added initial orig_id (#2010)

* added initial orig_id

* orig_id being set properly during transfer

* simplified code

* storing orig_id correctly in the comments

* fixed alignment detection

* updated dock and set default

* fixed a selection error

* remove console log

client/apollo/js/JSONUtils.js

@@ -222,7 +222,7 @@ JSONUtils.handleCigarSubFeatures = function(feature,type){
 
 JSONUtils.isAlignment = function(feature){
     try {
-        return feature.data.cigar !== undefined;
+        return feature.data && feature.data.cigar !== undefined;
     } catch (e) {
         console.error('Unable to process feature alignment.  Assuming not an alignment',feature,e);
         return false;
@@ -297,7 +297,6 @@ JSONUtils.generateSubFeaturesFromCigar = function(feature){
 *    currently, for features with lazy-loaded children, ignores children
 */
 JSONUtils.createApolloFeature = function( jfeature, specified_type, useName, specified_subtype )   {
-    console.log('creating apollo feature',jfeature);
     var diagnose =  (JSONUtils.verbose_conversion && jfeature.children() && jfeature.children().length > 0);
     if (diagnose)  {
         console.log("converting JBrowse feature to Apollo feture, specified type: " + specified_type);
@@ -350,8 +349,14 @@ JSONUtils.createApolloFeature = function( jfeature, specified_type, useName, spe
     var name = jfeature.get('name');
     if (useName) {
         // using 'id' attribute in the absence of 'name' attribute
-        name !== undefined ? afeature.name = name : afeature.name = id;
+        if( name !== undefined ) {
+            afeature.name = name;
+        }
+        else{
+            afeature.name = id;
+        }
     }
+    afeature.orig_id = id ;
 
     /*
     afeature.properties = [];
@@ -653,4 +658,4 @@ window.JSONUtils = JSONUtils;
 
 return JSONUtils;
 
-});
+});

client/apollo/js/View/Track/AnnotTrack.js

@@ -1035,7 +1035,7 @@ define([
                 var subfeatures = [];
                 var strand;
                 var parentFeature;
-                var variantSelectionRecords = new Array();
+                var variantSelectionRecords = [];
 
                 for (var i in selection_records) {
                     var type = selection_records[i].feature.get("type").toUpperCase();
@@ -1110,6 +1110,7 @@ define([
                     if (!featureToAdd.get('name')) {
                         featureToAdd.set('name', featureToAdd.get('id'));
                     }
+                    featureToAdd.set('orig_id', featureToAdd.get('id'));
                     featureToAdd.set("strand", strand);
                     var fmin;
                     var fmax;
@@ -1171,6 +1172,8 @@ define([
 
                     var afeat ;
                     featureToAdd = JSONUtils.handleCigarSubFeatures(featureToAdd,biotype);
+                    console.log('adding',featureToAdd)
+
                     if(biotype === 'mRNA'){
                         featureToAdd = JSONUtils.handleCigarSubFeatures(featureToAdd,biotype);
                         afeat = JSONUtils.createApolloFeature(featureToAdd, biotype, true);
@@ -1228,7 +1231,6 @@ define([
                         }
                     });
                     this.openDialog("Confirm", content);
-                    return;
                 }
                 else {
                     process();
@@ -1255,6 +1257,7 @@ define([
                                     }
                                     else {
                                         var afeat = JSONUtils.createApolloVariant(dragfeat, true);
+                                        afeat.orig_id = dojo.clone(dragfeat.id);
                                         featuresToAdd.push(afeat);
 
                                         var postData = {
@@ -1318,12 +1321,14 @@ define([
                         featureToAdd.set("start", fmin);
                         featureToAdd.set("end", fmax);
                         var afeat = JSONUtils.createApolloFeature(featureToAdd, type, true, subfeatType);
+                        console.log('created apollo feature',afeat)
                         if (topLevelType) {
-                            var topLevel = new Object();
+                            var topLevel = {};
+                            topLevel.orig_id = dojo.clone(afeat.id);
                             topLevel.location = dojo.clone(afeat.location);
                             topLevel.type = dojo.clone(afeat.type);
                             topLevel.type.name = topLevelType;
-                            topLevel.children = new Array();
+                            topLevel.children = [];
                             topLevel.children.push(afeat);
                             afeat = topLevel;
                         }
@@ -1335,6 +1340,7 @@ define([
                             var afeat = JSONUtils.createApolloFeature(dragfeat, type, true, subfeatType);
                             if (topLevelType) {
                                 var topLevel = new Object();
+                                topLevel.orig_id = dojo.clone(afeat.id);
                                 topLevel.location = dojo.clone(afeat.location);
                                 topLevel.type = dojo.clone(afeat.type);
                                 topLevel.type.name = topLevelType;

client/apollo/js/View/Track/DraggableHTMLFeatures.js

@@ -845,6 +845,10 @@ var draggableTrack = declare( HTMLFeatureTrack,
            }
        }
        else if (event.altKey) {
+           if(feat.parent()===undefined){
+            // do nothing
+           }
+           else
            if (already_selected) {
                // select entire feature
                selman.addToSelection({ feature: feat.parent(), track: this}, false);
@@ -1190,6 +1194,12 @@ var draggableTrack = declare( HTMLFeatureTrack,
         //  return this.getUiGenomeCoord(mouseEvent) - 1;
     },
 
+    _handleSelectedFeatures: function(){
+        var selFeats = this.selectionManager.getSelectedFeatures();
+        this.selectionManager.clearSelection();
+        return selFeats;
+    },
+
     _makeFeatureContextMenu: function( featDiv, menuTemplate ) {
         var atrack = this.webapollo.getAnnotTrack();
 
@@ -1211,91 +1221,61 @@ var draggableTrack = declare( HTMLFeatureTrack,
         createAnnotationMenu.addChild(new dijitMenuItem( {
             label: "pseudogene",
             onClick: dojo.hitch(this, function() {
-                var selection = this.selectionManager.getSelection();
-                var selFeats = this.selectionManager.getSelectedFeatures();
-                this.selectionManager.clearSelection();
-                atrack.createGenericAnnotations(selFeats, "transcript", null, "pseudogene");
+                atrack.createGenericAnnotations(this._handleSelectedFeatures(), "transcript", null, "pseudogene");
             })
         }));
         createAnnotationMenu.addChild(new dijitMenuItem( {
             label: "tRNA",
             onClick: dojo.hitch(this, function() {
-                var selection = this.selectionManager.getSelection();
-                var selFeats = this.selectionManager.getSelectedFeatures();
-                this.selectionManager.clearSelection();
-                atrack.createGenericAnnotations(selFeats, "tRNA", null, "gene");
+                atrack.createGenericAnnotations(this._handleSelectedFeatures(), "tRNA", null, "gene");
             })
         }));
         createAnnotationMenu.addChild(new dijitMenuItem( {
             label: "snRNA",
             onClick: dojo.hitch(this, function() {
-                var selection = this.selectionManager.getSelection();
-                var selFeats = this.selectionManager.getSelectedFeatures();
-                this.selectionManager.clearSelection();
-                atrack.createGenericAnnotations(selFeats, "snRNA", null, "gene");
+                atrack.createGenericAnnotations(this._handleSelectedFeatures(), "snRNA", null, "gene");
             })
         }));
         createAnnotationMenu.addChild(new dijitMenuItem( {
             label: "snoRNA",
             onClick: dojo.hitch(this, function() {
-                var selection = this.selectionManager.getSelection();
-                var selFeats = this.selectionManager.getSelectedFeatures();
-                this.selectionManager.clearSelection();
-                atrack.createGenericAnnotations(selFeats, "snoRNA", null, "gene");
+                atrack.createGenericAnnotations(this._handleSelectedFeatures(), "snoRNA", null, "gene");
             })
         }));
         createAnnotationMenu.addChild(new dijitMenuItem( {
             label: "ncRNA",
             onClick: dojo.hitch(this, function() {
-                var selection = this.selectionManager.getSelection();
-                var selFeats = this.selectionManager.getSelectedFeatures();
-                this.selectionManager.clearSelection();
-                atrack.createGenericAnnotations(selFeats, "ncRNA", null, "gene");
+                atrack.createGenericAnnotations(this._handleSelectedFeatures(), "ncRNA", null, "gene");
             })
         }));
         createAnnotationMenu.addChild(new dijitMenuItem( {
             label: "rRNA",
             onClick: dojo.hitch(this, function() {
-                var selection = this.selectionManager.getSelection();
-                var selFeats = this.selectionManager.getSelectedFeatures();
-                this.selectionManager.clearSelection();
-                atrack.createGenericAnnotations(selFeats, "rRNA", null, "gene");
+                atrack.createGenericAnnotations(this._handleSelectedFeatures(), "rRNA", null, "gene");
             })
         }));
         createAnnotationMenu.addChild(new dijitMenuItem( {
             label: "miRNA",
             onClick: dojo.hitch(this, function() {
-                var selection = this.selectionManager.getSelection();
-                var selFeats = this.selectionManager.getSelectedFeatures();
-                this.selectionManager.clearSelection();
-                atrack.createGenericAnnotations(selFeats, "miRNA", null, "gene");
+                atrack.createGenericAnnotations(this._handleSelectedFeatures(), "miRNA", null, "gene");
             })
         }));
         createAnnotationMenu.addChild(new dijitMenuItem( {
             label: "repeat_region",
             onClick: dojo.hitch(this, function() {
-                var selection = this.selectionManager.getSelection();
-                var selFeats = this.selectionManager.getSelectedFeatures();
-                this.selectionManager.clearSelection();
-                atrack.createGenericOneLevelAnnotations(selFeats, "repeat_region", true);
+                atrack.createGenericOneLevelAnnotations(this._handleSelectedFeatures(), "repeat_region", true);
             })
         }));
         createAnnotationMenu.addChild(new dijitMenuItem( {
             label: "terminator",
             onClick: dojo.hitch(this, function() {
-                var selection = this.selectionManager.getSelection();
-                var selFeats = this.selectionManager.getSelectedFeatures();
-                this.selectionManager.clearSelection();
-                atrack.createGenericOneLevelAnnotations(selFeats, "terminator", false);
+                atrack.createGenericOneLevelAnnotations(this._handleSelectedFeatures(), "terminator", false);
             })
         }));
         createAnnotationMenu.addChild(new dijitMenuItem( {
             label: "transposable_element",
             onClick: dojo.hitch(this, function() {
-                var selection = this.selectionManager.getSelection();
-                var selFeats = this.selectionManager.getSelectedFeatures();
-                this.selectionManager.clearSelection();
-                atrack.createGenericOneLevelAnnotations(selFeats, "transposable_element", true);
+                atrack.createGenericOneLevelAnnotations(this._handleSelectedFeatures(), "transposable_element", true);
             })
         }));
 

docs/Configure.md

@@ -18,46 +18,44 @@ that are defined in the Config.groovy file:
 ``` 
 // default apollo settings
 apollo {
-  default_minimum_intron_size = 1
-  history_size = 0
-  overlapper_class = "org.bbop.apollo.sequence.OrfOverlapper"
-  track_name_comparator = "/config/track_name_comparator.js"
-  use_cds_for_new_transcripts = true
-  user_pure_memory_store = true
-  translation_table = "/config/translation_tables/ncbi_1_translation_table.txt"
-  is_partial_translation_allowed = false // unused so far
-  get_translation_code = 1
-  only_owners_delete = false
-  sequence_search_tools = [
-    blat_nuc: [
-      search_exe: "/usr/local/bin/blat",
-      search_class: "org.bbop.apollo.sequence.search.blat.BlatCommandLineNucleotideToNucleotide",
-      name: "Blat nucleotide",
-      params: ""
-    ],
-    blat_prot: [
-      search_exe: "/usr/local/bin/blat",
-      search_class: "org.bbop.apollo.sequence.search.blat.BlatCommandLineProteinToNucleotide",
-      name: "Blat protein",
-      params: ""
+
+    // other translation codes are of the form ncbi_KEY_translation_table.txt
+    // under the web-app/translation_tables  directory
+    // to add your own add them to that directory and over-ride the translation code here
+    get_translation_code = 1
+    proxies = [
+            [
+                    referenceUrl : 'http://golr.geneontology.org/select',
+                    targetUrl    : 'http://golr.geneontology.org/solr/select',
+                    active       : true,
+                    fallbackOrder: 0,
+                    replace      : true
+            ]
+            ,
+            [
+                    referenceUrl : 'http://golr.geneontology.org/select',
+                    targetUrl    : 'http://golr.berkeleybop.org/solr/select',
+                    active       : false,
+                    fallbackOrder: 1,
+                    replace      : false
+            ]
     ]
-  ]    
-      
-
-
-  splice_donor_sites = [ "GT" ]
-  splice_acceptor_sites = [ "AG"]
-  gff3.source= "." 
-  bootstrap = false
-
-  info_editor = {
-    feature_types = "default"
-    attributes = true
-    dbxrefs = true
-    pubmed_ids = true
-    go_ids = true
-    comments = true
-  }
+    sequence_search_tools = [
+            blat_nuc : [
+                    search_exe  : "/usr/local/bin/blat",
+                    search_class: "org.bbop.apollo.sequence.search.blat.BlatCommandLineNucleotideToNucleotide",
+                    name        : "Blat nucleotide",
+                    params      : ""
+            ],
+            blat_prot: [
+                    search_exe  : "/usr/local/bin/blat",
+                    search_class: "org.bbop.apollo.sequence.search.blat.BlatCommandLineProteinToNucleotide",
+                    name        : "Blat protein",
+                    params      : ""
+                    //tmp_dir: "/opt/apollo/tmp" optional param
+            ]
+    ]
+    ...
 }
 ```
 
@@ -157,6 +155,12 @@ Additional links for log4j:
   http://blog.andresteingress.com/2012/03/22/grails-adding-more-than-one-log4j-configurations/
 - Grails log4j guide: http://grails.github.io/grails-doc/2.4.x/guide/single.html#logging
 
+### Add attribute for the original id of the object
+
+In the apollo config override set `store_orig_id=true` to store an `orid_id` attribute on the top-level feature that 
+represents the original id from the genomic evidence.  This is useful for re-merging code as Apollo will generate its own IDs because 
+annotations will be based on multiple evidence sources.
+
 
 ### Canned Elements
 

grails-app/conf/Config.groovy

@@ -215,6 +215,7 @@ apollo {
     user_pure_memory_store = true
     is_partial_translation_allowed = false // unused so far
     export_subfeature_attrs = false
+    store_orig_id = false // sets the orig_id to the original evidence id when first created
 
     // used for uploading
     common_data_directory = "/opt/apollo"

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

@@ -113,6 +113,10 @@ class ConfigWrapperService {
         grailsApplication.config.apollo.authentications
     }
 
+    def storeOrigId() {
+        grailsApplication.config.apollo.store_orig_id
+    }
+
     def getPingUrl() {
         Boolean phoneHome =  grailsApplication.config.apollo.phone.phoneHome
         if(phoneHome){

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

@@ -1423,6 +1423,16 @@ public void setTranslationEnd(Transcript transcript, int translationEnd) {
             } else {
                 gsolFeature.setLastUpdated(new Date());
             }
+            if(configWrapperService.storeOrigId()){
+                if (jsonFeature.has(FeatureStringEnum.ORIG_ID.value)) {
+                    FeatureProperty gsolProperty = new FeatureProperty()
+                    gsolProperty.setTag(FeatureStringEnum.ORIG_ID.value)
+                    gsolProperty.setValue(jsonFeature.get(FeatureStringEnum.ORIG_ID.value))
+                    gsolProperty.setFeature(gsolFeature)
+                    gsolProperty.save()
+                    gsolFeature.addToFeatureProperties(gsolProperty)
+                }
+            }
             if (jsonFeature.has(FeatureStringEnum.PROPERTIES.value)) {
                 JSONArray properties = jsonFeature.getJSONArray(FeatureStringEnum.PROPERTIES.value);
                 for (int i = 0; i < properties.length(); ++i) {

src/gwt/org/bbop/apollo/gwt/shared/FeatureStringEnum.java

@@ -167,6 +167,7 @@ public enum FeatureStringEnum {
         VARIANT_INFO,
         OLD_VARIANT_INFO,
         NEW_VARIANT_INFO,
+        ORIG_ID,
         ;