from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os import logging log = logging.getLogger( __name__ ) category_name = 'Test 0460 Automatic repository revision completion' category_description = 'Test 0460 Automatic repository revision completion' datatypes_repository_name = 'emboss_datatypes_0460' datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools." datatypes_repository_long_description = "Galaxy applicable data formats used by Emboss tools. This repository contains no tools." bwa_repository_name = 'package_bwa_0_5_9_0460' bwa_repository_description = "Contains a tool dependency definition that downloads and compiles version 0.5.9 of the BWA package" bwa_repository_long_description = "bwa (alignment via Burrows-Wheeler transformation) 0.5.9-r16 by Heng Li" ''' For all steps, verify that the generated dependency points to the tip of the specified repository. 1) Create and populate emboss_datatypes_0460. 2) Create and populate package_bwa_0_5_9_0460 3) Create complex_dependency_test_1_0460, complex_dependency_test_2_0460, complex_dependency_test_3_0460, complex_dependency_test_4_0460, complex_dependency_test_5_0460. 4) Upload an uncompressed tool_dependencies.xml to complex_dependency_test_1_0460 that specifies a complex repository dependency on package_bwa_0_5_9_0460 without a specified changeset revision or tool shed url. 5) Upload a tarball to complex_dependency_test_2_0460 with a tool_dependencies.xml in the root of the tarball. 6) Upload a tarball to complex_dependency_test_3_0460 with a tool_dependencies.xml in a subfolder within the tarball. 7) Create hg_tool_dependency_0460 and hg_subfolder_tool_dependency_0460 and populate with tool dependencies. 8) Upload to complex_dependency_test_4_0460 using the url hg:///repos/user1/hg_tool_dependency_0460. 9) Upload to complex_dependency_test_5_0460 using the url hg:///repos/user1/hg_subfolder_tool_dependency_0460. 10) Create repository_dependency_test_1_0460, repository_dependency_test_2_0460, repository_dependency_test_3_0460, repository_dependency_test_4_0460, repository_dependency_test_4_0460. 11) Upload an uncompressed repository_dependencies.xml to repository_dependency_test_1_0460 that specifies a repository dependency on emboss_datatypes_0460 without a specified changeset revision or tool shed url. 12) Upload a tarball to repository_dependency_test_1_0460 with a repository_dependencies.xml in the root of the tarball. 13) Upload a tarball to repository_dependency_test_1_0460 with a repository_dependencies.xml in a subfolder within the tarball. 14) Create hg_repository_dependency_0460 and populate with repository_dependencies.xml. 15) Upload to repository_dependency_test_4_0460 using the url hg:///repos/user1/hg_repository_dependency_0460. 16) Upload to repository_dependency_test_5_0460 using the url hg:///repos/user1/hg_repository_dependency_0460. ''' class TestAutomaticDependencyRevision( ShedTwillTestCase ): '''Test defining repository dependencies without specifying the changeset revision.''' def test_0000_initiate_users( 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' % common.test_user_1_email test_user_1_private_role = self.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 = self.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 = self.test_db_util.get_private_role( test_user_2 ) 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' % common.admin_email admin_user_private_role = self.test_db_util.get_private_role( admin_user ) def test_0005_create_datatypes_repository( self ): '''Create and populate the emboss_datatypes_0460 repository''' ''' This is step 1 - Create and populate emboss_datatypes_0460. ''' 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 ) category = self.test_db_util.get_category_by_name( category_name ) repository = self.get_or_create_repository( name=datatypes_repository_name, description=datatypes_repository_description, long_description=datatypes_repository_long_description, owner=common.test_user_1_name, category_id=self.security.encode_id( category.id ), strings_displayed=[] ) self.upload_file( repository, filename='emboss/datatypes/datatypes_conf.xml', filepath=None, valid_tools_only=True, uncompress_file=False, remove_repo_files_not_in_tar=False, commit_message='Populate emboss_datatypes_0460 with datatype definitions.', strings_displayed=[], strings_not_displayed=[] ) def test_0010_create_bwa_package_repository( self ): '''Create and populate the package_bwa_0_5_9_0460 repository.''' ''' This is step 2 - Create and populate package_bwa_0_5_9_0460. ''' category = self.test_db_util.get_category_by_name( category_name ) repository = self.get_or_create_repository( name=bwa_repository_name, description=bwa_repository_description, long_description=bwa_repository_long_description, owner=common.test_user_1_name, category_id=self.security.encode_id( category.id ), strings_displayed=[] ) self.upload_file( repository, filename='bwa/complex/tool_dependencies.xml', filepath=None, valid_tools_only=True, uncompress_file=False, remove_repo_files_not_in_tar=False, commit_message='Populate package_bwa_0_5_9_0460 with a tool dependency definition.', strings_displayed=[], strings_not_displayed=[] ) def test_0015_create_tool_dependency_repositories( self ): '''Create repositories for testing complex dependency generation.''' ''' This is step 3 - Create complex_dependency_test_1_0460, complex_dependency_test_2_0460, complex_dependency_test_3_0460, complex_dependency_test_4_0460, complex_dependency_test_5_0460. Each of these repositories will be populated in a way that tests a different way to achieve the same resulting dependency structure using complex tool dependencies. The different methods being tested are: - Upload an uncompressed tool_dependencies.xml to the root of the repository. - Upload a tool_dependencies.xml in a tarball, not in a subfolder. - Upload a tool_dependencies.xml in a subfolder within a tarball. - Upload via url, with the tool_dependencies.xml in the root of another repository. - Upload via url, with the tool_dependencies.xml in a subfolder within another repository. ''' category = self.test_db_util.get_category_by_name( category_name ) repository_base_name = 'complex_dependency_test_%d_0460' repository_base_description = 'Test #%d for complex repository dependency definitions.' repository_base_long_description = 'Test #%d for complex repository dependency definitions.' for number in range( 1, 6 ): repository = self.get_or_create_repository( name=repository_base_name % number, description=repository_base_description % number, long_description=repository_base_long_description % number, owner=common.test_user_1_name, category_id=self.security.encode_id( category.id ), strings_displayed=[] ) def test_0020_populate_complex_dependency_test_1_0460( self ): '''Populate complex_dependency_test_1_0460.''' ''' This is step 4 - Upload an uncompressed tool_dependencies.xml to complex_dependency_test_1_0460 that specifies a complex repository dependency on package_bwa_0_5_9_0460 without a specified changeset revision or tool shed url. ''' repository = self.test_db_util.get_repository_by_name_and_owner( 'complex_dependency_test_1_0460', common.test_user_1_name ) package_repository = self.test_db_util.get_repository_by_name_and_owner( 'package_bwa_0_5_9_0460', common.test_user_1_name ) self.upload_file( repository, filename='0460_files/tool_dependencies.xml', filepath=None, valid_tools_only=True, uncompress_file=False, remove_repo_files_not_in_tar=False, commit_message='Uploaded complex repository dependency definition.', strings_displayed=[], strings_not_displayed=[] ) changeset_revision = self.get_repository_tip( package_repository ) strings_displayed = [ 'package_bwa_0_5_9_0460', 'bwa', '0.5.9', 'package', changeset_revision ] self.display_manage_repository_page( repository, strings_displayed=strings_displayed ) self.display_repository_file_contents( repository, filename='tool_dependencies.xml', strings_displayed=[ changeset_revision ] ) def test_0025_populate_complex_dependency_test_2_0460( self ): '''Populate complex_dependency_test_2_0460.''' ''' This is step 5 - Upload an tarball with tool_dependencies.xml to complex_dependency_test_2_0460 that specifies a complex repository dependency on package_bwa_0_5_9_0460 without a specified changeset revision or tool shed url. ''' repository = self.test_db_util.get_repository_by_name_and_owner( 'complex_dependency_test_2_0460', common.test_user_1_name ) package_repository = self.test_db_util.get_repository_by_name_and_owner( 'package_bwa_0_5_9_0460', common.test_user_1_name ) self.upload_file( repository, filename='0460_files/tool_dependencies_in_root.tar', filepath=None, valid_tools_only=True, uncompress_file=False, remove_repo_files_not_in_tar=True, commit_message='Uploaded complex repository dependency definition.', strings_displayed=[], strings_not_displayed=[] ) changeset_revision = self.get_repository_tip( package_repository ) strings_displayed = [ 'package_bwa_0_5_9_0460', 'bwa', '0.5.9', 'package', changeset_revision ] self.display_manage_repository_page( repository, strings_displayed=strings_displayed ) self.display_repository_file_contents( repository, filename='tool_dependencies.xml', strings_displayed=[ changeset_revision ] ) def test_0030_populate_complex_dependency_test_3_0460( self ): '''Populate complex_dependency_test_3_0460.''' ''' This is step 6 - Upload an tarball with tool_dependencies.xml in a subfolder to complex_dependency_test_3_0460 that specifies a complex repository dependency on package_bwa_0_5_9_0460 without a specified changeset revision or tool shed url. ''' repository = self.test_db_util.get_repository_by_name_and_owner( 'complex_dependency_test_3_0460', common.test_user_1_name ) package_repository = self.test_db_util.get_repository_by_name_and_owner( 'package_bwa_0_5_9_0460', common.test_user_1_name ) self.upload_file( repository, filename='0460_files/tool_dependencies_in_subfolder.tar', filepath=None, valid_tools_only=True, uncompress_file=False, remove_repo_files_not_in_tar=True, commit_message='Uploaded complex repository dependency definition.', strings_displayed=[], strings_not_displayed=[] ) changeset_revision = self.get_repository_tip( package_repository ) strings_displayed = [ 'package_bwa_0_5_9_0460', 'bwa', '0.5.9', 'package', changeset_revision ] self.display_manage_repository_page( repository, strings_displayed=strings_displayed ) self.display_repository_file_contents( repository, filename='tool_dependencies.xml', filepath='subfolder', strings_displayed=[ changeset_revision ] ) def test_0035_create_repositories_for_url_upload( self ): '''Create and populate hg_tool_dependency_0460 and hg_subfolder_tool_dependency_0460.''' ''' This is step 7 - Create hg_tool_dependency_0460 and hg_subfolder_tool_dependency_0460 and populate with tool dependencies. ''' category = self.test_db_util.get_category_by_name( category_name ) repository = self.get_or_create_repository( name='hg_tool_dependency_0460', description=bwa_repository_description, long_description=bwa_repository_long_description, owner=common.test_user_1_name, category_id=self.security.encode_id( category.id ), strings_displayed=[] ) self.upload_file( repository, filename='0460_files/tool_dependencies.xml', filepath=None, valid_tools_only=True, uncompress_file=False, remove_repo_files_not_in_tar=False, commit_message='Populate hg_tool_dependency_0460 with a tool dependency definition.', strings_displayed=[], strings_not_displayed=[] ) repository = self.get_or_create_repository( name='hg_subfolder_tool_dependency_0460', description=bwa_repository_description, long_description=bwa_repository_long_description, owner=common.test_user_1_name, category_id=self.security.encode_id( category.id ), strings_displayed=[] ) self.upload_file( repository, filename='0460_files/tool_dependencies_in_subfolder.tar', filepath=None, valid_tools_only=True, uncompress_file=False, remove_repo_files_not_in_tar=False, commit_message='Populate hg_subfolder_tool_dependency_0460 with a tool dependency definition.', strings_displayed=[], strings_not_displayed=[] ) def test_0040_url_upload_to_complex_test( self ): '''Populate complex_dependency_test_4_0460.''' ''' This is step 8 - Upload to complex_dependency_test_4_0460 using the url hg:///repos/user1/hg_tool_dependency_0460. ''' url = 'hg://%s:%s/repos/user1/hg_tool_dependency_0460' % ( self.host, self.port ) repository = self.test_db_util.get_repository_by_name_and_owner( 'complex_dependency_test_4_0460', common.test_user_1_name ) package_repository = self.test_db_util.get_repository_by_name_and_owner( 'package_bwa_0_5_9_0460', common.test_user_1_name ) self.upload_url( repository, url=url, filepath=None, valid_tools_only=True, uncompress_file=False, remove_repo_files_not_in_tar=True, commit_message='Uploaded complex repository dependency definition.', strings_displayed=[], strings_not_displayed=[] ) changeset_revision = self.get_repository_tip( package_repository ) strings_displayed = [ 'package_bwa_0_5_9_0460', 'bwa', '0.5.9', 'package', changeset_revision ] self.display_manage_repository_page( repository, strings_displayed=strings_displayed ) self.display_repository_file_contents( repository, filename='tool_dependencies.xml', strings_displayed=[ changeset_revision ] ) def test_0045_url_upload_to_complex_test( self ): '''Populate complex_dependency_test_4_0460.''' ''' This is step 9 - Upload to complex_dependency_test_5_0460 using the url hg:///repos/user1/hg_subfolder_tool_dependency_0460. ''' url = 'hg://%s:%s/repos/user1/hg_subfolder_tool_dependency_0460' % ( self.host, self.port ) repository = self.test_db_util.get_repository_by_name_and_owner( 'complex_dependency_test_5_0460', common.test_user_1_name ) package_repository = self.test_db_util.get_repository_by_name_and_owner( 'package_bwa_0_5_9_0460', common.test_user_1_name ) self.upload_url( repository, url=url, filepath=None, valid_tools_only=True, uncompress_file=False, remove_repo_files_not_in_tar=True, commit_message='Uploaded complex repository dependency definition.', strings_displayed=[], strings_not_displayed=[] ) changeset_revision = self.get_repository_tip( package_repository ) strings_displayed = [ 'package_bwa_0_5_9_0460', 'bwa', '0.5.9', 'package', changeset_revision ] self.display_manage_repository_page( repository, strings_displayed=strings_displayed ) self.display_repository_file_contents( repository, filename='tool_dependencies.xml', filepath='subfolder', strings_displayed=[ changeset_revision ] ) def test_0050_create_repositories_for_simple_dependencies( self ): '''Create repositories for testing simple dependency generation.''' ''' This is step 10 - Create repository_dependency_test_1_0460, repository_dependency_test_2_0460, repository_dependency_test_3_0460, repository_dependency_test_4_0460, repository_dependency_test_4_0460.. Each of these repositories will be populated in a way that tests a different way to achieve the same resulting dependency structure using complex tool dependencies. The different methods being tested are: - Upload an uncompressed repository_dependencies.xml to the root of the repository. - Upload a repository_dependencies.xml in a tarball, not in a subfolder. - Upload a repository_dependencies.xml in a subfolder within a tarball. - Upload via url, with the repository_dependencies.xml in the root of another repository. - Upload via url, with the repository_dependencies.xml in a subfolder within another repository. ''' category = self.test_db_util.get_category_by_name( category_name ) repository_base_name = 'repository_dependency_test_%d_0460' repository_base_description = 'Test #%d for repository dependency definitions.' repository_base_long_description = 'Test #%d for repository dependency definitions.' for number in range( 1, 6 ): repository = self.get_or_create_repository( name=repository_base_name % number, description=repository_base_description % number, long_description=repository_base_long_description % number, owner=common.test_user_1_name, category_id=self.security.encode_id( category.id ), strings_displayed=[] ) def test_0055_populate_repository_dependency_test_1_0460( self ): '''Populate repository_dependency_test_1_0460.''' ''' This is step 11 - Upload an uncompressed repository_dependencies.xml to repository_dependency_test_1_0460 that specifies a repository dependency on emboss_datatypes_0460 without a specified changeset revision or tool shed url. ''' repository = self.test_db_util.get_repository_by_name_and_owner( 'repository_dependency_test_1_0460', common.test_user_1_name ) package_repository = self.test_db_util.get_repository_by_name_and_owner( 'emboss_datatypes_0460', common.test_user_1_name ) self.upload_file( repository, filename='0460_files/repository_dependencies.xml', filepath=None, valid_tools_only=True, uncompress_file=False, remove_repo_files_not_in_tar=False, commit_message='Uploaded complex repository dependency definition.', strings_displayed=[], strings_not_displayed=[] ) changeset_revision = self.get_repository_tip( package_repository ) strings_displayed = [ 'emboss_datatypes_0460', 'user1', changeset_revision ] self.display_manage_repository_page( repository, strings_displayed=strings_displayed ) self.display_repository_file_contents( repository, filename='repository_dependencies.xml', strings_displayed=[ changeset_revision ] ) def test_0060_populate_repository_dependency_test_2_0460( self ): '''Populate repository_dependency_test_2_0460.''' ''' This is step 12 - Upload a tarball to repository_dependency_test_2_0460 with a repository_dependencies.xml in the root of the tarball. ''' repository = self.test_db_util.get_repository_by_name_and_owner( 'repository_dependency_test_2_0460', common.test_user_1_name ) package_repository = self.test_db_util.get_repository_by_name_and_owner( 'emboss_datatypes_0460', common.test_user_1_name ) self.upload_file( repository, filename='0460_files/repository_dependencies_in_root.tar', filepath=None, valid_tools_only=True, uncompress_file=False, remove_repo_files_not_in_tar=True, commit_message='Uploaded complex repository dependency definition.', strings_displayed=[], strings_not_displayed=[] ) changeset_revision = self.get_repository_tip( package_repository ) strings_displayed = [ 'emboss_datatypes_0460', 'user1', changeset_revision ] self.display_manage_repository_page( repository, strings_displayed=strings_displayed ) self.display_repository_file_contents( repository, filename='repository_dependencies.xml', strings_displayed=[ changeset_revision ] ) def test_0065_populate_repository_dependency_test_3_0460( self ): '''Populate repository_dependency_test_3_0460.''' ''' This is step 13 - Upload a tarball to repository_dependency_test_3_0460 with a repository_dependencies.xml in a subfolder within the tarball. ''' repository = self.test_db_util.get_repository_by_name_and_owner( 'repository_dependency_test_3_0460', common.test_user_1_name ) package_repository = self.test_db_util.get_repository_by_name_and_owner( 'emboss_datatypes_0460', common.test_user_1_name ) self.upload_file( repository, filename='0460_files/repository_dependencies_in_subfolder.tar', filepath=None, valid_tools_only=True, uncompress_file=False, remove_repo_files_not_in_tar=True, commit_message='Uploaded complex repository dependency definition.', strings_displayed=[], strings_not_displayed=[] ) changeset_revision = self.get_repository_tip( package_repository ) strings_displayed = [ 'emboss_datatypes_0460', 'user1', changeset_revision ] self.display_manage_repository_page( repository, strings_displayed=strings_displayed ) self.display_repository_file_contents( repository, filename='repository_dependencies.xml', filepath='subfolder', strings_displayed=[ changeset_revision ] ) def test_0070_create_repositories_for_url_upload( self ): '''Create and populate hg_repository_dependency_0460 and hg_subfolder_repository_dependency_0460.''' ''' This is step 14 - Create hg_repository_dependency_0460 and hg_subfolder_repository_dependency_0460 and populate with repository dependencies. ''' category = self.test_db_util.get_category_by_name( category_name ) repository = self.get_or_create_repository( name='hg_repository_dependency_0460', description=bwa_repository_description, long_description=bwa_repository_long_description, owner=common.test_user_1_name, category_id=self.security.encode_id( category.id ), strings_displayed=[] ) self.upload_file( repository, filename='0460_files/repository_dependencies.xml', filepath=None, valid_tools_only=True, uncompress_file=False, remove_repo_files_not_in_tar=False, commit_message='Populate hg_repository_dependency_0460 with a tool dependency definition.', strings_displayed=[], strings_not_displayed=[] ) repository = self.get_or_create_repository( name='hg_subfolder_repository_dependency_0460', description=bwa_repository_description, long_description=bwa_repository_long_description, owner=common.test_user_1_name, category_id=self.security.encode_id( category.id ), strings_displayed=[] ) self.upload_file( repository, filename='0460_files/repository_dependencies_in_subfolder.tar', filepath=None, valid_tools_only=True, uncompress_file=False, remove_repo_files_not_in_tar=False, commit_message='Populate hg_subfolder_repository_dependency_0460 with a tool dependency definition.', strings_displayed=[], strings_not_displayed=[] ) def test_0075_url_upload_to_complex_test( self ): '''Populate repository_dependency_test_4_0460.''' ''' This is step 15 - Upload to repository_dependency_test_4_0460 using the url hg:///repos/user1/hg_repository_dependency_0460. ''' url = 'hg://%s:%s/repos/user1/hg_repository_dependency_0460' % ( self.host, self.port ) repository = self.test_db_util.get_repository_by_name_and_owner( 'repository_dependency_test_4_0460', common.test_user_1_name ) package_repository = self.test_db_util.get_repository_by_name_and_owner( 'emboss_datatypes_0460', common.test_user_1_name ) self.upload_url( repository, url=url, filepath=None, valid_tools_only=True, uncompress_file=False, remove_repo_files_not_in_tar=True, commit_message='Uploaded repository dependency definition.', strings_displayed=[], strings_not_displayed=[] ) changeset_revision = self.get_repository_tip( package_repository ) strings_displayed = [ 'emboss_datatypes_0460', 'user1', changeset_revision ] self.display_manage_repository_page( repository, strings_displayed=strings_displayed ) self.display_repository_file_contents( repository, filename='repository_dependencies.xml', strings_displayed=[ changeset_revision ] ) def test_0080_url_upload_to_complex_test( self ): '''Populate repository_dependency_test_4_0460.''' ''' This is step 16 - Upload to repository_dependency_test_5_0460 using the url hg:///repos/user1/hg_subfolder_repository_dependency_0460. ''' url = 'hg://%s:%s/repos/user1/hg_subfolder_repository_dependency_0460' % ( self.host, self.port ) repository = self.test_db_util.get_repository_by_name_and_owner( 'repository_dependency_test_5_0460', common.test_user_1_name ) package_repository = self.test_db_util.get_repository_by_name_and_owner( 'emboss_datatypes_0460', common.test_user_1_name ) self.upload_url( repository, url=url, filepath=None, valid_tools_only=True, uncompress_file=False, remove_repo_files_not_in_tar=True, commit_message='Uploaded repository dependency definition.', strings_displayed=[], strings_not_displayed=[] ) changeset_revision = self.get_repository_tip( package_repository ) strings_displayed = [ 'emboss_datatypes_0460', 'user1', changeset_revision ] self.display_manage_repository_page( repository, strings_displayed=strings_displayed ) self.display_repository_file_contents( repository, filename='repository_dependencies.xml', filepath='subfolder', strings_displayed=[ changeset_revision ] )