Merge pull request #453 from tcezard/Fix_Release_port

Fix release port
EBIvariation · Jun 13, 2024 · 95d2b5b · 95d2b5b
2 parents a593333 + f855371
commit 95d2b5b
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Showing 2 changed files with 4 additions and 2 deletions.
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
@@ -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

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
@@ -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 '',
@@ -147,7 +149,7 @@ 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()