DT-323 Update variant configs

underlay/src/main/resources/config/criteria/aouCT/criteriaselector/variant/selector.json

@@ -0,0 +1,15 @@
+{
+  "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
+}

underlay/src/main/resources/config/criteria/aouCT/criteriaselector/variant/variant.json

@@ -0,0 +1,137 @@
+{
+  "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"
+        }
+      ]
+    }
+  ]
+}

underlay/src/main/resources/config/datamapping/aouCT/entity/variant/all.sql

@@ -0,0 +1,49 @@
+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)

underlay/src/main/resources/config/datamapping/aouCT/entity/variant/entity.json

@@ -0,0 +1,24 @@
+{
+  "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" ] }
+  ]
+}

underlay/src/main/resources/config/datamapping/aouCT/entitygroup/variantPerson/entityGroup.json

@@ -0,0 +1,14 @@
+{
+  "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"
+  }
+}

underlay/src/main/resources/config/datamapping/aouCT/entitygroup/variantPerson/idPairs.sql

@@ -0,0 +1,3 @@
+SELECT DISTINCT vid, flattened_person_id
+FROM `${omopDataset}.cb_variant_to_person`
+CROSS JOIN UNNEST(person_ids) AS flattened_person_id

underlay/src/main/resources/config/datamapping/aouCT/entitygroup/variantPerson/rollupCounts.sql

@@ -0,0 +1,3 @@
+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}"))

underlay/src/main/resources/config/underlay/aouC2024Q3R4/underlay.json

@@ -59,7 +59,9 @@
     "aouRT/surveySocialDeterminantsOfHealth",
     "aouRT/surveyCovidVaccine",
     "aouRT/surveyCope",
-    "aouRT/surveyOccurrence"
+    "aouRT/surveyOccurrence",
+
+    "aouCT/variant"
   ],
   "groupItemsEntityGroups": [
     "aouRT/brandIngredientConcept",
@@ -79,7 +81,9 @@
     "aouRT/weightPerson",
     "aouRT/bmiPerson",
     "aouRT/waistCircumferencePerson",
-    "aouRT/hipCircumferencePerson"
+    "aouRT/hipCircumferencePerson",
+
+    "aouCT/variantPerson"
   ],
   "criteriaOccurrenceEntityGroups": [
     "aouRT/conditionPerson",
@@ -149,6 +153,7 @@
     "aouCT/longReadWGS",
     "aouCT/globalDiversityArray",
     "aouCT/structuralVariants",
+    "aouCT/variant",
     "aouRT/hasPMData",
     "aouRT/bloodPressure",
     "aouRT/heartRate",

underlay/src/main/resources/config/underlay/aouSC2023Q3R2/underlay.json

@@ -59,7 +59,9 @@
     "aouRT/surveySocialDeterminantsOfHealth",
     "aouRT/surveyCovidVaccine",
     "aouRT/surveyCope",
-    "aouRT/surveyOccurrence"
+    "aouRT/surveyOccurrence",
+
+    "aouCT/variant"
   ],
   "groupItemsEntityGroups": [
     "aouRT/brandIngredientConcept",
@@ -79,7 +81,9 @@
     "aouRT/weightPerson",
     "aouRT/bmiPerson",
     "aouRT/waistCircumferencePerson",
-    "aouRT/hipCircumferencePerson"
+    "aouRT/hipCircumferencePerson",
+
+    "aouCT/variantPerson"
   ],
   "criteriaOccurrenceEntityGroups": [
     "aouRT/conditionPerson",
@@ -149,6 +153,7 @@
     "aouCT/longReadWGS",
     "aouCT/globalDiversityArray",
     "aouCT/structuralVariants",
+    "aouCT/variant",
     "aouRT/hasPMData",
     "aouRT/bloodPressure",
     "aouRT/heartRate",