From 92c8797fd17f3c895f95b4884d50d34364abe975 Mon Sep 17 00:00:00 2001 From: tcezard Date: Wed, 12 Jun 2024 20:43:52 +0100 Subject: [PATCH 1/3] Fix resume option --- .../run_release_in_embassy/run_release_for_species.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/eva-accession-release-automation/run_release_in_embassy/run_release_for_species.py b/eva-accession-release-automation/run_release_in_embassy/run_release_for_species.py index 57417710d..7d5eb45ee 100644 --- a/eva-accession-release-automation/run_release_in_embassy/run_release_for_species.py +++ b/eva-accession-release-automation/run_release_in_embassy/run_release_for_species.py @@ -147,7 +147,7 @@ def main(): argparse.add_argument("--taxonomy_id", help="ex: 9913") argparse.add_argument("--assembly_accessions", nargs='+', help="ex: GCA_000003055.3") argparse.add_argument("--release_version") - argparse.add_argument("--resume", default=False, + argparse.add_argument("--resume", default=False, action='store_true', help="Resume the nextflow pipeline for the specified taxonomy and assembly") args = argparse.parse_args() load_config() From 7c98b8c75ac677cde30be70e0f517a40b0200ff8 Mon Sep 17 00:00:00 2001 From: tcezard Date: Wed, 12 Jun 2024 20:44:07 +0100 Subject: [PATCH 2/3] Fix mongodb port --- .../run_release_in_embassy/run_release_for_assembly.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/eva-accession-release-automation/run_release_in_embassy/run_release_for_assembly.py b/eva-accession-release-automation/run_release_in_embassy/run_release_for_assembly.py index 85b6f3264..b19c5df08 100644 --- a/eva-accession-release-automation/run_release_in_embassy/run_release_for_assembly.py +++ b/eva-accession-release-automation/run_release_in_embassy/run_release_for_assembly.py @@ -39,7 +39,7 @@ def run_release_for_assembly(private_config_xml_file, profile, taxonomy_id, asse taxonomy_id, assembly_accession, release_species_inventory_table, release_version, assembly_release_folder) - release_command = 'java -Xmx{0}g -jar {1} --spring.config.location=file:{2} -Dspring.data.mongodb.port={3}'\ + release_command = 'java -Xmx{0}g -jar {1} --spring.config.location=file:{2} --spring.data.mongodb.port={3}'\ .format(memory, release_jar_path, release_properties_file, mongo_port) run_command_with_output("Running release pipeline for assembly: " + assembly_accession, release_command) exit_code = 0 From f855371ed1e9bf55aa3b2bf2712a3123a38af22f Mon Sep 17 00:00:00 2001 From: tcezard Date: Thu, 13 Jun 2024 09:02:55 +0100 Subject: [PATCH 3/3] Also Add a name to the workflow run to make it easier to identify in tower --- .../run_release_in_embassy/run_release_for_species.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/eva-accession-release-automation/run_release_in_embassy/run_release_for_species.py b/eva-accession-release-automation/run_release_in_embassy/run_release_for_species.py index 7d5eb45ee..eb4072afe 100644 --- a/eva-accession-release-automation/run_release_in_embassy/run_release_for_species.py +++ b/eva-accession-release-automation/run_release_in_embassy/run_release_for_species.py @@ -102,9 +102,11 @@ def run_release_for_species(taxonomy_id, release_assemblies, release_version, re workflow_file_path = get_run_release_for_assembly_nextflow() release_dir = get_assembly_release_folder(release_version, taxonomy_id, assembly_accession) nextflow_config = get_nextflow_config() + run_name = f'release_{release_version}_{taxonomy_id}_{assembly_accession}' workflow_command = ' '.join(( f"cd {release_dir} &&", f"{cfg.query('executable', 'nextflow')} run {workflow_file_path}", + f"-name {run_name}", f"-params-file {nextflow_params}", f'-c {nextflow_config}' if nextflow_config else '', '-resume' if resume else '',