fix: utilities requests

cancervariants · Jul 29, 2024 · 17beba5 · 17beba5
1 parent 77f3088
commit 17beba5
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Showing 6 changed files with 48 additions and 45 deletions.
diff --git a/client/src/components/Pages/Structure/Input/GeneElementInput/GeneElementInput.tsx b/client/src/components/Pages/Structure/Input/GeneElementInput/GeneElementInput.tsx
@@ -52,7 +52,7 @@ const GeneElementInput: React.FC<GeneElementInputProps> = ({
             ) {
               const clientGeneElement: ClientGeneElement = {
                 ...geneElementResponse.element,
-                element_id: element.element_id,
+                elementId: element.elementId,
                 nomenclature: nomenclatureResponse.nomenclature,
               };
               handleSave(index, clientGeneElement);

diff --git a/client/src/services/ResponseModels.ts b/client/src/services/ResponseModels.ts
@@ -427,7 +427,7 @@ export interface Assay {
  * Response model for domain ID autocomplete suggestion endpoint.
  */
 export interface AssociatedDomainResponse {
-  warnings: string[] | null;
+  warnings?: string[] | null;
   geneId: string;
   suggestions: DomainParams[] | null;
 }
@@ -628,8 +628,8 @@ export interface ClientStructuralElement {
  * Response model for genomic coordinates retrieval
  */
 export interface CoordsUtilsResponse {
-  warnings: string[] | null;
-  coordinatesData: GenomicData | null;
+  warnings?: string[] | null;
+  coordinates_data: GenomicData | null;
 }
 /**
  * Model containing genomic and transcript exon data.
@@ -650,7 +650,7 @@ export interface GenomicData {
  * Response model for demo fusion object retrieval endpoints.
  */
 export interface DemoResponse {
-  warnings: string[] | null;
+  warnings?: string[] | null;
   fusion: ClientAssayedFusion | ClientCategoricalFusion;
 }
 /**
@@ -668,21 +668,21 @@ export interface ExonCoordsRequest {
  * Response model for gene element construction endoint.
  */
 export interface GeneElementResponse {
-  warnings: string[] | null;
+  warnings?: string[] | null;
   element: GeneElement | null;
 }
 /**
  * Response model for functional domain constructor endpoint.
  */
 export interface GetDomainResponse {
-  warnings: string[] | null;
+  warnings?: string[] | null;
   domain: FunctionalDomain | null;
 }
 /**
  * Response model for MANE transcript retrieval endpoint.
  */
 export interface GetTranscriptsResponse {
-  warnings: string[] | null;
+  warnings?: string[] | null;
   transcripts: ManeGeneTranscript[] | null;
 }
 /**
@@ -700,22 +700,22 @@ export interface ManeGeneTranscript {
   Ensembl_prot: string;
   MANE_status: string;
   GRCh38_chr: string;
-  chr_start: string;
-  chr_end: string;
+  chr_start: number;
+  chr_end: number;
   chr_strand: string;
 }
 /**
  * Response model for regulatory element nomenclature endpoint.
  */
 export interface NomenclatureResponse {
-  warnings: string[] | null;
+  warnings?: string[] | null;
   nomenclature: string | null;
 }
 /**
  * Response model for gene normalization endpoint.
  */
 export interface NormalizeGeneResponse {
-  warnings: string[] | null;
+  warnings?: string[] | null;
   term: string;
   conceptId: string | null;
   symbol: string | null;
@@ -725,20 +725,20 @@ export interface NormalizeGeneResponse {
  * Response model for regulatory element constructor.
  */
 export interface RegulatoryElementResponse {
-  warnings: string[] | null;
+  warnings?: string[] | null;
   regulatoryElement: RegulatoryElement;
 }
 /**
  * Abstract Response class for defining API response structures.
  */
 export interface Response {
-  warnings: string[] | null;
+  warnings?: string[] | null;
 }
 /**
  * Response model for sequence ID retrieval endpoint.
  */
 export interface SequenceIDResponse {
-  warnings: string[] | null;
+  warnings?: string[] | null;
   sequence: string;
   refseqId: string | null;
   ga4ghId: string | null;
@@ -748,7 +748,7 @@ export interface SequenceIDResponse {
  * Response model for service_info endpoint.
  */
 export interface ServiceInfoResponse {
-  warnings: string[] | null;
+  warnings?: string[] | null;
   curfu_version: string;
   fusor_version: string;
   cool_seq_tool_version: string;
@@ -757,32 +757,32 @@ export interface ServiceInfoResponse {
  * Response model for gene autocomplete suggestions endpoint.
  */
 export interface SuggestGeneResponse {
-  warnings: string[] | null;
+  warnings?: string[] | null;
   term: string;
-  matchesCount: number;
-  conceptId: [unknown, unknown, unknown, unknown, unknown][] | null;
+  matches_count: number;
+  concept_id: [unknown, unknown, unknown, unknown, unknown][] | null;
   symbol: [unknown, unknown, unknown, unknown, unknown][] | null;
-  prevSymbols: [unknown, unknown, unknown, unknown, unknown][] | null;
+  prev_symbols: [unknown, unknown, unknown, unknown, unknown][] | null;
   aliases: [unknown, unknown, unknown, unknown, unknown][] | null;
 }
 /**
  * Response model for transcript segment element construction endpoint.
  */
 export interface TemplatedSequenceElementResponse {
-  warnings: string[] | null;
+  warnings?: string[] | null;
   element: TemplatedSequenceElement | null;
 }
 /**
  * Response model for transcript segment element construction endpoint.
  */
 export interface TxSegmentElementResponse {
-  warnings: string[] | null;
+  warnings?: string[] | null;
   element: TranscriptSegmentElement | null;
 }
 /**
  * Response model for Fusion validation endpoint.
  */
 export interface ValidateFusionResponse {
-  warnings: string[] | null;
+  warnings?: string[] | null;
   fusion: CategoricalFusion | AssayedFusion | null;
 }
diff --git a/client/src/services/main.tsx b/client/src/services/main.tsx
@@ -241,13 +241,14 @@ export const getExonCoords = async (
   gene?: string,
   txAc?: string
 ): Promise<CoordsUtilsResponse> => {
+  console.log(txAc);
   const argsArray = [
     `chromosome=${chromosome}`,
     `strand=${strand === "+" ? "%2B" : "-"}`,
-    gene !== "" ? `gene=${gene}` : "",
-    txAc !== "" ? `transcript=${txAc}` : "",
-    start !== "" ? `start=${start}` : "",
-    end !== "" ? `end=${end}` : "",
+    gene && gene !== "" ? `gene=${gene}` : "",
+    txAc && txAc !== "" ? `transcript=${txAc}` : "",
+    start && start !== "" ? `start=${start}` : "",
+    end && end !== "" ? `end=${end}` : "",
   ];
   const args = argsArray.filter((a) => a !== "").join("&");
   const response = await fetch(`/api/utilities/get_exon?${args}`);

diff --git a/server/src/curfu/routers/utilities.py b/server/src/curfu/routers/utilities.py
@@ -39,7 +39,7 @@ def get_mane_transcripts(request: Request, term: str) -> dict:
     normalized = request.app.state.fusor.gene_normalizer.normalize(term)
     if normalized.match_type == gene_schemas.MatchType.NO_MATCH:
         return {"warnings": [f"Normalization error: {term}"]}
-    if not normalized.gene.id.lower().startswith("hgnc"):
+    if not normalized.gene.id.replace("normalize.gene.", "").lower().startswith("hgnc"):
         return {"warnings": [f"No HGNC symbol: {term}"]}
     symbol = normalized.gene.label
     transcripts = request.app.state.fusor.cool_seq_tool.mane_transcript_mappings.get_gene_mane_data(
@@ -99,7 +99,7 @@ async def get_genome_coords(
     if warnings:
         for warning in warnings:
             logger.warning(warning)
-        return CoordsUtilsResponse(warnings=warnings, coordinatesData=None)
+        return CoordsUtilsResponse(warnings=warnings, coordinates_data=None)
 
     # TODO necessary for now
     if exon_start is not None and exon_start_offset is None:
@@ -120,9 +120,9 @@ async def get_genome_coords(
     )
     warnings = response.warnings
     if warnings:
-        return CoordsUtilsResponse(warnings=warnings, coordinatesData=None)
+        return CoordsUtilsResponse(warnings=warnings, coordinates_data=None)
 
-    return CoordsUtilsResponse(coordinatesData=response.genomic_data, warnings=None)
+    return CoordsUtilsResponse(coordinates_data=response.genomic_data, warnings=None)
 
 
 @router.get(
@@ -168,10 +168,10 @@ async def get_exon_coords(
     if warnings:
         for warning in warnings:
             logger.warning(warning)
-        return CoordsUtilsResponse(warnings=warnings, coordinatesData=None)
+        return CoordsUtilsResponse(warnings=warnings, coordinates_data=None)
 
-    response = await request.app.state.fusor.cool_seq_tool.genomic_to_transcript_exon_coordinates(
-        chromosome,
+    response = await request.app.state.fusor.cool_seq_tool.ex_g_coords_mapper.genomic_to_transcript_exon_coordinates(
+        alt_ac=chromosome,
         start=start,
         end=end,
         strand=strand_validated,
@@ -180,9 +180,9 @@ async def get_exon_coords(
     )
     warnings = response.warnings
     if warnings:
-        return CoordsUtilsResponse(warnings=warnings, coordinatesData=None)
+        return CoordsUtilsResponse(warnings=warnings, coordinates_data=None)
 
-    return CoordsUtilsResponse(coordinatesData=response.genomic_data, warnings=None)
+    return CoordsUtilsResponse(coordinates_data=response.genomic_data, warnings=None)
 
 
 @router.get(

diff --git a/server/src/curfu/schemas.py b/server/src/curfu/schemas.py
@@ -103,7 +103,7 @@ class ClientRegulatoryElement(RegulatoryElement):
 class Response(BaseModel):
     """Abstract Response class for defining API response structures."""
 
-    warnings: ResponseWarnings
+    warnings: ResponseWarnings | None = None
 
     class Config:
         """Configure class"""
@@ -142,11 +142,11 @@ class SuggestGeneResponse(Response):
     """Response model for gene autocomplete suggestions endpoint."""
 
     term: StrictStr
-    matchesCount: int
+    matches_count: int
     # complete term, normalized symbol, normalized concept ID, chromosome ID, strand
-    conceptId: list[tuple[str, str, str, str, str]] | None
+    concept_id: list[tuple[str, str, str, str, str]] | None
     symbol: list[tuple[str, str, str, str, str]] | None
-    prevSymbols: list[tuple[str, str, str, str, str]] | None
+    prev_symbols: list[tuple[str, str, str, str, str]] | None
     aliases: list[tuple[str, str, str, str, str]] | None
 
 
@@ -207,7 +207,7 @@ def validate_number(cls, v) -> int:
 class CoordsUtilsResponse(Response):
     """Response model for genomic coordinates retrieval"""
 
-    coordinatesData: GenomicData | None
+    coordinates_data: GenomicData | None
 
 
 class SequenceIDResponse(Response):
@@ -233,8 +233,8 @@ class ManeGeneTranscript(BaseModel):
     Ensembl_prot: str
     MANE_status: str
     GRCh38_chr: str
-    chr_start: str
-    chr_end: str
+    chr_start: int
+    chr_end: int
     chr_strand: str
 
 

diff --git a/server/src/curfu/sequence_services.py b/server/src/curfu/sequence_services.py
@@ -2,6 +2,8 @@
 
 import logging
 
+from cool_seq_tool.schemas import Strand
+
 logger = logging.getLogger("curfu")
 logger.setLevel(logging.DEBUG)
 
@@ -18,7 +20,7 @@ def get_strand(strand_input: str) -> int:
     :raises InvalidInputException: if strand arg is invalid
     """
     if strand_input == "+":
-        return 1
+        return Strand.POSITIVE
     if strand_input == "-":
-        return -1
+        return Strand.NEGATIVE
     raise InvalidInputError