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._get_repository_by_name_and_owner(
            bwa_color_repository_name, common.test_user_1_name
        )
        bwa_base_repository = self._get_repository_by_name_and_owner(bwa_base_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
        )
        dependency_xml_path = self.generate_temp_path("test_0090", additional_paths=["freebayes"])
        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),
        )
        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=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._get_repository_by_name_and_owner(
            bwa_color_repository_name, common.test_user_1_name
        )
        bwa_base_repository = self._get_repository_by_name_and_owner(bwa_base_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
        )
        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)