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)
        test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
        assert (
            test_user_1 is not None
        ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
        self.test_db_util.get_private_role(test_user_1)
        self.login(email=common.admin_email, username=common.admin_username)
        admin_user = self.test_db_util.get_user(common.admin_email)
        assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
        self.test_db_util.get_private_role(admin_user)

[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_id=self.security.encode_id(category.id),
            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_id=self.security.encode_id(category.id),
            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_id=self.security.encode_id(category.id),
            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)