comparison data_manager/pangolearn_dm.py @ 5:29c738066906 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolearn commit b12eb7c784ce8e0f9b775530e710e47088711f76"

4:6e24e79d3d69

            ret.append(release)

    return ret


def download_and_unpack(url, output_directory):
    response = requests.get(url)
    if response.status_code == 200:
        tmp_filename = url.split("/")[-1]
        tmpfile = open(tmp_filename, "wb")
        tmpfile.write(response.content)
        tmpfile.close()
        shutil.copy(tmp_filename, "/tmp")
        tf = tarfile.open(tmp_filename)
        pl_path = tf.next().name
        tf.extractall(output_directory)
        os.unlink(tmp_filename)
        os.rename(
            output_directory + "/" + pl_path + "/" + "pangoLEARN",
            output_directory + "/" + tmp_filename,
        )
        shutil.rmtree(output_directory + "/" + pl_path)
        return tmp_filename
    else:
        response.raise_for_status()

        release
        for release in releases
        if release["tag_name"] not in existing_release_tags
    ]
    for release in releases_to_download:
        fname = download_and_unpack(release["tarball_url"], output_directory)
        if args.pangolearn_format_version is not None:
            version = args.pangolearn_format_version
        else:
            # 2021-05-27 was the first release of pangoLEARN for pangolin 3, which changed DB format
            if release["date"] >= datetime.datetime(2021, 5, 27):
                version = '3.0'
            else:
                version = '1.0'
        data_manager_dict["data_tables"][args.datatable_name].append(
            dict(
                value=release["tag_name"],
                description=release["name"],
                format_version=version,

5:29c738066906

            ret.append(release)

    return ret


def download_and_unpack(url, output_directory, v3datatree=True):
    response = requests.get(url)
    if response.status_code == 200:
        tmp_filename = url.split("/")[-1]
        tmpfile = open(tmp_filename, "wb")
        tmpfile.write(response.content)
        tmpfile.close()
        shutil.copy(tmp_filename, "/tmp")
        tf = tarfile.open(tmp_filename)
        pl_path = os.path.join(output_directory, tf.next().name)
        tf.extractall(output_directory)
        os.unlink(tmp_filename)
        pangolearn_unpacked_dir = os.path.join(pl_path, "pangoLEARN")
        if v3datatree:
            # pangolin v3 expects a datadir with the entire pangoLEARN
            # subfolder in it.
            # In addition, it will only use the data if the __init__.py file
            # contained within that subfolder declares a __version__ that is
            # newer than the version installed with pangolin.
            pangolearn_dir = os.path.join(
                output_directory, tmp_filename, "pangoLEARN"
            )
            os.mkdir(os.path.dirname(pangolearn_dir))
            # rewrite the __init__.py file and make the __version__ string
            # appear newer than anything that might come with pangolin by
            # prepending a "v" to it.
            pangolearn_init = open(
                os.path.join(pangolearn_unpacked_dir, "__init__.py")
            ).readlines()
            with open(
                os.path.join(pangolearn_unpacked_dir, "__init__.py"), "w"
            ) as o:
                for line in pangolearn_init:
                    if line.startswith('__version__ = "'):
                        line = line.replace(
                            '__version__ = "', '__version__ = "v'
                        )
                    o.write(line)
        else:
            # Earlier versions of pangolin expect a datadir with just the
            # contents of the downloaded pangoLEARN subfolder in it and don't
            # care about the declared version in __init__.py.
            pangolearn_dir = os.path.join(
                output_directory, tmp_filename
            )
        os.rename(
            pangolearn_unpacked_dir,
            pangolearn_dir
        )
        shutil.rmtree(pl_path)
        return tmp_filename
    else:
        response.raise_for_status()

        release
        for release in releases
        if release["tag_name"] not in existing_release_tags
    ]
    for release in releases_to_download:
        if args.pangolearn_format_version is not None:
            version = args.pangolearn_format_version
        else:
            # 2021-05-27 was the first release of pangoLEARN for pangolin 3, which changed DB format
            if release["date"] >= datetime.datetime(2021, 5, 27):
                version = '3.0'
            else:
                version = '1.0'
        fname = download_and_unpack(
            release["tarball_url"],
            output_directory,
            v3datatree=version == '3.0'
        )
        data_manager_dict["data_tables"][args.datatable_name].append(
            dict(
                value=release["tag_name"],
                description=release["name"],
                format_version=version,