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Source code for tool_shed.test.functional.test_0550_metadata_updated_dependencies

import logging

from ..base.twilltestcase import (
    common,
    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 = 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=[], ) assert freebayes is not None, f"Error creating freebayes {repositories['freebayes']['name']}" self.upload_file( freebayes, filename="0550_files/package_freebayes_1_0550.tgz", filepath=None, valid_tools_only=True, uncompress_file=False, remove_repo_files_not_in_tar=False, commit_message="Uploaded.", strings_displayed=["has been successfully uploaded to the repository", "contains a single file"], strings_not_displayed=None, ) # Visit the manage repository page for package_freebayes_0_5_9_0100. self.display_manage_repository_page( freebayes, 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 = 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=[], ) assert samtools is not None, f"Error creating samtools {repositories['samtools']['name']}" self.upload_file( samtools, filename="0550_files/package_samtools_1_0550.tgz", filepath=None, valid_tools_only=True, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message="Uploaded samtools 1.0.", strings_displayed=["has been successfully uncompressed and uploaded to the repository"], strings_not_displayed=[], )
[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=[], ) assert repository is not None, f"Error creating repository {repositories['filtering']['name']}" self.upload_file( repository, filename="0550_files/filtering_1.0.tgz", filepath=None, valid_tools_only=True, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message="Uploaded filtering 1.0.", strings_displayed=["has been successfully uncompressed and uploaded to the repository"], strings_not_displayed=[], )
[docs] def test_0020_check_repository_dependency(self): """Make filtering depend on samtools and freebayes.""" freebayes = self.test_db_util.get_repository_by_name_and_owner( repositories["freebayes"]["name"], common.test_user_1_name ) samtools = self.test_db_util.get_repository_by_name_and_owner( repositories["samtools"]["name"], common.test_user_1_name ) filtering = self.test_db_util.get_repository_by_name_and_owner( repositories["filtering"]["name"], common.test_user_1_name ) strings_displayed = [self.security.encode_id(freebayes.id), self.security.encode_id(samtools.id)] 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.test_db_util.get_repository_by_name_and_owner( repositories["freebayes"]["name"], common.test_user_1_name ) samtools = self.test_db_util.get_repository_by_name_and_owner( repositories["samtools"]["name"], common.test_user_1_name ) filtering = self.test_db_util.get_repository_by_name_and_owner( repositories["filtering"]["name"], common.test_user_1_name ) self.upload_file( freebayes, filename="0550_files/package_freebayes_2_0550.tgz", filepath=None, valid_tools_only=True, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message="Uploaded freebayes 2.0.", strings_displayed=["has been successfully uncompressed and uploaded to the repository"], strings_not_displayed=[], ) self.upload_file( samtools, filename="0550_files/package_samtools_2_0550.tgz", filepath=None, valid_tools_only=True, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message="Uploaded samtools 2.0.", strings_displayed=["has been successfully uncompressed and uploaded to the repository"], strings_not_displayed=[], ) strings_displayed = [ repositories["freebayes"]["name"], repositories["samtools"]["name"], repositories["filtering"]["name"], ] self.fetch_repository_metadata(filtering, strings_displayed=strings_displayed, strings_not_displayed=None)