feat: Add status field to spdi response (#17) (#18)

bihealth · Oct 16, 2023 · 152c414 · 152c414
1 parent 517bab4
commit 152c414
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Showing 2 changed files with 40 additions and 16 deletions.
diff --git a/dotty/main.py b/dotty/main.py
@@ -92,11 +92,13 @@ class Spdi(pydantic.BaseModel):
     alternate_inserted: str
 
 
-class Result(pydantic.BaseModel):
+class SpdiResult(pydantic.BaseModel):
     """The result of the query."""
 
+    #: The indicator if the query was successful.
+    success: bool
     #: The actual payload / SPDI representation of the variant.
-    spdi: Spdi
+    value: Spdi | None
 
 
 class ExonAlignment(pydantic.BaseModel):
@@ -186,13 +188,13 @@ class TranscriptResult(pydantic.BaseModel):
     transcripts: list[Transcript]
 
 
-@app.get("/api/v1/to-spdi", response_model=Result)
-async def to_spdi(q: str, assembly: Assembly = Assembly.GRCH38) -> Result:
+@app.get("/api/v1/to-spdi", response_model=SpdiResult)
+async def to_spdi(q: str, assembly: Assembly = Assembly.GRCH38) -> SpdiResult:
     """Resolve the given HGVS variant to SPDI representation."""
     try:
         parsed_var = driver.parser.parse(q)
     except hgvs.exceptions.HGVSParseError:
-        raise HTTPException(status_code=400, detail="Invalid HGVS description")
+        return SpdiResult(success=False, value=None)
 
     if parsed_var.type == "c":
         var_g = driver.assembly_mappers[assembly].c_to_g(parsed_var)
@@ -207,14 +209,15 @@ async def to_spdi(q: str, assembly: Assembly = Assembly.GRCH38) -> Result:
 
     contig, pos, reference, alternative, type_ = driver.babelfishes[assembly].hgvs_to_vcf(var_g)
 
-    return Result(
-        spdi=Spdi(
+    return SpdiResult(
+        success=True,
+        value=Spdi(
             assembly=assembly.value,
             contig=contig,
             pos=pos,
             reference_deleted=reference,
             alternate_inserted=alternative,
-        )
+        ),
     )
 
 

diff --git a/tests/test_main.py b/tests/test_main.py
@@ -2,6 +2,7 @@
 import typing
 from unittest.mock import Mock
 
+import hgvs.exceptions
 from _pytest.monkeypatch import MonkeyPatch
 from fastapi.testclient import TestClient
 from pytest_snapshot.plugin import Snapshot
@@ -85,13 +86,14 @@ def test_to_spdi_c(test_client: TestClient, monkeypatch: MonkeyPatch):
     response = test_client.get("/api/v1/to-spdi?q=NM_000059.3:c.274G>A")
     assert response.status_code == 200
     expected = {
-        "spdi": {
+        "success": True,
+        "value": {
             "alternate_inserted": "C",
             "contig": "chr1",
             "pos": 100,
             "reference_deleted": "A",
             "assembly": "GRCh38",
-        }
+        },
     }
     assert response.json() == expected
 
@@ -101,13 +103,14 @@ def test_to_spdi_n(test_client: TestClient, monkeypatch: MonkeyPatch):
     response = test_client.get("/api/v1/to-spdi?q=NM_000059.3:n.274G>A")
     assert response.status_code == 200
     expected = {
-        "spdi": {
+        "success": True,
+        "value": {
             "alternate_inserted": "C",
             "contig": "chr1",
             "pos": 100,
             "reference_deleted": "A",
             "assembly": "GRCh38",
-        }
+        },
     }
     assert response.json() == expected
 
@@ -117,13 +120,14 @@ def test_to_spdi_g_37(test_client: TestClient, monkeypatch: MonkeyPatch):
     response = test_client.get("/api/v1/to-spdi?q=NC_000017.10:g.41197699T>C")
     assert response.status_code == 200
     expected = {
-        "spdi": {
+        "success": True,
+        "value": {
             "alternate_inserted": "C",
             "contig": "chr1",
             "pos": 100,
             "reference_deleted": "A",
             "assembly": "GRCh37",
-        }
+        },
     }
     assert response.json() == expected
 
@@ -133,13 +137,30 @@ def test_to_spdi_g_38(test_client: TestClient, monkeypatch: MonkeyPatch):
     response = test_client.get("/api/v1/to-spdi?q=NC_000017.11:g.43045682T>C")
     assert response.status_code == 200
     expected = {
-        "spdi": {
+        "success": True,
+        "value": {
             "alternate_inserted": "C",
             "contig": "chr1",
             "pos": 100,
             "reference_deleted": "A",
             "assembly": "GRCh38",
-        }
+        },
+    }
+    assert response.json() == expected
+
+
+def test_to_spdi_invalid(test_client: TestClient, monkeypatch: MonkeyPatch):
+    mock_driver = Mock()
+    mock_driver.parser = Mock()
+    mock_driver.parser.parse = Mock()
+    mock_driver.parser.parse.side_effect = hgvs.exceptions.HGVSParseError
+    monkeypatch.setattr(dotty_main, "driver", mock_driver)
+
+    response = test_client.get("/api/v1/to-spdi?q=BRCA1")
+    assert response.status_code == 200
+    expected = {
+        "success": False,
+        "value": None,
     }
     assert response.json() == expected