only need to specify GATK Jar for legacy extractions

all-of-us · Nov 26, 2024 · 266d106 · 266d106
1 parent 1b4a121
commit 266d106
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Showing 5 changed files with 6 additions and 9 deletions.
diff --git a/api/config/config_local.json b/api/config/config_local.json
@@ -58,7 +58,6 @@
       "extractionScatterTasksPerSample": 4
     },
     "cdrv8plus": {
-      "gatkJarUri": "gs:\/\/all-of-us-workbench-test-genomics\/wgs\/gatk-package-after_master_merge-177-gbd0a99c-SNAPSHOT-local.jar",
       "methodNamespace": "aouwgscohortextraction-test",
       "methodName": "echo-prototyping",
       "methodRepoVersion": 3,

diff --git a/api/config/config_preprod.json b/api/config/config_preprod.json
@@ -58,7 +58,6 @@
       "extractionScatterTasksPerSample": 4
     },
     "cdrv8plus": {
-      "gatkJarUri": "gs:\/\/all-of-us-workbench-test-genomics\/wgs\/gatk-package-after_master_merge-177-gbd0a99c-SNAPSHOT-local.jar",
       "methodNamespace": "aouwgscohortextraction-preprod",
       "methodName": "GvsExtractCohortFromSampleNamesV8",
       "methodRepoVersion": 1,

diff --git a/api/config/config_test.json b/api/config/config_test.json
@@ -58,7 +58,6 @@
       "extractionScatterTasksPerSample": 4
     },
     "cdrv8plus": {
-      "gatkJarUri": "gs:\/\/all-of-us-workbench-test-genomics\/wgs\/gatk-package-after_master_merge-177-gbd0a99c-SNAPSHOT-local.jar",
       "methodNamespace": "aouwgscohortextraction-test",
       "methodName": "echo-prototyping",
       "methodRepoVersion": 3,

diff --git a/api/src/main/java/org/pmiops/workbench/config/WorkbenchConfig.java b/api/src/main/java/org/pmiops/workbench/config/WorkbenchConfig.java
@@ -180,7 +180,6 @@ public static class WgsCohortExtractionConfig {
     public boolean enableJiraTicketingOnFailure;
 
     public abstract static class VersionedConfig {
-      public String gatkJarUri;
       // 'method' values refer to both the stored Method and the generated Method Configuration
       public String methodNamespace;
       public String methodName;
@@ -196,6 +195,7 @@ public abstract static class VersionedConfig {
 
     // for extraction workflows compatible with CDR v7 and earlier
     public static class LegacyWorkflowConfig extends VersionedConfig {
+      public String gatkJarUri;
       // This should not exceed the value of GenomicExtractionService.MAX_EXTRACTION_SCATTER.
       public int minExtractionScatterTasks;
       public float extractionScatterTasksPerSample;

diff --git a/api/src/main/java/org/pmiops/workbench/genomics/GenomicExtractionService.java b/api/src/main/java/org/pmiops/workbench/genomics/GenomicExtractionService.java
@@ -321,8 +321,7 @@ private Map<String, String> getWorkflowInputs(
       List<String> personIds,
       String extractionFolder,
       String outputDir,
-      boolean useLegacyWorkflow,
-      String gatkJarUri) {
+      boolean useLegacyWorkflow) {
 
     String[] destinationParts = cohortExtractionConfig.extractionDestinationDataset.split("\\.");
     if (destinationParts.length != 2) {
@@ -361,6 +360,9 @@ private Map<String, String> getWorkflowInputs(
       // Added in https://github.com/broadinstitute/gatk/pull/7698
       maybeInputs.put(EXTRACT_WORKFLOW_NAME + ".extraction_uuid", "\"" + extractionUuid + "\"");
       maybeInputs.put(EXTRACT_WORKFLOW_NAME + ".cohort_table_prefix", "\"" + extractionUuid + "\"");
+      maybeInputs.put(
+          EXTRACT_WORKFLOW_NAME + ".gatk_override",
+          "\"" + cohortExtractionConfig.legacyVersions.gatkJarUri + "\"");
     } else {
       // Added Nov 2024
       // replaces extraction_uuid and cohort_table_prefix which are now set to this value
@@ -399,7 +401,6 @@ private Map<String, String> getWorkflowInputs(
         // etc
         .put(EXTRACT_WORKFLOW_NAME + ".output_file_base_name", "\"interval\"")
         .put(EXTRACT_WORKFLOW_NAME + ".output_gcs_dir", "\"" + outputDir + "\"")
-        .put(EXTRACT_WORKFLOW_NAME + ".gatk_override", "\"" + gatkJarUri + "\"")
         .putAll(maybeInputs)
         .build();
   }
@@ -470,8 +471,7 @@ public GenomicExtractionJob submitGenomicExtractionJob(
                             personIds,
                             extractionFolder,
                             outputDir,
-                            useLegacyWorkflow,
-                            versionedConfig.gatkJarUri))
+                            useLegacyWorkflow))
                     .methodConfigVersion(versionedConfig.methodRepoVersion)
                     .methodRepoMethod(createRepoMethodParameter(versionedConfig))
                     .name(extractionUuid)