Source code for tool_shed.test.functional.test_0550_metadata_updated_dependencies

import logging

from ..base import common
from ..base.twilltestcase import ShedTwillTestCase

log = logging.getLogger(__name__)

repositories = dict(
    freebayes=dict(
        name="package_freebayes_0550",
        description="Description for package_freebayes_0550",
        long_description="Long description for package_freebayes_0550",
    ),
    samtools=dict(
        name="package_samtools_0550",
        description="Description for package_samtools_0550",
        long_description="Long description for package_samtools_0550",
    ),
    filtering=dict(
        name="filtering_0550",
        description="Description for filtering_0550",
        long_description="Long description for filtering_0550",
    ),
)

category_name = "Test 0550"
category_description = "Verify metadata updates"

"""
1. Create repository package_freebayes_0550.

2. Create repository package_samtools_0550.

3. Create repository filtering_0550.

4. Create dependency on package_freebayes_0550 for filtering_0550.

5. Create dependency on package_samtools_0550 for filtering_0550.

6. Update package_freebayes_0550 and package_samtools_0550.

5. Load /api/repositories/{filtering_0550}.id/metadata and verify contents.
"""


[docs]class TestGetUpdatedMetadata(ShedTwillTestCase): """Verify that updated repositories still have correct dependency links."""
[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_freebayes_repository(self): """Create and populate package_freebayes_0550.""" category = self.create_category(name=category_name, description=category_description) self.login(email=common.test_user_1_email, username=common.test_user_1_name) # Create a repository named package_freebayes_0550 owned by user1. freebayes_repository = self.get_or_create_repository( name=repositories["freebayes"]["name"], description=repositories["freebayes"]["description"], long_description=repositories["freebayes"]["long_description"], owner=common.test_user_1_name, category=category, strings_displayed=[], ) self.commit_tar_to_repository( freebayes_repository, "0550_files/package_freebayes_1_0550.tgz", ) if not self.is_v2: # Visit the manage repository page for package_freebayes_0_5_9_0100. self.display_manage_repository_page( freebayes_repository, strings_displayed=["Tool dependencies", "will not be", "to this repository"] )
[docs] def test_0010_create_samtools_repository(self): """Create and populate the package_samtools_0550 repository.""" category = self.create_category(name=category_name, description=category_description) samtools_repository = self.get_or_create_repository( name=repositories["samtools"]["name"], description=repositories["samtools"]["description"], long_description=repositories["samtools"]["long_description"], owner=common.test_user_1_name, category=category, strings_displayed=[], ) self.commit_tar_to_repository( samtools_repository, "0550_files/package_samtools_1_0550.tgz", commit_message="Uploaded samtools 1.0.", )
[docs] def test_0015_create_filtering_repository(self): """Create the filtering_0550 repository.""" category = self.create_category(name=category_name, description=category_description) repository = self.get_or_create_repository( name=repositories["filtering"]["name"], description=repositories["filtering"]["description"], long_description=repositories["filtering"]["long_description"], owner=common.test_user_1_name, category=category, strings_displayed=[], ) self.commit_tar_to_repository( repository, "0550_files/filtering_1.0.tgz", commit_message="Uploaded filtering 1.0.", )
[docs] def test_0020_check_repository_dependency(self): """Make filtering depend on samtools and freebayes.""" freebayes = self._get_repository_by_name_and_owner(repositories["freebayes"]["name"], common.test_user_1_name) samtools = self._get_repository_by_name_and_owner(repositories["samtools"]["name"], common.test_user_1_name) filtering = self._get_repository_by_name_and_owner(repositories["filtering"]["name"], common.test_user_1_name) strings_displayed = [freebayes.id, samtools.id] if not self.is_v2: self.display_manage_repository_page(filtering, strings_displayed=strings_displayed)
[docs] def test_0025_update_dependent_repositories(self): """ Update freebayes and samtools, load the API endpoint again. """ freebayes = self._get_repository_by_name_and_owner(repositories["freebayes"]["name"], common.test_user_1_name) samtools = self._get_repository_by_name_and_owner(repositories["samtools"]["name"], common.test_user_1_name) filtering = self._get_repository_by_name_and_owner(repositories["filtering"]["name"], common.test_user_1_name) self.commit_tar_to_repository( freebayes, "0550_files/package_freebayes_2_0550.tgz", commit_message="Uploaded freebayes 2.0.", ) self.commit_tar_to_repository( samtools, "0550_files/package_samtools_2_0550.tgz", commit_message="Uploaded samtools 2.0.", ) strings_displayed = [ repositories["freebayes"]["name"], repositories["samtools"]["name"], repositories["filtering"]["name"], ] self.fetch_repository_metadata(filtering, strings_displayed=strings_displayed, strings_not_displayed=None)