Bug fix #47, all the primary and secondary files to the workflow need to

be attached to a workflow_attachment. Thereby uploaded to a tem location
for the server. workflow_url should always be assigned to the workflow
descriptor file, as described by wes-schemas.

Author: achave11-ucsc

testdata/md5sum.cwl

@@ -11,8 +11,9 @@ outputs:
 
 steps:
   md5sum:
-    run: https://raw.githubusercontent.com/common-workflow-language/workflow-service/master/testdata/dockstore-tool-md5sum.cwl
+    run: dockstore-tool-md5sum.cwl
     in:
       input_file: input_file
     out: [output_file]
 
+

wes_service/cwl_runner.py

@@ -2,7 +2,6 @@
 import json
 import os
 import subprocess
-import urllib
 import uuid
 
 from wes_service.util import WESBackend
@@ -46,13 +45,7 @@ def run(self, request, opts):
                 self.workdir, "cwl.input.json"), "w") as inputtemp:
             json.dump(request["workflow_params"], inputtemp)
 
-        if request.get("workflow_descriptor"):
-            workflow_descriptor = request.get('workflow_descriptor')
-            with open(os.path.join(self.workdir, "workflow.cwl"), "w") as f:
-                f.write(workflow_descriptor)
-            workflow_url = urllib.pathname2url(os.path.join(self.workdir, "workflow.cwl"))
-        else:
-            workflow_url = request.get("workflow_url")
+        workflow_url = request.get("workflow_url")  # Will always be local path to descriptor cwl, or url.
 
         output = open(os.path.join(self.workdir, "cwl.output.json"), "w")
         stderr = open(os.path.join(self.workdir, "stderr"), "w")

wes_service/util.py

@@ -47,9 +47,10 @@ def collect_attachments(self):
         body = {}
         for k, ls in connexion.request.files.iterlists():
             for v in ls:
-                if k == "workflow_descriptor":
+                if k == "workflow_attachment":
                     filename = secure_filename(v.filename)
                     v.save(os.path.join(tempdir, filename))
+                    body[k] = "file://%s" % os.path.join(tempdir)  # Reference to tem working dir.
                 elif k in ("workflow_params", "tags", "workflow_engine_parameters"):
                     body[k] = json.loads(v.read())
                 else: