fixed jbrowse assembly view without gene selection

EBI-Metagenomics · Nov 15, 2024 · d1d2577 · d1d2577
1 parent 67bb7af
commit d1d2577
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Showing 10 changed files with 56 additions and 50 deletions.
diff --git a/dataportal-app/src/components/interfaces/Gene.ts b/dataportal-app/src/components/interfaces/Gene.ts
@@ -0,0 +1,20 @@
+export interface GeneMeta {
+    id: number;
+    seq_id: string;
+    gene_name: string;
+    description: string;
+    strain_id: number;
+    strain: string;
+    assembly: string;
+    locus_tag: string;
+    cog: string | null;
+    kegg: string | null;
+    pfam: string | null;
+    interpro: string | null;
+    dbxref: string | null;
+    ec_number: string | null;
+    product: string | null;
+    start_position: number | null;
+    end_position: number | null;
+    annotations: Record<string, any> | null;
+}
diff --git a/dataportal-app/src/components/interfaces/Genome.ts b/dataportal-app/src/components/interfaces/Genome.ts
@@ -3,7 +3,7 @@ export interface Contig {
     length: number;
 }
 
-export interface Genome {
+export interface GenomeMeta {
     species: string;
     id: number;
     common_name: string;
@@ -18,10 +18,24 @@ export interface Genome {
 }
 
 export interface GenomeResponse {
-    results: Genome[];
+    results: GenomeMeta[];
     page_number: number;
     num_pages: number;
     has_previous: boolean;
     has_next: boolean;
     total_results: number;
 }
+
+
+export interface Genome11Meta {
+    species: number;
+    id: number;
+    common_name: string;
+    isolate_name: string;
+    assembly_name: string;
+    assembly_accession: string;
+    fasta_file: string;
+    gff_file: string;
+    fasta_url: string;
+    gff_url: string;
+}
diff --git a/dataportal-app/src/components/organisms/GeneSearch/GeneSearchForm.tsx b/dataportal-app/src/components/organisms/GeneSearch/GeneSearchForm.tsx
@@ -113,7 +113,6 @@ const GeneSearchForm: React.FC<GeneSearchFormProps> = ({
     // Fetch search results based on the query, selected species, page, sort field, and sort order
     const fetchSearchResults = useCallback(
         async (page = 1, sortField: string, sortOrder: string) => {
-            console.log('111111111111')
             const params = new URLSearchParams({
                 'query': query.trim() || '',
                 'page': String(page),

diff --git a/dataportal-app/src/components/organisms/GeneViewer/assembly.ts b/dataportal-app/src/components/organisms/GeneViewer/assembly.ts
@@ -1,4 +1,4 @@
-import {GenomeMeta} from '../../pages/GeneViewerPage';
+import {GenomeMeta} from "@components/interfaces/Genome";
 
 const getAssembly = (genomeMeta: GenomeMeta, fastaBaseUrl: string) => ({
     name: genomeMeta.assembly_name,

diff --git a/dataportal-app/src/components/organisms/GeneViewer/defaultSessionConfig.ts b/dataportal-app/src/components/organisms/GeneViewer/defaultSessionConfig.ts
@@ -1,4 +1,6 @@
-import { GeneMeta, GenomeMeta } from '../../pages/GeneViewerPage';
+import {GeneMeta} from "@components/interfaces/Gene";
+import {GenomeMeta} from "@components/interfaces/Genome";
+
 
 const getDefaultSessionConfig = (
     geneMeta: GeneMeta | null,
@@ -8,24 +10,26 @@ const getDefaultSessionConfig = (
 ) => {
     if (!genomeMeta) {
         console.log("Genome meta information not found");
-        return null; // Return null if genomeMeta is missing
+        return null;
     }
 
     const displayedRegions = geneMeta
         ? [
             {
                 refName: geneMeta.seq_id,
                 start: geneMeta.start_position || 0,
-                end: geneMeta.end_position || 50000,
+                end: geneMeta.end_position || 1000,
                 reversed: true,
                 assemblyName: genomeMeta.assembly_name,
             },
         ]
         : [
             {
-                refName: genomeMeta.assembly_name,
+                refName: genomeMeta.contigs[0].seq_id,
                 start: 0,
-                end: 5000000, // Adjust this default range
+                end: 1000,
+                reversed: true,
+                assemblyName: genomeMeta.assembly_name,
             },
         ];
 

diff --git a/dataportal-app/src/components/organisms/GeneViewer/tracks.ts b/dataportal-app/src/components/organisms/GeneViewer/tracks.ts
@@ -1,4 +1,4 @@
-import {GenomeMeta} from '../../pages/GeneViewerPage';
+import {GenomeMeta} from "@components/interfaces/Genome";
 
 const getTracks = (genomeMeta: GenomeMeta, gffBaseUrl: string) => [
     {

diff --git a/dataportal-app/src/components/pages/GeneViewerPage.tsx b/dataportal-app/src/components/pages/GeneViewerPage.tsx
@@ -9,40 +9,8 @@ import GeneSearchForm from "@components/organisms/GeneSearch/GeneSearchForm";
 import {fetchGenomeById} from "../../services/genomeService";
 import {fetchGeneById, fetchGeneBySearch} from "../../services/geneService";
 import {JBrowseApp} from "@jbrowse/react-app";
-
-export interface GeneMeta {
-    id: number;
-    seq_id: string;
-    gene_name: string;
-    description: string;
-    strain_id: number;
-    strain: string;
-    assembly: string;
-    locus_tag: string;
-    cog: string | null;
-    kegg: string | null;
-    pfam: string | null;
-    interpro: string | null;
-    dbxref: string | null;
-    ec_number: string | null;
-    product: string | null;
-    start_position: number | null;
-    end_position: number | null;
-    annotations: Record<string, any> | null;
-}
-
-export interface GenomeMeta {
-    species: number;
-    id: number;
-    common_name: string;
-    isolate_name: string;
-    assembly_name: string;
-    assembly_accession: string;
-    fasta_file: string;
-    gff_file: string;
-    fasta_url: string;
-    gff_url: string;
-}
+import {GenomeMeta} from "@components/interfaces/Genome";
+import {GeneMeta} from "@components/interfaces/Gene";
 
 const GeneViewerPage: React.FC = () => {
     const [geneMeta, setGeneMeta] = useState<GeneMeta | null>(null);
@@ -93,10 +61,12 @@ const GeneViewerPage: React.FC = () => {
     }, [genomeMeta]);
 
     const sessionConfig = useMemo(() => {
-        if (genomeMeta && geneMeta) {
+        if (genomeMeta) {
+            console.log('22222222222');
             return getDefaultSessionConfig(geneMeta, genomeMeta, assembly, tracks);
-        } else if (genomeMeta) {
+        } else {
             // Default session configuration if only genomeMeta is available
+            console.log('111111111111');
             return {
                 name: "Default Genome View",
                 views: [
@@ -106,7 +76,7 @@ const GeneViewerPage: React.FC = () => {
                         tracks: tracks,
                         displayedRegions: [
                             {
-                                refName: genomeMeta.assembly_name,
+                                refName: 'Default assembly',
                                 start: 0,
                                 end: 5000000
                             }

diff --git a/dataportal-app/src/services/geneService.ts b/dataportal-app/src/services/geneService.ts
@@ -51,7 +51,6 @@ export const fetchGeneSearchResults = async (
     selectedSpecies?: number [],
 ) => {
     try {
-        console.log('2222222222')
         const params = new URLSearchParams({
             query: gene,
             page: String(page),

diff --git a/k8s-hl/dev/mett-dataportal-api-deployment.yaml b/k8s-hl/dev/mett-dataportal-api-deployment.yaml
@@ -19,7 +19,7 @@ spec:
         runAsUser: 7123
         runAsGroup: 1347
       containers:
-        - image: quay.io/microbiome-informatics/mett-dataportal-api:v0.0.29
+        - image: quay.io/microbiome-informatics/mett-dataportal-api:v0.0.30
           imagePullPolicy: Always
           name: mett-dataportal-api-dev
           env:

diff --git a/k8s-hl/dev/mett-dataportal-app-deployment.yaml b/k8s-hl/dev/mett-dataportal-app-deployment.yaml
@@ -16,7 +16,7 @@ spec:
         app: mett-dataportal-react-app-dev
     spec:
       containers:
-        - image: quay.io/microbiome-informatics/mett-dataportal-react-app:v0.0.29
+        - image: quay.io/microbiome-informatics/mett-dataportal-react-app:v0.0.30
           imagePullPolicy: Always
           name: mett-dataportal-react-app-dev
           env: