more test updates/error handling

Author: jsstevenson

src/anyvlm/anyvar/http_client.py

@@ -2,6 +2,7 @@
 
 import logging
 from collections.abc import Iterable
+from http import HTTPStatus
 
 import requests
 from anyvar.utils.liftover_utils import ReferenceAssembly
@@ -73,17 +74,12 @@ def put_allele_expressions(
                     payload,
                     url,
                 )
-                raise AnyVarClientError from e
-            response_json = response.json()
-            if messages := response_json.get("messages"):
-                _logger.warning(
-                    "Variant expression `%s` seems to have failed to translate: %s",
-                    expression,
-                    messages,
-                )
-                results.append(None)
+                if response.status_code == HTTPStatus.UNPROCESSABLE_ENTITY:
+                    results.append(None)
+                else:
+                    raise AnyVarClientError from e
             else:
-                results.append(response_json["object_id"])
+                results.append(response.json()["object_id"])
         return results
 
     def search_by_interval(

src/anyvlm/anyvar/python_client.py

@@ -83,4 +83,5 @@ def search_by_interval(
 
     def close(self) -> None:
         """Clean up AnyVar instance."""
+        _logger.info("Closing AnyVar client.")
         self.av.object_store.close()

tests/unit/anyvar/cassettes/test_clients/test_put_allele_expressions[anyvar_http_client].yaml

@@ -1,82 +1,4 @@
 interactions:
-- request:
-    body: '{"definition": "7-140753336-A-T", "assembly_name": "GRCh38", "input_type":
-      "Allele"}'
-    headers: {}
-    method: PUT
-    uri: http://localhost:8000/variation
-  response:
-    body:
-      string: '{"messages":[],"object":{"id":"ga4gh:VA.Otc5ovrw906Ack087o1fhegB4jDRqCAe","type":"Allele","digest":"Otc5ovrw906Ack087o1fhegB4jDRqCAe","location":{"id":"ga4gh:SL.nhul5x5P_fKjGEpY9PEkMIekJfZaKom2","type":"SequenceLocation","digest":"nhul5x5P_fKjGEpY9PEkMIekJfZaKom2","sequenceReference":{"type":"SequenceReference","refgetAccession":"SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul"},"start":140753335,"end":140753336},"state":{"type":"LiteralSequenceExpression","sequence":"T"}},"object_id":"ga4gh:VA.Otc5ovrw906Ack087o1fhegB4jDRqCAe"}'
-    headers: {}
-    status:
-      code: 200
-      message: OK
-- request:
-    body: '{"definition": "Y-2781704-G-G", "assembly_name": "GRCh38", "input_type":
-      "Allele"}'
-    headers: {}
-    method: PUT
-    uri: http://localhost:8000/variation
-  response:
-    body:
-      string: '{"messages":[],"object":{"id":"ga4gh:VA.ruQCmfXJrEylHmOQF-1PG6bLwQesDU2g","type":"Allele","digest":"ruQCmfXJrEylHmOQF-1PG6bLwQesDU2g","location":{"id":"ga4gh:SL.JqeJ3V-75edWj03xbzw1gtSw3qPQVV2D","type":"SequenceLocation","digest":"JqeJ3V-75edWj03xbzw1gtSw3qPQVV2D","sequenceReference":{"type":"SequenceReference","refgetAccession":"SQ.8_liLu1aycC0tPQPFmUaGXJLDs5SbPZ5"},"start":2781703,"end":2781704},"state":{"type":"LiteralSequenceExpression","sequence":"G"}},"object_id":"ga4gh:VA.ruQCmfXJrEylHmOQF-1PG6bLwQesDU2g"}'
-    headers: {}
-    status:
-      code: 200
-      message: OK
-- request:
-    body: '{"definition": "Y-2781761-C-C", "assembly_name": "GRCh38", "input_type":
-      "Allele"}'
-    headers: {}
-    method: PUT
-    uri: http://localhost:8000/variation
-  response:
-    body:
-      string: '{"messages":[],"object":{"id":"ga4gh:VA.xbX035HgURWIUAjn6x3cS26jafP8Q_bk","type":"Allele","digest":"xbX035HgURWIUAjn6x3cS26jafP8Q_bk","location":{"id":"ga4gh:SL.sYiBcbbgF-1CANNCTfQ6zwZOU0iHhymR","type":"SequenceLocation","digest":"sYiBcbbgF-1CANNCTfQ6zwZOU0iHhymR","sequenceReference":{"type":"SequenceReference","refgetAccession":"SQ.8_liLu1aycC0tPQPFmUaGXJLDs5SbPZ5"},"start":2781760,"end":2781761},"state":{"type":"LiteralSequenceExpression","sequence":"C"}},"object_id":"ga4gh:VA.xbX035HgURWIUAjn6x3cS26jafP8Q_bk"}'
-    headers: {}
-    status:
-      code: 200
-      message: OK
-- request:
-    body: '{"definition": "Y-2781761-C-C", "assembly_name": "GRCh38", "input_type":
-      "Allele"}'
-    headers: {}
-    method: PUT
-    uri: http://localhost:8000/variation
-  response:
-    body:
-      string: '{"messages":[],"object":{"id":"ga4gh:VA.xbX035HgURWIUAjn6x3cS26jafP8Q_bk","type":"Allele","digest":"xbX035HgURWIUAjn6x3cS26jafP8Q_bk","location":{"id":"ga4gh:SL.sYiBcbbgF-1CANNCTfQ6zwZOU0iHhymR","type":"SequenceLocation","digest":"sYiBcbbgF-1CANNCTfQ6zwZOU0iHhymR","sequenceReference":{"type":"SequenceReference","refgetAccession":"SQ.8_liLu1aycC0tPQPFmUaGXJLDs5SbPZ5"},"start":2781760,"end":2781761},"state":{"type":"LiteralSequenceExpression","sequence":"C"}},"object_id":"ga4gh:VA.xbX035HgURWIUAjn6x3cS26jafP8Q_bk"}'
-    headers: {}
-    status:
-      code: 200
-      message: OK
-- request:
-    body: '{"definition": "Y-2781761-C-A", "assembly_name": "GRCh38", "input_type":
-      "Allele"}'
-    headers: {}
-    method: PUT
-    uri: http://localhost:8000/variation
-  response:
-    body:
-      string: '{"messages":[],"object":{"id":"ga4gh:VA.9VDxL0stMBOZwcTKw3yb3UoWQkpaI9OD","type":"Allele","digest":"9VDxL0stMBOZwcTKw3yb3UoWQkpaI9OD","location":{"id":"ga4gh:SL.sYiBcbbgF-1CANNCTfQ6zwZOU0iHhymR","type":"SequenceLocation","digest":"sYiBcbbgF-1CANNCTfQ6zwZOU0iHhymR","sequenceReference":{"type":"SequenceReference","refgetAccession":"SQ.8_liLu1aycC0tPQPFmUaGXJLDs5SbPZ5"},"start":2781760,"end":2781761},"state":{"type":"LiteralSequenceExpression","sequence":"A"}},"object_id":"ga4gh:VA.9VDxL0stMBOZwcTKw3yb3UoWQkpaI9OD"}'
-    headers: {}
-    status:
-      code: 200
-      message: OK
-- request:
-    body: '{"definition": "Y-2781761-CA-C", "assembly_name": "GRCh38", "input_type":
-      "Allele"}'
-    headers: {}
-    method: PUT
-    uri: http://localhost:8000/variation
-  response:
-    body:
-      string: '{"messages":[],"object":{"id":"ga4gh:VA.yi7A2l0uIUMaInQaJnHU_B2Cf_OuZRJg","type":"Allele","digest":"yi7A2l0uIUMaInQaJnHU_B2Cf_OuZRJg","location":{"id":"ga4gh:SL.JsFGLKlUDocinf7oWTXAvVT2WOso7R9u","type":"SequenceLocation","digest":"JsFGLKlUDocinf7oWTXAvVT2WOso7R9u","sequenceReference":{"type":"SequenceReference","refgetAccession":"SQ.8_liLu1aycC0tPQPFmUaGXJLDs5SbPZ5"},"start":2781761,"end":2781785},"state":{"type":"ReferenceLengthExpression","length":23,"sequence":"AAAAAAAAAAAAAAAAAAAAAAA","repeatSubunitLength":1}},"object_id":"ga4gh:VA.yi7A2l0uIUMaInQaJnHU_B2Cf_OuZRJg"}'
-    headers: {}
-    status:
-      code: 200
-      message: OK
 - request:
     body: '{"definition": "7-140753336-A-T", "assembly_name": "GRCh38", "input_type":
       "Allele"}'