Source code for tool_shed.test.functional.test_1450_installing_datatypes_sniffers

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

repository_name = "proteomics_datatypes_1450"
repository_description = "Proteomics datatypes"
repository_long_description = "Datatypes used in proteomics"

category_name = "Test 1450 Datatype Sniffers"
category_description = "Test 1450 - Installing Datatype Sniffers"
"""
1. Get a count of datatypes and sniffers.
2. Install proteomics_datatypes_1450.
3. Verify the count of datatypes and sniffers is the previous count + the datatypes contained within proteomics_datatypes_1450.
4. Deactivate proteomics_datatypes_1450, verify the count of datatypes and sniffers is equal to the count determined in step 1.
5. Reactivate proteomics_datatypes_1450, verify that the count of datatypes and sniffers has been increased by the contents of the repository.
6. Uninstall proteomics_datatypes_1450, verify the count of datatypes and sniffers is equal to the count determined in step 1.
7. Reinstall proteomics_datatypes_1450, verify that the count of datatypes and sniffers has been increased by the contents of the repository.
"""

base_datatypes_count = 0
repository_datatypes_count = 0
base_sniffers_count = 0


[docs]class TestInstallDatatypesSniffers(ShedTwillTestCase): """Test installing a repository that defines datatypes and datatype sniffers."""
[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) self.galaxy_login(email=common.admin_email, username=common.admin_username) galaxy_admin_user = self.test_db_util.get_galaxy_user(common.admin_email) assert ( galaxy_admin_user is not None ), f"Problem retrieving user with email {common.admin_email} from the database" self.test_db_util.get_galaxy_private_role(galaxy_admin_user)
[docs] def test_0005_ensure_repositories_and_categories_exist(self): """Create the 1450 category and proteomics_datatypes_1450 repository.""" global repository_datatypes_count self.login(email=common.admin_email, username=common.admin_username) 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=repository_name, description=repository_description, long_description=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="proteomics_datatypes/proteomics_datatypes.tar", filepath=None, valid_tools_only=True, uncompress_file=False, remove_repo_files_not_in_tar=False, commit_message="Uploaded datatype and sniffer definitions.", strings_displayed=[], strings_not_displayed=[], ) repository_datatypes_count = self.get_repository_datatypes_count(repository)
[docs] def test_0010_install_datatypes_repository(self): """Install the proteomics_datatypes_1450 repository into the Galaxy instance. This includes steps 1 and 2 - Get a count of datatypes and sniffers. Store a count of the current datatypes registry and sniffers in global variables, to compare with the updated count after changing the installation status of the proteomics_datatypes_1450 repository. """ global base_datatypes_count global base_sniffers_count base_datatypes_count = self.get_datatypes_count() base_sniffers_count = self.get_sniffers_count() self.galaxy_login(email=common.admin_email, username=common.admin_username) strings_displayed = ["proteomics"] self.install_repository( "proteomics_datatypes_1450", common.test_user_1_name, category_name, strings_displayed=strings_displayed, new_tool_panel_section_label="test_1450", ) installed_repository = self.test_db_util.get_installed_repository_by_name_owner( "proteomics_datatypes_1450", common.test_user_1_name ) strings_displayed = [ "user1", self.url.replace("http://", ""), installed_repository.installed_changeset_revision, ] self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed)
[docs] def test_0015_verify_datatypes_count(self): """Verify that datatypes were added in the previous step. This is step 3 - Verify the count of datatypes and sniffers is the previous count + the datatypes contained within proteomics_datatypes_1450. Compare the current datatypes registry and sniffers with the values that were retrieved in the previous step. """ current_datatypes = self.get_datatypes_count() assert ( current_datatypes == base_datatypes_count + repository_datatypes_count ), "Found %d datatypes, expected %d." % (current_datatypes, base_datatypes_count + repository_datatypes_count) current_sniffers = self.get_sniffers_count() assert ( current_sniffers > base_sniffers_count ), "Sniffer count after installing proteomics_datatypes_1450 is %d, which is not greater than %d" % ( current_sniffers, base_sniffers_count, )
[docs] def test_0020_deactivate_datatypes_repository(self): """Deactivate the installed proteomics_datatypes_1450 repository. This is step 4 - Deactivate proteomics_datatypes_1450, verify the count of datatypes and sniffers is equal to the count determined in step 1. Deactivate proteomics_datatypes_1450 and check that the in-memory datatypes and sniffers match the base values determined in the first step. """ repository = self.test_db_util.get_installed_repository_by_name_owner(repository_name, common.test_user_1_name) global base_datatypes_count global base_sniffers_count self.deactivate_repository(repository) new_datatypes_count = self.get_datatypes_count() assert new_datatypes_count == base_datatypes_count, "Expected %d datatypes, got %d" % ( base_datatypes_count, new_datatypes_count, ) current_sniffers = self.get_sniffers_count() assert ( current_sniffers == base_sniffers_count ), "Sniffer count after deactivating proteomics_datatypes_1450 is %d, expected %d" % ( current_sniffers, base_sniffers_count, )
[docs] def test_0025_reactivate_datatypes_repository(self): """Reactivate the deactivated proteomics_datatypes_1450 repository. This is step 5 - Reactivate proteomics_datatypes, verify that the count of datatypes and sniffers has been increased by the contents of the repository. """ repository = self.test_db_util.get_installed_repository_by_name_owner(repository_name, common.test_user_1_name) global repository_datatypes_count global base_datatypes_count global base_sniffers_count self.reactivate_repository(repository) new_datatypes_count = self.get_datatypes_count() assert ( new_datatypes_count == base_datatypes_count + repository_datatypes_count ), "Found %d datatypes, expected %d." % (new_datatypes_count, base_datatypes_count + repository_datatypes_count) current_sniffers = self.get_sniffers_count() assert ( current_sniffers > base_sniffers_count ), "Sniffer count after reactivating proteomics_datatypes_1450 is %d, which is not greater than %d" % ( current_sniffers, base_sniffers_count, )
[docs] def test_0030_uninstall_datatypes_repository(self): """Uninstall the installed proteomics_datatypes_1450 repository. This is step 6 - Uninstall proteomics_datatypes_1450, verify the count of datatypes and sniffers is equal to the count determined in step 1. Uninstall proteomics_datatypes_1450 and check that the in-memory datatypes and sniffers match the base values determined in the first step. """ repository = self.test_db_util.get_installed_repository_by_name_owner(repository_name, common.test_user_1_name) global base_datatypes_count self.uninstall_repository(repository) new_datatypes_count = self.get_datatypes_count() assert new_datatypes_count == base_datatypes_count, "Expected %d datatypes, got %d" % ( base_datatypes_count, new_datatypes_count, ) current_sniffers = self.get_sniffers_count() assert ( current_sniffers == base_sniffers_count ), "Sniffer count after uninstalling proteomics_datatypes_1450 is %d, expected %d" % ( current_sniffers, base_sniffers_count, )
[docs] def test_0035_reinstall_datatypes_repository(self): """Reinstall the uninstalled proteomics_datatypes_1450 repository. This is step 7 - Reinstall proteomics_datatypes_1450, verify that the count of datatypes and sniffers has been increased by the contents of the repository. """ repository = self.test_db_util.get_installed_repository_by_name_owner(repository_name, common.test_user_1_name) global repository_datatypes_count global base_datatypes_count self.reinstall_repository(repository) new_datatypes_count = self.get_datatypes_count() assert ( new_datatypes_count == base_datatypes_count + repository_datatypes_count ), "Found %d datatypes, expected %d." % (new_datatypes_count, base_datatypes_count + repository_datatypes_count) current_sniffers = self.get_sniffers_count() assert ( current_sniffers > base_sniffers_count ), "Sniffer count after reinstalling proteomics_datatypes_1450 is %d, which is not greater than %d" % ( current_sniffers, base_sniffers_count, )