Fixes after review, and removed submit script that wasn't part of this

PR

.git_ignore

@@ -4,7 +4,8 @@ entity_update.tsv
 __pycache__/
 *.py[cod]
 *$py.class
-
+scripts/*.py[cod]
+scripts/*$py.class
 # Environments
 .env
 .venv

Dockerfile

 FROM google/cloud-sdk:170.0.1-slim
 
 COPY install.sh /
-RUN /bin/bash -c "/install.sh"
+RUN /install.sh
 	
 # Tell gcloud to save state in /.config so it's easy to override as a mounted volume.
 ENV HOME=/

install.sh

@@ -3,6 +3,8 @@ pip install PyYAML
 pip install google-auth-httplib2
 pip install google-api-python-client
 pip install gcs-oauth2-boto-plugin
+pip install google-cloud-datastore
+pip install google-cloud
 pip install retrying
 pip install firecloud
 pip install xlrd

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 characters
-            inputs_1 = {k:v for k,v in inputs_json.iteritems() if '#' not in k}
-            inputs = json.loads(json.dumps(inputs_1).replace('"','"\\"'))
-    else:
-        inputs = {}
-
-    #Build JSON for method config
-    method_body = json.dumps({
-        '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_submission = firecloud_api.create_workspace_config(args.workspace_namespace, args.workspace_name, method_body)
-    config_submission_json = config_submission.json()
-    if config_submission.status_code != 201:
-        print("Failed request response:")
-        print(config_submission_json)
-        fail("Unable to create method config: %s %s " % (config_namespace, config_name))
-
-
-if __name__ == "__main__":
-    main()
\ No newline at end of file