diff --git a/eva-accession-release-automation/publish_release_to_ftp/publish_release_files_to_ftp.py b/eva-accession-release-automation/publish_release_to_ftp/publish_release_files_to_ftp.py index fddf06bca..5a6a2c2da 100644 --- a/eva-accession-release-automation/publish_release_to_ftp/publish_release_files_to_ftp.py +++ b/eva-accession-release-automation/publish_release_to_ftp/publish_release_files_to_ftp.py @@ -20,12 +20,14 @@ import os from argparse import ArgumentParser +from ebi_eva_common_pyutils.config import cfg + from publish_release_to_ftp.create_assembly_name_symlinks import create_assembly_name_symlinks from ebi_eva_common_pyutils.command_utils import run_command_with_output from ebi_eva_common_pyutils.logger import logging_config from ebi_eva_internal_pyutils.metadata_utils import get_metadata_connection_handle from ebi_eva_internal_pyutils.pg_utils import get_all_results_for_query -from run_release_in_embassy.run_release_for_species import get_common_release_properties +from run_release_in_embassy.run_release_for_species import load_config from run_release_in_embassy.release_metadata import release_vcf_file_categories, release_text_file_categories by_assembly_folder_name = "by_assembly" @@ -42,16 +44,15 @@ class ReleaseProperties: - def __init__(self, common_release_properties_file): + def __init__(self, release_version): """ Get release properties from common release properties file """ - common_release_properties = get_common_release_properties(common_release_properties_file) - self.private_config_xml_file = common_release_properties["private-config-xml-file"] - self.release_version = common_release_properties["release-version"] - self.release_species_inventory_table = common_release_properties["release-species-inventory-table"] - self.staging_release_folder = common_release_properties["release-folder"] - self.public_ftp_release_base_folder = common_release_properties["public-ftp-release-base-folder"] + self.private_config_xml_file = cfg["private-config-xml-file"] + self.release_version = release_version + self.release_species_inventory_table = cfg["inventory_table"] + self.staging_release_folder = cfg["release_output"] + self.public_ftp_release_base_folder = cfg["public_ftp_release_base_folder"] self.public_ftp_current_release_folder = os.path.join(self.public_ftp_release_base_folder, f"release_{self.release_version}") self.public_ftp_previous_release_folder = os.path.join(self.public_ftp_release_base_folder, @@ -289,8 +290,8 @@ def create_species_folder(release_properties, species_current_release_folder_nam f"rm -rf {species_current_release_folder_path} && mkdir {species_current_release_folder_path}") -def publish_release_files_to_ftp(common_release_properties_file, taxonomy_id): - release_properties = ReleaseProperties(common_release_properties_file) +def publish_release_files_to_ftp(release_version, taxonomy_id): + release_properties = ReleaseProperties(release_version) create_requisite_folders(release_properties) # Release README, known issues etc., publish_release_top_level_files_to_ftp(release_properties) @@ -333,13 +334,14 @@ def publish_release_files_to_ftp(common_release_properties_file, taxonomy_id): def main(): argparse = ArgumentParser(description='Publish release files to FTP') - argparse.add_argument('--common_release_properties_file', required=True, type=str, - help='ex: /path/to/release/properties.yml') + argparse.add_argument("--release_version", type=int, required=True) argparse.add_argument('--taxonomy_id', required=True, type=int, help='ex: 9913') args = argparse.parse_args() + load_config() + logging_config.add_stdout_handler() - publish_release_files_to_ftp(args.common_release_properties_file, args.taxonomy_id) + publish_release_files_to_ftp(args.release_version, args.taxonomy_id) if __name__ == "__main__":