Warning

This document is for an in-development version of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

Source code for tool_shed.test.functional.test_1090_repository_dependency_handling

import logging

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

column_repository_name = "column_maker_1085"
column_repository_description = "Add column"
column_repository_long_description = "Compute an expression on every row"

convert_repository_name = "convert_chars_1085"
convert_repository_description = "Convert delimiters"
convert_repository_long_description = "Convert delimiters to tab"

category_name = "Test 1085 Advanced Circular Dependencies"
category_description = "Test circular dependency features"

log = logging.getLogger(__name__)


[docs]class TestRepositoryDependencies(ShedTwillTestCase): """Testing the behavior of repository dependencies with tool panel sections."""
[docs] def test_0000_create_or_login_admin_user(self): """Create necessary user accounts and login as an admin user.""" self.galaxy_login(email=common.admin_email, username=common.admin_username) 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_and_populate_column_repository(self): """Create a category for this test suite and add repositories to it.""" 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=column_repository_name, description=column_repository_description, long_description=column_repository_long_description, owner=common.test_user_1_name, category=category, 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_0010_create_and_populate_convert_repository(self): 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=convert_repository_name, description=convert_repository_description, long_description=convert_repository_long_description, owner=common.test_user_1_name, category=category, strings_displayed=[], ) if self.repository_is_new(repository): 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_0015_create_and_upload_dependency_files(self): convert_repository = self.test_db_util.get_repository_by_name_and_owner( convert_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 ) repository_dependencies_path = self.generate_temp_path("test_1085", additional_paths=["column"]) repository_tuple = ( self.url, convert_repository.name, convert_repository.user.username, self.get_repository_tip(convert_repository), ) self.create_repository_dependency( repository=column_repository, repository_tuples=[repository_tuple], filepath=repository_dependencies_path ) repository_tuple = ( self.url, column_repository.name, column_repository.user.username, self.get_repository_tip(column_repository), ) self.create_repository_dependency( repository=convert_repository, repository_tuples=[repository_tuple], filepath=repository_dependencies_path )
[docs] def test_0020_install_repositories(self): """Install column_maker into column_maker tool panel section and install 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", strings_displayed=["install_repository_dependencies"], ) installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner( convert_repository_name, common.test_user_1_name ) installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner( column_repository_name, common.test_user_1_name ) browse_strings_displayed = [ "convert_chars_1085", "Convert delimiters", self.url.replace("http://", ""), installed_convert_repository.installed_changeset_revision, "column_maker_1085", "Add column", installed_column_repository.installed_changeset_revision, ] strings_displayed = [ "convert_chars_1085", "Convert delimiters", self.url.replace("http://", ""), installed_convert_repository.installed_changeset_revision, "column_maker_1085", installed_column_repository.installed_changeset_revision, "Installed repository dependencies", ] self.display_galaxy_browse_repositories_page(strings_displayed=browse_strings_displayed) self.display_installed_repository_manage_page(installed_convert_repository, strings_displayed=strings_displayed)
[docs] def test_0025_uninstall_column_repository(self): """uninstall column_maker, verify same section""" installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner( column_repository_name, common.test_user_1_name ) self.uninstall_repository(installed_column_repository) self.test_db_util.ga_refresh(installed_column_repository) self.check_galaxy_repository_tool_panel_section(installed_column_repository, "column_maker")
[docs] def test_0030_uninstall_convert_repository(self): installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner( convert_repository_name, common.test_user_1_name ) self.uninstall_repository(installed_convert_repository) self.test_db_util.ga_refresh(installed_convert_repository) self.check_galaxy_repository_tool_panel_section(installed_convert_repository, "column_maker")
[docs] def test_0035_reinstall_column_repository(self): """reinstall column_maker into new section 'new_column_maker' (no_changes = false), no dependencies""" installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner( column_repository_name, common.test_user_1_name ) self.reinstall_repository( installed_column_repository, install_tool_dependencies=False, install_repository_dependencies=False, new_tool_panel_section_label="new_column_maker", no_changes=False, ) strings_displayed = [ "column_maker_1085", "Add column", self.url.replace("http://", ""), installed_column_repository.installed_changeset_revision, ] self.display_installed_repository_manage_page(installed_column_repository, strings_displayed=strings_displayed)
[docs] def test_0040_reinstall_convert_repository(self): """reinstall convert_chars into new section 'new_convert_chars' (no_changes = false), no dependencies""" installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner( convert_repository_name, common.test_user_1_name ) self.reinstall_repository( installed_convert_repository, install_tool_dependencies=False, install_repository_dependencies=False, new_tool_panel_section_label="new_convert_chars", no_changes=False, ) strings_displayed = [ "convert_chars_1085", "Convert delimiters", self.url.replace("http://", ""), installed_convert_repository.installed_changeset_revision, ] self.display_installed_repository_manage_page(installed_convert_repository, strings_displayed=strings_displayed)
# The following check fails somewhere around 5% of the time maybe on Jenkins. # https://jenkins.galaxyproject.org/job/docker-toolshed/5578/ # https://jenkins.galaxyproject.org/job/docker-toolshed/5198/ # def test_0045_uninstall_and_verify_tool_panel_sections( self ): # '''uninstall both and verify tool panel sections''' # installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner( convert_repository_name, # common.test_user_1_name ) # installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner( column_repository_name, # common.test_user_1_name ) # self.uninstall_repository( installed_convert_repository ) # self.uninstall_repository( installed_column_repository ) # self.test_db_util.ga_refresh( installed_convert_repository ) # self.test_db_util.ga_refresh( installed_column_repository ) # self.check_galaxy_repository_tool_panel_section( installed_column_repository, 'new_column_maker' ) # self.check_galaxy_repository_tool_panel_section( installed_convert_repository, 'new_convert_chars' )