Merge pull request #650 from nsoranzo/dev

flake8 test/tool_shed/ . Fix 8 Tool Shed functional tests.

.ci/flake8_blacklist.txt

@@ -6,7 +6,6 @@ doc/patch.py
 doc/source/conf.py
 lib/galaxy/model/migrate/versions/
 lib/galaxy/model/tool_shed_install/migrate/versions/
-lib/galaxy/util/pastescript/serve.py
 lib/galaxy/util/jstree.py
 lib/galaxy/webapps/tool_shed/model/migrate/versions/
 lib/pkg_resources.py
@@ -23,5 +22,4 @@ scripts/transfer.py
 test/base/
 test/casperjs/
 test/install_and_test_tool_shed_repositories/
-test/tool_shed/
 tools/

lib/galaxy/webapps/tool_shed/controllers/repository.py

@@ -905,10 +905,8 @@ def check_for_updates( self, trans, **kwd ):
             params = dict( tool_shed_url=web.url_for( '/', qualified=True ),
                            name=str( repository.name ),
                            owner=str( repository.user.username ),
-                           changeset_revision=changeset_revision,
-                           latest_changeset_revision=latest_changeset_revision )
+                           changeset_revision=changeset_revision )
             pathspec = [ 'admin_toolshed', 'update_to_changeset_revision' ]
-            url = common_util.url_join( galaxy_url, pathspec=pathspec, params=params )
         else:
             message = 'Unable to check for updates due to an invalid Galaxy URL: <b>%s</b>.  ' % galaxy_url
             message += 'You may need to enable third-party cookies in your browser.  '
@@ -918,7 +916,6 @@ def check_for_updates( self, trans, **kwd ):
             if from_update_manager:
                 return no_update
             # Return the same value for changeset_revision and latest_changeset_revision.
-            url += latest_changeset_revision
         else:
             repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app,
                                                                                      trans.security.encode_id( repository.id ),
@@ -928,9 +925,7 @@ def check_for_updates( self, trans, **kwd ):
                 # additional updates.
                 if from_update_manager:
                     return no_update
-                else:
-                    # Return the same value for changeset_revision and latest_changeset_revision.
-                    url += latest_changeset_revision
+                # Return the same value for changeset_revision and latest_changeset_revision.
             else:
                 # The changeset_revision column in the repository_metadata table has been updated with a new
                 # changeset_revision value since the repository was installed.  We need to find the changeset_revision
@@ -963,8 +958,9 @@ def check_for_updates( self, trans, **kwd ):
                     if latest_changeset_revision == changeset_revision:
                         return no_update
                     return update
-                url += str( latest_changeset_revision )
-        url += '&latest_ctx_rev=%s' % str( update_to_ctx.rev() )
+        params['latest_changeset_revision'] = str( latest_changeset_revision )
+        params['latest_ctx_rev'] = str( update_to_ctx.rev() )
+        url = common_util.url_join( galaxy_url, pathspec=pathspec, params=params )
         return trans.response.send_redirect( url )
 
     @web.expose

test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py

@@ -1,4 +1,7 @@
-from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os
+import os
+
+from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+
 repository_name = 'freebayes_0010'
 repository_description = "Galaxy's freebayes tool"
 repository_long_description = "Long description of Galaxy's freebayes tool"
@@ -13,145 +16,146 @@
 7. Check for the appropriate strings on the manage repository page.
 '''
 
+
 class TestFreebayesRepository( ShedTwillTestCase ):
     '''Testing freebayes with tool data table entries, .loc files, and tool dependencies.'''
-    
+
     def test_0000_create_or_login_admin_user( self ):
         """Create necessary user accounts and login as an admin user."""
         self.logout()
         self.login( email=common.test_user_1_email, username=common.test_user_1_name )
         test_user_1 = self.test_db_util.get_user( common.test_user_1_email )
-        assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % test_user_1_email
-        test_user_1_private_role = self.test_db_util.get_private_role( test_user_1 )
+        assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % common.test_user_1_email
+        self.test_db_util.get_private_role( test_user_1 )
         self.logout()
         self.login( email=common.admin_email, username=common.admin_username )
         admin_user = self.test_db_util.get_user( common.admin_email )
-        assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email
-        admin_user_private_role = self.test_db_util.get_private_role( admin_user )
-        
+        assert admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email
+        self.test_db_util.get_private_role( admin_user )
+
     def test_0005_create_category( self ):
         """Create a category for this test suite"""
         self.create_category( name='Test 0010 Repository With Tool Dependencies', description='Tests for a repository with tool dependencies.' )
-        
+
     def test_0010_create_freebayes_repository_and_upload_tool_xml( self ):
         '''Create freebayes repository and upload only freebayes.xml.'''
         '''
         We are at step 1 - Create repository freebayes_0020 and upload only the tool XML.
-        Uploading only the tool XML file should result in an invalid tool and an error message on 
-        upload, as well as on the manage repository page. 
+        Uploading only the tool XML file should result in an invalid tool and an error message on
+        upload, as well as on the manage repository page.
         '''
         self.logout()
         self.login( email=common.test_user_1_email, username=common.test_user_1_name )
         category = self.test_db_util.get_category_by_name( 'Test 0010 Repository With Tool Dependencies' )
-        repository = self.get_or_create_repository( name=repository_name, 
-                                                    description=repository_description, 
-                                                    long_description=repository_long_description, 
+        repository = self.get_or_create_repository( name=repository_name,
+                                                    description=repository_description,
+                                                    long_description=repository_long_description,
                                                     owner=common.test_user_1_name,
-                                                    category_id=self.security.encode_id( category.id ), 
+                                                    category_id=self.security.encode_id( category.id ),
                                                     strings_displayed=[] )
-        self.upload_file( repository, 
-                          filename='freebayes/freebayes.xml', 
+        self.upload_file( repository,
+                          filename='freebayes/freebayes.xml',
                           filepath=None,
                           valid_tools_only=False,
                           uncompress_file=False,
                           remove_repo_files_not_in_tar=False,
                           commit_message='Uploaded the tool xml.',
-                          strings_displayed=[ 'Metadata may have been defined', 'This file requires an entry', 'tool_data_table_conf' ], 
+                          strings_displayed=[ 'Metadata may have been defined', 'This file requires an entry', 'tool_data_table_conf' ],
                           strings_not_displayed=[] )
         self.display_manage_repository_page( repository, strings_displayed=[ 'Invalid tools' ], strings_not_displayed=[ 'Valid tools' ] )
         tip = self.get_repository_tip( repository )
         strings_displayed = [ 'requires an entry', 'tool_data_table_conf.xml' ]
         self.check_repository_invalid_tools_for_changeset_revision( repository, tip, strings_displayed=strings_displayed )
-        
+
     def test_0015_upload_missing_tool_data_table_conf_file( self ):
         '''Upload the missing tool_data_table_conf.xml.sample file to the repository.'''
         '''
         We are at step 2 - Upload the tool_data_table_conf.xml.sample file.
         Uploading the tool_data_table_conf.xml.sample alone should not make the tool valid, but the error message should change.
         '''
         repository = self.test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name )
-        self.upload_file( repository, 
-                          filename='freebayes/tool_data_table_conf.xml.sample', 
+        self.upload_file( repository,
+                          filename='freebayes/tool_data_table_conf.xml.sample',
                           filepath=None,
                           valid_tools_only=False,
                           uncompress_file=False,
                           remove_repo_files_not_in_tar=False,
                           commit_message='Uploaded the tool data table sample file.',
-                          strings_displayed=[], 
+                          strings_displayed=[],
                           strings_not_displayed=[] )
         self.display_manage_repository_page( repository, strings_displayed=[ 'Invalid tools' ], strings_not_displayed=[ 'Valid tools' ] )
         tip = self.get_repository_tip( repository )
         strings_displayed = [ 'refers to a file', 'sam_fa_indices.loc' ]
         self.check_repository_invalid_tools_for_changeset_revision( repository, tip, strings_displayed=strings_displayed )
-        
+
     def test_0020_upload_missing_sample_loc_file( self ):
         '''Upload the missing sam_fa_indices.loc.sample file to the repository.'''
         '''
         We are at step 3 - Upload the tool_data_table_conf.xml.sample file.
         Uploading the tool_data_table_conf.xml.sample alone should not make the tool valid, but the error message should change.
         '''
         repository = self.test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name )
-        self.upload_file( repository, 
-                          filename='freebayes/sam_fa_indices.loc.sample', 
+        self.upload_file( repository,
+                          filename='freebayes/sam_fa_indices.loc.sample',
                           filepath=None,
                           valid_tools_only=True,
                           uncompress_file=False,
                           remove_repo_files_not_in_tar=False,
                           commit_message='Uploaded tool data table .loc file.',
-                          strings_displayed=[], 
+                          strings_displayed=[],
                           strings_not_displayed=[] )
-        
+
     def test_0025_upload_malformed_tool_dependency_xml( self ):
         '''Upload tool_dependencies.xml with bad characters in the readme tag.'''
         '''
         We are at step 4 - Upload a tool_dependencies.xml file that should not parse correctly.
         Upload a tool_dependencies.xml file that contains <> in the text of the readme tag. This should show an error message about malformed xml.
         '''
         repository = self.test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name )
-        self.upload_file( repository, 
-                          filename=os.path.join( 'freebayes', 'malformed_tool_dependencies', 'tool_dependencies.xml' ), 
+        self.upload_file( repository,
+                          filename=os.path.join( 'freebayes', 'malformed_tool_dependencies', 'tool_dependencies.xml' ),
                           filepath=None,
                           valid_tools_only=False,
                           uncompress_file=False,
                           remove_repo_files_not_in_tar=False,
                           commit_message='Uploaded malformed tool dependency XML.',
-                          strings_displayed=[ 'Exception attempting to parse', 'not well-formed' ], 
+                          strings_displayed=[ 'Exception attempting to parse', 'not well-formed' ],
                           strings_not_displayed=[] )
-        
+
     def test_0030_upload_invalid_tool_dependency_xml( self ):
         '''Upload tool_dependencies.xml defining version 0.9.5 of the freebayes package.'''
         '''
         We are at step 5 - Upload a tool_dependencies.xml file that specifies a version that does not match the tool's requirements.
         This should result in a message about the tool dependency configuration not matching the tool's requirements.
         '''
         repository = self.test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name )
-        self.upload_file( repository, 
-                          filename=os.path.join( 'freebayes', 'invalid_tool_dependencies', 'tool_dependencies.xml' ), 
+        self.upload_file( repository,
+                          filename=os.path.join( 'freebayes', 'invalid_tool_dependencies', 'tool_dependencies.xml' ),
                           filepath=None,
                           valid_tools_only=False,
                           uncompress_file=False,
                           remove_repo_files_not_in_tar=False,
                           commit_message='Uploaded invalid tool dependency XML.',
-                          strings_displayed=[ 'The settings for <b>name</b>, <b>version</b> and <b>type</b> from a contained tool configuration' ], 
+                          strings_displayed=[ 'The settings for <b>name</b>, <b>version</b> and <b>type</b> from a contained tool configuration' ],
                           strings_not_displayed=[] )
-        
+
     def test_0035_upload_valid_tool_dependency_xml( self ):
         '''Upload tool_dependencies.xml defining version 0.9.4_9696d0ce8a962f7bb61c4791be5ce44312b81cf8 of the freebayes package.'''
         '''
         We are at step 6 - Upload a valid tool_dependencies.xml file.
         At this stage, there should be no errors on the upload page, as every missing or invalid file has been corrected.
         '''
         repository = self.test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name )
-        self.upload_file( repository, 
-                          filename=os.path.join( 'freebayes', 'tool_dependencies.xml' ), 
+        self.upload_file( repository,
+                          filename=os.path.join( 'freebayes', 'tool_dependencies.xml' ),
                           filepath=None,
                           valid_tools_only=True,
                           uncompress_file=False,
                           remove_repo_files_not_in_tar=False,
                           commit_message='Uploaded valid tool dependency XML.',
-                          strings_displayed=[], 
+                          strings_displayed=[],
                           strings_not_displayed=[] )
-        
+
     def test_0040_verify_tool_dependencies( self ):
         '''Verify that the uploaded tool_dependencies.xml specifies the correct package versions.'''
         '''
@@ -160,5 +164,5 @@ def test_0040_verify_tool_dependencies( self ):
         '''
         repository = self.test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name )
         strings_displayed = [ 'freebayes', '0.9.4_9696d0ce8a9', 'samtools', '0.1.18', 'Valid tools', 'package' ]
-        strings_not_displayed = [ 'Invalid tools' ] 
+        strings_not_displayed = [ 'Invalid tools' ]
         self.display_manage_repository_page( repository, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed )