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_1170_prior_installation_required

import logging

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

log = logging.getLogger(__name__)

column_repository_name = "column_maker_0150"
column_repository_description = "Add column"
column_repository_long_description = "Compute an expression on every row"

convert_repository_name = "convert_chars_0150"
convert_repository_description = "Convert delimiters"
convert_repository_long_description = "Convert delimiters to tab"

category_name = "Test 0150 Simple Prior Installation"
category_description = "Test 0150 Simple Prior Installation"

"""
Create column_maker and convert_chars.

Column maker repository dependency:
<repository toolshed="self.url" name="convert_chars" owner="test" changeset_revision="c3041382815c" prior_installation_required="True" />

Verify display.

Galaxy side:

Install column_maker.
Verify that convert_chars was installed first, contrary to the ordering that would be present without prior_installation_required.
"""

running_standalone = False


[docs]class TestSimplePriorInstallation(ShedTwillTestCase): """Test features related to datatype converters."""
[docs] def test_0000_initiate_users(self): """Create necessary user accounts.""" 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_convert_repository(self): """Create and populate convert_chars_0150.""" global running_standalone 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): running_standalone = True 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_0010_create_column_repository(self): """Create and populate convert_chars_0150.""" global running_standalone category = self.create_category(name=category_name, description=category_description) 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 running_standalone: 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_0015_create_repository_dependency(self): """Create a repository dependency specifying convert_chars. Column maker repository dependency: <repository toolshed="self.url" name="convert_chars" owner="test" changeset_revision="<tip>" prior_installation_required="True" /> """ global running_standalone column_repository = self.test_db_util.get_repository_by_name_and_owner( column_repository_name, common.test_user_1_name ) convert_repository = self.test_db_util.get_repository_by_name_and_owner( convert_repository_name, common.test_user_1_name ) if running_standalone: dependency_xml_path = self.generate_temp_path("test_1150", additional_paths=["column"]) convert_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=[convert_tuple], filepath=dependency_xml_path, prior_installation_required=True, )
[docs] def test_0020_verify_repository_dependency(self): """Verify that the previously generated repositiory dependency displays correctly.""" column_repository = self.test_db_util.get_repository_by_name_and_owner( column_repository_name, common.test_user_1_name ) convert_repository = self.test_db_util.get_repository_by_name_and_owner( convert_repository_name, common.test_user_1_name ) self.check_repository_dependency( repository=column_repository, depends_on_repository=convert_repository, depends_on_changeset_revision=None, changeset_revision=None, )
[docs] def test_0025_install_column_repository(self): """Install column_maker_0150.""" self.galaxy_login(email=common.admin_email, username=common.admin_username) column_repository = self.test_db_util.get_repository_by_name_and_owner( column_repository_name, common.test_user_1_name ) preview_strings_displayed = ["column_maker_0150", self.get_repository_tip(column_repository)] strings_displayed = ["Choose the tool panel section"] self.install_repository( column_repository_name, common.test_user_1_name, category_name, install_tool_dependencies=False, install_repository_dependencies=True, preview_strings_displayed=preview_strings_displayed, strings_displayed=strings_displayed, strings_not_displayed=[], post_submit_strings_displayed=["column_maker_0150", "New"], includes_tools_for_display_in_tool_panel=True, )
[docs] def test_0030_verify_installation_order(self): """Verify that convert_chars_0150 was installed before column_maker_0150.""" column_repository = self.test_db_util.get_installed_repository_by_name_owner( column_repository_name, common.test_user_1_name ) convert_repository = self.test_db_util.get_installed_repository_by_name_owner( convert_repository_name, common.test_user_1_name ) # Column maker was selected for installation, so convert chars should have been installed first, as reflected by the update_time field. assert ( column_repository.update_time > convert_repository.update_time ), "Error: column_maker_0150 shows an earlier update time than convert_chars_0150"