Percolating schema changes to other backends, and fixing the client to

accept the new changes.

Author: achave11-ucsc

wes_client/wes_client_main.py

@@ -128,7 +128,7 @@ def fixpaths(d):
     ]
     if workflow_url.startswith("file://"):
         # with open(workflow_url[7:], "rb") as f:
-        #     body["workflow_descriptor"] = f.read()
+        #     body["workflow_attachment"] = f.read()
         rootdir = os.path.dirname(workflow_url[7:])
         dirpath = rootdir
         # for dirpath, dirnames, filenames in os.walk(rootdir):
@@ -137,7 +137,7 @@ def fixpaths(d):
                 continue
             fn = os.path.join(dirpath, f)
             if os.path.isfile(fn):
-                parts.append(('workflow_descriptor', (fn[len(rootdir)+1:], open(fn, "rb"))))
+                parts.append(('workflow_attachment', (fn[len(rootdir)+1:], open(fn, "rb"))))
         parts.append(("workflow_url", os.path.basename(workflow_url[7:])))
     else:
         parts.append(("workflow_url", workflow_url))

wes_service/arvados_wes.py

@@ -109,7 +109,7 @@ def ListRuns(self, page_size=None, page_token=None, state_search=None):
         }
 
     def invoke_cwl_runner(self, cr_uuid, workflow_url, workflow_params,
-                          env, workflow_descriptor_file, project_uuid,
+                          env, workflow_attachment_file, project_uuid,
                           tempdir):
         api = arvados.api_from_config(version="v1", apiconfig={
             "ARVADOS_API_HOST": env["ARVADOS_API_HOST"],
@@ -151,8 +151,8 @@ def invoke_cwl_runner(self, cr_uuid, workflow_url, workflow_params,
             api.container_requests().update(uuid=cr_uuid, body={"priority": 0,
                                                                 "properties": {"arvados-cwl-runner-log": str(e)}}).execute()
         finally:
-            if workflow_descriptor_file is not None:
-                workflow_descriptor_file.close()
+            if workflow_attachment_file is not None:
+                workflow_attachment_file.close()
 
     @catch_exceptions
     def RunWorkflow(self, **args):
@@ -184,20 +184,20 @@ def RunWorkflow(self, **args):
                                                     "priority": 500}}).execute()
 
         workflow_url = body.get("workflow_url")
-        workflow_descriptor_file = None
-        if body.get("workflow_descriptor"):
-            workflow_descriptor_file = tempfile.NamedTemporaryFile()
-            workflow_descriptor_file.write(body.get('workflow_descriptor'))
-            workflow_descriptor_file.flush()
-            workflow_url = workflow_descriptor_file.name
+        workflow_attachment_file = None
+        if body.get("workflow_attachment"):
+            workflow_attachment_file = tempfile.NamedTemporaryFile()
+            workflow_attachment_file.write(body.get('workflow_attachment'))
+            workflow_attachment_file.flush()
+            workflow_url = workflow_attachment_file.name
 
         project_uuid = body.get("workflow_engine_parameters", {}).get("project_uuid")
 
         threading.Thread(target=self.invoke_cwl_runner, args=(cr["uuid"],
                                                               workflow_url,
                                                               body["workflow_params"],
                                                               env,
-                                                              workflow_descriptor_file,
+                                                              workflow_attachment_file,
                                                               project_uuid,
                                                               tempdir)).start()
 

wes_service/cwl_runner.py

@@ -24,7 +24,7 @@ def run(self, request, opts):
         CWL (url):
         request["workflow_url"] == a url to a cwl file
         or
-        request["workflow_descriptor"] == input cwl text (written to a file and a url constructed for that file)
+        request["workflow_attachment"] == input cwl text (written to a file and a url constructed for that file)
 
         JSON File:
         request["workflow_params"] == input json text (to be written to a file)

wes_service/toil_wes.py

@@ -38,10 +38,10 @@ def write_workflow(self, request, opts, wftype='cwl'):
         """Writes a cwl, wdl, or python file as appropriate from the request dictionary."""
         self.input_wf_filename = os.path.join(self.workdir, 'workflow.' + wftype)
 
-        if request.get("workflow_descriptor"):
-            workflow_descriptor = request.get('workflow_descriptor')
+        if request.get("workflow_attachment"):
+            workflow_attachment = request.get('workflow_attachment')
             with open(self.input_wf_filename, "w") as f:
-                f.write(workflow_descriptor)
+                f.write(workflow_attachment)
             workflow_url = urllib.pathname2url(self.input_wf_filename)
         else:
             workflow_url = request.get("workflow_url")
@@ -147,7 +147,7 @@ def run(self, request, opts):
         CWL (url):
         request["workflow_url"] == a url to a cwl file
         or
-        request["workflow_descriptor"] == input cwl text (written to a file and a url constructed for that file)
+        request["workflow_attachment"] == input cwl text (written to a file and a url constructed for that file)
 
         JSON File:
         request["workflow_params"] == input json text (to be written to a file)