Merge pull request #839 from legumeinfo/feature-newlinkouts

Feature newlinkouts

src/app/core/models/index.ts

@@ -1,6 +1,6 @@
 import { AppConfig, Brand, Communication, DashboardView, Dashboard,
   Miscellaneous, Tour } from './app-config.model';
-import { OrganismPlaceholders } from './placeholders.model';
+import { OrganismPlaceholders, GenePlaceholders, RegionPlaceholders } from './placeholders.model';
 import { Script, isScript } from './script.model';
 import { GET, POST, Request, Server } from './server.model';
 
@@ -14,6 +14,8 @@ export const models: any[] = [
   Miscellaneous,
   Tour,
   OrganismPlaceholders,
+  GenePlaceholders,
+  RegionPlaceholders,
   GET,
   POST,
   Request,

src/app/core/models/placeholders.model.ts

@@ -3,3 +3,13 @@ export enum OrganismPlaceholders {
   Species = 'SPECIES',
   Chromosome = 'CHROMOSOME',
 }
+
+export enum GenePlaceholders {
+  Gene = 'GENE',
+}
+
+export enum RegionPlaceholders {
+  Chromosome = 'CHROMOSOME',
+  Start = 'START',
+  Stop = 'STOP',
+}

src/app/gene/services/gene.service.ts

@@ -9,9 +9,10 @@ import * as geneActions from '@gcv/gene/store/actions/gene.actions';
 import * as fromRoot from '@gcv/store/reducers';
 import * as fromGene from '@gcv/gene/store/selectors/gene/';
 // app
-import { AppConfig, ConfigError, GET, POST, GRPC } from '@gcv/core/models';
+import { AppConfig, GenePlaceholders, ConfigError, GET, POST, GRPC } from '@gcv/core/models';
 import { HttpService } from '@gcv/core/services/http.service';
 import { Gene, Track } from '@gcv/gene/models';
+import { placeholderReplace } from '@gcv/core/utils';
 // api
 import { GenesGetReply, GenesGetRequest, GenesPromiseClient }
   from 'legumeinfo-microservices/dist/genes_service/v1';
@@ -74,10 +75,17 @@ export class GeneService extends HttpService {
     return this._store.select(fromGene.getSelectedGenes);
   }
 
+  //fill in templated geneLinksURL
+  private geneToGeneLinksURL(urlTemplate: string, gene: string): string {
+    const placeholders = {};
+    placeholders[GenePlaceholders.Gene] = gene;
+    return placeholderReplace(urlTemplate, placeholders);
+  }
+
   // fetches source specific details for the given gene
   getGeneDetails(gene: string, source: string): Observable<any> {
     const request = this._appConfig.getServerRequest(source, 'geneLinks');
-    const makeUrl = (url: string) => url + gene + '/json';
+    const makeUrl = (url: string) => this.geneToGeneLinksURL(request.url, gene);
     return this._makeHttpRequest<any>(request, {}, makeUrl);
   }
 

src/app/gene/services/region.service.ts

@@ -8,10 +8,11 @@ import { Store } from '@ngrx/store';
 import * as regionActions from '@gcv/gene/store/actions/region.actions';
 import * as fromRoot from '@gcv/store/reducers';
 // app
-import { AppConfig, ConfigError, GET, POST, GRPC } from '@gcv/core/models';
+import { AppConfig, RegionPlaceholders, ConfigError, GET, POST, GRPC } from '@gcv/core/models';
 import { Region } from '@gcv/gene/models';
 import { HttpService } from '@gcv/core/services/http.service';
 import { grpcRegionToModel } from './shims';
+import { placeholderReplace } from '@gcv/core/utils';
 // api
 import { ChromosomeRegionGetReply, ChromosomeRegionGetRequest,
   ChromosomeRegionPromiseClient, } from 'legumeinfo-microservices/dist/chromosomeregion_service/v1';
@@ -61,10 +62,19 @@ export class RegionService extends HttpService {
     this._store.dispatch(new regionActions.Get({chromosome, start, stop, source}));
   }
 
+  //fill in templated regionLinksURL
+  private regionToRegionLinksURL(urlTemplate: string, chromosome: string, start: number, stop: number): string {
+    const placeholders = {};
+    placeholders[RegionPlaceholders.Chromosome] = chromosome;
+    placeholders[RegionPlaceholders.Start] = start.toString();
+    placeholders[RegionPlaceholders.Stop] = stop.toString();
+    return placeholderReplace(urlTemplate, placeholders);
+  }
+
   // fetches source specific details for the given region
   getRegionDetails(chromosome: string, start: number, end: number, source: string): Observable<any> {
     const request = this._appConfig.getServerRequest(source, 'regionLinks');
-    const makeUrl = (url: string) => url + chromosome + '&start=' + start + '&end=' + end ;
+    const makeUrl = (url: string) => this.regionToRegionLinksURL(request.url, chromosome, start, end);
     return this._makeHttpRequest<any>(request, {}, makeUrl);
   }
 

src/config/config.json

@@ -56,11 +56,15 @@
       },
       "geneLinks": {
         "type": "GET",
-        "url": "https://legumeinfo.org/gene_links/"
+        "url": "https://services.lis.ncgr.org/gene_linkouts?genes={GENE}"
+      },
+      "regionLinks": {
+        "type": "GET",
+        "url": "https://services.lis.ncgr.org/genomic_region_linkouts?genomic_regions={CHROMOSOME}:{START}-{STOP}"
       },
       "familyTreeLink": {
         "type": "GET",
-        "url": "http://legumeinfo.org/chado_gene_phylotree_v2?family="
+        "url": "https://funnotate.legumeinfo.org/?family="
       },
       "chromosome": {
         "type": "GRPC",