Merge pull request #71 from gogepp/dev

Release v0.4.16

CHANGELOG.md

@@ -5,6 +5,12 @@ 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)
 
+## [0.4.16] 2024-06-12
+
+- Better management for mongo error when adding annotation
+- Manage empty genes (no subentities)
+- Manage CDS with same IDs in the same gene
+
 ## [0.4.15] 2024-04-05
 
 ### Fixed

imports/api/genomes/annotation/addAnnotation.test.js

@@ -63,7 +63,15 @@ describe('AddAnnotation', function testAnnotation() {
     chai.assert.equal(gene.start, 13640);
     chai.assert.equal(gene.end, 15401);
 
-    chai.assert.lengthOf(gene.subfeatures, 13, 'Number of subfeatures is not 13');
+    chai.assert.lengthOf(gene.subfeatures, 14, 'Number of subfeatures is not 14');
+
+    // Check CDS with the same ID
+    has_default_cds = gene.subfeatures.some((sub) => sub.type == "CDS" && sub.ID == "Bni|B01g000010.2N.1.cds1")
+    has_new_cds = gene.subfeatures.some((sub) => sub.type == "CDS" && sub.ID == "Bni|B01g000010.2N.1.cds1.1")
+
+    chai.assert.isTrue(has_default_cds, "Bni|B01g000010.2N.1.cds1 was not found")
+    chai.assert.isTrue(has_default_cds, "Bni|B01g000010.2N.1.cds1.1 was not found")
+
   });
 
   it('Should add multiple copies of genes with different annotation names', function addAnnotationGff3() {

imports/api/genomes/annotation/parser/annotationParserGff3.js

@@ -51,6 +51,8 @@ class AnnotationProcessor {
     // (this.IdParents[parents[0]] in addChildren function).
     this.IdParents = {};
     this.indexIdParent = 0;
+
+    this.cds_ids = {};
   }
 
   /**
@@ -358,6 +360,8 @@ class AnnotationProcessor {
         features.attributes,
       );
       this.geneLevelHierarchy.attributes = attributesFiltered;
+
+      this.geneLevelHierarchy.subfeatures = [];
     } else {
       // Create an array if not exists for the subfeatures (exons, cds ...) of
       // the gene.
@@ -387,7 +391,18 @@ class AnnotationProcessor {
         );
       }
 
-      const identifiant = features.ID
+      let identifiant = features.ID
+
+      // Manage case of discontinuous CDS: Same ID -> we add a suffix to avoid crashing
+      if (typeAttr === 'CDS'){
+        if (identifiant in this.cds_ids){
+           identifiant = identifiant + "." + this.cds_ids[identifiant]
+           this.cds_ids[identifiant] += 1
+        } else {
+          this.cds_ids[identifiant] = 1
+        }
+      }
+
       let proteinID
 
       // Complete ID parents.
@@ -446,7 +461,7 @@ class AnnotationProcessor {
       GeneSchema.validate(geneWithoutId);
     } catch (err) {
       logger.error(err)
-      throw new Error('There is something wrong with the gene collection schema');
+      throw new Error('Current gene is not valid, stopping');
     }
     return true;
   };
@@ -528,7 +543,7 @@ class AnnotationProcessor {
           // Increment.
           this.nAnnotation += 1;
 
-	  const protein_ids = this.geneLevelHierarchy.subfeatures.flatMap(children => {
+      	  const protein_ids = this.geneLevelHierarchy.subfeatures.flatMap(children => {
             if(typeof children.protein_id === 'undefined'){
               return []
             } else {
@@ -538,6 +553,9 @@ class AnnotationProcessor {
 
           this.geneLevelHierarchy.children = this.geneLevelHierarchy.children.concat(protein_ids)
 
+          // Validate schema before adding to bulk
+          this.isValidateGeneSchema();
+
           // Add to bulk operation.
           this.geneBulkOperation.insert(this.geneLevelHierarchy)
 
@@ -547,14 +565,16 @@ class AnnotationProcessor {
           this.shiftSequence = 0;
           this.IdParents = {};
           this.indexIdParent = 0;
+          this.cds_ids = {};
 
           // Init new gene.
           this.initGeneHierarchy(features);
 
           // Arbitrary break up of batch size to save ram
           if (this.geneBulkOperation.length > 500) {
               this.isReset = true
-              return this.geneBulkOperation.execute();
+              let execute = Meteor.wrapAsync(this.geneBulkOperation.execute, this.geneBulkOperation);
+              return execute()
           }
         }
       } else {

package.json

@@ -1,6 +1,6 @@
 {
   "name": "genoboo",
-  "version": "0.4.15",
+  "version": "0.4.16",
   "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",

private/data/Bnigra.gff3

@@ -8,6 +8,7 @@ B1	AAFC_GIFS	exon	14210	14284	.	-	.	ID=Bni%7CB01g000010.2N.1.exon4;Parent=Bni%7C
 B1	AAFC_GIFS	exon	13970	14062	.	-	.	ID=Bni%7CB01g000010.2N.1.exon5;Parent=Bni%7CB01g000010.2N.1
 B1	AAFC_GIFS	exon	13640	13870	.	-	.	ID=Bni%7CB01g000010.2N.1.exon6;Parent=Bni%7CB01g000010.2N.1
 B1	AAFC_GIFS	CDS	14702	15401	.	-	0	ID=Bni%7CB01g000010.2N.1.cds1;Parent=Bni%7CB01g000010.2N.1
+B1	AAFC_GIFS	CDS	14702	15401	.	-	0	ID=Bni%7CB01g000010.2N.1.cds1;Parent=Bni%7CB01g000010.2N.1
 B1	AAFC_GIFS	CDS	14557	14636	.	-	2	ID=Bni%7CB01g000010.2N.1.cds2;Parent=Bni%7CB01g000010.2N.1
 B1	AAFC_GIFS	CDS	14403	14486	.	-	0	ID=Bni%7CB01g000010.2N.1.cds3;Parent=Bni%7CB01g000010.2N.1
 B1	AAFC_GIFS	CDS	14210	14284	.	-	0	ID=Bni%7CB01g000010.2N.1.cds4;Parent=Bni%7CB01g000010.2N.1