Merge pull request #164 from PathwayCommons/iss146_not-found

Updates to GET endpoint
PathwayCommons · Jul 31, 2024 · 230f449 · 230f449
2 parents 966f58b + 0b6a62b
commit 230f449
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Showing 3 changed files with 38 additions and 15 deletions.
diff --git a/src/server/db/db.js b/src/server/db/db.js
@@ -7,6 +7,8 @@ import { patches } from './patches';
 const NS_FIELD = 'namespace';
 const ORG_FIELD = 'organism';
 
+const xref2id = (namespace, id) => `${namespace}:${id}`.toUpperCase();
+
 /**
  * @exports db
  */
@@ -232,7 +234,8 @@ const db = {
       // remove the main name from the synonym list (if it exists) for the same reason
       _.remove(entry.synonyms, syn => syn.toLowerCase() === entry.name.toLowerCase());
 
-      body.push( { index: { _index: INDEX, _id: (entry.namespace + ':' + entry.id).toUpperCase() } } );
+      const { namespace, id } = entry;
+      body.push( { index: { _index: INDEX, _id: xref2id( namespace, id ) } } );
       body.push( entry );
     } );
 
@@ -258,7 +261,8 @@ const db = {
     let body = [];
 
     updates.forEach( update => {
-      body.push( { update: { _index: INDEX, _id: (namespace + ':' + update.id).toUpperCase() } } );
+      const { id } = update;
+      body.push( { update: { _index: INDEX, _id: xref2id( namespace, id ) } } );
       body.push( { doc: update.updates } );
     } );
 
@@ -358,20 +362,23 @@ const db = {
    * @param {string} id The id of entity to search
    * @param {string} [namespace=undefined] Namespace to seek the entity e.g. 'uniprot', 'chebi', ...
    * @returns {Promise} Promise objects represents the entity with the given id from the given namespace,
-   * if there is no such entity it represents null.
+   * if there is no such entity it will reject with err (status (404) and message ("Not Found")).
    */
   get: function( id, namespace ){
     let client = this.connect();
-    let body = {};
-
-    _.set( body, ['query', 'bool', 'must', 'multi_match', 'fields'], ['id', 'ids'] );
-    _.set( body, ['query', 'bool', 'must', 'multi_match', 'query'], id );
-    _.set( body, ['query', 'bool', 'filter', 'term', NS_FIELD], namespace );
-
-    return client.search({
-      body,
-      index: INDEX
-    }).then( res => res.hits.hits.map( e => e._source )[0] );
+    const _id = xref2id( namespace, id );
+
+    return client.get({
+      index: INDEX,
+      type: '_doc',
+      id: _id
+    }).then( res => {
+      if( res.found ){
+        return res._source;
+      } else {
+        throw new Error('Not Found');
+      }
+    });
   },
   /**
    * Retrieve dbXrefs in another database, given a db and one or more ids

diff --git a/src/server/routes/index.js b/src/server/routes/index.js
@@ -89,11 +89,16 @@ router.get('/search', function(req, res){
  *     responses:
  *       200:
  *         description: The metadata for the grounding
+ *       404:
+ *         description: The grounding was not found
  */
-router.post('/get', function(req, res){
+router.post('/get', function(req, res, next){
   const { namespace, id } = req.body;
 
-  aggregate.get(namespace, id).then(searchRes => res.json(searchRes));
+  aggregate
+    .get(namespace, id)
+    .then(searchRes => res.json(searchRes))
+    .catch(next);
 });
 
 /**

diff --git a/test/aggregate-quality.js b/test/aggregate-quality.js
@@ -87,4 +87,15 @@ describe('Search and Get Aggregate', function(){
 
   }); // SEARCH_OBJECTS
 
+  describe('GET', () => {
+    it('Should not throw when id does exist', function(){
+      const xref_ncbi_known = { namespace: 'ncbi', id: '1' };
+      return expect( getEnt( xref_ncbi_known.namespace, xref_ncbi_known.id ) ).not.to.be.rejected;
+    });
+    it('Should throw when id does not exist', function(){
+      const xref_ncbi_unknown = { namespace: 'ncbi', id: '0' };
+      return expect( getEnt( xref_ncbi_unknown.namespace, xref_ncbi_unknown.id ) ).to.be.rejected;
+    });
+  }); // GET
+
 }); // describe