comparison data_manager/bakta_build_database.py @ 11:c50e8b4f74d7 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 572bbceeba9a22cdb591d526abda362595f8f0c4

10:9c65e5da43e2

import sys
import tarfile
from datetime import datetime
from pathlib import Path

import bakta.constants as bc
import bakta.utils as bu
import requests
from alive_progress import alive_bar


class GetBaktaDatabaseInfo:

        self.db_url = None
        self.data_table_entry = None
        self.data_table_name = data_table_name
        self.db_name = db_name
        self.db_version = db_version

    def get_data_table_format(self):
        """
        Build a data table format for galaxy
        using the bakta database information

        db_version: a string of the version number
        in the galaxy wrapper list or just latest
        return: info for the select or the latest bakta db version
        """
        try:
            with requests.get(bc.DB_VERSIONS_URL) as resp:
                versions = json.loads(resp.content)
        except IOError as e:
            print(e, file=sys.stderr)
            raise e
        else:

                         dbkey=bakta_database_info['date'],
                         database_record=bakta_database_info['record'],
                         bakta_version=str(
                             f"{bakta_database_info['software-min']['major']}."
                             f"{bakta_database_info['software-min']['minor']}"
                         ), path=output_path)
        self.bakta_table_list["data_tables"][self.data_table_name] = data_info
        return self.bakta_table_list


class InstallBaktaDatabase(GetBaktaDatabaseInfo):

        self.md5 = None
        self.db_dir = db_dir
        self.db_name = db_name
        self.tarball_name = tarball_name
        self.tarball_path = None
        bu.test_dependency(bu.DEPENDENCY_AMRFINDERPLUS)

    def download(self):
        self.db_name = f'{self.db_name}_{self.db_version}'
        bakta_path = Path(self.db_dir).joinpath(self.tarball_name)
        try:

                            help='Select the database version '
                                 '(major and minor eg. 4.0),'
                                 'default is the latest version',
                            default="latest",
                            required=True)
    return arg_parser.parse_args()


def main():
    all_args = parse_arguments()

    os.makedirs(target_dir)

    # init the class to download bakta db
    bakta_upload = InstallBaktaDatabase()
    # extract the version
    bakta_db = bakta_upload.fetch_db_versions(
        db_version=all_args.database_version)
    # update the path for galaxy
    bakta_upload.db_dir = target_dir
    # download the database
    print(bakta_db)
    bakta_upload.download()
    # check md5 sum
    bakta_upload.calc_md5_sum()
    # untar db
    bakta_extracted_path = bakta_upload.untar()
    # update for amrfinderplus
    bakta_upload.update_amrfinderplus_db()
    # make the data_manager metadata
    bakta_data_manager = bakta_upload.get_data_manager(bakta_database_info=bakta_db, output_path=bakta_extracted_path)
    with open(all_args.data_manager_json, 'w') as fh:
        json.dump(bakta_data_manager, fh, indent=2, sort_keys=True)


if __name__ == '__main__':
    main()

11:c50e8b4f74d7

import sys
import tarfile
from datetime import datetime
from pathlib import Path

import requests
from alive_progress import alive_bar


class GetBaktaDatabaseInfo:

        self.db_url = None
        self.data_table_entry = None
        self.data_table_name = data_table_name
        self.db_name = db_name
        self.db_version = db_version
        self.DB_VERSIONS_URL = 'https://raw.githubusercontent.com/oschwengers/bakta/master/db-versions.json'

    def get_data_table_format(self):
        """
        Build a data table format for galaxy
        using the bakta database information

        db_version: a string of the version number
        in the galaxy wrapper list or just latest
        return: info for the select or the latest bakta db version
        """
        try:
            with requests.get(self.DB_VERSIONS_URL) as resp:
                versions = json.loads(resp.content)
        except IOError as e:
            print(e, file=sys.stderr)
            raise e
        else:

                         dbkey=bakta_database_info['date'],
                         database_record=bakta_database_info['record'],
                         bakta_version=str(
                             f"{bakta_database_info['software-min']['major']}."
                             f"{bakta_database_info['software-min']['minor']}"
                         ),
                         path=output_path)
        self.bakta_table_list["data_tables"][self.data_table_name] = data_info
        return self.bakta_table_list


class InstallBaktaDatabase(GetBaktaDatabaseInfo):

        self.md5 = None
        self.db_dir = db_dir
        self.db_name = db_name
        self.tarball_name = tarball_name
        self.tarball_path = None

    def download(self):
        self.db_name = f'{self.db_name}_{self.db_version}'
        bakta_path = Path(self.db_dir).joinpath(self.tarball_name)
        try:

                            help='Select the database version '
                                 '(major and minor eg. 4.0),'
                                 'default is the latest version',
                            default="latest",
                            required=True)
    arg_parser.add_argument("-t", "--test", action='store_true',
                            help="option to test the script with an empty database")
    return arg_parser.parse_args()


def main():
    all_args = parse_arguments()

    os.makedirs(target_dir)

    # init the class to download bakta db
    bakta_upload = InstallBaktaDatabase()
    # extract the version
    if all_args.test is True:
        bakta_db = bakta_upload.fetch_db_versions(
            db_version="test")
    else:
        bakta_db = bakta_upload.fetch_db_versions(
            db_version=all_args.database_version)
    # update the path for galaxy
    bakta_upload.db_dir = target_dir
    # download the database
    bakta_upload.download()
    # check md5 sum
    bakta_upload.calc_md5_sum()
    # untar db
    bakta_extracted_path = bakta_upload.untar()
    # update for amrfinderplus
    bakta_upload.update_amrfinderplus_db()
    # make the data_manager metadata
    bakta_data_manager = bakta_upload.get_data_manager(bakta_database_info=bakta_db, output_path=bakta_extracted_path)
    with open(all_args.data_manager_json, 'w') as fh:
        json.dump(bakta_data_manager, fh, sort_keys=True)


if __name__ == '__main__':
    main()