wes-client passes most conformance tests with shared filesystem/cwltool backend.

Author: Peter Amstutz

setup.py

@@ -10,11 +10,11 @@
 SETUP_DIR = os.path.dirname(__file__)
 README = os.path.join(SETUP_DIR, 'README.md')
 
-setup(name='cwltool_service',
+setup(name='wes_service',
       version='2.0',
-      description='Common workflow language runner service',
+      description='GA4GH Workflow Execution Service reference implementation',
       long_description=open(README).read(),
-      author='Common workflow language working group',
+      author='GA4GH Containers and Workflows task team',
       author_email='[email protected]',
       url="https://github.com/common-workflow-language/cwltool-service",
       download_url="https://github.com/common-workflow-language/cwltool-service",
@@ -24,7 +24,8 @@
       include_package_data=True,
       install_requires=[
           'connexion',
-          'bravado'
+          'bravado',
+          'ruamel.yaml >= 0.12.4, < 0.15',
         ],
       entry_points={
           'console_scripts': [ "wes-server=wes_service:main",

wes_client.py

@@ -10,6 +10,10 @@
 import argparse
 import logging
 import urlparse
+import pkg_resources  # part of setuptools
+from wes_service.util import visit
+import urllib
+import ruamel.yaml as yaml
 
 def main(argv=sys.argv[1:]):
 
@@ -18,17 +22,24 @@ def main(argv=sys.argv[1:]):
     parser.add_argument("--auth", type=str, default=os.environ.get("WES_API_TOKEN"))
     parser.add_argument("--proto", type=str, default=os.environ.get("WES_API_PROTO", "https"))
     parser.add_argument("--quiet", action="store_true", default=False)
+    parser.add_argument("--outdir", type=str)
 
     exgroup = parser.add_mutually_exclusive_group()
     exgroup.add_argument("--run", action="store_true", default=False)
     exgroup.add_argument("--get", type=str, default=None)
     exgroup.add_argument("--log", type=str, default=None)
     exgroup.add_argument("--list", action="store_true", default=False)
+    exgroup.add_argument("--version", action="store_true", default=False)
 
     parser.add_argument("workflow_url", type=str, nargs="?", default=None)
     parser.add_argument("job_order", type=str, nargs="?", default=None)
     args = parser.parse_args(argv)
 
+    if args.version:
+        pkg = pkg_resources.require("cwltool_service")
+        print u"%s %s" % (sys.argv[0], pkg[0].version)
+        exit(0)
+
     http_client = RequestsClient()
     split = urlparse.urlsplit("%s://%s/" % (args.proto, args.host))
 
@@ -54,7 +65,13 @@ def main(argv=sys.argv[1:]):
         return 0
 
     with open(args.job_order) as f:
-        input = json.load(f)
+        input = yaml.safe_load(f)
+        basedir = os.path.dirname(args.job_order)
+        def fixpaths(d):
+            if isinstance(d, dict) and "location" in d:
+                if not ":" in d["location"]:
+                    d["location"] = urllib.pathname2url(os.path.normpath(os.path.join(os.getcwd(), basedir, d["location"])))
+        visit(input, fixpaths)
 
     workflow_url = args.workflow_url
     if not workflow_url.startswith("/") and ":" not in workflow_url:

wes_service/arvados_wes.py

@@ -74,14 +74,6 @@ def RunWorkflow(body):
                                                body.get("workflow_url"), inputtemp.name], env=env).strip()
     return {"workflow_id": workflow_id}
 
-def visit(d, op):
-    op(d)
-    if isinstance(d, list):
-        for i in d:
-            visit(i, op)
-    elif isinstance(d, dict):
-        for i in d.itervalues():
-            visit(i, op)
 
 def GetWorkflowLog(workflow_id):
     api = get_api()

wes_service/cwl_runner.py

@@ -6,6 +6,7 @@
 import json
 import urllib
 import sys
+from wes_service.util import visit
 
 class Workflow(object):
     def __init__(self, workflow_id):

wes_service/util.py

@@ -0,0 +1,8 @@
+def visit(d, op):
+    op(d)
+    if isinstance(d, list):
+        for i in d:
+            visit(i, op)
+    elif isinstance(d, dict):
+        for i in d.itervalues():
+            visit(i, op)