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Use mapped HGNC name for assay facts gene text when available #597

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Merged
bencap merged 1 commit into from
Feb 5, 2026
Merged

Use mapped HGNC name for assay facts gene text when available #597

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21 changes: 18 additions & 3 deletions src/components/AssayFactSheet.vue
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,9 @@
<div class="mavedb-assay-facts-section mavedb-assay-facts-bottom-separator">
<div class="mavedb-assay-facts-row">
<div class="mavedb-assay-facts-label">Gene (HGNC symbol)</div>
<div class="mavedb-assay-facts-value">{{ scoreSet.targetGenes[0]?.name }}</div>
<div class="mavedb-assay-facts-value">
{{ geneTextForScoreSet ? geneTextForScoreSet : 'Not specified' }}
</div>
</div>
</div>
<div class="mavedb-assay-facts-section">
Expand Down Expand Up @@ -238,8 +240,7 @@ export default defineComponent({
},

geneAndYear: function () {
// TODO VariantEffect/mavedb-api#450
const gene = this.scoreSet.targetGenes?.[0]?.name
const gene = this.geneTextForScoreSet
const year = this.scoreSet.primaryPublicationIdentifiers[0]?.publicationYear
const parts = [gene, year?.toString()].filter((x) => x != null)
return parts.length > 0 ? parts.join(' ') : undefined
Expand All @@ -253,6 +254,20 @@ export default defineComponent({
return this.scoreSet.primaryPublicationIdentifiers[0]?.publicationJournal
},

distinctGenesForTargets: function () {
// empty when no target genes have mappedHgncName
const geneNames = this.scoreSet.targetGenes?.map((tg) => tg.mappedHgncName) || []
return _.uniq(geneNames.filter((name) => !_.isEmpty(name))) as string[]
},

geneTextForScoreSet: function () {
if (this.distinctGenesForTargets.length == 0) {
return this.scoreSet.targetGenes[0]?.name || null
}

return this.distinctGenesForTargets.length == 1 ? this.distinctGenesForTargets[0] : 'Multiple genes'
},

detectsNmd: function () {
const libraryCreationMethod = this.scoreSet.experiment?.keywords?.find(
(k) => k.keyword.key === 'Variant Library Creation Method'
Expand Down
61 changes: 37 additions & 24 deletions src/schema/openapi.d.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -667,7 +667,7 @@ export interface paths {
* The index to start from. If None, starts from the beginning.
* limit : Optional[int]
* The maximum number of variants to return. If None, returns all variants.
* namespaces: List[Literal["scores", "counts", "vep", "gnomad"]]
* namespaces: List[Literal["scores", "counts", "vep", "gnomad", "clingen"]]
* The namespaces of all columns except for accession, hgvs_nt, hgvs_pro, and hgvs_splice.
* We may add ClinVar in the future.
* drop_na_columns : bool, optional
Expand Down Expand Up @@ -2708,7 +2708,7 @@ export interface components {
/** Processingstate */
processingState?: string | null;
/** Officialcollections */
officialCollections: components["schemas"]["mavedb__view_models__score_set__OfficialCollection"][];
officialCollections: components["schemas"]["OfficialCollection"][];
};
/**
* ExperimentControlledKeyword
Expand Down Expand Up @@ -3542,6 +3542,15 @@ export interface components {
/** Privatekey */
privateKey: string;
};
/** OfficialCollection */
OfficialCollection: {
/** Badgename */
badgeName: string;
/** Name */
name: string;
/** Urn */
urn: string;
};
/** OrcidUser */
OrcidUser: {
/** Recordtype */
Expand Down Expand Up @@ -4092,11 +4101,11 @@ export interface components {
/** Functionalclassifications */
functionalClassifications?: components["schemas"]["mavedb__view_models__score_calibration__FunctionalClassification"][] | null;
/** Thresholdsources */
thresholdSources?: components["schemas"]["PublicationIdentifier"][] | null;
thresholdSources: components["schemas"]["PublicationIdentifier"][];
/** Classificationsources */
classificationSources?: components["schemas"]["PublicationIdentifier"][] | null;
classificationSources: components["schemas"]["PublicationIdentifier"][];
/** Methodsources */
methodSources?: components["schemas"]["PublicationIdentifier"][] | null;
methodSources: components["schemas"]["PublicationIdentifier"][];
/** Calibrationmetadata */
calibrationMetadata?: Record<string, never> | null;
/** Recordtype */
Expand Down Expand Up @@ -4153,11 +4162,11 @@ export interface components {
/** Functionalclassifications */
functionalClassifications?: components["schemas"]["FunctionalClassificationCreate"][] | null;
/** Thresholdsources */
thresholdSources?: components["schemas"]["PublicationIdentifierCreate"][] | null;
thresholdSources: components["schemas"]["PublicationIdentifierCreate"][];
/** Classificationsources */
classificationSources?: components["schemas"]["PublicationIdentifierCreate"][] | null;
classificationSources: components["schemas"]["PublicationIdentifierCreate"][];
/** Methodsources */
methodSources?: components["schemas"]["PublicationIdentifierCreate"][] | null;
methodSources: components["schemas"]["PublicationIdentifierCreate"][];
/** Calibrationmetadata */
calibrationMetadata?: Record<string, never> | null;
/** Scoreseturn */
Expand All @@ -4184,11 +4193,11 @@ export interface components {
/** Functionalclassifications */
functionalClassifications?: components["schemas"]["SavedFunctionalClassification"][] | null;
/** Thresholdsources */
thresholdSources?: components["schemas"]["SavedPublicationIdentifier"][] | null;
thresholdSources: components["schemas"]["SavedPublicationIdentifier"][];
/** Classificationsources */
classificationSources?: components["schemas"]["SavedPublicationIdentifier"][] | null;
classificationSources: components["schemas"]["SavedPublicationIdentifier"][];
/** Methodsources */
methodSources?: components["schemas"]["SavedPublicationIdentifier"][] | null;
methodSources: components["schemas"]["SavedPublicationIdentifier"][];
/** Calibrationmetadata */
calibrationMetadata?: Record<string, never> | null;
/** Recordtype */
Expand Down Expand Up @@ -4289,7 +4298,7 @@ export interface components {
scoreCalibrations?: components["schemas"]["ScoreCalibration"][] | null;
experiment: components["schemas"]["Experiment"];
/** Officialcollections */
officialCollections: components["schemas"]["mavedb__view_models__score_set__OfficialCollection"][];
officialCollections: components["schemas"]["OfficialCollection"][];
/** Private */
private: boolean;
processingState?: components["schemas"]["ProcessingState"] | null;
Expand Down Expand Up @@ -4714,6 +4723,8 @@ export interface components {
recordType?: string;
targetSequence?: components["schemas"]["SavedTargetSequence"] | null;
targetAccession?: components["schemas"]["SavedTargetAccession"] | null;
/** Mappedhgncname */
mappedHgncName?: string | null;
/** Uniprotidfrommappedmetadata */
uniprotIdFromMappedMetadata?: string | null;
};
Expand Down Expand Up @@ -4920,6 +4931,8 @@ export interface components {
recordType?: string;
targetSequence?: components["schemas"]["TargetSequence"] | null;
targetAccession?: components["schemas"]["TargetAccession"] | null;
/** Mappedhgncname */
mappedHgncName?: string | null;
/** Uniprotidfrommappedmetadata */
uniprotIdFromMappedMetadata?: string | null;
};
Expand Down Expand Up @@ -4952,6 +4965,8 @@ export interface components {
recordType?: string;
targetSequence?: components["schemas"]["TargetSequence"] | null;
targetAccession?: components["schemas"]["TargetAccession"] | null;
/** Mappedhgncname */
mappedHgncName?: string | null;
/** Uniprotidfrommappedmetadata */
uniprotIdFromMappedMetadata?: string | null;
/** Scoreseturn */
Expand Down Expand Up @@ -5756,15 +5771,6 @@ export interface components {
*/
variants?: components["schemas"]["VariantEffectMeasurement"][];
};
/** OfficialCollection */
mavedb__view_models__score_set__OfficialCollection: {
/** Badgename */
badgeName: string;
/** Name */
name: string;
/** Urn */
urn: string;
};
/**
* sequenceString
* @description A character string of Residues that represents a biological sequence using the conventional sequence order (5'-to-3' for nucleic acid sequences, and amino-to-carboxyl for amino acid sequences). IUPAC ambiguity codes are permitted in Sequence Strings.
Expand Down Expand Up @@ -8685,6 +8691,11 @@ export interface operations {
};
/** Get Filter Options For Search */
get_filter_options_for_search_api_v1_score_sets_search_filter_options_post: {
parameters: {
header?: {
"x-active-roles"?: string | null;
};
};
requestBody: {
content: {
"application/json": components["schemas"]["ScoreSetsSearch"];
Expand Down Expand Up @@ -8983,7 +8994,7 @@ export interface operations {
* The index to start from. If None, starts from the beginning.
* limit : Optional[int]
* The maximum number of variants to return. If None, returns all variants.
* namespaces: List[Literal["scores", "counts", "vep", "gnomad"]]
* namespaces: List[Literal["scores", "counts", "vep", "gnomad", "clingen"]]
* The namespaces of all columns except for accession, hgvs_nt, hgvs_pro, and hgvs_splice.
* We may add ClinVar in the future.
* drop_na_columns : bool, optional
Expand All @@ -9005,8 +9016,8 @@ export interface operations {
start?: number;
/** @description Maximum number of variants to return */
limit?: number;
/** @description One or more data types to include: scores, counts, clinVar, gnomAD, VEP */
namespaces?: ("scores" | "counts" | "vep" | "gnomad")[];
/** @description One or more data types to include: scores, counts, ClinGen, gnomAD, VEP */
namespaces?: ("scores" | "counts" | "vep" | "gnomad" | "clingen")[];
drop_na_columns?: boolean | null;
include_custom_columns?: boolean | null;
include_post_mapped_hgvs?: boolean | null;
Expand Down Expand Up @@ -9068,6 +9079,7 @@ export interface operations {
urn: string;
};
};
/** @description Score files, to be uploaded as multipart form data. The `scores_file` is required, while the `counts_file`, `score_columns_metadata`, and `count_columns_metadata` are optional. */
requestBody?: {
content: {
"multipart/form-data": components["schemas"]["Body_upload_score_set_variant_data_api_v1_score_sets__urn__variants_data_post"];
Expand Down Expand Up @@ -9604,6 +9616,7 @@ export interface operations {
urn: string;
};
};
/** @description Score set properties and score files, to be uploaded as multipart form data. All fields here are optional, and only those provided will be updated. */
requestBody?: {
content: {
"multipart/form-data": components["schemas"]["Body_update_score_set_with_variants_api_v1_score_sets_with_variants__urn__patch"];
Expand Down