For demo

Author: Peter Amstutz

client.py

@@ -27,8 +27,7 @@ def run(self, path, inputobj):
         output = open(os.path.join(self.workdir, "cwl.output.json"), "w")
         stderr = open(os.path.join(self.workdir, "stderr"), "w")
 
-        #proc = subprocess.Popen(["cwl-runner", path, inputtemp.name],
-        proc = subprocess.Popen(["cwltool", path, inputtemp.name],
+        proc = subprocess.Popen(["cwl-runner", path, inputtemp.name],
                                 stdout=output,
                                 stderr=stderr,
                                 close_fds=True,
@@ -73,7 +72,7 @@ def getstatus(self):
         with open(os.path.join(self.workdir, "workflow_url"), "r") as f:
             workflow_url = f.read()
 
-        outputobj = None
+        outputobj = {}
         if state == "Complete":
             with open(os.path.join(self.workdir, "cwl.output.json"), "r") as outputtemp:
                 outputobj = json.load(outputtemp)
@@ -96,7 +95,7 @@ def getlog(self):
         return {
             "workflow_ID": self.workflow_ID,
             "log": {
-                "cmd": "",
+                "cmd": [""],
                 "startTime": "",
                 "endTime": "",
                 "stdout": "",

cwl_runner_wes.py

@@ -8,7 +8,7 @@
 from setuptools import setup, find_packages
 
 SETUP_DIR = os.path.dirname(__file__)
-README = os.path.join(SETUP_DIR, 'README')
+README = os.path.join(SETUP_DIR, 'README.md')
 
 setup(name='cwltool_service',
       version='2.0',
@@ -19,7 +19,7 @@
       url="https://github.com/common-workflow-language/cwltool-service",
       download_url="https://github.com/common-workflow-language/cwltool-service",
       license='Apache 2.0',
-      py_modules=["cwltool_stream", "cwl_flask", "cwltool_client"],
+      py_modules=["cwl_runner_wes"],
       install_requires=[
           'connexion',
           'bravado'

setup.py

@@ -168,7 +168,7 @@
       "type": "object",
       "properties": {
         "workflow_ID": {
-          "$ref": "#/definitions/ga4gh_workflow_execWorkflowRunID"
+            "type": "string"
         },
         "log": {
           "$ref": "#/definitions/ga4gh_task_execJobLog"