From fa35ef524b683b111f40757f6e64636a9cf83574 Mon Sep 17 00:00:00 2001 From: tcezard Date: Thu, 27 Jun 2024 21:16:15 +0100 Subject: [PATCH] additional fixes --- .../publish_release_to_ftp/publish_release_files_to_ftp.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) 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 d4c75b589..63b224380 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 @@ -27,6 +27,7 @@ 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.release_common_utils import get_release_folder_name from run_release_in_embassy.run_release_for_species import load_config, get_release_folder from run_release_in_embassy.release_metadata import release_vcf_file_categories, release_text_file_categories @@ -53,7 +54,7 @@ def __init__(self, release_version): self.release_version = release_version self.release_species_inventory_table = cfg.query('release', 'inventory_table') self.staging_release_folder = get_release_folder(release_version) - self.public_ftp_release_base_folder = cfg["public_ftp_release_base_folder"] + self.public_ftp_release_base_folder = cfg.query('release', '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, @@ -147,7 +148,7 @@ def recreate_public_release_species_assembly_folder(assembly_accession, public_r def copy_current_assembly_data_to_ftp(current_release_assembly_info, release_properties, public_release_species_assembly_folder): assembly_accession = current_release_assembly_info["assembly_accession"] - species_release_folder_name = current_release_assembly_info["release_folder_name"] + species_release_source_folder_name = get_release_folder_name(current_release_assembly_info['taxonomy']) md5sum_output_file = os.path.join(public_release_species_assembly_folder, "md5checksums.txt") run_command_with_output(f"Removing md5 checksum file {md5sum_output_file} for assembly if it exists...", f"rm -f {md5sum_output_file}") @@ -155,7 +156,7 @@ def copy_current_assembly_data_to_ftp(current_release_assembly_info, release_pro recreate_public_release_species_assembly_folder(assembly_accession, public_release_species_assembly_folder) for filename in get_release_file_list_for_assembly(current_release_assembly_info): - source_file_path = os.path.join(release_properties.staging_release_folder, species_release_folder_name, + source_file_path = os.path.join(release_properties.staging_release_folder, species_release_source_folder_name, assembly_accession, filename) run_command_with_output(f"Copying {filename} to {public_release_species_assembly_folder}...", f"cp {source_file_path} {public_release_species_assembly_folder}")