Ena add address (#2965)

* Add address

# Conflicts:
#	ena-submission/scripts/create_assembly.py

* Fix address parsing

* fix tests

* fix tests

(cherry picked from commit 673786c)

* log error

ena-submission/scripts/create_assembly.py

@@ -7,6 +7,7 @@
 import click
 import pytz
 import yaml
+from call_loculus import get_group_info
 from ena_submission_helper import (
     CreationResult,
     create_chromosome_list,
@@ -134,6 +135,17 @@ def create_manifest_object(
     sample_accession = sample_table_entry["result"]["ena_sample_accession"]
     study_accession = project_table_entry["result"]["bioproject_accession"]
 
+    address_string = project_table_entry["center_name"]
+    if config.is_broker:
+        try:
+            group_info = get_group_info(config, project_table_entry["group_id"])[0]["group"]
+            address = group_info["address"]
+            address_string = (f'{address.get("line1", "")}, {address.get("line2", "")}, '
+                f'{address.get("city", "")}, {address.get("state", "")}, '
+                f'{address.get("postalCode", "")}, {address.get("country")}')
+        except Exception as e:
+            logger.error(f"Was unable to create address, setting address to center_name due to {e}")
+
     metadata = submission_table_entry["metadata"]
     unaligned_nucleotide_sequences = submission_table_entry["unaligned_nucleotide_sequences"]
     organism_metadata = config.organisms[group_key["organism"]]["enaDeposition"]
@@ -205,6 +217,7 @@ def create_manifest_object(
         description=description,
         moleculetype=moleculetype,
         authors=authors,
+        address=address_string,
     )
 
 

ena-submission/scripts/test_ena_submission.py

@@ -240,7 +240,10 @@ def test_create_manifest(self):
         study_accession = "Test Study Accession"
         sample_accession = "Test Sample Accession"
         results_in_sample_table = {"result": {"ena_sample_accession": sample_accession}}
-        results_in_project_table = {"result": {"bioproject_accession": study_accession}}
+        results_in_project_table = {
+            "result": {"bioproject_accession": study_accession},
+            "center_name": "generic_center_name",
+        }
         manifest = create_manifest_object(
             config,
             results_in_sample_table,