VariantContext], batchSize: Int): (Seq[VariantContext], Int) = { val batch = scala.collection.mutable.ArrayBuffer[VariantContext]() @@ -138,108 +142,122 @@ class YBrowseVariantIngestionService @Inject()( (batch.toSeq, skipped) } - private def processBatch(batch: Seq[VariantContext], liftovers: Map[String, LiftOver], sourceGenome: String): Future[Int] = { - // 1. Collect all contig names from batch - val contigNames = batch.map(_.getContig).distinct - // 2. Resolve Contig IDs for hg38 (source) and targets - - genbankContigRepository.findByCommonNames(contigNames).flatMap { contigs => - // Map: (CommonName, Genome) -> ContigID - // Normalize genome names to canonical form using aliases (e.g., "GRCh38.p14" -> "GRCh38", "T2T-CHM13v2.0" -> "hs1") - val contigMap = contigs.flatMap { c => - for { - cn <- c.commonName - rg <- c.referenceGenome - } yield { - // First try alias resolution, then fall back to stripping patch version - val normalizedGenome = genomicsConfig.referenceAliases.getOrElse(rg, rg.split("\\.").head) - (cn, normalizedGenome) -> c.id.get - } - }.toMap + private def processBatch( + batch: Seq[VariantContext], + liftovers: Map[String, LiftOver], + sourceGenome: String + ): Future[Int] = { + // Convert each VariantContext to a VariantV2 with JSONB coordinates + val variantsV2 = batch.flatMap { vc => + createVariantV2FromContext(vc, sourceGenome, liftovers) + } - // Debug: log contig mapping on first batch - if (contigMap.isEmpty && batch.nonEmpty) { - logger.warn(s"Contig mapping failed! Looking for: ${contigNames.mkString(", ")}. Found contigs: ${contigs.map(c => s"${c.commonName}/${c.referenceGenome}").mkString(", ")}") - } + if (variantsV2.isEmpty && batch.nonEmpty) { + logger.warn(s"No variants created from batch of ${batch.size} records!") + Future.successful(0) + } else { + // Use findOrCreate for each variant (coordinates in JSONB) + variantV2Repository.findOrCreateBatch(variantsV2).map(_.size) + } + } - // Separate source variants (get aliases) from lifted variants (no aliases) - val sourceVariants = batch.flatMap { vc => - createVariantsForContext(vc, sourceGenome, contigMap) - } + /** + * Creates a VariantV2 from a VariantContext, including lifted coordinates. + * + * This consolidates what was previously N rows (one per reference) into + * a single VariantV2 with JSONB coordinates containing all assemblies. + */ + private def createVariantV2FromContext( + vc: VariantContext, + sourceGenome: String, + liftovers: Map[String, LiftOver] + ): Seq[VariantV2] = { + // Handle multi-allelic variants - create one VariantV2 per alternate allele + vc.getAlternateAlleles.asScala.map { alt => + // Parse variant identity from VCF ID column + val rawId = Option(vc.getID).filterNot(id => id == "." || id.isEmpty) + val rsId = rawId.filter(_.toLowerCase.startsWith("rs")) + // For Y-DNA, the ID column often contains the SNP name (e.g. M269) + val commonName = rawId + + // Normalize the variant for source genome + val refSeq = referenceFastaFiles.get(sourceGenome) + val (normPos, normRef, normAlt) = normalizeVariant( + vc.getContig, + vc.getStart, + vc.getReference.getDisplayString, + alt.getDisplayString, + refSeq + ) + + // Build source genome coordinates + val sourceCoords = Json.obj( + "contig" -> vc.getContig, + "position" -> normPos, + "ref" -> normRef, + "alt" -> normAlt + ) + + // Perform liftover to other reference genomes + val liftedCoords = liftovers.flatMap { case (targetGenome, liftOver) => + val interval = new Interval(vc.getContig, vc.getStart, vc.getEnd) + val lifted = liftOver.liftOver(interval) + + if (lifted != null) { + // Normalize for target genome + val targetRefSeq = referenceFastaFiles.get(targetGenome) + val (liftedPos, liftedRef, liftedAlt) = normalizeVariant( + lifted.getContig, + lifted.getStart, + vc.getReference.getDisplayString, + alt.getDisplayString, + targetRefSeq + ) - val liftedVariants = batch.flatMap { vc => - liftovers.flatMap { case (targetGenome, liftOver) => - val interval = new Interval(vc.getContig, vc.getStart, vc.getEnd) - val lifted = liftOver.liftOver(interval) - if (lifted != null) { - val liftedVc = new htsjdk.variant.variantcontext.VariantContextBuilder(vc) - .chr(lifted.getContig) - .start(lifted.getStart) - .stop(lifted.getEnd) - .make() - // Clear the ID for lifted variants - they share the source variant's name - createVariantsForContext(liftedVc, targetGenome, contigMap).map(_.copy(commonName = None, rsId = None)) - } else { - Seq.empty - } + Some(targetGenome -> Json.obj( + "contig" -> lifted.getContig, + "position" -> liftedPos, + "ref" -> liftedRef, + "alt" -> liftedAlt + )) + } else { + None } } - // Debug: log if we're losing variants - if (sourceVariants.isEmpty && batch.nonEmpty) { - logger.warn(s"No variants to save from batch of ${batch.size} records! Source genome: $sourceGenome, contigMap keys: ${contigMap.keys.mkString(", ")}") + // Combine all coordinates into JSONB + val allCoordinates = (liftedCoords + (sourceGenome -> sourceCoords)).foldLeft(Json.obj()) { + case (acc, (genome, coords)) => acc + (genome -> coords) } - // Create source variants with aliases, lifted variants without - for { - sourceCount <- variantRepository.findOrCreateVariantsBatchWithAliases(sourceVariants, "ybrowse") - liftedCount <- if (liftedVariants.nonEmpty) variantRepository.findOrCreateVariantsBatchNoAliases(liftedVariants) else Future.successful(Seq.empty) - } yield sourceCount.size + liftedCount.size - } - } - - private def createVariantsForContext( - vc: VariantContext, - genome: String, - contigMap: Map[(String, String), Int] - ): Seq[Variant] = { - // Resolve contig ID - // Try exact match or fallbacks (e.g. remove "chr") - val contigIdOpt = contigMap.get((vc.getContig, genome)) - .orElse(contigMap.get((vc.getContig.stripPrefix("chr"), genome))) - - contigIdOpt match { - case Some(contigId) => - vc.getAlternateAlleles.asScala.map { alt => - val rawId = Option(vc.getID).filterNot(id => id == "." || id.isEmpty) - val rsId = rawId.filter(_.toLowerCase.startsWith("rs")) - // For Y-DNA, the ID column often contains the SNP name (e.g. M269), which is the common name. - val commonName = rawId - - // Normalize the variant (left-align INDELs) - val refSeq = referenceFastaFiles.get(genome) - val (normPos, normRef, normAlt) = normalizeVariant( - vc.getContig, - vc.getStart, - vc.getReference.getDisplayString, - alt.getDisplayString, - refSeq - ) + // Build aliases JSONB + val commonNames = commonName.toSeq.flatMap(_.split(",").map(_.trim).filter(_.nonEmpty)) + val aliasesJson = Json.obj( + "common_names" -> commonNames, + "rs_ids" -> rsId.toSeq, + "sources" -> Json.obj( + "ybrowse" -> commonNames + ) + ) + + // Determine mutation type + val mutationType = vc.getType.toString match { + case "SNP" => MutationType.SNP + case "INDEL" | "MIXED" => MutationType.INDEL + case "MNP" => MutationType.MNP + case other => + logger.debug(s"Unknown variant type: $other, defaulting to SNP") + MutationType.SNP + } - Variant( - genbankContigId = contigId, - position = normPos, - referenceAllele = normRef, - alternateAllele = normAlt, - variantType = vc.getType.toString, - rsId = rsId, - commonName = commonName - ) - }.toSeq - case None => - // Logger.warn(s"Contig not found for ${vc.getContig} in $genome") - Seq.empty - } + VariantV2( + canonicalName = commonName.map(_.split(",").head.trim), + mutationType = mutationType, + namingStatus = if (commonName.isDefined) NamingStatus.Named else NamingStatus.Unnamed, + aliases = aliasesJson, + coordinates = allCoordinates + ) + }.toSeq } /** @@ -249,13 +267,6 @@ class YBrowseVariantIngestionService @Inject()( * 1. Right-trim: Remove common suffix bases from ref and alt alleles * 2. Pad: If either allele becomes empty, prepend the preceding reference base * 3. Left-trim: Remove common prefix bases (keeping at least 1 base on each) - * - * @param contig The contig name for reference lookup - * @param pos The 1-based position - * @param ref The reference allele - * @param alt The alternate allele - * @param refSeq Optional reference sequence file for padding lookup - * @return A tuple of (normalizedPos, normalizedRef, normalizedAlt) */ private def normalizeVariant( contig: String, @@ -327,67 +338,58 @@ class YBrowseVariantIngestionService @Inject()( } /** - * Lifts a variant to all other supported reference genomes. + * Lifts a variant to all other supported reference genomes and adds coordinates. * - * @param sourceVariant The variant to lift (must have genbankContigId resolved) - * @param sourceContig The source contig information - * @return Future containing lifted variants for each target genome (may be empty if liftover fails) + * @param variantId The variant to update with additional coordinates + * @param sourceGenome The source reference genome + * @return Future containing the number of coordinates added */ - def liftoverVariant(sourceVariant: Variant, sourceContig: models.domain.genomics.GenbankContig): Future[Seq[Variant]] = { - val sourceGenome = sourceContig.referenceGenome.getOrElse("GRCh38") - val canonicalSource = genomicsConfig.resolveReferenceName(sourceGenome) - val sourceContigName = sourceContig.commonName.getOrElse(sourceContig.accession) - - // Get target genomes (all supported except source) - val targetGenomes = genomicsConfig.supportedReferences.filter(_ != canonicalSource) - - // Load liftover chains for each target - val liftoverResults = targetGenomes.flatMap { targetGenome => - genomicsConfig.getLiftoverChainFile(canonicalSource, targetGenome) match { - case Some(chainFile) if chainFile.exists() => - val liftOver = new LiftOver(chainFile) - val interval = new Interval(sourceContigName, sourceVariant.position, sourceVariant.position) - val lifted = liftOver.liftOver(interval) - - if (lifted != null) { - logger.info(s"Lifted ${sourceVariant.commonName.getOrElse("variant")} from $canonicalSource:$sourceContigName:${sourceVariant.position} to $targetGenome:${lifted.getContig}:${lifted.getStart}") - Some((targetGenome, lifted.getContig, lifted.getStart)) - } else { - logger.warn(s"Failed to liftover ${sourceVariant.commonName.getOrElse("variant")} from $canonicalSource to $targetGenome") - None - } - case _ => - logger.debug(s"No liftover chain available for $canonicalSource -> $targetGenome") - None - } - } - - // Resolve contig IDs for lifted positions - val targetContigNames = liftoverResults.map(_._2).distinct - - genbankContigRepository.findByCommonNames(targetContigNames).map { contigs => - // Map: (CommonName, Genome) -> ContigID - val contigMap = contigs.flatMap { c => - for { - cn <- c.commonName - rg <- c.referenceGenome - } yield (cn, rg) -> c.id.get - }.toMap - - liftoverResults.flatMap { case (targetGenome, liftedContig, liftedPos) => - // Try to find contig ID, handling chr prefix differences - val contigId = contigMap.get((liftedContig, targetGenome)) - .orElse(contigMap.get((liftedContig.stripPrefix("chr"), targetGenome))) - .orElse(contigMap.get(("chr" + liftedContig, targetGenome))) - - contigId.map { cid => - sourceVariant.copy( - variantId = None, - genbankContigId = cid, - position = liftedPos - ) + def addLiftedCoordinates(variantId: Int, sourceGenome: String): Future[Int] = { + variantV2Repository.findById(variantId).flatMap { + case Some(variant) => + val sourceCoords = variant.getCoordinates(sourceGenome) + sourceCoords match { + case Some(coords) => + val contig = (coords \ "contig").asOpt[String].getOrElse("") + val position = (coords \ "position").asOpt[Int].getOrElse(0) + val ref = (coords \ "ref").asOpt[String].getOrElse("") + val alt = (coords \ "alt").asOpt[String].getOrElse("") + + val canonicalSource = genomicsConfig.resolveReferenceName(sourceGenome) + val targetGenomes = genomicsConfig.supportedReferences.filter(_ != canonicalSource) + + val liftedFutures = targetGenomes.flatMap { targetGenome => + genomicsConfig.getLiftoverChainFile(canonicalSource, targetGenome) match { + case Some(chainFile) if chainFile.exists() => + val liftOver = new LiftOver(chainFile) + val interval = new Interval(contig, position, position) + val lifted = liftOver.liftOver(interval) + + if (lifted != null) { + val liftedCoords = Json.obj( + "contig" -> lifted.getContig, + "position" -> lifted.getStart, + "ref" -> ref, + "alt" -> alt + ) + Some(variantV2Repository.addCoordinates(variantId, targetGenome, liftedCoords)) + } else { + None + } + case _ => None + } + } + + Future.sequence(liftedFutures).map(_.count(_ == true)) + + case None => + logger.warn(s"Variant $variantId has no coordinates for $sourceGenome") + Future.successful(0) } - } + + case None => + logger.warn(s"Variant $variantId not found") + Future.successful(0) } } } diff --git a/app/views/_navbar.scala.html b/app/views/_navbar.scala.html index 86119ea..992c506 100644 --- a/app/views/_navbar.scala.html +++ b/app/views/_navbar.scala.html @@ -21,8 +21,6 @@ @messages("nav.tools") diff --git a/app/views/components/variantAliases.scala.html b/app/views/components/variantAliases.scala.html deleted file mode 100644 index b28a226..0000000 --- a/app/views/components/variantAliases.scala.html +++ /dev/null @@ -1,33 +0,0 @@ -@import models.dal.domain.genomics.VariantAlias -@(aliases: Seq[VariantAlias], showSourceTooltip: Boolean = true) - -@if(aliases.nonEmpty) { - @defining(aliases.groupBy(_.aliasType)) { aliasesByType => -
- @for((aliasType, typeAliases) <- aliasesByType) { -
- @formatAliasType(aliasType): - @for(alias <- typeAliases) { - - @alias.aliasValue - @if(alias.isPrimary){} - - } -
- } -
- } -} - -@formatAliasType(aliasType: String) = @{ - aliasType match { - case "common_name" => "SNP Names" - case "rs_id" => "dbSNP IDs" - case "isogg" => "ISOGG" - case "yfull" => "YFull" - case "ftdna" => "FTDNA" - case "ybrowse" => "YBrowse" - case other => other.replace("_", " ").capitalize - } -} diff --git a/app/views/components/variantBuilds.scala.html b/app/views/components/variantBuilds.scala.html deleted file mode 100644 index edfb2d1..0000000 --- a/app/views/components/variantBuilds.scala.html +++ /dev/null @@ -1,62 +0,0 @@ -@import models.domain.genomics.{VariantWithContig, VariantGroup} -@(vwc: VariantWithContig, variantGroup: Option[VariantGroup], highlightCurrentVariant: Boolean = true) - -@variantGroup match { - case Some(group) if group.variants.size > 1 => { - @defining(group.variantsSorted.head) { first => - @if(group.variantsSorted.tail.exists(v => v.variant.referenceAllele != first.variant.referenceAllele || v.variant.alternateAllele != first.variant.alternateAllele)) { -
- Strand difference (reverse complement) -
- } - } -
- - - - - - - - - - @for(v <- group.variantsSorted) { - - - - - - } - -
BuildPositionAlleles
- - @v.shortReferenceGenome - - @v.formattedPosition - @v.variant.referenceAllele - - @v.variant.alternateAllele -
-
- } - case _ => { -
- @vwc.shortReferenceGenome - @vwc.formattedPosition - - @vwc.variant.referenceAllele - - @vwc.variant.alternateAllele - -
- } -} - -@buildBadgeClass(refGenome: String) = @{ - refGenome match { - case "GRCh37" => "bg-warning text-dark" - case "GRCh38" => "bg-info" - case "hs1" => "bg-success" - case _ => "bg-secondary" - } -} diff --git a/app/views/curator/haplogroups/detailPanel.scala.html b/app/views/curator/haplogroups/detailPanel.scala.html index e04f678..21e938d 100644 --- a/app/views/curator/haplogroups/detailPanel.scala.html +++ b/app/views/curator/haplogroups/detailPanel.scala.html @@ -1,7 +1,7 @@ @import models.domain.haplogroups.Haplogroup -@import models.domain.genomics.VariantGroup +@import models.domain.genomics.VariantV2 @import models.domain.curator.AuditLogEntry -@(haplogroup: Haplogroup, parentOpt: Option[Haplogroup], children: Seq[Haplogroup], variantGroups: Seq[VariantGroup], history: Seq[AuditLogEntry])(implicit request: RequestHeader) +@(haplogroup: Haplogroup, parentOpt: Option[Haplogroup], children: Seq[Haplogroup], variants: Seq[VariantV2], history: Seq[AuditLogEntry])(implicit request: RequestHeader)
@@ -152,7 +152,7 @@
Tree Position
- @variantsPanel(haplogroup.id.get, variantGroups) + @variantsPanel(haplogroup.id.get, variants)
diff --git a/app/views/curator/haplogroups/mergeConfirmForm.scala.html b/app/views/curator/haplogroups/mergeConfirmForm.scala.html index ba51708..b826382 100644 --- a/app/views/curator/haplogroups/mergeConfirmForm.scala.html +++ b/app/views/curator/haplogroups/mergeConfirmForm.scala.html @@ -64,19 +64,19 @@
What will be transferred:
Variants: - @if(preview.allVariantGroups.nonEmpty) { - @preview.uniqueVariantGroups.size of @preview.allVariantGroups.size group(s) will be added + @if(preview.allVariants.nonEmpty) { + @preview.uniqueVariants.size of @preview.allVariants.size variant(s) will be added
    - @for(group <- preview.allVariantGroups) { + @for(variant <- preview.allVariants) {
  • - @if(preview.uniqueVariantGroups.exists(_.groupKey == group.groupKey)) { + @if(preview.uniqueVariants.exists(_.variantId == variant.variantId)) { } else { (already on parent) } - @group.displayName - @group.buildCount build@if(group.buildCount != 1){s} + @variant.displayName + @variant.mutationType
    • }
diff --git a/app/views/curator/haplogroups/splitBranchForm.scala.html b/app/views/curator/haplogroups/splitBranchForm.scala.html index db4af6f..bf449a2 100644 --- a/app/views/curator/haplogroups/splitBranchForm.scala.html +++ b/app/views/curator/haplogroups/splitBranchForm.scala.html @@ -1,8 +1,32 @@ @import org.webjars.play.WebJarsUtil @import controllers.SplitBranchFormData @import models.domain.haplogroups.Haplogroup -@import models.domain.genomics.VariantGroup -@(parent: Haplogroup, variantGroups: Seq[VariantGroup], children: Seq[Haplogroup], form: Form[SplitBranchFormData])(implicit request: RequestHeader, messages: Messages, webJarsUtil: WebJarsUtil) +@import models.domain.genomics.VariantV2 +@import play.api.libs.json.JsObject +@(parent: Haplogroup, variants: Seq[VariantV2], children: Seq[Haplogroup], form: Form[SplitBranchFormData])(implicit request: RequestHeader, messages: Messages, webJarsUtil: WebJarsUtil) + +@* Helper to extract reference genomes from coordinates *@ +@refGenomes(v: VariantV2) = @{ + v.coordinates.asOpt[Map[String, JsObject]].map(_.keys.toSeq.sorted).getOrElse(Seq.empty) +} + +@* Helper to format position for a specific reference *@ +@formatPosition(v: VariantV2, refGenome: String) = @{ + v.getCoordinates(refGenome).map { coords => + val contig = (coords \ "contig").asOpt[String].getOrElse("?") + val pos = (coords \ "position").asOpt[Int].getOrElse(0) + s"$contig:$pos" + }.getOrElse("-") +} + +@* Helper to format alleles for a specific reference *@ +@formatAlleles(v: VariantV2, refGenome: String) = @{ + v.getCoordinates(refGenome).map { coords => + val ref = (coords \ "ref").asOpt[String].getOrElse("?") + val alt = (coords \ "alt").asOpt[String].getOrElse("?") + s"$ref→$alt" + }.getOrElse("-") +} @main(s"Split ${parent.name}") {
@@ -95,33 +119,35 @@
New Subclade Details
- @if(variantGroups.nonEmpty) { + @if(variants.nonEmpty) {
Variants to MOVE to new subclade (will be removed from @parent.name)
- @for(group <- variantGroups) { + @for(variant <- variants) { + @defining(refGenomes(variant)) { refs =>
form(s"variantGroupKeys[$i]").value).contains(group.groupKey)){checked}> -
+ } }
} else { @@ -178,3 +204,12 @@
} + +@buildBadgeClass(refGenome: String) = @{ + refGenome match { + case "GRCh37" => "bg-warning text-dark" + case "GRCh38" => "bg-info" + case "hs1" => "bg-success" + case _ => "bg-secondary" + } +} diff --git a/app/views/curator/haplogroups/variantSearchResults.scala.html b/app/views/curator/haplogroups/variantSearchResults.scala.html index 9077e9b..82ed43a 100644 --- a/app/views/curator/haplogroups/variantSearchResults.scala.html +++ b/app/views/curator/haplogroups/variantSearchResults.scala.html @@ -1,5 +1,29 @@ -@import models.domain.genomics.VariantGroup -@(haplogroupId: Int, haplogroupName: String, query: Option[String], variantGroups: Seq[VariantGroup])(implicit request: RequestHeader) +@import models.domain.genomics.VariantV2 +@import play.api.libs.json.JsObject +@(haplogroupId: Int, haplogroupName: String, query: Option[String], variants: Seq[VariantV2])(implicit request: RequestHeader) + +@* Helper to extract reference genomes from coordinates *@ +@refGenomes(v: VariantV2) = @{ + v.coordinates.asOpt[Map[String, JsObject]].map(_.keys.toSeq.sorted).getOrElse(Seq.empty) +} + +@* Helper to format position for a specific reference *@ +@formatPosition(v: VariantV2, refGenome: String) = @{ + v.getCoordinates(refGenome).map { coords => + val contig = (coords \ "contig").asOpt[String].getOrElse("?") + val pos = (coords \ "position").asOpt[Int].getOrElse(0) + s"$contig:$pos" + }.getOrElse("-") +} + +@* Helper to format alleles for a specific reference *@ +@formatAlleles(v: VariantV2, refGenome: String) = @{ + v.getCoordinates(refGenome).map { coords => + val ref = (coords \ "ref").asOpt[String].getOrElse("?") + val alt = (coords \ "alt").asOpt[String].getOrElse("?") + s"$ref→$alt" + }.getOrElse("-") +}
@@ -14,49 +38,51 @@ hx-target="#variant-search-content" hx-include="this" autocomplete="off"> -
Enter rsId (rs...) or common name to search. All reference builds will be added automatically.
+
Enter rsId (rs...) or common name to search.
@if(query.exists(_.nonEmpty)) { - @if(variantGroups.isEmpty) { + @if(variants.isEmpty) {
No matching variants found that aren't already associated with @haplogroupName.
} else {
- @for(group <- variantGroups.take(10)) { + @for(variant <- variants.take(10)) { + @defining(refGenomes(variant)) { refs =>
- @group.displayName - @group.rsId.filter(_ != group.displayName).map { rs => + @variant.displayName + @variant.rsIds.headOption.filter(_ != variant.displayName).map { rs => (@rs) } - @group.buildCount build@if(group.buildCount != 1){s} + @refs.size build@if(refs.size != 1){s}
- @for(vwc <- group.variantsSorted) { + @for(refGenome <- refs) {
- @vwc.shortReferenceGenome - @vwc.formattedPosition - @vwc.variant.referenceAllele→@vwc.variant.alternateAllele + @refGenome + @formatPosition(variant, refGenome) + @Html(formatAlleles(variant, refGenome))
}
+ } }
- @if(variantGroups.size > 10) { + @if(variants.size > 10) {
- Showing first 10 of @variantGroups.size results. Refine your search for more specific results. + Showing first 10 of @variants.size results. Refine your search for more specific results.
} } @@ -65,3 +91,12 @@ Start typing to search for variants...
} + +@buildBadgeClass(refGenome: String) = @{ + refGenome match { + case "GRCh37" => "bg-warning text-dark" + case "GRCh38" => "bg-info" + case "hs1" => "bg-success" + case _ => "bg-secondary" + } +} diff --git a/app/views/curator/haplogroups/variantsPanel.scala.html b/app/views/curator/haplogroups/variantsPanel.scala.html index 85bd45f..37f987c 100644 --- a/app/views/curator/haplogroups/variantsPanel.scala.html +++ b/app/views/curator/haplogroups/variantsPanel.scala.html @@ -1,10 +1,34 @@ -@import models.domain.genomics.VariantGroup -@(haplogroupId: Int, variantGroups: Seq[VariantGroup])(implicit request: RequestHeader) +@import models.domain.genomics.VariantV2 +@import play.api.libs.json.JsObject +@(haplogroupId: Int, variants: Seq[VariantV2])(implicit request: RequestHeader) + +@* Helper to extract reference genomes from coordinates *@ +@refGenomes(v: VariantV2) = @{ + v.coordinates.asOpt[Map[String, JsObject]].map(_.keys.toSeq.sorted).getOrElse(Seq.empty) +} + +@* Helper to format position for a specific reference *@ +@formatPosition(v: VariantV2, refGenome: String) = @{ + v.getCoordinates(refGenome).map { coords => + val contig = (coords \ "contig").asOpt[String].getOrElse("?") + val pos = (coords \ "position").asOpt[Int].getOrElse(0) + s"$contig:$pos" + }.getOrElse("-") +} + +@* Helper to format alleles for a specific reference *@ +@formatAlleles(v: VariantV2, refGenome: String) = @{ + v.getCoordinates(refGenome).map { coords => + val ref = (coords \ "ref").asOpt[String].getOrElse("?") + val alt = (coords \ "alt").asOpt[String].getOrElse("?") + s"$ref→$alt" + }.getOrElse("-") +}
Defining Variants - @variantGroups.size + @variants.size
-@if(variantGroups.isEmpty) { +@if(variants.isEmpty) {

No variants associated with this haplogroup.

} else { @defining(s"variants-$haplogroupId") { containerId => @@ -28,42 +52,46 @@
placeholder="Filter variants...">
-
+
    - @for(group <- variantGroups) { -
  • + @for(variant <- variants) { + @defining(refGenomes(variant)) { refs => +
  • - @group.displayName - @group.rsId.filter(_ != group.displayName).map { rs => + @variant.displayName + @variant.rsIds.headOption.filter(_ != variant.canonicalName.getOrElse("")).map { rs => (@rs) } - @group.buildCount build@if(group.buildCount != 1){s} + @refs.size build@if(refs.size != 1){s}
    + @variant.variantId.map { vid => + }
    - @for(vwc <- group.variantsSorted) { + @for(refGenome <- refs) {
    - @vwc.shortReferenceGenome - @vwc.formattedPosition - @vwc.variant.referenceAllele→@vwc.variant.alternateAllele + @refGenome + @formatPosition(variant, refGenome) + @Html(formatAlleles(variant, refGenome))
    }
    • + } }
} diff --git a/app/views/curator/variants/detailPanel.scala.html b/app/views/curator/variants/detailPanel.scala.html index 9484ce0..7a441cd 100644 --- a/app/views/curator/variants/detailPanel.scala.html +++ b/app/views/curator/variants/detailPanel.scala.html @@ -1,42 +1,120 @@ -@import models.domain.genomics.{VariantWithContig, VariantGroup} -@import models.dal.domain.genomics.VariantAlias +@import models.domain.genomics.{NamingStatus, VariantV2} @import models.domain.haplogroups.Haplogroup @import models.domain.curator.AuditLogEntry -@(vwc: VariantWithContig, variantGroup: Option[VariantGroup], aliases: Seq[VariantAlias], haplogroups: Seq[Haplogroup], history: Seq[AuditLogEntry])(implicit request: RequestHeader) +@import play.api.libs.json.JsObject +@(variant: VariantV2, haplogroups: Seq[Haplogroup], history: Seq[AuditLogEntry])(implicit request: RequestHeader) + +@* Helper to extract reference genomes from coordinates *@ +@refGenomes = @{ + variant.coordinates.asOpt[Map[String, JsObject]].map(_.keys.toSeq.sorted).getOrElse(Seq.empty) +} + +@* Helper to format position for a specific reference *@ +@formatPosition(refGenome: String) = @{ + variant.getCoordinates(refGenome).map { coords => + val contig = (coords \ "contig").asOpt[String].getOrElse("?") + val pos = (coords \ "position").asOpt[Int].getOrElse(0) + s"$contig:$pos" + }.getOrElse("-") +} + +@* Helper to format alleles for a specific reference *@ +@formatAlleles(refGenome: String) = @{ + variant.getCoordinates(refGenome).map { coords => + val ref = (coords \ "ref").asOpt[String].getOrElse("?") + val alt = (coords \ "alt").asOpt[String].getOrElse("?") + s"$ref→$alt" + }.getOrElse("-") +} + +@* Helper to get primary alleles (prefer hs1, then GRCh38) *@ +@primaryAlleles = @{ + val coords = variant.coordinates.asOpt[Map[String, JsObject]].getOrElse(Map.empty) + val primary = coords.get("hs1").orElse(coords.get("GRCh38")).orElse(coords.headOption.map(_._2)) + primary.map { c => + val ref = (c \ "ref").asOpt[String].getOrElse("?") + val alt = (c \ "alt").asOpt[String].getOrElse("?") + (ref, alt) + }.getOrElse(("?", "?")) +}
-
@vwc.variant.rsId.orElse(vwc.variant.commonName).getOrElse(s"Variant ${vwc.variant.variantId.get}")
- @vwc.variant.variantType +
@variant.displayName
+ @variant.mutationType
-
rsId
-
@vwc.variant.rsId.getOrElse("-")
+
Canonical Name
+
@variant.canonicalName.getOrElse("-")
-
Common Name
-
@vwc.variant.commonName.getOrElse("-")
+
rsIds
+
+ @if(variant.rsIds.nonEmpty) { + @for(rsId <- variant.rsIds) { + @rsId + } + } else { - } +
-
Ancestral
-
@vwc.variant.referenceAllele
+ @defining(primaryAlleles) { alleles => +
Ancestral
+
@alleles._1
-
Derived
-
@vwc.variant.alternateAllele
+
Derived
+
@alleles._2
+ }
Type
-
@vwc.variant.variantType
+
@variant.mutationType.displayName
+ +
Naming Status
+
+ + @variant.namingStatus.displayName + +
- @if(aliases.nonEmpty) { + @if(variant.commonNames.nonEmpty) {
Alternative Names
- @views.html.components.variantAliases(aliases) +
+ @for(name <- variant.commonNames) { + @name + } +
}
Reference Builds
- @views.html.components.variantBuilds(vwc, variantGroup) + @if(refGenomes.isEmpty) { +

No coordinates available.

+ } else { +
+ + + + + + + + + + @for(ref <- refGenomes) { + + + + + + } + +
BuildPositionAlleles
+ @ref + @formatPosition(ref)@Html(formatAlleles(ref))
+
+ }
@@ -59,27 +137,23 @@
Used By Haplogroups
} + @variant.notes.map { notes => +
+
Notes
+

@notes

+ } +
- @variantGroup match { - case Some(group) if group.variants.size > 1 => { - - Edit Group (@group.variants.size builds) - - } - case _ => { - - Edit - - } - } + + Edit +
@@ -99,7 +173,7 @@
Recent History
@if(history.size > 5) { View all history... @@ -108,6 +182,15 @@
Recent History
+@buildBadgeClass(refGenome: String) = @{ + refGenome match { + case "GRCh37" => "bg-warning text-dark" + case "GRCh38" => "bg-info" + case "hs1" => "bg-success" + case _ => "bg-secondary" + } +} + @actionBadgeClass(action: String) = @{ action match { case "create" => "bg-success" diff --git a/app/views/curator/variants/editGroupForm.scala.html b/app/views/curator/variants/editGroupForm.scala.html deleted file mode 100644 index a280337..0000000 --- a/app/views/curator/variants/editGroupForm.scala.html +++ /dev/null @@ -1,156 +0,0 @@ -@import org.webjars.play.WebJarsUtil -@import controllers.VariantFormData -@import models.domain.genomics.VariantGroup -@(groupKey: String, variantGroup: VariantGroup, form: Form[VariantFormData])(implicit request: RequestHeader, messages: Messages, webJarsUtil: WebJarsUtil) - -@buildBadgeClass(refGenome: String) = @{ - refGenome match { - case "GRCh37" => "bg-warning text-dark" - case "GRCh38" => "bg-info" - case "hs1" => "bg-success" - case _ => "bg-secondary" - } -} - -@* Check if alleles differ from first variant (potential reverse complement) *@ -@hasAlleleDifference = @{ - variantGroup.variants.size > 1 && { - val first = variantGroup.variantsSorted.head - variantGroup.variantsSorted.tail.exists { v => - v.variant.referenceAllele != first.variant.referenceAllele || - v.variant.alternateAllele != first.variant.alternateAllele - } - } -} - -@main(s"Edit Variant Group: ${variantGroup.displayName}") { -
-
-
- - -
-
-
- Edit Variant Group - @variantGroup.variants.size builds -
-
-
-
- - Editing this group will update @variantGroup.variants.size variant@if(variantGroup.variants.size != 1){s} across different reference builds. -
- - @if(hasAlleleDifference) { -
- - Strand difference detected: Alleles vary between builds (likely reverse complement on different strand). -
- } - -
Variants in this group
-
- - - - - - - - - - @for(vwc <- variantGroup.variantsSorted) { - - - - - - } - -
BuildPositionAlleles (Anc→Der)
- - @vwc.shortReferenceGenome - - - @vwc.contig.commonName.getOrElse(vwc.contig.accession):@vwc.variant.position - - @vwc.variant.referenceAllele - - @vwc.variant.alternateAllele -
-
- -
- -
Shared Properties (applies to all builds)
- - @helper.form(controllers.routes.CuratorController.updateVariantGroup(groupKey)) { - @helper.CSRF.formField - - @* Hidden fields to preserve required form data *@ - - - - - -
- - - @form.error("variantType").map { error => -
@error.message
- } -
- -
-
- - -
dbSNP reference identifier
-
-
- - -
SNP name used in phylogenetic trees
-
-
- -
- - - Cancel - -
- } -
-
-
-
-
-} diff --git a/app/views/curator/variants/list.scala.html b/app/views/curator/variants/list.scala.html index a9c420e..38453e5 100644 --- a/app/views/curator/variants/list.scala.html +++ b/app/views/curator/variants/list.scala.html @@ -1,6 +1,6 @@ @import org.webjars.play.WebJarsUtil -@import models.domain.genomics.VariantGroup -@(variantGroups: Seq[VariantGroup], query: Option[String], currentPage: Int, totalPages: Int, pageSize: Int, totalCount: Int)(implicit request: RequestHeader, messages: Messages, webJarsUtil: WebJarsUtil) +@import models.domain.genomics.VariantV2 +@(variants: Seq[VariantV2], query: Option[String], currentPage: Int, totalPages: Int, pageSize: Int, totalCount: Int)(implicit request: RequestHeader, messages: Messages, webJarsUtil: WebJarsUtil) @main("Curator - Variants") { + + +
+
+ 🧬 +
+

Scheduled Maintenance

+

+ We're upgrading our database to serve you better.
+ This process typically takes 15-30 minutes. +

+ +
+

What's Happening

+

We're consolidating our variant data schema to improve search performance and support additional reference genomes.

+
+
+
+
+ +
+

When We'll Be Back

+

We expect to be back online shortly. Please check back soon.

+
+ +
+

Questions? Contact us at support@decodingus.com

+
+
+ + From 9287d3049c211461e12bb69365f7e7b4bde1a779 Mon Sep 17 00:00:00 2001 From: jkane Date: Sat, 13 Dec 2025 06:49:36 -0600 Subject: [PATCH 03/28] DU Naming Authority API --- app/controllers/VariantApiController.scala | 139 ++++++++++++++++++ app/models/api/VariantApiModels.scala | 59 ++++++++ app/repositories/VariantV2Repository.scala | 65 ++++++++ conf/evolutions/default/54.sql | 42 ++++++ conf/routes | 5 + .../variant-schema-simplification.md | 58 +++++++- 6 files changed, 367 insertions(+), 1 deletion(-) create mode 100644 conf/evolutions/default/54.sql diff --git a/app/controllers/VariantApiController.scala b/app/controllers/VariantApiController.scala index f0460db..bfdc6cf 100644 --- a/app/controllers/VariantApiController.scala +++ b/app/controllers/VariantApiController.scala @@ -262,4 +262,143 @@ class VariantApiController @Inject()( )) } } + + // ============================================================================ + // DU Naming Authority Endpoints + // ============================================================================ + + /** + * Assign a DU name to a single variant. + * The variant must exist and not already have a DU name. + */ + def assignDuName(variantId: Int): Action[AnyContent] = secureApi.async { _ => + variantRepository.findById(variantId).flatMap { + case None => + Future.successful(NotFound(Json.toJson(DuNameAssignmentResult( + variantId = variantId, + duName = None, + previousName = None, + status = "error", + message = Some(s"Variant $variantId not found") + )))) + + case Some(variant) => + // Check if already has a DU name + if (variant.canonicalName.exists(variantRepository.isDuName)) { + Future.successful(Ok(Json.toJson(DuNameAssignmentResult( + variantId = variantId, + duName = variant.canonicalName, + previousName = variant.canonicalName, + status = "skipped", + message = Some("Variant already has a DU name") + )))) + } else { + // Assign new DU name + assignDuNameToVariant(variant).map { result => + Ok(Json.toJson(result)) + } + } + } + } + + /** + * Bulk assign DU names to multiple variants. + * Skips variants that already have DU names. + */ + def bulkAssignDuNames(): Action[BulkAssignDuNamesRequest] = + secureApi.jsonAction[BulkAssignDuNamesRequest].async { request => + val variantIds = request.body.variantIds + logger.info(s"Bulk assign DU names request for ${variantIds.size} variants") + + // Process sequentially to maintain name ordering + variantIds.foldLeft(Future.successful(Seq.empty[DuNameAssignmentResult])) { (accFuture, variantId) => + accFuture.flatMap { acc => + processAssignDuName(variantId).map(result => acc :+ result) + } + }.map { results => + val succeeded = results.count(_.status == "success") + val failed = results.count(_.status == "error") + val skipped = results.count(_.status == "skipped") + + logger.info(s"Bulk assign DU names completed: $succeeded succeeded, $failed failed, $skipped skipped") + + Ok(Json.toJson(BulkDuNameAssignmentResponse( + total = results.size, + succeeded = succeeded, + failed = failed, + skipped = skipped, + results = results + ))) + } + } + + /** + * Get the next DU name that would be assigned (preview without consuming). + */ + def previewNextDuName(): Action[AnyContent] = secureApi.async { _ => + variantRepository.nextDuName().map { nextName => + Ok(Json.obj( + "nextDuName" -> nextName, + "note" -> "This name has been reserved. Use assignDuName to apply it to a variant." + )) + } + } + + private def processAssignDuName(variantId: Int): Future[DuNameAssignmentResult] = { + variantRepository.findById(variantId).flatMap { + case None => + Future.successful(DuNameAssignmentResult( + variantId = variantId, + duName = None, + previousName = None, + status = "error", + message = Some(s"Variant $variantId not found") + )) + + case Some(variant) => + if (variant.canonicalName.exists(variantRepository.isDuName)) { + Future.successful(DuNameAssignmentResult( + variantId = variantId, + duName = variant.canonicalName, + previousName = variant.canonicalName, + status = "skipped", + message = Some("Variant already has a DU name") + )) + } else { + assignDuNameToVariant(variant) + } + } + } + + private def assignDuNameToVariant(variant: VariantV2): Future[DuNameAssignmentResult] = { + val previousName = variant.canonicalName + + for { + duName <- variantRepository.nextDuName() + updated = variant.copy( + canonicalName = Some(duName), + namingStatus = models.domain.genomics.NamingStatus.Named + ) + success <- variantRepository.update(updated) + } yield { + if (success) { + logger.info(s"Assigned DU name $duName to variant ${variant.variantId.get} (was: ${previousName.getOrElse("unnamed")})") + DuNameAssignmentResult( + variantId = variant.variantId.get, + duName = Some(duName), + previousName = previousName, + status = "success", + message = Some(s"Assigned $duName") + ) + } else { + DuNameAssignmentResult( + variantId = variant.variantId.get, + duName = None, + previousName = previousName, + status = "error", + message = Some("Failed to update variant") + ) + } + } + } } diff --git a/app/models/api/VariantApiModels.scala b/app/models/api/VariantApiModels.scala index 8b7743b..80d5205 100644 --- a/app/models/api/VariantApiModels.scala +++ b/app/models/api/VariantApiModels.scala @@ -180,3 +180,62 @@ case class AliasSourceStatsResponse( object AliasSourceStatsResponse { implicit val format: OFormat[AliasSourceStatsResponse] = Json.format[AliasSourceStatsResponse] } + +// ============================================================================ +// DU Naming Authority Models +// ============================================================================ + +/** + * Request to assign a DU name to a variant. + * Variant is identified by variantId. + * + * @param variantId The variant ID to assign a DU name to + */ +case class AssignDuNameRequest( + variantId: Int +) + +object AssignDuNameRequest { + implicit val format: OFormat[AssignDuNameRequest] = Json.format[AssignDuNameRequest] +} + +/** + * Bulk request to assign DU names to multiple variants. + */ +case class BulkAssignDuNamesRequest( + variantIds: Seq[Int] +) + +object BulkAssignDuNamesRequest { + implicit val format: OFormat[BulkAssignDuNamesRequest] = Json.format[BulkAssignDuNamesRequest] +} + +/** + * Result of a DU name assignment operation. + */ +case class DuNameAssignmentResult( + variantId: Int, + duName: Option[String], + previousName: Option[String], + status: String, + message: Option[String] = None +) + +object DuNameAssignmentResult { + implicit val format: OFormat[DuNameAssignmentResult] = Json.format[DuNameAssignmentResult] +} + +/** + * Response for bulk DU name assignment. + */ +case class BulkDuNameAssignmentResponse( + total: Int, + succeeded: Int, + failed: Int, + skipped: Int, + results: Seq[DuNameAssignmentResult] +) + +object BulkDuNameAssignmentResponse { + implicit val format: OFormat[BulkDuNameAssignmentResponse] = Json.format[BulkDuNameAssignmentResponse] +} diff --git a/app/repositories/VariantV2Repository.scala b/app/repositories/VariantV2Repository.scala index 7abd4c9..ab8b91d 100644 --- a/app/repositories/VariantV2Repository.scala +++ b/app/repositories/VariantV2Repository.scala @@ -183,6 +183,31 @@ trait VariantV2Repository { * Get variants by IDs. */ def findByIds(ids: Seq[Int]): Future[Seq[VariantV2]] + + // === DU Naming Authority === + + /** + * Generate the next DU name from the sequence. + * Format: DU1, DU2, DU123 (no zero padding per ISOGG guidelines) + */ + def nextDuName(): Future[String] + + /** + * Get the current DU name without incrementing the sequence. + * Useful for previewing what name would be assigned. + */ + def currentDuName(): Future[Option[String]] + + /** + * Check if a name follows the DU naming convention. + */ + def isDuName(name: String): Boolean + + /** + * Create a variant with a new DU name. + * Atomically generates the name and creates the variant. + */ + def createWithDuName(variant: VariantV2): Future[VariantV2] } class VariantV2RepositoryImpl @Inject()( @@ -684,6 +709,46 @@ class VariantV2RepositoryImpl @Inject()( } } + // === DU Naming Authority === + + private val DuNamePattern = "^DU[1-9][0-9]*$".r + + override def nextDuName(): Future[String] = { + db.run(sql"SELECT next_du_name()".as[String].head) + } + + override def currentDuName(): Future[Option[String]] = { + // currval throws if nextval hasn't been called in this session + // So we handle this gracefully + db.run(sql"SELECT current_du_name()".as[String].headOption).recover { + case _: PSQLException => None + } + } + + override def isDuName(name: String): Boolean = { + DuNamePattern.matches(name) + } + + override def createWithDuName(variant: VariantV2): Future[VariantV2] = { + // Atomically get next DU name and create the variant + val action = for { + duName <- sql"SELECT next_du_name()".as[String].head + now = Instant.now() + id <- (variantsV2 returning variantsV2.map(_.variantId)) += variant.copy( + canonicalName = Some(duName), + namingStatus = NamingStatus.Named, + createdAt = now, + updatedAt = now + ) + } yield variant.copy( + variantId = Some(id), + canonicalName = Some(duName), + namingStatus = NamingStatus.Named + ) + + db.run(action.transactionally) + } + // === GetResult for raw SQL queries === private val variantV2GetResult: GetResult[VariantV2] = GetResult { r => diff --git a/conf/evolutions/default/54.sql b/conf/evolutions/default/54.sql new file mode 100644 index 0000000..9416204 --- /dev/null +++ b/conf/evolutions/default/54.sql @@ -0,0 +1,42 @@ +# --- !Ups + +-- ============================================================================= +-- DU Naming Authority: Sequence and function for DecodingUs variant names +-- Per ISOGG guidelines: No zero padding (DU1, DU2, ... not DU00001) +-- ============================================================================= + +-- Sequence for DecodingUs variant names +CREATE SEQUENCE du_variant_name_seq START WITH 1; + +-- Function to get next DU name (no zero padding per ISOGG request) +CREATE OR REPLACE FUNCTION next_du_name() RETURNS TEXT AS $$ +BEGIN + RETURN 'DU' || nextval('du_variant_name_seq')::TEXT; +END; +$$ LANGUAGE plpgsql; + +-- Function to peek at current value without incrementing +CREATE OR REPLACE FUNCTION current_du_name() RETURNS TEXT AS $$ +BEGIN + RETURN 'DU' || currval('du_variant_name_seq')::TEXT; +END; +$$ LANGUAGE plpgsql; + +-- Function to check if a name is a valid DU name +CREATE OR REPLACE FUNCTION is_du_name(name TEXT) RETURNS BOOLEAN AS $$ +BEGIN + RETURN name ~ '^DU[1-9][0-9]*$'; +END; +$$ LANGUAGE plpgsql; + +COMMENT ON SEQUENCE du_variant_name_seq IS 'Sequence for DecodingUs (DU) variant naming authority'; +COMMENT ON FUNCTION next_du_name() IS 'Returns next available DU name (e.g., DU1, DU2, DU123)'; +COMMENT ON FUNCTION current_du_name() IS 'Returns current DU name without incrementing sequence'; +COMMENT ON FUNCTION is_du_name(TEXT) IS 'Validates if a name follows DU naming convention'; + +# --- !Downs + +DROP FUNCTION IF EXISTS is_du_name(TEXT); +DROP FUNCTION IF EXISTS current_du_name(); +DROP FUNCTION IF EXISTS next_du_name(); +DROP SEQUENCE IF EXISTS du_variant_name_seq; diff --git a/conf/routes b/conf/routes index 234f468..25b029e 100644 --- a/conf/routes +++ b/conf/routes @@ -126,6 +126,11 @@ GET /api/private/aliases/sources/stats GET /api/private/aliases/sources/preview controllers.VariantApiController.previewAliasSourceUpdate(aliasPrefix: String, currentSource: String) POST /api/private/aliases/sources controllers.VariantApiController.bulkUpdateAliasSources() +# DU Naming Authority API (X-API-Key secured) +POST /api/private/variants/:variantId/du-name controllers.VariantApiController.assignDuName(variantId: Int) +POST /api/private/variants/du-names controllers.VariantApiController.bulkAssignDuNames() +GET /api/private/variants/du-names/next controllers.VariantApiController.previewNextDuName() + # Authentication GET /login controllers.AuthController.login POST /login controllers.AuthController.authenticate diff --git a/documents/proposals/variant-schema-simplification.md b/documents/proposals/variant-schema-simplification.md index c397d11..4332e53 100644 --- a/documents/proposals/variant-schema-simplification.md +++ b/documents/proposals/variant-schema-simplification.md @@ -1,10 +1,66 @@ # Variant Schema Simplification with Universal Coordinates -**Status:** Backlog +**Status:** Implementation Complete - Pending Data Migration **Priority:** Medium **Complexity:** Large **Author:** DecodingUs Team **Created:** 2025-12-10 +**Updated:** 2025-12-13 + +--- + +## Implementation Status + +### Completed + +| Component | Status | Notes | +|-----------|--------|-------| +| **Evolution 53.sql** | ✅ Done | Creates `variant_v2`, ASR tables. Does NOT drop old tables. | +| **Domain Models** | ✅ Done | `VariantV2`, `MutationType` enum, `NamingStatus` enum in `models.domain.genomics` | +| **VariantV2Repository** | ✅ Done | Full CRUD, JSONB operations, search | +| **HaplogroupVariantRepository** | ✅ Done | Updated to use `variant_v2` | +| **YBrowseVariantIngestionService** | ✅ Done | Refactored for single-row-per-variant with JSONB coordinates | +| **VariantPublicApiService** | ✅ Done | Simplified (no grouping needed) | +| **VariantExportService** | ✅ Done | Updated for VariantV2 | +| **VariantBrowserController** | ✅ Done | Public read-only browser restored | +| **VariantApiController** | ✅ Done | Private bulk API restored | +| **CuratorController** | ✅ Done | Updated for VariantV2 | +| **View Templates** | ✅ Done | All curator and public views updated | +| **DatabaseSchema/BaseModule** | ✅ Done | Configuration updated | +| **Old files removed** | ✅ Done | Variant.scala, VariantAlias*.scala, VariantGroup.scala, old repositories | + +### Pending (Production Deployment) + +| Task | Notes | +|------|-------| +| **Run data migration** | `scripts/migrate_variant_to_v2.sql` - consolidates old data | +| **Verify migration** | Check counts, orphaned FKs | +| **Drop old tables** | `variant`, `variant_alias`, `str_marker` (after verification) | +| **Update haplogroup_variant FK** | Done in migration script | + +### Files Created + +| File | Purpose | +|------|---------| +| `conf/evolutions/default/53.sql` | Schema evolution (creates new tables) | +| `conf/evolutions/default/54.sql` | DU naming authority (sequence + functions) | +| `scripts/migrate_variant_to_v2.sql` | Data migration script (run manually) | +| `scripts/maintenance.html` | NGINX maintenance page for downtime | +| `app/models/domain/genomics/VariantV2.scala` | Domain model | +| `app/models/domain/genomics/MutationType.scala` | Scala 3 parameterized enum | +| `app/models/domain/genomics/NamingStatus.scala` | Scala 3 parameterized enum | +| `app/repositories/VariantV2Repository.scala` | Repository layer (includes DU naming methods) | +| `app/controllers/VariantBrowserController.scala` | Public browser | +| `app/controllers/VariantApiController.scala` | Private bulk API | +| `app/views/variants/*.scala.html` | Public browser views | + +### DU Naming Authority + +| Component | Status | Notes | +|-----------|--------|-------| +| **Evolution 54.sql** | ✅ Done | `du_variant_name_seq`, `next_du_name()`, `is_du_name()` | +| **Repository methods** | ✅ Done | `nextDuName()`, `currentDuName()`, `isDuName()`, `createWithDuName()` | +| **Format** | DU1, DU2, ... | No zero padding per ISOGG guidelines | --- From d292b6894137eccc0f1f09c8c7028cf6dc9ae441 Mon Sep 17 00:00:00 2001 From: jkane Date: Sat, 13 Dec 2025 08:07:43 -0600 Subject: [PATCH 04/28] **refactor(variants): Update forms and backend for simplified reference genome and variant metadata handling** - Replaced `genbankContigId` with `refGenome` and `contig` in forms and backend logic. - Enhanced `editForm` and `createForm` to support clearer metadata fields and additional variant types. - Made genomic coordinates immutable, restricting edits to metadata fields only. - Added improved validation and context for editable and optional fields. - Streamlined templates and controller logic to align with `VariantV2` schema. --- app/controllers/CuratorController.scala | 170 ++++++++++++++---- .../curator/variants/createForm.scala.html | 91 ++++++---- .../curator/variants/editForm.scala.html | 43 +++-- 3 files changed, 214 insertions(+), 90 deletions(-) diff --git a/app/controllers/CuratorController.scala b/app/controllers/CuratorController.scala index bc678f6..0b7b5b7 100644 --- a/app/controllers/CuratorController.scala +++ b/app/controllers/CuratorController.scala @@ -3,12 +3,13 @@ package controllers import actions.{AuthenticatedAction, AuthenticatedRequest, PermissionAction} import jakarta.inject.{Inject, Singleton} import models.HaplogroupType -import models.domain.genomics.VariantV2 +import models.domain.genomics.{MutationType, NamingStatus, PointVariantCoordinates, VariantAliases, VariantV2} import models.domain.haplogroups.Haplogroup import org.webjars.play.WebJarsUtil import play.api.Logging import play.api.data.Form import play.api.data.Forms.* +import play.api.libs.json.Json import play.api.i18n.I18nSupport import play.api.mvc.* import repositories.{GenbankContigRepository, HaplogroupCoreRepository, HaplogroupVariantRepository, VariantV2Repository} @@ -46,7 +47,8 @@ case class CreateHaplogroupFormData( ) case class VariantFormData( - genbankContigId: Int, + refGenome: String, + contig: String, position: Int, referenceAllele: String, alternateAllele: String, @@ -105,14 +107,15 @@ class CuratorController @Inject()( private val variantForm: Form[VariantFormData] = Form( mapping( - "genbankContigId" -> number, + "refGenome" -> nonEmptyText.verifying("Invalid reference genome", r => Seq("hs1", "GRCh38", "GRCh37").contains(r)), + "contig" -> nonEmptyText(1, 50), "position" -> number, "referenceAllele" -> nonEmptyText(1, 1000), "alternateAllele" -> nonEmptyText(1, 1000), - "variantType" -> nonEmptyText(1, 50), + "variantType" -> nonEmptyText.verifying("Invalid variant type", t => MutationType.fromString(t).isDefined), "rsId" -> optional(text(maxLength = 50)), "commonName" -> optional(text(maxLength = 100)) - )(VariantFormData.apply)(v => Some((v.genbankContigId, v.position, v.referenceAllele, v.alternateAllele, v.variantType, v.rsId, v.commonName))) + )(VariantFormData.apply)(v => Some((v.refGenome, v.contig, v.position, v.referenceAllele, v.alternateAllele, v.variantType, v.rsId, v.commonName))) ) private val splitBranchForm: Form[SplitBranchFormData] = Form( @@ -466,58 +469,153 @@ class CuratorController @Inject()( } } - // TODO: Redesign variant creation for VariantV2 with JSONB coordinates def createVariantForm: Action[AnyContent] = - withPermission("variant.create").async { implicit request => - Future.successful( - Redirect(routes.CuratorController.listVariants(None, 1, 20)) - .flashing("warning" -> "Variant creation is being updated for the new schema. Use YBrowse ingestion for now.") - ) + withPermission("variant.create") { implicit request => + Ok(views.html.curator.variants.createForm(variantForm)) } - // TODO: Redesign variant creation for VariantV2 with JSONB coordinates def createVariant: Action[AnyContent] = withPermission("variant.create").async { implicit request => - Future.successful( - Redirect(routes.CuratorController.listVariants(None, 1, 20)) - .flashing("warning" -> "Variant creation is being updated for the new schema.") + variantForm.bindFromRequest().fold( + formWithErrors => { + Future.successful(BadRequest(views.html.curator.variants.createForm(formWithErrors))) + }, + data => { + val coordinates = Json.obj( + data.refGenome -> Json.toJson(PointVariantCoordinates( + contig = data.contig, + position = data.position, + ref = data.referenceAllele.toUpperCase, + alt = data.alternateAllele.toUpperCase + )) + ) + + val aliases = (data.commonName, data.rsId) match { + case (Some(name), Some(rs)) => + Json.toJson(VariantAliases(commonNames = Seq(name), rsIds = Seq(rs))) + case (Some(name), None) => + Json.toJson(VariantAliases(commonNames = Seq(name))) + case (None, Some(rs)) => + Json.toJson(VariantAliases(rsIds = Seq(rs))) + case _ => + Json.obj() + } + + val variant = VariantV2( + canonicalName = data.commonName, + mutationType = MutationType.fromStringOrDefault(data.variantType), + namingStatus = if (data.commonName.isDefined) NamingStatus.Named else NamingStatus.Unnamed, + aliases = aliases, + coordinates = coordinates + ) + + for { + createdId <- variantV2Repository.create(variant) + createdVariant = variant.copy(variantId = Some(createdId)) + _ <- auditService.logVariantCreate(request.user.id.get, createdVariant, Some("Created via curator interface")) + } yield { + Redirect(routes.CuratorController.listVariants(None, 1, 20)) + .flashing("success" -> s"Variant ${createdVariant.displayName} created successfully") + } + } ) } - // TODO: Redesign variant editing for VariantV2 with JSONB coordinates def editVariantForm(id: Int): Action[AnyContent] = withPermission("variant.update").async { implicit request => - Future.successful( - Redirect(routes.CuratorController.listVariants(None, 1, 20)) - .flashing("warning" -> "Variant editing is being updated for the new schema.") - ) + variantV2Repository.findById(id).map { + case Some(variant) => + // Get the primary reference genome coordinates (prefer hs1) + val refGenome = variant.availableReferences.find(_ == "hs1") + .orElse(variant.availableReferences.headOption) + .getOrElse("hs1") + + val coords = variant.getCoordinates(refGenome) + val contig = coords.flatMap(c => (c \ "contig").asOpt[String]).getOrElse("") + val position = coords.flatMap(c => (c \ "position").asOpt[Int]).getOrElse(0) + val ref = coords.flatMap(c => (c \ "ref").asOpt[String]).getOrElse("") + val alt = coords.flatMap(c => (c \ "alt").asOpt[String]).getOrElse("") + + val filledForm = variantForm.fill(VariantFormData( + refGenome = refGenome, + contig = contig, + position = position, + referenceAllele = ref, + alternateAllele = alt, + variantType = variant.mutationType.dbValue, + rsId = variant.rsIds.headOption, + commonName = variant.canonicalName + )) + + Ok(views.html.curator.variants.editForm(id, filledForm, s"$refGenome:$contig")) + + case None => + NotFound("Variant not found") + } } - // TODO: Redesign variant editing for VariantV2 with JSONB coordinates def updateVariant(id: Int): Action[AnyContent] = withPermission("variant.update").async { implicit request => - Future.successful( - Redirect(routes.CuratorController.listVariants(None, 1, 20)) - .flashing("warning" -> "Variant editing is being updated for the new schema.") + variantForm.bindFromRequest().fold( + formWithErrors => { + Future.successful(BadRequest(views.html.curator.variants.editForm(id, formWithErrors, ""))) + }, + data => { + variantV2Repository.findById(id).flatMap { + case None => + Future.successful(NotFound("Variant not found")) + + case Some(existing) => + // Update editable fields (metadata only - coordinates are immutable after creation) + val updatedAliases = (data.commonName, data.rsId) match { + case (Some(name), Some(rs)) => + Json.toJson(VariantAliases(commonNames = Seq(name), rsIds = Seq(rs))) + case (Some(name), None) => + Json.toJson(VariantAliases(commonNames = Seq(name))) + case (None, Some(rs)) => + Json.toJson(VariantAliases(rsIds = Seq(rs))) + case _ => + existing.aliases + } + + val updated = existing.copy( + canonicalName = data.commonName.orElse(existing.canonicalName), + mutationType = MutationType.fromStringOrDefault(data.variantType), + namingStatus = if (data.commonName.isDefined) NamingStatus.Named else existing.namingStatus, + aliases = updatedAliases + ) + + for { + success <- variantV2Repository.update(updated) + _ <- if (success) { + auditService.logVariantUpdate(request.user.id.get, existing, updated, Some("Updated via curator interface")) + } else { + Future.successful(()) + } + } yield { + if (success) { + Redirect(routes.CuratorController.listVariants(None, 1, 20)) + .flashing("success" -> s"Variant ${updated.displayName} updated successfully") + } else { + BadRequest("Failed to update variant") + } + } + } + } ) } - // TODO: Remove variant group concept - VariantV2 is already consolidated + // Variant groups are obsolete - VariantV2 is already consolidated def editVariantGroupForm(groupKey: String): Action[AnyContent] = - withPermission("variant.update").async { implicit request => - Future.successful( - Redirect(routes.CuratorController.listVariants(None, 1, 20)) - .flashing("warning" -> "Variant group editing is being updated for the new schema.") - ) + withPermission("variant.update") { implicit request => + Redirect(routes.CuratorController.listVariants(Some(groupKey), 1, 20)) + .flashing("info" -> "Variant groups have been replaced with consolidated variants. Edit each variant directly.") } - // TODO: Remove variant group concept - VariantV2 is already consolidated def updateVariantGroup(groupKey: String): Action[AnyContent] = - withPermission("variant.update").async { implicit request => - Future.successful( - Redirect(routes.CuratorController.listVariants(None, 1, 20)) - .flashing("warning" -> "Variant group editing is being updated for the new schema.") - ) + withPermission("variant.update") { implicit request => + Redirect(routes.CuratorController.listVariants(Some(groupKey), 1, 20)) + .flashing("info" -> "Variant groups have been replaced with consolidated variants.") } def deleteVariant(id: Int): Action[AnyContent] = diff --git a/app/views/curator/variants/createForm.scala.html b/app/views/curator/variants/createForm.scala.html index 3659773..5bf92d9 100644 --- a/app/views/curator/variants/createForm.scala.html +++ b/app/views/curator/variants/createForm.scala.html @@ -1,13 +1,6 @@ @import org.webjars.play.WebJarsUtil @import controllers.VariantFormData -@import models.domain.genomics.GenbankContig -@(form: Form[VariantFormData], contigs: Seq[GenbankContig])(implicit request: RequestHeader, messages: Messages, webJarsUtil: WebJarsUtil) - -@contigLabel(c: GenbankContig) = @{ - val refGenome = c.referenceGenome.getOrElse("Unknown") - val name = c.commonName.getOrElse(c.accession) - s"$refGenome:$name" -} +@(form: Form[VariantFormData])(implicit request: RequestHeader, messages: Messages, webJarsUtil: WebJarsUtil) @main("Create Variant") {
@@ -31,24 +24,37 @@
Create Variant
- - - - @for(contig <- contigs) { - - } + + + + - @form.error("genbankContigId").map { error => + @form.error("refGenome").map { error =>
@error.message
}
+ + + @form.error("contig").map { error => +
@error.message
+ } +
+
+ +
+
Create Variant
@error.message
}
-
- -
-
+
Create Variant style="text-transform: uppercase;" placeholder="e.g., A" required> -
The allele present in the reference genome (ancestral state)
+
Reference genome allele (ancestral)
@form.error("referenceAllele").map { error =>
@error.message
}
-
+
Create Variant style="text-transform: uppercase;" placeholder="e.g., G" required> -
The mutated allele that defines this variant (derived state)
+
Mutated allele (derived)
@form.error("alternateAllele").map { error =>
@error.message
} @@ -102,25 +105,25 @@
Create Variant
name="variantType" required> - - - + + + + + + + + + @form.error("variantType").map { error =>
@error.message
}
+
+
Optional Identifiers
+
-
- - -
Create Variant name="commonName" value="@form("commonName").value.getOrElse("")" placeholder="e.g., M269"> +
Becomes canonical name if provided
+
+
+ +
diff --git a/app/views/curator/variants/editForm.scala.html b/app/views/curator/variants/editForm.scala.html index c49094c..7a92d53 100644 --- a/app/views/curator/variants/editForm.scala.html +++ b/app/views/curator/variants/editForm.scala.html @@ -22,14 +22,19 @@
Edit Variant
@helper.form(controllers.routes.CuratorController.updateVariant(id)) { @helper.CSRF.formField +
+ Genomic coordinates are immutable after creation. Only metadata fields can be edited. +
+
- + - + +
@@ -60,7 +65,8 @@
Edit Variant
- Genomic coordinates cannot be changed after creation +
+
Editable Fields
@@ -69,9 +75,15 @@
Edit Variant
name="variantType" required> - - - + + + + + + + + + @form.error("variantType").map { error =>
@error.message
@@ -79,15 +91,6 @@
Edit Variant
-
- - -
Edit Variant name="commonName" value="@form("commonName").value.getOrElse("")" placeholder="e.g., M269"> +
Becomes canonical name if provided
+
+
+ +
From a89c332018c82c3b9312a8b7b11629dc8b916ce8 Mon Sep 17 00:00:00 2001 From: jkane Date: Sat, 13 Dec 2025 08:26:19 -0600 Subject: [PATCH 05/28] **chore(curator): Remove legacy Cytoband and STR Marker templates and models** - Deleted unused templates (`createForm`, `editForm`, `detailPanel`) for Cytobands and STR Markers. - Removed associated Scala models (`Cytoband`, `StrMarker`), streamlining codebase maintenance. - Cleaned up controllers and routes referencing deprecated Cytoband and STR Marker logic. --- ...GenomeRegionsApiManagementController.scala | 110 +---- .../GenomeRegionsCuratorController.scala | 427 ++++-------------- .../GenomeRegionsManagementModels.scala | 151 +------ app/models/dal/DatabaseSchema.scala | 1 - app/models/dal/MyPostgresProfile.scala | 6 + .../domain/genomics/GenomeRegionTables.scala | 50 +- app/models/domain/genomics/Cytoband.scala | 21 - app/models/domain/genomics/GenomeRegion.scala | 41 +- .../GenomeRegionsRepository.scala | 244 ++-------- .../GenomeRegionsManagementService.scala | 390 ++-------------- app/services/GenomeRegionsService.scala | 112 +++-- .../curator/cytobands/createForm.scala.html | 117 ----- .../curator/cytobands/detailPanel.scala.html | 86 ---- .../curator/cytobands/editForm.scala.html | 116 ----- app/views/curator/cytobands/list.scala.html | 99 ---- .../curator/cytobands/listFragment.scala.html | 125 ----- .../genomeregions/detailPanel.scala.html | 61 +-- .../curator/genomeregions/list.scala.html | 4 +- .../genomeregions/listFragment.scala.html | 28 +- .../curator/strmarkers/createForm.scala.html | 145 ------ .../curator/strmarkers/detailPanel.scala.html | 86 ---- .../curator/strmarkers/editForm.scala.html | 143 ------ app/views/curator/strmarkers/list.scala.html | 99 ---- .../strmarkers/listFragment.scala.html | 119 ----- conf/evolutions/default/55.sql | 45 ++ conf/routes | 42 +- 26 files changed, 401 insertions(+), 2467 deletions(-) delete mode 100644 app/models/domain/genomics/Cytoband.scala delete mode 100644 app/views/curator/cytobands/createForm.scala.html delete mode 100644 app/views/curator/cytobands/detailPanel.scala.html delete mode 100644 app/views/curator/cytobands/editForm.scala.html delete mode 100644 app/views/curator/cytobands/list.scala.html delete mode 100644 app/views/curator/cytobands/listFragment.scala.html delete mode 100644 app/views/curator/strmarkers/createForm.scala.html delete mode 100644 app/views/curator/strmarkers/detailPanel.scala.html delete mode 100644 app/views/curator/strmarkers/editForm.scala.html delete mode 100644 app/views/curator/strmarkers/list.scala.html delete mode 100644 app/views/curator/strmarkers/listFragment.scala.html create mode 100644 conf/evolutions/default/55.sql diff --git a/app/controllers/GenomeRegionsApiManagementController.scala b/app/controllers/GenomeRegionsApiManagementController.scala index 64cb45a..0d0fa0a 100644 --- a/app/controllers/GenomeRegionsApiManagementController.scala +++ b/app/controllers/GenomeRegionsApiManagementController.scala @@ -11,7 +11,7 @@ import services.GenomeRegionsManagementService import scala.concurrent.{ExecutionContext, Future} /** - * Private API controller for managing genome regions, cytobands, and STR markers. + * Private API controller for managing genome regions. * Secured with X-API-Key authentication. * * API changes are logged as "system" user in the audit log. @@ -29,8 +29,8 @@ class GenomeRegionsApiManagementController @Inject()( // GenomeRegion Endpoints // ============================================================================ - def listRegions(build: Option[String], page: Int = 1, pageSize: Int = 25): Action[AnyContent] = secureApi.async { _ => - managementService.listRegions(build, page, pageSize).map { response => + def listRegions(regionType: Option[String], build: Option[String], page: Int = 1, pageSize: Int = 25): Action[AnyContent] = secureApi.async { _ => + managementService.listRegions(regionType, build, page, pageSize).map { response => Ok(Json.toJson(response)) } } @@ -75,106 +75,4 @@ class GenomeRegionsApiManagementController @Inject()( Ok(Json.toJson(response)) } } - - // ============================================================================ - // Cytoband Endpoints - // ============================================================================ - - def listCytobands(build: Option[String], page: Int = 1, pageSize: Int = 25): Action[AnyContent] = secureApi.async { _ => - managementService.listCytobands(build, page, pageSize).map { response => - Ok(Json.toJson(response)) - } - } - - def getCytoband(id: Int): Action[AnyContent] = secureApi.async { _ => - managementService.getCytoband(id).map { - case Some(cytoband) => Ok(Json.toJson(cytoband)) - case None => NotFound(Json.obj("error" -> "Cytoband not found")) - } - } - - def createCytoband(): Action[CreateCytobandRequest] = - secureApi.jsonAction[CreateCytobandRequest].async { request => - logger.info(s"API: Creating cytoband") - managementService.createCytoband(request.body, None).map { - case Right(cytoband) => Created(Json.toJson(cytoband)) - case Left(error) => BadRequest(Json.obj("error" -> error)) - } - } - - def updateCytoband(id: Int): Action[UpdateCytobandRequest] = - secureApi.jsonAction[UpdateCytobandRequest].async { request => - logger.info(s"API: Updating cytoband $id") - managementService.updateCytoband(id, request.body, None).map { - case Right(cytoband) => Ok(Json.toJson(cytoband)) - case Left(error) => BadRequest(Json.obj("error" -> error)) - } - } - - def deleteCytoband(id: Int): Action[AnyContent] = secureApi.async { _ => - logger.info(s"API: Deleting cytoband $id") - managementService.deleteCytoband(id, None).map { - case Right(_) => NoContent - case Left(error) => BadRequest(Json.obj("error" -> error)) - } - } - - def bulkCreateCytobands(): Action[BulkCreateCytobandsRequest] = - secureApi.jsonAction[BulkCreateCytobandsRequest].async { request => - logger.info(s"API: Bulk creating ${request.body.cytobands.size} cytobands") - managementService.bulkCreateCytobands(request.body, None).map { response => - Ok(Json.toJson(response)) - } - } - - // ============================================================================ - // STR Marker Endpoints - // ============================================================================ - - def listStrMarkers(build: Option[String], page: Int = 1, pageSize: Int = 25): Action[AnyContent] = secureApi.async { _ => - managementService.listStrMarkers(build, page, pageSize).map { response => - Ok(Json.toJson(response)) - } - } - - def getStrMarker(id: Int): Action[AnyContent] = secureApi.async { _ => - managementService.getStrMarker(id).map { - case Some(marker) => Ok(Json.toJson(marker)) - case None => NotFound(Json.obj("error" -> "STR marker not found")) - } - } - - def createStrMarker(): Action[CreateStrMarkerRequest] = - secureApi.jsonAction[CreateStrMarkerRequest].async { request => - logger.info(s"API: Creating STR marker") - managementService.createStrMarker(request.body, None).map { - case Right(marker) => Created(Json.toJson(marker)) - case Left(error) => BadRequest(Json.obj("error" -> error)) - } - } - - def updateStrMarker(id: Int): Action[UpdateStrMarkerRequest] = - secureApi.jsonAction[UpdateStrMarkerRequest].async { request => - logger.info(s"API: Updating STR marker $id") - managementService.updateStrMarker(id, request.body, None).map { - case Right(marker) => Ok(Json.toJson(marker)) - case Left(error) => BadRequest(Json.obj("error" -> error)) - } - } - - def deleteStrMarker(id: Int): Action[AnyContent] = secureApi.async { _ => - logger.info(s"API: Deleting STR marker $id") - managementService.deleteStrMarker(id, None).map { - case Right(_) => NoContent - case Left(error) => BadRequest(Json.obj("error" -> error)) - } - } - - def bulkCreateStrMarkers(): Action[BulkCreateStrMarkersRequest] = - secureApi.jsonAction[BulkCreateStrMarkersRequest].async { request => - logger.info(s"API: Bulk creating ${request.body.markers.size} STR markers") - managementService.bulkCreateStrMarkers(request.body, None).map { response => - Ok(Json.toJson(response)) - } - } -} +} \ No newline at end of file diff --git a/app/controllers/GenomeRegionsCuratorController.scala b/app/controllers/GenomeRegionsCuratorController.scala index d4ce447..2cddb58 100644 --- a/app/controllers/GenomeRegionsCuratorController.scala +++ b/app/controllers/GenomeRegionsCuratorController.scala @@ -10,6 +10,7 @@ import play.api.Logging import play.api.data.Form import play.api.data.Forms.* import play.api.i18n.I18nSupport +import play.api.libs.json.Json import play.api.mvc.* import repositories.GenbankContigRepository import services.GenomeRegionsManagementService @@ -26,26 +27,8 @@ case class GenomeRegionFormData( modifier: Option[BigDecimal] ) -case class CytobandFormData( - genbankContigId: Int, - name: String, - startPos: Long, - endPos: Long, - stain: String -) - -case class StrMarkerFormData( - genbankContigId: Int, - name: String, - startPos: Long, - endPos: Long, - period: Int, - verified: Boolean, - note: Option[String] -) - /** - * UI Controller for managing genome regions, cytobands, and STR markers. + * UI Controller for managing genome regions. * Uses session-based authentication with permission checks. */ @Singleton @@ -75,46 +58,24 @@ class GenomeRegionsCuratorController @Inject()( )(GenomeRegionFormData.apply)(g => Some((g.genbankContigId, g.regionType, g.name, g.startPos, g.endPos, g.modifier))) ) - private val cytobandForm: Form[CytobandFormData] = Form( - mapping( - "genbankContigId" -> number, - "name" -> nonEmptyText(1, 20), - "startPos" -> longNumber(min = 0), - "endPos" -> longNumber(min = 0), - "stain" -> nonEmptyText(1, 10) - )(CytobandFormData.apply)(c => Some((c.genbankContigId, c.name, c.startPos, c.endPos, c.stain))) - ) - - private val strMarkerForm: Form[StrMarkerFormData] = Form( - mapping( - "genbankContigId" -> number, - "name" -> nonEmptyText(1, 30), - "startPos" -> longNumber(min = 0), - "endPos" -> longNumber(min = 0), - "period" -> number(min = 1), - "verified" -> boolean, - "note" -> optional(text) - )(StrMarkerFormData.apply)(s => Some((s.genbankContigId, s.name, s.startPos, s.endPos, s.period, s.verified, s.note))) - ) - // ============================================================================ // GenomeRegion UI Endpoints // ============================================================================ - def listRegions(build: Option[String], page: Int = 1, pageSize: Int = 25): Action[AnyContent] = + def listRegions(regionType: Option[String], build: Option[String], page: Int = 1, pageSize: Int = 25): Action[AnyContent] = withPermission("genome_region.view").async { implicit request => for { - response <- managementService.listRegions(build, page, pageSize) + response <- managementService.listRegions(regionType, build, page, pageSize) } yield { val totalPages = Math.max(1, (response.total + pageSize - 1) / pageSize) Ok(views.html.curator.genomeregions.list(response.regions, build, page, totalPages, pageSize, response.total, genomicsConfig.supportedReferences)) } } - def regionsFragment(build: Option[String], page: Int = 1, pageSize: Int = 25): Action[AnyContent] = + def regionsFragment(regionType: Option[String], build: Option[String], page: Int = 1, pageSize: Int = 25): Action[AnyContent] = withPermission("genome_region.view").async { implicit request => for { - response <- managementService.listRegions(build, page, pageSize) + response <- managementService.listRegions(regionType, build, page, pageSize) } yield { val totalPages = Math.max(1, (response.total + pageSize - 1) / pageSize) Ok(views.html.curator.genomeregions.listFragment(response.regions, build, page, totalPages, pageSize, response.total)) @@ -145,26 +106,34 @@ class GenomeRegionsCuratorController @Inject()( } }, formData => { - val createRequest = CreateGenomeRegionRequest( - genbankContigId = formData.genbankContigId, - regionType = formData.regionType, - name = formData.name, - startPos = formData.startPos, - endPos = formData.endPos, - modifier = formData.modifier - ) - managementService.createRegion(createRequest, request.user.id).map { - case Right(_) => - Redirect(routes.GenomeRegionsCuratorController.listRegions(None, 1, 25)) - .flashing("success" -> "Genome region created successfully") - case Left(error) => - getContigsForFormSync.map { contigs => - BadRequest(views.html.curator.genomeregions.createForm( - genomeRegionForm.fill(formData).withGlobalError(error), - contigs, - genomicsConfig.supportedReferences - )) - }.getOrElse(BadRequest(error)) + // Resolve contig to get build name and common name + genbankContigRepository.getById(formData.genbankContigId).flatMap { + case Some(contig) => + val build = contig.referenceGenome.getOrElse("unknown") + val contigName = contig.commonName.getOrElse("unknown") + + val createRequest = CreateGenomeRegionRequest( + regionType = formData.regionType, + name = formData.name, + coordinates = Map(build -> RegionCoordinateDto(contigName, formData.startPos, formData.endPos)), + properties = formData.modifier.map(m => Json.obj("modifier" -> m)) + ) + + managementService.createRegion(createRequest, request.user.id).map { + case Right(_) => + Redirect(routes.GenomeRegionsCuratorController.listRegions(None, None, 1, 25)) + .flashing("success" -> "Genome region created successfully") + case Left(error) => + getContigsForFormSync.map { contigs => + BadRequest(views.html.curator.genomeregions.createForm( + genomeRegionForm.fill(formData).withGlobalError(error), + contigs, + genomicsConfig.supportedReferences + )) + }.getOrElse(BadRequest(error)) + } + case None => + Future.successful(BadRequest("Invalid contig ID")) } } ) @@ -177,13 +146,24 @@ class GenomeRegionsCuratorController @Inject()( contigs <- getContigsForForm } yield regionOpt match { case Some(region) => + // Try to map back to form data using the first coordinate found (limitation of this UI) + val (build, coord) = region.coordinates.headOption.getOrElse("unknown" -> RegionCoordinateDto("", 0, 0)) + // We need a genbankContigId for the form dropdown. + // This is tricky without a reverse lookup or storing it. + // For now, we might leave it 0 or try to find it in the list of contigs if possible. + // Or just pick the first contig that matches name and build. + val contigId = contigs.find(c => c.commonName.contains(coord.contig) && c.referenceGenome.contains(build)) + .flatMap(_.id).getOrElse(0) + + val modifier = (region.properties \ "modifier").asOpt[BigDecimal] + val formData = GenomeRegionFormData( - region.genbankContigId, + contigId, region.regionType, region.name, - region.startPos, - region.endPos, - region.modifier + coord.start, + coord.end, + modifier ) Ok(views.html.curator.genomeregions.editForm(id, genomeRegionForm.fill(formData), contigs, genomicsConfig.supportedReferences)) case None => @@ -200,27 +180,38 @@ class GenomeRegionsCuratorController @Inject()( } }, formData => { - val updateRequest = UpdateGenomeRegionRequest( - regionType = Some(formData.regionType), - name = formData.name, - startPos = Some(formData.startPos), - endPos = Some(formData.endPos), - modifier = formData.modifier - ) - managementService.updateRegion(id, updateRequest, request.user.id).map { - case Right(_) => - Redirect(routes.GenomeRegionsCuratorController.listRegions(None, 1, 25)) - .flashing("success" -> "Genome region updated successfully") - case Left(error) => - getContigsForFormSync.map { contigs => - BadRequest(views.html.curator.genomeregions.editForm( - id, - genomeRegionForm.fill(formData).withGlobalError(error), - contigs, - genomicsConfig.supportedReferences - )) - }.getOrElse(BadRequest(error)) - } + genbankContigRepository.getById(formData.genbankContigId).flatMap { + case Some(contig) => + val build = contig.referenceGenome.getOrElse("unknown") + val contigName = contig.commonName.getOrElse("unknown") + + val updateRequest = UpdateGenomeRegionRequest( + regionType = Some(formData.regionType), + name = formData.name, + // Merging coordinates is complex. This simplistic update might overwrite other builds' coordinates + // if the service replaces the map. The Service logic currently REPLACES if provided. + // To support multi-build editing, the UI needs to change. + // For now, we assume single-build editing flow. + coordinates = Some(Map(build -> RegionCoordinateDto(contigName, formData.startPos, formData.endPos))), + properties = formData.modifier.map(m => Json.obj("modifier" -> m)) + ) + + managementService.updateRegion(id, updateRequest, request.user.id).map { + case Right(_) => + Redirect(routes.GenomeRegionsCuratorController.listRegions(None, None, 1, 25)) + .flashing("success" -> "Genome region updated successfully") + case Left(error) => + getContigsForFormSync.map { contigs => + BadRequest(views.html.curator.genomeregions.editForm( + id, + genomeRegionForm.fill(formData).withGlobalError(error), + contigs, + genomicsConfig.supportedReferences + )) + }.getOrElse(BadRequest(error)) + } + case None => Future.successful(BadRequest("Invalid Contig")) + } } ) } @@ -235,260 +226,6 @@ class GenomeRegionsCuratorController @Inject()( } } - // ============================================================================ - // Cytoband UI Endpoints - // ============================================================================ - - def listCytobands(build: Option[String], page: Int = 1, pageSize: Int = 25): Action[AnyContent] = - withPermission("cytoband.view").async { implicit request => - for { - response <- managementService.listCytobands(build, page, pageSize) - } yield { - val totalPages = Math.max(1, (response.total + pageSize - 1) / pageSize) - Ok(views.html.curator.cytobands.list(response.cytobands, build, page, totalPages, pageSize, response.total, genomicsConfig.supportedReferences)) - } - } - - def cytobandsFragment(build: Option[String], page: Int = 1, pageSize: Int = 25): Action[AnyContent] = - withPermission("cytoband.view").async { implicit request => - for { - response <- managementService.listCytobands(build, page, pageSize) - } yield { - val totalPages = Math.max(1, (response.total + pageSize - 1) / pageSize) - Ok(views.html.curator.cytobands.listFragment(response.cytobands, build, page, totalPages, pageSize, response.total)) - } - } - - def cytobandDetailPanel(id: Int): Action[AnyContent] = - withPermission("cytoband.view").async { implicit request => - managementService.getCytoband(id).map { - case Some(cytoband) => Ok(views.html.curator.cytobands.detailPanel(cytoband)) - case None => NotFound("Cytoband not found") - } - } - - def createCytobandForm: Action[AnyContent] = - withPermission("cytoband.create").async { implicit request => - getContigsForForm.map { contigs => - Ok(views.html.curator.cytobands.createForm(cytobandForm, contigs, genomicsConfig.supportedReferences)) - } - } - - def createCytoband: Action[AnyContent] = - withPermission("cytoband.create").async { implicit request => - cytobandForm.bindFromRequest().fold( - formWithErrors => { - getContigsForForm.map { contigs => - BadRequest(views.html.curator.cytobands.createForm(formWithErrors, contigs, genomicsConfig.supportedReferences)) - } - }, - formData => { - val createRequest = CreateCytobandRequest( - genbankContigId = formData.genbankContigId, - name = formData.name, - startPos = formData.startPos, - endPos = formData.endPos, - stain = formData.stain - ) - managementService.createCytoband(createRequest, request.user.id).map { - case Right(_) => - Redirect(routes.GenomeRegionsCuratorController.listCytobands(None, 1, 25)) - .flashing("success" -> "Cytoband created successfully") - case Left(error) => - Redirect(routes.GenomeRegionsCuratorController.createCytobandForm) - .flashing("error" -> error) - } - } - ) - } - - def editCytobandForm(id: Int): Action[AnyContent] = - withPermission("cytoband.update").async { implicit request => - for { - cytobandOpt <- managementService.getCytoband(id) - contigs <- getContigsForForm - } yield cytobandOpt match { - case Some(cytoband) => - val formData = CytobandFormData( - cytoband.genbankContigId, - cytoband.name, - cytoband.startPos, - cytoband.endPos, - cytoband.stain - ) - Ok(views.html.curator.cytobands.editForm(id, cytobandForm.fill(formData), contigs, genomicsConfig.supportedReferences)) - case None => - NotFound("Cytoband not found") - } - } - - def updateCytoband(id: Int): Action[AnyContent] = - withPermission("cytoband.update").async { implicit request => - cytobandForm.bindFromRequest().fold( - formWithErrors => { - getContigsForForm.map { contigs => - BadRequest(views.html.curator.cytobands.editForm(id, formWithErrors, contigs, genomicsConfig.supportedReferences)) - } - }, - formData => { - val updateRequest = UpdateCytobandRequest( - name = Some(formData.name), - startPos = Some(formData.startPos), - endPos = Some(formData.endPos), - stain = Some(formData.stain) - ) - managementService.updateCytoband(id, updateRequest, request.user.id).map { - case Right(_) => - Redirect(routes.GenomeRegionsCuratorController.listCytobands(None, 1, 25)) - .flashing("success" -> "Cytoband updated successfully") - case Left(error) => - Redirect(routes.GenomeRegionsCuratorController.editCytobandForm(id)) - .flashing("error" -> error) - } - } - ) - } - - def deleteCytoband(id: Int): Action[AnyContent] = - withPermission("cytoband.delete").async { implicit request => - managementService.deleteCytoband(id, request.user.id).map { - case Right(_) => - Ok("").withHeaders("HX-Trigger" -> "cytobandDeleted") - case Left(error) => - BadRequest(error) - } - } - - // ============================================================================ - // STR Marker UI Endpoints - // ============================================================================ - - def listStrMarkers(build: Option[String], page: Int = 1, pageSize: Int = 25): Action[AnyContent] = - withPermission("str_marker.view").async { implicit request => - for { - response <- managementService.listStrMarkers(build, page, pageSize) - } yield { - val totalPages = Math.max(1, (response.total + pageSize - 1) / pageSize) - Ok(views.html.curator.strmarkers.list(response.markers, build, page, totalPages, pageSize, response.total, genomicsConfig.supportedReferences)) - } - } - - def strMarkersFragment(build: Option[String], page: Int = 1, pageSize: Int = 25): Action[AnyContent] = - withPermission("str_marker.view").async { implicit request => - for { - response <- managementService.listStrMarkers(build, page, pageSize) - } yield { - val totalPages = Math.max(1, (response.total + pageSize - 1) / pageSize) - Ok(views.html.curator.strmarkers.listFragment(response.markers, build, page, totalPages, pageSize, response.total)) - } - } - - def strMarkerDetailPanel(id: Int): Action[AnyContent] = - withPermission("str_marker.view").async { implicit request => - managementService.getStrMarker(id).map { - case Some(marker) => Ok(views.html.curator.strmarkers.detailPanel(marker)) - case None => NotFound("STR marker not found") - } - } - - def createStrMarkerForm: Action[AnyContent] = - withPermission("str_marker.create").async { implicit request => - getContigsForForm.map { contigs => - Ok(views.html.curator.strmarkers.createForm(strMarkerForm, contigs, genomicsConfig.supportedReferences)) - } - } - - def createStrMarker: Action[AnyContent] = - withPermission("str_marker.create").async { implicit request => - strMarkerForm.bindFromRequest().fold( - formWithErrors => { - getContigsForForm.map { contigs => - BadRequest(views.html.curator.strmarkers.createForm(formWithErrors, contigs, genomicsConfig.supportedReferences)) - } - }, - formData => { - val createRequest = CreateStrMarkerRequest( - genbankContigId = formData.genbankContigId, - name = formData.name, - startPos = formData.startPos, - endPos = formData.endPos, - period = formData.period, - verified = formData.verified, - note = formData.note - ) - managementService.createStrMarker(createRequest, request.user.id).map { - case Right(_) => - Redirect(routes.GenomeRegionsCuratorController.listStrMarkers(None, 1, 25)) - .flashing("success" -> "STR marker created successfully") - case Left(error) => - Redirect(routes.GenomeRegionsCuratorController.createStrMarkerForm) - .flashing("error" -> error) - } - } - ) - } - - def editStrMarkerForm(id: Int): Action[AnyContent] = - withPermission("str_marker.update").async { implicit request => - for { - markerOpt <- managementService.getStrMarker(id) - contigs <- getContigsForForm - } yield markerOpt match { - case Some(marker) => - val formData = StrMarkerFormData( - marker.genbankContigId, - marker.name, - marker.startPos, - marker.endPos, - marker.period, - marker.verified, - marker.note - ) - Ok(views.html.curator.strmarkers.editForm(id, strMarkerForm.fill(formData), contigs, genomicsConfig.supportedReferences)) - case None => - NotFound("STR marker not found") - } - } - - def updateStrMarker(id: Int): Action[AnyContent] = - withPermission("str_marker.update").async { implicit request => - strMarkerForm.bindFromRequest().fold( - formWithErrors => { - getContigsForForm.map { contigs => - BadRequest(views.html.curator.strmarkers.editForm(id, formWithErrors, contigs, genomicsConfig.supportedReferences)) - } - }, - formData => { - val updateRequest = UpdateStrMarkerRequest( - name = Some(formData.name), - startPos = Some(formData.startPos), - endPos = Some(formData.endPos), - period = Some(formData.period), - verified = Some(formData.verified), - note = formData.note - ) - managementService.updateStrMarker(id, updateRequest, request.user.id).map { - case Right(_) => - Redirect(routes.GenomeRegionsCuratorController.listStrMarkers(None, 1, 25)) - .flashing("success" -> "STR marker updated successfully") - case Left(error) => - Redirect(routes.GenomeRegionsCuratorController.editStrMarkerForm(id)) - .flashing("error" -> error) - } - } - ) - } - - def deleteStrMarker(id: Int): Action[AnyContent] = - withPermission("str_marker.delete").async { implicit request => - managementService.deleteStrMarker(id, request.user.id).map { - case Right(_) => - Ok("").withHeaders("HX-Trigger" -> "strMarkerDeleted") - case Left(error) => - BadRequest(error) - } - } - // ============================================================================ // Helper Methods // ============================================================================ @@ -504,4 +241,4 @@ class GenomeRegionsCuratorController @Inject()( // This is a fallback for sync error handling - not ideal but simple None } -} +} \ No newline at end of file diff --git a/app/models/api/genomics/GenomeRegionsManagementModels.scala b/app/models/api/genomics/GenomeRegionsManagementModels.scala index 6b0c228..0fb5d76 100644 --- a/app/models/api/genomics/GenomeRegionsManagementModels.scala +++ b/app/models/api/genomics/GenomeRegionsManagementModels.scala @@ -1,22 +1,30 @@ package models.api.genomics -import play.api.libs.json.{Json, OFormat, Reads} +import play.api.libs.json.{JsValue, Json, OFormat} /** * API DTOs for Genome Regions Management (CRUD operations). */ +case class RegionCoordinateDto( + contig: String, + start: Long, + end: Long +) + +object RegionCoordinateDto { + implicit val format: OFormat[RegionCoordinateDto] = Json.format[RegionCoordinateDto] +} + // ============================================================================ // Request DTOs // ============================================================================ case class CreateGenomeRegionRequest( - genbankContigId: Int, regionType: String, name: Option[String] = None, - startPos: Long, - endPos: Long, - modifier: Option[BigDecimal] = None + coordinates: Map[String, RegionCoordinateDto], + properties: Option[JsValue] = None ) object CreateGenomeRegionRequest { @@ -26,65 +34,14 @@ object CreateGenomeRegionRequest { case class UpdateGenomeRegionRequest( regionType: Option[String] = None, name: Option[String] = None, - startPos: Option[Long] = None, - endPos: Option[Long] = None, - modifier: Option[BigDecimal] = None + coordinates: Option[Map[String, RegionCoordinateDto]] = None, + properties: Option[JsValue] = None ) object UpdateGenomeRegionRequest { implicit val format: OFormat[UpdateGenomeRegionRequest] = Json.format[UpdateGenomeRegionRequest] } -case class CreateCytobandRequest( - genbankContigId: Int, - name: String, - startPos: Long, - endPos: Long, - stain: String -) - -object CreateCytobandRequest { - implicit val format: OFormat[CreateCytobandRequest] = Json.format[CreateCytobandRequest] -} - -case class UpdateCytobandRequest( - name: Option[String] = None, - startPos: Option[Long] = None, - endPos: Option[Long] = None, - stain: Option[String] = None -) - -object UpdateCytobandRequest { - implicit val format: OFormat[UpdateCytobandRequest] = Json.format[UpdateCytobandRequest] -} - -case class CreateStrMarkerRequest( - genbankContigId: Int, - name: String, - startPos: Long, - endPos: Long, - period: Int, - verified: Boolean = false, - note: Option[String] = None -) - -object CreateStrMarkerRequest { - implicit val format: OFormat[CreateStrMarkerRequest] = Json.format[CreateStrMarkerRequest] -} - -case class UpdateStrMarkerRequest( - name: Option[String] = None, - startPos: Option[Long] = None, - endPos: Option[Long] = None, - period: Option[Int] = None, - verified: Option[Boolean] = None, - note: Option[String] = None -) - -object UpdateStrMarkerRequest { - implicit val format: OFormat[UpdateStrMarkerRequest] = Json.format[UpdateStrMarkerRequest] -} - // ============================================================================ // Bulk Request DTOs // ============================================================================ @@ -95,70 +52,22 @@ object BulkCreateGenomeRegionsRequest { implicit val format: OFormat[BulkCreateGenomeRegionsRequest] = Json.format[BulkCreateGenomeRegionsRequest] } -case class BulkCreateCytobandsRequest(cytobands: Seq[CreateCytobandRequest]) - -object BulkCreateCytobandsRequest { - implicit val format: OFormat[BulkCreateCytobandsRequest] = Json.format[BulkCreateCytobandsRequest] -} - -case class BulkCreateStrMarkersRequest(markers: Seq[CreateStrMarkerRequest]) - -object BulkCreateStrMarkersRequest { - implicit val format: OFormat[BulkCreateStrMarkersRequest] = Json.format[BulkCreateStrMarkersRequest] -} - // ============================================================================ -// Response DTOs (with additional contig info) +// Response DTOs // ============================================================================ case class GenomeRegionDetailDto( id: Int, - genbankContigId: Int, - contigName: Option[String], - referenceGenome: Option[String], regionType: String, name: Option[String], - startPos: Long, - endPos: Long, - modifier: Option[BigDecimal] + coordinates: Map[String, RegionCoordinateDto], + properties: JsValue ) object GenomeRegionDetailDto { implicit val format: OFormat[GenomeRegionDetailDto] = Json.format[GenomeRegionDetailDto] } -case class CytobandDetailDto( - id: Int, - genbankContigId: Int, - contigName: Option[String], - referenceGenome: Option[String], - name: String, - startPos: Long, - endPos: Long, - stain: String -) - -object CytobandDetailDto { - implicit val format: OFormat[CytobandDetailDto] = Json.format[CytobandDetailDto] -} - -case class StrMarkerDetailDto( - id: Int, - genbankContigId: Int, - contigName: Option[String], - referenceGenome: Option[String], - name: String, - startPos: Long, - endPos: Long, - period: Int, - verified: Boolean, - note: Option[String] -) - -object StrMarkerDetailDto { - implicit val format: OFormat[StrMarkerDetailDto] = Json.format[StrMarkerDetailDto] -} - // ============================================================================ // List Response DTOs // ============================================================================ @@ -174,28 +83,6 @@ object GenomeRegionListResponse { implicit val format: OFormat[GenomeRegionListResponse] = Json.format[GenomeRegionListResponse] } -case class CytobandListResponse( - cytobands: Seq[CytobandDetailDto], - total: Int, - page: Int, - pageSize: Int -) - -object CytobandListResponse { - implicit val format: OFormat[CytobandListResponse] = Json.format[CytobandListResponse] -} - -case class StrMarkerListResponse( - markers: Seq[StrMarkerDetailDto], - total: Int, - page: Int, - pageSize: Int -) - -object StrMarkerListResponse { - implicit val format: OFormat[StrMarkerListResponse] = Json.format[StrMarkerListResponse] -} - // ============================================================================ // Bulk Operation Response // ============================================================================ @@ -220,4 +107,4 @@ case class BulkOperationResponse( object BulkOperationResponse { implicit val format: OFormat[BulkOperationResponse] = Json.format[BulkOperationResponse] -} +} \ No newline at end of file diff --git a/app/models/dal/DatabaseSchema.scala b/app/models/dal/DatabaseSchema.scala index 0a9d06e..bfd88d5 100644 --- a/app/models/dal/DatabaseSchema.scala +++ b/app/models/dal/DatabaseSchema.scala @@ -96,7 +96,6 @@ object DatabaseSchema { // Genome regions API tables val genomeRegions = TableQuery[GenomeRegionTable] val genomeRegionVersions = TableQuery[GenomeRegionVersionTable] - val cytobands = TableQuery[CytobandTable] } object haplogroups { diff --git a/app/models/dal/MyPostgresProfile.scala b/app/models/dal/MyPostgresProfile.scala index 36b675c..a9f3389 100644 --- a/app/models/dal/MyPostgresProfile.scala +++ b/app/models/dal/MyPostgresProfile.scala @@ -321,6 +321,12 @@ trait MyPostgresProfile extends ExPostgresProfile implicit val haplogroupProvenanceJsonbTypeMapper: JdbcType[HaplogroupProvenance] with BaseTypedType[HaplogroupProvenance] = MappedJdbcType.base[HaplogroupProvenance, JsValue](Json.toJson(_), _.as[HaplogroupProvenance]) + // --- Genome Region JSONB Type Mappers --- + import models.domain.genomics.RegionCoordinate + + implicit val regionCoordinatesJsonbTypeMapper: JdbcType[Map[String, RegionCoordinate]] with BaseTypedType[Map[String, RegionCoordinate]] = + MappedJdbcType.base[Map[String, RegionCoordinate], JsValue](Json.toJson(_), _.as[Map[String, RegionCoordinate]]) + // Declare the name of an aggregate function: val ArrayAgg = new SqlAggregateFunction("array_agg") diff --git a/app/models/dal/domain/genomics/GenomeRegionTables.scala b/app/models/dal/domain/genomics/GenomeRegionTables.scala index 0156dcb..ba41e19 100644 --- a/app/models/dal/domain/genomics/GenomeRegionTables.scala +++ b/app/models/dal/domain/genomics/GenomeRegionTables.scala @@ -1,8 +1,8 @@ package models.dal.domain.genomics import models.dal.MyPostgresProfile.api.* -import models.domain.genomics.{Cytoband, GenomeRegion, GenomeRegionVersion, StrMarker} - +import models.domain.genomics.{GenomeRegion, GenomeRegionVersion, RegionCoordinate, StrMarker} +import play.api.libs.json.JsValue import java.time.Instant /** @@ -19,44 +19,20 @@ class GenomeRegionVersionTable(tag: Tag) extends Table[GenomeRegionVersion](tag, } /** - * Slick table definition for genome_region table. - * Stores structural regions (centromere, telomere, PAR, XTR, etc.). + * Slick table definition for genome_region_v2 table. + * Stores structural regions (centromere, telomere, PAR, XTR, etc.) and Cytobands. + * Supports multi-reference coordinates via JSONB. */ -class GenomeRegionTable(tag: Tag) extends Table[GenomeRegion](tag, "genome_region") { - def id = column[Int]("id", O.PrimaryKey, O.AutoInc) - def genbankContigId = column[Int]("genbank_contig_id") +class GenomeRegionTable(tag: Tag) extends Table[GenomeRegion](tag, "genome_region_v2") { + def id = column[Int]("region_id", O.PrimaryKey, O.AutoInc) // Column name changed to region_id def regionType = column[String]("region_type") def name = column[Option[String]]("name") - def startPos = column[Long]("start_pos") - def endPos = column[Long]("end_pos") - def modifier = column[Option[BigDecimal]]("modifier") - - def * = (id.?, genbankContigId, regionType, name, startPos, endPos, modifier).mapTo[GenomeRegion] - - def genbankContigFk = foreignKey("genome_region_genbank_contig_fk", genbankContigId, - TableQuery[GenbankContigsTable])(_.genbankContigId, onDelete = ForeignKeyAction.Cascade) - - def idxContig = index("idx_genome_region_contig", genbankContigId) -} - -/** - * Slick table definition for cytoband table. - * Stores cytoband annotations for chromosome ideogram display. - */ -class CytobandTable(tag: Tag) extends Table[Cytoband](tag, "cytoband") { - def id = column[Int]("id", O.PrimaryKey, O.AutoInc) - def genbankContigId = column[Int]("genbank_contig_id") - def name = column[String]("name") - def startPos = column[Long]("start_pos") - def endPos = column[Long]("end_pos") - def stain = column[String]("stain") - - def * = (id.?, genbankContigId, name, startPos, endPos, stain).mapTo[Cytoband] + def coordinates = column[Map[String, RegionCoordinate]]("coordinates") + def properties = column[JsValue]("properties") - def genbankContigFk = foreignKey("cytoband_genbank_contig_fk", genbankContigId, - TableQuery[GenbankContigsTable])(_.genbankContigId, onDelete = ForeignKeyAction.Cascade) - - def idxContig = index("idx_cytoband_contig", genbankContigId) + def * = (id.?, regionType, name, coordinates, properties).mapTo[GenomeRegion] + + // No Foreign Key to Contig anymore, as coordinates are embedded } /** @@ -79,4 +55,4 @@ class StrMarkerTable(tag: Tag) extends Table[StrMarker](tag, "str_marker") { TableQuery[GenbankContigsTable])(_.genbankContigId, onDelete = ForeignKeyAction.Cascade) def idxContig = index("idx_str_marker_contig", genbankContigId) -} +} \ No newline at end of file diff --git a/app/models/domain/genomics/Cytoband.scala b/app/models/domain/genomics/Cytoband.scala deleted file mode 100644 index db4bee7..0000000 --- a/app/models/domain/genomics/Cytoband.scala +++ /dev/null @@ -1,21 +0,0 @@ -package models.domain.genomics - -/** - * Represents a cytoband annotation for chromosome ideogram display. - * Cytobands are banding patterns visible under microscopy after Giemsa staining. - * - * @param id Optional unique identifier for the cytoband. - * @param genbankContigId The ID of the associated GenBank contig (chromosome). - * @param name Band name (e.g., "p11.32", "q11.21"). - * @param startPos Start position (1-based, inclusive). - * @param endPos End position (1-based, inclusive). - * @param stain Giemsa stain pattern: gneg, gpos25, gpos50, gpos75, gpos100, acen, gvar, stalk. - */ -case class Cytoband( - id: Option[Int] = None, - genbankContigId: Int, - name: String, - startPos: Long, - endPos: Long, - stain: String -) diff --git a/app/models/domain/genomics/GenomeRegion.scala b/app/models/domain/genomics/GenomeRegion.scala index 1b48f8c..d086f4d 100644 --- a/app/models/domain/genomics/GenomeRegion.scala +++ b/app/models/domain/genomics/GenomeRegion.scala @@ -1,23 +1,38 @@ package models.domain.genomics +import play.api.libs.json.{Format, JsValue, Json} + /** - * Represents a structural region within a chromosome, such as centromeres, telomeres, - * pseudoautosomal regions (PAR), X-transposed regions (XTR), ampliconic regions, etc. + * Coordinate information for a specific reference genome build. + */ +case class RegionCoordinate( + contig: String, + start: Long, + end: Long +) + +object RegionCoordinate { + implicit val format: Format[RegionCoordinate] = Json.format[RegionCoordinate] +} + +/** + * Represents a structural region within a chromosome (or a cytoband). + * Supports multi-reference coordinates. * - * @param id Optional unique identifier for the genome region. - * @param genbankContigId The ID of the associated GenBank contig (chromosome). - * @param regionType The type of region (e.g., "Centromere", "Telomere_P", "PAR1", "XTR"). - * @param name Optional name for named regions (e.g., "P1" for palindrome 1). - * @param startPos Start position (1-based, inclusive). - * @param endPos End position (1-based, inclusive). - * @param modifier Optional quality modifier (0.1-1.0) indicating confidence in variant calls within this region. + * @param id Optional unique identifier (region_id). + * @param regionType The type of region (e.g., "Centromere", "Cytoband", "PAR1"). + * @param name Optional name (e.g., "p11.32" for cytobands, "P1" for palindromes). + * @param coordinates Map of BuildName -> Coordinate (e.g., "GRCh38" -> {contig: "chrY", start: ...}). + * @param properties Additional properties as JSON (e.g., {"stain": "gpos75", "modifier": 0.5}). */ case class GenomeRegion( id: Option[Int] = None, - genbankContigId: Int, regionType: String, name: Option[String], - startPos: Long, - endPos: Long, - modifier: Option[BigDecimal] + coordinates: Map[String, RegionCoordinate], + properties: JsValue ) + +object GenomeRegion { + implicit val format: Format[GenomeRegion] = Json.format[GenomeRegion] +} \ No newline at end of file diff --git a/app/repositories/GenomeRegionsRepository.scala b/app/repositories/GenomeRegionsRepository.scala index d254ea7..bdc4293 100644 --- a/app/repositories/GenomeRegionsRepository.scala +++ b/app/repositories/GenomeRegionsRepository.scala @@ -3,14 +3,14 @@ package repositories import jakarta.inject.Inject import models.dal.MyPostgresProfile import models.dal.MyPostgresProfile.api.* -import models.domain.genomics.{Cytoband, GenbankContig, GenomeRegion, GenomeRegionVersion, StrMarker} +import models.domain.genomics.{GenbankContig, GenomeRegion, GenomeRegionVersion} import play.api.db.slick.{DatabaseConfigProvider, HasDatabaseConfigProvider} import scala.concurrent.{ExecutionContext, Future} /** * Repository interface for genome region data. - * Provides access to structural annotations, cytobands, and STR markers. + * Provides access to structural annotations and cytobands (now unified). */ trait GenomeRegionsRepository { @@ -25,23 +25,12 @@ trait GenomeRegionsRepository { def getContigsForBuild(referenceGenome: String): Future[Seq[GenbankContig]] /** - * Get all structural regions for a specific contig. + * Get all regions (including cytobands) that have coordinates for the specified build. */ - def getRegionsForContig(contigId: Int): Future[Seq[GenomeRegion]] - - /** - * Get all cytobands for a specific contig. - */ - def getCytobandsForContig(contigId: Int): Future[Seq[Cytoband]] - - /** - * Get all STR markers for a specific contig. - */ - def getStrMarkersForContig(contigId: Int): Future[Seq[StrMarker]] + def getRegionsForBuild(referenceGenome: String): Future[Seq[GenomeRegion]] /** * Get all data for a build in a single composed query. - * Returns contigs with their associated regions, cytobands, and STR markers. */ def getFullBuildData(referenceGenome: String): Future[FullBuildData] @@ -50,39 +39,17 @@ trait GenomeRegionsRepository { // ============================================================================ def findRegionById(id: Int): Future[Option[GenomeRegion]] - def findRegionByIdWithContig(id: Int): Future[Option[(GenomeRegion, GenbankContig)]] - def findRegionsByBuild(referenceGenome: String, offset: Int, limit: Int): Future[Seq[(GenomeRegion, GenbankContig)]] - def countRegionsByBuild(referenceGenome: Option[String]): Future[Int] + + // Note: Pagination with JSONB filtering can be slow without specific indices. + // For the management API, we might iterate all or allow filtering by type. + def findRegions(regionType: Option[String], build: Option[String], offset: Int, limit: Int): Future[Seq[GenomeRegion]] + + def countRegions(regionType: Option[String], build: Option[String]): Future[Int] + def createRegion(region: GenomeRegion): Future[Int] def updateRegion(id: Int, region: GenomeRegion): Future[Boolean] def deleteRegion(id: Int): Future[Boolean] def bulkCreateRegions(regions: Seq[GenomeRegion]): Future[Seq[Int]] - - // ============================================================================ - // Cytoband CRUD operations - // ============================================================================ - - def findCytobandById(id: Int): Future[Option[Cytoband]] - def findCytobandByIdWithContig(id: Int): Future[Option[(Cytoband, GenbankContig)]] - def findCytobandsByBuild(referenceGenome: String, offset: Int, limit: Int): Future[Seq[(Cytoband, GenbankContig)]] - def countCytobandsByBuild(referenceGenome: Option[String]): Future[Int] - def createCytoband(cytoband: Cytoband): Future[Int] - def updateCytoband(id: Int, cytoband: Cytoband): Future[Boolean] - def deleteCytoband(id: Int): Future[Boolean] - def bulkCreateCytobands(cytobands: Seq[Cytoband]): Future[Seq[Int]] - - // ============================================================================ - // StrMarker CRUD operations - // ============================================================================ - - def findStrMarkerById(id: Int): Future[Option[StrMarker]] - def findStrMarkerByIdWithContig(id: Int): Future[Option[(StrMarker, GenbankContig)]] - def findStrMarkersByBuild(referenceGenome: String, offset: Int, limit: Int): Future[Seq[(StrMarker, GenbankContig)]] - def countStrMarkersByBuild(referenceGenome: Option[String]): Future[Int] - def createStrMarker(marker: StrMarker): Future[Int] - def updateStrMarker(id: Int, marker: StrMarker): Future[Boolean] - def deleteStrMarker(id: Int): Future[Boolean] - def bulkCreateStrMarkers(markers: Seq[StrMarker]): Future[Seq[Int]] } /** @@ -91,9 +58,7 @@ trait GenomeRegionsRepository { case class FullBuildData( version: Option[GenomeRegionVersion], contigs: Seq[GenbankContig], - regions: Map[Int, Seq[GenomeRegion]], // contigId -> regions - cytobands: Map[Int, Seq[Cytoband]], // contigId -> cytobands - strMarkers: Map[Int, Seq[StrMarker]] // contigId -> markers + regions: Seq[GenomeRegion] ) class GenomeRegionsRepositoryImpl @Inject()( @@ -120,57 +85,23 @@ class GenomeRegionsRepositoryImpl @Inject()( db.run(query) } - override def getRegionsForContig(contigId: Int): Future[Seq[GenomeRegion]] = { + override def getRegionsForBuild(referenceGenome: String): Future[Seq[GenomeRegion]] = { + // Select regions where coordinates -> buildName exists val query = genomeRegions - .filter(_.genbankContigId === contigId) - .sortBy(_.startPos) + .filter(r => (r.coordinates +> referenceGenome).isDefined) .result db.run(query) } - override def getCytobandsForContig(contigId: Int): Future[Seq[Cytoband]] = { - val query = cytobands - .filter(_.genbankContigId === contigId) - .sortBy(_.startPos) - .result - db.run(query) - } - - // STR marker table was replaced in schema migration - stub for now - override def getStrMarkersForContig(contigId: Int): Future[Seq[StrMarker]] = { - Future.successful(Seq.empty) - } - override def getFullBuildData(referenceGenome: String): Future[FullBuildData] = { for { version <- getVersion(referenceGenome) contigs <- getContigsForBuild(referenceGenome) - contigIds = contigs.flatMap(_.id) - - // Fetch all regions for the build's contigs - allRegions <- if (contigIds.nonEmpty) { - val query = genomeRegions - .filter(_.genbankContigId.inSet(contigIds)) - .sortBy(r => (r.genbankContigId, r.startPos)) - .result - db.run(query) - } else Future.successful(Seq.empty) - - // Fetch all cytobands for the build's contigs - allCytobands <- if (contigIds.nonEmpty) { - val query = cytobands - .filter(_.genbankContigId.inSet(contigIds)) - .sortBy(c => (c.genbankContigId, c.startPos)) - .result - db.run(query) - } else Future.successful(Seq.empty) - + regions <- getRegionsForBuild(referenceGenome) } yield FullBuildData( version = version, contigs = contigs, - regions = allRegions.groupBy(_.genbankContigId), - cytobands = allCytobands.groupBy(_.genbankContigId), - strMarkers = Map.empty // STR marker table was replaced in schema migration + regions = regions ) } @@ -182,31 +113,31 @@ class GenomeRegionsRepositoryImpl @Inject()( db.run(genomeRegions.filter(_.id === id).result.headOption) } - override def findRegionByIdWithContig(id: Int): Future[Option[(GenomeRegion, GenbankContig)]] = { - val query = for { - region <- genomeRegions if region.id === id - contig <- genbankContigs if contig.genbankContigId === region.genbankContigId - } yield (region, contig) - db.run(query.result.headOption) - } + override def findRegions(regionType: Option[String], build: Option[String], offset: Int, limit: Int): Future[Seq[GenomeRegion]] = { + var query = genomeRegions.sortBy(_.id) + + if (regionType.isDefined) { + query = query.filter(_.regionType === regionType.get) + } + + if (build.isDefined) { + query = query.filter(r => (r.coordinates +> build.get).isDefined) + } - override def findRegionsByBuild(referenceGenome: String, offset: Int, limit: Int): Future[Seq[(GenomeRegion, GenbankContig)]] = { - val query = for { - region <- genomeRegions - contig <- genbankContigs if contig.genbankContigId === region.genbankContigId && contig.referenceGenome === referenceGenome - } yield (region, contig) - db.run(query.sortBy(_._1.startPos).drop(offset).take(limit).result) + db.run(query.drop(offset).take(limit).result) } - override def countRegionsByBuild(referenceGenome: Option[String]): Future[Int] = { - val query = referenceGenome match { - case Some(ref) => - for { - region <- genomeRegions - contig <- genbankContigs if contig.genbankContigId === region.genbankContigId && contig.referenceGenome === ref - } yield region - case None => genomeRegions + override def countRegions(regionType: Option[String], build: Option[String]): Future[Int] = { + var query = genomeRegions.sortBy(_.id) // Sort irrelevant for count but type checks + + if (regionType.isDefined) { + query = query.filter(_.regionType === regionType.get) + } + + if (build.isDefined) { + query = query.filter(r => (r.coordinates +> build.get).isDefined) } + db.run(query.length.result) } @@ -216,8 +147,8 @@ class GenomeRegionsRepositoryImpl @Inject()( override def updateRegion(id: Int, region: GenomeRegion): Future[Boolean] = { val query = genomeRegions.filter(_.id === id).map(r => - (r.genbankContigId, r.regionType, r.name, r.startPos, r.endPos, r.modifier) - ).update((region.genbankContigId, region.regionType, region.name, region.startPos, region.endPos, region.modifier)) + (r.regionType, r.name, r.coordinates, r.properties) + ).update((region.regionType, region.name, region.coordinates, region.properties)) db.run(query).map(_ > 0) } @@ -228,97 +159,4 @@ class GenomeRegionsRepositoryImpl @Inject()( override def bulkCreateRegions(regions: Seq[GenomeRegion]): Future[Seq[Int]] = { db.run((genomeRegions returning genomeRegions.map(_.id)) ++= regions) } - - // ============================================================================ - // Cytoband CRUD implementations - // ============================================================================ - - override def findCytobandById(id: Int): Future[Option[Cytoband]] = { - db.run(cytobands.filter(_.id === id).result.headOption) - } - - override def findCytobandByIdWithContig(id: Int): Future[Option[(Cytoband, GenbankContig)]] = { - val query = for { - cytoband <- cytobands if cytoband.id === id - contig <- genbankContigs if contig.genbankContigId === cytoband.genbankContigId - } yield (cytoband, contig) - db.run(query.result.headOption) - } - - override def findCytobandsByBuild(referenceGenome: String, offset: Int, limit: Int): Future[Seq[(Cytoband, GenbankContig)]] = { - val query = for { - cytoband <- cytobands - contig <- genbankContigs if contig.genbankContigId === cytoband.genbankContigId && contig.referenceGenome === referenceGenome - } yield (cytoband, contig) - db.run(query.sortBy(_._1.startPos).drop(offset).take(limit).result) - } - - override def countCytobandsByBuild(referenceGenome: Option[String]): Future[Int] = { - val query = referenceGenome match { - case Some(ref) => - for { - cytoband <- cytobands - contig <- genbankContigs if contig.genbankContigId === cytoband.genbankContigId && contig.referenceGenome === ref - } yield cytoband - case None => cytobands - } - db.run(query.length.result) - } - - override def createCytoband(cytoband: Cytoband): Future[Int] = { - db.run((cytobands returning cytobands.map(_.id)) += cytoband) - } - - override def updateCytoband(id: Int, cytoband: Cytoband): Future[Boolean] = { - val query = cytobands.filter(_.id === id).map(c => - (c.genbankContigId, c.name, c.startPos, c.endPos, c.stain) - ).update((cytoband.genbankContigId, cytoband.name, cytoband.startPos, cytoband.endPos, cytoband.stain)) - db.run(query).map(_ > 0) - } - - override def deleteCytoband(id: Int): Future[Boolean] = { - db.run(cytobands.filter(_.id === id).delete).map(_ > 0) - } - - override def bulkCreateCytobands(cytobandList: Seq[Cytoband]): Future[Seq[Int]] = { - db.run((cytobands returning cytobands.map(_.id)) ++= cytobandList) - } - - // ============================================================================ - // StrMarker CRUD implementations - // NOTE: STR marker table was replaced with str_mutation_rate in schema migration. - // These methods are stubbed to maintain API compatibility. - // ============================================================================ - - override def findStrMarkerById(id: Int): Future[Option[StrMarker]] = { - Future.successful(None) - } - - override def findStrMarkerByIdWithContig(id: Int): Future[Option[(StrMarker, GenbankContig)]] = { - Future.successful(None) - } - - override def findStrMarkersByBuild(referenceGenome: String, offset: Int, limit: Int): Future[Seq[(StrMarker, GenbankContig)]] = { - Future.successful(Seq.empty) - } - - override def countStrMarkersByBuild(referenceGenome: Option[String]): Future[Int] = { - Future.successful(0) - } - - override def createStrMarker(marker: StrMarker): Future[Int] = { - Future.failed(new UnsupportedOperationException("STR marker table has been replaced with str_mutation_rate")) - } - - override def updateStrMarker(id: Int, marker: StrMarker): Future[Boolean] = { - Future.successful(false) - } - - override def deleteStrMarker(id: Int): Future[Boolean] = { - Future.successful(false) - } - - override def bulkCreateStrMarkers(markers: Seq[StrMarker]): Future[Seq[Int]] = { - Future.failed(new UnsupportedOperationException("STR marker table has been replaced with str_mutation_rate")) - } -} +} \ No newline at end of file diff --git a/app/services/GenomeRegionsManagementService.scala b/app/services/GenomeRegionsManagementService.scala index 66a8f01..1442841 100644 --- a/app/services/GenomeRegionsManagementService.scala +++ b/app/services/GenomeRegionsManagementService.scala @@ -4,17 +4,17 @@ import config.GenomicsConfig import jakarta.inject.{Inject, Singleton} import models.api.genomics.* import models.domain.curator.AuditLogEntry -import models.domain.genomics.{Cytoband, GenbankContig, GenomeRegion, StrMarker} +import models.domain.genomics.{GenomeRegion, RegionCoordinate} import play.api.Logging import play.api.cache.AsyncCacheApi -import play.api.libs.json.{Format, Json} +import play.api.libs.json.{Format, JsValue, Json} import repositories.{CuratorAuditRepository, GenomeRegionsRepository} import java.util.UUID import scala.concurrent.{ExecutionContext, Future} /** - * Service for managing genome regions, cytobands, and STR markers. + * Service for managing genome regions (including cytobands). * Provides CRUD operations with audit logging. */ @Singleton @@ -30,60 +30,45 @@ class GenomeRegionsManagementService @Inject()( // JSON formats for domain objects private given Format[GenomeRegion] = Json.format[GenomeRegion] - private given Format[Cytoband] = Json.format[Cytoband] - private given Format[StrMarker] = Json.format[StrMarker] // ============================================================================ // GenomeRegion Operations // ============================================================================ - def listRegions(build: Option[String], page: Int, pageSize: Int): Future[GenomeRegionListResponse] = { + def listRegions(regionType: Option[String], build: Option[String], page: Int, pageSize: Int): Future[GenomeRegionListResponse] = { val offset = (page - 1) * pageSize - build match { - case Some(buildName) => - val canonicalName = genomicsConfig.resolveReferenceName(buildName) - for { - regions <- genomeRegionsRepository.findRegionsByBuild(canonicalName, offset, pageSize) - total <- genomeRegionsRepository.countRegionsByBuild(Some(canonicalName)) - } yield GenomeRegionListResponse( - regions = regions.map(toRegionDetailDto), - total = total, - page = page, - pageSize = pageSize - ) - case None => - for { - total <- genomeRegionsRepository.countRegionsByBuild(None) - } yield GenomeRegionListResponse( - regions = Seq.empty, - total = total, - page = page, - pageSize = pageSize - ) - } + val canonicalBuild = build.map(genomicsConfig.resolveReferenceName) + + for { + regions <- genomeRegionsRepository.findRegions(regionType, canonicalBuild, offset, pageSize) + total <- genomeRegionsRepository.countRegions(regionType, canonicalBuild) + } yield GenomeRegionListResponse( + regions = regions.map(toRegionDetailDto), + total = total, + page = page, + pageSize = pageSize + ) } def getRegion(id: Int): Future[Option[GenomeRegionDetailDto]] = { - genomeRegionsRepository.findRegionByIdWithContig(id).map(_.map(toRegionDetailDto)) + genomeRegionsRepository.findRegionById(id).map(_.map(toRegionDetailDto)) } def createRegion(request: CreateGenomeRegionRequest, userId: Option[UUID]): Future[Either[String, GenomeRegionDetailDto]] = { val region = GenomeRegion( id = None, - genbankContigId = request.genbankContigId, regionType = request.regionType, name = request.name, - startPos = request.startPos, - endPos = request.endPos, - modifier = request.modifier + coordinates = request.coordinates.map { case (k, v) => k -> RegionCoordinate(v.contig, v.start, v.end) }, + properties = request.properties.getOrElse(Json.obj()) ) genomeRegionsRepository.createRegion(region).flatMap { id => - genomeRegionsRepository.findRegionByIdWithContig(id).flatMap { - case Some((createdRegion, contig)) => + genomeRegionsRepository.findRegionById(id).flatMap { + case Some(createdRegion) => logAudit(userId, "genome_region", id, "create", None, Some(createdRegion)).map { _ => - invalidateCacheForContig(contig) - Right(toRegionDetailDto((createdRegion, contig))) + invalidateCache() + Right(toRegionDetailDto(createdRegion)) } case None => Future.successful(Left("Failed to retrieve created region")) @@ -96,22 +81,21 @@ class GenomeRegionsManagementService @Inject()( } def updateRegion(id: Int, request: UpdateGenomeRegionRequest, userId: Option[UUID]): Future[Either[String, GenomeRegionDetailDto]] = { - genomeRegionsRepository.findRegionByIdWithContig(id).flatMap { + genomeRegionsRepository.findRegionById(id).flatMap { case None => Future.successful(Left("Region not found")) - case Some((oldRegion, contig)) => + case Some(oldRegion) => val updatedRegion = oldRegion.copy( regionType = request.regionType.getOrElse(oldRegion.regionType), name = request.name.orElse(oldRegion.name), - startPos = request.startPos.getOrElse(oldRegion.startPos), - endPos = request.endPos.getOrElse(oldRegion.endPos), - modifier = request.modifier.orElse(oldRegion.modifier) + coordinates = request.coordinates.map(_.map { case (k, v) => k -> RegionCoordinate(v.contig, v.start, v.end) }).getOrElse(oldRegion.coordinates), + properties = request.properties.getOrElse(oldRegion.properties) ) genomeRegionsRepository.updateRegion(id, updatedRegion).flatMap { success => if (success) { logAudit(userId, "genome_region", id, "update", Some(oldRegion), Some(updatedRegion)).map { _ => - invalidateCacheForContig(contig) - Right(toRegionDetailDto((updatedRegion.copy(id = Some(id)), contig))) + invalidateCache() + Right(toRegionDetailDto(updatedRegion.copy(id = Some(id)))) } } else { Future.successful(Left("Failed to update region")) @@ -125,13 +109,13 @@ class GenomeRegionsManagementService @Inject()( } def deleteRegion(id: Int, userId: Option[UUID]): Future[Either[String, Unit]] = { - genomeRegionsRepository.findRegionByIdWithContig(id).flatMap { + genomeRegionsRepository.findRegionById(id).flatMap { case None => Future.successful(Left("Region not found")) - case Some((oldRegion, contig)) => + case Some(oldRegion) => genomeRegionsRepository.deleteRegion(id).flatMap { success => if (success) { logAudit(userId, "genome_region", id, "delete", Some(oldRegion), None).map { _ => - invalidateCacheForContig(contig) + invalidateCache() Right(()) } } else { @@ -165,316 +149,17 @@ class GenomeRegionsManagementService @Inject()( } } - // ============================================================================ - // Cytoband Operations - // ============================================================================ - - def listCytobands(build: Option[String], page: Int, pageSize: Int): Future[CytobandListResponse] = { - val offset = (page - 1) * pageSize - build match { - case Some(buildName) => - val canonicalName = genomicsConfig.resolveReferenceName(buildName) - for { - cytobands <- genomeRegionsRepository.findCytobandsByBuild(canonicalName, offset, pageSize) - total <- genomeRegionsRepository.countCytobandsByBuild(Some(canonicalName)) - } yield CytobandListResponse( - cytobands = cytobands.map(toCytobandDetailDto), - total = total, - page = page, - pageSize = pageSize - ) - case None => - for { - total <- genomeRegionsRepository.countCytobandsByBuild(None) - } yield CytobandListResponse( - cytobands = Seq.empty, - total = total, - page = page, - pageSize = pageSize - ) - } - } - - def getCytoband(id: Int): Future[Option[CytobandDetailDto]] = { - genomeRegionsRepository.findCytobandByIdWithContig(id).map(_.map(toCytobandDetailDto)) - } - - def createCytoband(request: CreateCytobandRequest, userId: Option[UUID]): Future[Either[String, CytobandDetailDto]] = { - val cytoband = Cytoband( - id = None, - genbankContigId = request.genbankContigId, - name = request.name, - startPos = request.startPos, - endPos = request.endPos, - stain = request.stain - ) - - genomeRegionsRepository.createCytoband(cytoband).flatMap { id => - genomeRegionsRepository.findCytobandByIdWithContig(id).flatMap { - case Some((createdCytoband, contig)) => - logAudit(userId, "cytoband", id, "create", None, Some(createdCytoband)).map { _ => - invalidateCacheForContig(contig) - Right(toCytobandDetailDto((createdCytoband, contig))) - } - case None => - Future.successful(Left("Failed to retrieve created cytoband")) - } - }.recover { - case e: Exception => - logger.error(s"Failed to create cytoband: ${e.getMessage}", e) - Left(s"Failed to create cytoband: ${e.getMessage}") - } - } - - def updateCytoband(id: Int, request: UpdateCytobandRequest, userId: Option[UUID]): Future[Either[String, CytobandDetailDto]] = { - genomeRegionsRepository.findCytobandByIdWithContig(id).flatMap { - case None => Future.successful(Left("Cytoband not found")) - case Some((oldCytoband, contig)) => - val updatedCytoband = oldCytoband.copy( - name = request.name.getOrElse(oldCytoband.name), - startPos = request.startPos.getOrElse(oldCytoband.startPos), - endPos = request.endPos.getOrElse(oldCytoband.endPos), - stain = request.stain.getOrElse(oldCytoband.stain) - ) - - genomeRegionsRepository.updateCytoband(id, updatedCytoband).flatMap { success => - if (success) { - logAudit(userId, "cytoband", id, "update", Some(oldCytoband), Some(updatedCytoband)).map { _ => - invalidateCacheForContig(contig) - Right(toCytobandDetailDto((updatedCytoband.copy(id = Some(id)), contig))) - } - } else { - Future.successful(Left("Failed to update cytoband")) - } - } - }.recover { - case e: Exception => - logger.error(s"Failed to update cytoband: ${e.getMessage}", e) - Left(s"Failed to update cytoband: ${e.getMessage}") - } - } - - def deleteCytoband(id: Int, userId: Option[UUID]): Future[Either[String, Unit]] = { - genomeRegionsRepository.findCytobandByIdWithContig(id).flatMap { - case None => Future.successful(Left("Cytoband not found")) - case Some((oldCytoband, contig)) => - genomeRegionsRepository.deleteCytoband(id).flatMap { success => - if (success) { - logAudit(userId, "cytoband", id, "delete", Some(oldCytoband), None).map { _ => - invalidateCacheForContig(contig) - Right(()) - } - } else { - Future.successful(Left("Failed to delete cytoband")) - } - } - }.recover { - case e: Exception => - logger.error(s"Failed to delete cytoband: ${e.getMessage}", e) - Left(s"Failed to delete cytoband: ${e.getMessage}") - } - } - - def bulkCreateCytobands(request: BulkCreateCytobandsRequest, userId: Option[UUID]): Future[BulkOperationResponse] = { - val results = request.cytobands.zipWithIndex.map { case (req, idx) => - createCytoband(req, userId).map { - case Right(dto) => BulkOperationResult(idx, "success", Some(dto.id), None) - case Left(error) => BulkOperationResult(idx, "error", None, Some(error)) - }.recover { - case e: Exception => BulkOperationResult(idx, "error", None, Some(e.getMessage)) - } - } - - Future.sequence(results).map { resultList => - BulkOperationResponse( - total = resultList.size, - succeeded = resultList.count(_.status == "success"), - failed = resultList.count(_.status == "error"), - results = resultList - ) - } - } - - // ============================================================================ - // StrMarker Operations - // ============================================================================ - - def listStrMarkers(build: Option[String], page: Int, pageSize: Int): Future[StrMarkerListResponse] = { - val offset = (page - 1) * pageSize - build match { - case Some(buildName) => - val canonicalName = genomicsConfig.resolveReferenceName(buildName) - for { - markers <- genomeRegionsRepository.findStrMarkersByBuild(canonicalName, offset, pageSize) - total <- genomeRegionsRepository.countStrMarkersByBuild(Some(canonicalName)) - } yield StrMarkerListResponse( - markers = markers.map(toStrMarkerDetailDto), - total = total, - page = page, - pageSize = pageSize - ) - case None => - for { - total <- genomeRegionsRepository.countStrMarkersByBuild(None) - } yield StrMarkerListResponse( - markers = Seq.empty, - total = total, - page = page, - pageSize = pageSize - ) - } - } - - def getStrMarker(id: Int): Future[Option[StrMarkerDetailDto]] = { - genomeRegionsRepository.findStrMarkerByIdWithContig(id).map(_.map(toStrMarkerDetailDto)) - } - - def createStrMarker(request: CreateStrMarkerRequest, userId: Option[UUID]): Future[Either[String, StrMarkerDetailDto]] = { - val marker = StrMarker( - id = None, - genbankContigId = request.genbankContigId, - name = request.name, - startPos = request.startPos, - endPos = request.endPos, - period = request.period, - verified = request.verified, - note = request.note - ) - - genomeRegionsRepository.createStrMarker(marker).flatMap { id => - genomeRegionsRepository.findStrMarkerByIdWithContig(id).flatMap { - case Some((createdMarker, contig)) => - logAudit(userId, "str_marker", id, "create", None, Some(createdMarker)).map { _ => - invalidateCacheForContig(contig) - Right(toStrMarkerDetailDto((createdMarker, contig))) - } - case None => - Future.successful(Left("Failed to retrieve created STR marker")) - } - }.recover { - case e: Exception => - logger.error(s"Failed to create STR marker: ${e.getMessage}", e) - Left(s"Failed to create STR marker: ${e.getMessage}") - } - } - - def updateStrMarker(id: Int, request: UpdateStrMarkerRequest, userId: Option[UUID]): Future[Either[String, StrMarkerDetailDto]] = { - genomeRegionsRepository.findStrMarkerByIdWithContig(id).flatMap { - case None => Future.successful(Left("STR marker not found")) - case Some((oldMarker, contig)) => - val updatedMarker = oldMarker.copy( - name = request.name.getOrElse(oldMarker.name), - startPos = request.startPos.getOrElse(oldMarker.startPos), - endPos = request.endPos.getOrElse(oldMarker.endPos), - period = request.period.getOrElse(oldMarker.period), - verified = request.verified.getOrElse(oldMarker.verified), - note = request.note.orElse(oldMarker.note) - ) - - genomeRegionsRepository.updateStrMarker(id, updatedMarker).flatMap { success => - if (success) { - logAudit(userId, "str_marker", id, "update", Some(oldMarker), Some(updatedMarker)).map { _ => - invalidateCacheForContig(contig) - Right(toStrMarkerDetailDto((updatedMarker.copy(id = Some(id)), contig))) - } - } else { - Future.successful(Left("Failed to update STR marker")) - } - } - }.recover { - case e: Exception => - logger.error(s"Failed to update STR marker: ${e.getMessage}", e) - Left(s"Failed to update STR marker: ${e.getMessage}") - } - } - - def deleteStrMarker(id: Int, userId: Option[UUID]): Future[Either[String, Unit]] = { - genomeRegionsRepository.findStrMarkerByIdWithContig(id).flatMap { - case None => Future.successful(Left("STR marker not found")) - case Some((oldMarker, contig)) => - genomeRegionsRepository.deleteStrMarker(id).flatMap { success => - if (success) { - logAudit(userId, "str_marker", id, "delete", Some(oldMarker), None).map { _ => - invalidateCacheForContig(contig) - Right(()) - } - } else { - Future.successful(Left("Failed to delete STR marker")) - } - } - }.recover { - case e: Exception => - logger.error(s"Failed to delete STR marker: ${e.getMessage}", e) - Left(s"Failed to delete STR marker: ${e.getMessage}") - } - } - - def bulkCreateStrMarkers(request: BulkCreateStrMarkersRequest, userId: Option[UUID]): Future[BulkOperationResponse] = { - val results = request.markers.zipWithIndex.map { case (req, idx) => - createStrMarker(req, userId).map { - case Right(dto) => BulkOperationResult(idx, "success", Some(dto.id), None) - case Left(error) => BulkOperationResult(idx, "error", None, Some(error)) - }.recover { - case e: Exception => BulkOperationResult(idx, "error", None, Some(e.getMessage)) - } - } - - Future.sequence(results).map { resultList => - BulkOperationResponse( - total = resultList.size, - succeeded = resultList.count(_.status == "success"), - failed = resultList.count(_.status == "error"), - results = resultList - ) - } - } - // ============================================================================ // Helper Methods // ============================================================================ - private def toRegionDetailDto(data: (GenomeRegion, GenbankContig)): GenomeRegionDetailDto = { - val (region, contig) = data + private def toRegionDetailDto(region: GenomeRegion): GenomeRegionDetailDto = { GenomeRegionDetailDto( id = region.id.getOrElse(0), - genbankContigId = region.genbankContigId, - contigName = contig.commonName, - referenceGenome = contig.referenceGenome, regionType = region.regionType, name = region.name, - startPos = region.startPos, - endPos = region.endPos, - modifier = region.modifier - ) - } - - private def toCytobandDetailDto(data: (Cytoband, GenbankContig)): CytobandDetailDto = { - val (cytoband, contig) = data - CytobandDetailDto( - id = cytoband.id.getOrElse(0), - genbankContigId = cytoband.genbankContigId, - contigName = contig.commonName, - referenceGenome = contig.referenceGenome, - name = cytoband.name, - startPos = cytoband.startPos, - endPos = cytoband.endPos, - stain = cytoband.stain - ) - } - - private def toStrMarkerDetailDto(data: (StrMarker, GenbankContig)): StrMarkerDetailDto = { - val (marker, contig) = data - StrMarkerDetailDto( - id = marker.id.getOrElse(0), - genbankContigId = marker.genbankContigId, - contigName = contig.commonName, - referenceGenome = contig.referenceGenome, - name = marker.name, - startPos = marker.startPos, - endPos = marker.endPos, - period = marker.period, - verified = marker.verified, - note = marker.note + coordinates = region.coordinates.map { case (k, v) => k -> RegionCoordinateDto(v.contig, v.start, v.end) }, + properties = region.properties ) } @@ -493,10 +178,11 @@ class GenomeRegionsManagementService @Inject()( auditRepository.logAction(entry) } - private def invalidateCacheForContig(contig: GenbankContig): Unit = { - contig.referenceGenome.foreach { refGenome => + private def invalidateCache(): Unit = { + // Invalidate all build caches as we don't know easily which builds are affected by coordinates update + genomicsConfig.supportedReferences.foreach { refGenome => cache.remove(s"genome-regions:$refGenome") logger.debug(s"Invalidated cache for genome-regions:$refGenome") } } -} +} \ No newline at end of file diff --git a/app/services/GenomeRegionsService.scala b/app/services/GenomeRegionsService.scala index 6809c3c..93e0b43 100644 --- a/app/services/GenomeRegionsService.scala +++ b/app/services/GenomeRegionsService.scala @@ -3,8 +3,9 @@ package services import config.GenomicsConfig import jakarta.inject.{Inject, Singleton} import models.api.genomics.* -import models.domain.genomics.{GenomeRegion, GenbankContig} +import models.domain.genomics.{GenbankContig, GenomeRegion} import play.api.cache.AsyncCacheApi +import play.api.libs.json.{JsValue, Reads} import repositories.{FullBuildData, GenomeRegionsRepository} import java.security.MessageDigest @@ -78,14 +79,24 @@ class GenomeRegionsService @Inject()( */ private def buildResponse(canonicalName: String): Future[GenomeRegionsResponse] = { genomeRegionsRepository.getFullBuildData(canonicalName).map { data => + + // Group regions by contig name for efficient lookup. + // We check for exact match or "chr"+name match to handle common naming conventions. + val regionsByContig = data.regions.flatMap { region => + region.coordinates.get(canonicalName).map(coord => coord.contig -> region) + }.groupBy(_._1).map { case (k, v) => k -> v.map(_._2) } + val chromosomeMap = data.contigs.flatMap { contig => contig.commonName.map { chromName => - val contigId = contig.id.getOrElse(0) - val regions = data.regions.getOrElse(contigId, Seq.empty) - val cytobands = data.cytobands.getOrElse(contigId, Seq.empty) - val markers = data.strMarkers.getOrElse(contigId, Seq.empty) - - chromName -> buildChromosomeRegions(contig, regions, cytobands, markers) + // Try to find regions for this contig using common variations + val relevantRegions = regionsByContig.getOrElse(chromName, Seq.empty) ++ + regionsByContig.getOrElse("chr" + chromName, Seq.empty) ++ + regionsByContig.getOrElse(chromName.replace("chr", ""), Seq.empty) + + // Deduplicate if needed (though mapping logic usually prevents duplicate keys in map unless source has duplicates) + val uniqueRegions = relevantRegions.distinctBy(_.id) + + chromName -> buildChromosomeRegions(contig, uniqueRegions, canonicalName) } }.toMap @@ -104,58 +115,95 @@ class GenomeRegionsService @Inject()( private def buildChromosomeRegions( contig: GenbankContig, regions: Seq[GenomeRegion], - cytobands: Seq[models.domain.genomics.Cytoband], - markers: Seq[models.domain.genomics.StrMarker] + buildName: String ): ChromosomeRegionsDto = { + // Helper to convert to DTO with current build context + def toDto(r: GenomeRegion): Option[RegionDto] = toRegionDto(r, buildName) + // Extract specific region types - val centromere = regions.find(_.regionType == "Centromere").map(toRegionDto) - val telomereP = regions.find(_.regionType == "Telomere_P").map(toRegionDto) - val telomereQ = regions.find(_.regionType == "Telomere_Q").map(toRegionDto) + val centromere = regions.find(_.regionType == "Centromere").flatMap(toDto) + val telomereP = regions.find(_.regionType == "Telomere_P").flatMap(toDto) + val telomereQ = regions.find(_.regionType == "Telomere_Q").flatMap(toDto) val telomeres = if (telomereP.isDefined || telomereQ.isDefined) { Some(TelomeresDto(p = telomereP, q = telomereQ)) } else None + // Cytobands + val cytobands = regions.filter(_.regionType == "Cytoband") + .flatMap(r => toCytobandDto(r, buildName)) + .sortBy(_.start) + // Build Y-chromosome specific regions if this is chrY val yRegions = if (contig.commonName.exists(name => name.toLowerCase.contains("chry") || name == "Y")) { - Some(buildYRegions(regions)) + Some(buildYRegions(regions, buildName)) } else None ChromosomeRegionsDto( length = contig.seqLength.toLong, centromere = centromere, telomeres = telomeres, - cytobands = cytobands.map(toCytobandDto), + cytobands = cytobands, regions = yRegions, - strMarkers = markers.map(toStrMarkerDto) + strMarkers = Seq.empty // STR markers handled by separate service/table now ) } /** * Build Y-chromosome specific regions grouped by type. */ - private def buildYRegions(regions: Seq[GenomeRegion]): YChromosomeRegionsDto = { + private def buildYRegions(regions: Seq[GenomeRegion], buildName: String): YChromosomeRegionsDto = { + def toDto(r: GenomeRegion) = toRegionDto(r, buildName) + def toNamedDto(r: GenomeRegion) = toNamedRegionDto(r, buildName) + YChromosomeRegionsDto( - par1 = regions.find(_.regionType == "PAR1").map(toRegionDto), - par2 = regions.find(_.regionType == "PAR2").map(toRegionDto), - xtr = regions.filter(_.regionType == "XTR").map(toRegionDto), - ampliconic = regions.filter(_.regionType == "Ampliconic").map(toRegionDto), - palindromes = regions.filter(_.regionType == "Palindrome").map(toNamedRegionDto), - heterochromatin = regions.find(_.regionType == "Heterochromatin").map(toRegionDto), - xDegenerate = regions.filter(_.regionType == "XDegenerate").map(toRegionDto) + par1 = regions.find(_.regionType == "PAR1").flatMap(toDto), + par2 = regions.find(_.regionType == "PAR2").flatMap(toDto), + xtr = regions.filter(_.regionType == "XTR").flatMap(toDto), + ampliconic = regions.filter(_.regionType == "Ampliconic").flatMap(toDto), + palindromes = regions.filter(_.regionType == "Palindrome").flatMap(toNamedDto), + heterochromatin = regions.find(_.regionType == "Heterochromatin").flatMap(toDto), + xDegenerate = regions.filter(_.regionType == "XDegenerate").flatMap(toDto) ) } // Domain to DTO conversions - private def toRegionDto(r: GenomeRegion): RegionDto = - RegionDto(r.startPos, r.endPos, Some(r.regionType), r.modifier.map(_.toDouble)) - private def toNamedRegionDto(r: GenomeRegion): NamedRegionDto = - NamedRegionDto(r.name.getOrElse(""), r.startPos, r.endPos, r.regionType, r.modifier.map(_.toDouble)) + private def getProperty[T](r: GenomeRegion, key: String)(implicit reads: Reads[T]): Option[T] = { + (r.properties \ key).asOpt[T] + } - private def toCytobandDto(c: models.domain.genomics.Cytoband): CytobandDto = - CytobandDto(c.name, c.startPos, c.endPos, c.stain) + private def toRegionDto(r: GenomeRegion, buildName: String): Option[RegionDto] = { + r.coordinates.get(buildName).map { coord => + RegionDto( + start = coord.start, + end = coord.end, + `type` = Some(r.regionType), + modifier = getProperty[Double](r, "modifier") + ) + } + } - private def toStrMarkerDto(s: models.domain.genomics.StrMarker): StrMarkerDto = - StrMarkerDto(s.name, s.startPos, s.endPos, s.period, s.verified, s.note) -} + private def toNamedRegionDto(r: GenomeRegion, buildName: String): Option[NamedRegionDto] = { + r.coordinates.get(buildName).map { coord => + NamedRegionDto( + name = r.name.getOrElse(""), + start = coord.start, + end = coord.end, + `type` = r.regionType, + modifier = getProperty[Double](r, "modifier") + ) + } + } + + private def toCytobandDto(r: GenomeRegion, buildName: String): Option[CytobandDto] = { + r.coordinates.get(buildName).map { coord => + CytobandDto( + name = r.name.getOrElse(""), + start = coord.start, + end = coord.end, + stain = getProperty[String](r, "stain").getOrElse("gneg") + ) + } + } +} \ No newline at end of file diff --git a/app/views/curator/cytobands/createForm.scala.html b/app/views/curator/cytobands/createForm.scala.html deleted file mode 100644 index 488574e..0000000 --- a/app/views/curator/cytobands/createForm.scala.html +++ /dev/null @@ -1,117 +0,0 @@ -@import org.webjars.play.WebJarsUtil -@import models.domain.genomics.GenbankContig -@import controllers.CytobandFormData -@(form: Form[CytobandFormData], contigs: Seq[GenbankContig], supportedBuilds: Seq[String])(implicit request: RequestHeader, messages: Messages, webJarsUtil: WebJarsUtil) - -@main("Create Cytoband") { -
-
-
- -
-
- -
-
-
-
-
Create Cytoband
-
-
- @helper.form(action = controllers.routes.GenomeRegionsCuratorController.createCytoband, Symbol("class") -> "needs-validation") { - @helper.CSRF.formField - -
- - -
- -
- - -
- -
-
- - -
-
- - -
-
- -
- - -
- -
- - - Cancel - -
- } -
-
-
-
-
-} diff --git a/app/views/curator/cytobands/detailPanel.scala.html b/app/views/curator/cytobands/detailPanel.scala.html deleted file mode 100644 index 219c338..0000000 --- a/app/views/curator/cytobands/detailPanel.scala.html +++ /dev/null @@ -1,86 +0,0 @@ -@import models.api.genomics.CytobandDetailDto -@(cytoband: CytobandDetailDto)(implicit request: RequestHeader) - -
-
-
Cytoband Details
-
- - Edit - - -
-
-
-
-
ID
-
@cytoband.id
- -
Chromosome
-
- @cytoband.contigName.getOrElse("Unknown") -
- -
Build
-
- - @cytoband.referenceGenome.getOrElse("Unknown") - -
- -
Band Name
-
- @cytoband.name -
- -
Start Position
-
- @{java.text.NumberFormat.getIntegerInstance().format(cytoband.startPos)} -
- -
End Position
-
- @{java.text.NumberFormat.getIntegerInstance().format(cytoband.endPos)} -
- -
Length
-
- @{java.text.NumberFormat.getIntegerInstance().format(cytoband.endPos - cytoband.startPos)} bp -
- -
Stain
-
- @cytoband.stain -
-
-
-
- -@buildBadgeClass(refGenome: String) = @{ - refGenome match { - case "GRCh37" => "bg-warning text-dark" - case "GRCh38" => "bg-info" - case "hs1" => "bg-success" - case _ => "bg-secondary" - } -} - -@stainBadgeClass(stain: String) = @{ - stain match { - case "gneg" => "bg-light text-dark" - case "gpos25" => "bg-secondary" - case "gpos50" => "bg-secondary" - case "gpos75" => "bg-dark" - case "gpos100" => "bg-dark" - case "acen" => "bg-danger" - case "gvar" => "bg-info" - case "stalk" => "bg-primary" - case _ => "bg-secondary" - } -} diff --git a/app/views/curator/cytobands/editForm.scala.html b/app/views/curator/cytobands/editForm.scala.html deleted file mode 100644 index 4b1ea0c..0000000 --- a/app/views/curator/cytobands/editForm.scala.html +++ /dev/null @@ -1,116 +0,0 @@ -@import org.webjars.play.WebJarsUtil -@import models.domain.genomics.GenbankContig -@import controllers.CytobandFormData -@(id: Int, form: Form[CytobandFormData], contigs: Seq[GenbankContig], supportedBuilds: Seq[String])(implicit request: RequestHeader, messages: Messages, webJarsUtil: WebJarsUtil) - -@main("Edit Cytoband") { -
-
-
- -
-
- -
-
-
-
-
Edit Cytoband #@id
-
-
- @helper.form(action = controllers.routes.GenomeRegionsCuratorController.updateCytoband(id), Symbol("class") -> "needs-validation") { - @helper.CSRF.formField - -
- - -
- -
- - -
- -
-
- - -
-
- - -
-
- -
- - -
- -
- - - Cancel - -
- } -
-
-
-
-
-} diff --git a/app/views/curator/cytobands/list.scala.html b/app/views/curator/cytobands/list.scala.html deleted file mode 100644 index 6f79145..0000000 --- a/app/views/curator/cytobands/list.scala.html +++ /dev/null @@ -1,99 +0,0 @@ -@import org.webjars.play.WebJarsUtil -@import models.api.genomics.CytobandDetailDto -@(cytobands: Seq[CytobandDetailDto], build: Option[String], currentPage: Int, totalPages: Int, pageSize: Int, totalCount: Int, supportedBuilds: Seq[String])(implicit request: RequestHeader, messages: Messages, webJarsUtil: WebJarsUtil) - -@main("Curator - Cytobands") { - - -
-
-
- -
-
- - @request.flash.get("success").map { msg => - - } - - @request.flash.get("error").map { msg => - - } - -
-
-
-
-
Cytobands
- - Create - -
-
-
-
-
- - - - - -
-
-
- -
- @listFragment(cytobands, build, currentPage, totalPages, pageSize, totalCount) -
-
-
-
- -
-
-
-
- -

Select a cytoband to view details

-
-
-
-
-
-
- - -} diff --git a/app/views/curator/cytobands/listFragment.scala.html b/app/views/curator/cytobands/listFragment.scala.html deleted file mode 100644 index 149f4c9..0000000 --- a/app/views/curator/cytobands/listFragment.scala.html +++ /dev/null @@ -1,125 +0,0 @@ -@import models.api.genomics.CytobandDetailDto -@(cytobands: Seq[CytobandDetailDto], build: Option[String], currentPage: Int, totalPages: Int, pageSize: Int, totalCount: Int)(implicit request: RequestHeader) - -@defining(java.text.NumberFormat.getIntegerInstance()) { nf => -
- - @if(build.nonEmpty) { - Found @nf.format(totalCount) cytobands for @build.get - } else { - Showing @nf.format(totalCount) total cytobands - } - - @if(totalPages > 1) { - Page @currentPage of @nf.format(totalPages) - } -
-} - -@if(cytobands.isEmpty) { -
- @if(build.nonEmpty) { - No cytobands found for @build.get. - } else { - Select a build to view cytobands. - } -
-} else { -
- - - - - - - - - - - - @for(cytoband <- cytobands) { - - - - - - - - } - -
ChromosomeBandPositionStainBuild
- @cytoband.contigName.getOrElse("Unknown") - - @cytoband.name - - @{java.text.NumberFormat.getIntegerInstance().format(cytoband.startPos)} - - @{java.text.NumberFormat.getIntegerInstance().format(cytoband.endPos)} - - @cytoband.stain - - - @cytoband.referenceGenome.getOrElse("Unknown") - -
-
- - @if(totalPages > 1) { - - } -} - -@buildBadgeClass(refGenome: String) = @{ - refGenome match { - case "GRCh37" => "bg-warning text-dark" - case "GRCh38" => "bg-info" - case "hs1" => "bg-success" - case _ => "bg-secondary" - } -} - -@stainBadgeClass(stain: String) = @{ - stain match { - case "gneg" => "bg-light text-dark" - case "gpos25" => "bg-secondary" - case "gpos50" => "bg-secondary" - case "gpos75" => "bg-dark" - case "gpos100" => "bg-dark" - case "acen" => "bg-danger" - case "gvar" => "bg-info" - case "stalk" => "bg-primary" - case _ => "bg-secondary" - } -} diff --git a/app/views/curator/genomeregions/detailPanel.scala.html b/app/views/curator/genomeregions/detailPanel.scala.html index e6c0102..7ee66af 100644 --- a/app/views/curator/genomeregions/detailPanel.scala.html +++ b/app/views/curator/genomeregions/detailPanel.scala.html @@ -22,18 +22,6 @@
Region Details
ID
@region.id
-
Chromosome
-
- @region.contigName.getOrElse("Unknown") -
- -
Build
-
- - @region.referenceGenome.getOrElse("Unknown") - -
-
Type
@region.regionType @@ -44,34 +32,31 @@
Region Details
@name
} -
Start Position
-
- @{java.text.NumberFormat.getIntegerInstance().format(region.startPos)} -
- -
End Position
-
- @{java.text.NumberFormat.getIntegerInstance().format(region.endPos)} -
- -
Length
-
- @{java.text.NumberFormat.getIntegerInstance().format(region.endPos - region.startPos)} bp -
+ @if(region.coordinates.nonEmpty) { +
Coordinates
+ @for((build, coord) <- region.coordinates) { +
@build
+
+ @coord.contig: + @{java.text.NumberFormat.getIntegerInstance().format(coord.start)} - + @{java.text.NumberFormat.getIntegerInstance().format(coord.end)} + (@{java.text.NumberFormat.getIntegerInstance().format(coord.end - coord.start)} bp) +
+ } + } else { +
Coordinates
+
No coordinates defined
+ } - @region.modifier.map { mod => + @if((region.properties \ "modifier").asOpt[BigDecimal].isDefined) {
Modifier
-
@mod
+
@{(region.properties \ "modifier").as[BigDecimal]}
+ } + + @if((region.properties \ "stain").asOpt[String].isDefined) { +
Stain
+
@{(region.properties \ "stain").as[String]}
}
-
- -@buildBadgeClass(refGenome: String) = @{ - refGenome match { - case "GRCh37" => "bg-warning text-dark" - case "GRCh38" => "bg-info" - case "hs1" => "bg-success" - case _ => "bg-secondary" - } -} +
\ No newline at end of file diff --git a/app/views/curator/genomeregions/list.scala.html b/app/views/curator/genomeregions/list.scala.html index 3f07644..8be6de5 100644 --- a/app/views/curator/genomeregions/list.scala.html +++ b/app/views/curator/genomeregions/list.scala.html @@ -57,7 +57,7 @@
Genome Regions
- - @for(build <- supportedBuilds) { - - @for(contig <- contigs.filter(_.referenceGenome.contains(build))) { - - } - - } - -
- -
- - -
- -
-
- - -
-
- - -
-
- -
-
- - -
The repeat unit length in base pairs
-
-
- -
- - -
-
- - -
-
-
- -
- - -
Optional notes about this marker
-
- -
- - - Cancel - -
- } - - - - - -} diff --git a/app/views/curator/strmarkers/detailPanel.scala.html b/app/views/curator/strmarkers/detailPanel.scala.html deleted file mode 100644 index 424c3e6..0000000 --- a/app/views/curator/strmarkers/detailPanel.scala.html +++ /dev/null @@ -1,86 +0,0 @@ -@import models.api.genomics.StrMarkerDetailDto -@(marker: StrMarkerDetailDto)(implicit request: RequestHeader) - -
-
-
STR Marker Details
-
- - Edit - - -
-
-
-
-
ID
-
@marker.id
- -
Chromosome
-
- @marker.contigName.getOrElse("Unknown") -
- -
Build
-
- - @marker.referenceGenome.getOrElse("Unknown") - -
- -
Name
-
- @marker.name -
- -
Start Position
-
- @{java.text.NumberFormat.getIntegerInstance().format(marker.startPos)} -
- -
End Position
-
- @{java.text.NumberFormat.getIntegerInstance().format(marker.endPos)} -
- -
Length
-
- @{java.text.NumberFormat.getIntegerInstance().format(marker.endPos - marker.startPos)} bp -
- -
Period
-
- @marker.period bp -
- -
Verified
-
- @if(marker.verified) { - Yes - } else { - No - } -
- - @marker.note.map { n => -
Note
-
@n
- } -
-
-
- -@buildBadgeClass(refGenome: String) = @{ - refGenome match { - case "GRCh37" => "bg-warning text-dark" - case "GRCh38" => "bg-info" - case "hs1" => "bg-success" - case _ => "bg-secondary" - } -} diff --git a/app/views/curator/strmarkers/editForm.scala.html b/app/views/curator/strmarkers/editForm.scala.html deleted file mode 100644 index efc8ecf..0000000 --- a/app/views/curator/strmarkers/editForm.scala.html +++ /dev/null @@ -1,143 +0,0 @@ -@import org.webjars.play.WebJarsUtil -@import models.domain.genomics.GenbankContig -@import controllers.StrMarkerFormData -@(id: Int, form: Form[StrMarkerFormData], contigs: Seq[GenbankContig], supportedBuilds: Seq[String])(implicit request: RequestHeader, messages: Messages, webJarsUtil: WebJarsUtil) - -@main("Edit STR Marker") { -
-
-
- -
-
- -
-
-
-
-
Edit STR Marker #@id
-
-
- @helper.form(action = controllers.routes.GenomeRegionsCuratorController.updateStrMarker(id), Symbol("class") -> "needs-validation") { - @helper.CSRF.formField - -
- - -
- -
- - -
- -
-
- - -
-
- - -
-
- -
-
- - -
The repeat unit length in base pairs
-
-
- -
- - -
-
- - -
-
-
- -
- - -
Optional notes about this marker
-
- -
- - - Cancel - -
- } -
-
-
-
-
-} diff --git a/app/views/curator/strmarkers/list.scala.html b/app/views/curator/strmarkers/list.scala.html deleted file mode 100644 index fa9006b..0000000 --- a/app/views/curator/strmarkers/list.scala.html +++ /dev/null @@ -1,99 +0,0 @@ -@import org.webjars.play.WebJarsUtil -@import models.api.genomics.StrMarkerDetailDto -@(markers: Seq[StrMarkerDetailDto], build: Option[String], currentPage: Int, totalPages: Int, pageSize: Int, totalCount: Int, supportedBuilds: Seq[String])(implicit request: RequestHeader, messages: Messages, webJarsUtil: WebJarsUtil) - -@main("Curator - STR Markers") { - - -
-
-
- -
-
- - @request.flash.get("success").map { msg => - - } - - @request.flash.get("error").map { msg => - - } - -
-
-
-
-
STR Markers
- - Create - -
-
-
-
-
- - - - - -
-
-
- -
- @listFragment(markers, build, currentPage, totalPages, pageSize, totalCount) -
-
-
-
- -
-
-
-
- -

Select a marker to view details

-
-
-
-
-
-
- - -} diff --git a/app/views/curator/strmarkers/listFragment.scala.html b/app/views/curator/strmarkers/listFragment.scala.html deleted file mode 100644 index 80586d0..0000000 --- a/app/views/curator/strmarkers/listFragment.scala.html +++ /dev/null @@ -1,119 +0,0 @@ -@import models.api.genomics.StrMarkerDetailDto -@(markers: Seq[StrMarkerDetailDto], build: Option[String], currentPage: Int, totalPages: Int, pageSize: Int, totalCount: Int)(implicit request: RequestHeader) - -@defining(java.text.NumberFormat.getIntegerInstance()) { nf => -
- - @if(build.nonEmpty) { - Found @nf.format(totalCount) markers for @build.get - } else { - Showing @nf.format(totalCount) total markers - } - - @if(totalPages > 1) { - Page @currentPage of @nf.format(totalPages) - } -
-} - -@if(markers.isEmpty) { -
- @if(build.nonEmpty) { - No STR markers found for @build.get. - } else { - Select a build to view STR markers. - } -
-} else { -
- - - - - - - - - - - - - @for(marker <- markers) { - - - - - - - - - } - -
ChromosomeNamePositionPeriodVerifiedBuild
- @marker.contigName.getOrElse("Unknown") - - @marker.name - - @{java.text.NumberFormat.getIntegerInstance().format(marker.startPos)} - - @{java.text.NumberFormat.getIntegerInstance().format(marker.endPos)} - - @marker.period bp - - @if(marker.verified) { - Yes - } else { - No - } - - - @marker.referenceGenome.getOrElse("Unknown") - -
-
- - @if(totalPages > 1) { - - } -} - -@buildBadgeClass(refGenome: String) = @{ - refGenome match { - case "GRCh37" => "bg-warning text-dark" - case "GRCh38" => "bg-info" - case "hs1" => "bg-success" - case _ => "bg-secondary" - } -} diff --git a/conf/evolutions/default/55.sql b/conf/evolutions/default/55.sql new file mode 100644 index 0000000..58236a1 --- /dev/null +++ b/conf/evolutions/default/55.sql @@ -0,0 +1,45 @@ +# --- !Ups + +DROP TABLE IF EXISTS genome_region; +DROP TABLE IF EXISTS cytoband; + +CREATE TABLE genome_region_v2 ( + region_id SERIAL PRIMARY KEY, + region_type TEXT NOT NULL, + name TEXT, + coordinates JSONB NOT NULL, + properties JSONB DEFAULT '{}', + UNIQUE(region_type, name) +); + +CREATE INDEX idx_genome_region_v2_coords ON genome_region_v2 USING GIN(coordinates); + +-- Efficient lookup: "What region contains GRCh38:chrY:15000000?" +CREATE INDEX idx_genome_region_v2_grch38_range ON genome_region_v2 ( + (coordinates->'GRCh38'->>'contig'), + ((coordinates->'GRCh38'->>'start')::bigint), + ((coordinates->'GRCh38'->>'end')::bigint) +); + +# --- !Downs + +DROP TABLE IF EXISTS genome_region_v2; + +CREATE TABLE genome_region ( + id SERIAL PRIMARY KEY, + genbank_contig_id INT NOT NULL, + region_type TEXT NOT NULL, + name TEXT, + start_pos BIGINT NOT NULL, + end_pos BIGINT NOT NULL, + modifier NUMERIC +); + +CREATE TABLE cytoband ( + id SERIAL PRIMARY KEY, + genbank_contig_id INT NOT NULL, + name TEXT NOT NULL, + start_pos BIGINT NOT NULL, + end_pos BIGINT NOT NULL, + stain TEXT NOT NULL +); diff --git a/conf/routes b/conf/routes index 25b029e..8d7137c 100644 --- a/conf/routes +++ b/conf/routes @@ -163,29 +163,13 @@ GET /api/v1/genome-regions/:build # Genome Regions API Management (X-API-Key secured) # ============================================= # Genome Regions -GET /api/v1/manage/genome-regions controllers.GenomeRegionsApiManagementController.listRegions(build: Option[String]) +GET /api/v1/manage/genome-regions controllers.GenomeRegionsApiManagementController.listRegions(regionType: Option[String], build: Option[String], page: Int ?= 1, pageSize: Int ?= 25) GET /api/v1/manage/genome-regions/:id controllers.GenomeRegionsApiManagementController.getRegion(id: Int) POST /api/v1/manage/genome-regions controllers.GenomeRegionsApiManagementController.createRegion() PUT /api/v1/manage/genome-regions/:id controllers.GenomeRegionsApiManagementController.updateRegion(id: Int) DELETE /api/v1/manage/genome-regions/:id controllers.GenomeRegionsApiManagementController.deleteRegion(id: Int) POST /api/v1/manage/genome-regions/bulk controllers.GenomeRegionsApiManagementController.bulkCreateRegions() -# Cytobands -GET /api/v1/manage/cytobands controllers.GenomeRegionsApiManagementController.listCytobands(build: Option[String]) -GET /api/v1/manage/cytobands/:id controllers.GenomeRegionsApiManagementController.getCytoband(id: Int) -POST /api/v1/manage/cytobands controllers.GenomeRegionsApiManagementController.createCytoband() -PUT /api/v1/manage/cytobands/:id controllers.GenomeRegionsApiManagementController.updateCytoband(id: Int) -DELETE /api/v1/manage/cytobands/:id controllers.GenomeRegionsApiManagementController.deleteCytoband(id: Int) -POST /api/v1/manage/cytobands/bulk controllers.GenomeRegionsApiManagementController.bulkCreateCytobands() - -# STR Markers -GET /api/v1/manage/str-markers controllers.GenomeRegionsApiManagementController.listStrMarkers(build: Option[String]) -GET /api/v1/manage/str-markers/:id controllers.GenomeRegionsApiManagementController.getStrMarker(id: Int) -POST /api/v1/manage/str-markers controllers.GenomeRegionsApiManagementController.createStrMarker() -PUT /api/v1/manage/str-markers/:id controllers.GenomeRegionsApiManagementController.updateStrMarker(id: Int) -DELETE /api/v1/manage/str-markers/:id controllers.GenomeRegionsApiManagementController.deleteStrMarker(id: Int) -POST /api/v1/manage/str-markers/bulk controllers.GenomeRegionsApiManagementController.bulkCreateStrMarkers() - # ============================================= # Haplogroup Tree Merge API (X-API-Key secured) # ============================================= @@ -242,8 +226,8 @@ GET /curator/audit/:entityType/:entityId # Curator - Genome Regions (session auth + permissions) # ============================================= # Genome Regions -GET /curator/genome-regions controllers.GenomeRegionsCuratorController.listRegions(build: Option[String], page: Int ?= 1, pageSize: Int ?= 25) -GET /curator/genome-regions/fragment controllers.GenomeRegionsCuratorController.regionsFragment(build: Option[String], page: Int ?= 1, pageSize: Int ?= 25) +GET /curator/genome-regions controllers.GenomeRegionsCuratorController.listRegions(regionType: Option[String], build: Option[String], page: Int ?= 1, pageSize: Int ?= 25) +GET /curator/genome-regions/fragment controllers.GenomeRegionsCuratorController.regionsFragment(regionType: Option[String], build: Option[String], page: Int ?= 1, pageSize: Int ?= 25) GET /curator/genome-regions/:id/detail controllers.GenomeRegionsCuratorController.regionDetailPanel(id: Int) GET /curator/genome-regions/new controllers.GenomeRegionsCuratorController.createRegionForm POST /curator/genome-regions controllers.GenomeRegionsCuratorController.createRegion @@ -251,26 +235,6 @@ GET /curator/genome-regions/:id/edit POST /curator/genome-regions/:id controllers.GenomeRegionsCuratorController.updateRegion(id: Int) DELETE /curator/genome-regions/:id controllers.GenomeRegionsCuratorController.deleteRegion(id: Int) -# Cytobands -GET /curator/cytobands controllers.GenomeRegionsCuratorController.listCytobands(build: Option[String], page: Int ?= 1, pageSize: Int ?= 25) -GET /curator/cytobands/fragment controllers.GenomeRegionsCuratorController.cytobandsFragment(build: Option[String], page: Int ?= 1, pageSize: Int ?= 25) -GET /curator/cytobands/:id/detail controllers.GenomeRegionsCuratorController.cytobandDetailPanel(id: Int) -GET /curator/cytobands/new controllers.GenomeRegionsCuratorController.createCytobandForm -POST /curator/cytobands controllers.GenomeRegionsCuratorController.createCytoband -GET /curator/cytobands/:id/edit controllers.GenomeRegionsCuratorController.editCytobandForm(id: Int) -POST /curator/cytobands/:id controllers.GenomeRegionsCuratorController.updateCytoband(id: Int) -DELETE /curator/cytobands/:id controllers.GenomeRegionsCuratorController.deleteCytoband(id: Int) - -# STR Markers -GET /curator/str-markers controllers.GenomeRegionsCuratorController.listStrMarkers(build: Option[String], page: Int ?= 1, pageSize: Int ?= 25) -GET /curator/str-markers/fragment controllers.GenomeRegionsCuratorController.strMarkersFragment(build: Option[String], page: Int ?= 1, pageSize: Int ?= 25) -GET /curator/str-markers/:id/detail controllers.GenomeRegionsCuratorController.strMarkerDetailPanel(id: Int) -GET /curator/str-markers/new controllers.GenomeRegionsCuratorController.createStrMarkerForm -POST /curator/str-markers controllers.GenomeRegionsCuratorController.createStrMarker -GET /curator/str-markers/:id/edit controllers.GenomeRegionsCuratorController.editStrMarkerForm(id: Int) -POST /curator/str-markers/:id controllers.GenomeRegionsCuratorController.updateStrMarker(id: Int) -DELETE /curator/str-markers/:id controllers.GenomeRegionsCuratorController.deleteStrMarker(id: Int) - # --- API Routes (Handled by Tapir, including Swagger UI) --- POST /api/registerPDS controllers.PDSRegistrationController.registerPDS() From 8538d45e1a7030539a86a8f665ecf7474cdd0ab0 Mon Sep 17 00:00:00 2001 From: jkane Date: Sat, 13 Dec 2025 08:50:56 -0600 Subject: [PATCH 06/28] **chore(curator): Remove legacy Cytoband and STR Marker templates and models** - Deleted unused templates (`createForm`, `editForm`, `detailPanel`) for Cytobands and STR Markers. - Removed associated Scala models (`Cytoband`, `StrMarker`), streamlining codebase maintenance. - Cleaned up controllers and routes referencing deprecated Cytoband and STR Marker logic. --- .../GenomeRegionsCuratorController.scala | 4 +-- .../domain/genomics/GenomeRegionTables.scala | 9 ++++-- .../GenomeRegionsRepository.scala | 9 +++--- .../genomeregions/createForm.scala.html | 4 +-- .../curator/genomeregions/editForm.scala.html | 4 +-- conf/evolutions/default/54.sql | 31 +------------------ scripts/naming_functions.sql | 31 +++++++++++++++++++ 7 files changed, 50 insertions(+), 42 deletions(-) create mode 100644 scripts/naming_functions.sql diff --git a/app/controllers/GenomeRegionsCuratorController.scala b/app/controllers/GenomeRegionsCuratorController.scala index 2cddb58..14f08d8 100644 --- a/app/controllers/GenomeRegionsCuratorController.scala +++ b/app/controllers/GenomeRegionsCuratorController.scala @@ -107,7 +107,7 @@ class GenomeRegionsCuratorController @Inject()( }, formData => { // Resolve contig to get build name and common name - genbankContigRepository.getById(formData.genbankContigId).flatMap { + genbankContigRepository.findById(formData.genbankContigId).flatMap { case Some(contig) => val build = contig.referenceGenome.getOrElse("unknown") val contigName = contig.commonName.getOrElse("unknown") @@ -180,7 +180,7 @@ class GenomeRegionsCuratorController @Inject()( } }, formData => { - genbankContigRepository.getById(formData.genbankContigId).flatMap { + genbankContigRepository.findById(formData.genbankContigId).flatMap { case Some(contig) => val build = contig.referenceGenome.getOrElse("unknown") val contigName = contig.commonName.getOrElse("unknown") diff --git a/app/models/dal/domain/genomics/GenomeRegionTables.scala b/app/models/dal/domain/genomics/GenomeRegionTables.scala index ba41e19..3c4895c 100644 --- a/app/models/dal/domain/genomics/GenomeRegionTables.scala +++ b/app/models/dal/domain/genomics/GenomeRegionTables.scala @@ -27,10 +27,15 @@ class GenomeRegionTable(tag: Tag) extends Table[GenomeRegion](tag, "genome_regio def id = column[Int]("region_id", O.PrimaryKey, O.AutoInc) // Column name changed to region_id def regionType = column[String]("region_type") def name = column[Option[String]]("name") - def coordinates = column[Map[String, RegionCoordinate]]("coordinates") + def coordinates = column[JsValue]("coordinates") def properties = column[JsValue]("properties") - def * = (id.?, regionType, name, coordinates, properties).mapTo[GenomeRegion] + def * = (id.?, regionType, name, coordinates, properties).<> ( + (t: (Option[Int], String, Option[String], JsValue, JsValue)) => GenomeRegion( + t._1, t._2, t._3, t._4.as[Map[String, RegionCoordinate]], t._5 + ), + (r: GenomeRegion) => Some((r.id, r.regionType, r.name, play.api.libs.json.Json.toJson(r.coordinates), r.properties)) + ) // No Foreign Key to Contig anymore, as coordinates are embedded } diff --git a/app/repositories/GenomeRegionsRepository.scala b/app/repositories/GenomeRegionsRepository.scala index bdc4293..a1a3aea 100644 --- a/app/repositories/GenomeRegionsRepository.scala +++ b/app/repositories/GenomeRegionsRepository.scala @@ -5,6 +5,7 @@ import models.dal.MyPostgresProfile import models.dal.MyPostgresProfile.api.* import models.domain.genomics.{GenbankContig, GenomeRegion, GenomeRegionVersion} import play.api.db.slick.{DatabaseConfigProvider, HasDatabaseConfigProvider} +import play.api.libs.json.Json import scala.concurrent.{ExecutionContext, Future} @@ -88,7 +89,7 @@ class GenomeRegionsRepositoryImpl @Inject()( override def getRegionsForBuild(referenceGenome: String): Future[Seq[GenomeRegion]] = { // Select regions where coordinates -> buildName exists val query = genomeRegions - .filter(r => (r.coordinates +> referenceGenome).isDefined) + .filter(r => r.coordinates ?? referenceGenome) .result db.run(query) } @@ -121,7 +122,7 @@ class GenomeRegionsRepositoryImpl @Inject()( } if (build.isDefined) { - query = query.filter(r => (r.coordinates +> build.get).isDefined) + query = query.filter(r => r.coordinates ?? build.get) } db.run(query.drop(offset).take(limit).result) @@ -135,7 +136,7 @@ class GenomeRegionsRepositoryImpl @Inject()( } if (build.isDefined) { - query = query.filter(r => (r.coordinates +> build.get).isDefined) + query = query.filter(r => r.coordinates ?? build.get) } db.run(query.length.result) @@ -148,7 +149,7 @@ class GenomeRegionsRepositoryImpl @Inject()( override def updateRegion(id: Int, region: GenomeRegion): Future[Boolean] = { val query = genomeRegions.filter(_.id === id).map(r => (r.regionType, r.name, r.coordinates, r.properties) - ).update((region.regionType, region.name, region.coordinates, region.properties)) + ).update((region.regionType, region.name, Json.toJson(region.coordinates), region.properties)) db.run(query).map(_ > 0) } diff --git a/app/views/curator/genomeregions/createForm.scala.html b/app/views/curator/genomeregions/createForm.scala.html index 8f78480..cd6c908 100644 --- a/app/views/curator/genomeregions/createForm.scala.html +++ b/app/views/curator/genomeregions/createForm.scala.html @@ -10,7 +10,7 @@ @@ -140,7 +140,7 @@
Create Genome Region
- + Cancel diff --git a/app/views/curator/genomeregions/editForm.scala.html b/app/views/curator/genomeregions/editForm.scala.html index b5a4f3d..2e373d8 100644 --- a/app/views/curator/genomeregions/editForm.scala.html +++ b/app/views/curator/genomeregions/editForm.scala.html @@ -10,7 +10,7 @@ @@ -138,7 +138,7 @@
Edit Genome Region #@id
- + Cancel diff --git a/conf/evolutions/default/54.sql b/conf/evolutions/default/54.sql index 9416204..644c7bf 100644 --- a/conf/evolutions/default/54.sql +++ b/conf/evolutions/default/54.sql @@ -1,38 +1,9 @@ # --- !Ups --- ============================================================================= --- DU Naming Authority: Sequence and function for DecodingUs variant names --- Per ISOGG guidelines: No zero padding (DU1, DU2, ... not DU00001) --- ============================================================================= - -- Sequence for DecodingUs variant names -CREATE SEQUENCE du_variant_name_seq START WITH 1; - --- Function to get next DU name (no zero padding per ISOGG request) -CREATE OR REPLACE FUNCTION next_du_name() RETURNS TEXT AS $$ -BEGIN - RETURN 'DU' || nextval('du_variant_name_seq')::TEXT; -END; -$$ LANGUAGE plpgsql; - --- Function to peek at current value without incrementing -CREATE OR REPLACE FUNCTION current_du_name() RETURNS TEXT AS $$ -BEGIN - RETURN 'DU' || currval('du_variant_name_seq')::TEXT; -END; -$$ LANGUAGE plpgsql; - --- Function to check if a name is a valid DU name -CREATE OR REPLACE FUNCTION is_du_name(name TEXT) RETURNS BOOLEAN AS $$ -BEGIN - RETURN name ~ '^DU[1-9][0-9]*$'; -END; -$$ LANGUAGE plpgsql; +CREATE SEQUENCE IF NOT EXISTS du_variant_name_seq START WITH 1; COMMENT ON SEQUENCE du_variant_name_seq IS 'Sequence for DecodingUs (DU) variant naming authority'; -COMMENT ON FUNCTION next_du_name() IS 'Returns next available DU name (e.g., DU1, DU2, DU123)'; -COMMENT ON FUNCTION current_du_name() IS 'Returns current DU name without incrementing sequence'; -COMMENT ON FUNCTION is_du_name(TEXT) IS 'Validates if a name follows DU naming convention'; # --- !Downs diff --git a/scripts/naming_functions.sql b/scripts/naming_functions.sql new file mode 100644 index 0000000..a1ae24b --- /dev/null +++ b/scripts/naming_functions.sql @@ -0,0 +1,31 @@ +-- ============================================================================= +-- DU Naming Authority: Sequence and function for DecodingUs variant names +-- Per ISOGG guidelines: No zero padding (DU1, DU2, ... not DU00001) +-- ============================================================================= + + + +-- Function to get next DU name (no zero padding per ISOGG request) +CREATE OR REPLACE FUNCTION next_du_name() RETURNS TEXT AS $func$ +BEGIN + RETURN 'DU' || nextval('du_variant_name_seq')::TEXT; +END; +$func$ LANGUAGE plpgsql; + +-- Function to peek at current value without incrementing +CREATE OR REPLACE FUNCTION current_du_name() RETURNS TEXT AS $func$ +BEGIN + RETURN 'DU' || currval('du_variant_name_seq')::TEXT; +END; +$func$ LANGUAGE plpgsql; + +-- Function to check if a name is a valid DU name +CREATE OR REPLACE FUNCTION is_du_name(name TEXT) RETURNS BOOLEAN AS $func$ +BEGIN + RETURN name ~ '^DU[1-9][0-9]*$'; +END; +$func$ LANGUAGE plpgsql; + +COMMENT ON FUNCTION next_du_name() IS 'Returns next available DU name (e.g., DU1, DU2, DU123)'; +COMMENT ON FUNCTION current_du_name() IS 'Returns current DU name without incrementing sequence'; +COMMENT ON FUNCTION is_du_name(TEXT) IS 'Validates if a name follows DU naming convention'; \ No newline at end of file From 50318168a4e1922e65f35e40d6229eceae9f5704 Mon Sep 17 00:00:00 2001 From: jkane Date: Sat, 13 Dec 2025 09:03:33 -0600 Subject: [PATCH 07/28] **refactor(views/utils): Centralize badge and variant rendering utilities** - Extracted reusable badge class and variant formatting logic into `CuratorViewUtils` and `VariantViewUtils`. - Updated multiple views to utilize the new utilities, reducing redundancy and improving maintainability. - Replaced inline helper methods with calls to centralized utility functions across various curator and variant templates. --- app/utils/CuratorViewUtils.scala | 21 ++++ app/utils/VariantViewUtils.scala | 62 ++++++++++ .../curator/audit/historyPanel.scala.html | 14 +-- .../haplogroups/detailPanel.scala.html | 14 +-- .../haplogroups/splitBranchForm.scala.html | 43 +------ .../variantHistoryPanel.scala.html | 14 +-- .../variantSearchResults.scala.html | 43 +------ .../haplogroups/variantsPanel.scala.html | 32 +----- .../curator/variants/detailPanel.scala.html | 88 +------------- .../curator/variants/listFragment.scala.html | 76 +++---------- app/views/fragments/pagination.scala.html | 34 ++++++ .../variant/referenceBuilds.scala.html | 54 +++++++++ app/views/variants/detailPanel.scala.html | 107 ++---------------- app/views/variants/listFragment.scala.html | 85 +++----------- 14 files changed, 237 insertions(+), 450 deletions(-) create mode 100644 app/utils/CuratorViewUtils.scala create mode 100644 app/utils/VariantViewUtils.scala create mode 100644 app/views/fragments/pagination.scala.html create mode 100644 app/views/fragments/variant/referenceBuilds.scala.html diff --git a/app/utils/CuratorViewUtils.scala b/app/utils/CuratorViewUtils.scala new file mode 100644 index 0000000..6139a2f --- /dev/null +++ b/app/utils/CuratorViewUtils.scala @@ -0,0 +1,21 @@ +package utils + +object CuratorViewUtils { + def actionBadgeClass(action: String): String = { + action match { + case "create" => "bg-success" + case "update" => "bg-warning text-dark" + case "delete" => "bg-danger" + case _ => "bg-secondary" + } + } + + def changeTypeBadgeClass(changeType: String): String = { + changeType match { + case "add" => "bg-success" + case "remove" => "bg-danger" + case "update" => "bg-warning text-dark" + case _ => "bg-secondary" + } + } +} \ No newline at end of file diff --git a/app/utils/VariantViewUtils.scala b/app/utils/VariantViewUtils.scala new file mode 100644 index 0000000..b9aa57c --- /dev/null +++ b/app/utils/VariantViewUtils.scala @@ -0,0 +1,62 @@ +package utils + +import models.domain.genomics.VariantV2 +import play.api.libs.json.JsObject + +object VariantViewUtils { + def refGenomes(v: VariantV2): Seq[String] = { + v.coordinates.asOpt[Map[String, JsObject]].map(_.keys.toSeq.sorted).getOrElse(Seq.empty) + } + + def formatPosition(v: VariantV2, refGenome: String): String = { + v.getCoordinates(refGenome).map { coords => + val contig = (coords \ "contig").asOpt[String].getOrElse("?") + val pos = (coords \ "position").asOpt[Int].getOrElse(0) + s"$contig:$pos" + }.getOrElse("-") + } + + def formatAlleles(v: VariantV2, refGenome: String): String = { + v.getCoordinates(refGenome).map { coords => + val ref = (coords \ "ref").asOpt[String].getOrElse("?") + val alt = (coords \ "alt").asOpt[String].getOrElse("?") + s"$ref→$alt" + }.getOrElse("-") + } + + def formatAllelesTuple(v: VariantV2, refGenome: String): (String, String) = { + v.getCoordinates(refGenome).map { coords => + val ref = (coords \ "ref").asOpt[String].getOrElse("?") + val alt = (coords \ "alt").asOpt[String].getOrElse("?") + (ref, alt) + }.getOrElse(("?", "?")) + } + + def primaryAlleles(v: VariantV2): (String, String) = { + val coords = v.coordinates.asOpt[Map[String, JsObject]].getOrElse(Map.empty) + val primary = coords.get("hs1").orElse(coords.get("GRCh38")).orElse(coords.headOption.map(_._2)) + primary.map { c => + val ref = (c \ "ref").asOpt[String].getOrElse("?") + val alt = (c \ "alt").asOpt[String].getOrElse("?") + (ref, alt) + }.getOrElse(("?", "?")) + } + + def buildBadgeClass(refGenome: String): String = { + refGenome match { + case "GRCh37" => "bg-warning text-dark" + case "GRCh38" => "bg-info" + case "hs1" => "bg-success" + case _ => "bg-secondary" + } + } + + def shortRefGenome(refGenome: String): String = { + refGenome match { + case "GRCh37" => "GRCh37" + case "GRCh38" => "GRCh38" + case "hs1" => "T2T" + case other => other + } + } +} diff --git a/app/views/curator/audit/historyPanel.scala.html b/app/views/curator/audit/historyPanel.scala.html index dcbeded..75738fe 100644 --- a/app/views/curator/audit/historyPanel.scala.html +++ b/app/views/curator/audit/historyPanel.scala.html @@ -1,5 +1,6 @@ @import models.domain.curator.AuditLogEntry @import play.api.libs.json.Json +@import utils.CuratorViewUtils @(entityType: String, entityId: Int, history: Seq[AuditLogEntry])(implicit request: RequestHeader)
@@ -15,7 +16,7 @@
Audit History
@for(entry <- history) {
- @entry.action + @entry.action @entry.createdAt.toLocalDate @entry.createdAt.toLocalTime.toString.take(5)
@@ -75,13 +76,4 @@
Audit History
}
- - -@actionBadgeClass(action: String) = @{ - action match { - case "create" => "bg-success" - case "update" => "bg-warning text-dark" - case "delete" => "bg-danger" - case _ => "bg-secondary" - } -} + \ No newline at end of file diff --git a/app/views/curator/haplogroups/detailPanel.scala.html b/app/views/curator/haplogroups/detailPanel.scala.html index 21e938d..91304de 100644 --- a/app/views/curator/haplogroups/detailPanel.scala.html +++ b/app/views/curator/haplogroups/detailPanel.scala.html @@ -1,6 +1,7 @@ @import models.domain.haplogroups.Haplogroup @import models.domain.genomics.VariantV2 @import models.domain.curator.AuditLogEntry +@import utils.CuratorViewUtils @(haplogroup: Haplogroup, parentOpt: Option[Haplogroup], children: Seq[Haplogroup], variants: Seq[VariantV2], history: Seq[AuditLogEntry])(implicit request: RequestHeader)
@@ -186,7 +187,7 @@
Recent History
    @for(entry <- history.take(5)) {
  • - @entry.action + @entry.action @entry.createdAt.toLocalDate @entry.comment.map { c =>
    @c }
    • @@ -202,13 +203,4 @@
    Recent History
    } }
- - -@actionBadgeClass(action: String) = @{ - action match { - case "create" => "bg-success" - case "update" => "bg-warning text-dark" - case "delete" => "bg-danger" - case _ => "bg-secondary" - } -} + \ No newline at end of file diff --git a/app/views/curator/haplogroups/splitBranchForm.scala.html b/app/views/curator/haplogroups/splitBranchForm.scala.html index bf449a2..4a65444 100644 --- a/app/views/curator/haplogroups/splitBranchForm.scala.html +++ b/app/views/curator/haplogroups/splitBranchForm.scala.html @@ -3,31 +3,9 @@ @import models.domain.haplogroups.Haplogroup @import models.domain.genomics.VariantV2 @import play.api.libs.json.JsObject +@import utils.VariantViewUtils @(parent: Haplogroup, variants: Seq[VariantV2], children: Seq[Haplogroup], form: Form[SplitBranchFormData])(implicit request: RequestHeader, messages: Messages, webJarsUtil: WebJarsUtil) -@* Helper to extract reference genomes from coordinates *@ -@refGenomes(v: VariantV2) = @{ - v.coordinates.asOpt[Map[String, JsObject]].map(_.keys.toSeq.sorted).getOrElse(Seq.empty) -} - -@* Helper to format position for a specific reference *@ -@formatPosition(v: VariantV2, refGenome: String) = @{ - v.getCoordinates(refGenome).map { coords => - val contig = (coords \ "contig").asOpt[String].getOrElse("?") - val pos = (coords \ "position").asOpt[Int].getOrElse(0) - s"$contig:$pos" - }.getOrElse("-") -} - -@* Helper to format alleles for a specific reference *@ -@formatAlleles(v: VariantV2, refGenome: String) = @{ - v.getCoordinates(refGenome).map { coords => - val ref = (coords \ "ref").asOpt[String].getOrElse("?") - val alt = (coords \ "alt").asOpt[String].getOrElse("?") - s"$ref→$alt" - }.getOrElse("-") -} - @main(s"Split ${parent.name}") {
@@ -127,7 +105,7 @@
@for(variant <- variants) { - @defining(refGenomes(variant)) { refs => + @defining(VariantViewUtils.refGenomes(variant)) { refs =>
@refs.size build@if(refs.size != 1){s}
@for(refGenome <- refs) { - @refGenome - @formatPosition(variant, refGenome) - @Html(formatAlleles(variant, refGenome)) + @refGenome + @VariantViewUtils.formatPosition(variant, refGenome) + @Html(VariantViewUtils.formatAlleles(variant, refGenome)) }
@@ -203,13 +181,4 @@
-} - -@buildBadgeClass(refGenome: String) = @{ - refGenome match { - case "GRCh37" => "bg-warning text-dark" - case "GRCh38" => "bg-info" - case "hs1" => "bg-success" - case _ => "bg-secondary" - } -} +} \ No newline at end of file diff --git a/app/views/curator/haplogroups/variantHistoryPanel.scala.html b/app/views/curator/haplogroups/variantHistoryPanel.scala.html index b1409ed..3836497 100644 --- a/app/views/curator/haplogroups/variantHistoryPanel.scala.html +++ b/app/views/curator/haplogroups/variantHistoryPanel.scala.html @@ -1,4 +1,5 @@ @import models.domain.haplogroups.HaplogroupVariantMetadata +@import utils.CuratorViewUtils @(haplogroupVariantId: Int, history: Seq[HaplogroupVariantMetadata])(implicit request: RequestHeader)
@@ -14,7 +15,7 @@
Haplogroup-Variant History<
  • - @entry.change_type + @entry.change_type Revision @entry.revision_id
    @entry.timestamp.toLocalDate @@ -30,13 +31,4 @@
    Haplogroup-Variant History< }
    -
    • - -@changeTypeBadgeClass(changeType: String) = @{ - changeType match { - case "add" => "bg-success" - case "remove" => "bg-danger" - case "update" => "bg-warning text-dark" - case _ => "bg-secondary" - } -} +
    \ No newline at end of file diff --git a/app/views/curator/haplogroups/variantSearchResults.scala.html b/app/views/curator/haplogroups/variantSearchResults.scala.html index 82ed43a..79c5923 100644 --- a/app/views/curator/haplogroups/variantSearchResults.scala.html +++ b/app/views/curator/haplogroups/variantSearchResults.scala.html @@ -1,30 +1,8 @@ @import models.domain.genomics.VariantV2 @import play.api.libs.json.JsObject +@import utils.VariantViewUtils @(haplogroupId: Int, haplogroupName: String, query: Option[String], variants: Seq[VariantV2])(implicit request: RequestHeader) -@* Helper to extract reference genomes from coordinates *@ -@refGenomes(v: VariantV2) = @{ - v.coordinates.asOpt[Map[String, JsObject]].map(_.keys.toSeq.sorted).getOrElse(Seq.empty) -} - -@* Helper to format position for a specific reference *@ -@formatPosition(v: VariantV2, refGenome: String) = @{ - v.getCoordinates(refGenome).map { coords => - val contig = (coords \ "contig").asOpt[String].getOrElse("?") - val pos = (coords \ "position").asOpt[Int].getOrElse(0) - s"$contig:$pos" - }.getOrElse("-") -} - -@* Helper to format alleles for a specific reference *@ -@formatAlleles(v: VariantV2, refGenome: String) = @{ - v.getCoordinates(refGenome).map { coords => - val ref = (coords \ "ref").asOpt[String].getOrElse("?") - val alt = (coords \ "alt").asOpt[String].getOrElse("?") - s"$ref→$alt" - }.getOrElse("-") -} -
    @for(variant <- variants.take(10)) { - @defining(refGenomes(variant)) { refs => + @defining(VariantViewUtils.refGenomes(variant)) { refs =>
    @@ -70,9 +48,9 @@
    @for(refGenome <- refs) {
    - @refGenome - @formatPosition(variant, refGenome) - @Html(formatAlleles(variant, refGenome)) + @refGenome + @VariantViewUtils.formatPosition(variant, refGenome) + @Html(VariantViewUtils.formatAlleles(variant, refGenome))
    }
    @@ -90,13 +68,4 @@
    Start typing to search for variants...
    -} - -@buildBadgeClass(refGenome: String) = @{ - refGenome match { - case "GRCh37" => "bg-warning text-dark" - case "GRCh38" => "bg-info" - case "hs1" => "bg-success" - case _ => "bg-secondary" - } -} +} \ No newline at end of file diff --git a/app/views/curator/haplogroups/variantsPanel.scala.html b/app/views/curator/haplogroups/variantsPanel.scala.html index 37f987c..3fa3f04 100644 --- a/app/views/curator/haplogroups/variantsPanel.scala.html +++ b/app/views/curator/haplogroups/variantsPanel.scala.html @@ -1,30 +1,8 @@ @import models.domain.genomics.VariantV2 @import play.api.libs.json.JsObject +@import utils.VariantViewUtils @(haplogroupId: Int, variants: Seq[VariantV2])(implicit request: RequestHeader) -@* Helper to extract reference genomes from coordinates *@ -@refGenomes(v: VariantV2) = @{ - v.coordinates.asOpt[Map[String, JsObject]].map(_.keys.toSeq.sorted).getOrElse(Seq.empty) -} - -@* Helper to format position for a specific reference *@ -@formatPosition(v: VariantV2, refGenome: String) = @{ - v.getCoordinates(refGenome).map { coords => - val contig = (coords \ "contig").asOpt[String].getOrElse("?") - val pos = (coords \ "position").asOpt[Int].getOrElse(0) - s"$contig:$pos" - }.getOrElse("-") -} - -@* Helper to format alleles for a specific reference *@ -@formatAlleles(v: VariantV2, refGenome: String) = @{ - v.getCoordinates(refGenome).map { coords => - val ref = (coords \ "ref").asOpt[String].getOrElse("?") - val alt = (coords \ "alt").asOpt[String].getOrElse("?") - s"$ref→$alt" - }.getOrElse("-") -} -
    Defining Variants @@ -55,7 +33,7 @@
      @for(variant <- variants) { - @defining(refGenomes(variant)) { refs => + @defining(VariantViewUtils.refGenomes(variant)) { refs =>
    • @@ -79,8 +57,8 @@
      @for(refGenome <- refs) {
      @refGenome - @formatPosition(variant, refGenome) - @Html(formatAlleles(variant, refGenome)) + @VariantViewUtils.formatPosition(variant, refGenome) + @Html(VariantViewUtils.formatAlleles(variant, refGenome))
      }
      @@ -146,4 +124,4 @@
    -
    +
    \ No newline at end of file diff --git a/app/views/curator/variants/detailPanel.scala.html b/app/views/curator/variants/detailPanel.scala.html index 7a441cd..8a9a543 100644 --- a/app/views/curator/variants/detailPanel.scala.html +++ b/app/views/curator/variants/detailPanel.scala.html @@ -2,46 +2,13 @@ @import models.domain.haplogroups.Haplogroup @import models.domain.curator.AuditLogEntry @import play.api.libs.json.JsObject -@(variant: VariantV2, haplogroups: Seq[Haplogroup], history: Seq[AuditLogEntry])(implicit request: RequestHeader) - -@* Helper to extract reference genomes from coordinates *@ -@refGenomes = @{ - variant.coordinates.asOpt[Map[String, JsObject]].map(_.keys.toSeq.sorted).getOrElse(Seq.empty) -} - -@* Helper to format position for a specific reference *@ -@formatPosition(refGenome: String) = @{ - variant.getCoordinates(refGenome).map { coords => - val contig = (coords \ "contig").asOpt[String].getOrElse("?") - val pos = (coords \ "position").asOpt[Int].getOrElse(0) - s"$contig:$pos" - }.getOrElse("-") -} - -@* Helper to format alleles for a specific reference *@ -@formatAlleles(refGenome: String) = @{ - variant.getCoordinates(refGenome).map { coords => - val ref = (coords \ "ref").asOpt[String].getOrElse("?") - val alt = (coords \ "alt").asOpt[String].getOrElse("?") - s"$ref→$alt" - }.getOrElse("-") -} - -@* Helper to get primary alleles (prefer hs1, then GRCh38) *@ -@primaryAlleles = @{ - val coords = variant.coordinates.asOpt[Map[String, JsObject]].getOrElse(Map.empty) - val primary = coords.get("hs1").orElse(coords.get("GRCh38")).orElse(coords.headOption.map(_._2)) - primary.map { c => - val ref = (c \ "ref").asOpt[String].getOrElse("?") - val alt = (c \ "alt").asOpt[String].getOrElse("?") - (ref, alt) - }.getOrElse(("?", "?")) -} +@import utils.{CuratorViewUtils, VariantViewUtils} +@(variant: VariantV2, haplogroups: Seq[Haplogroup], history: Seq[AuditLogEntry])(implicit request: RequestHeader, messages: Messages)
    @variant.displayName
    - @variant.mutationType + @variant.mutationType.displayName
    @@ -57,7 +24,7 @@
    @variant.displayName
    } else { - } - @defining(primaryAlleles) { alleles => + @defining(VariantViewUtils.primaryAlleles(variant)) { alleles =>
    Ancestral
    @alleles._1
    @@ -89,32 +56,7 @@
    Alternative Names
    Reference Builds
    - @if(refGenomes.isEmpty) { -

    No coordinates available.

    - } else { -
    - - - - - - - - - - @for(ref <- refGenomes) { - - - - - - } - -
    BuildPositionAlleles
    - @ref - @formatPosition(ref)@Html(formatAlleles(ref))
    -
    - } + @views.html.fragments.variant.referenceBuilds(variant)
    @@ -164,7 +106,7 @@
    Recent History
      @for(entry <- history.take(5)) {
    • - @entry.action + @entry.action @entry.createdAt.toLocalDate @entry.comment.map { c =>
      @c }
      • @@ -181,21 +123,3 @@
      Recent History
      }
    - -@buildBadgeClass(refGenome: String) = @{ - refGenome match { - case "GRCh37" => "bg-warning text-dark" - case "GRCh38" => "bg-info" - case "hs1" => "bg-success" - case _ => "bg-secondary" - } -} - -@actionBadgeClass(action: String) = @{ - action match { - case "create" => "bg-success" - case "update" => "bg-warning text-dark" - case "delete" => "bg-danger" - case _ => "bg-secondary" - } -} diff --git a/app/views/curator/variants/listFragment.scala.html b/app/views/curator/variants/listFragment.scala.html index 2570c00..dbb9f12 100644 --- a/app/views/curator/variants/listFragment.scala.html +++ b/app/views/curator/variants/listFragment.scala.html @@ -1,22 +1,6 @@ @import models.domain.genomics.VariantV2 -@import play.api.libs.json.JsObject -@(variants: Seq[VariantV2], query: Option[String], currentPage: Int, totalPages: Int, pageSize: Int, totalCount: Int)(implicit request: RequestHeader) - -@* Helper to extract reference genomes from coordinates *@ -@refGenomes(v: VariantV2) = @{ - v.coordinates.asOpt[Map[String, JsObject]].map(_.keys.toSeq.sorted).getOrElse(Seq.empty) -} - -@* Helper to get alleles from primary reference (prefer hs1, then GRCh38) *@ -@primaryAlleles(v: VariantV2) = @{ - val coords = v.coordinates.asOpt[Map[String, JsObject]].getOrElse(Map.empty) - val primary = coords.get("hs1").orElse(coords.get("GRCh38")).orElse(coords.headOption.map(_._2)) - primary.map { c => - val ref = (c \ "ref").asOpt[String].getOrElse("?") - val alt = (c \ "alt").asOpt[String].getOrElse("?") - (ref, alt) - }.getOrElse(("?", "?")) -} +@import utils.VariantViewUtils +@(variants: Seq[VariantV2], query: Option[String], currentPage: Int, totalPages: Int, pageSize: Int, totalCount: Int)(implicit request: RequestHeader, messages: Messages) @defining(java.text.NumberFormat.getIntegerInstance()) { nf =>
    @@ -55,8 +39,8 @@ @for(variant <- variants) { - @defining(primaryAlleles(variant)) { alleles => - @defining(refGenomes(variant)) { refs => + @defining(VariantViewUtils.primaryAlleles(variant)) { alleles => + @defining(VariantViewUtils.refGenomes(variant)) { refs => @for(refGenome <- refs) { - + @refGenome } @@ -96,45 +80,11 @@
    - @if(totalPages > 1) { - - } -} - -@buildBadgeClass(refGenome: String) = @{ - refGenome match { - case "GRCh37" => "bg-warning text-dark" - case "GRCh38" => "bg-info" - case "hs1" => "bg-success" - case _ => "bg-secondary" - } -} + @views.html.fragments.pagination( + currentPage, + totalPages, + p => controllers.routes.CuratorController.variantsFragment(query, p, pageSize), + "#variants-table", + "#variant-search" + ) +} \ No newline at end of file diff --git a/app/views/fragments/pagination.scala.html b/app/views/fragments/pagination.scala.html new file mode 100644 index 0000000..4fe7eb1 --- /dev/null +++ b/app/views/fragments/pagination.scala.html @@ -0,0 +1,34 @@ +@(currentPage: Int, totalPages: Int, pageCall: Int => play.api.mvc.Call, target: String, include: String)(implicit messages: Messages) + +@if(totalPages > 1) { + +} diff --git a/app/views/fragments/variant/referenceBuilds.scala.html b/app/views/fragments/variant/referenceBuilds.scala.html new file mode 100644 index 0000000..8fff0f9 --- /dev/null +++ b/app/views/fragments/variant/referenceBuilds.scala.html @@ -0,0 +1,54 @@ +@import models.domain.genomics.VariantV2 +@import utils.VariantViewUtils +@(variant: VariantV2)(implicit messages: Messages) + +@defining(VariantViewUtils.refGenomes(variant)) { refs => + @if(refs.size > 1) { +
    + + + + + + + + + + @for(refGenome <- refs) { + @defining(VariantViewUtils.formatAllelesTuple(variant, refGenome)) { alleles => + + + + + + } + } + +
    @messages("variants.detail.build")@messages("variants.detail.position")@messages("variants.detail.alleles")
    + + @VariantViewUtils.shortRefGenome(refGenome) + + @VariantViewUtils.formatPosition(variant, refGenome) + @alleles._1 + + @alleles._2 +
    +
    + } else if(refs.nonEmpty) { + @defining(refs.head) { refGenome => + @defining(VariantViewUtils.formatAllelesTuple(variant, refGenome)) { alleles => +
    + @VariantViewUtils.shortRefGenome(refGenome) + @VariantViewUtils.formatPosition(variant, refGenome) + + @alleles._1 + + @alleles._2 + +
    + } + } + } else { +

    @messages("variants.detail.noCoordinates")

    + } +} diff --git a/app/views/variants/detailPanel.scala.html b/app/views/variants/detailPanel.scala.html index 7e538f3..68f87c7 100644 --- a/app/views/variants/detailPanel.scala.html +++ b/app/views/variants/detailPanel.scala.html @@ -1,31 +1,9 @@ @import models.domain.genomics.{NamingStatus, VariantV2} @import models.domain.haplogroups.Haplogroup @import play.api.libs.json.JsObject +@import utils.VariantViewUtils @(variant: VariantV2, haplogroups: Seq[Haplogroup])(implicit request: RequestHeader, messages: Messages) -@* Helper to extract reference genomes from coordinates *@ -@refGenomes = @{ - variant.coordinates.asOpt[Map[String, JsObject]].map(_.keys.toSeq.sorted).getOrElse(Seq.empty) -} - -@* Helper to format position for a specific reference *@ -@formatPosition(refGenome: String) = @{ - variant.getCoordinates(refGenome).map { coords => - val contig = (coords \ "contig").asOpt[String].getOrElse("?") - val pos = (coords \ "position").asOpt[Int].getOrElse(0) - s"$contig:$pos" - }.getOrElse("-") -} - -@* Helper to format alleles for a specific reference *@ -@formatAlleles(refGenome: String) = @{ - variant.getCoordinates(refGenome).map { coords => - val ref = (coords \ "ref").asOpt[String].getOrElse("?") - val alt = (coords \ "alt").asOpt[String].getOrElse("?") - (ref, alt) - }.getOrElse(("?", "?")) -} -
    @variant.displayName
    @@ -43,14 +21,12 @@
    @variant.displayName
    @messages("variants.detail.commonName")
    @variant.canonicalName.getOrElse("-")
    - @defining(variant.getCoordinates("hs1").orElse(variant.getCoordinates("GRCh38"))) { primaryCoords => - @primaryCoords.map { coords => -
    @messages("variants.detail.ancestral")
    -
    @((coords \ "ref").asOpt[String].getOrElse("?"))
    + @defining(VariantViewUtils.primaryAlleles(variant)) { alleles => +
    @messages("variants.detail.ancestral")
    +
    @alleles._1
    -
    @messages("variants.detail.derived")
    -
    @((coords \ "alt").asOpt[String].getOrElse("?"))
    - } +
    @messages("variants.detail.derived")
    +
    @alleles._2
    }
    @messages("variants.detail.type")
    @@ -90,56 +66,7 @@
    @messages("variants.detail.altNames")
    @messages("variants.detail.refBuilds")
    - @defining(refGenomes) { refs => - @if(refs.size > 1) { -
    - - - - - - - - - - @for(refGenome <- refs) { - @defining(formatAlleles(refGenome)) { alleles => - - - - - - } - } - -
    @messages("variants.detail.build")@messages("variants.detail.position")@messages("variants.detail.alleles")
    - - @shortRefGenome(refGenome) - - @formatPosition(refGenome) - @alleles._1 - - @alleles._2 -
    -
    - } else if(refs.nonEmpty) { - @defining(refs.head) { refGenome => - @defining(formatAlleles(refGenome)) { alleles => -
    - @shortRefGenome(refGenome) - @formatPosition(refGenome) - - @alleles._1 - - @alleles._2 - -
    - } - } - } else { -

    @messages("variants.detail.noCoordinates")

    - } - } + @views.html.fragments.variant.referenceBuilds(variant)
    @@ -168,22 +95,4 @@
    @messages("variants.detail.notes")

    @notes

    }
    -
    - -@buildBadgeClass(refGenome: String) = @{ - refGenome match { - case "GRCh37" => "bg-warning text-dark" - case "GRCh38" => "bg-info" - case "hs1" => "bg-success" - case _ => "bg-secondary" - } -} - -@shortRefGenome(refGenome: String) = @{ - refGenome match { - case "GRCh37" => "GRCh37" - case "GRCh38" => "GRCh38" - case "hs1" => "T2T" - case other => other - } -} +
    \ No newline at end of file diff --git a/app/views/variants/listFragment.scala.html b/app/views/variants/listFragment.scala.html index 68e97a8..0b85699 100644 --- a/app/views/variants/listFragment.scala.html +++ b/app/views/variants/listFragment.scala.html @@ -1,23 +1,7 @@ @import models.domain.genomics.VariantV2 -@import play.api.libs.json.JsObject +@import utils.VariantViewUtils @(variants: Seq[VariantV2], query: Option[String], currentPage: Int, totalPages: Int, pageSize: Int, totalCount: Int)(implicit request: RequestHeader, messages: Messages) -@* Helper to extract reference genomes from coordinates *@ -@refGenomes(v: VariantV2) = @{ - v.coordinates.asOpt[Map[String, JsObject]].map(_.keys.toSeq.sorted).getOrElse(Seq.empty) -} - -@* Helper to get alleles from primary reference (prefer hs1, then GRCh38) *@ -@primaryAlleles(v: VariantV2) = @{ - val coords = v.coordinates.asOpt[Map[String, JsObject]].getOrElse(Map.empty) - val primary = coords.get("hs1").orElse(coords.get("GRCh38")).orElse(coords.headOption.map(_._2)) - primary.map { c => - val ref = (c \ "ref").asOpt[String].getOrElse("?") - val alt = (c \ "alt").asOpt[String].getOrElse("?") - (ref, alt) - }.getOrElse(("?", "?")) -} - @defining(java.text.NumberFormat.getIntegerInstance()) { nf =>
    @@ -54,8 +38,8 @@ @for(variant <- variants) { - @defining(primaryAlleles(variant)) { alleles => - @defining(refGenomes(variant)) { refs => + @defining(VariantViewUtils.primaryAlleles(variant)) { alleles => + @defining(VariantViewUtils.refGenomes(variant)) { refs => @for(refGenome <- refs) { - - @shortRefGenome(refGenome) + + @VariantViewUtils.shortRefGenome(refGenome) } @@ -88,54 +72,11 @@
    - @if(totalPages > 1) { - - } -} - -@buildBadgeClass(refGenome: String) = @{ - refGenome match { - case "GRCh37" => "bg-warning text-dark" - case "GRCh38" => "bg-info" - case "hs1" => "bg-success" - case _ => "bg-secondary" - } -} - -@shortRefGenome(refGenome: String) = @{ - refGenome match { - case "GRCh37" => "GRCh37" - case "GRCh38" => "GRCh38" - case "hs1" => "T2T" - case other => other - } -} + @views.html.fragments.pagination( + currentPage, + totalPages, + p => controllers.routes.VariantBrowserController.listFragment(query, p, pageSize), + "#variants-table", + "#variant-search" + ) +} \ No newline at end of file From 87350f536162f58448589a7418035d24f03459b3 Mon Sep 17 00:00:00 2001 From: jkane Date: Sat, 13 Dec 2025 09:12:48 -0600 Subject: [PATCH 08/28] **refactor(views): Extract and reuse breadcrumb, flash message, and search input components** - Added reusable templates for breadcrumbs, flash messages, and search inputs in `fragments`. - Updated variant browser and curator views to utilize the new components, reducing redundancy. - Simplified and centralized layout structures for improved maintainability. --- .../genomeregions/createForm.scala.html | 20 +++------ .../curator/genomeregions/editForm.scala.html | 20 +++------ .../curator/genomeregions/list.scala.html | 24 +++------- .../curator/haplogroups/createForm.scala.html | 16 +++---- .../curator/haplogroups/editForm.scala.html | 14 +++--- app/views/curator/haplogroups/list.scala.html | 42 ++++++------------ .../curator/variants/createForm.scala.html | 14 +++--- .../curator/variants/editForm.scala.html | 14 +++--- app/views/curator/variants/list.scala.html | 42 ++++++------------ app/views/fragments/breadcrumbs.scala.html | 13 ++++++ app/views/fragments/flashMessages.scala.html | 29 ++++++++++++ app/views/fragments/searchInput.scala.html | 39 ++++++++++++++++ app/views/references.scala.html | 44 +++++-------------- app/views/variants/browser.scala.html | 25 ++++------- 14 files changed, 169 insertions(+), 187 deletions(-) create mode 100644 app/views/fragments/breadcrumbs.scala.html create mode 100644 app/views/fragments/flashMessages.scala.html create mode 100644 app/views/fragments/searchInput.scala.html diff --git a/app/views/curator/genomeregions/createForm.scala.html b/app/views/curator/genomeregions/createForm.scala.html index cd6c908..a00ea0d 100644 --- a/app/views/curator/genomeregions/createForm.scala.html +++ b/app/views/curator/genomeregions/createForm.scala.html @@ -7,13 +7,11 @@
    - + @views.html.fragments.breadcrumbs(Seq( + ("Curator", controllers.routes.CuratorController.dashboard), + ("Genome Regions", controllers.routes.GenomeRegionsCuratorController.listRegions(None, None, 1, 25)), + ("Create", controllers.routes.GenomeRegionsCuratorController.createRegionForm) + ))
    @@ -24,13 +22,7 @@
    Create Genome Region
    - @if(form.hasGlobalErrors) { -
    - @for(error <- form.globalErrors) { - @error.message - } -
    - } + @views.html.fragments.flashMessages(request.flash, Some(form)) @helper.form(action = controllers.routes.GenomeRegionsCuratorController.createRegion, Symbol("class") -> "needs-validation") { @helper.CSRF.formField diff --git a/app/views/curator/genomeregions/editForm.scala.html b/app/views/curator/genomeregions/editForm.scala.html index 2e373d8..20ad415 100644 --- a/app/views/curator/genomeregions/editForm.scala.html +++ b/app/views/curator/genomeregions/editForm.scala.html @@ -7,13 +7,11 @@
    - + @views.html.fragments.breadcrumbs(Seq( + ("Curator", controllers.routes.CuratorController.dashboard), + ("Genome Regions", controllers.routes.GenomeRegionsCuratorController.listRegions(None, None, 1, 25)), + ("Edit", controllers.routes.GenomeRegionsCuratorController.editRegionForm(id)) + ))
    @@ -24,13 +22,7 @@
    Edit Genome Region #@id
    - @if(form.hasGlobalErrors) { -
    - @for(error <- form.globalErrors) { - @error.message - } -
    - } + @views.html.fragments.flashMessages(request.flash, Some(form)) @helper.form(action = controllers.routes.GenomeRegionsCuratorController.updateRegion(id), Symbol("class") -> "needs-validation") { @helper.CSRF.formField diff --git a/app/views/curator/genomeregions/list.scala.html b/app/views/curator/genomeregions/list.scala.html index 8be6de5..bb50f80 100644 --- a/app/views/curator/genomeregions/list.scala.html +++ b/app/views/curator/genomeregions/list.scala.html @@ -14,28 +14,14 @@
    - + @views.html.fragments.breadcrumbs(Seq( + ("Curator", controllers.routes.CuratorController.dashboard), + ("Genome Regions", controllers.routes.GenomeRegionsCuratorController.listRegions(None, None, 1, 25)) + ))
    - @request.flash.get("success").map { msg => - - } - - @request.flash.get("error").map { msg => - - } + @views.html.fragments.flashMessages(request.flash)
    diff --git a/app/views/curator/haplogroups/createForm.scala.html b/app/views/curator/haplogroups/createForm.scala.html index 55bb145..1c4c3e3 100644 --- a/app/views/curator/haplogroups/createForm.scala.html +++ b/app/views/curator/haplogroups/createForm.scala.html @@ -7,22 +7,18 @@
    - + @views.html.fragments.breadcrumbs(Seq( + ("Curator", controllers.routes.CuratorController.dashboard), + ("Haplogroups", controllers.routes.CuratorController.listHaplogroups(None, None, 1, 20)), + ("Create", controllers.routes.CuratorController.createHaplogroupForm) + ))
    Create Haplogroup
    - @form.globalError.map { error => -
    @error.message
    - } + @views.html.fragments.flashMessages(request.flash, Some(form))
    Creation Rules: diff --git a/app/views/curator/haplogroups/editForm.scala.html b/app/views/curator/haplogroups/editForm.scala.html index afc0ada..1a5b531 100644 --- a/app/views/curator/haplogroups/editForm.scala.html +++ b/app/views/curator/haplogroups/editForm.scala.html @@ -6,13 +6,11 @@
    - + @views.html.fragments.breadcrumbs(Seq( + ("Curator", controllers.routes.CuratorController.dashboard), + ("Haplogroups", controllers.routes.CuratorController.listHaplogroups(None, None, 1, 20)), + ("Edit", controllers.routes.CuratorController.editHaplogroupForm(id)) + ))
    @@ -23,6 +21,8 @@
    Edit Haplogroup
    + @views.html.fragments.flashMessages(request.flash, Some(form)) + @helper.form(controllers.routes.CuratorController.updateHaplogroup(id)) { @helper.CSRF.formField diff --git a/app/views/curator/haplogroups/list.scala.html b/app/views/curator/haplogroups/list.scala.html index a8b827e..23a2b81 100644 --- a/app/views/curator/haplogroups/list.scala.html +++ b/app/views/curator/haplogroups/list.scala.html @@ -13,21 +13,14 @@
    - + @views.html.fragments.breadcrumbs(Seq( + ("Curator", controllers.routes.CuratorController.dashboard), + ("Haplogroups", controllers.routes.CuratorController.listHaplogroups(None, None, 1, 20)) + ))
    - @request.flash.get("success").map { msg => - - } + @views.html.fragments.flashMessages(request.flash)
    @@ -41,23 +34,14 @@
    Haplogroups
    - + @views.html.fragments.searchInput( + id = "haplogroup-search", + name = "query", + value = query, + placeholder = "Search haplogroups...", + hxGet = controllers.routes.CuratorController.haplogroupsFragment(None, hgType, 1, pageSize), + hxTarget = "#haplogroups-table" + )
    -
    + @views.html.fragments.searchInput( + id = "variant-search", + name = "query", + value = query, + placeholder = "Search by rsId or common name...", + hxGet = controllers.routes.CuratorController.variantsFragment(None, 1, pageSize), + hxTarget = "#variants-table" + )
    diff --git a/app/views/fragments/breadcrumbs.scala.html b/app/views/fragments/breadcrumbs.scala.html new file mode 100644 index 0000000..036fe12 --- /dev/null +++ b/app/views/fragments/breadcrumbs.scala.html @@ -0,0 +1,13 @@ +@(crumbs: Seq[(String, play.api.mvc.Call)]) + + diff --git a/app/views/fragments/flashMessages.scala.html b/app/views/fragments/flashMessages.scala.html new file mode 100644 index 0000000..057ae4a --- /dev/null +++ b/app/views/fragments/flashMessages.scala.html @@ -0,0 +1,29 @@ +@(flash: Flash, form: Option[Form[?]] = None)(implicit messages: Messages) + +@flash.get("success").map { msg => + +} + +@flash.get("error").map { msg => + +} + +@form.map { f => + @if(f.hasGlobalErrors) { + + } +} diff --git a/app/views/fragments/searchInput.scala.html b/app/views/fragments/searchInput.scala.html new file mode 100644 index 0000000..db37684 --- /dev/null +++ b/app/views/fragments/searchInput.scala.html @@ -0,0 +1,39 @@ +@( + id: String, + name: String, + value: Option[String], + placeholder: String, + hxGet: play.api.mvc.Call, + hxTarget: String, + hxIndicator: String = "", + hxTrigger: String = "input changed delay:300ms, search" +)(implicit messages: Messages) + +
    + + + + + + @if(value.exists(_.nonEmpty)) { + + } +
    diff --git a/app/views/references.scala.html b/app/views/references.scala.html index fdb1c24..5bbb5d4 100644 --- a/app/views/references.scala.html +++ b/app/views/references.scala.html @@ -45,32 +45,16 @@
    - + @views.html.fragments.searchInput( + id = "publication-search", + name = "query", + value = None, + placeholder = messages("references.search.placeholder"), + hxGet = controllers.routes.PublicationController.getAllPublicationsWithDetailsHtml(Some(1), None, None), + hxTarget = "#publications-container", + hxIndicator = "#search-box", + hxTrigger = "input changed delay:300ms, search" + ) @messages("references.search.help")
    @@ -84,12 +68,4 @@
    - - } \ No newline at end of file diff --git a/app/views/variants/browser.scala.html b/app/views/variants/browser.scala.html index adb1075..0eb6184 100644 --- a/app/views/variants/browser.scala.html +++ b/app/views/variants/browser.scala.html @@ -27,23 +27,14 @@
    @messages("variants.browser.v
    - + @views.html.fragments.searchInput( + id = "variant-search", + name = "query", + value = query, + placeholder = messages("variants.browser.searchPlaceholder"), + hxGet = controllers.routes.VariantBrowserController.listFragment(None, 1, pageSize), + hxTarget = "#variants-table" + ) @messages("variants.browser.searchHelp")
    From e885f5e4ff0e484385e6f4a3e524bbf3c83a4a2a Mon Sep 17 00:00:00 2001 From: jkane Date: Sat, 13 Dec 2025 09:33:27 -0600 Subject: [PATCH 09/28] **refactor(views): Extract and reuse breadcrumb, flash message, and search input components** - Added reusable templates for breadcrumbs, flash messages, and search inputs in `fragments`. - Updated variant browser and curator views to utilize the new components, reducing redundancy. - Simplified and centralized layout structures for improved maintainability. --- app/utils/CuratorViewUtils.scala | 13 +- app/views/admin/genomics/dashboard.scala.html | 2 + app/views/auth/appPasswordHelp.scala.html | 1 + app/views/auth/login.scala.html | 7 +- app/views/contact.scala.html | 18 +-- app/views/curator/dashboard.scala.html | 7 +- app/views/fragments/haplogroup.scala.html | 140 ++++++++++++++---- app/views/fragments/htmlPagination.scala.html | 32 ++++ app/views/fragments/treeView.scala.html | 31 ++++ app/views/mtree.scala.html | 32 +--- .../publicationCandidates/list.scala.html | 50 +------ app/views/publicationList.scala.html | 21 +-- app/views/publications/submitPaper.scala.html | 12 +- .../support/admin/messageDetail.scala.html | 10 +- .../support/admin/messageList.scala.html | 46 ++---- app/views/support/myMessages.scala.html | 4 + app/views/user/profile.scala.html | 7 +- app/views/ytree.scala.html | 31 +--- 18 files changed, 238 insertions(+), 226 deletions(-) create mode 100644 app/views/fragments/htmlPagination.scala.html create mode 100644 app/views/fragments/treeView.scala.html diff --git a/app/utils/CuratorViewUtils.scala b/app/utils/CuratorViewUtils.scala index 6139a2f..a7d6155 100644 --- a/app/utils/CuratorViewUtils.scala +++ b/app/utils/CuratorViewUtils.scala @@ -1,5 +1,7 @@ package utils +import models.domain.support.MessageStatus + object CuratorViewUtils { def actionBadgeClass(action: String): String = { action match { @@ -18,4 +20,13 @@ object CuratorViewUtils { case _ => "bg-secondary" } } -} \ No newline at end of file + + def statusBadgeClass(status: MessageStatus): String = { + status match { + case MessageStatus.New => "bg-primary" + case MessageStatus.Read => "bg-info" + case MessageStatus.Replied => "bg-success" + case MessageStatus.Closed => "bg-secondary" + } + } +} diff --git a/app/views/admin/genomics/dashboard.scala.html b/app/views/admin/genomics/dashboard.scala.html index 2fdd6c0..7889d38 100644 --- a/app/views/admin/genomics/dashboard.scala.html +++ b/app/views/admin/genomics/dashboard.scala.html @@ -5,6 +5,8 @@

    Genomics Admin

    + @views.html.fragments.flashMessages(request.flash) +
    diff --git a/app/views/auth/appPasswordHelp.scala.html b/app/views/auth/appPasswordHelp.scala.html index 38e497c..0295447 100644 --- a/app/views/auth/appPasswordHelp.scala.html +++ b/app/views/auth/appPasswordHelp.scala.html @@ -3,6 +3,7 @@ @main(messages("auth.appPasswordHelp.title")) {
    + @views.html.fragments.flashMessages(request.flash)
    diff --git a/app/views/auth/login.scala.html b/app/views/auth/login.scala.html index 01ed6b6..9bf2a0b 100644 --- a/app/views/auth/login.scala.html +++ b/app/views/auth/login.scala.html @@ -9,12 +9,7 @@

    @messages("auth.login.heading")

    - @request.flash.get("error").map { msg => - - } - @request.flash.get("success").map { msg => - - } + @views.html.fragments.flashMessages(request.flash) } - @request.flash.get("success").map { message => - - } - - @if(contactForm.hasGlobalErrors) { - - } + @views.html.fragments.flashMessages(request.flash, Some(contactForm)) @helper.form(action = routes.ContactController.submit(), Symbol("class") -> "needs-validation", Symbol("autocomplete") -> "off") { @helper.CSRF.formField diff --git a/app/views/curator/dashboard.scala.html b/app/views/curator/dashboard.scala.html index 2c34a95..1a14998 100644 --- a/app/views/curator/dashboard.scala.html +++ b/app/views/curator/dashboard.scala.html @@ -5,12 +5,7 @@

    Curator Dashboard

    - @request.flash.get("success").map { msg => - - } + @views.html.fragments.flashMessages(request.flash)
    diff --git a/app/views/fragments/haplogroup.scala.html b/app/views/fragments/haplogroup.scala.html index e1996b9..9dfbbe0 100644 --- a/app/views/fragments/haplogroup.scala.html +++ b/app/views/fragments/haplogroup.scala.html @@ -39,27 +39,27 @@ -
    +
    - ✓ @messages("tree.legend.established") - ★ @messages("tree.legend.updated") + ✓ @messages("tree.legend.established") + ★ @messages("tree.legend.updated") + @if(renderedTreeData.isDefined) { + + }
    -
    -
    +
    + @* Loading Overlay *@ +
    + +
    + +
    @renderedTreeData.map { rtd => @@ -68,7 +68,13 @@ } @for(node <- rtd.allNodes) { - + + + @* Node Rectangle *@ - @node.name (@messages("tree.reRoot")) + @* Header bar *@ + @* Name row with icon *@ @if(node.isBackbone){✓ }@if(node.isRecentlyUpdated){★ }@node.name + @* Variants row *@ + hx-trigger="click" + data-bs-toggle="tooltip" + title="@messages("tree.clickToSeeVariants", node.variantsCount.getOrElse(0))"> @node.variantsCount.map(c => s"$c variants ▸").getOrElse("—") - @messages("tree.clickToSeeVariants", node.variantsCount.getOrElse(0)) + @if(showBranchAgeEstimates) { @* Formed row *@
    - + + /* Legend Icons */ + .legend-icon { + display: inline-block; + width: 24px; + height: 24px; + border-radius: 3px; + vertical-align: middle; + } + + .legend-icon.established { + background-color: #d4edda; + border: 2px solid #2e7d32; + } + + .legend-icon.updated { + background-color: #ffeeba; + border: 2px dashed #e65100; + } + \ No newline at end of file diff --git a/app/views/fragments/htmlPagination.scala.html b/app/views/fragments/htmlPagination.scala.html new file mode 100644 index 0000000..9917b61 --- /dev/null +++ b/app/views/fragments/htmlPagination.scala.html @@ -0,0 +1,32 @@ +@(currentPage: Int, totalPages: Int, linkGenerator: (Int, Int) => play.api.mvc.Call, pageSize: Int)(implicit messages: Messages) + +@if(totalPages > 1) { + +} diff --git a/app/views/fragments/treeView.scala.html b/app/views/fragments/treeView.scala.html new file mode 100644 index 0000000..d9a929a --- /dev/null +++ b/app/views/fragments/treeView.scala.html @@ -0,0 +1,31 @@ +@(titleKey: String, + fragmentCall: Option[String] => play.api.mvc.Call, + fullPageCall: Option[String] => play.api.mvc.Call, + rootHaplogroup: Option[String], + searchPlaceholder: String, + searchInputTitle: String)(implicit webJarsUtil: org.webjars.play.WebJarsUtil, messages: Messages, request: RequestHeader) + +@main(messages(titleKey)) { +
    +

    @messages(titleKey)

    + +
    +
    + + + +
    +
    + +
    +
    @messages("tree.loading")
    +
    +
    +} diff --git a/app/views/mtree.scala.html b/app/views/mtree.scala.html index 14450f1..b5e98cc 100644 --- a/app/views/mtree.scala.html +++ b/app/views/mtree.scala.html @@ -1,27 +1,11 @@ @import org.webjars.play.WebJarsUtil @(rootHaplogroup: Option[String])(implicit webJarsUtil: WebJarsUtil, messages: Messages, request: RequestHeader) -@main(messages("nav.mtree")) { -
    -

    @messages("nav.mtree")

    -
    -
    @messages("tree.loading")
    -
    - -
    -
    - - - -
    -
    - -
    -} +@views.html.fragments.treeView( + titleKey = "nav.mtree", + fragmentCall = controllers.routes.TreeController.mTreeFragment, + fullPageCall = controllers.routes.TreeController.mtree, + rootHaplogroup = rootHaplogroup, + searchPlaceholder = "e.g. H1", + searchInputTitle = "Enter a valid MT-DNA haplogroup" +) \ No newline at end of file diff --git a/app/views/publicationCandidates/list.scala.html b/app/views/publicationCandidates/list.scala.html index 85dc8bf..4c00f35 100644 --- a/app/views/publicationCandidates/list.scala.html +++ b/app/views/publicationCandidates/list.scala.html @@ -10,21 +10,7 @@

    @messages("publicationCandidates.heading")

    - @request.flash.get("success").map { message => - - } - - @request.flash.get("error").map { message => - - } + @views.html.fragments.flashMessages(request.flash) @if(candidates.isEmpty) { @* Pagination *@ - @defining({ - val totalPages = (totalCandidates + pageSize - 1) / pageSize - val startPage = Math.max(1, currentPage - 2) - val endPage = Math.min(totalPages, currentPage + 2) - (totalPages, startPage, endPage) - }) { case (totalPages, startPage, endPage) => - - } + @views.html.fragments.htmlPagination( + currentPage = currentPage, + totalPages = (totalCandidates + pageSize - 1) / pageSize, + pageSize = pageSize, + linkGenerator = (p, ps) => controllers.routes.PublicationCandidateController.listCandidates(p, ps) + ) }
    } diff --git a/app/views/publicationList.scala.html b/app/views/publicationList.scala.html index 9c46d4b..9c80bac 100644 --- a/app/views/publicationList.scala.html +++ b/app/views/publicationList.scala.html @@ -37,21 +37,12 @@
    @messages("publication.list.total", paginatedPublications.totalItems) - @if(paginatedPublications.hasPreviousPage) { - - } - @messages("pagination.pageOf", paginatedPublications.currentPage, paginatedPublications.totalPages) - @if(paginatedPublications.hasNextPage) { - - } + @views.html.fragments.htmlPagination( + currentPage = paginatedPublications.currentPage, + totalPages = paginatedPublications.totalPages, + pageSize = paginatedPublications.pageSize, + linkGenerator = (p, ps) => controllers.routes.PublicationController.getAllPublicationsWithDetailsHtml(Some(p), Some(ps), searchQuery) + )
    } diff --git a/app/views/publications/submitPaper.scala.html b/app/views/publications/submitPaper.scala.html index a4f5e32..4fbc9e4 100644 --- a/app/views/publications/submitPaper.scala.html +++ b/app/views/publications/submitPaper.scala.html @@ -7,17 +7,7 @@

    @messages("publication.submit.title")

    - @request.flash.get("error").map { message => -
    - @message -
    - } - - @request.flash.get("success").map { message => -
    - @message -
    - } + @views.html.fragments.flashMessages(request.flash) @form(routes.PublicationController.submitPaper()) { @CSRF.formField diff --git a/app/views/support/admin/messageDetail.scala.html b/app/views/support/admin/messageDetail.scala.html index a18aa50..b9d6dc6 100644 --- a/app/views/support/admin/messageDetail.scala.html +++ b/app/views/support/admin/messageDetail.scala.html @@ -2,6 +2,7 @@ @import models.domain.support.{ContactMessage, MessageReply, MessageStatus} @import models.domain.user.User @import controllers.ReplyFormData +@import utils.CuratorViewUtils @(message: ContactMessage, replies: Seq[MessageReply], sender: Option[User], replyForm: Form[ReplyFormData])(implicit request: RequestHeader, messagesProvider: Messages, webJarsUtil: WebJarsUtil) @main(messagesProvider("support.admin.messageDetail.title")) { @@ -12,19 +13,14 @@
    - @request.flash.get("success").map { msg => - - } + @views.html.fragments.flashMessages(request.flash)
    @message.subject
    - + @messagesProvider(s"support.status.${message.status.value}")
    diff --git a/app/views/support/admin/messageList.scala.html b/app/views/support/admin/messageList.scala.html index f266b49..00b9cd4 100644 --- a/app/views/support/admin/messageList.scala.html +++ b/app/views/support/admin/messageList.scala.html @@ -1,17 +1,13 @@ @import org.webjars.play.WebJarsUtil @import models.domain.support.{ContactMessage, MessageStatus} +@import utils.CuratorViewUtils @(messages: Seq[ContactMessage], statusFilter: Option[MessageStatus], currentPage: Int, totalPages: Int, pageSize: Int)(implicit request: RequestHeader, messagesProvider: Messages, webJarsUtil: WebJarsUtil) @main(messagesProvider("support.admin.title")) {

    @messagesProvider("support.admin.heading")

    - @request.flash.get("success").map { msg => - - } + @views.html.fragments.flashMessages(request.flash)
    @@ -51,7 +47,7 @@

    @messagesProvider("support.admin.heading")

    @for(msg <- messages) { - + @messagesProvider(s"support.status.${msg.status.value}") @@ -74,36 +70,12 @@

    @messagesProvider("support.admin.heading")

    - @if(totalPages > 1) { - - } + @views.html.fragments.htmlPagination( + currentPage = currentPage, + totalPages = totalPages, + pageSize = pageSize, + linkGenerator = (p, ps) => controllers.routes.SupportAdminController.listMessages(statusFilter.map(_.value), p, ps) + ) }
    } - -@statusBadgeClass(status: MessageStatus) = @{ - status match { - case MessageStatus.New => "bg-primary" - case MessageStatus.Read => "bg-info" - case MessageStatus.Replied => "bg-success" - case MessageStatus.Closed => "bg-secondary" - } -} diff --git a/app/views/support/myMessages.scala.html b/app/views/support/myMessages.scala.html index 77b929a..8162758 100644 --- a/app/views/support/myMessages.scala.html +++ b/app/views/support/myMessages.scala.html @@ -1,5 +1,6 @@ @import org.webjars.play.WebJarsUtil @import models.domain.support.{ContactMessage, MessageStatus} +@import utils.CuratorViewUtils @(messages: Seq[ContactMessage])(implicit request: RequestHeader, messagesProvider: Messages, webJarsUtil: WebJarsUtil) @main(messagesProvider("support.myMessages.title")) { @@ -13,7 +14,10 @@

    @messagesProvider("support.myMessages.heading")

    + @views.html.fragments.flashMessages(request.flash) + @if(messages.isEmpty) { +
    @messagesProvider("support.myMessages.empty")
    diff --git a/app/views/user/profile.scala.html b/app/views/user/profile.scala.html index d57709e..c3c2571 100644 --- a/app/views/user/profile.scala.html +++ b/app/views/user/profile.scala.html @@ -11,12 +11,7 @@

    @messages("profile.heading")

    - @request.flash.get("success").map { msg => - - } + @views.html.fragments.flashMessages(request.flash)
    @messages("profile.accountDetails")
    diff --git a/app/views/ytree.scala.html b/app/views/ytree.scala.html index 816adcf..2d006d8 100644 --- a/app/views/ytree.scala.html +++ b/app/views/ytree.scala.html @@ -1,26 +1,11 @@ @import org.webjars.play.WebJarsUtil @(rootHaplogroup: Option[String])(implicit webJarsUtil: WebJarsUtil, messages: Messages, request: RequestHeader) -@main(messages("nav.ytree")) { -
    -

    @messages("nav.ytree")

    -
    -
    @messages("tree.loading")
    -
    - -
    -
    - - - -
    -
    -
    -} +@views.html.fragments.treeView( + titleKey = "nav.ytree", + fragmentCall = controllers.routes.TreeController.yTreeFragment, + fullPageCall = controllers.routes.TreeController.ytree, + rootHaplogroup = rootHaplogroup, + searchPlaceholder = "e.g. R1b", + searchInputTitle = "Enter a valid Y-DNA haplogroup" +) \ No newline at end of file From cd3a139b288441f2b4d2dcc67c0c922c805a772d Mon Sep 17 00:00:00 2001 From: jkane Date: Sat, 13 Dec 2025 22:30:43 -0600 Subject: [PATCH 10/28] feat(tree): add user opt-in preference for block layout This feature allows users to toggle between the standard tree layout and the block layout on the main tree pages. The preference is saved in a cookie and respected across sessions. --- app/config/FeatureFlags.scala | 5 + app/controllers/TreeController.scala | 29 ++- app/views/fragments/blockTree.scala.html | 290 +++++++++++++++++++++++ app/views/fragments/treeView.scala.html | 17 +- app/views/mtree.scala.html | 5 +- app/views/ytree.scala.html | 5 +- conf/messages | 1 + 7 files changed, 338 insertions(+), 14 deletions(-) create mode 100644 app/views/fragments/blockTree.scala.html diff --git a/app/config/FeatureFlags.scala b/app/config/FeatureFlags.scala index 3520042..25e14e3 100644 --- a/app/config/FeatureFlags.scala +++ b/app/config/FeatureFlags.scala @@ -17,4 +17,9 @@ class FeatureFlags @Inject()(config: Configuration) { * Disabled by default until age data is populated. */ val showBranchAgeEstimates: Boolean = featuresConfig.getOptional[Boolean]("tree.showBranchAgeEstimates").getOrElse(false) + + /** + * Show the alternative "Block Layout" (ytree.net style) for the tree. + */ + val showBlockLayout: Boolean = featuresConfig.getOptional[Boolean]("tree.showBlockLayout").getOrElse(false) } diff --git a/app/controllers/TreeController.scala b/app/controllers/TreeController.scala index 1de184b..8e5f27a 100644 --- a/app/controllers/TreeController.scala +++ b/app/controllers/TreeController.scala @@ -52,6 +52,11 @@ class TreeController @Inject()(val controllerComponents: MessagesControllerCompo private val YConfig = TreeConfig(Y, "Y") private val MTConfig = TreeConfig(MT, "L") + private val BLOCK_LAYOUT_COOKIE = "showBlockLayout" + + private def shouldShowBlockLayout(request: RequestHeader): Boolean = { + request.cookies.get(BLOCK_LAYOUT_COOKIE).map(_.value.toBoolean).getOrElse(featureFlags.showBlockLayout) + } /** * Renders the Y-DNA tree page. @@ -65,7 +70,7 @@ class TreeController @Inject()(val controllerComponents: MessagesControllerCompo * @return an action that renders the Y-DNA tree page as an HTML response */ def ytree(rootHaplogroup: Option[String]): Action[AnyContent] = Action { implicit request => - Ok(views.html.ytree(rootHaplogroup)) + Ok(views.html.ytree(rootHaplogroup, shouldShowBlockLayout(request))) } /** @@ -80,7 +85,7 @@ class TreeController @Inject()(val controllerComponents: MessagesControllerCompo * @return an action that renders the MT-DNA tree page as an HTML response */ def mtree(rootHaplogroup: Option[String]): Action[AnyContent] = Action { implicit request => - Ok(views.html.mtree(rootHaplogroup)) + Ok(views.html.mtree(rootHaplogroup, shouldShowBlockLayout(request))) } /** @@ -188,8 +193,11 @@ class TreeController @Inject()(val controllerComponents: MessagesControllerCompo config: TreeConfig, cacheKey: String )(using request: Request[AnyContent]): Future[Result] = { - cache.getOrElseUpdate(cacheKey, 24.hours) { - buildTreeFragment(rootHaplogroup, config) + val useBlockLayout = shouldShowBlockLayout(request) + val effectiveCacheKey = s"$cacheKey-block:$useBlockLayout" + + cache.getOrElseUpdate(effectiveCacheKey, 24.hours) { + buildTreeFragment(rootHaplogroup, config, useBlockLayout) } } @@ -198,17 +206,22 @@ class TreeController @Inject()(val controllerComponents: MessagesControllerCompo */ private def buildTreeFragment( rootHaplogroup: Option[String], - config: TreeConfig + config: TreeConfig, + showBlockLayout: Boolean )(using request: Request[AnyContent]): Future[Result] = { val haplogroupName = rootHaplogroup.getOrElse(config.defaultRoot) val isAbsoluteTopRootView = haplogroupName == config.defaultRoot treeService.buildTreeResponse(haplogroupName, config.haplogroupType, FragmentRoute) .map { treeDto => - val treeViewModel: Option[TreeViewModel] = treeDto.subclade.flatMap { _ => - services.TreeLayoutService.layoutTree(treeDto, isAbsoluteTopRootView) + if (showBlockLayout) { + Ok(views.html.fragments.blockTree(treeDto, config.haplogroupType, request.uri)) + } else { + val treeViewModel: Option[TreeViewModel] = treeDto.subclade.flatMap { _ => + services.TreeLayoutService.layoutTree(treeDto, isAbsoluteTopRootView) + } + Ok(views.html.fragments.haplogroup(treeDto, config.haplogroupType, treeViewModel, request.uri, featureFlags.showBranchAgeEstimates)) } - Ok(views.html.fragments.haplogroup(treeDto, config.haplogroupType, treeViewModel, request.uri, featureFlags.showBranchAgeEstimates)) } .recover { case _: IllegalArgumentException => diff --git a/app/views/fragments/blockTree.scala.html b/app/views/fragments/blockTree.scala.html new file mode 100644 index 0000000..7caf507 --- /dev/null +++ b/app/views/fragments/blockTree.scala.html @@ -0,0 +1,290 @@ +@import models.api.{TreeDTO, TreeNodeDTO} +@import models.HaplogroupType +@import models.HaplogroupType.{MT, Y} +@import controllers.routes.TreeController + +@(tree: TreeDTO, hapType: HaplogroupType, currentUrl: String)(implicit messages: Messages) + +@fullPageUrl(haplogroup: Option[String]) = @{ + hapType match { + case Y => TreeController.ytree(haplogroup) + case MT => TreeController.mtree(haplogroup) + } +} + +@fragmentUrl(haplogroup: Option[String]) = @{ + hapType match { + case Y => TreeController.yTreeFragment(haplogroup) + case MT => TreeController.mTreeFragment(haplogroup) + } +} + + + +@* Recursive Node Renderer *@ +@renderNode(node: TreeNodeDTO) = { +
    +
    + +
    + @if(node.isBackbone){✓} @node.name +
    + + @if(node.variants.nonEmpty) { +
    + @for(variant <- node.variants.take(5)) { +
    @variant
    + } + @if(node.variants.size > 5) { +
    + @(node.variants.size - 5) more
    + } +
    + } +
    + + @if(node.children.nonEmpty) { +
    +
    +
    + @for(child <- node.children) { + @renderNode(child) + } +
    +
    + } +
    +} + +
    + @* Loading Overlay *@ +
    + +
    + +
    + @tree.subclade.map { root => +
    + @renderNode(root) +
    + }.getOrElse { +
    @messages("tree.noData")
    + } +
    + +
    +
    + + diff --git a/app/views/fragments/treeView.scala.html b/app/views/fragments/treeView.scala.html index d9a929a..9caeb4e 100644 --- a/app/views/fragments/treeView.scala.html +++ b/app/views/fragments/treeView.scala.html @@ -3,13 +3,14 @@ fullPageCall: Option[String] => play.api.mvc.Call, rootHaplogroup: Option[String], searchPlaceholder: String, - searchInputTitle: String)(implicit webJarsUtil: org.webjars.play.WebJarsUtil, messages: Messages, request: RequestHeader) + searchInputTitle: String, + showBlockLayout: Boolean = false)(implicit webJarsUtil: org.webjars.play.WebJarsUtil, messages: Messages, request: RequestHeader) @main(messages(titleKey)) {

    @messages(titleKey)

    -
    +
    @messages(titleKey)
    title="@searchInputTitle"> + +
    + + +
    + +
    diff --git a/app/views/mtree.scala.html b/app/views/mtree.scala.html index b5e98cc..0ad2d76 100644 --- a/app/views/mtree.scala.html +++ b/app/views/mtree.scala.html @@ -1,5 +1,5 @@ @import org.webjars.play.WebJarsUtil -@(rootHaplogroup: Option[String])(implicit webJarsUtil: WebJarsUtil, messages: Messages, request: RequestHeader) +@(rootHaplogroup: Option[String], showBlockLayout: Boolean = false)(implicit webJarsUtil: WebJarsUtil, messages: Messages, request: RequestHeader) @views.html.fragments.treeView( titleKey = "nav.mtree", @@ -7,5 +7,6 @@ fullPageCall = controllers.routes.TreeController.mtree, rootHaplogroup = rootHaplogroup, searchPlaceholder = "e.g. H1", - searchInputTitle = "Enter a valid MT-DNA haplogroup" + searchInputTitle = "Enter a valid MT-DNA haplogroup", + showBlockLayout = showBlockLayout ) \ No newline at end of file diff --git a/app/views/ytree.scala.html b/app/views/ytree.scala.html index 2d006d8..feb672f 100644 --- a/app/views/ytree.scala.html +++ b/app/views/ytree.scala.html @@ -1,5 +1,5 @@ @import org.webjars.play.WebJarsUtil -@(rootHaplogroup: Option[String])(implicit webJarsUtil: WebJarsUtil, messages: Messages, request: RequestHeader) +@(rootHaplogroup: Option[String], showBlockLayout: Boolean = false)(implicit webJarsUtil: WebJarsUtil, messages: Messages, request: RequestHeader) @views.html.fragments.treeView( titleKey = "nav.ytree", @@ -7,5 +7,6 @@ fullPageCall = controllers.routes.TreeController.ytree, rootHaplogroup = rootHaplogroup, searchPlaceholder = "e.g. R1b", - searchInputTitle = "Enter a valid Y-DNA haplogroup" + searchInputTitle = "Enter a valid Y-DNA haplogroup", + showBlockLayout = showBlockLayout ) \ No newline at end of file diff --git a/conf/messages b/conf/messages index fdaedbf..fa42ce5 100644 --- a/conf/messages +++ b/conf/messages @@ -179,6 +179,7 @@ tree.loading = Loading haplogroup tree... tree.jumpTo = Jump to haplogroup: tree.go = Go tree.reRoot = Click to re-root +tree.blockLayout = Block Layout tree.clickToSeeVariants = Click to see {0} defining Variants(s) # Sidebar From 24c3c6f8d3929987636ae213c8e6a0fbc3edc81b Mon Sep 17 00:00:00 2001 From: jkane Date: Sat, 13 Dec 2025 22:33:10 -0600 Subject: [PATCH 11/28] **refactor(sql): Optimize variant migration script for performance and clarity** - Added a temporary index to speed up grouping and joining during variant migration. - Combined variant name and coordinates insertion into a single pass. - Simplified alias aggregation using filtered JSONB operations. - Improved maintainability by removing redundant steps and optimizing query structure. - Dropped temporary index after migration steps to clean up. --- scripts/migrate_variant_to_v2.sql | 127 +++++++++++++----------------- 1 file changed, 55 insertions(+), 72 deletions(-) diff --git a/scripts/migrate_variant_to_v2.sql b/scripts/migrate_variant_to_v2.sql index 86e43f4..677a363 100644 --- a/scripts/migrate_variant_to_v2.sql +++ b/scripts/migrate_variant_to_v2.sql @@ -18,95 +18,76 @@ BEGIN; -- ============================================================================= --- Step 1: Insert variants into variant_v2 (one row per unique name) +-- Optimization: Create temporary index to speed up grouping and joining +-- ============================================================================= +CREATE INDEX IF NOT EXISTS idx_tmp_variant_group_key ON variant (COALESCE(common_name, rs_id)); + +-- ============================================================================= +-- Step 1: Insert variants into variant_v2 (Name + Coordinates in one pass) -- ============================================================================= INSERT INTO variant_v2 (canonical_name, mutation_type, naming_status, aliases, coordinates) SELECT - group_key as canonical_name, - MAX(variant_type) as mutation_type, - CASE WHEN group_key IS NOT NULL THEN 'NAMED' ELSE 'UNNAMED' END as naming_status, + COALESCE(v.common_name, v.rs_id) as group_key, + MAX(v.variant_type) as mutation_type, + CASE WHEN COALESCE(v.common_name, v.rs_id) IS NOT NULL THEN 'NAMED' ELSE 'UNNAMED' END, '{}'::jsonb as aliases, - '{}'::jsonb as coordinates -FROM ( - SELECT - COALESCE(v.common_name, v.rs_id) as group_key, - v.variant_type - FROM variant v -) grouped -GROUP BY group_key + jsonb_object_agg( + COALESCE(gc.reference_genome, 'unknown'), + jsonb_build_object( + 'contig', COALESCE(gc.common_name, gc.accession), + 'position', v.position, + 'ref', v.reference_allele, + 'alt', v.alternate_allele + ) + ) as coordinates +FROM variant v +JOIN genbank_contig gc ON v.genbank_contig_id = gc.genbank_contig_id +GROUP BY COALESCE(v.common_name, v.rs_id) ON CONFLICT DO NOTHING; -- ============================================================================= --- Step 2: Add coordinates for each reference genome +-- Step 2: Migrate aliases into JSONB structure -- ============================================================================= --- Update coordinates by merging all builds for each variant -WITH coord_data AS ( +WITH raw_aliases AS ( + -- Collect all aliases linked to any variant instance in the group SELECT COALESCE(v.common_name, v.rs_id) as group_key, - jsonb_object_agg( - gc.reference_genome, - jsonb_build_object( - 'contig', COALESCE(gc.common_name, gc.accession), - 'position', v.position, - 'ref', v.reference_allele, - 'alt', v.alternate_allele - ) - ) as coords + va.alias_type, + va.alias_value, + va.source FROM variant v - JOIN genbank_contig gc ON v.genbank_contig_id = gc.genbank_contig_id - GROUP BY COALESCE(v.common_name, v.rs_id) -) -UPDATE variant_v2 v2 -SET coordinates = cd.coords -FROM coord_data cd -WHERE v2.canonical_name IS NOT DISTINCT FROM cd.group_key; - --- ============================================================================= --- Step 3: Migrate aliases into JSONB structure --- ============================================================================= - -WITH alias_data AS ( + JOIN variant_alias va ON v.variant_id = va.variant_id +), +grouped_aliases AS ( + -- Aggregate aliases by type for each variant group SELECT - COALESCE(v.common_name, v.rs_id) as group_key, + group_key, jsonb_build_object( - 'common_names', COALESCE( - (SELECT jsonb_agg(DISTINCT va.alias_value) - FROM variant_alias va - JOIN variant v2 ON va.variant_id = v2.variant_id - WHERE COALESCE(v2.common_name, v2.rs_id) IS NOT DISTINCT FROM COALESCE(v.common_name, v.rs_id) - AND va.alias_type = 'common_name'), - '[]'::jsonb - ), - 'rs_ids', COALESCE( - (SELECT jsonb_agg(DISTINCT va.alias_value) - FROM variant_alias va - JOIN variant v2 ON va.variant_id = v2.variant_id - WHERE COALESCE(v2.common_name, v2.rs_id) IS NOT DISTINCT FROM COALESCE(v.common_name, v.rs_id) - AND va.alias_type = 'rs_id'), - '[]'::jsonb - ), - 'sources', COALESCE( - (SELECT jsonb_object_agg(source, names) - FROM ( - SELECT va.source, jsonb_agg(DISTINCT va.alias_value) as names - FROM variant_alias va - JOIN variant v2 ON va.variant_id = v2.variant_id - WHERE COALESCE(v2.common_name, v2.rs_id) IS NOT DISTINCT FROM COALESCE(v.common_name, v.rs_id) - AND va.source IS NOT NULL - GROUP BY va.source - ) src), - '{}'::jsonb - ) - ) as aliases - FROM variant v - GROUP BY COALESCE(v.common_name, v.rs_id) + 'common_names', COALESCE(jsonb_agg(DISTINCT alias_value) FILTER (WHERE alias_type = 'common_name'), '[]'::jsonb), + 'rs_ids', COALESCE(jsonb_agg(DISTINCT alias_value) FILTER (WHERE alias_type = 'rs_id'), '[]'::jsonb), + 'sources', COALESCE( + ( + SELECT jsonb_object_agg(source, names) + FROM ( + SELECT source, jsonb_agg(DISTINCT alias_value) as names + FROM raw_aliases ra2 + WHERE ra2.group_key = ra1.group_key + AND source IS NOT NULL + GROUP BY source + ) src + ), + '{}'::jsonb + ) + ) as alias_json + FROM raw_aliases ra1 + GROUP BY group_key ) UPDATE variant_v2 v2 -SET aliases = ad.aliases -FROM alias_data ad -WHERE v2.canonical_name IS NOT DISTINCT FROM ad.group_key; +SET aliases = ga.alias_json +FROM grouped_aliases ga +WHERE v2.canonical_name IS NOT DISTINCT FROM ga.group_key; -- ============================================================================= -- Step 4: Update haplogroup_variant FK references @@ -152,6 +133,8 @@ FROM tree.haplogroup_variant hv LEFT JOIN variant_v2 v2 ON hv.variant_id = v2.variant_id WHERE v2.variant_id IS NULL; +DROP INDEX IF EXISTS idx_tmp_variant_group_key; + COMMIT; -- ============================================================================= From 2b758c920a583b5bd93714f7500126e96cb39875 Mon Sep 17 00:00:00 2001 From: jkane Date: Sat, 13 Dec 2025 22:44:24 -0600 Subject: [PATCH 12/28] **refactor(views/controllers): Simplify variant and haplogroup pagination with dynamic fragment loading** - Replaced server-side pagination logic for variants and haplogroups with HTMX-driven fragment updates for improved responsiveness. - Simplified controller actions and templates, removing unused parameters and reducing complexity. - Added loading spinner and placeholder text for better user experience during content updates. --- app/controllers/CuratorController.scala | 26 +++---------------- .../VariantBrowserController.scala | 10 ++----- app/views/curator/haplogroups/list.scala.html | 16 +++++++++--- app/views/curator/variants/list.scala.html | 15 ++++++++--- app/views/variants/browser.scala.html | 15 ++++++++--- 5 files changed, 40 insertions(+), 42 deletions(-) diff --git a/app/controllers/CuratorController.scala b/app/controllers/CuratorController.scala index 0b7b5b7..b0f2a2d 100644 --- a/app/controllers/CuratorController.scala +++ b/app/controllers/CuratorController.scala @@ -158,20 +158,8 @@ class CuratorController @Inject()( // === Haplogroups === def listHaplogroups(query: Option[String], hgType: Option[String], page: Int, pageSize: Int): Action[AnyContent] = - withPermission("haplogroup.view").async { implicit request => - val haplogroupType = hgType.flatMap(HaplogroupType.fromString) - val offset = (page - 1) * pageSize - - for { - haplogroups <- query match { - case Some(q) if q.nonEmpty => haplogroupRepository.search(q, haplogroupType, pageSize, offset) - case _ => haplogroupRepository.search("", haplogroupType, pageSize, offset) - } - totalCount <- haplogroupRepository.count(query.filter(_.nonEmpty), haplogroupType) - } yield { - val totalPages = Math.max(1, (totalCount + pageSize - 1) / pageSize) - Ok(views.html.curator.haplogroups.list(haplogroups, query, hgType, page, totalPages, pageSize)) - } + withPermission("haplogroup.view") { implicit request => + Ok(views.html.curator.haplogroups.list(query, hgType, pageSize)) } def haplogroupsFragment(query: Option[String], hgType: Option[String], page: Int, pageSize: Int): Action[AnyContent] = @@ -432,14 +420,8 @@ class CuratorController @Inject()( // === Variants === def listVariants(query: Option[String], page: Int, pageSize: Int): Action[AnyContent] = - withPermission("variant.view").async { implicit request => - val offset = (page - 1) * pageSize - for { - (variants, totalCount) <- variantV2Repository.searchPaginated(query.getOrElse(""), offset, pageSize) - } yield { - val totalPages = Math.max(1, (totalCount + pageSize - 1) / pageSize) - Ok(views.html.curator.variants.list(variants, query, page, totalPages, pageSize, totalCount)) - } + withPermission("variant.view") { implicit request => + Ok(views.html.curator.variants.list(query, pageSize)) } def variantsFragment(query: Option[String], page: Int, pageSize: Int): Action[AnyContent] = diff --git a/app/controllers/VariantBrowserController.scala b/app/controllers/VariantBrowserController.scala index e519718..15daa4c 100644 --- a/app/controllers/VariantBrowserController.scala +++ b/app/controllers/VariantBrowserController.scala @@ -35,15 +35,9 @@ class VariantBrowserController @Inject()( /** * Main variant browser page with search functionality. */ - def index(query: Option[String], page: Int, pageSize: Int): Action[AnyContent] = Action.async { + def index(query: Option[String], page: Int, pageSize: Int): Action[AnyContent] = Action { implicit request: Request[AnyContent] => - val offset = (page - 1) * pageSize - for { - (variants, totalCount) <- getCachedSearchResults(query.getOrElse(""), offset, pageSize) - } yield { - val totalPages = Math.max(1, (totalCount + pageSize - 1) / pageSize) - Ok(views.html.variants.browser(variants, query, page, totalPages, pageSize, totalCount)) - } + Ok(views.html.variants.browser(query, page, pageSize)) } /** diff --git a/app/views/curator/haplogroups/list.scala.html b/app/views/curator/haplogroups/list.scala.html index 23a2b81..66e878e 100644 --- a/app/views/curator/haplogroups/list.scala.html +++ b/app/views/curator/haplogroups/list.scala.html @@ -1,6 +1,5 @@ @import org.webjars.play.WebJarsUtil -@import models.domain.haplogroups.Haplogroup -@(haplogroups: Seq[Haplogroup], query: Option[String], hgType: Option[String], currentPage: Int, totalPages: Int, pageSize: Int)(implicit request: RequestHeader, messages: Messages, webJarsUtil: WebJarsUtil) +@(query: Option[String], hgType: Option[String], pageSize: Int)(implicit request: RequestHeader, messages: Messages, webJarsUtil: WebJarsUtil) @main("Curator - Haplogroups") { + \ No newline at end of file From 0ba93244c53d08c8a06bbde8454edecef65f37a0 Mon Sep 17 00:00:00 2001 From: jkane Date: Sun, 14 Dec 2025 09:02:41 -0600 Subject: [PATCH 18/28] Search the tree by SNP name as well as subclade name --- .../HaplogroupVariantRepository.scala | 4 +- app/services/HaplogroupTreeService.scala | 40 +++++++++++++++++-- app/views/fragments/treeView.scala.html | 1 - 3 files changed, 39 insertions(+), 6 deletions(-) diff --git a/app/repositories/HaplogroupVariantRepository.scala b/app/repositories/HaplogroupVariantRepository.scala index e57c998..8189bb6 100644 --- a/app/repositories/HaplogroupVariantRepository.scala +++ b/app/repositories/HaplogroupVariantRepository.scala @@ -124,7 +124,7 @@ class HaplogroupVariantRepositoryImpl @Inject()( // Search rs_ids in aliases val rsQuery = sql""" SELECT * FROM variant_v2 - WHERE aliases->'rs_ids' ? $normalizedQuery + WHERE aliases->'rs_ids' ?? $normalizedQuery """.as[VariantV2] runQuery(rsQuery) } else if (normalizedQuery.contains(":")) { @@ -167,7 +167,7 @@ class HaplogroupVariantRepositoryImpl @Inject()( val nameQuery = sql""" SELECT * FROM variant_v2 WHERE UPPER(canonical_name) LIKE $searchPattern - OR aliases->'common_names' ? $normalizedQuery + OR aliases->'common_names' ?? $normalizedQuery OR EXISTS ( SELECT 1 FROM jsonb_array_elements_text(aliases->'common_names') AS name WHERE UPPER(name) LIKE $searchPattern diff --git a/app/services/HaplogroupTreeService.scala b/app/services/HaplogroupTreeService.scala index 89a4dbe..794a0c0 100644 --- a/app/services/HaplogroupTreeService.scala +++ b/app/services/HaplogroupTreeService.scala @@ -30,10 +30,11 @@ class HaplogroupTreeService @Inject()( /** * Builds a TreeDTO representation for a specified haplogroup with related breadcrumbs and subtree. */ - def buildTreeResponse(haplogroupName: String, haplogroupType: HaplogroupType, routeType: RouteType): Future[TreeDTO] = { + def buildTreeResponse(haplogroupQuery: String, haplogroupType: HaplogroupType, routeType: RouteType): Future[TreeDTO] = { for { - rootHaplogroupOpt <- coreRepository.getHaplogroupByName(haplogroupName, haplogroupType) - rootHaplogroup = rootHaplogroupOpt.getOrElse(throw new IllegalArgumentException(s"Haplogroup $haplogroupName not found")) + resolvedHaplogroupName <- resolveHaplogroupByNameOrVariant(haplogroupQuery, haplogroupType) + rootHaplogroupOpt <- coreRepository.getHaplogroupByName(resolvedHaplogroupName, haplogroupType) + rootHaplogroup = rootHaplogroupOpt.getOrElse(throw new IllegalArgumentException(s"Haplogroup $resolvedHaplogroupName not found after variant lookup")) ancestors <- coreRepository.getAncestors(rootHaplogroup.id.get) crumbs = buildCrumbs(ancestors, haplogroupType, routeType) @@ -50,6 +51,39 @@ class HaplogroupTreeService @Inject()( ) } + /** + * Resolves a haplogroup name by either direct lookup or by finding a variant. + */ + private def resolveHaplogroupByNameOrVariant(query: String, haplogroupType: HaplogroupType): Future[String] = { + coreRepository.getHaplogroupByName(query, haplogroupType).flatMap { + case Some(haplogroup) => Future.successful(haplogroup.name) + case None => + // Haplogroup not found by direct name, try searching by variant + logger.debug(s"Haplogroup '$query' not found by direct name. Attempting variant lookup.") + val normalizedQuery = normalizeVariantId(query) + variantRepository.findVariants(normalizedQuery).flatMap { + case variants if variants.nonEmpty => + // Found variants, now find their defining haplogroups + val variantIds = variants.flatMap(_.variantId).map(_.toString) + Future.sequence(variantIds.map(vid => variantRepository.findHaplogroupsByDefiningVariant(vid, haplogroupType))).map { + haplogroupLists => + val definingHaplogroups = haplogroupLists.flatten + definingHaplogroups.sortBy(_.validFrom).lastOption match { + case Some(latestHaplogroup) => + logger.info(s"Resolved variant '$query' to haplogroup '${latestHaplogroup.name}'.") + latestHaplogroup.name + case None => + logger.warn(s"Variant '$query' found, but no defining haplogroups for type $haplogroupType.") + throw new IllegalArgumentException(s"Haplogroup or variant '$query' not found") + } + } + case _ => + logger.debug(s"Variant '$query' not found.") + Future.failed(new IllegalArgumentException(s"Haplogroup or variant '$query' not found")) + } + } + } + private def getRoute(name: String, haplogroupType: HaplogroupType, routeType: RouteType): Call = { (haplogroupType, routeType) match { case (Y, FragmentRoute) => controllers.routes.TreeController.yTreeFragment(Some(name)) diff --git a/app/views/fragments/treeView.scala.html b/app/views/fragments/treeView.scala.html index 9caeb4e..3ae0733 100644 --- a/app/views/fragments/treeView.scala.html +++ b/app/views/fragments/treeView.scala.html @@ -17,7 +17,6 @@

    @messages(titleKey)

    id="haplogroup-search" name="rootHaplogroup" placeholder="@searchPlaceholder" - pattern="[A-Z0-9-]+" title="@searchInputTitle"> From 958defb9144e06cb81294f0c69ddec8a47489cce Mon Sep 17 00:00:00 2001 From: jkane Date: Sun, 14 Dec 2025 09:21:37 -0600 Subject: [PATCH 19/28] Using the more correct terminology for cladograms --- app/config/FeatureFlags.scala | 2 +- app/controllers/TreeController.scala | 32 +++++++++---------- app/views/fragments/treeView.scala.html | 10 +++--- ...ree.scala.html => verticalTree.scala.html} | 23 ++++++++++--- app/views/mtree.scala.html | 17 +++++----- app/views/ytree.scala.html | 17 +++++----- conf/messages | 2 +- 7 files changed, 59 insertions(+), 44 deletions(-) rename app/views/fragments/{blockTree.scala.html => verticalTree.scala.html} (91%) diff --git a/app/config/FeatureFlags.scala b/app/config/FeatureFlags.scala index 25e14e3..eb9dba5 100644 --- a/app/config/FeatureFlags.scala +++ b/app/config/FeatureFlags.scala @@ -21,5 +21,5 @@ class FeatureFlags @Inject()(config: Configuration) { /** * Show the alternative "Block Layout" (ytree.net style) for the tree. */ - val showBlockLayout: Boolean = featuresConfig.getOptional[Boolean]("tree.showBlockLayout").getOrElse(false) + val showVerticalTree: Boolean = featuresConfig.getOptional[Boolean]("tree.showVerticalTree").getOrElse(false) } diff --git a/app/controllers/TreeController.scala b/app/controllers/TreeController.scala index 22b1759..25bdf96 100644 --- a/app/controllers/TreeController.scala +++ b/app/controllers/TreeController.scala @@ -52,10 +52,10 @@ class TreeController @Inject()(val controllerComponents: MessagesControllerCompo private val YConfig = TreeConfig(Y, "Y") private val MTConfig = TreeConfig(MT, "L") - private val BLOCK_LAYOUT_COOKIE = "showBlockLayout" + private val VERTICAL_TREE_COOKIE = "showVerticalTree" - private def shouldShowBlockLayout(request: RequestHeader): Boolean = { - request.cookies.get(BLOCK_LAYOUT_COOKIE).map(_.value.toBoolean).getOrElse(featureFlags.showBlockLayout) + private def shouldShowVerticalTree(request: RequestHeader): Boolean = { + request.cookies.get(VERTICAL_TREE_COOKIE).map(_.value.toBoolean).getOrElse(featureFlags.showVerticalTree) } /** @@ -70,7 +70,7 @@ class TreeController @Inject()(val controllerComponents: MessagesControllerCompo * @return an action that renders the Y-DNA tree page as an HTML response */ def ytree(rootHaplogroup: Option[String]): Action[AnyContent] = Action { implicit request => - Ok(views.html.ytree(rootHaplogroup, shouldShowBlockLayout(request))) + Ok(views.html.ytree(rootHaplogroup, shouldShowVerticalTree(request))) } /** @@ -85,7 +85,7 @@ class TreeController @Inject()(val controllerComponents: MessagesControllerCompo * @return an action that renders the MT-DNA tree page as an HTML response */ def mtree(rootHaplogroup: Option[String]): Action[AnyContent] = Action { implicit request => - Ok(views.html.mtree(rootHaplogroup, shouldShowBlockLayout(request))) + Ok(views.html.mtree(rootHaplogroup, shouldShowVerticalTree(request))) } /** @@ -193,11 +193,11 @@ class TreeController @Inject()(val controllerComponents: MessagesControllerCompo config: TreeConfig, cacheKey: String )(using request: Request[AnyContent]): Future[Result] = { - val useBlockLayout = shouldShowBlockLayout(request) - val effectiveCacheKey = s"$cacheKey-block:$useBlockLayout" + val useVerticalTree = shouldShowVerticalTree(request) + val effectiveCacheKey = s"$cacheKey-vertical:$useVerticalTree" cache.getOrElseUpdate(effectiveCacheKey, 24.hours) { - buildTreeFragment(rootHaplogroup, config, useBlockLayout) + buildTreeFragment(rootHaplogroup, config, useVerticalTree) } } @@ -207,12 +207,12 @@ class TreeController @Inject()(val controllerComponents: MessagesControllerCompo private def buildTreeFragment( rootHaplogroup: Option[String], config: TreeConfig, - showBlockLayout: Boolean + showVerticalTree: Boolean )(using request: Request[AnyContent]): Future[Result] = { val haplogroupName = rootHaplogroup.getOrElse(config.defaultRoot) val isAbsoluteTopRootView = haplogroupName == config.defaultRoot - val orientation = if (showBlockLayout) services.TreeOrientation.Vertical else services.TreeOrientation.Horizontal + val orientation = if (showVerticalTree) services.TreeOrientation.Vertical else services.TreeOrientation.Horizontal treeService.buildTreeResponse(haplogroupName, config.haplogroupType, FragmentRoute) .map { treeDto => @@ -220,8 +220,8 @@ class TreeController @Inject()(val controllerComponents: MessagesControllerCompo services.TreeLayoutService.layoutTree(treeDto, isAbsoluteTopRootView, orientation) } - if (showBlockLayout) { - Ok(views.html.fragments.blockTree(treeDto, config.haplogroupType, treeViewModel, request.uri)) + if (showVerticalTree) { + Ok(views.html.fragments.verticalTree(treeDto, config.haplogroupType, treeViewModel, request.uri)) } else { Ok(views.html.fragments.haplogroup(treeDto, config.haplogroupType, treeViewModel, request.uri, featureFlags.showBranchAgeEstimates)) } @@ -258,8 +258,8 @@ class TreeController @Inject()(val controllerComponents: MessagesControllerCompo val haplogroupName = rootHaplogroup.getOrElse(config.defaultRoot) val isAbsoluteTopRootView = haplogroupName == config.defaultRoot - val showBlockLayout = shouldShowBlockLayout(request) - val orientation = if (showBlockLayout) services.TreeOrientation.Vertical else services.TreeOrientation.Horizontal + val showVerticalTree = shouldShowVerticalTree(request) + val orientation = if (showVerticalTree) services.TreeOrientation.Vertical else services.TreeOrientation.Horizontal treeService.buildTreeResponse(haplogroupName, config.haplogroupType, routeType) .map { treeDto => @@ -273,8 +273,8 @@ class TreeController @Inject()(val controllerComponents: MessagesControllerCompo services.TreeLayoutService.layoutTree(treeDto, isAbsoluteTopRootView, orientation) } - if (showBlockLayout) { - Ok(views.html.fragments.blockTree(treeDto, config.haplogroupType, treeViewModel, request.uri)) + if (showVerticalTree) { + Ok(views.html.fragments.verticalTree(treeDto, config.haplogroupType, treeViewModel, request.uri)) } else { Ok(views.html.fragments.haplogroup(treeDto, config.haplogroupType, treeViewModel, request.uri, featureFlags.showBranchAgeEstimates)) } diff --git a/app/views/fragments/treeView.scala.html b/app/views/fragments/treeView.scala.html index 3ae0733..de1930b 100644 --- a/app/views/fragments/treeView.scala.html +++ b/app/views/fragments/treeView.scala.html @@ -4,7 +4,7 @@ rootHaplogroup: Option[String], searchPlaceholder: String, searchInputTitle: String, - showBlockLayout: Boolean = false)(implicit webJarsUtil: org.webjars.play.WebJarsUtil, messages: Messages, request: RequestHeader) + showVerticalTree: Boolean = false)(implicit webJarsUtil: org.webjars.play.WebJarsUtil, messages: Messages, request: RequestHeader) @main(messages(titleKey)) {
    @@ -22,14 +22,14 @@

    @messages(titleKey)

    - - + +
    diff --git a/app/views/fragments/blockTree.scala.html b/app/views/fragments/verticalTree.scala.html similarity index 91% rename from app/views/fragments/blockTree.scala.html rename to app/views/fragments/verticalTree.scala.html index 5b58bab..0a04b0a 100644 --- a/app/views/fragments/blockTree.scala.html +++ b/app/views/fragments/verticalTree.scala.html @@ -46,7 +46,7 @@
    -
    +
    @* Loading Overlay *@
    -
    +
    @renderedTreeData.map { rtd => - + @for(link <- rtd.allLinks) { } @@ -78,6 +78,9 @@ hx-target="#tree-container" hx-push-url="@fullPageUrl(Option(node.name))" hx-indicator=".tree-loading-indicator" + data-bs-toggle="tooltip" + data-bs-placement="top" + title="@messages("tree.reRoot") @node.name" style="fill: @node.fillColor; cursor: pointer;"> @@ -133,12 +136,22 @@
    + +