Merge pull request #91 from KeithKelleher/master

updates to support Pharos version 3.16
ncats · Apr 13, 2023 · 8182661 · 8182661
2 parents d0cd95f + 01e97f6
commit 8182661
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Showing 6 changed files with 69 additions and 3 deletions.
diff --git a/package.json b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "pharos-graphql-server",
-  "version": "3.15.1",
+  "version": "3.16.0",
   "description": "",
   "main": "src/index.js",
   "scripts": {

diff --git a/src/db_credentials.js b/src/db_credentials.js
@@ -3,9 +3,9 @@
 //
 const cred = {
     DBHOST: 'tcrd-cluster.cluster-ceyknq0yekb3.us-east-1.rds.amazonaws.com',
-    DBNAME: 'tcrd6134pharos2',
+    DBNAME: 'pharos316',
     USER: 'tcrd',
     PWORD: '',
-    LASTMOD: '2023-01-13'
+    LASTMOD: '2023-03-30'
 };
 module.exports.cred = cred;
diff --git a/src/models/databaseConfig.ts b/src/models/databaseConfig.ts
@@ -121,6 +121,7 @@ export class DatabaseConfig {
 
     modelList: Map<string, ModelInfo> = new Map<string, { name: string, table: string, column: string }>();
     communityDataList: Map<string, any[]> = new Map<string, any[]>();
+    communityDataSequenceList: Map<string, any> = new Map<string, any>();
     database: any;
     dbName: string;
     settingsDB: any;
@@ -143,6 +144,13 @@ export class DatabaseConfig {
         return {community_data: 'community_data'};
     }
 
+    get communitySequenceDataTables(): {community_sequence_data: string, community_sequence_tracks: string} {
+        return {
+            community_sequence_data: 'community_sequence_data',
+            community_sequence_tracks: 'community_sequence_tracks'
+        };
+    }
+
     get assocModelTable(): { associated_model: string } {
         return {associated_model: 'model'};
     };
@@ -175,6 +183,54 @@ export class DatabaseConfig {
                 list.push(row);
             });
         });
+        const seqQuery = this.settingsDB({...this.communitySequenceDataTables})
+            .select({
+                code: 'code',
+                category_label: 'community_sequence_data.label',
+                category_type: 'community_sequence_data.trackType',
+                track_label: 'community_sequence_tracks.label',
+                instructions: 'community_sequence_tracks.instructions',
+                track_type: 'community_sequence_tracks.trackType',
+                adapter: 'community_sequence_tracks.adapter',
+                url: 'community_sequence_tracks.url',
+                tooltip: 'community_sequence_tracks.tooltip',
+                row: 'community_sequence_tracks.row',
+                filter: 'community_sequence_tracks.filter'
+            })
+            .whereRaw('community_sequence_tracks.sequence_category = community_sequence_data.code')
+            .where('community_sequence_data.default', true)
+            .then((rows: any[]) => {
+                rows.forEach(row => {
+                    const appendTrack = (list: any[], currentRow: any) => {
+                        list.push({
+                            name: row.code + '-' + row.row,
+                            row: row.row,
+                            label: row.track_label,
+                            instructions: row.instructions,
+                            filter: JSON.parse(row.filter),
+                            trackType: row.track_type,
+                            data: [{
+                                adapter: row.adapter,
+                                url: row.url
+                            }],
+                            tooltip: row.tooltip
+                        });
+                    }
+                    if (this.communityDataSequenceList.has(row.code)) {
+                        const categoryObj = this.communityDataSequenceList.get(row.code);
+                        appendTrack(categoryObj.tracks, row);
+                    } else {
+                        const categoryObj = {
+                            name: row.code,
+                            label: row.category_label,
+                            trackType: row.category_type,
+                            tracks: []
+                        };
+                        appendTrack(categoryObj.tracks, row);
+                        this.communityDataSequenceList.set(row.code, categoryObj);
+                    }
+                });
+            });
     }
     loadMondoMap() {
         const query = this.database('mondo_xref').distinct({

diff --git a/src/pharos_config.sqlite b/src/pharos_config.sqlite
diff --git a/src/unfiltered_counts.sqlite b/src/unfiltered_counts.sqlite
diff --git a/src/utils.js b/src/utils.js
@@ -61,6 +61,16 @@ module.exports.applySpecialRoutes = (app, tcrd) => {
     res.end(JSON.stringify(parseResidueData(results)));
   });
 
+  app.get("/sources", async (req, res) => {
+    res.setHeader('Content-Type', 'application/json');
+    res.setHeader('Access-Control-Allow-Origin', '*');
+    const list = [];
+    tcrd.tableInfo.communityDataSequenceList.forEach((v,k) => {
+      list.push(v);
+   })
+    res.end(JSON.stringify(list));
+  });
+
   app.get("/sitemap.xml", async (req, res) => {
     res.setHeader('Content-Type', 'application/xml');
     res.setHeader('Access-Control-Allow-Origin', '*');