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

@@ -1,89 +1,66 @@
-aiofiles==23.1.0
-anyio==3.7.1
-appdirs==1.4.4
-appnope==0.1.3
-asttokens==2.2.1
-asyncpg==0.28.0
-attrs==23.1.0
-backcall==0.2.0
-beautifulsoup4==4.12.2
-biocommons.seqrepo==0.6.5
+agct==0.1.0.dev2
+aiofiles==24.1.0
+annotated-types==0.7.0
+anyio==4.4.0
+asttokens==2.4.1
+async-timeout==4.0.3
+asyncpg==0.29.0
+attrs==24.2.0
+biocommons.seqrepo==0.6.9
 bioutils==0.5.8.post1
-boto3==1.28.11
-botocore==1.31.11
-bs4==0.0.1
+boto3==1.35.4
+botocore==1.35.4
 canonicaljson==2.0.0
-certifi==2023.7.22
-charset-normalizer==3.2.0
-click==8.1.6
+certifi==2024.7.4
+charset-normalizer==3.3.2
+click==8.1.7
 coloredlogs==15.0.1
-configparser==6.0.0
-cool-seq-tool==0.5.1
-cssselect==1.2.0
-Cython==3.0.0
+configparser==7.1.0
+cool_seq_tool==0.7.0
 decorator==5.1.1
-executing==1.2.0
-fake-useragent==1.1.3
-fastapi==0.100.0
-fusor==0.2.0
+executing==2.0.1
+fastapi==0.112.1
+fusor==0.4.1
 ga4gh.vrs==2.0.0a10
 gene-normalizer==0.4.0
 h11==0.14.0
 hgvs==1.5.4
 humanfriendly==10.0
-idna==3.4
-importlib-metadata==6.8.0
-inflection==0.5.1
-ipython==8.14.0
-jedi==0.18.2
-Jinja2==3.1.2
+idna==3.7
+importlib_metadata==8.4.0
+ipython==8.26.0
+jedi==0.19.1
+Jinja2==3.1.4
 jmespath==1.0.1
-jsonschema==3.2.0
-lxml==4.9.3
-Markdown==3.4.4
-MarkupSafe==2.1.3
-matplotlib-inline==0.1.6
-numpy==1.25.1
-pandas==2.0.3
-parse==1.19.1
+MarkupSafe==2.1.5
+matplotlib-inline==0.1.7
 Parsley==1.3
-parso==0.8.3
-pexpect==4.8.0
-pickleshare==0.7.5
-prompt-toolkit==3.0.39
-psycopg2==2.9.6
+parso==0.8.4
+pexpect==4.9.0
+polars==1.5.0
+prompt_toolkit==3.0.47
+psycopg2==2.9.9
 ptyprocess==0.7.0
-pure-eval==0.2.2
+pure_eval==0.2.3
 pydantic==2.4.2
-pyee==8.2.2
-Pygments==2.15.1
-pyliftover==0.4
-pyppeteer==1.0.2
-pyquery==2.0.0
-pyrsistent==0.19.3
-pysam==0.21.0
-python-dateutil==2.8.2
-python-jsonschema-objects==0.4.2
-pytz==2023.3
-PyYAML==6.0.1
-requests==2.31.0
-requests-html==0.10.0
-s3transfer==0.6.1
+pydantic_core==2.10.1
+Pygments==2.18.0
+pysam==0.22.1
+python-dateutil==2.9.0.post0
+requests==2.32.3
+s3transfer==0.10.2
 six==1.16.0
-sniffio==1.3.0
-soupsieve==2.4.1
-sqlparse==0.4.4
-stack-data==0.6.2
-starlette==0.27.0
+sniffio==1.3.1
+sqlparse==0.5.1
+stack-data==0.6.3
+starlette==0.38.2
 tabulate==0.9.0
-tqdm==4.65.0
-traitlets==5.9.0
-typing_extensions==4.7.1
-tzdata==2023.3
-urllib3==1.26.16
-uvicorn==0.23.1
-w3lib==2.1.1
-wcwidth==0.2.6
-websockets==10.4
+tqdm==4.66.5
+traitlets==5.14.3
+typing_extensions==4.12.2
+urllib3==1.26.19
+uvicorn==0.30.6
+wags_tails==0.1.4
+wcwidth==0.2.13
 yoyo-migrations==8.2.0
-zipp==3.16.2
+zipp==3.20.0

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",
 ]