Np kill jobs from previous commits

.github/workflows/test_cram_to_unmapped_bams.yml

@@ -57,12 +57,7 @@ env:
 
 
 jobs:
-  check-authorization:
-    uses: ./.github/workflows/authorized_users.yml
-
   TestCramToUnmappedBams:
-    needs: check-authorization
-    if: ${{ needs.check-authorization.outputs.approved == 'true' }}
     runs-on: ubuntu-latest
     # Add "id-token" with the intended permissions.
     permissions:

.github/workflows/test_exome_germline_single_sample.yml

@@ -70,12 +70,7 @@ env:
 
 
 jobs:
-  check-authorization:
-    uses: ./.github/workflows/authorized_users.yml
-
   TestExomeGermlineSingleSample:
-    needs: check-authorization
-    if: ${{ needs.check-authorization.outputs.approved == 'true' }}
     runs-on: ubuntu-latest
     # Add "id-token" with the intended permissions.
     permissions:

.github/workflows/test_exome_reprocessing.yml

@@ -73,12 +73,7 @@ env:
 
 
 jobs:
-  check-authorization:
-    uses: ./.github/workflows/authorized_users.yml
-
   TestExomeReprocessing:
-    needs: check-authorization
-    if: ${{ needs.check-authorization.outputs.approved == 'true' }}
     runs-on: ubuntu-latest
     # Add "id-token" with the intended permissions.
     permissions:

.github/workflows/test_illumina_genotyping_array.yml

@@ -58,12 +58,7 @@ env:
 
 
 jobs:
-  check-authorization:
-    uses: ./.github/workflows/authorized_users.yml
-
   TestIlluminaGenotypingArray:
-    needs: check-authorization
-    if: ${{ needs.check-authorization.outputs.approved == 'true' }}
     runs-on: ubuntu-latest
     # Add "id-token" with the intended permissions.
     permissions:
@@ -98,6 +93,17 @@ jobs:
             echo "BRANCH_NAME=${{ github.head_ref }}" >> $GITHUB_ENV
           fi
 
+      - name: Cancel Previous Runs
+        run: |
+          python3 scripts/firecloud_api/firecloud_api.py \
+            --workspace-namespace "${{ env.WORKSPACE_NAMESPACE }}" \
+            --workspace-name "${{ env.TESTING_WORKSPACE }}" \
+            --pipeline_name "${{ env.PIPELINE_NAME }}" \
+            --branch_name "${{ env.BRANCH_NAME }}" \
+            --sa-json-b64 "${{ secrets.PDT_TESTER_SA_B64 }}" \
+            --user "${{ env.USER }}" \
+            cancel_old_submissions
+
       - name: Determine Github Commit Hash
         id: determine_github_commit_hash
         run: |
@@ -112,42 +118,67 @@ jobs:
             exit 1
           fi
 
-      - name: Fetch Dockstore Workflow Commit Hash
+     # - name: Fetch Dockstore Workflow Commit Hash
+     #   run: |
+     #     # Wait 5.5 minutes for Dockstore to update
+     #     sleep 3
+     #
+     #     DOCKSTORE_COMMIT_HASH_FROM_FETCH=$(python scripts/dockstore_api/fetch_dockstore_commit.py \
+     #       $DOCKSTORE_TOKEN \
+     #       $DOCKSTORE_PIPELINE_NAME \
+     #       $BRANCH_NAME)
+     #
+     #     # Export the commit hash as an environment variable
+     #     echo "DOCKSTORE_COMMIT_HASH=$DOCKSTORE_COMMIT_HASH_FROM_FETCH" >> $GITHUB_ENV
+     #     echo "Dockstore Commit Hash: $DOCKSTORE_COMMIT_HASH_FROM_FETCH"
+#
+     #   env:
+     #     ## TODO NEED TO ADD DOCKSTORE_TOKEN FOR SERVICE ACCOUNT ##
+     #     DOCKSTORE_TOKEN: ${{ secrets.DOCKSTORE_TOKEN }}
+     #     DOCKSTORE_PIPELINE_NAME: ${{ env.DOCKSTORE_PIPELINE_NAME }}
+     #     BRANCH_NAME: ${{ env.BRANCH_NAME }}
+
+
+      - name: Compare Dockstore and Commit Hashes with Retry
+        id: compare_hashes
         run: |
+
           # Wait 5.5 minutes for Dockstore to update
           sleep 330
 
-          DOCKSTORE_COMMIT_HASH_FROM_FETCH=$(python scripts/dockstore_api/fetch_dockstore_commit.py \
-            $DOCKSTORE_TOKEN \
-            $DOCKSTORE_PIPELINE_NAME \
-            $BRANCH_NAME)
-
-          # Export the commit hash as an environment variable
-          echo "DOCKSTORE_COMMIT_HASH=$DOCKSTORE_COMMIT_HASH_FROM_FETCH" >> $GITHUB_ENV
-          echo "Dockstore Commit Hash: $DOCKSTORE_COMMIT_HASH_FROM_FETCH"
+          MAX_WAIT_TIME=$((15 * 60)) # 15 minutes in seconds
+          WAIT_INTERVAL=60          # 1 minute in seconds
+          TOTAL_WAITED=0
 
+          echo "Starting hash comparison with retry mechanism..."
+
+          while [ $TOTAL_WAITED -lt $MAX_WAIT_TIME ]; do
+            echo "Fetching Dockstore Commit Hash..."
+            DOCKSTORE_COMMIT_HASH=$(python scripts/dockstore_api/fetch_dockstore_commit.py \
+              $DOCKSTORE_TOKEN \
+              $DOCKSTORE_PIPELINE_NAME \
+              $BRANCH_NAME)
+            echo "Fetched Dockstore Commit Hash: $DOCKSTORE_COMMIT_HASH"
+
+            echo "GitHub Commit Hash: $GITHUB_COMMIT_HASH"
+
+            if [ "$DOCKSTORE_COMMIT_HASH" == "$GITHUB_COMMIT_HASH" ]; then
+              echo "Success: The Dockstore Commit Hash matches the GitHub Commit Hash."
+              exit 0
+            else
+              echo "Mismatch found: $DOCKSTORE_COMMIT_HASH != $GITHUB_COMMIT_HASH"
+              echo "Retrying in $WAIT_INTERVAL seconds..."
+              sleep $WAIT_INTERVAL
+              TOTAL_WAITED=$((TOTAL_WAITED + WAIT_INTERVAL))
+            fi
+          done
+
+          echo "Error: The Dockstore Commit Hash does not match the GitHub Commit Hash after 15 minutes of retries!"
+          exit 1
         env:
-          ## TODO NEED TO ADD DOCKSTORE_TOKEN FOR SERVICE ACCOUNT ##
           DOCKSTORE_TOKEN: ${{ secrets.DOCKSTORE_TOKEN }}
           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: Set Test Type

.github/workflows/test_imputation.yml

@@ -58,12 +58,7 @@ env:
 
 
 jobs:
-  check-authorization:
-    uses: ./.github/workflows/authorized_users.yml
-
   TestImputation:
-    needs: check-authorization
-    if: ${{ needs.check-authorization.outputs.approved == 'true' }}
     runs-on: ubuntu-latest
     # Add "id-token" with the intended permissions.
     permissions:

.github/workflows/test_joint_genotyping.yml

@@ -62,12 +62,7 @@ env:
 
 
 jobs:
-  check-authorization:
-    uses: ./.github/workflows/authorized_users.yml
-
   TestJointGenotyping:
-    needs: check-authorization
-    if: ${{ needs.check-authorization.outputs.approved == 'true' }}
     runs-on: ubuntu-latest
     # Add "id-token" with the intended permissions.
     permissions:

.github/workflows/test_multisamplesmartseq2singlenucleus.yml

@@ -66,12 +66,7 @@ env:
 
 
 jobs:
-  check-authorization:
-    uses: ./.github/workflows/authorized_users.yml
-
   TestMultiSampleSmartSeq2SingleNucleus:
-    needs: check-authorization
-    if: ${{ needs.check-authorization.outputs.approved == 'true' }}
     runs-on: ubuntu-latest
     # Add "id-token" with the intended permissions.
     permissions:

.github/workflows/test_optimus.yml

@@ -66,12 +66,7 @@ env:
 
 
 jobs:
-  check-authorization:
-    uses: ./.github/workflows/authorized_users.yml
-
   TestOptimus:
-    needs: check-authorization
-    if: ${{ needs.check-authorization.outputs.approved == 'true' }}
     runs-on: ubuntu-latest
     # Add "id-token" with the intended permissions.
     permissions:

.github/workflows/test_pairedtag.yml

@@ -68,12 +68,7 @@ env:
 
 
 jobs:
-  check-authorization:
-    uses: ./.github/workflows/authorized_users.yml
-
   TestPairedTag:
-    needs: check-authorization
-    if: ${{ needs.check-authorization.outputs.approved == 'true' }}
     runs-on: ubuntu-latest
     # Add "id-token" with the intended permissions.
     permissions:

.github/workflows/test_reblockGVCF.yml

@@ -60,12 +60,7 @@ env:
 
 
 jobs:
-  check-authorization:
-    uses: ./.github/workflows/authorized_users.yml
-
   TestReblockGVCF:
-    needs: check-authorization
-    if: ${{ needs.check-authorization.outputs.approved == 'true' }}
     runs-on: ubuntu-latest
     # Add "id-token" with the intended permissions.
     permissions:

.github/workflows/test_rna_with_umis.yml

@@ -61,12 +61,7 @@ env:
 
 
 jobs:
-  check-authorization:
-    uses: ./.github/workflows/authorized_users.yml
-
   TestRNAWithUMIsPipeline:
-    needs: check-authorization
-    if: ${{ needs.check-authorization.outputs.approved == 'true' }}
     runs-on: ubuntu-latest
     # Add "id-token" with the intended permissions.
     permissions:

.github/workflows/test_slideseq.yml

@@ -64,12 +64,7 @@ env:
 
 
 jobs:
-  check-authorization:
-    uses: ./.github/workflows/authorized_users.yml
-
   TestSlideSeq:
-    needs: check-authorization
-    if: ${{ needs.check-authorization.outputs.approved == 'true' }}
     runs-on: ubuntu-latest
     # Add "id-token" with the intended permissions.
     permissions:

.github/workflows/test_snm3c.yml

@@ -57,12 +57,7 @@ env:
 
 
 jobs:
-  check-authorization:
-    uses: ./.github/workflows/authorized_users.yml
-
   Testsnm3C:
-    needs: check-authorization
-    if: ${{ needs.check-authorization.outputs.approved == 'true' }}
     runs-on: ubuntu-latest
     # Add "id-token" with the intended permissions.
     permissions:

.github/workflows/test_ultima_genomics_joint_genotyping.yml

@@ -64,12 +64,7 @@ env:
 
 
 jobs:
-  check-authorization:
-    uses: ./.github/workflows/authorized_users.yml
-
   TestUltimaGenomicsJointGenotyping:
-    needs: check-authorization
-    if: ${{ needs.check-authorization.outputs.approved == 'true' }}
     runs-on: ubuntu-latest
     # Add "id-token" with the intended permissions.
     permissions:

.github/workflows/test_ultima_genomics_whole_genome_cram_only.yml

@@ -71,12 +71,7 @@ env:
 
 
 jobs:
-  check-authorization:
-    uses: ./.github/workflows/authorized_users.yml
-
   TestUltimaGenomicsWholeGenomeCramOnly:
-    needs: check-authorization
-    if: ${{ needs.check-authorization.outputs.approved == 'true' }}
     runs-on: ubuntu-latest
     # Add "id-token" with the intended permissions.
     permissions:

.github/workflows/test_ultima_genomics_whole_genome_germline.yml

@@ -71,12 +71,7 @@ env:
 
 
 jobs:
-  check-authorization:
-    uses: ./.github/workflows/authorized_users.yml
-
   TestUltimaGenomicsWholeGenomeGermline:
-    needs: check-authorization
-    if: ${{ needs.check-authorization.outputs.approved == 'true' }}
     runs-on: ubuntu-latest
     # Add "id-token" with the intended permissions.
     permissions:

.github/workflows/test_variant_calling.yml

@@ -62,12 +62,7 @@ env:
 
 
 jobs:
-  check-authorization:
-    uses: ./.github/workflows/authorized_users.yml
-
   TestVariantCalling:
-    needs: check-authorization
-    if: ${{ needs.check-authorization.outputs.approved == 'true' }}
     runs-on: ubuntu-latest
     # Add "id-token" with the intended permissions.
     permissions: