Merge pull request #64 from gijzelaerr/py3compat

fix a py3 compat issue

Author: tetron

.travis.yml

@@ -1,6 +1,9 @@
 language: python
 python:
 - '2.7'
+- '3.5'
+- '3.6'
+- '3.7'
 before_install:
 - sudo apt-get update -qq
 - pip install toil[all]==3.17.0

test/test_client_util.py

@@ -64,8 +64,8 @@ def testSupportedFormatChecking(self):
         for file_format, location in self.local.items():
             if file_format != 'unsupported':
                 # Tests the behavior after receiving supported file types with and without the 'file://' prefix
-                self.assertEquals(wf_info(location), self.expected[file_format])
-                self.assertEquals(wf_info(location[7:]), self.expected[file_format])
+                self.assertEqual(wf_info(location), self.expected[file_format])
+                self.assertEqual(wf_info(location[7:]), self.expected[file_format])
 
             else:
                 # Tests behavior after receiving a non supported file type.
@@ -91,7 +91,7 @@ def testFileLocationChecking(self):
                     wf_info(location)
 
             else:
-                self.assertEquals(wf_info(location), self.expected[file_format])
+                self.assertEqual(wf_info(location), self.expected[file_format])
                 self.assertFalse(os.path.isfile(os.path.join(os.getcwd(), 'fetchedFromRemote.' + file_format)))
 
 

wes_client/util.py

@@ -5,11 +5,14 @@
 import yaml
 import glob
 import requests
-import urllib
 import logging
 
 from wes_service.util import visit
-from urllib import urlopen
+
+from future.standard_library import hooks
+
+with hooks():
+    from urllib.request import urlopen, pathname2url
 
 
 def two_seven_compatible(filePath):
@@ -56,7 +59,7 @@ def wf_info(workflow_path):
             html = urlopen(workflow_path).read()
             local_loc = os.path.join(os.getcwd(), 'fetchedFromRemote.' + file_type)
             with open(local_loc, 'w') as f:
-                f.write(html)
+                f.write(html.decode())
             version = wf_info('file://' + local_loc)[0]  # Don't take the file_type here, found it above.
             os.remove(local_loc)  # TODO: Find a way to avoid recreating file before version determination.
         else:
@@ -86,7 +89,7 @@ def fixpaths(d):
             if "path" in d:
                 if ":" not in d["path"]:
                     local_path = os.path.normpath(os.path.join(os.getcwd(), basedir, d["path"]))
-                    d["location"] = urllib.pathname2url(local_path)
+                    d["location"] = pathname2url(local_path)
                 else:
                     d["location"] = d["path"]
                 del d["path"]

wes_service/util.py

@@ -67,7 +67,7 @@ def collect_attachments(self, run_id=None):
                     content = v.read()
                     body[k] = json.loads(content)
                 else:
-                    body[k] = v.read()
+                    body[k] = v.read().decode()
 
         if ":" not in body["workflow_url"]:
             body["workflow_url"] = "file://%s" % os.path.join(tempdir, secure_filename(body["workflow_url"]))