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Source code for tool_shed.test.functional.test_0300_reset_all_metadata

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

column_maker_repository_name = "column_maker_0020"
column_maker_repository_description = "A flexible aligner."
column_maker_repository_long_description = "A flexible aligner and methylation caller for Bisulfite-Seq applications."

emboss_repository_description = "Galaxy wrappers for Emboss version 5.0.0 tools"
emboss_repository_long_description = "Galaxy wrappers for Emboss version 5.0.0 tools"

emboss_repository_name = "emboss_0050"
emboss_5_repository_name = "emboss_5_0050"
emboss_6_repository_name = "emboss_6_0050"

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_0050_name = "Test 0050 Circular Dependencies 5 Levels"
category_0050_description = "Test circular dependency features"

running_standalone = False


[docs]class TestResetAllRepositoryMetadata(ShedTwillTestCase): """Verify that the "Reset selected metadata" feature works."""
[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) self.login(email=common.admin_email, username=common.admin_username)
[docs] def test_0005_create_filtering_repository(self): """Create and populate the filtering_0000 repository.""" global running_standalone self.login(email=common.admin_email, username=common.admin_username) category_0000 = self.create_category( name="Test 0000 Basic Repository Features 1", description="Test 0000 Basic Repository Features 1" ) self.login(email=common.test_user_1_email, username=common.test_user_1_name) repository = self.get_or_create_repository( name="filtering_0000", description="Galaxy's filtering tool", long_description="Long description of Galaxy's filtering tool", owner=common.test_user_1_name, category=category_0000, ) if self.repository_is_new(repository): running_standalone = True 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_2.2.0.tar", filepath=None, valid_tools_only=True, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message="Uploaded filtering 2.2.0 tarball.", strings_displayed=[], strings_not_displayed=[], )
[docs] def test_0010_create_freebayes_repository(self): """Create and populate the freebayes_0010 repository.""" global running_standalone self.login(email=common.admin_email, username=common.admin_username) category_0010 = self.create_category( name="Test 0010 Repository With Tool Dependencies", description="Tests for a repository with tool dependencies.", ) self.login(email=common.test_user_1_email, username=common.test_user_1_name) repository = self.get_or_create_repository( name="freebayes_0010", description="Galaxy's freebayes tool", long_description="Long description of Galaxy's freebayes tool", owner=common.test_user_1_name, category=category_0010, strings_displayed=[], ) if running_standalone: self.upload_file( repository, filename="freebayes/freebayes.xml", filepath=None, valid_tools_only=False, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message="Uploaded freebayes.xml.", strings_displayed=[], strings_not_displayed=[], ) self.upload_file( repository, filename="freebayes/tool_data_table_conf.xml.sample", filepath=None, valid_tools_only=False, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message="Uploaded tool_data_table_conf.xml.sample", strings_displayed=[], strings_not_displayed=[], ) self.upload_file( repository, filename="freebayes/sam_fa_indices.loc.sample", filepath=None, valid_tools_only=False, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message="Uploaded sam_fa_indices.loc.sample", strings_displayed=[], strings_not_displayed=[], ) self.upload_file( repository, filename="freebayes/tool_dependencies.xml", filepath=None, valid_tools_only=False, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message="Uploaded tool_dependencies.xml", strings_displayed=[], strings_not_displayed=[], )
[docs] def test_0015_create_datatypes_0020_repository(self): """Create and populate the column_maker_0020 repository.""" global running_standalone if running_standalone: self.login(email=common.admin_email, username=common.admin_username) category_0020 = self.create_category( name="Test 0020 Basic Repository Dependencies", description="Testing basic repository dependency features.", ) self.login(email=common.test_user_1_email, username=common.test_user_1_name) repository = self.get_or_create_repository( name="column_maker_0020", description=column_maker_repository_description, long_description=column_maker_repository_long_description, owner=common.test_user_1_name, category=category_0020, 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 tarball.", strings_displayed=[], strings_not_displayed=[], )
[docs] def test_0020_create_emboss_0020_repository(self): """Create and populate the emboss_0020 repository.""" global running_standalone if running_standalone: self.login(email=common.admin_email, username=common.admin_username) category_0020 = self.create_category( name="Test 0020 Basic Repository Dependencies", description="Testing basic repository dependency features.", ) self.login(email=common.test_user_1_email, username=common.test_user_1_name) repository = self.get_or_create_repository( name="emboss_0020", description=emboss_repository_long_description, long_description=emboss_repository_long_description, owner=common.test_user_1_name, category=category_0020, strings_displayed=[], ) 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.tar", strings_displayed=[], strings_not_displayed=[], )
[docs] def test_0025_create_emboss_datatypes_0030_repository(self): """Create and populate the emboss_0030 repository.""" global running_standalone if running_standalone: self.login(email=common.admin_email, username=common.admin_username) category_0030 = self.create_category( name="Test 0030 Repository Dependency Revisions", description="Testing repository dependencies by revision.", ) self.login(email=common.test_user_1_email, username=common.test_user_1_name) column_maker_repository = self.get_or_create_repository( name="column_maker_0030", description=column_maker_repository_description, long_description=column_maker_repository_long_description, owner=common.test_user_1_name, category=category_0030, strings_displayed=[], ) self.upload_file( column_maker_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_0030_create_emboss_5_repository(self): """Create and populate the emboss_5_0030 repository.""" global running_standalone if running_standalone: self.login(email=common.admin_email, username=common.admin_username) category_0030 = self.create_category( name="Test 0030 Repository Dependency Revisions", description="Testing repository dependencies by revision.", ) self.login(email=common.test_user_1_email, username=common.test_user_1_name) emboss_5_repository = self.get_or_create_repository( name="emboss_5_0030", description=emboss_repository_description, long_description=emboss_repository_long_description, owner=common.test_user_1_name, category=category_0030, strings_displayed=[], ) self.upload_file( emboss_5_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.tar", strings_displayed=[], strings_not_displayed=[], )
[docs] def test_0035_create_emboss_6_repository(self): """Create and populate the emboss_6_0030 repository.""" global running_standalone if running_standalone: self.login(email=common.admin_email, username=common.admin_username) category_0030 = self.create_category( name="Test 0030 Repository Dependency Revisions", description="Testing repository dependencies by revision.", ) self.login(email=common.test_user_1_email, username=common.test_user_1_name) emboss_6_repository = self.get_or_create_repository( name="emboss_6_0030", description=emboss_repository_description, long_description=emboss_repository_long_description, owner=common.test_user_1_name, category=category_0030, strings_displayed=[], ) self.upload_file( emboss_6_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.tar", strings_displayed=[], strings_not_displayed=[], )
[docs] def test_0040_create_emboss_0030_repository(self): """Create and populate the emboss_0030 repository.""" global running_standalone if running_standalone: self.login(email=common.admin_email, username=common.admin_username) category_0030 = self.create_category( name="Test 0030 Repository Dependency Revisions", description="Testing repository dependencies by revision.", ) self.login(email=common.test_user_1_email, username=common.test_user_1_name) emboss_repository = self.get_or_create_repository( name="emboss_0030", description=emboss_repository_description, long_description=emboss_repository_long_description, owner=common.test_user_1_name, category=category_0030, strings_displayed=[], ) self.upload_file( emboss_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.tar", strings_displayed=[], strings_not_displayed=[], )
[docs] def test_0045_create_repository_dependencies_for_0030(self): """Create the dependency structure for test 0030.""" global running_standalone if running_standalone: column_maker_repository = self._get_repository_by_name_and_owner( "column_maker_0030", common.test_user_1_name ) emboss_repository = self._get_repository_by_name_and_owner("emboss_0030", common.test_user_1_name) emboss_5_repository = self._get_repository_by_name_and_owner("emboss_5_0030", common.test_user_1_name) emboss_6_repository = self._get_repository_by_name_and_owner("emboss_6_0030", common.test_user_1_name) repository_dependencies_path = self.generate_temp_path("test_0330", additional_paths=["emboss"]) column_maker_tuple = ( self.url, column_maker_repository.name, column_maker_repository.owner, self.get_repository_tip(column_maker_repository), ) emboss_5_tuple = ( self.url, emboss_5_repository.name, emboss_5_repository.owner, self.get_repository_tip(emboss_5_repository), ) emboss_6_tuple = ( self.url, emboss_6_repository.name, emboss_6_repository.owner, self.get_repository_tip(emboss_6_repository), ) self.create_repository_dependency( repository=emboss_5_repository, repository_tuples=[column_maker_tuple], filepath=repository_dependencies_path, ) self.create_repository_dependency( repository=emboss_6_repository, repository_tuples=[column_maker_tuple], filepath=repository_dependencies_path, ) self.create_repository_dependency( repository=emboss_repository, repository_tuples=[emboss_5_tuple], filepath=repository_dependencies_path ) self.create_repository_dependency( repository=emboss_repository, repository_tuples=[emboss_6_tuple], filepath=repository_dependencies_path )
[docs] def test_0050_create_freebayes_repository(self): """Create and populate the freebayes_0040 repository.""" global running_standalone self.login(email=common.admin_email, username=common.admin_username) category_0040 = self.create_category( name="test_0040_repository_circular_dependencies", description="Testing handling of circular repository dependencies.", ) self.login(email=common.test_user_1_email, username=common.test_user_1_name) repository = self.get_or_create_repository( name="freebayes_0040", description="Galaxy's freebayes tool", long_description="Long description of Galaxy's freebayes tool", owner=common.test_user_1_name, category=category_0040, strings_displayed=[], ) if running_standalone: 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_0055_create_filtering_repository(self): """Create and populate the filtering_0040 repository.""" global running_standalone if running_standalone: self.login(email=common.admin_email, username=common.admin_username) category_0040 = self.create_category( name="test_0040_repository_circular_dependencies", description="Testing handling of circular repository dependencies.", ) self.login(email=common.test_user_1_email, username=common.test_user_1_name) repository = self.get_or_create_repository( name="filtering_0040", description="Galaxy's filtering tool", long_description="Long description of Galaxy's filtering tool", owner=common.test_user_1_name, category=category_0040, 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=[], )
[docs] def test_0060_create_dependency_structure(self): """Create the dependency structure for test 0040.""" global running_standalone if running_standalone: freebayes_repository = self._get_repository_by_name_and_owner("freebayes_0040", common.test_user_1_name) filtering_repository = self._get_repository_by_name_and_owner("filtering_0040", common.test_user_1_name) repository_dependencies_path = self.generate_temp_path("test_0340", additional_paths=["dependencies"]) freebayes_tuple = ( self.url, freebayes_repository.name, freebayes_repository.owner, self.get_repository_tip(freebayes_repository), ) filtering_tuple = ( self.url, filtering_repository.name, filtering_repository.owner, self.get_repository_tip(filtering_repository), ) self.create_repository_dependency( repository=filtering_repository, repository_tuples=[freebayes_tuple], filepath=repository_dependencies_path, ) self.create_repository_dependency( repository=freebayes_repository, repository_tuples=[filtering_tuple], filepath=repository_dependencies_path, )
[docs] def test_0065_create_convert_repository(self): """Create and populate convert_chars_0050.""" global running_standalone if running_standalone: self.login(email=common.admin_email, username=common.admin_username) category = self.create_category(name=category_0050_name, description=category_0050_description) 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=category, 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 tarball.", strings_displayed=[], strings_not_displayed=[], )
[docs] def test_0070_create_column_repository(self): """Create and populate convert_chars_0050.""" global running_standalone if running_standalone: self.login(email=common.admin_email, username=common.admin_username) category = self.create_category(name=category_0050_name, description=category_0050_description) self.login(email=common.test_user_1_email, username=common.test_user_1_name) 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=category, 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 tarball.", strings_displayed=[], strings_not_displayed=[], )
[docs] def test_0075_create_emboss_datatypes_repository(self): """noop now..."""
[docs] def test_0080_create_emboss_repository(self): """Create and populate emboss_0050.""" global running_standalone if running_standalone: self.login(email=common.admin_email, username=common.admin_username) category = self.create_category(name=category_0050_name, description=category_0050_description) self.login(email=common.test_user_1_email, username=common.test_user_1_name) 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=category, strings_displayed=[], ) 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_0085_create_filtering_repository(self): """Create and populate filtering_0050.""" global running_standalone if running_standalone: self.login(email=common.admin_email, username=common.admin_username) category = self.create_category(name=category_0050_name, description=category_0050_description) self.login(email=common.test_user_1_email, username=common.test_user_1_name) filtering_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=category, strings_displayed=[], ) self.upload_file( filtering_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_0090_create_freebayes_repository(self): """Create and populate freebayes_0050.""" global running_standalone if running_standalone: self.login(email=common.admin_email, username=common.admin_username) category = self.create_category(name=category_0050_name, description=category_0050_description) self.login(email=common.test_user_1_email, username=common.test_user_1_name) 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=category, strings_displayed=[], ) 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_0095_create_bismark_repository(self): """Create and populate bismark_0050.""" global running_standalone if running_standalone: self.login(email=common.admin_email, username=common.admin_username) category = self.create_category(name=category_0050_name, description=category_0050_description) self.login(email=common.test_user_1_email, username=common.test_user_1_name) 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=category, strings_displayed=[], ) 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_0100_create_and_upload_dependency_definitions(self): """Create the dependency structure for test 0050.""" global running_standalone if running_standalone: self.login(email=common.test_user_1_email, username=common.test_user_1_name) column_repository = self._get_repository_by_name_and_owner(column_repository_name, common.test_user_1_name) convert_repository = self._get_repository_by_name_and_owner( convert_repository_name, common.test_user_1_name ) emboss_repository = self._get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name) filtering_repository = self._get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name ) freebayes_repository = self._get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) bismark_repository = self._get_repository_by_name_and_owner( bismark_repository_name, common.test_user_1_name ) dependency_xml_path = self.generate_temp_path("test_0050", additional_paths=["freebayes"]) # 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.owner, self.get_repository_tip(column_repository), ) convert_tuple = ( self.url, convert_repository.name, convert_repository.owner, self.get_repository_tip(convert_repository), ) freebayes_tuple = ( self.url, freebayes_repository.name, freebayes_repository.owner, self.get_repository_tip(freebayes_repository), ) emboss_tuple = ( self.url, emboss_repository.name, emboss_repository.owner, self.get_repository_tip(emboss_repository), ) bismark_tuple = ( self.url, bismark_repository.name, bismark_repository.owner, 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=emboss_repository, repository_tuples=[bismark_tuple], filepath=dependency_xml_path ) self.create_repository_dependency( repository=freebayes_repository, repository_tuples=[freebayes_tuple, bismark_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_0110_reset_metadata_on_all_repositories(self): """Reset metadata on all repositories, then verify that it has not changed.""" self.login(email=common.admin_email, username=common.admin_username) old_metadata = dict() new_metadata = dict() repositories = self.test_db_util.get_all_repositories() for repository in repositories: old_metadata[self.security.encode_id(repository.id)] = dict() for metadata in self.get_repository_metadata_for_db_object(repository): old_metadata[self.security.encode_id(repository.id)][metadata.changeset_revision] = metadata.metadata self.reset_metadata_on_selected_repositories(list(old_metadata.keys())) for repository in repositories: new_metadata[self.security.encode_id(repository.id)] = dict() for metadata in self.get_repository_metadata_for_db_object(repository): new_metadata[self.security.encode_id(repository.id)][metadata.changeset_revision] = metadata.metadata if ( old_metadata[self.security.encode_id(repository.id)] != new_metadata[self.security.encode_id(repository.id)] ): raise AssertionError(f"Metadata changed after reset for repository {repository.name}.")