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"primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::donors.specimens.samples.sample_id", + "field": "donors.specimens.samples.sample_id", + "type": "keyword", + "displayName": "SampleId", + "active": true, + "isArray": false, + "primaryKey": true, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::donors.specimens.samples.sample_type", + "field": "donors.specimens.samples.sample_type", + "type": "keyword", + "displayName": "Sample Type", + "active": true, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::donors.specimens.samples.submitter_sample_id", + "field": "donors.specimens.samples.submitter_sample_id", + "type": "keyword", + "displayName": "Submitter Sample Id", + "active": true, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::donors.specimens.specimen_id", + "field": "donors.specimens.specimen_id", + "type": "keyword", + "displayName": "SpecimenId", + "active": true, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::donors.specimens.specimen_tissue_source", + "field": "donors.specimens.specimen_tissue_source", + "type": "keyword", + "displayName": "Specimen Tissue Source", + "active": true, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::donors.specimens.specimen_type", + "field": "donors.specimens.specimen_type", + "type": "keyword", + "displayName": "Specimen Type", + "active": true, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::donors.specimens.submitter_specimen_id", + "field": "donors.specimens.submitter_specimen_id", + "type": "keyword", + "displayName": "Submitter Specimen Id", + "active": true, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::donors.specimens.tumour_normal_designation", + "field": "donors.specimens.tumour_normal_designation", + "type": "keyword", + "displayName": "Tumour Normal Designation", + "active": true, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::donors.submitter_donor_id", + "field": "donors.submitter_donor_id", + "type": "keyword", + "displayName": "Submitter Donor Id", + "active": true, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::file", + "field": "file", + "type": "object", + "displayName": "File", + "active": false, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::file.index_file", + "field": "file.index_file", + "type": "object", + "displayName": "File Index File", + "active": false, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::file.index_file.file_type", + "field": "file.index_file.file_type", + "type": "keyword", + "displayName": "Index File Type", + "active": true, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::file.index_file.md5sum", + "field": "file.index_file.md5sum", + "type": "keyword", + "displayName": "Index File Md5sum", + "active": true, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::file.index_file.name", + "field": "file.index_file.name", + "type": "keyword", + "displayName": "Index File Name", + "active": true, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::file.index_file.object_id", + "field": "file.index_file.object_id", + "type": "keyword", + "displayName": "Index File Object Id", + "active": true, + "isArray": false, + "primaryKey": true, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::file.index_file.size", + "field": "file.index_file.size", + "type": "long", + "displayName": "Index File Size", + "active": true, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::file.md5sum", + "field": "file.md5sum", + "type": "keyword", + "displayName": "File Md5sum", + "active": true, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::file.name", + "field": "file.name", + "type": "keyword", + "displayName": "File Name", + "active": true, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::file.size", + "field": "file.size", + "type": "long", + "displayName": "File Size", + "active": true, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::file_access", + "field": "file_access", + "type": "keyword", + "displayName": "File Access", + "active": true, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::file_autocomplete", + "field": "file_autocomplete", + "type": "keyword", + "displayName": "File Autocomplete", + "active": false, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::file_type", + "field": "file_type", + "type": "keyword", + "displayName": "File Type", + "active": true, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::object_id", + "field": "object_id", + "type": "keyword", + "displayName": "Object Id", + "active": true, + "isArray": false, + "primaryKey": true, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::repositories", + "field": "repositories", + "type": "nested", + "displayName": "Repositories", + "active": false, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::repositories.code", + "field": "repositories.code", + "type": "keyword", + "displayName": "Repositories Code", + "active": true, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::repositories.country", + "field": "repositories.country", + "type": "keyword", + "displayName": "Repositories Country", + "active": true, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::repositories.name", + "field": "repositories.name", + "type": "keyword", + "displayName": "Repositories Name", + "active": true, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::repositories.organization", + "field": "repositories.organization", + "type": "keyword", + "displayName": "Repositories Organization", + "active": true, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::repositories.url", + "field": "repositories.url", + "type": "keyword", + "displayName": "Repositories Url", + "active": true, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::study_id", + "field": "study_id", + "type": "keyword", + "displayName": "Study Id", + "active": true, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::analysis.first_published_at", + "field": "analysis.first_published_at", + "type": "date", + "displayName": "Analysis First Published At", + "active": false, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::analysis.published_at", + "field": "analysis.published_at", + "type": "date", + "displayName": "Analysis Published At", + "active": false, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::analysis.updated_at", + "field": "analysis.updated_at", + "type": "date", + "displayName": "Analysis Updated At", + "active": false, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + } +] \ No newline at end of file diff --git a/playground-data/arranger-metadata/matchbox-state.json b/playground-data/arranger-metadata/matchbox-state.json new file mode 100644 index 0000000..1929bf4 --- /dev/null +++ b/playground-data/arranger-metadata/matchbox-state.json @@ -0,0 +1,42 @@ +[ + { + "displayName": "some_alias", + "field": "", + "isActive": false, + "keyField": null, + "searchFields": [], + "__typename": "MatchBoxField" + }, + { + "displayName": "Donors", + "field": "donors", + "isActive": true, + "keyField": null, + "searchFields": [], + "__typename": "MatchBoxField" + }, + { + "displayName": "Donors Specimens", + "field": "donors.specimens", + "isActive": true, + "keyField": null, + "searchFields": [], + "__typename": "MatchBoxField" + }, + { + "displayName": "Donors Specimens Samples", + "field": "donors.specimens.samples", + "isActive": true, + "keyField": null, + "searchFields": [], + "__typename": "MatchBoxField" + }, + { + "displayName": "Repositories", + "field": "repositories", + "isActive": true, + "keyField": null, + "searchFields": [], + "__typename": "MatchBoxField" + } +] \ No newline at end of file diff --git a/playground-data/song-schemas/VariantCall.json b/playground-data/song-schemas/VariantCall.json new file mode 100644 index 0000000..c658fd6 --- /dev/null +++ b/playground-data/song-schemas/VariantCall.json @@ -0,0 +1,81 @@ +{ + "studyId" : "ABC123", + "analysisType" : { + "name" : "variantCall" + }, + "experiment": { + "variantCallingTool": "silver bullet", + "matchedNormalSampleSubmitterId": "sample-x24-11a", + "randomField14" : "we can define any EXPERIMENT field. For example, randomField14", + "randomField15" : "as a second example, we can define another random EXPERIMENT field called randomField15", + "info" : { + "randomField16" : "alternatively, put some extra EXPERIMENT fields here" + } + }, + "samples": [ + { + "submitterSampleId": "internal_sample_1", + "sampleType": "Total RNA", + "matchedNormalSubmitterSampleId": "sample-x24-11a", + "specimen": { + "submitterSpecimenId": "internal_specimen_1", + "specimenType": "Primary tumour", + "specimenTissueSource": "Solid tissue", + "tumourNormalDesignation": "Tumour", + "randomField1" : "we can define any SPECIMEN field. For example, randomField1", + "randomField2" : "as a second example, we can define another random SPECIMEN field called randomField2", + "info" : { + "randomField3" : "alternatively, put some extra SPECIMEN fields here" + } + }, + "donor": { + "submitterDonorId": "internal_donor_123456789-00", + "gender": "Female", + "age": 30, + "randomField4" : "we can define any DONOR field. For example, randomField4", + "randomField5" : "as a second example, we can define another random DONOR field called randomField5", + "info" : { + "randomField6" : "alternatively, put some extra DONOR fields here" + } + }, + "randomField7" : "we can define any SAMPLE field. For example, randomField7", + "randomField8" : "as a second example, we can define another random SAMPLE field called randomField8", + "info" : { + "randomField9" : "alternatively, put some extra SAMPLE fields here" + } + } + ], + "files": [ + { + "dataType": "Variant Calling Data", + "fileName": "example.vcf.gz", + "fileSize": 52, + "fileMd5sum": "9a793e90d0d1e11301ea8da996446e59", + "fileAccess" : "open", + "fileType": "VCF", + "randomField10" : "we can define any FILE field. For example, randomField10", + "randomField11" : "as a second example, we can define another random FILE field called randomField11", + "info" : { + "randomField12" : "alternatively, put some extra FILE fields here" + } + }, + { + "dataType": "Variant Calling Index", + "fileName": "example.vcf.gz.idx", + "fileSize": 24, + "fileMd5sum": "c03274816eb4907a92b8e5632cd6eb81", + "fileAccess" : "open", + "fileType": "IDX", + "randomField10" : "we can define any FILE field. For example, randomField10", + "randomField13" : "as a second example, we can define another random FILE field called randomField13", + "info" : { + "randomField12" : "alternatively, put some extra FILE fields here" + } + } + ], + "randomField17" : "we can define any ANALYSIS field. For example, randomField17", + "randomField18" : "as a second example, we can define another random ANALYSIS field called randomField18", + "info" : { + "randomField19" : "alternatively, put some extra ANALYSIS fields here" + } +}