Merge pull request #52 from mboudet/dev_version

Fix redirect and add annotation management in ES.

Author: mboudet

CHANGELOG.md

@@ -5,6 +5,14 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html)
 
+## [0.4.10] 2023-11-29
+
+### Added
+
+- Added 'annotation_field" config option, for external ES search
+- Added redirection from Gene subentity to Gene in url
+
+
 ## [0.4.10] 2023-11-23
 
 ### Added

config.json.template

@@ -13,6 +13,7 @@
   "externalSearchOptions": {
     "url": "http://0.0.0.0:80",
     "gene_field": "gene_id",
+    "annotation_field": "annotation",
     "query_param": "q",
     "field_param": "display_fields",
     "count_param": "max_results"

imports/api/publications.js

@@ -86,13 +86,17 @@ Meteor.publish({
       let url = config.externalSearchOptions.url.replace(/,+$/, "") + "/";
       let paramsDict = {}
       let geneField = config.externalSearchOptions.gene_field ? config.externalSearchOptions.gene_field : "geneId"
+      let annotationField = config.externalSearchOptions.annotation_field ? config.externalSearchOptions.annotation_field : ""
       if (config.externalSearchOptions.query_param){
         paramsDict[config.externalSearchOptions.query_param] = query.query
       } else {
         url += query.query
       }
       if (config.externalSearchOptions.field_param){
         paramsDict[config.externalSearchOptions.field_param] = geneField
+        if (config.externalSearchOptions.annotation_field) {
+          paramsDict[config.externalSearchOptions.field_param] += "," + annotationField
+        }
       }
 
       if (config.externalSearchOptions.count_param){
@@ -103,9 +107,15 @@ Meteor.publish({
       url = url + "?" + new URLSearchParams(paramsDict)
       const response = HTTP.get(url);
       if (response.statusCode === 200){
-        geneResults = response.data.data.map(result => result._source[geneField])
+        geneResults = response.data.data.map(result => {
+          if (config.externalSearchOptions.annotation_field){
+            return {"ID": result._source[geneField], "annotationName": result._source[annotationField]}
+          } else {
+            return {"ID": result._source[geneField]}
+          }
+        })
       }
-      transformedQuery = {genomeId: { $in: queryGenomeIds }, ID: { $in: geneResults }}
+      transformedQuery = {genomeId: { $in: queryGenomeIds }, $or: geneResults}
     } else {
       transformedQuery = { ...query, genomeId: { $in: queryGenomeIds } };
     }
@@ -120,7 +130,13 @@ Meteor.publish({
     if (typeof geneId === 'undefined') {
       Object.assign(query, { 'subfeatures.ID': transcriptId });
     } else {
-      Object.assign(query, { ID: geneId });
+      Object.assign(query, {
+        $or: [
+          {'ID': geneId},
+          { 'subfeatures.ID': geneId },
+          { 'subfeatures.protein_id': geneId },
+        ],
+      });
     }
 
     return Genes.find(query);

imports/ui/singleGenePage/SingleGenePage.jsx

@@ -84,9 +84,22 @@ function geneDataTracker({ match, genomeDataCache, location }) {
   const geneSub = Meteor.subscribe('singleGene', { geneId });
   let genes
   if (annotation) {
-    genes = Genes.find({ ID: geneId, annotationName: annotation }).fetch();
+    genes = Genes.find({
+      $or: [
+        {'ID': geneId},
+        { 'subfeatures.ID': geneId },
+        { 'subfeatures.protein_id': geneId },
+      ],
+      annotationName: annotation
+    }).fetch();
   } else {
-    genes = Genes.find({ ID: geneId }).fetch();
+    genes = Genes.find({
+      $or: [
+        {'ID': geneId},
+        { 'subfeatures.ID': geneId },
+        { 'subfeatures.protein_id': geneId },
+      ]
+    }).fetch();
   }
 
   const loading = !geneSub.ready();

package.json

@@ -1,6 +1,6 @@
 {
   "name": "genoboo",
-  "version": "0.4.10",
+  "version": "0.4.11",
   "repository": "https://github.com/gogepp/genoboo",
   "description": "A portable website for browsing and querying genome sequences and annotations. Forked from genenotebook",
   "license": "AGPL-3.0",