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Source code for tool_shed.test.functional.test_0540_get_all_metadata_from_api

import logging

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

log = logging.getLogger(__name__)

repositories = dict(
    column=dict(
        name="column_maker_0540",
        description="Description for column_maker_0540",
        long_description="Long description for column_maker_0540",
    ),
    convert=dict(
        name="convert_chars_0540",
        description="Description for convert_chars_0540",
        long_description="Long description for convert_chars_0540",
    ),
    bwa=dict(
        name="package_bwa_0_5_9_0540",
        description="Description for package_bwa_0_5_9_0540",
        long_description="Long description for package_bwa_0_5_9_0540",
    ),
)

category_name = "Test 0540"
category_description = "Verify API endpoint to retrieve all metadata"

"""
1. Create repository column_maker_0540 as user user1.

2. Create repository convert_chars_0540 with dependency on column_maker_0540.

3. Create repository package_bwa_0_5_9_0540.

4. Create dependency on package_bwa_0_5_9_0540 for convert_chars_0540.

5. Load /api/repositories/convert_chars_0540.id/metadata and verify contents.
"""


[docs]class TestGetAllMetadata(ShedTwillTestCase): """Verify that the code correctly handles the repository admin role."""
[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_create_bwa_package_repository(self): """Create and populate package_bwa_0_5_9_0540.""" 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_bwa_0_5_9_0100 owned by user1. repository = self.get_or_create_repository( name=repositories["bwa"]["name"], description=repositories["bwa"]["description"], long_description=repositories["bwa"]["long_description"], owner=common.test_user_1_name, category=category, strings_displayed=[], ) assert repository is not None, f"Error creating repository {repositories['bwa']['name']}" self.upload_file( repository, filename="0540_files/package_bwa/tool_dependencies.xml", filepath=None, valid_tools_only=True, uncompress_file=False, remove_repo_files_not_in_tar=False, commit_message="Uploaded tool_dependencies.xml.", strings_displayed=["This repository currently contains a single file named <b>tool_dependencies.xml</b>"], strings_not_displayed=[], ) # Visit the manage repository page for package_bwa_0_5_9_0100. self.display_manage_repository_page( repository, strings_displayed=["Tool dependencies", "will not be", "to this repository"] )
[docs] def test_0010_create_convert_repository(self): """Create the convert_chars_0540 repository.""" category = self.create_category(name=category_name, description=category_description) repository = self.get_or_create_repository( name=repositories["convert"]["name"], description=repositories["convert"]["description"], long_description=repositories["convert"]["long_description"], owner=common.test_user_1_name, category=category, strings_displayed=[], ) assert repository is not None, f"Error creating repository {repositories['convert']['name']}" self.upload_file( repository, filename="0540_files/convert_chars/convert_chars.tar", filepath=None, valid_tools_only=True, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message="Uploaded column maker 1.0.", strings_displayed=[], strings_not_displayed=[], ) # Add a dependency on BWA. self.upload_file( repository, filename="0540_files/convert_chars/tool_dependencies.xml", filepath=None, valid_tools_only=True, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message="Uploaded column maker 1.0.", strings_displayed=[], strings_not_displayed=[], ) # Visit the manage repository page for convert_chars_0540. self.display_manage_repository_page(repository, strings_displayed=[repositories["bwa"]["name"]])
[docs] def test_0015_create_column_repository(self): """Create the column_maker_0540 repository.""" category = self.create_category(name=category_name, description=category_description) repository = self.get_or_create_repository( name=repositories["column"]["name"], description=repositories["column"]["description"], long_description=repositories["column"]["long_description"], owner=common.test_user_1_name, category=category, strings_displayed=[], ) assert repository is not None, f"Error creating repository {repositories['column']['name']}" self.upload_file( repository, filename="0540_files/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 1.0.", strings_displayed=[], strings_not_displayed=[], )
[docs] def test_0020_create_repository_dependency(self): """Make column_maker depend on convert_chars.""" repository = self.test_db_util.get_repository_by_name_and_owner( repositories["column"]["name"], common.test_user_1_name ) self.upload_file( repository, filename="0540_files/column_maker/repository_dependencies.xml", filepath=None, valid_tools_only=True, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message="Uploaded column maker 2.0.", strings_displayed=[], strings_not_displayed=[], )
[docs] def test_0025_verify_dependency_json(self): """ Load the API endpoint to retrieve all repository metadata and verify that all three repository names are displayed. """ repository = self.test_db_util.get_repository_by_name_and_owner( repositories["column"]["name"], common.test_user_1_name ) strings_displayed = [ repositories["column"]["name"], repositories["convert"]["name"], repositories["bwa"]["name"], ] self.fetch_repository_metadata(repository, strings_displayed=strings_displayed, strings_not_displayed=None)