fixing tests and adjusting variable casing

cancervariants · Aug 3, 2024 · d28870f · d28870f
1 parent aa3af6c
commit d28870f
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Showing 6 changed files with 33 additions and 56 deletions.
diff --git a/...nt/src/components/Pages/Structure/Input/RegulatoryElementInput/RegulatoryElementInput.tsx b/...nt/src/components/Pages/Structure/Input/RegulatoryElementInput/RegulatoryElementInput.tsx
@@ -75,7 +75,7 @@ const RegulatoryElementInput: React.FC<RegulatoryElementInputProps> = ({
       if (reResponse.warnings && reResponse.warnings.length > 0) {
         throw new Error(reResponse.warnings[0]);
       }
-      getRegElementNomenclature(reResponse.regulatory_element).then(
+      getRegElementNomenclature(reResponse.regulatoryElement).then(
         (nomenclatureResponse) => {
           if (
             nomenclatureResponse.warnings &&
@@ -84,7 +84,7 @@ const RegulatoryElementInput: React.FC<RegulatoryElementInputProps> = ({
             throw new Error(nomenclatureResponse.warnings[0]);
           }
           const newRegElement: ClientRegulatoryElement = {
-            ...reResponse.regulatory_element,
+            ...reResponse.regulatoryElement,
             elementId: element.elementId,
             displayClass: regulatoryClassItems[elementClass][1],
             nomenclature: nomenclatureResponse.nomenclature || "",

diff --git a/client/src/services/ResponseModels.ts b/client/src/services/ResponseModels.ts
@@ -762,7 +762,7 @@ export interface NormalizeGeneResponse {
  */
 export interface RegulatoryElementResponse {
   warnings?: string[] | null;
-  regulatory_element: RegulatoryElement;
+  regulatoryElement: RegulatoryElement;
 }
 /**
  * Abstract Response class for defining API response structures.
@@ -820,5 +820,5 @@ export interface TxSegmentElementResponse {
  */
 export interface ValidateFusionResponse {
   warnings?: string[] | null;
-  fusion: CategoricalFusion | AssayedFusion | null;
+  fusion?: CategoricalFusion | AssayedFusion | null;
 }
diff --git a/client/src/services/main.tsx b/client/src/services/main.tsx
@@ -30,8 +30,6 @@ import {
   ClientCategoricalFusion,
   ClientAssayedFusion,
   ValidateFusionResponse,
-  AssayedFusion,
-  CategoricalFusion,
   NomenclatureResponse,
   RegulatoryElement,
   RegulatoryClass,
@@ -427,7 +425,7 @@ export const getRegulatoryElement = async (
   geneName: string
 ): Promise<RegulatoryElementResponse> => {
   const response = await fetch(
-    `/api/construct/regulatoryElement?element_class=${regulatoryClass}&gene_name=${geneName}`
+    `/api/construct/regulatory_element?element_class=${regulatoryClass}&gene_name=${geneName}`
   );
   const responseJson = await response.json();
   return responseJson;

diff --git a/server/src/curfu/routers/constructors.py b/server/src/curfu/routers/constructors.py
@@ -283,4 +283,4 @@ def build_regulatory_element(
     element, warnings = request.app.state.fusor.regulatory_element(
         normalized_class, gene_name
     )
-    return {"regulatory_element": element, "warnings": warnings}
+    return {"regulatoryElement": element, "warnings": warnings}
diff --git a/server/src/curfu/schemas.py b/server/src/curfu/schemas.py
@@ -23,7 +23,7 @@
     TranscriptSegmentElement,
     UnknownGeneElement,
 )
-from pydantic import BaseModel, Extra, Field, StrictInt, StrictStr, validator
+from pydantic import BaseModel, Field, StrictInt, StrictStr, field_validator
 
 ResponseWarnings = list[StrictStr] | None
 
@@ -95,7 +95,7 @@ class ClientFunctionalDomain(FunctionalDomain):
     class Config:
         """Configure class."""
 
-        extra = Extra.forbid
+        extra = "forbid"
 
 
 class ClientRegulatoryElement(RegulatoryElement, ClientStructuralElement):
@@ -113,7 +113,7 @@ class Response(BaseModel):
     class Config:
         """Configure class"""
 
-        extra = Extra.forbid
+        extra = "forbid"
 
 
 class GeneElementResponse(Response):
@@ -194,14 +194,14 @@ class ExonCoordsRequest(BaseModel):
     exonEnd: StrictInt | None = 0
     exonEndOffset: StrictInt | None = 0
 
-    @validator("gene")
+    @field_validator("gene")
     def validate_gene(cls, v) -> str:
         """Replace None with empty string."""
         if v is None:
             return ""
         return v
 
-    @validator("exonStart", "exonStartOffset", "exonEnd", "exonEndOffset")
+    @field_validator("exonStart", "exonStartOffset", "exonEnd", "exonEndOffset")
     def validate_number(cls, v) -> int:
         """Replace None with 0 for numeric fields."""
         if v is None:
@@ -329,7 +329,7 @@ class NomenclatureResponse(Response):
 class RegulatoryElementResponse(Response):
     """Response model for regulatory element constructor."""
 
-    regulatory_element: RegulatoryElement
+    regulatoryElement: RegulatoryElement
 
 
 class DemoResponse(Response):

diff --git a/server/tests/integration/test_constructors.py b/server/tests/integration/test_constructors.py
@@ -135,7 +135,7 @@ async def test_build_tx_segment_ect(
     coordinates and transcript.
     """
     await check_response(
-        "/api/construct/structural_element/tx_segment_ect?transcript=NM_002529.3&exonStart=2&exonStartOffset=1",
+        "/api/construct/structural_element/tx_segment_ect?transcript=NM_002529.3&exon_start=2&exon_start_offset=1",
         {"element": ntrk1_tx_element_start},
         check_tx_element_response,
     )
@@ -149,7 +149,7 @@ async def test_build_tx_segment_ect(
 
     # test handle invalid transcript
     await check_response(
-        "/api/construct/structural_element/tx_segment_ect?transcript=NM_0012529.3&exonStart=3",
+        "/api/construct/structural_element/tx_segment_ect?transcript=NM_0012529.3&exon_start=3",
         {"warnings": ["Unable to get exons for NM_0012529.3"]},
         check_tx_element_response,
     )
@@ -192,7 +192,7 @@ async def test_build_segment_gcg(
 async def test_build_reg_element(check_response, check_reg_element_response):
     """Test correctness of regulatory element constructor endpoint."""
     await check_response(
-        "/api/construct/regulatoryElement?element_class=promoter&gene_name=braf",
+        "/api/construct/regulatory_element?element_class=promoter&gene_name=braf",
         {
             "regulatoryElement": {
                 "associatedGene": {
@@ -213,52 +213,31 @@ async def test_build_templated_sequence(
     check_response, check_templated_sequence_response
 ):
     """Test correct functioning of templated sequence constructor"""
-    await check_response(
-        "/api/construct/structural_element/templated_sequence?start=154171415&end=154171417&sequence_id=NC_000001.11&strand=-",
-        {
-            "element": {
-                "type": "TemplatedSequenceElement",
-                "region": {
-                    "id": "fusor.location_descriptor:NC_000001.11",
-                    "type": "SequenceLocation",
-                    "location_id": "ga4gh:VSL.K_suWpotWJZL0EFYUqoZckNq4bqEjH-z",
-                    "location": {
-                        "type": "SequenceLocation",
-                        "sequence_id": "refseq:NC_000001.11",
-                        "interval": {
-                            "type": "SequenceInterval",
-                            "start": {"type": "Number", "value": 154171414},
-                            "end": {"type": "Number", "value": 154171417},
-                        },
-                    },
+    expected = {
+        "element": {
+            "type": "TemplatedSequenceElement",
+            "region": {
+                "id": "ga4gh:SL.thjDCmA1u2mB0vLGjgQbCOEg81eP5hdO",
+                "type": "SequenceLocation",
+                "sequenceReference": {
+                    "id": "refseq:NC_000001.11",
+                    "refgetAccession": "",
+                    "type": "SequenceReference",
                 },
-                "strand": "-",
+                "start": 154171414,
+                "end": 154171417,
             },
+            "strand": -1,
         },
+    }
+    await check_response(
+        "/api/construct/structural_element/templated_sequence?start=154171415&end=154171417&sequence_id=NC_000001.11&strand=-",
+        expected,
         check_templated_sequence_response,
     )
 
     await check_response(
         "/api/construct/structural_element/templated_sequence?start=154171415&end=154171417&sequence_id=refseq%3ANC_000001.11&strand=-",
-        {
-            "element": {
-                "type": "TemplatedSequenceElement",
-                "region": {
-                    "id": "fusor.location_descriptor:NC_000001.11",
-                    "type": "SequenceLocation",
-                    "location_id": "ga4gh:VSL.K_suWpotWJZL0EFYUqoZckNq4bqEjH-z",
-                    "location": {
-                        "type": "SequenceLocation",
-                        "sequence_id": "refseq:NC_000001.11",
-                        "interval": {
-                            "type": "SequenceInterval",
-                            "start": {"type": "Number", "value": 154171414},
-                            "end": {"type": "Number", "value": 154171417},
-                        },
-                    },
-                },
-                "strand": "-",
-            },
-        },
+        expected,
         check_templated_sequence_response,
     )