Source code for tool_shed.test.functional.test_1050_circular_dependencies_4_levels

from ..base.twilltestcase import (
    common,
    ShedTwillTestCase,
)

emboss_datatypes_repository_name = "emboss_datatypes_0050"
emboss_datatypes_repository_description = "Datatypes for emboss"
emboss_datatypes_repository_long_description = "Long description of Emboss' datatypes"

emboss_repository_name = "emboss_0050"
emboss_repository_description = "Galaxy's emboss tool"
emboss_repository_long_description = "Long description of Galaxy's emboss tool"

filtering_repository_name = "filtering_0050"
filtering_repository_description = "Galaxy's filtering tool"
filtering_repository_long_description = "Long description of Galaxy's filtering tool"

freebayes_repository_name = "freebayes_0050"
freebayes_repository_description = "Galaxy's freebayes tool"
freebayes_repository_long_description = "Long description of Galaxy's freebayes tool"

column_repository_name = "column_maker_0050"
column_repository_description = "Add column"
column_repository_long_description = "Compute an expression on every row"

convert_repository_name = "convert_chars_0050"
convert_repository_description = "Convert delimiters"
convert_repository_long_description = "Convert delimiters to tab"

bismark_repository_name = "bismark_0050"
bismark_repository_description = "A flexible aligner."
bismark_repository_long_description = "A flexible aligner and methylation caller for Bisulfite-Seq applications."

category_name = "Test 0050 Circular Dependencies 5 Levels"
category_description = "Test circular dependency features"

running_standalone = False


[docs]class TestInstallRepositoryCircularDependencies(ShedTwillTestCase): """Verify that the code correctly handles circular dependencies down to n levels."""
[docs] def test_0000_initiate_users(self): """Create necessary user accounts.""" 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 ), f"Problem retrieving user with email {common.test_user_1_email} from the database" self.test_db_util.get_private_role(test_user_1) 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, f"Problem retrieving user with email {common.admin_email} from the database" self.test_db_util.get_private_role(admin_user)
[docs] def test_0005_create_convert_repository(self): """Create and populate convert_chars_0050.""" category = self.create_category(name=category_name, description=category_description) global running_standalone self.login(email=common.test_user_1_email, username=common.test_user_1_name) 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=[], ) if self.repository_is_new(repository): running_standalone = True 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 tarball.", strings_displayed=[], strings_not_displayed=[], )
[docs] def test_0010_create_column_repository(self): """Create and populate convert_chars_0050.""" category = self.create_category(name=category_name, description=category_description) 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=[], ) if self.repository_is_new(repository): 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 tarball.", strings_displayed=[], strings_not_displayed=[], )
[docs] def test_0015_create_emboss_datatypes_repository(self): """Create and populate emboss_datatypes_0050.""" category = self.create_category(name=category_name, description=category_description) repository = self.get_or_create_repository( name=emboss_datatypes_repository_name, description=emboss_datatypes_repository_description, long_description=emboss_datatypes_repository_long_description, owner=common.test_user_1_name, category_id=self.security.encode_id(category.id), strings_displayed=[], ) if self.repository_is_new(repository): 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="Uploaded datatypes_conf.xml.", strings_displayed=[], strings_not_displayed=[], )
[docs] def test_0020_create_emboss_repository(self): """Create and populate emboss_0050.""" category = self.create_category(name=category_name, description=category_description) repository = self.get_or_create_repository( name=emboss_repository_name, description=emboss_repository_description, long_description=emboss_repository_long_description, owner=common.test_user_1_name, category_id=self.security.encode_id(category.id), strings_displayed=[], ) if self.repository_is_new(repository): self.upload_file( repository, filename="emboss/emboss.tar", filepath=None, valid_tools_only=True, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message="Uploaded emboss tarball.", strings_displayed=[], strings_not_displayed=[], )
[docs] def test_0025_create_filtering_repository(self): """Create and populate filtering_0050.""" category = self.create_category(name=category_name, description=category_description) repository = self.get_or_create_repository( name=filtering_repository_name, description=filtering_repository_description, long_description=filtering_repository_long_description, owner=common.test_user_1_name, category_id=self.security.encode_id(category.id), strings_displayed=[], ) if self.repository_is_new(repository): 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=[], )
[docs] def test_0030_create_freebayes_repository(self): """Create and populate freebayes_0050.""" category = self.create_category(name=category_name, description=category_description) repository = self.get_or_create_repository( name=freebayes_repository_name, description=freebayes_repository_description, long_description=freebayes_repository_long_description, owner=common.test_user_1_name, category_id=self.security.encode_id(category.id), strings_displayed=[], ) if self.repository_is_new(repository): self.upload_file( repository, filename="freebayes/freebayes.tar", filepath=None, valid_tools_only=True, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message="Uploaded freebayes tarball.", strings_displayed=[], strings_not_displayed=[], )
[docs] def test_0035_create_bismark_repository(self): """Create and populate bismark_0050.""" category = self.create_category(name=category_name, description=category_description) repository = self.get_or_create_repository( name=bismark_repository_name, description=bismark_repository_description, long_description=bismark_repository_long_description, owner=common.test_user_1_name, category_id=self.security.encode_id(category.id), strings_displayed=[], ) if self.repository_is_new(repository): self.upload_file( repository, filename="bismark/bismark.tar", filepath=None, valid_tools_only=False, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message="Uploaded bismark tarball.", strings_displayed=[], strings_not_displayed=[], )
[docs] def test_0040_create_and_upload_dependency_definitions(self): """Set up the dependency structure.""" global running_standalone if running_standalone: column_repository = self.test_db_util.get_repository_by_name_and_owner( column_repository_name, common.test_user_1_name ) convert_repository = self.test_db_util.get_repository_by_name_and_owner( convert_repository_name, common.test_user_1_name ) datatypes_repository = self.test_db_util.get_repository_by_name_and_owner( emboss_datatypes_repository_name, common.test_user_1_name ) emboss_repository = self.test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) filtering_repository = self.test_db_util.get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name ) freebayes_repository = self.test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) bismark_repository = self.test_db_util.get_repository_by_name_and_owner( bismark_repository_name, common.test_user_1_name ) dependency_xml_path = self.generate_temp_path("test_1050", additional_paths=["dependencies"]) # convert_chars depends on column_maker # column_maker depends on convert_chars # emboss depends on emboss_datatypes # emboss_datatypes depends on bismark # freebayes depends on freebayes, emboss, emboss_datatypes, and column_maker # filtering depends on emboss column_tuple = ( self.url, column_repository.name, column_repository.user.username, self.get_repository_tip(column_repository), ) convert_tuple = ( self.url, convert_repository.name, convert_repository.user.username, self.get_repository_tip(convert_repository), ) freebayes_tuple = ( self.url, freebayes_repository.name, freebayes_repository.user.username, self.get_repository_tip(freebayes_repository), ) emboss_tuple = ( self.url, emboss_repository.name, emboss_repository.user.username, self.get_repository_tip(emboss_repository), ) datatypes_tuple = ( self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip(datatypes_repository), ) bismark_tuple = ( self.url, bismark_repository.name, bismark_repository.user.username, self.get_repository_tip(bismark_repository), ) self.create_repository_dependency( repository=convert_repository, repository_tuples=[column_tuple], filepath=dependency_xml_path ) self.create_repository_dependency( repository=column_repository, repository_tuples=[convert_tuple], filepath=dependency_xml_path ) self.create_repository_dependency( repository=datatypes_repository, repository_tuples=[bismark_tuple], filepath=dependency_xml_path ) self.create_repository_dependency( repository=emboss_repository, repository_tuples=[datatypes_tuple], filepath=dependency_xml_path ) self.create_repository_dependency( repository=freebayes_repository, repository_tuples=[freebayes_tuple, datatypes_tuple, emboss_tuple, column_tuple], filepath=dependency_xml_path, ) self.create_repository_dependency( repository=filtering_repository, repository_tuples=[emboss_tuple], filepath=dependency_xml_path )
[docs] def test_0045_verify_repository_dependencies(self): """Verify that the generated dependency circle does not cause an infinite loop. Expected structure: id: 2 key: http://toolshed.local:10001__ESEP__filtering__ESEP__test__ESEP__871602b4276b ['http://toolshed.local:10001', 'emboss_5', 'test', '8de5fe0d7b04'] id: 3 key: http://toolshed.local:10001__ESEP__emboss_datatypes__ESEP__test__ESEP__dbd4f68bf507 ['http://toolshed.local:10001', 'freebayes', 'test', 'f40028114098'] id: 4 key: http://toolshed.local:10001__ESEP__freebayes__ESEP__test__ESEP__f40028114098 ['http://toolshed.local:10001', 'emboss_datatypes', 'test', 'dbd4f68bf507'] ['http://toolshed.local:10001', 'emboss_5', 'test', '8de5fe0d7b04'] ['http://toolshed.local:10001', 'column_maker', 'test', '83e956bdbac0'] id: 5 key: http://toolshed.local:10001__ESEP__column_maker__ESEP__test__ESEP__83e956bdbac0 ['http://toolshed.local:10001', 'convert_chars', 'test', 'b28134220c8a'] id: 6 key: http://toolshed.local:10001__ESEP__convert_chars__ESEP__test__ESEP__b28134220c8a ['http://toolshed.local:10001', 'column_maker', 'test', '83e956bdbac0'] id: 7 key: http://toolshed.local:10001__ESEP__emboss_5__ESEP__test__ESEP__8de5fe0d7b04 ['http://toolshed.local:10001', 'emboss_datatypes', 'test', 'dbd4f68bf507'] """ emboss_datatypes_repository = self.test_db_util.get_repository_by_name_and_owner( emboss_datatypes_repository_name, common.test_user_1_name ) emboss_repository = self.test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) filtering_repository = self.test_db_util.get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name ) freebayes_repository = self.test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) column_repository = self.test_db_util.get_repository_by_name_and_owner( column_repository_name, common.test_user_1_name ) convert_repository = self.test_db_util.get_repository_by_name_and_owner( convert_repository_name, common.test_user_1_name ) bismark_repository = self.test_db_util.get_repository_by_name_and_owner( bismark_repository_name, common.test_user_1_name ) self.check_repository_dependency(convert_repository, column_repository) self.check_repository_dependency(column_repository, convert_repository) self.check_repository_dependency(emboss_datatypes_repository, bismark_repository) self.check_repository_dependency(emboss_repository, emboss_datatypes_repository) self.check_repository_dependency(filtering_repository, emboss_repository) 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 = [ f"{freebayes_repository.name} depends on {', '.join(repo.name for repo in freebayes_dependencies)}." ] self.display_manage_repository_page(freebayes_repository, strings_displayed=strings_displayed)
[docs] def test_0050_verify_tool_dependencies(self): """Check that freebayes and emboss display tool dependencies.""" freebayes_repository = self.test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) emboss_repository = self.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"], ) self.display_manage_repository_page( emboss_repository, strings_displayed=["Tool dependencies", "emboss", "5.0.0", "package"] )
[docs] def test_0055_install_column_repository(self): """Install column_maker with repository dependencies.""" self.galaxy_login(email=common.admin_email, username=common.admin_username) self.install_repository( column_repository_name, common.test_user_1_name, category_name, install_tool_dependencies=False, install_repository_dependencies=True, new_tool_panel_section_label="column_maker", ) # 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), ] 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)
[docs] def test_0060_install_emboss_repository(self): """Install emboss_5 with repository dependencies.""" global running_standalone original_datatypes = self.get_datatypes_count() self.install_repository( emboss_repository_name, common.test_user_1_name, category_name, install_tool_dependencies=False, install_repository_dependencies=True, new_tool_panel_section_label="emboss_5_0050", ) if running_standalone: assert ( original_datatypes < self.get_datatypes_count() ), "Installing a repository that depends on emboss_datatypes did not add datatypes." # Now we have emboss_datatypes, emboss, bismark, column_maker, and convert_chars installed, filtering and freebayes never installed. installed_repositories = [ (emboss_datatypes_repository_name, common.test_user_1_name), (column_repository_name, common.test_user_1_name), (emboss_repository_name, common.test_user_1_name), (convert_repository_name, common.test_user_1_name), (bismark_repository_name, common.test_user_1_name), ] 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)
[docs] def test_0065_deactivate_datatypes_repository(self): """Deactivate emboss_datatypes and verify that the datatypes count is reduced.""" original_datatypes = self.get_datatypes_count() repository = self.test_db_util.get_installed_repository_by_name_owner( emboss_datatypes_repository_name, common.test_user_1_name ) self.deactivate_repository(repository) assert ( original_datatypes > self.get_datatypes_count() ), "Deactivating emboss_datatypes did not remove datatypes." # Now we have emboss, bismark, column_maker, and convert_chars installed, filtering and freebayes never installed, and emboss_datatypes deactivated. installed_repositories = [ (column_repository_name, common.test_user_1_name), (emboss_repository_name, common.test_user_1_name), (convert_repository_name, common.test_user_1_name), (bismark_repository_name, common.test_user_1_name), ] 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)
[docs] def test_0070_uninstall_emboss_repository(self): """Uninstall the emboss_5 repository.""" repository = self.test_db_util.get_installed_repository_by_name_owner( emboss_repository_name, common.test_user_1_name ) self.uninstall_repository(repository) strings_not_displayed = [repository.name, repository.installed_changeset_revision] self.display_galaxy_browse_repositories_page(strings_not_displayed=strings_not_displayed) self.test_db_util.ga_refresh(repository) self.check_galaxy_repository_tool_panel_section(repository, "emboss_5_0050") # Now we have bismark, column_maker, and convert_chars installed, filtering and freebayes never installed, emboss_datatypes deactivated, # and emboss uninstalled. 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), ] 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)
[docs] 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() strings_displayed = ["Handle", "tool dependencies", "freebayes", "0.9.4_9696d0ce8a9", "samtools", "0.1.18"] self.install_repository( freebayes_repository_name, common.test_user_1_name, category_name, strings_displayed=strings_displayed, install_tool_dependencies=False, install_repository_dependencies=True, new_tool_panel_section_label="freebayes", ) assert ( original_datatypes < self.get_datatypes_count() ), "Installing a repository that depends on emboss_datatypes did not add datatypes." emboss_repository = self.test_db_util.get_installed_repository_by_name_owner( emboss_repository_name, common.test_user_1_name ) datatypes_repository = self.test_db_util.get_installed_repository_by_name_owner( emboss_datatypes_repository_name, common.test_user_1_name ) strings_displayed = [ "emboss_0050", "emboss_datatypes_0050", emboss_repository.installed_changeset_revision, datatypes_repository.installed_changeset_revision, ] self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed) # Installing freebayes should automatically reinstall emboss and reactivate emboss_datatypes. # Now column_maker, convert_chars, emboss, emboss_datatypes, freebayes, and bismark should be installed. installed_repositories = [ (column_repository_name, common.test_user_1_name), (emboss_datatypes_repository_name, common.test_user_1_name), (emboss_repository_name, common.test_user_1_name), (freebayes_repository_name, common.test_user_1_name), (convert_repository_name, common.test_user_1_name), (bismark_repository_name, common.test_user_1_name), ] 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)