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._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._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)