From 50897cfe851920188b8479a596bc954c6164ce5b Mon Sep 17 00:00:00 2001
From: npetrill <npetrill@broadinstitute.org>
Date: Wed, 4 Dec 2024 13:18:47 -0500
Subject: [PATCH] wait before submitting any workflows

---
 .../test_illumina_genotyping_array.yml        | 15 ++++++----
 scripts/firecloud_api/firecloud_api.py        | 30 +++++++++----------
 2 files changed, 25 insertions(+), 20 deletions(-)

diff --git a/.github/workflows/test_illumina_genotyping_array.yml b/.github/workflows/test_illumina_genotyping_array.yml
index 5b993b87a2..9a9e878e7f 100644
--- a/.github/workflows/test_illumina_genotyping_array.yml
+++ b/.github/workflows/test_illumina_genotyping_array.yml
@@ -106,6 +106,11 @@ jobs:
           # Use the testType provided by the user
           echo "testType=${{ github.event.inputs.testType }}" >> $GITHUB_ENV
 
+      - name: Delay before submitting workflows
+        run: |
+          echo "Waiting for 5 minutes before submitting workflows..."
+          sleep 300  # 300 seconds = 5 minutes
+
       - name: Submit job, poll status, and get outputs
         id: pipeline_run
         run: |
@@ -188,11 +193,11 @@ jobs:
           MAX_RETRIES=2
           RETRY_DELAY=300  # 300 seconds = 5 minutes
                     
-          while true; do
-            echo "Refreshing token..."
-            TOKEN=$(gcloud auth print-access-token)
-            sleep 3000 # sleep for 50 minutes
-          done &
+          #while true; do
+          #  echo "Refreshing token..."
+          #  TOKEN=$(gcloud auth print-access-token)
+          #  sleep 3000 # sleep for 50 minutes
+          #done &
           
           for input_file in "$INPUTS_DIR"/*.json; do
             echo "Processing input file: $input_file"
diff --git a/scripts/firecloud_api/firecloud_api.py b/scripts/firecloud_api/firecloud_api.py
index f01c784129..9961af4e10 100644
--- a/scripts/firecloud_api/firecloud_api.py
+++ b/scripts/firecloud_api/firecloud_api.py
@@ -64,21 +64,21 @@ def get_workflow_outputs(self, submission_id, workflow_id, pipeline_name):
             print(f"Failed to retrieve workflow outputs. Status code: {response.status_code}")
             return None, None
 
-    def refresh_token(self):
-        """
-        Refreshes the API token using gcloud's application default credentials.
-        :return: The new token as a string
-        """
-        try:
-            # Execute the gcloud command to get the new access token
-            result = subprocess.run(
-                ["gcloud", "auth", "application-default", "print-access-token"],
-                capture_output=True, text=True, check=True
-            )
-            return result.stdout.strip()  # Return the new token
-        except subprocess.CalledProcessError as e:
-            print(f"Error refreshing token: {e.stderr}", file=sys.stderr)
-            return None
+    #def refresh_token(self):
+    #    """
+    #    Refreshes the API token using gcloud's application default credentials.
+    #    :return: The new token as a string
+    #    """
+    #    try:
+    #        # Execute the gcloud command to get the new access token
+    #        result = subprocess.run(
+    #            ["gcloud", "auth", "application-default", "print-access-token"],
+    #            capture_output=True, text=True, check=True
+    #        )
+    #        return result.stdout.strip()  # Return the new token
+    #    except subprocess.CalledProcessError as e:
+    #        print(f"Error refreshing token: {e.stderr}", file=sys.stderr)
+    #        return None
 
     def create_submission(self, submission_data):
         """