Merge branch 'main' of github.com:cytoscape/enrichment-map-webapp

cytoscape · Jun 3, 2024 · ab41ede · ab41ede
2 parents 8840dc6 + 89ff049
commit ab41ede
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Showing 4 changed files with 5 additions and 121 deletions.
diff --git a/src/client/components/network-editor/gene-list-panel.js b/src/client/components/network-editor/gene-list-panel.js
@@ -88,16 +88,8 @@ const GeneMetadataPanel = ({ controller, symbol, showSymbol }) => {
     }
   );
 
-  const queryNodes = useQuery(
-    ['related-node-ids', symbol],
-    () => fetch(`/api/${controller.cy.data('id')}/${symbol}/nodes`)
-          .then(res => res.json())
-          .then(res => res.nodeIDs),
-    { retry: false }
-  );
-
   const data = queryGeneData.data;
-  const isLoading = queryGeneData.isLoading || queryNodes.isLoading;
+  const isLoading = queryGeneData.isLoading;
 
   let error = queryGeneData.error;
   let description, ncbiId;

diff --git a/src/server/datastore.js b/src/server/datastore.js
@@ -208,6 +208,8 @@ class Datastore {
     networkJson['_id'] = networkID.bson;
     networkJson['networkIDStr'] = networkID.string;
     networkJson['creationTime'] = new Date();
+
+    delete networkJson['summaryNetwork'];
 
     if(networkName)
       networkJson['networkName'] = networkName;
@@ -283,7 +285,6 @@ class Datastore {
 
     // Create an initialize the documents in the GENE_RANKS_COLLECTION, used for quick lookups.
     await this.createGeneRanksDocuments(networkID);
-    await this.mergeSummaryNodeIDsIntoGeneRanks(geneSetCollection, networkID);
     await this.mergePathwayNamesIntoGeneRanks(geneSetCollection, networkID);
 
     return geneListID.string;
@@ -311,51 +312,6 @@ class Datastore {
   }
 
 
-  /**
-   * Update the documents in the geneRanks collection to add the 'summaryNodeIDs' field.
-   */
-  async mergeSummaryNodeIDsIntoGeneRanks(geneSetCollection, networkID) {
-    await this.db
-      .collection(NETWORKS_COLLECTION)
-      .aggregate([
-        // Get the nodeIDs and the names of the Pathways they represent
-        { $match: { _id: networkID.bson } },
-        { $replaceWith: { path: "$summaryNetwork.elements.nodes.data" } },
-        { $unwind: { path: "$path" } },
-        { $replaceRoot: { newRoot: "$path" } },
-        { $addFields: { splitNames: { 
-            $cond: {
-              if: { $isArray: "$name" },
-              then: { $getField: "name" },
-              else: { $split: [ "$name", "," ] }
-            }
-        } } },
-        { $unwind: { path: "$splitNames" } },
-
-        // Lookup the genes contained in each node
-        { $lookup: {
-            from: geneSetCollection,
-            localField: "splitNames",
-            foreignField: "name",
-            as: "geneSet"
-        }},
-        { $replaceRoot: { newRoot: { $mergeObjects: [ { $arrayElemAt: [ "$geneSet", 0 ] }, "$$ROOT" ] } } },
-        { $unwind: { path: "$genes" } },
-        { $group: { _id: "$genes", nodeIDs: { $addToSet: "$id" } }},
-        { $project: { _id: 0, gene: "$_id", nodeIDs: 1, networkID: networkID.bson } },
-
-        // Update the geneRanks collection
-        { $merge: {
-            into: GENE_RANKS_COLLECTION,
-            on: [ "networkID", "gene" ],
-            whenNotMatched: "discard",
-            let: { nodeIDs: "$nodeIDs" },
-            whenMatched: [{ $addFields: { summaryNodeIDs: "$$nodeIDs" } }],
-          }
-        }
-      ]).toArray(); 
-  }
-
   /**
    * Update the documents in the geneRanks collection to add the 'pathways' field.
    */
@@ -608,7 +564,7 @@ class Datastore {
       .aggregate([
         // Get the node data in the network
         { $match: { _id: networkID.bson } },
-        { $replaceWith: { path: "$summaryNetwork.elements.nodes.data" } },
+        { $replaceWith: { path: "$network.elements.nodes.data" } },
         { $unwind: { path: "$path" } },
         { $replaceRoot: { newRoot: "$path" } },
         // Get the names
@@ -651,19 +607,6 @@ class Datastore {
   }
 
 
-  /**
-   * Returns the IDs of nodes that contain the given gene.
-   */
-  async getNodesContainingGene(networkIDString, geneName) {
-    const networkID = makeID(networkIDString);
-    return await this.db
-      .collection(GENE_RANKS_COLLECTION)
-      .findOne(
-        { networkID: networkID.bson, gene: geneName },
-        { projection: { _id: 0, nodeIDs: "$summaryNodeIDs" } }
-      );
-  }
-
   /**
    * Returns the values of the min and max ranks in the network.
    */
@@ -693,6 +636,7 @@ class Datastore {
 
     if(geneSetNames === undefined || geneSetNames.length == 0) {
       geneSetNames = await this.getNodeDataSetNames(networkID);
+      console.log("geneSetNames", geneSetNames);
     }
 
     const geneListWithRanks = await this.db

diff --git a/src/server/routes/api/index.js b/src/server/routes/api/index.js
@@ -126,23 +126,6 @@ http.get('/:netid/ranks', async function(req, res, next) {
   }
 });
 
-/**
- * Returns the IDs of nodes that contain the given gene.
- */
-http.get('/:netid/:gene/nodes', async function(req, res, next) {
-  try {
-    const { netid, gene } = req.params;
-    const nodeIDs = await Datastore.getNodesContainingGene(netid, gene);
-    if(!nodeIDs) {
-      res.sendStatus(404);
-    } else {
-      res.send(JSON.stringify(nodeIDs));
-    }
-  } catch (err) {
-    next(err);
-  }
-});
-
 
 /*
  * Returns the contents of multiple gene sets, including ranks.

diff --git a/test/test_datastore.js b/test/test_datastore.js
@@ -26,8 +26,6 @@ describe('Gene Set Queries', () => {
   it('gets a network', async () => {
     const network = await Datastore.getNetwork(networkID, { nodeLimit: 100 });
     expect(network.networkIDStr).to.eql(networkID);
-    expect(network.summaryNetwork.elements.nodes.length).to.eql(4);
-    expect(network.summaryNetwork.elements.edges.length).to.eql(2);
   });
 
   it('get a gene sets', async () => {
@@ -128,37 +126,4 @@ describe('Gene Set Queries', () => {
     });
   });
 
-  it('gets nodes for genes', async () => { 
-    const lookup = async gene => {
-      const results = await Datastore.getNodesContainingGene(networkID, gene);
-      results.nodeIDs.sort();
-      return results;
-    };
-    {  
-      const results = await lookup("AAA");
-      expect(results).to.eql({
-        nodeIDs: [
-          '3f9549bd-17f3-4625-88da-86f33794aac5',
-          '9aaa7dea-8353-4cb6-9e8b-dd0b52927821',
-          'aae5d32b-04ac-4aa7-a440-81843921e258',
-          'ccc53527-c85f-411d-8b96-bd317522b6a7',
-        ]
-      });
-    } {
-      const results = await lookup("CCC");
-      expect(results).to.eql({
-        nodeIDs: [
-          '9aaa7dea-8353-4cb6-9e8b-dd0b52927821',
-          'ccc53527-c85f-411d-8b96-bd317522b6a7',
-        ]
-      });
-    } {
-      const results = await lookup("LLL");
-      expect(results).to.eql({
-        nodeIDs: [
-          'aae5d32b-04ac-4aa7-a440-81843921e258',
-        ]
-      });
-    } 
-  });
 });