Merge pull request #96 from gogepp/dev

Release 0.4.19

Author: mboudet

CHANGELOG.md

@@ -5,6 +5,19 @@ 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)
 
+## [0.4.19] 2026-03-12
+
+- Properly raises error when failing to add an annotation (#82)
+- Fix eggnog seed link (#89)
+- Add --silent option to add genome (#92) and add Eggnog
+- Allow a 'range' (ex: `5:19`) of columns to be passed when loading expression files (#88)
+- Allow '--genome' to be passed when loading expression. This skips trying to predict genome based on first 10 genes (#87)
+- Cleanup mongo files at startup to avoid crashes (#86)
+- Open dbxref in newTab + allow using any of the gff attribute in the link (#85)
+- Add cleaner error when document size is exceeded
+- Add optionnal GO json file when loading eggnog, to store used goterms, and avoid requests later.
+- Add conf option to display a warning message related to isoforms
+
 ## [0.4.18] 2025-07-11
 
 - Fix GO API call

cli/genoboo.js

@@ -4,7 +4,7 @@
 const fs = require('fs');
 const commander = require('commander');
 const { Tail } = require('tail');
-const { spawn, execFileSync } = require('child_process');
+const { spawn, execFileSync, execSync } = require('child_process');
 const path = require('path');
 const asteroid = require('asteroid');
 const WebSocket = require('ws');
@@ -64,18 +64,23 @@ class GeneNoteBookConnection {
         } else if (jobStatus) {
           if (jobStatus === 'failed') {
             logger.error('The job failed, something went wrong! (Look at the logs for more details).');
+            this.connection.disconnect();
+            process.exit(1);
           } else {
             logger.log(`Job status: ${jobStatus}`);
           }
         } else {
           logger.error('Undefined server response');
+          this.connection.disconnect();
+          process.exit(1);
         }
         this.connection.disconnect();
       })
       .catch((error) => {
         logger.error(error);
         console.log(error);
         this.connection.disconnect();
+        process.exit(1);
       });
   }
 }
@@ -103,6 +108,16 @@ function startMongoDaemon(
   execFileSync('mkdir', ['-p', dataFolderPath, logFolderPath]);
   const logPath = `${dbPath}/log/mongod.log`;
 
+  // Delete log file if it exists to avoid rotation issues
+  try {
+    logger.log("Clearing log file if it exists")
+    fs.unlinkSync(logPath);
+  } catch (err) {
+    if (err.code !== "ENOENT") {
+      throw err;
+    }
+  }
+
   logger.log(`Using DB path: ${dbPath}`);
   logger.log(`MongoDB data files are in ${dataFolderPath}`);
   logger.log(`MongoDB logs are in ${logFolderPath}`);
@@ -124,6 +139,10 @@ function startMongoDaemon(
 
   const mongoDaemon = spawn('mongod', mongodOptionArray);
 
+  // wait a bit to make sure the log files are setup
+  logger.log("Waiting 10 seconds for mongo to start")
+  execSync("sleep 10");
+
   mongoDaemon.on('error', (err) => {
     logger.error(err);
   });
@@ -283,7 +302,12 @@ addGenome
     '--port [port]',
     'Port on which GeneNoteBook is running. Default: 3000'
   )
-  .action((file, { username, password, name, port = 3000, public = false }) => {
+  .option(
+    '--silent',
+    'Keep the upload process silent. Default: false',
+    false
+  )
+  .action((file, { username, password, name, port = 3000, public = false, silent = false }) => {
     if (typeof file !== 'string') addGenome.help();
     const fileName = path.resolve(file);
 
@@ -297,6 +321,7 @@ addGenome
       fileName,
       public,
       async: false,
+      silent
     });
   })
   .on('--help', () => {
@@ -621,9 +646,9 @@ const addExpression = add.command('expression');
 
 addExpression
   .description(
-    'Add gene expression to a running GeneNoteBook server'
+    'Add gene expression to a running GeneNoteBook server. Will use the first 10 genes to find the genome, using the genome name is passed'
   )
-  .usage('[options] <Kallisto abundance.tsv file>')
+  .usage('[options] <expression.tsv file>')
   .arguments('<file>')
   .option('-u, --username <username>', 'GeneNoteBook admin username')
   .option('-p, --password <password>', 'GeneNoteBook admin password')
@@ -636,16 +661,20 @@ addExpression
     'Description of the experiment'
   )
   .option(
-    '--annot <annotation-ame>',
+    '--annot <annotation-name>',
     'Annotation name',
   )
+  .option(
+    '--genome <genome-name>',
+    'Genome name',
+  )
   .option(
     '-r, --replicas <replicas...>',
     'Comma-separated column positions, which are part of the same replica group. Can be set multiple times for multiple groups. The replica group name will be the first column, unless replica-names is set'
   )
   .option(
     '-n, --replica-names <replicaNames...>',
-    'Name of the replica group. Will defaut to the first column header if not set. Can be set multiple time (for each replica group). Will match replica groups in order, whether they are multiple of single columns.'
+    'Name of the replica group. Will defaut to the first column header if not set. Can be set multiple time (for each replica group). Will match replica groups in order, whether they are multiple or single columns.'
   )
   .option(
     '--public',
@@ -660,6 +689,7 @@ addExpression
     const replicaNames = opts.replicaNames || [];
     const isPublic = opts.public;
     const annot = opts.annot
+    const genome = opts.genome
     if (!(fileName && username && password)) {
       program.help();
     }
@@ -669,6 +699,7 @@ addExpression
         fileName,
         description,
         annot,
+        genome,
         replicas,
         replicaNames,
         isPublic
@@ -818,6 +849,15 @@ addEggnog
   .description('Add EggNog-mapper results to a running GeneNoteBook server')
   .usage('[options] <EggNog-mapper tsv output file>')
   .arguments('<file>')
+  .option(
+    '--gofile <gofile>',
+    'Path to Gene Ontology json file',
+  )
+  .option(
+    '--silent',
+    'Keep the upload process silent. Default: false',
+    false
+  )
   .requiredOption(
     '-u, --username <adminUsername>',
     'GeneNoteBook admin username'
@@ -834,7 +874,7 @@ addEggnog
     '--port [port]',
     'Port on which GeneNoteBook is running. Default: 3000'
   )
-  .action((file, { username, password, port = 3000, annot }) => {
+  .action((file, { username, password, port = 3000, annot, gofile, silent = false }) => {
     if (typeof file !== 'string') addEggnog.help();
 
     const fileName = path.resolve(file);
@@ -844,7 +884,9 @@ addEggnog
 
     new GeneNoteBookConnection({ username, password, port }).call('addEggnog', {
       fileName,
-      annot: annot
+      annot: annot,
+      goFile: gofile,
+      silent
     });
   })
   .on('--help', () => {

config.json.template

@@ -1,6 +1,7 @@
 {
   "public":{
     "disable_blast": false,
+    "enable_hectar": false,
     "disable_user_login": false,
     "disable_user_registration": false,
     "disable_header": false,
@@ -14,7 +15,8 @@
     ],
     "protein_dbxref": [
        {"url": "https://test_url_protein/#PROTEINID", "label": "my protein label", "assembly": "", "annotation": ""}
-    ]
+    ],
+    "isoform_filtered": false
   },
   "externalSearchOptions": {
     "url": "http://0.0.0.0:80",

imports/api/genes/eggnog/addEggnog.js

@@ -6,13 +6,75 @@ import logger from '/imports/api/util/logger.js';
 import { Roles } from 'meteor/alanning:roles';
 import SimpleSchema from 'simpl-schema';
 import { Meteor } from 'meteor/meteor';
+import { dbxrefCollection } from '/imports/api/genes/dbxrefCollection.js';
+
+import fs from 'fs';
+import path from 'path';
 
 class EggnogProcessor {
-  constructor(annot) {
+  constructor(annot, goFile) {
     // Not a bulk mongo suite.
     this.genesDb = Genes.rawCollection();
     this.nEggnog = 0;
     this.annot = annot;
+    this.goContent = {}
+    this.addGo = new Set()
+    this.hasGO = false
+    this.loadGoContent(goFile)
+  }
+
+  /**
+  Function that load an option go.json file and store it as dict
+  */
+  loadGoContent(goFile){
+    if (! goFile) {
+      return
+    }
+    try {
+      logger.log("Loading GO annotation from :" + goFile)
+      const raw = fs.readFileSync(goFile, 'utf8');
+      const goData = JSON.parse(raw);
+      goData.graphs[0].nodes.forEach(node => {
+        if (node.id && node.lbl) {
+          this.goContent[node.id.replace("http://purl.obolibrary.org/obo/", "").replace("_", ":")] = node.lbl;
+          if (node.meta && node.meta.basicPropertyValues){
+            node.meta.basicPropertyValues.forEach(bpv => {
+              if (bpv.pred == "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId" && bpv.val){
+                this.goContent[bpv.val] = node.lbl
+              }
+            })
+          }
+        }
+      })
+      this.hasGO = true
+    } catch (error) {
+      logger.error(error)
+      logger.warn("Failed to load from " + goFile)
+      this.hasGO = false
+      this.goContent = {}
+    }
+  }
+  /** Function that add the GOterms in eggnog row into db */
+  createGOterms(){
+
+    this.addGo.forEach(goID => {
+      if (!(goID in this.goContent) || !(this.goContent[goID])){
+        logger.warn(`Missing ${goID} in GO ontology`)
+        return
+      }
+
+      dbxrefCollection.upsert(
+        { dbxrefId: goID},
+        { $set: {
+            dbxrefId: goID,
+            url: `http://amigo.geneontology.org/amigo/term/${goID}`,
+            description: this.goContent[goID],
+            updated: new Date(),
+            dbType: "go",
+          }
+        }
+      );
+    })
   }
 
   /**
@@ -64,7 +126,7 @@ class EggnogProcessor {
         eggNOG_OGs: eggnogOGs,
         max_annot_lvl: maxAnnotLvl,
         COG_category: cogCategory,
-        Description: description,
+         Description: description,
         Preferred_name: preferredName,
         GOs: gos,
         EC: ec,
@@ -118,6 +180,11 @@ class EggnogProcessor {
           annotations, // modifier.
         );
 
+
+        if (this.hasGO && annotations.GOs){
+	  annotations.GOs.forEach(item => this.addGo.add(item))
+        }
+
         // Update eggnogId in genes database.
         if (typeof documentEggnog.insertedId !== 'undefined') {
           // Eggnog _id is created.
@@ -150,20 +217,27 @@ const addEggnog = new ValidatedMethod({
       type: String,
       optional: true,
     },
+    goFile: {
+      type: String,
+      optional: true,
+    },
+    silent: {
+      type: Boolean,
+      optional: true,
+    },
   }).validator(),
   applyOptions: {
     noRetry: true,
   },
-  run({ fileName, annot }) {
+  run({ fileName, annot, goFile, silent }) {
     if (!this.userId) {
       throw new Meteor.Error('not-authorized');
     }
     if (!Roles.userIsInRole(this.userId, 'admin')) {
       throw new Meteor.Error('not-authorized');
     }
 
-    logger.log('file :', { fileName });
-    const job = new Job(jobQueue, 'addEggnog', { fileName, annot });
+    const job = new Job(jobQueue, 'addEggnog', { fileName, annot, goFile, silent });
     const jobId = job.priority('high').save();
 
     let { status } = job.doc;