galaxy/test/unit/files/_util.py

"""Utilities for unit test suite for galaxy.files."""
import os
import tempfile

from galaxy.files import (
    ConfiguredFileSources,
    ConfiguredFileSourcesConfig,
    DictFileSourcesUserContext,
)

TEST_USERNAME = "alice"
TEST_EMAIL = "alice@galaxyproject.org"


def serialize_and_recover(file_sources_o, user_context=None):
    as_dict = file_sources_o.to_dict(for_serialization=True, user_context=user_context)
    file_sources = ConfiguredFileSources.from_dict(as_dict)
    return file_sources


def find_file_a(dir_list):
    return find(dir_list, class_="File", name="a")


def find(dir_list, class_=None, name=None):
    for ent in dir_list:
        if class_ is not None and ent["class"] != class_:
            continue
        if name is not None and ent["name"] == name:
            return ent

    return None


def list_root(file_sources, uri, recursive, user_context=None):
    file_source_pair = file_sources.get_file_source_path(uri)
    file_source = file_source_pair.file_source
    res = file_source.list("/", recursive=recursive, user_context=user_context)
    return res


def list_dir(file_sources, uri, recursive, user_context=None):
    file_source_pair = file_sources.get_file_source_path(uri)
    file_source = file_source_pair.file_source
    print(file_source_pair.path)
    print(uri)
    res = file_source.list(file_source_pair.path, recursive=recursive, user_context=user_context)
    return res


def user_context_fixture(user_ftp_dir=None, role_names=None, group_names=None, is_admin=False):
    user_context = DictFileSourcesUserContext(
        username=TEST_USERNAME,
        email=TEST_EMAIL,
        user_ftp_dir=user_ftp_dir,
        preferences={
            "webdav|password": "secret1234",
            "dropbox|access_token": os.environ.get("GALAXY_TEST_DROPBOX_ACCESS_TOKEN"),
            "googledrive|client_id": os.environ.get("GALAXY_TEST_GOOGLE_DRIVE_CLIENT_ID"),
            "googledrive|client_secret": os.environ.get("GALAXY_TEST_GOOGLE_DRIVE_CLIENT_SECRET"),
            "googledrive|access_token": os.environ.get("GALAXY_TEST_GOOGLE_DRIVE_ACCESS_TOKEN"),
            "googledrive|refresh_token": os.environ.get("GALAXY_TEST_GOOGLE_DRIVE_REFRESH_TOKEN"),
            "googlecloudstorage|project": os.environ.get("GALAXY_TEST_GCS_PROJECT"),
            "googlecloudstorage|bucket_name": os.environ.get("GALAXY_TEST_GCS_BUCKET"),
            "googlecloudstorage|client_id": os.environ.get("GALAXY_TEST_GCS_CLIENT_ID"),
            "googlecloudstorage|client_secret": os.environ.get("GALAXY_TEST_GCS_CLIENT_SECRET"),
            "googlecloudstorage|access_token": os.environ.get("GALAXY_TEST_GCS_ACCESS_TOKEN"),
            "googlecloudstorage|refresh_token": os.environ.get("GALAXY_TEST_GCS_REFRESH_TOKEN"),
            "onedata|provider_host": os.environ.get("GALAXY_TEST_ONEDATA_PROVIDER_HOST"),
            "onedata|access_token": os.environ.get("GALAXY_TEST_ONEDATA_ACCESS_TOKEN"),
            "basespace|client_id": os.environ.get("GALAXY_TEST_ONEDATA_CLIENT_ID"),
            "basespace|client_secret": os.environ.get("GALAXY_TEST_ONEDATA_CLIENT_SECRET"),
            "basespace|access_token": os.environ.get("GALAXY_TEST_ONEDATA_ACCESS_TOKEN"),
        },
        role_names=role_names or set(),
        group_names=group_names or set(),
        is_admin=is_admin,
    )
    return user_context


def realize_to_temp_file(file_sources, uri, user_context=None):
    file_source_path = file_sources.get_file_source_path(uri)
    with tempfile.NamedTemporaryFile(mode="r") as temp:
        file_source_path.file_source.realize_to(file_source_path.path, temp.name, user_context=user_context)
        with open(temp.name) as f:
            realized_contents = f.read()
            return realized_contents


def assert_realizes_as(file_sources, uri, expected, user_context=None):
    realized_contents = realize_to_temp_file(file_sources, uri, user_context=user_context)
    if realized_contents != expected:
        message = "Expected to realize contents at [{}] as [{}], instead found [{}]".format(
            uri,
            expected,
            realized_contents,
        )
        raise AssertionError(message)


def assert_realizes_contains(file_sources, uri, expected, user_context=None):
    realized_contents = realize_to_temp_file(file_sources, uri, user_context=user_context)
    if expected not in realized_contents:
        message = "Expected to realize contents at [{}] to contain [{}], instead found [{}]".format(
            uri,
            expected,
            realized_contents,
        )
        raise AssertionError(message)


def assert_realizes_throws_exception(file_sources, uri, user_context=None) -> Exception:
    exception = None
    try:
        realize_to_temp_file(file_sources, uri, user_context=user_context)
    except Exception as e:
        exception = e
    assert exception
    return exception


def write_from(file_sources, uri, content, user_context=None):
    file_source_path = file_sources.get_file_source_path(uri)
    with tempfile.NamedTemporaryFile(mode="w") as f:
        f.write(content)
        f.flush()
        file_source_path.file_source.write_from(file_source_path.path, f.name, user_context=user_context)


def configured_file_sources(conf_file):
    file_sources_config = ConfiguredFileSourcesConfig()
    return ConfiguredFileSources(file_sources_config, conf_file=conf_file)


def assert_simple_file_realize(conf_file, recursive=False, filename="a", contents="a\n", contains=False):
    user_context = user_context_fixture()
    file_sources = configured_file_sources(conf_file)
    file_source_pair = file_sources.get_file_source_path("gxfiles://test1")

    assert file_source_pair.path == "/"
    file_source = file_source_pair.file_source
    res = file_source.list("/", recursive=recursive, user_context=user_context)
    a_file = find(res, class_="File", name=filename)
    assert a_file

    if contains:
        assert_realizes_contains(file_sources, f"gxfiles://test1/{filename}", contents, user_context=user_context)
    else:
        assert_realizes_as(file_sources, f"gxfiles://test1/{filename}", contents, user_context=user_context)