From 7872add87f2151b86f1b022447d998964f9df676 Mon Sep 17 00:00:00 2001
From: npetrill <npetrill@broadinstitute.org>
Date: Fri, 10 Jan 2025 12:22:41 -0500
Subject: [PATCH] try updating usercomment

---
 .../test_illumina_genotyping_array.yml        | 92 +++++++++++--------
 1 file changed, 56 insertions(+), 36 deletions(-)

diff --git a/.github/workflows/test_illumina_genotyping_array.yml b/.github/workflows/test_illumina_genotyping_array.yml
index c57a84ce4f..1abbcc06ce 100644
--- a/.github/workflows/test_illumina_genotyping_array.yml
+++ b/.github/workflows/test_illumina_genotyping_array.yml
@@ -111,7 +111,7 @@ jobs:
       - name: Fetch Dockstore Workflow Commit Hash
         run: |
           # Wait 5.5 minutes for Dockstore to update
-          sleep 330
+          sleep 3
           
           DOCKSTORE_COMMIT_HASH_FROM_FETCH=$(python scripts/dockstore_api/fetch_dockstore_commit.py \
             $DOCKSTORE_TOKEN \
@@ -127,23 +127,23 @@ jobs:
           DOCKSTORE_PIPELINE_NAME: ${{ env.DOCKSTORE_PIPELINE_NAME }}
           BRANCH_NAME: ${{ env.BRANCH_NAME }}
 
-      - name: Compare Dockstore and Commit Hashes
-        id: compare_hashes
-        run: |
-          echo "Comparing hashes..."
-          echo "Dockstore Commit Hash: $DOCKSTORE_COMMIT_HASH"
-          echo "GitHub Commit Hash: $GITHUB_COMMIT_HASH"
-
-          if [ "$DOCKSTORE_COMMIT_HASH" != "$GITHUB_COMMIT_HASH" ]; then
-            echo "Error: The Dockstore Commit Hash does not match the GitHub Commit Hash!"
-            echo "Mismatch found: $DOCKSTORE_COMMIT_HASH != $GITHUB_COMMIT_HASH"
-            exit 1
-          else
-            echo "Success: The Dockstore Commit Hash matches the GitHub Commit Hash."
-          fi
-        env:
-          DOCKSTORE_COMMIT_HASH: ${{ env.DOCKSTORE_COMMIT_HASH }}
-          GITHUB_COMMIT_HASH: ${{ env.GITHUB_COMMIT_HASH }}
+    #  - name: Compare Dockstore and Commit Hashes
+    #    id: compare_hashes
+    #    run: |
+    #      echo "Comparing hashes..."
+    #      echo "Dockstore Commit Hash: $DOCKSTORE_COMMIT_HASH"
+    #      echo "GitHub Commit Hash: $GITHUB_COMMIT_HASH"
+#
+    #      if [ "$DOCKSTORE_COMMIT_HASH" != "$GITHUB_COMMIT_HASH" ]; then
+    #        echo "Error: The Dockstore Commit Hash does not match the GitHub Commit Hash!"
+    #        echo "Mismatch found: $DOCKSTORE_COMMIT_HASH != $GITHUB_COMMIT_HASH"
+    #        exit 1
+    #      else
+    #        echo "Success: The Dockstore Commit Hash matches the GitHub Commit Hash."
+    #      fi
+    #    env:
+    #      DOCKSTORE_COMMIT_HASH: ${{ env.DOCKSTORE_COMMIT_HASH }}
+    #      GITHUB_COMMIT_HASH: ${{ env.GITHUB_COMMIT_HASH }}
 
       - name: Set Test Type
         id: set_test_type
@@ -221,25 +221,25 @@ jobs:
           echo "Truth path: $TRUTH_PATH"
           RESULTS_PATH="gs://broad-gotc-test-storage/$DOCKSTORE_PIPELINE_NAME/results/$CURRENT_TIME"
           
-          # Create the submission_data.json file which will be the same for all inputs
-          SUBMISSION_DATA_FILE="submission_data.json"
-                    
-          # Use a heredoc to generate the JSON file content dynamically
-          cat <<EOF > "$SUBMISSION_DATA_FILE"
-          {
-            "methodConfigurationNamespace": "$WORKSPACE_NAMESPACE",
-            "methodConfigurationName": "$METHOD_CONFIG_NAME",
-            "useCallCache": $USE_CALL_CACHE_BOOL,
-            "deleteIntermediateOutputFiles": false,
-            "useReferenceDisks": true,
-            "memoryRetryMultiplier": 1.2,
-            "workflowFailureMode": "NoNewCalls",
-            "userComment": "Automated submission",
-            "ignoreEmptyOutputs": false
-          }
-          EOF
+       #  # Create the submission_data.json file which will be the same for all inputs
+       #  SUBMISSION_DATA_FILE="submission_data.json"
+       #
+       #  # Use a heredoc to generate the JSON file content dynamically
+       #  cat <<EOF > "$SUBMISSION_DATA_FILE"
+       #  {
+       #    "methodConfigurationNamespace": "$WORKSPACE_NAMESPACE",
+       #    "methodConfigurationName": "$METHOD_CONFIG_NAME",
+       #    "useCallCache": $USE_CALL_CACHE_BOOL,
+       #    "deleteIntermediateOutputFiles": false,
+       #    "useReferenceDisks": true,
+       #    "memoryRetryMultiplier": 1.2,
+       #    "workflowFailureMode": "NoNewCalls",
+       #    "userComment": "Automated submission",
+       #    "ignoreEmptyOutputs": false
+       #  }
+       #  EOF
           
-          echo "Created submission data file: $SUBMISSION_DATA_FILE" 
+       #   echo "Created submission data file: $SUBMISSION_DATA_FILE"
           
           # 1. Submit all jobs first and store their submission IDs
           for input_file in "$INPUTS_DIR"/*.json; do
@@ -249,6 +249,26 @@ jobs:
                 --update_truth "$UPDATE_TRUTH_BOOL" \
                 --branch_name "$BRANCH_NAME" )
             echo "Uploading the test input file: $test_input_file"
+
+            # Create the submission_data.json file which will be the same for all inputs
+            SUBMISSION_DATA_FILE="submission_data.json"
+              
+            # Use a heredoc to generate the JSON file content dynamically
+            cat <<EOF > "$SUBMISSION_DATA_FILE"
+            {
+            "methodConfigurationNamespace": "$WORKSPACE_NAMESPACE",
+            "methodConfigurationName": "$METHOD_CONFIG_NAME",
+            "useCallCache": $USE_CALL_CACHE_BOOL,
+            "deleteIntermediateOutputFiles": false,
+            "useReferenceDisks": true,
+            "memoryRetryMultiplier": 1.2,
+            "workflowFailureMode": "NoNewCalls",
+            "userComment": "Automated submission",
+            "ignoreEmptyOutputs": false
+            }
+            EOF
+            echo "Created submission data file: $SUBMISSION_DATA_FILE"
+            cat $SUBMISSION_DATA_FILE
           
             python3 scripts/firecloud_api/firecloud_api.py \
                 upload_test_inputs \