feat!: update tx segment element with updated cool-seq-tool structure changes

client/src/components/Pages/Structure/Input/TxSegmentElementInput/TxSegmentElementInput.tsx

@@ -267,8 +267,7 @@ const TxSegmentCompInput: React.FC<TxSegmentElementInputProps> = ({
           txAc,
           txChrom,
           txStartingGenomic,
-          txEndingGenomic,
-          txStrand
+          txEndingGenomic
         ).then((txSegmentResponse) => {
           if (
             txSegmentResponse.warnings &&

client/src/components/Pages/Summary/Main/Summary.tsx

@@ -162,8 +162,6 @@ export const Summary: React.FC<Props> = ({ setVisibleTab }) => {
     setFormattedFusion(formattedFusion);
   }, [fusion]);
 
-  console.log(formattedFusion);
-
   return (
     <>
       {(!validationErrors || validationErrors.length === 0) &&

client/src/components/Utilities/GetCoordinates/GetCoordinates.tsx

@@ -193,12 +193,12 @@ const GetCoordinates: React.FC = () => {
         exonEndOffset
       ).then((coordsResponse) => handleResponse(coordsResponse));
     } else if (inputType == "genomic_coords_gene") {
-      getExonCoords(chromosome, start, end, strand, gene).then(
-        (coordsResponse) => handleResponse(coordsResponse)
+      getExonCoords(chromosome, start, end, gene).then((coordsResponse) =>
+        handleResponse(coordsResponse)
       );
     } else if (inputType == "genomic_coords_tx") {
-      getExonCoords(chromosome, start, end, strand, "", txAc).then(
-        (coordsResponse) => handleResponse(coordsResponse)
+      getExonCoords(chromosome, start, end, "", txAc).then((coordsResponse) =>
+        handleResponse(coordsResponse)
       );
     }
   };
@@ -215,25 +215,38 @@ const GetCoordinates: React.FC = () => {
   const renderResults = (): React.ReactFragment => {
     if (inputValid) {
       if (results) {
+        const txSegStart = results.seg_start;
+        const txSegEnd = results.seg_end;
+
+        const genomicStart =
+          txSegStart?.genomic_location.start ||
+          txSegStart?.genomic_location.end;
+        const genomicEnd =
+          txSegEnd?.genomic_location.start || txSegEnd?.genomic_location.end;
+
         return (
           <Table>
             {renderRow("Gene", results.gene)}
-            {renderRow("Chromosome", results.chr)}
-            {results.start ? renderRow("Genomic start", results.start) : null}
-            {results.end ? renderRow("Genomic end", results.end) : null}
+            {renderRow("Chromosome", results.genomic_ac)}
+            {genomicStart != null
+              ? renderRow("Genomic start", genomicStart)
+              : null}
+            {genomicEnd != null ? renderRow("Genomic end", genomicEnd) : null}
             {results.strand
               ? renderRow("Strand", results.strand === 1 ? "+" : "-")
               : null}
-            {renderRow("Transcript", results.transcript)}
-            {results.exon_start
-              ? renderRow("Exon start", results.exon_start)
+            {renderRow("Transcript", results.tx_ac)}
+            {txSegStart?.exon_ord != null
+              ? renderRow("Exon start", txSegStart.exon_ord)
+              : null}
+            {txSegStart?.offset != null
+              ? renderRow("Exon start offset", txSegStart.offset)
               : null}
-            {results.exon_start_offset
-              ? renderRow("Exon start offset", results.exon_start_offset)
+            {txSegEnd?.exon_ord != null
+              ? renderRow("Exon end", txSegEnd.exon_ord)
               : null}
-            {results.exon_end ? renderRow("Exon end", results.exon_end) : null}
-            {results.exon_end_offset
-              ? renderRow("Exon end offset", results.exon_end_offset)
+            {txSegEnd?.offset != null
+              ? renderRow("Exon end offset", txSegEnd.offset)
               : null}
           </Table>
         );
@@ -250,10 +263,7 @@ const GetCoordinates: React.FC = () => {
   const genomicCoordinateInfo = (
     <>
       <Box display="flex" justifyContent="space-between" width="100%">
-        <ChromosomeField
-          fieldValue={chromosome}
-          errorText={chromosomeText}
-        />
+        <ChromosomeField fieldValue={chromosome} errorText={chromosomeText} />
         <Box mt="18px">
           <Box className={classes.strand} width="125px">
             <StrandSwitch

client/src/services/ResponseModels.ts

@@ -638,22 +638,66 @@ export interface ClientStructuralElement {
  */
 export interface CoordsUtilsResponse {
   warnings?: string[] | null;
-  coordinates_data: GenomicData | null;
+  coordinates_data: GenomicTxSegService | null;
 }
 /**
- * Model containing genomic and transcript exon data.
+ * Service model for genomic and transcript data.
  */
-export interface GenomicData {
-  gene: string;
-  chr: string;
-  start?: number | null;
-  end?: number | null;
-  exon_start?: number | null;
-  exon_start_offset?: number | null;
-  exon_end?: number | null;
-  exon_end_offset?: number | null;
-  transcript: string;
-  strand: Strand;
+export interface GenomicTxSegService {
+  /**
+   * HGNC gene symbol.
+   */
+  gene?: string | null;
+  /**
+   * RefSeq genomic accession.
+   */
+  genomic_ac?: string | null;
+  /**
+   * RefSeq transcript accession.
+   */
+  tx_ac?: string | null;
+  /**
+   * Start transcript segment.
+   */
+  seg_start?: TxSegment | null;
+  /**
+   * End transcript segment.
+   */
+  seg_end?: TxSegment | null;
+  /**
+   * Error messages.
+   */
+  errors?: string[];
+  /**
+   * Service metadata.
+   */
+  service_meta: ServiceMeta;
+}
+/**
+ * Model for representing transcript segment data.
+ */
+export interface TxSegment {
+  /**
+   * Exon number. 0-based.
+   */
+  exon_ord: number;
+  /**
+   * The value added to or subtracted from the `genomic_location` to find the start or end of an exon.
+   */
+  offset?: number;
+  /**
+   * The genomic position of a transcript segment.
+   */
+  genomic_location: SequenceLocation;
+}
+/**
+ * Metadata for cool_seq_tool service
+ */
+export interface ServiceMeta {
+  name?: "cool_seq_tool";
+  version: string;
+  response_datetime: string;
+  url?: "https://github.com/GenomicMedLab/cool-seq-tool";
 }
 /**
  * Response model for demo fusion object retrieval endpoints.

client/src/services/main.tsx

@@ -163,13 +163,11 @@ export const getTxSegmentElementGCT = async (
   transcript: string,
   chromosome: string,
   start: string,
-  end: string,
-  strand: string
+  end: string
 ): Promise<TxSegmentElementResponse> => {
   const params: Array<string> = [
     `transcript=${transcript}`,
     `chromosome=${chromosome}`,
-    `strand=${strand === "+" ? "%2B" : "-"}`,
   ];
   if (start !== "") params.push(`start=${start}`);
   if (end !== "") params.push(`end=${end}`);
@@ -251,13 +249,11 @@ export const getExonCoords = async (
   chromosome: string,
   start: string,
   end: string,
-  strand: string,
   gene?: string,
   txAc?: string
 ): Promise<CoordsUtilsResponse> => {
   const argsArray = [
     `chromosome=${chromosome}`,
-    `strand=${strand === "+" ? "%2B" : "-"}`,
     gene && gene !== "" ? `gene=${gene}` : "",
     txAc && txAc !== "" ? `transcript=${txAc}` : "",
     start && start !== "" ? `start=${start}` : "",

requirements.txt

@@ -25,7 +25,7 @@ decorator==5.1.1
 executing==1.2.0
 fake-useragent==1.1.3
 fastapi==0.100.0
-fusor==0.2.0
+fusor==0.4.1
 ga4gh.vrs==2.0.0a10
 gene-normalizer==0.4.0
 h11==0.14.0

server/pyproject.toml

@@ -28,8 +28,8 @@ dependencies = [
     "click",
     "boto3",
     "botocore",
-    "fusor ~= 0.3.0",
-    "cool-seq-tool ~= 0.5.1",
+    "fusor ~= 0.4.1",
+    "cool-seq-tool ~= 0.7.0",
     "pydantic == 2.4.2",
     "gene-normalizer ~= 0.4.0",
 ]

server/src/curfu/routers/constructors.py

@@ -15,7 +15,7 @@
     TemplatedSequenceElementResponse,
     TxSegmentElementResponse,
 )
-from curfu.sequence_services import InvalidInputError, get_strand
+from curfu.sequence_services import get_strand
 
 router = APIRouter()
 
@@ -93,7 +93,6 @@ async def build_tx_segment_gct(
     chromosome: str,
     start: int | None = Query(None),
     end: int | None = Query(None),
-    strand: str | None = Query(None),
 ) -> TxSegmentElementResponse:
     """Construct Transcript Segment element by providing transcript and genomic
     coordinates (chromosome, start, end positions).
@@ -107,23 +106,12 @@ async def build_tx_segment_gct(
     :return: Pydantic class with TranscriptSegment element if successful, and
         warnings otherwise.
     """
-    if strand is not None:
-        try:
-            strand_validated = get_strand(strand)
-        except InvalidInputError:
-            warning = f"Received invalid strand value: {strand}"
-            logger.warning(warning)
-            return TxSegmentElementResponse(warnings=[warning], element=None)
-    else:
-        strand_validated = strand
     tx_segment, warnings = await request.app.state.fusor.transcript_segment_element(
         tx_to_genomic_coords=False,
         transcript=parse_identifier(transcript),
-        chromosome=parse_identifier(chromosome),
-        start=start,
-        end=end,
-        strand=strand_validated,
-        residue_mode="inter-residue",
+        genomic_ac=parse_identifier(chromosome),
+        seg_start_genomic=start,
+        seg_end_genomic=end,
     )
     return TxSegmentElementResponse(element=tx_segment, warnings=warnings)
 
@@ -141,7 +129,6 @@ async def build_tx_segment_gcg(
     chromosome: str,
     start: int | None = Query(None),
     end: int | None = Query(None),
-    strand: str | None = Query(None),
 ) -> TxSegmentElementResponse:
     """Construct Transcript Segment element by providing gene and genomic
     coordinates (chromosome, start, end positions).
@@ -155,23 +142,12 @@ async def build_tx_segment_gcg(
     :return: Pydantic class with TranscriptSegment element if successful, and
         warnings otherwise.
     """
-    if strand is not None:
-        try:
-            strand_validated = get_strand(strand)
-        except InvalidInputError:
-            warning = f"Received invalid strand value: {strand}"
-            logger.warning(warning)
-            return TxSegmentElementResponse(warnings=[warning], element=None)
-    else:
-        strand_validated = strand
     tx_segment, warnings = await request.app.state.fusor.transcript_segment_element(
         tx_to_genomic_coords=False,
         gene=gene,
-        chromosome=parse_identifier(chromosome),
-        strand=strand_validated,
-        start=start,
-        end=end,
-        residue_mode="inter-residue",
+        genomic_ac=parse_identifier(chromosome),
+        seg_start_genomic=start,
+        seg_end_genomic=end,
     )
     return TxSegmentElementResponse(element=tx_segment, warnings=warnings)
 

server/src/curfu/routers/demo.py

@@ -71,7 +71,7 @@ def clientify_structural_element(
         context
     :return: client-ready structural element
     """
-    element_args = element.dict()
+    element_args = element.model_dump()
     element_args["elementId"] = str(uuid4())
 
     if element.type == StructuralElementType.UNKNOWN_GENE_ELEMENT:
@@ -119,7 +119,7 @@ def clientify_fusion(fusion: Fusion, fusor_instance: FUSOR) -> ClientFusion:
     :param fusor_instance: FUSOR object instance provided by FastAPI request context
     :return: completed client-ready fusion
     """
-    fusion_args = fusion.dict()
+    fusion_args = fusion.model_dump()
     client_elements = [
         clientify_structural_element(element, fusor_instance)
         for element in fusion.structure
@@ -145,7 +145,7 @@ def clientify_fusion(fusion: Fusion, fusor_instance: FUSOR) -> ClientFusion:
         if fusion.criticalFunctionalDomains:
             client_domains = []
             for domain in fusion.criticalFunctionalDomains:
-                client_domain = domain.dict()
+                client_domain = domain.model_dump()
                 client_domain["domainId"] = str(uuid4())
                 client_domains.append(client_domain)
             fusion_args["criticalFunctionalDomains"] = client_domains