Fix tests

.travis.yml

@@ -1,9 +1,14 @@
+branches:
+  only:
+    - main
 language: python
 python:
 - '3.6'
 - '3.7'
 - '3.8'
+- '3.9'
 before_install:
+- pip install -U pip wheel
 - pip install .[toil]
 - pip install -r dev-requirements.txt
 script:

setup.py

@@ -21,14 +21,15 @@
     download_url="https://github.com/common-workflow-language/cwltool-service",
     license="Apache 2.0",
     python_requires="~=3.5",
-    setup_requires=['pytest-runner'],
-    tests_require=['pytest'],
+    setup_requires=["pytest-runner"],
+    tests_require=["pytest"],
     packages=["wes_service", "wes_client"],
     package_data={"wes_service": ["openapi/workflow_execution_service.swagger.yaml"]},
     include_package_data=True,
     install_requires=[
         "connexion >= 2.0.2, < 3",
         "ruamel.yaml >= 0.15.78, <= 0.16.5",
+        "schema-salad",
     ],
     entry_points={
         "console_scripts": [
@@ -39,7 +40,7 @@
     extras_require={
         "cwltool": ["cwlref-runner"],
         "arvados": ["arvados-cwl-runner"],
-        "toil": ["toil[cwl]==4.1.0"],
+        "toil": ["toil[cwl]==5.4.0"],
     },
     zip_safe=False,
     platforms=["MacOS X", "Posix"],

test/test_integration.py

@@ -22,7 +22,7 @@ class IntegrationTest(unittest.TestCase):
     @classmethod
     def setUpClass(cls):
         # cwl
-        cls.cwl_dockstore_url = 'https://dockstore.org:8443/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/master/plain-CWL/descriptor/%2FDockstore.cwl'
+        cls.cwl_dockstore_url = 'https://dockstore.org/api/ga4gh/trs/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/plain-CWL/descriptor//Dockstore.cwl'
         cls.cwl_local_path = "file://" + os.path.abspath('testdata/md5sum.cwl')
         cls.cwl_json_input = "file://" + os.path.abspath('testdata/md5sum.json')
         cls.cwl_attachments = ['file://' + os.path.abspath('testdata/md5sum.input'),

wes_client/util.py

@@ -9,10 +9,7 @@
 
 from wes_service.util import visit
 
-from future.standard_library import hooks
-
-with hooks():
-    from urllib.request import urlopen, pathname2url
+from urllib.request import urlopen, pathname2url
 
 
 def two_seven_compatible(filePath):

wes_service/toil_wes.py

@@ -74,7 +74,9 @@ def write_workflow(self, request, opts, cwd, wftype="cwl"):
             try:
                 os.link(workflow_url[7:], os.path.join(cwd, "wes_workflow." + wftype))
             except OSError:
-                os.symlink(workflow_url[7:], os.path.join(cwd, "wes_workflow." + wftype))
+                os.symlink(
+                    workflow_url[7:], os.path.join(cwd, "wes_workflow." + wftype)
+                )
             workflow_url = os.path.join(cwd, "wes_workflow." + wftype)
         try:
             os.link(self.input_json, os.path.join(cwd, "wes_input.json"))

wes_service/wes_service_main.py

@@ -65,7 +65,7 @@ def get_parser() -> argparse.Namespace:
 
 
 def main(argv=sys.argv[1:]):
-    args = get_parser.parse_args(argv)
+    args = get_parser().parse_args(argv)
 
     if args.version:
         pkg = pkg_resources.require("wes_service")