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Source code for tool_shed.test.functional.test_0090_tool_search

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

emboss_repository_name = "emboss_0090"
emboss_repository_description = "Galaxy's emboss tool"
emboss_repository_long_description = "Long description of Galaxy's emboss tool"

filtering_repository_name = "filtering_0090"
filtering_repository_description = "Galaxy's filtering tool"
filtering_repository_long_description = "Long description of Galaxy's filtering tool"

freebayes_repository_name = "freebayes_0090"
freebayes_repository_description = "Galaxy's freebayes tool"
freebayes_repository_long_description = "Long description of Galaxy's freebayes tool"

bwa_base_repository_name = "bwa_base_0090"
bwa_base_repository_description = "BWA Base"
bwa_base_repository_long_description = "NT space mapping with BWA"

bwa_color_repository_name = "bwa_color_0090"
bwa_color_repository_description = "BWA Color"
bwa_color_repository_long_description = "Color space mapping with BWA"

category_name = "Test 0090 Tool Search And Installation"
category_description = "Test 0090 Tool Search And Installation"


[docs]class TestRepositoryCircularDependenciesAgain(ShedTwillTestCase): """Test more features related to repository dependencies."""
[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_bwa_base_repository(self): """Create and populate bwa_base_0090.""" category = self.create_category(name=category_name, description=category_description) self.login(email=common.test_user_1_email, username=common.test_user_1_name) 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=category, strings_displayed=[], ) self.upload_file( repository, filename="bwa/bwa_base.tar", filepath=None, valid_tools_only=True, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message="Uploaded BWA tarball.", strings_displayed=[], strings_not_displayed=[], )
[docs] def test_0010_create_bwa_color_repository(self): """Create and populate bwa_color_0090.""" category = self.create_category(name=category_name, description=category_description) self.login(email=common.test_user_1_email, username=common.test_user_1_name) repository = self.get_or_create_repository( name=bwa_color_repository_name, description=bwa_color_repository_description, long_description=bwa_color_repository_long_description, owner=common.test_user_1_name, category=category, strings_displayed=[], ) self.upload_file( repository, filename="bwa/bwa_color.tar", filepath=None, valid_tools_only=True, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message="Uploaded BWA color tarball.", strings_displayed=[], strings_not_displayed=[], )
[docs] def test_0020_create_emboss_repository(self): """Create and populate emboss_0090.""" 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=category, strings_displayed=[], ) self.upload_file( repository, filename="emboss/emboss.tar", filepath=None, valid_tools_only=True, uncompress_file=False, 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_0090.""" category = self.create_category(name=category_name, description=category_description) 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_0030_create_freebayes_repository(self): """Create and populate freebayes_0090.""" 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=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_0035_create_and_upload_dependency_definitions(self): """Create and upload repository dependency definitions.""" bwa_color_repository = self.test_db_util.get_repository_by_name_and_owner( bwa_color_repository_name, common.test_user_1_name ) bwa_base_repository = self.test_db_util.get_repository_by_name_and_owner( bwa_base_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 ) dependency_xml_path = self.generate_temp_path("test_0090", additional_paths=["freebayes"]) 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), ) filtering_tuple = ( self.url, filtering_repository.name, filtering_repository.user.username, self.get_repository_tip(filtering_repository), ) self.create_repository_dependency( repository=filtering_repository, repository_tuples=[freebayes_tuple], filepath=dependency_xml_path ) self.create_repository_dependency( repository=bwa_base_repository, repository_tuples=[emboss_tuple], filepath=dependency_xml_path ) self.create_repository_dependency( repository=bwa_color_repository, repository_tuples=[filtering_tuple], filepath=dependency_xml_path )
[docs] def test_0040_verify_repository_dependencies(self): """Verify the generated dependency structure.""" bwa_color_repository = self.test_db_util.get_repository_by_name_and_owner( bwa_color_repository_name, common.test_user_1_name ) bwa_base_repository = self.test_db_util.get_repository_by_name_and_owner( bwa_base_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 ) self.check_repository_dependency(filtering_repository, freebayes_repository) self.check_repository_dependency(bwa_base_repository, emboss_repository) self.check_repository_dependency(bwa_color_repository, filtering_repository)