Some changes and prepare release

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

@@ -86,14 +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 : "annotation"
+      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 + "," + annotationField
+        paramsDict[config.externalSearchOptions.field_param] = geneField
+        if (config.externalSearchOptions.annotation_field) {
+          paramsDict[config.externalSearchOptions.field_param] += "," + annotationField
+        }
       }
 
       if (config.externalSearchOptions.count_param){
@@ -105,7 +108,11 @@ Meteor.publish({
       const response = HTTP.get(url);
       if (response.statusCode === 200){
         geneResults = response.data.data.map(result => {
-          return {"ID": result._source[geneField], "annotationName": result._source[annotationField]}
+          if (config.externalSearchOptions.annotation_field){
+            return {"ID": result._source[geneField], "annotationName": result._source[annotationField]}
+          } else {
+            return {"ID": result._source[geneField]}
+          }
         })
       }
       transformedQuery = {genomeId: { $in: queryGenomeIds }, $or: geneResults}

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",