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EVA-3568 - Update publish_release_files_to_ftp.py to use the new config file #450

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merged 2 commits into from
Jun 3, 2024
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EVA-3568 - Update publish_release_files_to_ftp.py to use the new config file #450

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c47bab2
Update publish_release_files_to_ftp.py to use the new config file
tcezard May 24, 2024
ad5b37b
Correct link to maven file
tcezard May 24, 2024
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31 changes: 17 additions & 14 deletions eva-accession-release-automation/publish_release_to_ftp/publish_release_files_to_ftp.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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"
Expand All @@ -42,16 +44,16 @@


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.query('maven', 'settings_file')
self.profile = cfg.query('maven', 'environment')
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,
Expand Down Expand Up @@ -289,14 +291,14 @@ 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)

with get_metadata_connection_handle(
"production_processing", release_properties.private_config_xml_file) as metadata_connection_handle:
release_properties.profile, release_properties.private_config_xml_file) as metadata_connection_handle:
assemblies_to_process = get_release_assemblies_info_for_taxonomy(taxonomy_id, release_properties,
metadata_connection_handle)
species_has_unmapped_data = "Unmapped" in set([assembly_info["assembly_accession"] for assembly_info in
Expand Down Expand Up @@ -333,13 +335,14 @@ 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__":
Expand Down
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