From 78c0197f400f3f53109535a7dc209b4c1f7ccdf9 Mon Sep 17 00:00:00 2001
From: adf-ncgr <adf@ncgr.org>
Date: Mon, 19 Jun 2023 09:08:41 -0600
Subject: [PATCH] templated replacement of info in linkout urls

---
 src/app/core/models/placeholders.model.ts |  9 +++++++--
 src/app/gene/services/gene.service.ts     | 13 +++++--------
 src/app/gene/services/region.service.ts   | 15 ++++++++++++---
 src/config/config.json                    |  6 +++---
 4 files changed, 27 insertions(+), 16 deletions(-)

diff --git a/src/app/core/models/placeholders.model.ts b/src/app/core/models/placeholders.model.ts
index c0380ce1..88e72e27 100644
--- a/src/app/core/models/placeholders.model.ts
+++ b/src/app/core/models/placeholders.model.ts
@@ -3,8 +3,13 @@ export enum OrganismPlaceholders {
   Species = 'SPECIES',
   Chromosome = 'CHROMOSOME',
 }
+
 export enum GenePlaceholders {
-  GeneID = 'GENE_ID',
-  Species = 'SPECIES',
+  Gene = 'GENE',
+}
+
+export enum RegionPlaceholders {
   Chromosome = 'CHROMOSOME',
+  Start = 'START',
+  Stop = 'STOP',
 }
diff --git a/src/app/gene/services/gene.service.ts b/src/app/gene/services/gene.service.ts
index db58e89d..3833c3c9 100644
--- a/src/app/gene/services/gene.service.ts
+++ b/src/app/gene/services/gene.service.ts
@@ -76,19 +76,16 @@ export class GeneService extends HttpService {
   }
 
   //fill in templated geneLinksURL
-  //TODO: should different servers be able to specify their own geneLinks?
-  export function geneToGeneLinksURL(gene) {
-    let name = AppConfig.geneLinks.url;
+  geneToGeneLinksURL(urlTemplate: string, gene: string): string {
     const placeholders = {};
-    placeholders[GenePlaceholders.GeneID] = gene;
-    return placeholderReplace(name, 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');
-    //TODO: make this more configurable via template substitution
-    const makeUrl = (url: string) => geneToGeneLinksURL(gene);
+    const makeUrl = (url: string) => this.geneToGeneLinksURL(request.url, gene);
     return this._makeHttpRequest<any>(request, {}, makeUrl);
   }
 
diff --git a/src/app/gene/services/region.service.ts b/src/app/gene/services/region.service.ts
index 692bceb2..8bfd8934 100644
--- a/src/app/gene/services/region.service.ts
+++ b/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';
@@ -61,11 +62,19 @@ export class RegionService extends HttpService {
     this._store.dispatch(new regionActions.Get({chromosome, start, stop, source}));
   }
 
+  //fill in templated regionLinksURL
+  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');
-    //TODO: make this more configurable via template-based substitution
-    const makeUrl = (url: string) => url + chromosome + ':' + start + '-' + end ;
+    const makeUrl = (url: string) => this.regionToRegionLinksURL(request.url, chromosome, start, end);
     return this._makeHttpRequest<any>(request, {}, makeUrl);
   }
 
diff --git a/src/config/config.json b/src/config/config.json
index b1101fec..14b41f17 100644
--- a/src/config/config.json
+++ b/src/config/config.json
@@ -56,15 +56,15 @@
       },
       "geneLinks": {
         "type": "GET",
-        "url": "https://services.lis.ncgr.org/gene_linkouts?genes={GENE_ID}"
+        "url": "https://services.lis.ncgr.org/gene_linkouts?genes={GENE}"
       },
       "regionLinks": {
         "type": "GET",
-        "url": "https://services.lis.ncgr.org/linkouts/genomic_region_linkouts?"
+        "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",