Handle form parameters in POST that are not attachments

Author: Peter Amstutz

wes_service/arvados_wes.py

@@ -129,7 +129,7 @@ def invoke_cwl_runner(self, cr_uuid, workflow_url, workflow_params,
         })
 
         try:
-            with tempfile.NamedTemporaryFile(dir=tempdir, suffix=".json") as inputtemp:
+            with tempfile.NamedTemporaryFile("wt", dir=tempdir, suffix=".json") as inputtemp:
                 json.dump(workflow_params, inputtemp)
                 inputtemp.flush()
 
@@ -163,7 +163,7 @@ def invoke_cwl_runner(self, cr_uuid, workflow_url, workflow_params,
                 if proc.returncode != 0:
                     api.container_requests().update(uuid=cr_uuid, body={"priority": 0}).execute()
 
-                self.log_for_run(cr_uuid, stderrdata, env['ARVADOS_API_TOKEN'])
+                self.log_for_run(cr_uuid, stderrdata.decode("utf-8"), env['ARVADOS_API_TOKEN'])
 
             if tempdir:
                 shutil.rmtree(tempdir)
@@ -212,7 +212,8 @@ def RunWorkflow(self, **args):
                                                                   tempdir)).start()
 
         except Exception as e:
-            self.log_for_run(cr["uuid"], str(e))
+            logging.exception("Error")
+            self.log_for_run(cr["uuid"], "An exception ocurred while handling your request: " + str(e))
             cr = api.container_requests().update(uuid=cr["uuid"],
                                                  body={"container_request":
                                                        {"priority": 0}}).execute()

wes_service/util.py

@@ -68,10 +68,18 @@ def collect_attachments(self, run_id=None):
                     body[k] = json.loads(content.decode("utf-8"))
                 else:
                     body[k] = v.read().decode()
+        for k, ls in iterlists(connexion.request.form):
+            for v in ls:
+                if k in ("workflow_params", "tags", "workflow_engine_parameters"):
+                    body[k] = json.loads(v)
+                else:
+                    body[k] = v
 
-        if ":" not in body["workflow_url"]:
-            body["workflow_url"] = "file://%s" % os.path.join(tempdir, secure_filename(body["workflow_url"]))
-
-        self.log_for_run(run_id, "Using workflow_url '%s'" % body.get("workflow_url"))
+        if "workflow_url" in body:
+            if ":" not in body["workflow_url"]:
+                body["workflow_url"] = "file://%s" % os.path.join(tempdir, secure_filename(body["workflow_url"]))
+            self.log_for_run(run_id, "Using workflow_url '%s'" % body.get("workflow_url"))
+        else:
+            raise Exception("Missing 'workflow_url' in submission")
 
         return tempdir, body