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

run.sh

@@ -22,7 +22,7 @@ if [ ! -d ~/.firecloud-tools ]; then
 	#pip install .
 fi
 
-export PYTHONPATH=./:$PYTHONPATH
+export PYTHONPATH=./:scripts:$PYTHONPATH
 source ~/.firecloud-tools/venv/bin/activate
 
-python -u $@
\ No newline at end of file
+python -u $@

submit_workflow_source_files/submit_workflow_source_files.py → scripts/submit_workflow_source_files/submit_workflow_source_files.py

@@ -60,14 +60,13 @@ def main():
     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('"','"\\"'))
+            #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 = json.dumps({
+    method_body = {
         'name': config_name,
         'namespace': config_namespace,
         'methodRepoMethod': { 'methodNamespace': args.method_namespace,
@@ -79,18 +78,35 @@ def main():
         "methodConfigVersion": 1,
         "deleted": False,
         "inputs": inputs,
-        "outputs": {}
-        })
+        "outputs": {} 
+        }
 
 
-    print("method body: ")
-    print(method_body)
+    #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_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 config_submission.status_code != 201:
+    if failed:
         print("Failed request response:")
         print(config_submission_json)
         fail("Unable to create method config: %s %s " % (config_namespace, config_name))