Np add firecloud api scripts (#1358)

* pin all latest docker version

* add firecloud scripts

* add testing scripts

scripts/firecloud_api/GetWorkflowOutputs.py

@@ -0,0 +1,53 @@
+import requests
+import argparse
+
+def get_workflow_outputs(token, namespace, workspace_name, submission_id, workflow_id, pipeline_name):
+    # API endpoint to get the workflow outputs
+    url = f"https://api.firecloud.org/api/workspaces/{namespace}/{workspace_name}/submissions/{submission_id}/workflows/{workflow_id}/outputs"
+    print(f"Requesting URL: {url}")
+
+    # Headers including the authorization token
+    headers = {
+        'accept': '*/*',
+        'Authorization': f'Bearer {token}',
+    }
+
+    # Make the GET request
+    response = requests.get(url, headers=headers)
+
+    # Check if the request was successful
+    if response.status_code == 200:
+        json_response = response.json()  # parse the JSON response
+        # extract the outputs section using the task name
+        outputs = json_response.get('tasks', {}).get(pipeline_name, {}).get('outputs', {})
+
+        # Turn the outputs dictionary into a list of values
+        output_values = list(outputs.values())
+
+        return outputs, output_values
+    else:
+        print(f"Failed to retrieve workflow outputs. Status code: {response.status_code}")
+        return None, None
+
+if __name__ == "__main__":
+    # Define the command-line arguments
+    parser = argparse.ArgumentParser(description='Fetch workflow outputs from the API.')
+    parser.add_argument('--token', required=True, help='Authentication token')
+    parser.add_argument('--namespace', required=True, help='Workspace namespace')
+    parser.add_argument('--workspace', required=True, help='Workspace name')
+    parser.add_argument('--submission_id', required=True, help='Submission ID')
+    parser.add_argument('--workflow_id', required=True, help='Workflow ID')
+    parser.add_argument('--pipeline_name', required=True, help='Name of the pipeline')
+
+    # Parse the arguments
+    args = parser.parse_args()
+
+    # Call the function with the parsed arguments
+    outputs, output_values = get_workflow_outputs(args.token, args.namespace, args.workspace, args.submission_id, args.workflow_id, args.pipeline_name)
+
+    if outputs:
+        print("Outputs:")
+        print(outputs)
+
+        print("\nOutput Values:")
+        print(output_values)

scripts/firecloud_api/SubmitWorkflowAndGetStatus.py

@@ -0,0 +1,90 @@
+import requests
+import time
+import argparse
+import json
+
+def create_submission(token, workspace_namespace, workspace_name, submission_data):
+    # API endpoint
+    base_url = f'https://api.firecloud.org/api/workspaces/{workspace_namespace}/{workspace_name}/submissions'
+
+    # Headers to make API requests
+    headers = {
+        'accept': 'application/json',
+        'Authorization': f'Bearer {token}',
+        'Content-Type': 'application/json'
+    }
+
+    # Create the submission
+    # send an HTTP POST request to the API endpoint
+    response = requests.post(base_url, headers=headers, json=submission_data)
+    # convert the response json into a dictionary
+    submission_response = response.json()
+    # extract the submission ID from the response dictionary
+    submission_id = submission_response.get("submissionId")
+
+    if not submission_id:
+        print("Failed to create submission.")
+    else:
+        print(f"Submission created with ID: {submission_id}")
+        return submission_id
+
+def poll_submission_status(token, workspace_namespace, workspace_name, submission_id):
+
+    # Status endpoint
+    status_url = f'https://api.firecloud.org/api/workspaces/{workspace_namespace}/{workspace_name}/submissions/{submission_id}'
+
+    # Headers to make API requests
+    headers = {
+        'accept': 'application/json',
+        'Authorization': f'Bearer {token}'
+    }
+
+    # polling the submission status
+    # create an emptu list to store the previous workflow status
+    previous_workflow_status = []
+
+    # loop until the submission is done
+    while True:
+        # send a get request and convert the response json into a dictionary
+        status_response = requests.get(status_url, headers=headers)
+        status_data = status_response.json()
+
+        # get the submission status
+        submission_status = status_data.get("status")
+        # get the workflow status of each workflow in the submission
+        workflows_status = [workflow.get("status") for workflow in status_data.get("workflows", [])]
+
+        # print the workflow status to stdout if it has changed
+        if workflows_status != previous_workflow_status:
+            print(f"Workflows Status: {workflows_status}")
+            previous_workflow_status = workflows_status
+
+        # Check if the submission has completed
+        if submission_status == "Done" and "Failed" in workflows_status:
+            print("At least one workflow has failed.")
+            break
+        elif submission_status == "Done":
+            break
+
+        # Wait for 10 seconds before polling again
+        time.sleep(10)
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description='Submit and monitor a job.')
+    parser.add_argument('--token', required=True, help='API access token')
+    parser.add_argument('--workspace-namespace', required=True, help='Workspace namespace')
+    parser.add_argument('--workspace-name', required=True, help='Workspace name')
+    parser.add_argument('--submission-data-file', required=True, help='Path to the JSON file containing submission data')
+
+    args = parser.parse_args()
+
+    # load submission data from JSON file
+    with open(args.submission_data_file, 'r') as file:
+        submission_data = json.load(file)
+
+    # create submission and get submission ID
+    submission_id = create_submission(args.token, args.workspace_namespace, args.workspace_name, submission_data)
+
+    if submission_id:
+        # Poll submission status
+        poll_submission_status(args.token, args.workspace_namespace, args.workspace_name, submission_id)