Fixed issues with escaping strings and setup script to either create new or...

Fixed issues with escaping strings and setup script to either create new or update existing method configs

scripts/submit_workflow_source_files/submit_workflow_source_files.py

+from common import *
+from pprint import pprint
+
+def escapedText(fileName):
+
+    with open(fileName, 'r') as f:
+        fileContent = f.read()
+        escapedText = json.dumps(fileContent)
+
+    return escapedText
+
+
+def main():
+    setup()
+
+    # The main argument parser
+    parser = DefaultArgsParser(description="Create Method and Method Config from WDL source file and inputs json")
+
+    # Core application arguments
+    parser.add_argument('-mns', '--method-namespace', dest='method_namespace', action='store', required=True, help='Method namespace')
+    parser.add_argument('-mn', '--method-name', dest='method_name', action='store', required=True, help='Method name')
+
+    parser.add_argument('-wns', '--workspace-namespace', dest='workspace_namespace', action='store', required=True, help='Workspace namespace')
+    parser.add_argument('-wn', '--workspace-name', dest='workspace_name', action='store', required=True, help='Workspace name')
+
+    parser.add_argument('-w', '--wdl-file', dest='wdl_file', action='store', required=True, help='WDL source (File)')
+    parser.add_argument('-i', '--wdl-inputs', dest='wdl_inputs', action='store', required=False, help='WDL inputs (File)')
+
+    #Optional arguments
+    parser.add_argument('-s', '--method-synopsis', dest='method_synopsis', action='store', required=False, help='Method Synopsis (File)')
+    parser.add_argument('-d', '--method-docs', dest='method_docs', action='store', required=False, help='Method Docs (File)')
+
+    parser.add_argument('-cns', '--config-namespace', dest='config_namespace', action='store', required=False, help='Config namespace (Default: Method namespace')
+    parser.add_argument('-cn', '--config-name', dest='config_name', action='store', required=False, help='Config name (Default: Method name)')
+
+    parser.add_argument('-e', '--root-entity', dest='root_entity', action='store', required=False, help='Method config root entity (Default: participant)')
+
+    args = parser.parse_args()
+
+    docs = args.method_docs if (args.method_docs) else None
+
+    if args.method_synopsis is not None:
+        with open (args.method_synopsis, 'r') as f:
+            synopsis = f.read()
+    else:
+        synopsis = ""
+
+    #TODO: Add error handling for failed method creation requests
+    method_submission = firecloud_api.update_repository_method(args.method_namespace, args.method_name, synopsis, args.wdl_file, docs)
+
+    if method_submission.status_code != 201:
+        print method_submission
+        fail("Unable to create method: %s %s" % (args.method_namespace, args.method_name))
+    submission_json = method_submission.json()
+
+    config_name = args.config_name if (args.config_name) else args.method_name
+    config_namespace = args.config_namespace if (args.config_namespace) else args.method_namespace
+    root_entity = args.root_entity if (args.root_entity) else "participant"
+    #get inputs
+    if args.wdl_inputs is not None:
+        with open (args.wdl_inputs, 'r') as f:
+            inputs_json = json.loads(f.read())
+            #Filter out any key/values that contain #, and escape strings with quotes as MCs need this to not be treated as expressions
+            inputs = {k:"\"{}\"".format(v) if isinstance(v, basestring) else v for k,v in inputs_json.iteritems() if '#' not in k}
+    else:
+        inputs = {}
+
+    #Build JSON for method config
+    method_body = {
+        'name': config_name,
+        'namespace': config_namespace,
+        'methodRepoMethod': { 'methodNamespace': args.method_namespace,
+                              'methodName': args.method_name,
+                              'methodVersion': submission_json["snapshotId"]
+                            },
+        'rootEntityType': root_entity,
+        "prerequisites": {},
+        "methodConfigVersion": 1,
+        "deleted": False,
+        "inputs": inputs,
+        "outputs": {} 
+        }
+
+
+    #print("method body: ")
+    #print(method_body)
+
+    #TODO: perform GET to see if the method config already exists and use update_workspace_config instead
+
+    config_exists = firecloud_api.get_workspace_config(args.workspace_namespace, args.workspace_name, config_namespace, config_name)
+    
+    failed = False
+    if config_exists.status_code == 200:
+        config_submission = firecloud_api.update_workspace_config(args.workspace_namespace, args.workspace_name, config_namespace, config_name, method_body)
+        if config_submission.status_code == 200:
+            print "method config updated."
+        else:
+            failed = True
+        
+    else:
+        config_submission = firecloud_api.create_workspace_config(args.workspace_namespace, args.workspace_name, method_body)
+        update_status = config_submission.status_code
+        if config_submission.status_code == 201:
+            print "method config created."
+        else:
+            failed = True
+        
+    config_submission_json = config_submission.json()
+    if failed:
+        print("Failed request response:")
+        print(config_submission_json)
+        fail("Unable to create method config: %s %s " % (config_namespace, config_name))
+
+
+if __name__ == "__main__":
+    main()
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