WDL support.

Author: DailyDreaming

wes_client/wes_client_main.py

@@ -10,7 +10,7 @@
 import logging
 import schema_salad.ref_resolver
 import requests
-from requests.exceptions import InvalidSchema
+from requests.exceptions import InvalidSchema, MissingSchema
 from wes_service.util import visit
 from bravado.client import SwaggerClient
 from bravado.requests_client import RequestsClient
@@ -81,6 +81,13 @@ def main(argv=sys.argv[1:]):
         json.dump(response.result(), sys.stdout, indent=4)
         return 0
 
+    if args.workflow_url.lower().endswith('wdl'):
+        wf_type = 'WDL'
+    elif args.workflow_url.lower().endswith('cwl'):
+        wf_type = 'CWL'
+    elif args.workflow_url.lower().endswith('py'):
+        wf_type = 'PY'
+
     loader = schema_salad.ref_resolver.Loader({
         "location": {"@type": "@id"},
         "path": {"@type": "@id"}
@@ -112,7 +119,7 @@ def fixpaths(d):
 
     parts = [
         ("workflow_params", json.dumps(input_dict)),
-        ("workflow_type", "CWL"),
+        ("workflow_type", wf_type),
         ("workflow_type_version", "v1.0")
     ]
     if workflow_url.startswith("file://"):
@@ -163,6 +170,8 @@ def fixpaths(d):
         logging.info("Workflow log:\n" + logs)
     except InvalidSchema:
         logging.info("Workflow log:\n" + str(s["workflow_log"]["stderr"]))
+    except MissingSchema:
+        logging.info("Workflow log:\n" + str(s["workflow_log"]["stderr"]))
 
     if "fields" in s["outputs"] and s["outputs"]["fields"] is None:
         del s["outputs"]["fields"]

wes_service/toil_wes.py

@@ -53,6 +53,9 @@ def write_workflow(self, request, opts, wftype='cwl'):
         if wftype == 'cwl':
             command_args = ['toil-cwl-runner'] + extra + [workflow_url, self.input_json]
         elif wftype == 'wdl':
+            if workflow_url.startswith('http://') or workflow_url.startswith('https://'):
+                subprocess.check_call(['wget', workflow_url])
+                workflow_url = os.path.abspath(workflow_url.split('/')[-1])
             command_args = ['toil-wdl-runner'] + extra + [workflow_url, self.input_json]
             assert(os.path.exists(workflow_url), workflow_url)
             with open(workflow_url, 'r') as f: