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DT-323 Update variant configs (#1138)
* DT-323 adding config for variants * updating config for variant search
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15 changes: 15 additions & 0 deletions
15
underlay/src/main/resources/config/criteria/aouCT/criteriaselector/variant/selector.json
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| { | ||
| "name": "tanagra-variant", | ||
| "displayName": "SNP/Indel Variant", | ||
| "isEnabledForCohorts": true, | ||
| "isEnabledForDataFeatureSets": false, | ||
| "display": { | ||
| "category": "Genomics", | ||
| "tags": null | ||
| }, | ||
| "filterBuilder": "core.FilterableGroupFilterBuilder", | ||
| "plugin": "filterableGroup", | ||
| "pluginConfig": null, | ||
| "pluginConfigFile": "variant.json", | ||
| "modifiers": null | ||
| } |
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137
underlay/src/main/resources/config/criteria/aouCT/criteriaselector/variant/variant.json
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| { | ||
| "columns": [ | ||
| { | ||
| "key": "id", | ||
| "widthString": "100%", | ||
| "title": "Variant id" | ||
| }, | ||
| { | ||
| "key": "gene", | ||
| "widthDouble": 100, | ||
| "title": "Gene" | ||
| }, | ||
| { | ||
| "key": "rs_number", | ||
| "widthDouble": 100, | ||
| "title": "RS number" | ||
| }, | ||
| { | ||
| "key": "consequence", | ||
| "widthDouble": 100, | ||
| "title": "Consequence" | ||
| }, | ||
| { | ||
| "key": "clinvar_significance", | ||
| "widthDouble": 100, | ||
| "title": "ClinVar significance" | ||
| }, | ||
| { | ||
| "key": "protein_change", | ||
| "widthDouble": 100, | ||
| "title": "Protein change" | ||
| }, | ||
| { | ||
| "key": "allele_count", | ||
| "widthDouble": 100, | ||
| "title": "Allele count" | ||
| }, | ||
| { | ||
| "key": "allele_number", | ||
| "widthDouble": 100, | ||
| "title": "Allele number" | ||
| }, | ||
| { | ||
| "key": "allele_frequency", | ||
| "widthDouble": 100, | ||
| "title": "Allele frequency" | ||
| }, | ||
| { | ||
| "key": "t_item_count", | ||
| "widthDouble": 150, | ||
| "title": "Participant count" | ||
| } | ||
| ], | ||
| "entityGroup": "variantPerson", | ||
| "valueConfigs": [ | ||
| { | ||
| "attribute": "gene", | ||
| "title": "Gene" | ||
| }, | ||
| { | ||
| "attribute": "consequence", | ||
| "title": "Consequence" | ||
| }, | ||
| { | ||
| "attribute": "clinvar_significance", | ||
| "title": "ClinVar significance" | ||
| }, | ||
| { | ||
| "attribute": "allele_count", | ||
| "title": "Allele count" | ||
| }, | ||
| { | ||
| "attribute": "allele_number", | ||
| "title": "Allele number" | ||
| }, | ||
| { | ||
| "attribute": "allele_frequency", | ||
| "title": "Allele frequency" | ||
| } | ||
| ], | ||
| "searchConfigs": [ | ||
| { | ||
| "name": "RS number", | ||
| "example": "rs558865434", | ||
| "regex": "rs\\d+", | ||
| "parameters": [ | ||
| { | ||
| "attribute": "rs_number", | ||
| "operator": "OPERATOR_EQUALS" | ||
| } | ||
| ] | ||
| }, | ||
| { | ||
| "name": "Variant id", | ||
| "example": "20-38623282-G-A", | ||
| "regex": "\\d+-\\d+-\\w+-\\w+", | ||
| "parameters": [ | ||
| { | ||
| "attribute": "id", | ||
| "operator": "OPERATOR_EQUALS" | ||
| } | ||
| ] | ||
| }, | ||
| { | ||
| "name": "Genomic region", | ||
| "example": "chr20:38623000-38623379", | ||
| "regex": "(\\w+):(\\d+)-(\\d+)", | ||
| "parameters": [ | ||
| { | ||
| "attribute": "contig", | ||
| "operator": "OPERATOR_EQUALS" | ||
| }, | ||
| { | ||
| "attribute": "position", | ||
| "operator": "OPERATOR_GREATER_THAN_OR_EQUAL" | ||
| }, | ||
| { | ||
| "attribute": "position", | ||
| "operator": "OPERATOR_LESS_THAN_OR_EQUAL" | ||
| } | ||
| ] | ||
| }, | ||
| { | ||
| "name": "Gene", | ||
| "example": "WFDC2", | ||
| "regex": "\\w+", | ||
| "displayOrder": -1, | ||
| "parameters": [ | ||
| { | ||
| "attribute": "gene", | ||
| "operator": "OPERATOR_EQUALS", | ||
| "case": "CASE_UPPER" | ||
| } | ||
| ] | ||
| } | ||
| ] | ||
| } |
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underlay/src/main/resources/config/datamapping/aouCT/entity/variant/all.sql
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| WITH sorted_transcripts AS ( | ||
| SELECT vid, | ||
| consequence, | ||
| aa_change, | ||
| contig, | ||
| position, | ||
| ref_allele, | ||
| alt_allele, | ||
| dbsnp_rsid, | ||
| transcript, | ||
| dna_change_in_transcript, | ||
| clinvar_classification, | ||
| gvs_all_ac, | ||
| gvs_all_an, | ||
| gvs_all_af, | ||
| ROW_NUMBER() OVER( | ||
| PARTITION BY vid ORDER BY | ||
| CASE ARRAY_TO_STRING(consequence, ', ') | ||
| WHEN 'upstream_gene_variant' | ||
| THEN 4 | ||
| WHEN 'downstream_gene_variant' | ||
| THEN 5 | ||
| ELSE 1 | ||
| END) AS row_number | ||
| FROM `${omopDataset}.prep_vat` | ||
| WHERE is_canonical_transcript OR transcript IS NULL | ||
| ORDER BY vid, row_number), | ||
|
|
||
| genes AS ( | ||
| SELECT vid, ARRAY_AGG(DISTINCT gene_symbol IGNORE NULLS ORDER BY gene_symbol) AS genes | ||
| FROM `${omopDataset}.prep_vat` | ||
| GROUP BY vid | ||
| ) | ||
|
|
||
| SELECT | ||
| sorted_transcripts.vid, | ||
| genes.genes as gene_symbol, | ||
| sorted_transcripts.dbsnp_rsid, | ||
| sorted_transcripts.consequence, | ||
| sorted_transcripts.aa_change, | ||
| sorted_transcripts.clinvar_classification, | ||
| sorted_transcripts.gvs_all_ac, | ||
| sorted_transcripts.gvs_all_an, | ||
| sorted_transcripts.gvs_all_af, | ||
| sorted_transcripts.contig, | ||
| sorted_transcripts.position | ||
| FROM sorted_transcripts, genes | ||
| WHERE genes.vid = sorted_transcripts.vid | ||
| AND (sorted_transcripts.row_number =1 or sorted_transcripts.transcript is NULL) |
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underlay/src/main/resources/config/datamapping/aouCT/entity/variant/entity.json
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| { | ||
| "name": "variant", | ||
| "allInstancesSqlFile": "all.sql", | ||
| "attributes": [ | ||
| { "name": "id", "dataType": "STRING", "valueFieldName": "vid" }, | ||
| { "name": "gene", "dataType": "STRING", "isDataTypeRepeated": true, "valueFieldName": "gene_symbol", "isComputeDisplayHint": true }, | ||
| { "name": "rs_number", "dataType": "STRING", "isDataTypeRepeated": true, "valueFieldName": "dbsnp_rsid" }, | ||
| { "name": "consequence", "dataType": "STRING", "isDataTypeRepeated": true, "isComputeDisplayHint": true }, | ||
| { "name": "protein_change", "dataType": "STRING", "valueFieldName": "aa_change" }, | ||
| { "name": "clinvar_significance", "dataType": "STRING", "isDataTypeRepeated": true, "valueFieldName": "clinvar_classification", "isComputeDisplayHint": true }, | ||
| { "name": "allele_count", "dataType": "INT64", "valueFieldName": "gvs_all_ac", "isComputeDisplayHint": true }, | ||
| { "name": "allele_number", "dataType": "INT64", "valueFieldName": "gvs_all_an", "isComputeDisplayHint": true }, | ||
| { "name": "allele_frequency", "dataType": "DOUBLE", "valueFieldName": "gvs_all_af", "isComputeDisplayHint": true }, | ||
| { "name": "contig", "dataType": "STRING" }, | ||
| { "name": "position", "dataType": "INT64" } | ||
| ], | ||
| "idAttribute": "id", | ||
| "optimizeGroupByAttributes": [ "id" ], | ||
| "optimizeSearchByAttributes": [ | ||
| { "attributes": [ "gene" ] }, | ||
| { "attributes": [ "rs_number" ] }, | ||
| { "attributes": [ "contig", "position" ] } | ||
| ] | ||
| } |
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...ay/src/main/resources/config/datamapping/aouCT/entitygroup/variantPerson/entityGroup.json
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| { | ||
| "name": "variantPerson", | ||
| "groupEntity": "variant", | ||
| "itemsEntity": "person", | ||
| "idPairsSqlFile": "idPairs.sql", | ||
| "useSourceIdPairsSql": true, | ||
| "groupEntityIdFieldName": "vid", | ||
| "itemsEntityIdFieldName": "flattened_person_id", | ||
| "rollupCountsSql": { | ||
| "sqlFile": "rollupCounts.sql", | ||
| "entityIdFieldName": "vid", | ||
| "rollupCountFieldName": "num_persons" | ||
| } | ||
| } |
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underlay/src/main/resources/config/datamapping/aouCT/entitygroup/variantPerson/idPairs.sql
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| SELECT DISTINCT vid, flattened_person_id | ||
| FROM `${omopDataset}.cb_variant_to_person` | ||
| CROSS JOIN UNNEST(person_ids) AS flattened_person_id |
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...ay/src/main/resources/config/datamapping/aouCT/entitygroup/variantPerson/rollupCounts.sql
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| SELECT vid, ARRAY_LENGTH(person_ids) AS num_persons | ||
| /* Wrap variant_to_person table in a SELECT DISTINCT because there is a duplicate row in the test data. */ | ||
| FROM (SELECT DISTINCT vid, person_ids FROM `${omopDataset}.cb_variant_to_person` WHERE REGEXP_CONTAINS(vid, r"{indexIdRegex}")) |
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