Add task for VAT validation #3 (#7360)

scripts/variantstore/wdl/GvsValidateVAT.wdl

@@ -27,11 +27,19 @@ workflow GvsValidateVatTable {
             last_modified_timestamp = GetBQTableLastModifiedDatetime.last_modified_timestamp
     }
 
+    call SpotCheckForExpectedTranscripts {
+        input:
+            query_project_id = query_project_id,
+            fq_vat_table = fq_vat_table,
+            service_account_json_path = service_account_json_path,
+            last_modified_timestamp = GetBQTableLastModifiedDatetime.last_modified_timestamp
+    }
+
     # once there is more than one check, they will be gathered into this workflow output, in the format
     # [{ValidationRule1: "PASS/FAIL Extra info from this test"},
     #  {ValidationRule2: "PASS/FAIL Extra from this test"}]
     output {
-        Array[Map[String, String]] validation_results = [EnsureVatTableHasVariants.result]
+        Array[Map[String, String]] validation_results = [EnsureVatTableHasVariants.result, SpotCheckForExpectedTranscripts.result]
     }
 }
 
@@ -85,6 +93,68 @@ task EnsureVatTableHasVariants {
     }
 }
 
+task SpotCheckForExpectedTranscripts {
+    input {
+        String query_project_id
+        String fq_vat_table
+        String? service_account_json_path
+        String last_modified_timestamp
+    }
+
+    String has_service_account_file = if (defined(service_account_json_path)) then 'true' else 'false'
+
+    command <<<
+        if [ ~{has_service_account_file} = 'true' ]; then
+            gsutil cp ~{service_account_json_path} local.service_account.json
+            gcloud auth activate-service-account --key-file=local.service_account.json
+            gcloud config set project ~{query_project_id}
+        fi
+        echo "project_id = ~{query_project_id}" > ~/.bigqueryrc
+
+        bq query --nouse_legacy_sql --project_id=~{query_project_id} --format=csv 'SELECT
+            contig,
+            position,
+            vid,
+            gene_symbol,
+            variant_consequence
+        FROM
+            ~{fq_vat_table},
+            UNNEST(consequence) AS variant_consequence
+        WHERE
+            contig = "chr19" AND
+            position >= 35740407 AND
+            position <= 35740469 AND
+            variant_consequence NOT IN ("downstream_gene_variant","upstream_gene_variant") AND
+            gene_symbol NOT IN ("IGFLR1","AD000671.2")' > bq_query_output.csv
+
+        # get number of lines in bq query output
+        NUMRESULTS=$(awk 'END{print NR}' bq_query_output.csv)
+
+        # if the result of the query has any rows, that means there were unexpected transcripts at the
+        # specified location, so report those back in the output
+        if [[ $NUMRESULTS = "0" ]]; then
+            echo "PASS: The VAT table ~{fq_vat_table} only has the expected transcripts at the tested location ('IGFLR1' and 'AD000671.2' in chromosome 19, between positions 35,740,407 - 35,740,469)." > validation_results.txt
+        else
+            echo "FAIL: The VAT table ~{fq_vat_table} had unexpected transcripts at the tested location: [csv output follows] " > validation_results.txt
+            cat bq_query_output.csv >> validation_results.txt
+        fi
+    >>>
+    # ------------------------------------------------
+    # Runtime settings:
+    runtime {
+        docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:305.0.0"
+        memory: "1 GB"
+        preemptible: 3
+        cpu: "1"
+        disks: "local-disk 100 HDD"
+    }
+    # ------------------------------------------------
+    # Output: {"Name of validation rule": "PASS/FAIL plus additional validation results"}
+    output {
+        Map[String, String] result = {"SpotCheckForExpectedTranscripts": read_string('validation_results.txt')}
+    }
+}
+
 task GetBQTableLastModifiedDatetime {
     # because this is being used to determine if the data has changed, never use call cache
     meta {