Update unit tests to match the new VRS 2.0 digests (#92)

* Update expected VRS IDs for VCF tests

* Update VRS IDs for variation tests

* Update variation test data to match VRS 2.0 changes

* Comment out response model to return full VRS objects instead of serialized version

* Make get location/variation behave consistently even when the object store does not throw a KeyError on missing key

* Remove code added to make debugging easier

* Storage implementations should be consistent with MutableMapping API and throw KeyError when an item is not found

* Remove VRS model classes from response objects because the serialization used internally is not correct for API responses

* Corrected path used for missing allele id test

* Get location and get variation should be consistent in behavior when id is not found

* Revert unecessary change

src/anyvar/restapi/main.py

@@ -100,11 +100,16 @@ def get_location_by_id(
     try:
         location = av.get_object(location_id)
     except KeyError:
-        return HTTPException(status_code=HTTPStatus.NOT_FOUND)
+        raise HTTPException(
+            status_code=HTTPStatus.NOT_FOUND, detail=f"Location {location_id} not found"
+        )
+
     if location:
         return {"location": location.model_dump(exclude_none=True)}
     else:
-        return {"location": None}
+        raise HTTPException(
+            status_code=HTTPStatus.NOT_FOUND, detail=f"Location {location_id} not found"
+        )
 
 
 @app.put(
@@ -273,17 +278,19 @@ def get_variation_by_id(
     :raise HTTPException: if no variation matches provided ID
     """
     av: AnyVar = request.app.state.anyvar
-
     try:
         variation = av.get_object(variation_id, deref=True)
     except KeyError:
         raise HTTPException(
             status_code=HTTPStatus.NOT_FOUND, detail=f"Variation {variation_id} not found"
         )
 
-    result = {"messages": [], "data": variation.model_dump(exclude_none=True)}
-
-    return result
+    if variation:
+        return {"messages": [], "data": variation.model_dump(exclude_none=True)}
+    else:
+        raise HTTPException(
+            status_code=HTTPStatus.NOT_FOUND, detail=f"Variation {variation_id} not found"
+        )
 
 
 @app.get(

src/anyvar/restapi/schema.py

@@ -50,7 +50,7 @@ def schema_extra(schema: Dict[str, Any], model: Type["InfoResponse"]) -> None:
 class GetSequenceLocationResponse(BaseModel):
     """Describe response for the /locations/ endpoint"""
 
-    location: Optional[models.SequenceLocation]
+    location: Optional[Dict]
 
 
 class RegisterVariationRequest(BaseModel):
@@ -124,7 +124,7 @@ class GetVariationResponse(BaseModel):
     """Describe response for the /variation get endpoint"""
 
     messages: List[StrictStr]
-    data: models.Variation
+    data: Dict
 
     class Config:
         """Configure GetVariationResponse class"""
@@ -139,27 +139,29 @@ def schema_extra(schema: Dict[str, Any], model: Type["GetVariationResponse"]) ->
             schema["example"] = {
                 "messages": [],
                 "data": {
-                    "_id": "ga4gh:VA.ZDdoQdURgO2Daj2NxLj4pcDnjiiAsfbO",
-                    "type": "Allele",
+                    "digest": "K7akyz9PHB0wg8wBNVlWAAdvMbJUJJfU",
+                    "id": "ga4gh:VA.K7akyz9PHB0wg8wBNVlWAAdvMbJUJJfU",
                     "location": {
-                        "_id": "ga4gh:VSL.2cHIgn7iLKk4x9z3zLkSTTFMV0e48DR4",
-                        "type": "SequenceLocation",
-                        "sequence_id": "ga4gh:SQ.cQvw4UsHHRRlogxbWCB8W-mKD4AraM9y",
-                        "interval": {
-                            "type": "SequenceInterval",
-                            "start": {"type": "Number", "value": 599},
-                            "end": {"type": "Number", "value": 600},
+                        "digest": "01EH5o6V6VEyNUq68gpeTwKE7xOo-WAy",
+                        "id": "ga4gh:SL.01EH5o6V6VEyNUq68gpeTwKE7xOo-WAy",
+                        "start": 87894076,
+                        "end": 87894077,
+                        "sequenceReference": {
+                            "refgetAccession": "SQ.ss8r_wB0-b9r44TQTMmVTI92884QvBiB",
+                            "type": "SequenceReference",
                         },
+                        "type": "SequenceLocation",
                     },
-                    "state": {"type": "LiteralSequenceExpression", "sequence": "E"},
+                    "state": {"sequence": "T", "type": "LiteralSequenceExpression"},
+                    "type": "Allele",
                 },
             }
 
 
 class SearchResponse(BaseModel):
     """Describe response for the /search endpoint"""
 
-    variations: List[models.Variation]
+    variations: List[Dict]
 
 
 class VariationStatisticType(str, Enum):

src/anyvar/storage/postgres.py

@@ -105,6 +105,8 @@ def __getitem__(self, name: str) -> Optional[Any]:
                 return models.SequenceLocation(**result)
             else:
                 raise NotImplementedError
+        else:
+            raise KeyError(name)
 
     def __contains__(self, name: str) -> bool:
         """Check whether VRS objects table contains ID.

src/anyvar/storage/snowflake.py

@@ -203,6 +203,8 @@ def __getitem__(self, name: str) -> Optional[Any]:
                 return models.SequenceLocation(**result)
             else:
                 raise NotImplementedError
+        else:
+            raise KeyError(name)
 
     def __contains__(self, name: str) -> bool:
         """Check whether VRS objects table contains ID.

tests/data/variations.json

@@ -1,17 +1,19 @@
 {
   "alleles": {
-    "ga4gh:VA.GbDZmcmmWJngURaODSrbbLWgNEeSYhFB": {
+    "ga4gh:VA.K7akyz9PHB0wg8wBNVlWAAdvMbJUJJfU": {
       "params": {
         "definition": "NC_000010.11:g.87894077C>T"
       },
       "allele_response": {
         "messages": [],
         "object": {
-          "id": "ga4gh:VA.GbDZmcmmWJngURaODSrbbLWgNEeSYhFB",
+          "digest": "K7akyz9PHB0wg8wBNVlWAAdvMbJUJJfU",
+          "id": "ga4gh:VA.K7akyz9PHB0wg8wBNVlWAAdvMbJUJJfU",
           "location": {
-            "id": "ga4gh:SL.aCMcqLGKClwMWEDx3QWe4XSiGDlKXdB8",
-            "end": 87894077,
+            "digest": "01EH5o6V6VEyNUq68gpeTwKE7xOo-WAy",
+            "id": "ga4gh:SL.01EH5o6V6VEyNUq68gpeTwKE7xOo-WAy",
             "start": 87894076,
+            "end": 87894077,
             "sequenceReference": {
               "refgetAccession": "SQ.ss8r_wB0-b9r44TQTMmVTI92884QvBiB",
               "type": "SequenceReference"
@@ -25,38 +27,40 @@
           "type": "Allele"
         }
       },
-      "location_id": "ga4gh:SL.aCMcqLGKClwMWEDx3QWe4XSiGDlKXdB8"
+      "location_id": "ga4gh:SL.01EH5o6V6VEyNUq68gpeTwKE7xOo-WAy"
     },
-    "ga4gh:VA.EB-JEr9jnAjzL_zjxzBqRgGMREVCv31v": {
+    "ga4gh:VA.1FzYrqG-7jB3Wr46eIL_L5BWElQZEB7i": {
       "params": {
         "definition": "NM_000551.3:c.1A>T"
       },
       "allele_response": {
         "messages": [],
         "object": {
-          "id": "ga4gh:VA.EB-JEr9jnAjzL_zjxzBqRgGMREVCv31v",
-          "type": "Allele",
+          "digest": "1FzYrqG-7jB3Wr46eIL_L5BWElQZEB7i",
+          "id": "ga4gh:VA.1FzYrqG-7jB3Wr46eIL_L5BWElQZEB7i",
           "location": {
-            "id": "ga4gh:SL.-FaQ9J0LDvasaUpfLKstbyDx8nUld9fl",
-            "type": "SequenceLocation",
+            "digest": "WoWgQNl0L6EkWkW_xRl0TSwzmzh-Z3FD",
+            "id": "ga4gh:SL.WoWgQNl0L6EkWkW_xRl0TSwzmzh-Z3FD",
+            "start": 213,
+            "end": 214,
             "sequenceReference": {
               "refgetAccession": "SQ.v_QTc1p-MUYdgrRv4LMT6ByXIOsdw3C_",
               "type": "SequenceReference"
             },
-            "start": 0,
-            "end": 1
+            "type": "SequenceLocation"
           },
           "state": {
             "type": "LiteralSequenceExpression",
             "sequence": "T"
-          }
+          },
+          "type": "Allele"
         }
       },
-      "location_id": "ga4gh:SL.-FaQ9J0LDvasaUpfLKstbyDx8nUld9fl"
+      "location_id": "ga4gh:SL.WoWgQNl0L6EkWkW_xRl0TSwzmzh-Z3FD"
     }
   },
   "copy_numbers": {
-    "ga4gh:CX.UvIENZGNmCM5j38yHueYdd-BZLn-aLJM": {
+    "ga4gh:CX.TvAhuGK6HYf53mXoUnon60cZ7DC_UgM3": {
       "params": {
         "definition": "NC_000013.11:g.26440969_26443305del",
         "copy_change": "efo:0030069",
@@ -65,9 +69,11 @@
       "copy_number_response": {
         "messages": [],
         "object": {
-          "id": "ga4gh:CX.UvIENZGNmCM5j38yHueYdd-BZLn-aLJM",
+          "digest": "TvAhuGK6HYf53mXoUnon60cZ7DC_UgM3",
+          "id": "ga4gh:CX.TvAhuGK6HYf53mXoUnon60cZ7DC_UgM3",
           "location": {
-            "id": "ga4gh:SL.XBjSbazxe6h8lI14zfXIxqt6J718QEec",
+            "digest": "4akcjXlbAu4xBKnxjOL_b4DM_20HOCA3",
+            "id": "ga4gh:SL.4akcjXlbAu4xBKnxjOL_b4DM_20HOCA3",
             "start": 26440968,
             "end": 26443305,
             "sequenceReference": {
@@ -80,9 +86,9 @@
           "type": "CopyNumberChange"
         }
       },
-      "location_id": "ga4gh:SL.XBjSbazxe6h8lI14zfXIxqt6J718QEec"
+      "location_id": "ga4gh:SL.4akcjXlbAu4xBKnxjOL_b4DM_20HOCA3"
     },
-    "ga4gh:CN.tPLSlUBW6j2dVHv0G81U_IFXt4Xawo7J": {
+    "ga4gh:CN.QnU97C-cRW431O9qWia9UCVRBDvGDH7I": {
       "params": {
         "definition": "NC_000013.11:g.26440969_26443305del",
         "copies": 1,
@@ -91,9 +97,11 @@
       "copy_number_response": {
         "messages": [],
         "object": {
-          "id": "ga4gh:CN.tPLSlUBW6j2dVHv0G81U_IFXt4Xawo7J",
+          "digest": "QnU97C-cRW431O9qWia9UCVRBDvGDH7I",
+          "id": "ga4gh:CN.QnU97C-cRW431O9qWia9UCVRBDvGDH7I",
           "location": {
-            "id": "ga4gh:SL.XBjSbazxe6h8lI14zfXIxqt6J718QEec",
+            "digest": "4akcjXlbAu4xBKnxjOL_b4DM_20HOCA3",
+            "id": "ga4gh:SL.4akcjXlbAu4xBKnxjOL_b4DM_20HOCA3",
             "start": 26440968,
             "end": 26443305,
             "sequenceReference": {
@@ -106,7 +114,7 @@
           "type": "CopyNumberCount"
         }
       },
-      "location_id": "ga4gh:SL.XBjSbazxe6h8lI14zfXIxqt6J718QEec"
+      "location_id": "ga4gh:SL.4akcjXlbAu4xBKnxjOL_b4DM_20HOCA3"
     }
   }
 }

tests/test_location.py

@@ -11,6 +11,5 @@ def test_location(client, alleles):
         assert resp.json()["location"] == allele["allele_response"]["object"]["location"]
 
     # invalid ID
-    resp = client.get("/locations/not_a_real_location")
-    assert resp.status_code == HTTPStatus.OK
-    assert "location" not in resp.json()
+    bad_resp = client.get("/locations/not_a_real_location")
+    assert bad_resp.status_code == HTTPStatus.NOT_FOUND

tests/test_variation.py

@@ -52,14 +52,12 @@ def test_put_copy_number(client, copy_numbers):
 def test_put_vrs_variation(client, alleles, copy_numbers):
     for allele_id, allele in alleles.items():
         params = deepcopy(allele["allele_response"]["object"])
-        params.pop("id")
         resp = client.put("/vrs_variation", json=params)
         assert resp.status_code == HTTPStatus.OK
         assert resp.json()["object_id"] == allele_id
 
     for copy_number_id, copy_number in copy_numbers.items():
         params = deepcopy(copy_number["copy_number_response"]["object"])
-        params.pop("id")
         resp = client.put("/vrs_variation", json=params)
         assert resp.status_code == HTTPStatus.OK
         assert resp.json()["object_id"] == copy_number_id
@@ -71,7 +69,7 @@ def test_get_allele(client, alleles):
         assert resp.status_code == HTTPStatus.OK
         assert resp.json()["data"] == allele["allele_response"]["object"]
 
-    bad_resp = client.get("/allele/ga4gh:VA.invalid7DSM9KE3Z0LntAukLqm0K2ENn")
+    bad_resp = client.get("/variation/ga4gh:VA.invalid7DSM9KE3Z0LntAukLqm0K2ENn")
     assert bad_resp.status_code == HTTPStatus.NOT_FOUND
 
 

tests/test_vcf.py

@@ -49,7 +49,7 @@ def test_vcf_registration_default_assembly(client, sample_vcf_grch38):
     resp = client.put("/vcf", files={"vcf": ("test.vcf", sample_vcf_grch38)})
     assert resp.status_code == HTTPStatus.OK
     assert (
-        b"VRS_Allele_IDs=ga4gh:VA.8MVWsPFeScEY_19U32k4LVI_3lEOKGUL,ga4gh:VA.l7crC9qxgcDtexejZkfp6yPNevEMnZ5y"
+        b"VRS_Allele_IDs=ga4gh:VA.ryPubD68BB0D-D78L_kK4993mXmsNNWe,ga4gh:VA._QhHH18HBAIeLos6npRgR-S_0lAX5KR6"
         in resp.content
     )
 
@@ -58,7 +58,7 @@ def test_vcf_registration_grch38(client, sample_vcf_grch38):
     resp = client.put("/vcf", params={"assembly": "GRCh38"}, files={"vcf": ("test.vcf", sample_vcf_grch38)})
     assert resp.status_code == HTTPStatus.OK
     assert (
-        b"VRS_Allele_IDs=ga4gh:VA.8MVWsPFeScEY_19U32k4LVI_3lEOKGUL,ga4gh:VA.l7crC9qxgcDtexejZkfp6yPNevEMnZ5y"
+        b"VRS_Allele_IDs=ga4gh:VA.ryPubD68BB0D-D78L_kK4993mXmsNNWe,ga4gh:VA._QhHH18HBAIeLos6npRgR-S_0lAX5KR6"
         in resp.content
     )
 
@@ -106,7 +106,7 @@ def test_vcf_registration_grch37(client, sample_vcf_grch37):
     resp = client.put("/vcf", params={"assembly": "GRCh37"}, files={"vcf": ("test.vcf", sample_vcf_grch37)})
     assert resp.status_code == HTTPStatus.OK
     assert (
-        b"VRS_Allele_IDs=ga4gh:VA.R-tU3agvAtsRD59MXZaCymsVE4yjMpt3,ga4gh:VA.f_EzEO6CLZmubm1gbL20F9EV8GZPLAJz"
+        b"VRS_Allele_IDs=ga4gh:VA.iwk6beQfvJGkeW33NBbSqalr29XkDBE5,ga4gh:VA.CNSRLQlBrly3rRcdldN85dw2Tjos7Cas"
         in resp.content
     )