1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/8e93ca10b0e2/ changeset: 8e93ca10b0e2 user: inithello date: 2013-02-15 22:55:29 summary: Tool shed functional test refactoring for clarity. Functional tests for limiting access to repository component reviews. affected #: 22 files
diff -r ec4da708e45175610a33d16fcfc68732e425f54f -r 8e93ca10b0e2523ba78a02bfb36e371db5f17e0a test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -83,20 +83,20 @@ tool_panel_section = tool_panel_section_metadata[ tool_guid ][ 0 ][ 'name' ] assert tool_panel_section == expected_tool_panel_section, 'Expected tool panel section %s, found %s\nMetadata: %s\n' % \ ( expected_tool_panel_section, tool_panel_section, metadata ) - def check_installed_repository_tool_dependencies( self, installed_repository, dependencies_installed=False ): + def check_installed_repository_tool_dependencies( self, + installed_repository, + strings_displayed=[], + strings_not_displayed=[], + dependencies_installed=False ): # Tool dependencies are not being installed in these functional tests. If this is changed, the test method will also need to be updated. - strings_not_displayed = [] if not dependencies_installed: - strings_displayed = [ 'Missing tool dependencies' ] + strings_displayed.append( 'Missing tool dependencies' ) else: - strings_displayed = [ 'Tool dependencies' ] - for dependency in installed_repository.metadata[ 'tool_dependencies' ]: - tool_dependency = installed_repository.metadata[ 'tool_dependencies' ][ dependency ] - strings_displayed.extend( [ tool_dependency[ 'name' ], tool_dependency[ 'version' ], tool_dependency[ 'type' ] ] ) - if dependencies_installed: - strings_displayed.append( 'Installed' ) - else: - strings_displayed.append( 'Never installed' ) + strings_displayed.append( 'Tool dependencies' ) + if dependencies_installed: + strings_displayed.append( 'Installed' ) + else: + strings_displayed.append( 'Never installed' ) url = '/admin_toolshed/manage_repository?id=%s' % self.security.encode_id( installed_repository.id ) self.visit_galaxy_url( url ) self.check_for_strings( strings_displayed, strings_not_displayed ) @@ -122,6 +122,7 @@ Loop through each tool dictionary in the repository metadata associated with the received changeset_revision. For each of these, check for a tools attribute, and load the tool metadata page if it exists, then display that tool's page. ''' + test_db_util.refresh( repository ) repository_metadata = self.get_repository_metadata_by_changeset_revision( repository, changeset_revision ) metadata = repository_metadata.metadata if 'tools' not in metadata: @@ -297,11 +298,7 @@ def display_installed_repository_manage_page( self, installed_repository, strings_displayed=[], strings_not_displayed=[] ): url = '/admin_toolshed/manage_repository?id=%s' % self.security.encode_id( installed_repository.id ) self.visit_galaxy_url( url ) - strings_displayed.extend( [ installed_repository.name, - installed_repository.description, - installed_repository.owner, - installed_repository.tool_shed, - installed_repository.installed_changeset_revision ] ) + strings_displayed.append( installed_repository.installed_changeset_revision ) self.check_for_strings( strings_displayed, strings_not_displayed ) def display_installed_workflow_image( self, repository, workflow_name, strings_displayed=[], strings_not_displayed=[] ): url = '/admin_toolshed/generate_workflow_image?repository_id=%s&workflow_name=%s' % \ @@ -316,19 +313,6 @@ changeset_revision = self.get_repository_tip( repository ) url = base_url self.visit_url( url ) - metadata = self.get_repository_metadata_by_changeset_revision( repository, changeset_revision ) - if metadata: - if 'tool_dependencies' in metadata.metadata: - strings_displayed.append( 'Tool dependencies' ) - for dependency in metadata.metadata[ 'tool_dependencies' ]: - if dependency == 'set_environment': - for environment_dependency in metadata.metadata[ 'tool_dependencies' ][ dependency ]: - strings_displayed.append( environment_dependency[ 'name' ] ) - strings_displayed.append( environment_dependency[ 'type' ] ) - else: - strings_displayed.append( metadata.metadata[ 'tool_dependencies' ][ dependency ][ 'name' ] ) - strings_displayed.append( metadata.metadata[ 'tool_dependencies' ][ dependency ][ 'version' ] ) - strings_displayed.append( metadata.metadata[ 'tool_dependencies' ][ dependency ][ 'type' ] ) self.check_for_strings( strings_displayed, strings_not_displayed ) def display_repository_clone_page( self, owner_name, repository_name, strings_displayed=[], strings_not_displayed=[] ): url = '/repos/%s/%s' % ( owner_name, repository_name ) @@ -907,19 +891,12 @@ # else: # time.sleep( 1 ) # continue - def verify_installed_uninstalled_repositories( self, installed_repositories=[], uninstalled_repositories=[] ): - strings_displayed = [] - strings_not_displayed = [] - for repository_name, repository_owner in uninstalled_repositories: - repository = test_db_util.get_repository_by_name_and_owner( repository_name, repository_owner ) - strings_not_displayed.extend( [ repository_name, self.get_repository_tip( repository ) ] ) + def verify_installed_repositories( self, installed_repositories=[], uninstalled_repositories=[] ): for repository_name, repository_owner in installed_repositories: - repository = test_db_util.get_repository_by_name_and_owner( repository_name, repository_owner ) galaxy_repository = test_db_util.get_installed_repository_by_name_owner( repository_name, repository_owner ) if galaxy_repository: - assert galaxy_repository.status == 'Installed', 'Repository %s should be installed, but is %s' % ( repository_name, galaxy_repository.status ) - strings_displayed.extend( [ repository_name, self.get_repository_tip( repository ) ] ) - self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed ) + assert galaxy_repository.status == 'Installed', \ + 'Repository %s should be installed, but is %s' % ( repository_name, galaxy_repository.status ) def verify_installed_repository_metadata_unchanged( self, name, owner ): installed_repository = test_db_util.get_installed_repository_by_name_owner( name, owner ) metadata = installed_repository.metadata
diff -r ec4da708e45175610a33d16fcfc68732e425f54f -r 8e93ca10b0e2523ba78a02bfb36e371db5f17e0a test/tool_shed/functional/test_0000_basic_repository_features.py --- a/test/tool_shed/functional/test_0000_basic_repository_features.py +++ b/test/tool_shed/functional/test_0000_basic_repository_features.py @@ -157,7 +157,7 @@ category = test_db_util.get_category_by_name( 'Test 0000 Basic Repository Features 1' ) tip = self.get_repository_tip( repository ) self.check_for_valid_tools( repository ) - strings_displayed = self.get_repository_metadata_revisions( repository ).append( 'Select a revision' ) + strings_displayed = [ 'Select a revision' ] self.display_manage_repository_page( repository, strings_displayed=strings_displayed ) self.check_count_of_metadata_revisions_associated_with_repository( repository, metadata_count=2 ) self.check_repository_tools_for_changeset_revision( repository, tip )
diff -r ec4da708e45175610a33d16fcfc68732e425f54f -r 8e93ca10b0e2523ba78a02bfb36e371db5f17e0a test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py --- a/test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py +++ b/test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py @@ -116,5 +116,5 @@ '''Verify that the uploaded tool_dependencies.xml specifies the correct package versions.''' repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) self.display_manage_repository_page( repository, - strings_displayed=[ 'freebayes', '0.9.4_9696d0ce8a9', 'samtools', '0.1.18', 'Valid tools' ], + strings_displayed=[ 'freebayes', '0.9.4_9696d0ce8a9', 'samtools', '0.1.18', 'Valid tools', 'package' ], strings_not_displayed=[ 'Invalid tools' ] )
diff -r ec4da708e45175610a33d16fcfc68732e425f54f -r 8e93ca10b0e2523ba78a02bfb36e371db5f17e0a test/tool_shed/functional/test_0030_repository_dependency_revisions.py --- a/test/tool_shed/functional/test_0030_repository_dependency_revisions.py +++ b/test/tool_shed/functional/test_0030_repository_dependency_revisions.py @@ -178,7 +178,7 @@ # Iterate through all metadata revisions and check for repository dependencies. for metadata, changeset_revision in repository_metadata: # Add the dependency description and datatypes repository details to the strings to check. - strings_displayed.extend( [ 'Emboss requires the Emboss', 'emboss_datatypes_0030', 'user1', datatypes_tip ] ) + strings_displayed = [ 'Emboss requires the Emboss', 'emboss_datatypes_0030', 'user1', datatypes_tip ] strings_displayed.extend( [ 'Tool dependencies', 'emboss', '5.0.0', 'package' ] ) self.display_manage_repository_page( repository, changeset_revision=changeset_revision,
diff -r ec4da708e45175610a33d16fcfc68732e425f54f -r 8e93ca10b0e2523ba78a02bfb36e371db5f17e0a test/tool_shed/functional/test_0040_repository_circular_dependencies.py --- a/test/tool_shed/functional/test_0040_repository_circular_dependencies.py +++ b/test/tool_shed/functional/test_0040_repository_circular_dependencies.py @@ -127,5 +127,5 @@ '''Verify that freebayes displays tool dependencies.''' repository = test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) self.display_manage_repository_page( repository, - strings_displayed=[ 'freebayes', '0.9.4_9696d0ce8a9', 'samtools', '0.1.18', 'Valid tools' ], + strings_displayed=[ 'freebayes', '0.9.4_9696d0ce8a9', 'samtools', '0.1.18', 'Valid tools', 'package' ], strings_not_displayed=[ 'Invalid tools' ] )
diff -r ec4da708e45175610a33d16fcfc68732e425f54f -r 8e93ca10b0e2523ba78a02bfb36e371db5f17e0a test/tool_shed/functional/test_0050_circular_dependencies_4_levels.py --- a/test/tool_shed/functional/test_0050_circular_dependencies_4_levels.py +++ b/test/tool_shed/functional/test_0050_circular_dependencies_4_levels.py @@ -261,7 +261,7 @@ for repository in [ emboss_datatypes_repository, emboss_repository, column_repository ]: self.check_repository_dependency( freebayes_repository, repository ) freebayes_dependencies = [ freebayes_repository, emboss_datatypes_repository, emboss_repository, column_repository ] - strings_displayed = [ '%s depends on %s.' % ( freebayes_repository.name, ', '.join( repo.name for repo in freebayes_dependencies ) ) ] + strings_displayed = [ 'freebayes_0050 depends on freebayes_0050, emboss_datatypes_0050, emboss_0050, column_maker_0050.' ] self.display_manage_repository_page( freebayes_repository, strings_displayed=strings_displayed ) def test_0050_verify_tool_dependencies( self ): @@ -269,7 +269,7 @@ freebayes_repository = test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) self.display_manage_repository_page( freebayes_repository, - strings_displayed=[ 'freebayes', '0.9.4_9696d0ce8a9', 'samtools', '0.1.18', 'Tool dependencies' ] ) + strings_displayed=[ 'freebayes', '0.9.4_9696d0ce8a9', 'samtools', '0.1.18', 'Tool dependencies', 'package' ] ) self.display_manage_repository_page( emboss_repository, strings_displayed=[ 'Tool dependencies', 'emboss', '5.0.0', 'package' ] ) def test_0055_verify_repository_metadata( self ): '''Verify that resetting the metadata does not change it.'''
diff -r ec4da708e45175610a33d16fcfc68732e425f54f -r 8e93ca10b0e2523ba78a02bfb36e371db5f17e0a test/tool_shed/functional/test_0410_repository_component_review_access_control.py --- /dev/null +++ b/test/tool_shed/functional/test_0410_repository_component_review_access_control.py @@ -0,0 +1,196 @@ +from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os +import tool_shed.base.test_db_util as test_db_util + +repository_name = 'filtering_0410' +repository_description = 'Galaxy filtering tool for test 0410' +repository_long_description = 'Long description of Galaxy filtering tool for test 0410' + +''' +1. Create a repository in the tool shed owned by test_user_1. +2. Have test_user_2 complete a review of the repository. +3. Have test_user_1 browse the review. +4. Have test_user_3 browse the repository and make sure they are not allowed to browse the review. +5. Have test_user_1 give write permission on the repository to the test_user_3. +6. Have test_user_3 browse the repository again and they should now have the ability to browse the review. +7. Have test_user_3 browse the review. +''' + +class TestRepositoryComponentReviews( ShedTwillTestCase ): + '''Test repository component review features.''' + def test_0000_initiate_users( self ): + """Create necessary user accounts and login as an admin user.""" + """ + Create all the user accounts that are needed for this test script to run independently of other test. + Previously created accounts will not be re-created. + """ + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + test_user_1 = 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' % common.test_user_1_email + test_user_1_private_role = test_db_util.get_private_role( test_user_1 ) + self.logout() + self.login( email=common.test_user_2_email, username=common.test_user_2_name ) + test_user_2 = test_db_util.get_user( common.test_user_2_email ) + assert test_user_2 is not None, 'Problem retrieving user with email %s from the database' % common.test_user_2_email + test_user_2_private_role = test_db_util.get_private_role( test_user_2 ) + self.logout() + self.login( email=common.test_user_3_email, username=common.test_user_3_name ) + test_user_3 = test_db_util.get_user( common.test_user_3_email ) + assert test_user_3 is not None, 'Problem retrieving user with email %s from the database' % common.test_user_3_email + test_user_3_private_role = test_db_util.get_private_role( test_user_3 ) + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + admin_user = test_db_util.get_user( common.admin_email ) + assert admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email + admin_user_private_role = test_db_util.get_private_role( admin_user ) + def test_0005_grant_reviewer_role( self ): + '''Grant the repository reviewer role to test_user_2.''' + """ + We now have an admin user (admin_user) and three non-admin users (test_user_1, test_user_2, and test_user_3). Grant the repository + reviewer role to test_user_2, who will not be the owner of the reviewed repositories, and do not grant any roles to test_user_3 yet. + """ + reviewer_role = test_db_util.get_role_by_name( 'Repository Reviewer' ) + test_user_2 = test_db_util.get_user( common.test_user_2_email ) + self.grant_role_to_user( test_user_2, reviewer_role ) + def test_0010_verify_repository_review_components( self ): + '''Ensure that the required review components exist.''' + """ + Make sure all the components we are to review are recorded in the database. + """ + self.add_repository_review_component( name='Repository dependencies', + description='Repository dependencies defined in a file named repository_dependencies.xml included in the repository' ) + strings_displayed=[ 'Data types', 'Functional tests', 'README', 'Repository dependencies', 'Tool dependencies', 'Tools', 'Workflows' ] + self.manage_review_components( strings_displayed=strings_displayed ) + def test_0015_create_repository( self ): + """Create and populate the filtering repository""" + """ + We are at step 1. + Log in as test_user_1 and create the filtering repository, then upload a basic set of + components to be reviewed in subsequent tests. + """ + category = self.create_category( name='Test 0400 Repository Component Reviews', description='Test 0400 Repository Component Reviews' ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + strings_displayed = [ 'Repository %s' % "'%s'" % repository_name, + 'Repository %s has been created' % "'%s'" % repository_name ] + 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 ), + strings_displayed=strings_displayed ) + self.upload_file( repository, + filename='filtering/filtering_1.1.0.tar', + filepath=None, + valid_tools_only=True, + uncompress_file=True, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded filtering 1.1.0 tarball.', + strings_displayed=[], + strings_not_displayed=[] ) + self.upload_file( repository, + filename='filtering/filtering_test_data.tar', + filepath=None, + valid_tools_only=True, + uncompress_file=True, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded filtering test data.', + strings_displayed=[], + strings_not_displayed=[] ) + self.upload_file( repository, + filename='readme.txt', + filepath=None, + valid_tools_only=True, + uncompress_file=True, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded readme.txt.', + strings_displayed=[], + strings_not_displayed=[] ) + def test_0020_review_repository( self ): + '''Complete a review of the filtering repository.''' + ''' + We are at step 2 - Have test_user_2 complete a review of the repository. + Review all components of the filtering repository, with the appropriate contents and approved/not approved/not applicable status. + ''' + self.logout() + self.login( email=common.test_user_2_email, username=common.test_user_2_name ) + repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + user = test_db_util.get_user( common.test_user_2_email ) + review_contents_dict = { + 'Data types': dict(), + 'README': dict( rating=5, comment='Clear and concise readme file, a true pleasure to read.', approved='yes', private='no' ), + 'Functional tests': dict( rating=5, comment='A good set of functional tests.', approved='yes', private='no' ), + 'Repository dependencies': dict(), + 'Tool dependencies': dict(), + 'Tools': dict( rating=5, comment='Excellent tool, easy to use.', approved='yes', private='no' ), + 'Workflows': dict() + } + self.create_repository_review( repository, review_contents_dict ) + def test_0025_verify_repository_review( self ): + '''Verify that the review was completed and displays properly.''' + ''' + We are at step 3 - Have test_user_1 browse the review. + Verify that all the review components were submitted, and that the repository owner can see the review. + ''' + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + user = test_db_util.get_user( common.test_user_2_email ) + strings_displayed = [ 'Data types', 'Functional tests', 'yes', 'A good set of functional tests.', 'README', 'yes', 'Workflows', 'Tools' ] + strings_displayed.extend( [ 'Clear and concise readme file, a true pleasure to read.', 'Tool dependencies', 'not_applicable' ] ) + strings_displayed.extend( [ 'Repository dependencies', 'Excellent tool, easy to use.' ] ) + strings_displayed = [ 'Browse reviews of this repository' ] + self.display_manage_repository_page( repository, strings_displayed=strings_displayed ) + self.verify_repository_reviews( repository, reviewer=user, strings_displayed=strings_displayed ) + def test_0030_browse_with_other_user( self ): + '''Verify that test_user_3 is blocked from browsing the review.''' + ''' + We are at step 4 - Have test_user_3 browse the repository and make sure they are not allowed to browse the review. + ''' + self.logout() + self.login( email=common.test_user_3_email, username=common.test_user_3_name ) + repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + user = test_db_util.get_user( common.test_user_2_email ) + strings_not_displayed = [ 'Browse reviews of this repository' ] + self.display_manage_repository_page( repository, strings_not_displayed=strings_not_displayed ) + strings_not_displayed = [ 'A good set of functional tests.', 'Clear and concise readme file, a true pleasure to read.' ] + strings_not_displayed.append( 'Excellent tool, easy to use.' ) + changeset_revision = self.get_repository_tip( repository ) + review = test_db_util.get_repository_review_by_user_id_changeset_revision( user.id, repository.id, changeset_revision ) + self.browse_component_review( review, strings_not_displayed=strings_not_displayed ) + def test_0035_grant_write_access_to_other_user( self ): + '''Grant write access on the filtering_0410 repository to test_user_3.''' + ''' + We are at step 5 - Have test_user_1 give write permission on the repository to the test_user_3. + ''' + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + self.grant_write_access( repository, usernames=[ common.test_user_3_name ] ) + def test_0040_verify_test_user_3_can_browse_reviews( self ): + '''Check that test_user_3 can now browse reviews.''' + ''' + We are at step 6 - Have test_user_3 browse the repository again and they should now have the ability to browse the review. + ''' + self.logout() + self.login( email=common.test_user_3_email, username=common.test_user_3_name ) + repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + strings_displayed = [ 'Browse reviews of this repository' ] + self.display_manage_repository_page( repository, strings_displayed=strings_displayed ) + def test_0045_verify_browse_review_with_write_access( self ): + '''Check that test_user_3 can now display reviews.''' + ''' + We are at step 7 - Have test_user_3 browse the review. + ''' + self.logout() + self.login( email=common.test_user_3_email, username=common.test_user_3_name ) + repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + user = test_db_util.get_user( common.test_user_2_email ) + strings_displayed = [ 'A good set of functional tests.', + 'Clear and concise readme file', + 'a true pleasure to read.', + 'Excellent tool, easy to use.' ] + changeset_revision = self.get_repository_tip( repository ) + review = test_db_util.get_repository_review_by_user_id_changeset_revision( user.id, repository.id, changeset_revision ) + self.browse_component_review( review, strings_displayed=strings_displayed ) + \ No newline at end of file
diff -r ec4da708e45175610a33d16fcfc68732e425f54f -r 8e93ca10b0e2523ba78a02bfb36e371db5f17e0a test/tool_shed/functional/test_1000_install_basic_repository.py --- a/test/tool_shed/functional/test_1000_install_basic_repository.py +++ b/test/tool_shed/functional/test_1000_install_basic_repository.py @@ -88,14 +88,14 @@ 'Test 0000 Basic Repository Features 1', new_tool_panel_section='test_1000' ) installed_repository = test_db_util.get_installed_repository_by_name_owner( 'filtering_0000', common.test_user_1_name ) - strings_displayed = [ installed_repository.name, - installed_repository.description, - installed_repository.owner, - installed_repository.tool_shed, + strings_displayed = [ 'filtering_0000', + "Galaxy's filtering tool", + 'user1', + self.url.replace( 'http://', '' ), installed_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) - self.display_installed_repository_manage_page( installed_repository, - strings_displayed=[ 'Installed tool shed repository', 'Valid tools', 'Filter1' ] ) + strings_displayed.extend( [ 'Installed tool shed repository', 'Valid tools', 'Filter1' ] ) + self.display_installed_repository_manage_page( installed_repository, strings_displayed=strings_displayed ) self.verify_tool_metadata_for_installed_repository( installed_repository ) def test_0030_verify_installed_repository_metadata( self ): '''Verify that resetting the metadata on an installed repository does not change the metadata.'''
diff -r ec4da708e45175610a33d16fcfc68732e425f54f -r 8e93ca10b0e2523ba78a02bfb36e371db5f17e0a test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py --- a/test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py +++ b/test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py @@ -117,9 +117,10 @@ self.url.replace( 'http://', '' ), installed_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) - self.display_installed_repository_manage_page( installed_repository, - strings_displayed=[ 'Installed tool shed repository', 'Valid tools', 'FreeBayes' ] ) - self.check_installed_repository_tool_dependencies( installed_repository, dependencies_installed=False ) + strings_displayed.extend( [ 'Installed tool shed repository', 'Valid tools', 'FreeBayes' ] ) + self.display_installed_repository_manage_page( installed_repository, strings_displayed=strings_displayed ) + strings_displayed = [ 'freebayes', '0.9.4_9696d0ce8a9', 'samtools', '0.1.18' ] + self.check_installed_repository_tool_dependencies( installed_repository, strings_displayed=strings_displayed, dependencies_installed=False ) self.verify_tool_metadata_for_installed_repository( installed_repository ) def test_0020_verify_installed_repository_metadata( self ): '''Verify that resetting the metadata on an installed repository does not change the metadata.'''
diff -r ec4da708e45175610a33d16fcfc68732e425f54f -r 8e93ca10b0e2523ba78a02bfb36e371db5f17e0a test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py --- a/test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py +++ b/test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py @@ -109,9 +109,10 @@ self.url.replace( 'http://', '' ), installed_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) - self.display_installed_repository_manage_page( installed_repository, - strings_displayed=[ 'Installed tool shed repository', 'Valid tools', 'antigenic' ] ) - self.check_installed_repository_tool_dependencies( installed_repository, dependencies_installed=False ) + strings_displayed.extend( [ 'Installed tool shed repository', 'Valid tools', 'antigenic' ] ) + self.display_installed_repository_manage_page( installed_repository, strings_displayed=strings_displayed ) + strings_displayed = [ 'emboss', '5.0.0', 'package' ] + self.check_installed_repository_tool_dependencies( installed_repository, strings_displayed=strings_displayed, dependencies_installed=False ) self.verify_tool_metadata_for_installed_repository( installed_repository ) current_datatypes = int( self.get_datatypes_count() ) assert current_datatypes == base_datatypes_count + repository_datatypes_count, 'Installing emboss did not add new datatypes. Expected: %d. Found: %d' % \
diff -r ec4da708e45175610a33d16fcfc68732e425f54f -r 8e93ca10b0e2523ba78a02bfb36e371db5f17e0a test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py --- a/test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py +++ b/test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py @@ -175,13 +175,14 @@ installed_repository = test_db_util.get_installed_repository_by_name_owner( 'emboss_0030', common.test_user_1_name ) strings_displayed = [ 'emboss_0030', 'Galaxy wrappers for Emboss version 5.0.0 tools for test 0030', - installed_repository.owner, - installed_repository.tool_shed, + 'user1', + self.url.replace( 'http://', '' ), installed_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) - self.display_installed_repository_manage_page( installed_repository, - strings_displayed=[ 'Installed tool shed repository', 'Valid tools', 'antigenic' ] ) - self.check_installed_repository_tool_dependencies( installed_repository, dependencies_installed=False ) + strings_displayed.extend( [ 'Installed tool shed repository', 'Valid tools', 'antigenic' ] ) + self.display_installed_repository_manage_page( installed_repository, strings_displayed=strings_displayed ) + strings_displayed = [ 'emboss', '5.0.0', 'package' ] + self.check_installed_repository_tool_dependencies( installed_repository, strings_displayed=strings_displayed, dependencies_installed=False ) self.verify_tool_metadata_for_installed_repository( installed_repository ) self.update_installed_repository( installed_repository, strings_displayed=[ "there are no updates available" ] ) current_datatypes = int( self.get_datatypes_count() )
diff -r ec4da708e45175610a33d16fcfc68732e425f54f -r 8e93ca10b0e2523ba78a02bfb36e371db5f17e0a test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py --- a/test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py +++ b/test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py @@ -129,7 +129,7 @@ self.uninstall_repository( installed_freebayes_repository, remove_from_disk=True ) test_db_util.ga_refresh( installed_freebayes_repository ) self.check_galaxy_repository_tool_panel_section( installed_freebayes_repository, '' ) - strings_displayed = [ 'Missing repository', 'freebayes' ] + strings_displayed = [ 'Missing repository', 'freebayes', 'filtering_0040', 'user1', "Galaxy's filtering tool for test 0040" ] self.display_installed_repository_manage_page( installed_filtering_repository, strings_displayed=strings_displayed ) self.check_galaxy_repository_db_status( freebayes_repository_name, common.test_user_1_name, @@ -150,7 +150,7 @@ self.uninstall_repository( installed_filtering_repository, remove_from_disk=True ) test_db_util.ga_refresh( installed_filtering_repository ) self.check_galaxy_repository_tool_panel_section( installed_filtering_repository, '' ) - strings_displayed = [ 'Missing repository', 'filtering' ] + strings_displayed = [ 'Missing repository', 'filtering', 'freebayes_0040', 'user1', "Galaxy's freebayes tool for test 0040" ] self.display_installed_repository_manage_page( installed_freebayes_repository, strings_displayed=strings_displayed ) self.check_galaxy_repository_db_status( filtering_repository_name, common.test_user_1_name, @@ -162,7 +162,7 @@ self.uninstall_repository( installed_freebayes_repository, remove_from_disk=True ) test_db_util.ga_refresh( installed_freebayes_repository ) self.check_galaxy_repository_tool_panel_section( installed_freebayes_repository, 'freebayes' ) - strings_displayed = [ 'Missing repository', 'freebayes' ] + strings_displayed = [ 'Missing repository', 'freebayes', 'filtering_0040', 'user1', "Galaxy's filtering tool for test 0040" ] self.display_installed_repository_manage_page( installed_filtering_repository, strings_displayed=strings_displayed ) self.check_galaxy_repository_db_status( 'freebayes_0040', 'user1',
diff -r ec4da708e45175610a33d16fcfc68732e425f54f -r 8e93ca10b0e2523ba78a02bfb36e371db5f17e0a test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py --- a/test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py +++ b/test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py @@ -267,12 +267,10 @@ # This should result in column_maker and convert_chars being installed, and the rest never installed. installed_repositories = [ ( column_repository_name, common.test_user_1_name ), ( convert_repository_name, common.test_user_1_name ) ] - uninstalled_repositories = [ ( emboss_datatypes_repository_name, common.test_user_1_name ), - ( emboss_repository_name, common.test_user_1_name ), - ( filtering_repository_name, common.test_user_1_name ), - ( freebayes_repository_name, common.test_user_1_name ), - ( bismark_repository_name, common.test_user_1_name ) ] - self.verify_installed_uninstalled_repositories( installed_repositories=installed_repositories, uninstalled_repositories=uninstalled_repositories ) + strings_displayed = [ 'column_maker_0050', 'convert_chars_0050' ] + strings_not_displayed = [ 'emboss_datatypes_0050', 'emboss_0050', 'filtering_0050', 'freebayes_0050', 'bismark_0050' ] + self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed ) + self.verify_installed_repositories( installed_repositories=installed_repositories ) def test_0060_install_emboss_repository( self ): '''Install emboss_5 with repository dependencies.''' global running_standalone @@ -291,9 +289,10 @@ ( emboss_repository_name, common.test_user_1_name ), ( convert_repository_name, common.test_user_1_name ), ( bismark_repository_name, common.test_user_1_name ) ] - uninstalled_repositories = [ ( filtering_repository_name, common.test_user_1_name ), - ( freebayes_repository_name, common.test_user_1_name ) ] - self.verify_installed_uninstalled_repositories( installed_repositories=installed_repositories, uninstalled_repositories=uninstalled_repositories ) + strings_displayed = [ 'emboss_datatypes_0050', 'emboss_0050', 'column_maker_0050', 'convert_chars_0050', 'bismark_0050' ] + strings_not_displayed = [ 'filtering_0050', 'freebayes_0050' ] + self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed ) + self.verify_installed_repositories( installed_repositories ) def test_0065_deactivate_datatypes_repository( self ): '''Deactivate emboss_datatypes and verify that the datatypes count is reduced.''' original_datatypes = self.get_datatypes_count() @@ -305,12 +304,10 @@ ( emboss_repository_name, common.test_user_1_name ), ( convert_repository_name, common.test_user_1_name ), ( bismark_repository_name, common.test_user_1_name ) ] - uninstalled_repositories = [ ( emboss_datatypes_repository_name, common.test_user_1_name ), - ( filtering_repository_name, common.test_user_1_name ), - ( freebayes_repository_name, common.test_user_1_name ) ] - self.verify_installed_uninstalled_repositories( installed_repositories=installed_repositories, uninstalled_repositories=uninstalled_repositories ) - strings_not_displayed = [ repository.name, repository.installed_changeset_revision ] - self.display_galaxy_browse_repositories_page( strings_not_displayed=strings_not_displayed ) + strings_displayed = [ 'emboss_0050', 'column_maker_0050', 'convert_chars_0050', 'bismark_0050' ] + strings_not_displayed = [ 'emboss_datatypes_0050', 'filtering_0050', 'freebayes_0050' ] + self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed ) + self.verify_installed_repositories( installed_repositories ) def test_0070_uninstall_emboss_repository( self ): '''Uninstall the emboss_5 repository.''' repository = test_db_util.get_installed_repository_by_name_owner( emboss_repository_name, common.test_user_1_name ) @@ -324,11 +321,10 @@ installed_repositories = [ ( column_repository_name, common.test_user_1_name ), ( convert_repository_name, common.test_user_1_name ), ( bismark_repository_name, common.test_user_1_name ) ] - uninstalled_repositories = [ ( emboss_datatypes_repository_name, common.test_user_1_name ), - ( emboss_repository_name, common.test_user_1_name ), - ( filtering_repository_name, common.test_user_1_name ), - ( freebayes_repository_name, common.test_user_1_name ) ] - self.verify_installed_uninstalled_repositories( installed_repositories=installed_repositories, uninstalled_repositories=uninstalled_repositories ) + strings_displayed = [ 'column_maker_0050', 'convert_chars_0050', 'bismark_0050' ] + strings_not_displayed = [ 'emboss_0050', 'emboss_datatypes_0050', 'filtering_0050', 'freebayes_0050' ] + self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed ) + self.verify_installed_repositories( installed_repositories ) def test_0075_install_freebayes_repository( self ): '''Install freebayes with repository dependencies. This should also automatically reactivate emboss_datatypes and reinstall emboss_5.''' original_datatypes = self.get_datatypes_count() @@ -356,6 +352,8 @@ ( freebayes_repository_name, common.test_user_1_name ), ( convert_repository_name, common.test_user_1_name ), ( bismark_repository_name, common.test_user_1_name ) ] - uninstalled_repositories = [ ( filtering_repository_name, common.test_user_1_name ) ] - self.verify_installed_uninstalled_repositories( installed_repositories=installed_repositories, uninstalled_repositories=uninstalled_repositories ) + strings_displayed = [ 'emboss_0050', 'emboss_datatypes_0050', 'column_maker_0050', 'convert_chars_0050', 'bismark_0050', 'freebayes_0050' ] + strings_not_displayed = [ 'filtering_0050' ] + self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed ) + self.verify_installed_repositories( installed_repositories )
diff -r ec4da708e45175610a33d16fcfc68732e425f54f -r 8e93ca10b0e2523ba78a02bfb36e371db5f17e0a test/tool_shed/functional/test_1070_invalid_tool.py --- a/test/tool_shed/functional/test_1070_invalid_tool.py +++ b/test/tool_shed/functional/test_1070_invalid_tool.py @@ -79,8 +79,9 @@ self.url.replace( 'http://', '' ), installed_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) + strings_displayed.extend( [ 'methylation extractor', 'Invalid tools' ] ) self.display_installed_repository_manage_page( installed_repository, - strings_displayed=[ 'methylation extractor', 'Invalid tools' ], + strings_displayed=strings_displayed, strings_not_displayed=[ 'bisulfite mapper' ] ) self.verify_tool_metadata_for_installed_repository( installed_repository ) self.update_installed_repository( installed_repository, strings_displayed=[ "there are no updates available" ] )
diff -r ec4da708e45175610a33d16fcfc68732e425f54f -r 8e93ca10b0e2523ba78a02bfb36e371db5f17e0a test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py --- a/test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py +++ b/test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py @@ -199,12 +199,16 @@ common.test_user_1_name ) self.reactivate_repository( installed_convert_repository ) strings_displayed = [ 'convert_chars_0080', - 'Convert delimiters', - self.url.replace( 'http://', '' ), - installed_convert_repository.installed_changeset_revision, + 'Compute', + 'an expression on every row', + '1.1.0', 'column_maker_0080', - installed_column_repository.installed_changeset_revision, - 'Installed repository dependencies' ] + 'Installed repository dependencies', + self.url.replace( 'http://', '' ), + installed_column_repository.installed_changeset_revision, + installed_convert_repository.installed_changeset_revision ] + self.display_installed_repository_manage_page( installed_column_repository, + strings_displayed=strings_displayed ) def test_0040_deactivate_column_repository( self ): '''Deactivate column_maker, verify that convert_chars is installed and missing repository dependencies.''' installed_convert_repository = test_db_util.get_installed_repository_by_name_owner( convert_repository_name,
diff -r ec4da708e45175610a33d16fcfc68732e425f54f -r 8e93ca10b0e2523ba78a02bfb36e371db5f17e0a test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py --- a/test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py +++ b/test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py @@ -108,5 +108,5 @@ url = '/admin_toolshed/browse_repositories?operation=activate+or+reinstall&id=%s' % self.security.encode_id( installed_column_repository.id ) self.visit_galaxy_url( url ) self.check_for_strings( strings_displayed ) - uninstalled_repositories = [ ( column_repository_name, common.test_user_1_name ) ] - self.verify_installed_uninstalled_repositories( uninstalled_repositories=uninstalled_repositories, installed_repositories=[] ) + strings_not_displayed = [ 'column_maker_1087' ] + self.display_galaxy_browse_repositories_page( strings_not_displayed=strings_not_displayed )
diff -r ec4da708e45175610a33d16fcfc68732e425f54f -r 8e93ca10b0e2523ba78a02bfb36e371db5f17e0a test/tool_shed/functional/test_1090_install_tool_from_tool_search.py --- a/test/tool_shed/functional/test_1090_install_tool_from_tool_search.py +++ b/test/tool_shed/functional/test_1090_install_tool_from_tool_search.py @@ -213,12 +213,10 @@ install_repository_dependencies=False, new_tool_panel_section='freebayes_1090' ) installed_repositories = [ ( freebayes_repository_name, common.test_user_1_name ) ] - uninstalled_repositories = [ ( filtering_repository_name, common.test_user_1_name ), - ( emboss_repository_name, common.test_user_1_name ), - ( emboss_datatypes_repository_name, common.test_user_1_name ), - ( bwa_color_repository_name, common.test_user_1_name ), - ( bwa_base_repository_name, common.test_user_1_name ) ] - self.verify_installed_uninstalled_repositories( installed_repositories=installed_repositories, uninstalled_repositories=uninstalled_repositories ) + strings_displayed = [ 'freebayes_0090' ] + strings_not_displayed = [ 'filtering_0090', 'emboss_0090', 'emboss_datatypes_0090', 'bwa_color_0090', 'bwa_base_0090' ] + self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed ) + self.verify_installed_repositories( installed_repositories ) def test_0050_install_deactivate_filtering_repository( self ): '''Install and deactivate filtering.''' global running_standalone @@ -235,13 +233,15 @@ new_tool_panel_section='filtering_1090' ) installed_repositories = [ ( filtering_repository_name, common.test_user_1_name ), ( freebayes_repository_name, common.test_user_1_name ) ] - uninstalled_repositories = [ ( emboss_repository_name, common.test_user_1_name ), - ( emboss_datatypes_repository_name, common.test_user_1_name ), - ( bwa_color_repository_name, common.test_user_1_name ), - ( bwa_base_repository_name, common.test_user_1_name ) ] - self.verify_installed_uninstalled_repositories( installed_repositories=installed_repositories, uninstalled_repositories=uninstalled_repositories ) + strings_displayed = [ 'filtering_0090', 'freebayes_0090' ] + strings_not_displayed = [ 'emboss_0090', 'emboss_datatypes_0090', 'bwa_color_0090', 'bwa_base_0090' ] + self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed ) + self.verify_installed_repositories( installed_repositories ) filtering_repository = test_db_util.get_installed_repository_by_name_owner( filtering_repository_name, common.test_user_1_name ) self.uninstall_repository( filtering_repository, remove_from_disk=False ) + strings_displayed = [ 'freebayes_0090' ] + strings_not_displayed = [ 'filtering_0090', 'emboss_0090', 'emboss_datatypes_0090', 'bwa_color_0090', 'bwa_base_0090' ] + self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed ) def test_0055_install_uninstall_datatypes_repository( self ): '''Install and uninstall emboss_datatypes.''' # After this test, the repositories should be in the following states: @@ -259,9 +259,15 @@ ( filtering_repository_name, common.test_user_1_name ), ( bwa_color_repository_name, common.test_user_1_name ), ( bwa_base_repository_name, common.test_user_1_name ) ] - self.verify_installed_uninstalled_repositories( installed_repositories=installed_repositories, uninstalled_repositories=uninstalled_repositories ) + strings_displayed = [ 'emboss_datatypes_0090', 'freebayes_0090' ] + strings_not_displayed = [ 'filtering_0090', 'emboss_0090', 'bwa_color_0090', 'bwa_base_0090' ] + self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed ) + self.verify_installed_repositories( installed_repositories ) datatypes_repository = test_db_util.get_installed_repository_by_name_owner( emboss_datatypes_repository_name, common.test_user_1_name ) self.uninstall_repository( datatypes_repository, remove_from_disk=True ) + strings_displayed = [ 'freebayes_0090' ] + strings_not_displayed = [ 'emboss_datatypes_0090', 'filtering_0090', 'emboss_0090', 'bwa_color_0090', 'bwa_base_0090' ] + self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed ) def test_0060_search_for_bwa_tools( self ): '''Search for and install the repositories with BWA tools, and verify that this reinstalls emboss_datatypes and reactivates filtering.''' bwa_color_repository = test_db_util.get_repository_by_name_and_owner( bwa_color_repository_name, common.test_user_1_name ) @@ -292,5 +298,6 @@ ( bwa_base_repository_name, common.test_user_1_name ), ( emboss_datatypes_repository_name, common.test_user_1_name ), ( freebayes_repository_name, common.test_user_1_name ) ] - uninstalled_repositories = [] - self.verify_installed_uninstalled_repositories( installed_repositories=installed_repositories, uninstalled_repositories=uninstalled_repositories ) + strings_displayed = [ 'emboss_datatypes_0090', 'filtering_0090', 'emboss_0090', 'bwa_color_0090', 'bwa_base_0090', 'freebayes_0090' ] + self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) + self.verify_installed_repositories( installed_repositories )
diff -r ec4da708e45175610a33d16fcfc68732e425f54f -r 8e93ca10b0e2523ba78a02bfb36e371db5f17e0a test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py --- a/test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py +++ b/test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py @@ -238,19 +238,24 @@ '''Verify that the installed repositories are displayed properly.''' base_repository = test_db_util.get_installed_repository_by_name_owner( bwa_base_repository_name, common.test_user_1_name ) tool_repository = test_db_util.get_installed_repository_by_name_owner( bwa_tool_repository_name, common.test_user_1_name ) - strings_displayed = [ base_repository.name, base_repository.owner, base_repository.installed_changeset_revision ] - strings_displayed.extend( [ tool_repository.name, tool_repository.owner, tool_repository.installed_changeset_revision ] ) + strings_displayed = [ 'bwa_base_repository_0100', 'user1', base_repository.installed_changeset_revision ] + strings_displayed.extend( [ 'bwa_tool_repository_0100', 'user1', tool_repository.installed_changeset_revision ] ) strings_displayed.append( self.url.replace( 'http://', '' ) ) self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed, strings_not_displayed=[] ) - checks = [ ( tool_repository, - [ 'bwa_tool_repository_0100', 'user1', tool_repository.installed_changeset_revision ], - [ 'Missing tool dependencies' ] ), - ( base_repository, - [ 'bwa_base_repository_0100', 'user1', base_repository.installed_changeset_revision, 'bwa_tool_repository_0100', - tool_repository.installed_changeset_revision ], - [ 'Missing tool dependencies' ] ) ] - for repository, strings_displayed, strings_not_displayed in checks: - self.display_installed_repository_manage_page( repository, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed ) + strings_displayed = [ 'bwa_tool_repository_0100', 'user1', tool_repository.installed_changeset_revision ] + strings_not_displayed = [ 'Missing tool dependencies' ] + self.display_installed_repository_manage_page( tool_repository, + strings_displayed=strings_displayed, + strings_not_displayed=strings_not_displayed ) + strings_displayed = [ 'bwa_base_repository_0100', + 'user1', + 'bwa_tool_repository_0100', + base_repository.installed_changeset_revision, + tool_repository.installed_changeset_revision ] + strings_not_displayed = [ 'Missing tool dependencies' ] + self.display_installed_repository_manage_page( base_repository, + strings_displayed=strings_displayed, + strings_not_displayed=strings_not_displayed ) def test_0055_verify_complex_tool_dependency( self ): '''Verify that the generated env.sh contains the right data.''' base_repository = test_db_util.get_installed_repository_by_name_owner( bwa_base_repository_name, common.test_user_1_name )
diff -r ec4da708e45175610a33d16fcfc68732e425f54f -r 8e93ca10b0e2523ba78a02bfb36e371db5f17e0a test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py --- a/test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py +++ b/test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py @@ -101,8 +101,8 @@ self.url.replace( 'http://', '' ), installed_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) - self.display_installed_repository_manage_page( installed_repository, - strings_displayed=[ 'Installed tool shed repository', 'Valid tools', 'Filter1' ] ) + strings_displayed.extend( [ 'Installed tool shed repository', 'Valid tools', 'Filter1' ] ) + self.display_installed_repository_manage_page( installed_repository, strings_displayed=strings_displayed ) self.verify_tool_metadata_for_installed_repository( installed_repository ) def test_0025_deactivate_filtering_repository( self ): '''Deactivate the filtering repository without removing it from disk.''' @@ -122,6 +122,6 @@ self.url.replace( 'http://', '' ), installed_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) - self.display_installed_repository_manage_page( installed_repository, - strings_displayed=[ 'Installed tool shed repository', 'Valid tools', 'Filter1' ] ) + strings_displayed.extend( [ 'Installed tool shed repository', 'Valid tools', 'Filter1' ] ) + self.display_installed_repository_manage_page( installed_repository, strings_displayed=strings_displayed ) self.verify_tool_metadata_for_installed_repository( installed_repository )
diff -r ec4da708e45175610a33d16fcfc68732e425f54f -r 8e93ca10b0e2523ba78a02bfb36e371db5f17e0a test/tool_shed/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py --- a/test/tool_shed/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py +++ b/test/tool_shed/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py @@ -118,8 +118,8 @@ self.url.replace( 'http://', '' ), installed_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) - self.display_installed_repository_manage_page( installed_repository, - strings_displayed=[ 'Installed tool shed repository', 'Valid tools', 'FreeBayes' ] ) + strings_displayed.extend( [ 'Installed tool shed repository', 'Valid tools', 'FreeBayes' ] ) + self.display_installed_repository_manage_page( installed_repository, strings_displayed=strings_displayed ) self.verify_tool_metadata_for_installed_repository( installed_repository ) def test_0025_deactivate_freebayes_repository( self ): '''Deactivate the freebayes repository without removing it from disk.''' @@ -137,6 +137,6 @@ self.url.replace( 'http://', '' ), installed_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) - self.display_installed_repository_manage_page( installed_repository, - strings_displayed=[ 'Installed tool shed repository', 'Valid tools', 'FreeBayes' ] ) + strings_displayed.extend( [ 'Installed tool shed repository', 'Valid tools', 'FreeBayes' ] ) + self.display_installed_repository_manage_page( installed_repository, strings_displayed=strings_displayed ) self.verify_tool_metadata_for_installed_repository( installed_repository )
diff -r ec4da708e45175610a33d16fcfc68732e425f54f -r 8e93ca10b0e2523ba78a02bfb36e371db5f17e0a test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py --- a/test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py +++ b/test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py @@ -128,8 +128,8 @@ self.url.replace( 'http://', '' ), installed_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) - self.display_installed_repository_manage_page( installed_repository, - strings_displayed=[ 'Installed tool shed repository', 'Valid tools', 'emboss' ] ) + strings_displayed.extend( [ 'Installed tool shed repository', 'Valid tools', 'emboss' ] ) + self.display_installed_repository_manage_page( installed_repository, strings_displayed=strings_displayed ) self.verify_tool_metadata_for_installed_repository( installed_repository ) def test_0025_deactivate_emboss_repository( self ): '''Deactivate the emboss repository without removing it from disk.''' @@ -148,6 +148,6 @@ self.url.replace( 'http://', '' ), installed_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) - self.display_installed_repository_manage_page( installed_repository, - strings_displayed=[ 'Installed tool shed repository', 'Valid tools', 'emboss' ] ) + strings_displayed.extend( [ 'Installed tool shed repository', 'Valid tools', 'emboss' ] ) + self.display_installed_repository_manage_page( installed_repository, strings_displayed=strings_displayed ) self.verify_tool_metadata_for_installed_repository( installed_repository )
diff -r ec4da708e45175610a33d16fcfc68732e425f54f -r 8e93ca10b0e2523ba78a02bfb36e371db5f17e0a test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py --- a/test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py +++ b/test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py @@ -188,8 +188,8 @@ self.url.replace( 'http://', '' ), installed_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) - self.display_installed_repository_manage_page( installed_repository, - strings_displayed=[ 'Installed tool shed repository', 'Valid tools', 'emboss' ] ) + strings_displayed.extend( [ 'Installed tool shed repository', 'Valid tools', 'emboss' ] ) + self.display_installed_repository_manage_page( installed_repository, strings_displayed=strings_displayed ) self.verify_tool_metadata_for_installed_repository( installed_repository ) def test_0025_deactivate_emboss_repository( self ): '''Deactivate the emboss repository without removing it from disk.''' @@ -207,6 +207,6 @@ self.url.replace( 'http://', '' ), installed_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) - self.display_installed_repository_manage_page( installed_repository, - strings_displayed=[ 'Installed tool shed repository', 'Valid tools', 'emboss' ] ) + strings_displayed.extend( [ 'Installed tool shed repository', 'Valid tools', 'emboss' ] ) + self.display_installed_repository_manage_page( installed_repository, strings_displayed=strings_displayed ) self.verify_tool_metadata_for_installed_repository( installed_repository )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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