1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/7c5912105551/ Changeset: 7c5912105551 User: inithello Date: 2013-04-23 20:46:53 Summary: Functional tests to verify correct setting of metadata when dependency definitions are deleted. Affected #: 1 file

diff -r 1e3d92ec22b2794bfa2294edb74695c580791406 -r 7c59121055516595937b83d51eaf98b60723b622 test/tool_shed/functional/test_0440_deleting_dependency_definitions.py --- /dev/null +++ b/test/tool_shed/functional/test_0440_deleting_dependency_definitions.py @@ -0,0 +1,365 @@ +from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os +import tool_shed.base.test_db_util as test_db_util + +column_repository_name = 'column_maker_0440' +column_repository_description = "Add column" +column_repository_long_description = "Compute an expression on every row" + +convert_repository_name = 'convert_chars_0440' +convert_repository_description = "Convert delimiters" +convert_repository_long_description = "Convert delimiters to tab" + +bwa_package_repository_name = 'bwa_package_0440' +bwa_package_repository_description = "BWA Package Repository" +bwa_package_repository_long_description = "BWA repository with a package tool dependency defined for BWA 0.5.9." + +bwa_base_repository_name = 'bwa_base_0440' +bwa_base_repository_description = "BWA Base" +bwa_base_repository_long_description = "NT space mapping with BWA" + +bwa_tool_dependency_repository_name = 'bwa_tool_dependency_0440' +bwa_tool_dependency_repository_description = "BWA Base" +bwa_tool_dependency_repository_long_description = "NT space mapping with BWA" + +''' +Simple repository dependencies: +1. Create and populate column_maker_0440 so that it has an installable revision 0. +2. Create and populate convert_chars_0440 so that it has an installable revision 0. +3. Add a valid simple repository_dependencies.xml to convert_chars_0440 that points to the installable revision of column_maker_0440. +4. Make sure the installable revision of convert_chars_0440 is now revision 1 instead of revision 0. +5. Delete repository_dependencies.xml from convert_chars_0440, and make sure convert_chars_0440 now has two installable revisions: 1 and 2 + +Complex repository dependencies: +1. Create and populate bwa_package_0440 so that it has a valid orphan tool dependency definition and an installable revision 0. +2. Create and populate bwa_base_0440 so that it has an installable revision 0. +3. Add a valid complex repository dependency tool_dependencies.xml to bwa_base_0440 that points to the installable revision 0 of bwa_package_0440. +4. Make sure that bwa_base_0440 installable revision is now revision 1 instead of revision 0. +5. Delete tool_dependencies.xml from bwa_base_0440, and make sure bwa_base_0440 now has two installable revisions: 1 and 2 + +Tool dependencies: +1. Create and populate bwa_tool_dependency_0440 so that it has a valid orphan tool dependency definition and an installable revision 0. +2. Delete tool_dependencies.xml from bwa_tool_dependency_0440, and make sure that bwa_tool_dependency_0440 still has + a single installable revision 0. +3. Add the same tool_dependencies.xml file to bwa_tool_dependency_0440, and make sure that bwa_tool_dependency_0440 + still has a single installable revision 0. +''' + + +class TestDeletedDependencies( ShedTwillTestCase ): + '''Test metadata setting when dependency definitions are deleted.''' + + 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 tests. + 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.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_create_column_maker_repository( self ): + '''Create and populate a repository named column_maker_0440.''' + ''' + We are at simple repository dependencies, step 1 - Create and populate column_maker_0440 so that it has an installable revision 0. + ''' + category = self.create_category( name='Test 0440 Deleted Dependency Definitions', + description='Description of Deleted Dependency Definitions category for test 0440' ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + strings_displayed = [ "Repository 'column_maker_0440' has been created" ] + repository = self.get_or_create_repository( name=column_repository_name, + description=column_repository_description, + long_description=column_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='column_maker/column_maker.tar', + filepath=None, + valid_tools_only=True, + uncompress_file=True, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded column maker tool tarball.', + strings_displayed=[], + strings_not_displayed=[] ) + + def test_0010_create_convert_chars_repository( self ): + '''Create and populate a repository named convert_chars_0440.''' + ''' + We are at simple repository dependencies, step 2 - Create and populate convert_chars_0440 so that it has an installable revision 0. + ''' + category = test_db_util.get_category_by_name( 'Test 0440 Deleted Dependency Definitions' ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + strings_displayed = [ "Repository 'convert_chars_0440' has been created" ] + repository = self.get_or_create_repository( name=convert_repository_name, + description=convert_repository_description, + long_description=convert_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='convert_chars/convert_chars.tar', + filepath=None, + valid_tools_only=True, + uncompress_file=True, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded convert chars tool tarball.', + strings_displayed=[], + strings_not_displayed=[] ) + + def test_0015_create_dependency_on_convert_chars( self ): + '''Create a dependency definition file that specifies column_maker_0440 and upload it to convert_chars_0440.''' + ''' + We are at simple repository dependencies, step 3 - Add a valid simple repository_dependencies.xml to + convert_chars_0440 that points to the installable revision of column_maker_0440. + ''' + convert_repository = test_db_util.get_repository_by_name_and_owner( convert_repository_name, common.test_user_1_name ) + column_repository = test_db_util.get_repository_by_name_and_owner( column_repository_name, common.test_user_1_name ) + dependency_xml_path = self.generate_temp_path( 'test_0440', additional_paths=[ 'dependencies' ] ) + column_tuple = ( self.url, column_repository.name, column_repository.user.username, self.get_repository_tip( column_repository ) ) + # After this, convert_chars_0440 should depend on column_maker_0440. + self.create_repository_dependency( repository=convert_repository, + repository_tuples=[ column_tuple ], + filepath=dependency_xml_path, + prior_installation_required=True ) + self.check_repository_dependency( convert_repository, column_repository ) + + def test_0020_verify_dependency_metadata( self ): + '''Verify that uploading the dependency moved metadata to the tip.''' + ''' + We are at simple repository dependencies, step 4 - Make sure the installable revision of convert_chars_0440 is now + revision 1 (the tip) instead of revision 0. + ''' + repository = test_db_util.get_repository_by_name_and_owner( convert_repository_name, common.test_user_1_name ) + tip = self.get_repository_tip( repository ) + metadata_record = self.get_repository_metadata_by_changeset_revision( repository, tip ) + # Make sure that the new tip is now downloadable, and that there are no other downloadable revisions. + assert metadata_record.downloadable, 'Tip is not downloadable.' + assert len( repository.downloadable_revisions ) == 1, 'Repository %s has %d downloadable revisions, expected 1.' % \ + ( repository.name, len( repository.downloadable_revisions ) ) + + def test_0025_delete_repository_dependency( self ): + '''Delete the repository_dependencies.xml from convert_chars_0440.''' + ''' + We are at simple repository dependencies, steps 5 and 6 - Delete repository_dependencies.xml from convert_chars_0440. + Make sure convert_chars_0440 now has two installable revisions: 1 and 2 + ''' + repository = test_db_util.get_repository_by_name_and_owner( convert_repository_name, common.test_user_1_name ) + # Record the current tip, so we can verify that it's still a downloadable revision after repository_dependencies.xml + # is deleted and a new downloadable revision is created. + old_changeset_revision = self.get_repository_tip( repository ) + self.delete_files_from_repository( repository, filenames=[ 'repository_dependencies.xml' ] ) + new_changeset_revision = self.get_repository_tip( repository ) + # Check that the old changeset revision is still downloadable. + metadata_record = self.get_repository_metadata_by_changeset_revision( repository, old_changeset_revision ) + assert metadata_record.downloadable, 'The revision of %s that contains repository_dependencies.xml is no longer downloadable.' % \ + repository.name + # Check that the new tip is also downloadable. + metadata_record = self.get_repository_metadata_by_changeset_revision( repository, new_changeset_revision ) + assert metadata_record.downloadable, 'The revision of %s that does not contain repository_dependencies.xml is not downloadable.' % \ + repository.name + # Explicitly reload the repository instance from the database, to avoid potential caching issues. + test_db_util.refresh( repository ) + # Verify that there are only two downloadable revisions. + assert len( repository.downloadable_revisions ) == 2, 'Repository %s has %d downloadable revisions, expected 2.' % \ + ( repository.name, len( repository.downloadable_revisions ) ) + + def test_0030_create_bwa_package_repository( self ): + '''Create and populate the bwa_package_0440 repository.''' + ''' + We are at complex repository dependencies, step 1 - Create and populate bwa_package_0440 so that it has a valid orphan + tool dependency definition and an installable revision 0. + ''' + category = test_db_util.get_category_by_name( 'Test 0440 Deleted Dependency Definitions' ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + strings_displayed = [ "Repository 'bwa_package_0440' has been created" ] + repository = self.get_or_create_repository( name=bwa_package_repository_name, + description=bwa_package_repository_description, + long_description=bwa_package_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='bwa/complex/tool_dependencies.xml', + filepath=None, + valid_tools_only=True, + uncompress_file=True, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded package tool dependency definition.', + strings_displayed=[], + strings_not_displayed=[] ) + + def test_0035_create_bwa_base_repository( self ): + '''Create and populate the bwa_base_0440 repository.''' + ''' + We are at complex repository dependencies, step 2 - Create and populate bwa_base_0440 so that it has an installable revision 0. + This repository should contain a tool with a defined dependency that will be satisfied by the tool dependency defined in bwa_package_0440. + ''' + category = test_db_util.get_category_by_name( 'Test 0440 Deleted Dependency Definitions' ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + strings_displayed = [ "Repository 'bwa_base_0440' has been created" ] + 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=strings_displayed ) + self.upload_file( repository, + filename='bwa/complex/bwa_base.tar', + filepath=None, + valid_tools_only=True, + uncompress_file=True, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded BWA nucleotide space mapping tool tarball.', + strings_displayed=[], + strings_not_displayed=[] ) + + def test_0040_create_dependency_on_bwa_package_repository( self ): + '''Create a complex repository dependency on bwa_package_0440 and upload it to bwa_tool_0440.''' + ''' + We are at complex repository dependencies, step 3 - Add a valid complex repository dependency tool_dependencies.xml to + bwa_base_0440 that points to the installable revision 0 of bwa_package_0440. + ''' + bwa_package_repository = test_db_util.get_repository_by_name_and_owner( bwa_package_repository_name, common.test_user_1_name ) + bwa_base_repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) + dependency_path = self.generate_temp_path( 'test_0440', additional_paths=[ 'complex' ] ) + changeset_revision = self.get_repository_tip( bwa_package_repository ) + bwa_tuple = ( self.url, bwa_package_repository.name, bwa_package_repository.user.username, changeset_revision ) + self.create_repository_dependency( repository=bwa_base_repository, + repository_tuples=[ bwa_tuple ], + filepath=dependency_path, + prior_installation_required=True, + complex=True, + package='bwa', + version='0.5.9' ) + + def test_0045_verify_dependency_metadata( self ): + '''Verify that uploading the dependency moved metadata to the tip.''' + ''' + We are at complex repository dependencies, step 4 - Make sure that bwa_base_0440 installable revision is now revision 1 + instead of revision 0. + ''' + repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) + tip = self.get_repository_tip( repository ) + metadata_record = self.get_repository_metadata_by_changeset_revision( repository, tip ) + # Make sure that the new tip is now downloadable, and that there are no other downloadable revisions. + assert metadata_record.downloadable, 'Tip is not downloadable.' + assert len( repository.downloadable_revisions ) == 1, 'Repository %s has %d downloadable revisions, expected 1.' % \ + ( repository.name, len( repository.downloadable_revisions ) ) + + def test_0050_delete_complex_repository_dependency( self ): + '''Delete the tool_dependencies.xml from bwa_base_0440.''' + ''' + We are at complex repository dependencies, step 5 - Delete tool_dependencies.xml from bwa_base_0440, + and make sure bwa_base_0440 now has two installable revisions: 1 and 2 + ''' + repository = test_db_util.get_repository_by_name_and_owner( bwa_base_repository_name, common.test_user_1_name ) + # Record the current tip, so we can verify that it's still a downloadable revision after tool_dependencies.xml + # is deleted and a new downloadable revision is created. + old_changeset_revision = self.get_repository_tip( repository ) + self.delete_files_from_repository( repository, filenames=[ 'tool_dependencies.xml' ] ) + new_changeset_revision = self.get_repository_tip( repository ) + # Check that the old changeset revision is still downloadable. + metadata_record = self.get_repository_metadata_by_changeset_revision( repository, old_changeset_revision ) + assert metadata_record.downloadable, 'The revision of %s that contains tool_dependencies.xml is no longer downloadable.' % \ + repository.name + # Check that the new tip is also downloadable. + metadata_record = self.get_repository_metadata_by_changeset_revision( repository, new_changeset_revision ) + assert metadata_record.downloadable, 'The revision of %s that does not contain tool_dependencies.xml is not downloadable.' % \ + repository.name + # Verify that there are only two downloadable revisions. + assert len( repository.downloadable_revisions ) == 2, 'Repository %s has %d downloadable revisions, expected 2.' % \ + ( repository.name, len( repository.downloadable_revisions ) ) + + def test_0055_create_bwa_tool_dependency_repository( self ): + '''Create and populate the bwa_tool_dependency_0440 repository.''' + ''' + We are at tool dependencies, step 1 - Create and populate bwa_tool_dependency_0440 so that it has a valid orphan tool + dependency definition and an installable revision 0. + ''' + category = test_db_util.get_category_by_name( 'Test 0440 Deleted Dependency Definitions' ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + strings_displayed = [ "Repository 'bwa_tool_dependency_0440' has been created" ] + repository = self.get_or_create_repository( name=bwa_tool_dependency_repository_name, + description=bwa_tool_dependency_repository_description, + long_description=bwa_tool_dependency_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='bwa/complex/tool_dependencies.xml', + filepath=None, + valid_tools_only=True, + uncompress_file=True, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded package tool dependency definition.', + strings_displayed=[], + strings_not_displayed=[] ) + + def test_0060_delete_bwa_tool_dependency_definition( self ): + '''Delete the tool_dependencies.xml file from bwa_tool_dependency_0440.''' + ''' + We are at tool dependencies, step 2 - Delete tool_dependencies.xml from bwa_tool_dependency_0440. + Make sure bwa_tool_dependency_0440 still has a downloadable changeset revision at the old tip. + ''' + repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_dependency_repository_name, common.test_user_1_name ) + # Record the current tip, so we can verify that it's still a downloadable revision after repository_dependencies.xml + # is deleted and a new downloadable revision is created. + old_changeset_revision = self.get_repository_tip( repository ) + self.delete_files_from_repository( repository, filenames=[ 'tool_dependencies.xml' ] ) + new_changeset_revision = self.get_repository_tip( repository ) + # Check that the old changeset revision is still downloadable. + metadata_record = self.get_repository_metadata_by_changeset_revision( repository, old_changeset_revision ) + assert metadata_record.downloadable, 'The revision of %s that contains tool_dependencies.xml is no longer downloadable.' % \ + repository.name + # Check that the new tip does not have a metadata revision. + metadata_record = self.get_repository_metadata_by_changeset_revision( repository, new_changeset_revision ) + # If a changeset revision does not have metadata, the above method will return None. + assert metadata_record is None, 'The tip revision of %s should not have metadata, but metadata was found.' % repository.name + # Verify that the new changeset revision is not downloadable. + assert len( repository.downloadable_revisions ) == 1, 'Repository %s has %d downloadable revisions, expected 1.' % \ + ( repository.name, len( repository.downloadable_revisions ) ) + + def test_0065_reupload_bwa_tool_dependency_definition( self ): + '''Reupload the tool_dependencies.xml file to bwa_tool_dependency_0440.''' + ''' + We are at tool dependencies, step 3 - Add the same tool_dependencies.xml file to bwa_tool_dependency_0440, and make sure + that bwa_tool_dependency_0440 still has a single installable revision 0. + ''' + repository = test_db_util.get_repository_by_name_and_owner( bwa_tool_dependency_repository_name, common.test_user_1_name ) + # Record the current tip, so we can verify that it's still not a downloadable revision after tool_dependencies.xml + # is re-uploaded and a new downloadable revision is created. + old_changeset_revision = self.get_repository_tip( repository ) + self.upload_file( repository, + filename='bwa/complex/tool_dependencies.xml', + filepath=None, + valid_tools_only=True, + uncompress_file=True, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded package tool dependency definition.', + strings_displayed=[], + strings_not_displayed=[] ) + new_changeset_revision = self.get_repository_tip( repository ) + # Check that the old changeset revision is still downloadable. + metadata_record = self.get_repository_metadata_by_changeset_revision( repository, old_changeset_revision ) + assert metadata_record is None, 'The revision of %s that does not contain tool_dependencies.xml should not be downloadable, but is.' % \ + repository.name + # Check that the new tip is also downloadable. + metadata_record = self.get_repository_metadata_by_changeset_revision( repository, new_changeset_revision ) + assert metadata_record.downloadable, 'The revision of %s that contains tool_dependencies.xml is not downloadable.' % \ + repository.name + # Verify that there are only two downloadable revisions. + assert len( repository.downloadable_revisions ) == 1, 'Repository %s has %d downloadable revisions, expected 1.' % \ + ( repository.name, len( repository.downloadable_revisions ) )

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