Support multiple status

eva-accession-release-automation/run_release_in_embassy/release_metadata.py

@@ -92,11 +92,23 @@ def get_release_inventory_info_for_assembly(taxonomy_id, assembly_accession, rel
     return results[0][0]
 
 
-def get_release_pending(release_species_inventory_table, metadata_connection_handle):
-    results = get_all_results_for_query(metadata_connection_handle,
-                                        "select taxonomy, assembly_accession, release_version from {0} "
-                                        "where should_be_released "
-                                        "and num_rs_to_release > 0"
-                                        "ORDER BY release_version, taxonomy, assembly_accession"
-                                        .format(release_species_inventory_table))
+def get_release_pending(release_species_inventory_table, metadata_connection_handle, status=None):
+    def format_status(status_list):
+        return f"({str(status_list).strip('[]')})"
+
+    if 'Pending' in status:
+        status.remove('Pending')
+        if status:
+            status_statement = f"and (release_status in {format_status(status)} or release_status is null)"
+        else:
+            status_statement = f"and release_status is null"
+    else:
+        status_statement = f"and release_status in {format_status(status)}"
+
+    query = (f"select taxonomy, assembly_accession, release_version from {release_species_inventory_table} "
+              "where should_be_released "
+              "and num_rs_to_release > 0 "
+              f"{status_statement}" if status_statement else ''
+              "ORDER BY release_version, taxonomy, assembly_accession")
+    results = get_all_results_for_query(metadata_connection_handle, query)
     yield results

eva-accession-release-automation/run_release_in_embassy/run_release_for_species.py

@@ -106,15 +106,15 @@ def run_release_for_species(taxonomy_id, release_assemblies, release_version, re
             run_command_with_output(f"Running workflow file {workflow_file_path}", workflow_command)
 
 
-def list_pending_release():
+def list_pending_release(status):
     private_config_xml_file = cfg.query("maven", "settings_file")
     profile = cfg.query("maven", "environment")
     release_species_inventory_table = cfg.query('release', 'inventory_table')
     with get_metadata_connection_handle(profile, private_config_xml_file) as metadata_connection_handle:
         header = ['taxonomy', 'assembly_accession', 'release_version']
         table = []
         for taxonomy, assembly_accession, release_version in get_release_pending(release_species_inventory_table,
-                                                                                 metadata_connection_handle):
+                                                                                 metadata_connection_handle, status):
             table.append((taxonomy, assembly_accession, release_version))
         pretty_print(header, table)
 
@@ -129,7 +129,9 @@ def load_config(*args):
 
 def main():
     argparse = ArgumentParser()
-    argparse.add_argument("--list", help="Generate the list of species and assembly that needs to be released", action='store_true', default=False)
+    argparse.add_argument("--list", nargs='+',
+                          help="Generate the list of species and assembly that needs to be released",
+                          choices=['Pending', 'Started', 'Completed'])
     argparse.add_argument("--taxonomy_id", help="ex: 9913", required=True)
     argparse.add_argument("--assembly_accessions", nargs='+', help="ex: GCA_000003055.3")
     argparse.add_argument("--release_version", required=True)
@@ -139,7 +141,7 @@ def main():
     load_config()
     logging_config.add_stdout_handler()
     if args.list:
-        list_pending_release()
+        list_pending_release(args.list)
     else:
         run_release_for_species(args.taxonomy_id, args.assembly_accessions, args.release_version, args.resume)