fix path to inventory_table in config + other fixes

Update the release readme files
EBIvariation · Jun 27, 2024 · 0cad932 · 0cad932
1 parent 203b559
commit 0cad932
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Showing 4 changed files with 14 additions and 5 deletions.
diff --git a/eva-accession-release-automation/publish_release_to_ftp/README_release_changelog.txt b/eva-accession-release-automation/publish_release_to_ftp/README_release_changelog.txt
@@ -1,5 +1,11 @@
 This document describes technical changes associated with the EVA RefSNP release.
 
+EVA RefSNP release 6
+====================
+
+- No significant changes compare to release 5
+
+
 EVA RefSNP release 5
 ====================
 

diff --git a/eva-accession-release-automation/publish_release_to_ftp/README_release_general_info.txt b/eva-accession-release-automation/publish_release_to_ftp/README_release_general_info.txt
@@ -1,4 +1,4 @@
-EVA RefSNP release 5
+EVA RefSNP release 6
 
 Feedback
 ==================================

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
@@ -27,7 +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.run_release_for_species import load_config
+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
 
 by_assembly_folder_name = "by_assembly"
@@ -51,8 +51,8 @@ def __init__(self, release_version):
         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.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_current_release_folder = os.path.join(self.public_ftp_release_base_folder,
                                                               f"release_{self.release_version}")

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
@@ -16,6 +16,8 @@
 
 import os
 from functools import lru_cache
+from random import choice
+from string import ascii_lowercase
 
 import yaml
 from ebi_eva_common_pyutils.command_utils import run_command_with_output
@@ -102,7 +104,8 @@ 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}'
+            random_string = ''.join(choice(ascii_lowercase) for i in range(4))
+            run_name = f'release_{release_version}_{taxonomy_id}_{assembly_accession}_{random_string}'.replace('.', '_')
             workflow_command = ' '.join((
                 f"cd {release_dir} &&",
                 f"{cfg.query('executable', 'nextflow')} run {workflow_file_path}",