1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/64b4ef5e2cc8/ changeset: 64b4ef5e2cc8 user: greg date: 2013-02-16 22:21:40 summary: Add some comments to the tool shed functional test script that tests behavior of complex repository dependencies. affected #: 1 file diff -r a41446bf66fda81772b6fe7d02f921a4955f7ce9 -r 64b4ef5e2cc8e18a2872eaeb64fa46f50ae7f814 test/tool_shed/functional/test_0100_complex_repository_dependencies.py --- a/test/tool_shed/functional/test_0100_complex_repository_dependencies.py +++ b/test/tool_shed/functional/test_0100_complex_repository_dependencies.py @@ -27,10 +27,11 @@ assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email admin_user_private_role = test_db_util.get_private_role( admin_user ) def test_0005_create_bwa_tool_repository( self ): - '''Create and populate bwa_tool_0100.''' + '''Create and populate bwa_tool_repository_0100.''' category = self.create_category( name=category_name, description=category_description ) self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + # Create a repository named bwa_tool_repository_0100 owned by user1. repository = self.get_or_create_repository( name=bwa_tool_repository_name, description=bwa_tool_repository_description, long_description=bwa_tool_repository_long_description, @@ -46,19 +47,21 @@ commit_message='Uploaded tool_dependencies.xml.', strings_displayed=[ 'The settings for <b>name</b>, <b>version</b> and <b>type</b> from a contained tool' ], strings_not_displayed=[] ) + # Visit the manage repository page for bwa_tool_repository_0100. self.display_manage_repository_page( repository, strings_displayed=[ 'Tool dependencies', 'may not be', 'in this repository' ] ) def test_0010_create_bwa_base_repository( self ): '''Create and populate bwa_base_0100.''' category = self.create_category( name=category_name, description=category_description ) self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + # Create a repository named bwa_base_repository_0100 owned by user1. repository = self.get_or_create_repository( name=bwa_base_repository_name, description=bwa_base_repository_description, long_description=bwa_base_repository_long_description, owner=common.test_user_1_name, category_id=self.security.encode_id( category.id ), strings_displayed=[] ) - tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) + # Populate the repository named bwa_base_repository_0100 with a bwa_base tool archive. self.upload_file( repository, filename='bwa/complex/bwa_base.tar', filepath=None, @@ -72,14 +75,17 @@ '''Generate and upload a complex repository definition that specifies an invalid tool shed URL.''' dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'invalid' ] ) xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path ) + # The repository named bwa_base_repository_0100 is the dependent repository. repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) + # The tool_repository named bwa_tool_repository_0100 is the required repository. tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) url = 'http://http://this is not an url!' - name = tool_repository.name - owner = tool_repository.user.username + name = 'bwa_tool_repository_0100' + owner = 'user1' changeset_revision = self.get_repository_tip( tool_repository ) self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=True, package='bwa', version='0.5.9' ) strings_displayed = [ 'Repository dependencies are currently supported only within the same tool shed' ] + # Populate the dependent repository named bwa_base_repository_0100 with an invalid tool_dependencies.xml file. self.upload_file( repository, filename='tool_dependencies.xml', filepath=dependency_path, @@ -93,14 +99,17 @@ '''Generate and upload a complex repository definition that specifies an invalid repository name.''' dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'invalid' ] ) xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path ) + # The base_repository named bwa_base_repository_0100 is the dependent repository. base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) + # The tool_repository named bwa_tool_repository_0100 is the required repository. tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) url = self.url name = 'invalid_repository!?' - owner = tool_repository.user.username + owner = 'user1' changeset_revision = self.get_repository_tip( tool_repository ) self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=True, package='bwa', version='0.5.9' ) - strings_displayed = [ 'because the name is invalid' ] + strings_displayed = [ 'because the name is invalid' ] + # # Populate the dependent base_repository named bwa_tool_repository_0100 with an invalid tool_dependencies.xml file. self.upload_file( base_repository, filename='tool_dependencies.xml', filepath=dependency_path, @@ -114,10 +123,12 @@ '''Generate and upload a complex repository definition that specifies an invalid owner.''' dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'invalid' ] ) xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path ) + # The base_repository named bwa_base_repository_0100 is the dependent repository. base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) + # The tool_repository named bwa_tool_repository_0100 is the required repository. tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) url = self.url - name = tool_repository.name + name = 'bwa_tool_repository_0100' owner = 'invalid_owner!?' changeset_revision = self.get_repository_tip( tool_repository ) self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=True, package='bwa', version='0.5.9' ) @@ -135,11 +146,13 @@ '''Generate and upload a complex repository definition that specifies an invalid changeset revision.''' dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex', 'invalid' ] ) xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path ) + # The base_repository named bwa_base_repository_0100 is the dependent repository. base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) + # The tool_repository named bwa_tool_repository_0100 is the required repository. tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) url = self.url - name = tool_repository.name - owner = tool_repository.user.username + name = 'bwa_tool_repository_0100' + owner = 'user1' changeset_revision = '1234abcd' self.generate_invalid_dependency_xml( xml_filename, url, name, owner, changeset_revision, complex=True, package='bwa', version='0.5.9' ) strings_displayed = [ 'because the changeset revision is invalid.' ] @@ -154,15 +167,19 @@ strings_not_displayed=[] ) def test_0035_generate_complex_repository_dependency( self ): '''Generate and upload a valid tool_dependencies.xml file that specifies bwa_tool_repository_0100.''' + # The base_repository named bwa_base_repository_0100 is the dependent repository. base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) + # The tool_repository named bwa_tool_repository_0100 is the required repository. tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) dependency_path = self.generate_temp_path( 'test_0100', additional_paths=[ 'complex' ] ) xml_filename = self.get_filename( 'tool_dependencies.xml', filepath=dependency_path ) url = self.url - name = tool_repository.name - owner = tool_repository.user.username + name = 'bwa_tool_repository_0100' + owner = 'user1' changeset_revision = self.get_repository_tip( tool_repository ) self.generate_repository_dependency_xml( [ tool_repository ], xml_filename, complex=True, package='bwa', version='0.5.9' ) + # Upload the valid tool_dependencies.xml file to bwa_base_repository_0100 that specifies bwa_tool_repository_0100 + # as a repository dependency via a complex repository dependency definition. self.upload_file( base_repository, filename='tool_dependencies.xml', filepath=dependency_path, @@ -176,7 +193,9 @@ self.display_manage_repository_page( base_repository, strings_displayed=[ 'bwa', '0.5.9', 'package' ] ) def test_0040_generate_tool_dependency( self ): '''Generate and upload a new tool_dependencies.xml file that specifies an arbitrary file on the filesystem, and verify that bwa_base depends on the new changeset revision.''' + # The base_repository named bwa_base_repository_0100 is the dependent repository. base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) + # The tool_repository named bwa_tool_repository_0100 is the required repository. tool_repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_repository_name, common.test_user_1_name ) previous_changeset = self.get_repository_tip( tool_repository ) old_tool_dependency = self.get_filename( os.path.join( 'bwa', 'complex', 'readme', 'tool_dependencies.xml' ) ) @@ -195,6 +214,21 @@ strings_displayed=[], strings_not_displayed=[] ) # Verify that the dependency display has been updated as a result of the new tool_dependencies.xml file. + repository_tip = self.get_repository_tip( tool_repository ) + strings_displayed = [ 'bwa', '0.5.9', 'package' ] + strings_displayed.append( repository_tip ) + strings_not_displayed=[ previous_changeset ] + self.display_manage_repository_page( tool_repository, + strings_displayed=strings_displayed, + strings_not_displayed=strings_not_displayed ) + # Visit the manage page of the bwa_tool_repository_0100 to confirm the valid tool dependency definition. + self.display_manage_repository_page( tool_repository, + strings_displayed=strings_displayed, + strings_not_displayed=strings_not_displayed ) + # Visit the manage page of the bwa_base_repository_0100 to confirm the valid tool dependency definition + # and the updated changeset revision (updated tip) of the bwa_tool_repository_0100 repository is displayed + # as the required repository revision. The original revision defined in the previously uploaded + # tool_dependencies.xml file will be updated. self.display_manage_repository_page( base_repository, - strings_displayed=[ self.get_repository_tip( tool_repository ), 'bwa', '0.5.9', 'package' ], - strings_not_displayed=[ previous_changeset ] ) + strings_displayed=strings_displayed, + strings_not_displayed=strings_not_displayed ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.