fixes #2567 (#2572)

ChangeLog.md

@@ -6,8 +6,10 @@ Features
 - Fix empty attribute list in annotation panel [2552](https://github.com/GMOD/Apollo/issues/2552).
 - Added ability to use posts to sequence methods [2555](https://github.com/GMOD/Apollo/pull/2558).
 - Added system info web service [2557](https://github.com/GMOD/Apollo/pull/2557).
+- Add "merged from" comment to merged in transcript and gene [2567](https://github.com/GMOD/Apollo/issues/2567).
 
 Bug Fixes:
+
 - Bad coordinate value in genomic element details screen in annotator panel [2559](https://github.com/GMOD/Apollo/issues/2559).
 - Web services indicated user had no organism permissions when checking the login [2554](https://github.com/GMOD/Apollo/issues/2554).
 - Vcf reads as ISO-8859-1 instead of UTF-8 from reader mangling some symbols. [2498](https://github.com/GMOD/Apollo/issues/2498).

docker-files/docker-apollo-config.groovy

@@ -101,6 +101,7 @@ apollo {
     overlapper_class = System.getenv("WEBAPOLLO_OVERLAPPER_CLASS") ?: "org.bbop.apollo.sequence.OrfOverlapper"
     use_cds_for_new_transcripts = checkBooleanEnvironment("WEBAPOLLO_CDS_FOR_NEW_TRANSCRIPTS",false)
     count_annotations = checkBooleanEnvironment("WEBAPOLLO_COUNT_ANNOTATIONS",true)
+    add_merged_commented = checkBooleanEnvironment("WEBAPOLLO_ADD_MERGED_COMMENT",true)
     phone.phoneHome = checkBooleanEnvironment("WEBAPOLLO_PHONE_HOME",true)
     feature_has_dbxrefs = checkBooleanEnvironment("WEBAPOLLO_FEATURE_HAS_DBXREFS",true)
     feature_has_attributes = checkBooleanEnvironment("WEBAPOLLO_FEATURE_HAS_ATTRS",true)

docs/Configure.md

@@ -96,6 +96,21 @@ grails {
 }
 ```
 
+### Suppress add merged comments
+
+By default, when you merge two isoforms, it will automatically create a comment indicating the name and unique ID from the 
+consumed isoform that was used as a comment.
+
+
+```
+grails {
+  apollo.add_merged_comment = false
+  apollo {
+    add_merged_comment = false
+  }
+}
+```
+
 
 
 ### JBrowse Plugins and Configuration

grails-app/conf/Config.groovy

@@ -215,6 +215,7 @@ apollo {
     track_name_comparator = "/config/track_name_comparator.js"
     use_cds_for_new_transcripts = false
     count_annotations = true
+    add_merged_comment = true
     transcript_overlapper = "CDS"
     feature_has_dbxrefs = true
     feature_has_attributes = true

grails-app/controllers/org/bbop/apollo/AnnotationEditorController.groovy

@@ -3,7 +3,6 @@ package org.bbop.apollo
 import grails.converters.JSON
 import groovy.json.JsonBuilder
 import org.apache.shiro.SecurityUtils
-import org.bbop.apollo.Feature
 import org.bbop.apollo.event.AnnotationEvent
 import org.bbop.apollo.event.AnnotationListener
 import org.bbop.apollo.gwt.shared.FeatureStringEnum

grails-app/services/org/bbop/apollo/ConfigWrapperService.groovy

@@ -31,6 +31,10 @@ class ConfigWrapperService {
         return grailsApplication.config.apollo.count_annotations
     }
 
+    Boolean getAddMergedComment(){
+        return grailsApplication.config.apollo.add_merged_comment
+    }
+
     String getTranscriptOverlapper() {
         return grailsApplication.config.apollo.transcript_overlapper
     }

grails-app/services/org/bbop/apollo/PermissionService.groovy

@@ -359,7 +359,8 @@ class PermissionService {
     Sequence checkPermissions(JSONObject inputObject, PermissionEnum requiredPermissionEnum) {
         Organism organism
 
-        validateSessionForJsonObject(inputObject)
+        // NOTE: if coming through web-socket, we will not have a session
+//        validateSessionForJsonObject(inputObject)
         String sequenceName = getSequenceNameFromInput(inputObject)
 
         User user = getCurrentUser(inputObject)

grails-app/services/org/bbop/apollo/TranscriptService.groovy

@@ -16,10 +16,12 @@ class TranscriptService {
 
     // services
     def featureService
+    def featurePropertyService
     def featureRelationshipService
     def nameService
     def nonCanonicalSplitSiteService
     def sequenceService
+    def configWrapperService
 
     /** Retrieve the CDS associated with this transcript.  Uses the configuration to determine
      *  which child is a CDS.  The CDS object is generated on the fly.  Returns <code>null</code>
@@ -483,6 +485,10 @@ class TranscriptService {
         if (gene1 && gene2) {
             if (gene1 != gene2) {
                 log.debug "Gene1 != Gene2; merging genes together"
+                if(configWrapperService.addMergedComment) {
+                    Comment geneMergeComment = new Comment(value: "Merged from ${gene2.name} / ${gene2.uniqueName} ", feature: gene1).save()
+                    featurePropertyService.addComment(gene1, geneMergeComment)
+                }
                 List<Transcript> gene2Transcripts = getTranscripts(gene2)
                 if (gene2Transcripts) {
                     gene2Transcripts.retainAll(featureService.getOverlappingTranscripts(transcript1))
@@ -505,6 +511,10 @@ class TranscriptService {
 
         // Delete the empty transcript from the gene, if gene not already deleted
         if (!flag) {
+            if(configWrapperService.addMergedComment){
+                Comment transcriptMergeComment = new Comment(value: "Merged from ${transcript2.name} / ${transcript2.uniqueName} ", feature: transcript1).save()
+                featurePropertyService.addComment(transcript1,transcriptMergeComment)
+            }
             featureService.mergeIsoformBoundaries(transcript1,transcript2)
             def childFeatures = featureRelationshipService.getChildren(transcript2)
             featureRelationshipService.deleteChildrenForTypes(transcript2)

sample-h2-apollo-config.groovy

@@ -67,6 +67,7 @@ environments {
 //    common_data_directory = "/opt/temporary/apollo"
 //    calculate_non_canonical_splice_sites = false
 //    store_orig_id = false
+//    add_merged_comment = true
 //    count_annotations = false
 //    fa_to_twobit_exe = "/usr/local/bin/blat" // get form https://genome.ucsc.edu/goldenPath/help/blatSpec.html
 //    sequence_search_tools {

sample-mysql-apollo-config.groovy

@@ -66,6 +66,7 @@ environments {
 //    common_data_directory = "/opt/temporary/apollo"
 //    store_orig_id = false
 //    count_annotations = false
+//    add_merged_comment = true
 //    calculate_non_canonical_splice_sites = false
 //    fa_to_twobit_exe = "/usr/local/bin/faToTwoBit" // get from // https://genome.ucsc.edu/goldenPath/help/blatSpec.html
 //    sequence_search_tools {

sample-postgres-apollo-config.groovy

@@ -110,6 +110,7 @@ environments {
 //    only_owners_delete = true
 //    common_data_directory = "/opt/temporary/apollo"
 //    calculate_non_canonical_splice_sites = false
+//    add_merged_comment = true
 //    count_annotations = false
 //    store_orig_id = false
 //    fa_to_twobit_exe = "/usr/local/bin/faToTwoBit" // get from // https://genome.ucsc.edu/goldenPath/help/blatSpec.html