Formatting changes

Author: bencvdb

test/test_wesclient_utils.py

@@ -1,29 +1,38 @@
 import unittest
 import os
+import sys
+
+pkg_root = os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))  # noqa
+sys.path.insert(0, pkg_root) # noqa
+
 from wes_client.util import wf_info
 
+
 class WorkflowInfoTest(unittest.TestCase):
 
-    local = {'cwl': 'file://' + os.path.join(os.getcwd() + '/workflow-service/testdata/md5sum.cwl'),
-             'wdl': 'file://' + os.path.join(os.getcwd() + '/workflow-service/testdata/md5sum.wdl'),
-             'py': 'file://' + os.path.join(os.getcwd() + '/workflow-service/test/test_integration.py'),
-             'unsupported':'fake.txt'}
+    local = {'cwl': 'file://' + os.path.join(os.getcwd() + '/testdata/md5sum.cwl'),
+             'wdl': 'file://' + os.path.join(os.getcwd() + '/testdata/md5sum.wdl'),
+             'py': 'file://' + os.path.join(os.getcwd() + '/test/test_integration.py'),
+             'unsupported': 'fake.txt'}
 
-    remote = {'cwl':'https://raw.githubusercontent.com/common-workflow-language/workflow-service/master/testdata/md5sum.cwl',
-              'wdl':'https://raw.githubusercontent.com/common-workflow-language/workflow-service/master/testdata/md5sum.wdl',
+    remote = {'cwl': 'https://raw.githubusercontent.com/common-workflow-language/workflow-service/master/testdata/md5sum.cwl',
+              'wdl': 'https://raw.githubusercontent.com/common-workflow-language/workflow-service/master/testdata/md5sum.wdl',
               'py': 'https://raw.githubusercontent.com/common-workflow-language/workflow-service/master/test/test_integration.py',
               'unsupported': 'gs://topmed_workflow_testing/topmed_aligner/small_test_files_sbg/example_human_known_snp.py', # TODO: find real external file of .py, .cwl, .wdl
-              'unreachable':'https://fake.py'}
+              'unreachable': 'https://fake.py'}
 
-    expected = {'cwl':('v1.0', 'CWL'),
-                'wdl':('draft-2','WDL'),
+    expected = {'cwl': ('v1.0', 'CWL'),
+                'wdl': ('draft-2','WDL'),
                 'py': ('2.7','PY'),
-                'pyWithPrefix' : ('2.7','PY')}
+                'pyWithPrefix': ('2.7','PY')}
 
     def testSupportedFormatChecking(self):
-        """Check that non-wdl, -python, -cwl files are rejected."""
+        """
+        Check that non-wdl, -python, -cwl files are rejected.
+
+        This test is run only on local files to avoid downloading and removing a new file.
+        """
 
-        # The choice to run this on local files prevents the irrelevant steps of creating and removing a new file.
         for format, location in self.local.items():
             if format != 'unsupported':
                 # Tests the behavior after receiving supported file types with and without the 'file://' prefix
@@ -37,17 +46,23 @@ def testSupportedFormatChecking(self):
 
 
     def testFileLocationChecking(self):
-        """Check that the function rejects unsupported file locations."""
-        # This needs to be run on remote files to get to the location checking step.
+        """
+        Check that the function rejects unsupported file locations.
+
+        This test needs to be run on remote files to test the location checking functionality of wf_info().
+        """
+
         for format, location in self.remote.items():
             if format == 'unsupported':
-                # Tests behavior after receiving a non-existant file.
+                # Tests behavior after receiving a file hosted at an unsupported location.
                 with self.assertRaises(NotImplementedError):
                     wf_info(location)
+
             elif format == 'unreachable':
-                # Tests behavior after receiving a non-existant file.
+                # Tests behavior after receiving a non-existent file.
                 with self.assertRaises(IOError):
                     wf_info(location)
+
             else:
                 self.assertEquals(wf_info(location), self.expected[format])
                 self.assertFalse(os.path.isfile(os.path.join(os.getcwd(), 'fetchedFromRemote.' + format)))

wes_client/util.py

@@ -27,7 +27,7 @@ def _getVersion(extension, workflow_file):
             return 'draft-2'
 
 
-def wf_info(workflow_file):
+def wf_info(workflow_path):
     """
     Returns the version of the file and the file extension.
 
@@ -37,21 +37,22 @@ def wf_info(workflow_file):
     """
 
     supportedFormats = ['py', 'wdl', 'cwl']
-    fileType = workflow_file.lower().split('.')[-1]  # Grab the file extension
-    workflow_file = workflow_file if ':' in workflow_file else 'file://' + workflow_file
+    fileType = workflow_path.lower().split('.')[-1]  # Grab the file extension
+    workflow_path = workflow_path if ':' in workflow_path else 'file://' + workflow_path
 
     if fileType in supportedFormats:
-        if workflow_file.startswith('file://'):
-            version = _getVersion(fileType, workflow_file[7:])
-        elif workflow_file.startswith('https://') or workflow_file.startswith('http://'):  # If file not local go fetch it.
-            html = urlopen(workflow_file).read()
+        if workflow_path.startswith('file://'):
+            version = _getVersion(fileType, workflow_path[7:])
+        elif workflow_path.startswith('https://') or workflow_path.startswith('http://'):
+            # If file not local go fetch it.
+            html = urlopen(workflow_path).read()
             localLoc = os.path.join(os.getcwd(), 'fetchedFromRemote.' + fileType)
             with open(localLoc, 'w') as f:
                 f.write(html)
-            version = wf_info('file://' + localLoc)[0] # Dont take the filetype here.
+            version = wf_info('file://' + localLoc)[0] # Don't take the fileType here, found it above.
             os.remove(localLoc)  # TODO: Find a way to avoid recreating file before version determination.
         else:
-            raise NotImplementedError('Unsupported workflow file location: {}. Must be local or HTTP(S).'.format(workflow_file))
+            raise NotImplementedError('Unsupported workflow file location: {}. Must be local or HTTP(S).'.format(workflow_path))
     else:
         raise TypeError('Unsupported workflow type: .{}. Must be {}.'.format(fileType, '.py, .cwl, or .wdl'))
     return version, fileType.upper()