fixes #2565 - removes featureLocationPublications (#2573)

* fixes #2565 - removes featureLocationPublications * partial fmin and fmax get in there , but not yet saved to the DB * added obsolete to client * fixed JSON output * fixed some broken errors * udpate partials for genes properly now * implemented in GFF3 output * fixed partial children * in transcript panel now * fixed look and feel * finished obsoletes * updated changedoc and rest doc
GMOD · Feb 16, 2021 · 8149e2a · 8149e2a
1 parent 0afb683
commit 8149e2a
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Showing 16 changed files with 2,253 additions and 1,913 deletions.
diff --git a/ChangeLog.md b/ChangeLog.md
@@ -7,6 +7,7 @@ Features
 - 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).
+- Added support for "obsolete", and partials in the interface for GFF3s [2573](https://github.com/GMOD/Apollo/pull/2573).
 
 Bug Fixes:
 

diff --git a/grails-app/controllers/org/bbop/apollo/AnnotatorController.groovy b/grails-app/controllers/org/bbop/apollo/AnnotatorController.groovy
@@ -236,6 +236,7 @@ class AnnotatorController {
         feature.name = data.name
         feature.symbol = data.symbol
         feature.description = data.description
+        feature.isObsolete = data.obsolete
         if(data.containsKey("obsolete")) {
             feature.isObsolete = data.getBoolean("obsolete")
         }
@@ -328,6 +329,76 @@ class AnnotatorController {
         render updateFeatureContainer
     }
 
+/**
+ * updates shallow properties of gene / feature
+ * @return
+ */
+    @RestApiMethod(description = "Update partial fmin / famx", path = "/annotator/updatePartials", verb = RestApiVerb.POST)
+    @RestApiParams(params = [
+            @RestApiParam(name = "username", type = "email", paramType = RestApiParamType.QUERY)
+            , @RestApiParam(name = "password", type = "password", paramType = RestApiParamType.QUERY)
+            , @RestApiParam(name = "uniquename", type = "string", paramType = RestApiParamType.QUERY, description = "Uniquename (UUID) of the feature we are editing")
+            , @RestApiParam(name = "data", type = "string", paramType = RestApiParamType.QUERY, description = "Annotation Info object")
+    ]
+    )
+    @Transactional
+    def updatePartials() {
+        log.debug "update partials  ${params.data}"
+        JSONObject data = permissionService.handleInput(request, params)
+        if (!permissionService.hasPermissions(data, PermissionEnum.WRITE)) {
+            render status: HttpStatus.UNAUTHORIZED
+            return
+        }
+        Feature feature = Feature.findByUniqueName(data.uniquename)
+        FeatureLocation featureLocation = feature.featureLocation
+
+        boolean isFminPartial = feature.featureLocation.isFminPartial
+        boolean isFmaxPartial = feature.featureLocation.isFmaxPartial
+
+        JSONObject originalFeatureJsonObject = featureService.convertFeatureToJSON(feature)
+        FeatureOperation featureOperation
+        if(data.containsKey(FeatureStringEnum.IS_FMIN_PARTIAL.value)
+            &&
+                data.getBoolean(FeatureStringEnum.IS_FMIN_PARTIAL.value) != isFminPartial
+        ){
+            featureOperation = FeatureOperation.SET_PARTIAL_FMIN
+//            featureLocation.isFminPartial = data.getBoolean(FeatureStringEnum.IS_FMIN_PARTIAL.value)
+            featureService.setPartialFmin(feature,data.getBoolean(FeatureStringEnum.IS_FMIN_PARTIAL.value).booleanValue(),feature.featureLocation.fmin)
+        }
+        else
+        if(data.containsKey(FeatureStringEnum.IS_FMAX_PARTIAL.value)
+                &&
+                data.getBoolean(FeatureStringEnum.IS_FMAX_PARTIAL.value) != isFmaxPartial
+        ){
+            featureOperation = FeatureOperation.SET_PARTIAL_FMAX
+            featureService.setPartialFmax(feature,data.getBoolean(FeatureStringEnum.IS_FMAX_PARTIAL.value).booleanValue(),feature.featureLocation.fmax)
+        }
+        else{
+            throw new AnnotationException("Partials have not changed, so not doing anything")
+        }
+        featureLocation.save(flush: true, failOnError: true,insert:false)
+
+        JSONObject updateFeatureContainer = jsonWebUtilityService.createJSONFeatureContainer();
+        // its either a gene or
+
+        User user = permissionService.getCurrentUser(data)
+        JSONObject currentFeatureJsonObject = featureService.convertFeatureToJSON(feature)
+
+        JSONArray oldFeaturesJsonArray = new JSONArray()
+        oldFeaturesJsonArray.add(originalFeatureJsonObject)
+        JSONArray newFeaturesJsonArray = new JSONArray()
+        newFeaturesJsonArray.add(currentFeatureJsonObject)
+        featureEventService.addNewFeatureEvent(featureOperation,
+                feature.name,
+                feature.uniqueName,
+                data,
+                oldFeaturesJsonArray,
+                newFeaturesJsonArray,
+                user)
+
+        render updateFeatureContainer
+    }
+
 
     @RestApiMethod(description = "Update exon boundaries", path = "/annotator/setExonBoundaries", verb = RestApiVerb.POST)
     @RestApiParams(params = [
@@ -991,6 +1062,7 @@ class AnnotatorController {
         if (!compareNullToBlank(feature.symbol,data.symbol)) return FeatureOperation.SET_SYMBOL
         if (!compareNullToBlank(feature.description,data.description)) return FeatureOperation.SET_DESCRIPTION
         if (!compareNullToBlank(feature.status,data.status)) return FeatureOperation.SET_STATUS
+        if(feature.isObsolete != data.obsolete ) return FeatureOperation.SET_OBSOLETE
 
         log.warn("Updated generic feature")
         null

diff --git a/grails-app/domain/org/bbop/apollo/FeatureLocation.groovy b/grails-app/domain/org/bbop/apollo/FeatureLocation.groovy
@@ -35,20 +35,15 @@ class FeatureLocation {
     static belongsTo = [Feature]
 
 
-    static hasMany = [
-            featureLocationPublications: Publication
-    ]
-
-
-    public boolean equals(Object other) {
+    boolean equals(Object other) {
         if (this.is(other)) return true
         if (getClass() != other.class) return false
         FeatureLocation castOther = (FeatureLocation) other;
 
         return ((this.getFeature() == castOther.getFeature()) || (this.getFeature() != null && castOther.getFeature() != null && this.getFeature().equals(castOther.getFeature()))) && (this.getLocgroup() == castOther.getLocgroup()) && (this.getRank() == castOther.getRank());
     }
 
-    public int hashCode() {
+    int hashCode() {
         int result = 17;
 
         result = 37 * result + (getFeature() == null ? 0 : this.getFeature().hashCode());
@@ -63,10 +58,10 @@ class FeatureLocation {
      * We use this as an artificial accessor in case the property has not been calculatd
      * @return
      */
-    public Integer calculateLength(){
+    Integer calculateLength(){
         return fmax-fmin
     }
-    public FeatureLocation generateClone() {
+    FeatureLocation generateClone() {
         FeatureLocation cloned = new FeatureLocation();
         cloned.sequence = this.sequence;
         cloned.feature = this.feature;
@@ -79,7 +74,6 @@ class FeatureLocation {
         cloned.residueInfo = this.residueInfo;
         cloned.locgroup = this.locgroup;
         cloned.rank = this.rank;
-        cloned.featureLocationPublications = this.featureLocationPublications;
         return cloned;
     }
 

diff --git a/grails-app/services/org/bbop/apollo/ChadoHandlerService.groovy b/grails-app/services/org/bbop/apollo/ChadoHandlerService.groovy
@@ -456,9 +456,9 @@ class ChadoHandlerService {
         endTime = System.currentTimeMillis()
         log.debug "Time taken to create Chado featureloc for feature fmin: ${feature.fmin} fmax: ${feature.fmax}: ${endTime - startTime} ms"
         exportStatisticsMap['featureloc_count'] += 1
-        feature.featureLocation.featureLocationPublications.each { featureLocationPublication ->
-            createChadoFeaturelocPub(chadoFeatureLoc, featureLocationPublication)
-        }
+//        feature.featureLocation.featureLocationPublications.each { featureLocationPublication ->
+//            createChadoFeaturelocPub(chadoFeatureLoc, featureLocationPublication)
+//        }
         return chadoFeatureLoc
     }
 

diff --git a/grails-app/services/org/bbop/apollo/FeatureService.groovy b/grails-app/services/org/bbop/apollo/FeatureService.groovy
@@ -6,6 +6,7 @@ import org.bbop.apollo.alteration.SequenceAlterationInContext
 import org.bbop.apollo.geneProduct.GeneProduct
 import org.bbop.apollo.go.GoAnnotation
 import org.bbop.apollo.gwt.shared.FeatureStringEnum
+import org.bbop.apollo.history.FeatureOperation
 import org.bbop.apollo.sequence.SequenceTranslationHandler
 import org.bbop.apollo.sequence.Strand
 import org.bbop.apollo.sequence.TranslationTable
@@ -1966,6 +1967,9 @@ public void setTranslationEnd(Transcript transcript, int translationEnd) {
     if (gsolFeature.symbol) {
       jsonFeature.put(FeatureStringEnum.SYMBOL.value, gsolFeature.symbol);
     }
+    if (gsolFeature.isObsolete) {
+      jsonFeature.put(FeatureStringEnum.OBSOLETE.value, gsolFeature.isObsolete);
+    }
     if (gsolFeature.description) {
       jsonFeature.put(FeatureStringEnum.DESCRIPTION.value, gsolFeature.description);
     }
@@ -2356,20 +2360,21 @@ public void setTranslationEnd(Transcript transcript, int translationEnd) {
 
   @Timed
   JSONObject convertFeatureLocationToJSON(FeatureLocation gsolFeatureLocation) throws JSONException {
-    JSONObject jsonFeatureLocation = new JSONObject();
+    JSONObject jsonFeatureLocation = new JSONObject()
     if (gsolFeatureLocation.id) {
-      jsonFeatureLocation.put(FeatureStringEnum.ID.value, gsolFeatureLocation.id);
+      jsonFeatureLocation.put(FeatureStringEnum.ID.value, gsolFeatureLocation.id)
     }
-    jsonFeatureLocation.put(FeatureStringEnum.FMIN.value, gsolFeatureLocation.getFmin());
-    jsonFeatureLocation.put(FeatureStringEnum.FMAX.value, gsolFeatureLocation.getFmax());
-    if (gsolFeatureLocation.isIsFminPartial()) {
-      jsonFeatureLocation.put(FeatureStringEnum.IS_FMIN_PARTIAL.value, true);
+    jsonFeatureLocation.put(FeatureStringEnum.FMIN.value, gsolFeatureLocation.getFmin())
+    jsonFeatureLocation.put(FeatureStringEnum.FMAX.value, gsolFeatureLocation.getFmax())
+    if(gsolFeatureLocation.getIsFminPartial()){
+      jsonFeatureLocation.put(FeatureStringEnum.IS_FMIN_PARTIAL.value, gsolFeatureLocation.getIsFminPartial())
     }
-    if (gsolFeatureLocation.isIsFmaxPartial()) {
-      jsonFeatureLocation.put(FeatureStringEnum.IS_FMAX_PARTIAL.value, true);
+
+    if(gsolFeatureLocation.getIsFmaxPartial()){
+      jsonFeatureLocation.put(FeatureStringEnum.IS_FMAX_PARTIAL.value, gsolFeatureLocation.getIsFmaxPartial())
     }
-    jsonFeatureLocation.put(FeatureStringEnum.STRAND.value, gsolFeatureLocation.getStrand());
-    return jsonFeatureLocation;
+    jsonFeatureLocation.put(FeatureStringEnum.STRAND.value, gsolFeatureLocation.getStrand())
+    return jsonFeatureLocation
   }
 
   @Transactional
@@ -3584,4 +3589,38 @@ public void setTranslationEnd(Transcript transcript, int translationEnd) {
 
     return false
   }
+
+  @Transactional
+  def setPartialFmin(Feature feature,boolean fminPartial,int fmin){
+    FeatureLocation featureLocation = feature.featureLocation
+    if(fmin==featureLocation.fmin){
+      featureLocation.isFminPartial = fminPartial
+      featureLocation.save()
+    }
+
+    List<Feature> childFeatures = feature.parentFeatureRelationships*.childFeature
+    if(childFeatures){
+      for(childFeature in childFeatures){
+        setPartialFmin(childFeature,fminPartial,fmin)
+      }
+    }
+  }
+
+  @Transactional
+  def setPartialFmax(Feature feature,boolean fmaxPartial,int fmax){
+    FeatureLocation featureLocation = feature.featureLocation
+    if(fmax==featureLocation.fmax){
+      featureLocation.isFmaxPartial = fmaxPartial
+      featureLocation.save()
+    }
+
+    List<Feature> childFeatures = feature.parentFeatureRelationships*.childFeature
+    if(childFeatures){
+      for(childFeature in childFeatures){
+        setPartialFmax(childFeature,fmaxPartial,fmax)
+      }
+    }
+
+  }
+
 }
diff --git a/grails-app/services/org/bbop/apollo/Gff3HandlerService.groovy b/grails-app/services/org/bbop/apollo/Gff3HandlerService.groovy
@@ -1,12 +1,9 @@
 package org.bbop.apollo
 
 import org.apache.commons.lang.WordUtils
-import org.bbop.apollo.geneProduct.GeneProduct
-import org.bbop.apollo.go.GoAnnotation
 import org.bbop.apollo.gwt.shared.FeatureStringEnum
 import org.bbop.apollo.sequence.Strand
 import org.grails.plugins.metrics.groovy.Timed
-import org.springframework.format.datetime.DateFormatter
 import java.text.SimpleDateFormat
 
 
@@ -53,6 +50,9 @@ class Gff3HandlerService {
         writeObject.attributesToExport.add(FeatureStringEnum.COMMENTS.value);
         writeObject.attributesToExport.add(FeatureStringEnum.DATE_CREATION.value);
         writeObject.attributesToExport.add(FeatureStringEnum.DATE_LAST_MODIFIED.value);
+        writeObject.attributesToExport.add(FeatureStringEnum.IS_FMIN_PARTIAL.value);
+        writeObject.attributesToExport.add(FeatureStringEnum.IS_FMAX_PARTIAL.value);
+        writeObject.attributesToExport.add(FeatureStringEnum.OBSOLETE.value);
 
         if (!writeObject.file.canWrite()) {
             throw new IOException("Cannot write GFF3 to: " + writeObject.file.getAbsolutePath());
@@ -355,6 +355,15 @@ class Gff3HandlerService {
                 String productString  = geneProductService.convertGeneProductsToGff3String(feature.geneProducts)
                 attributes.put(FeatureStringEnum.GENE_PRODUCT.value, encodeString(productString))
             }
+            if (writeObject.attributesToExport.contains(FeatureStringEnum.IS_FMIN_PARTIAL.value) &&  feature.featureLocation.isFminPartial) {
+                attributes.put(FeatureStringEnum.IS_FMIN_PARTIAL.value, feature.featureLocation.isFminPartial.toString())
+            }
+            if (writeObject.attributesToExport.contains(FeatureStringEnum.OBSOLETE.value) &&  feature.isObsolete) {
+                attributes.put(FeatureStringEnum.OBSOLETE.value, feature.isObsolete.toString())
+            }
+            if (writeObject.attributesToExport.contains(FeatureStringEnum.IS_FMAX_PARTIAL.value) &&  feature.featureLocation.isFmaxPartial) {
+                attributes.put(FeatureStringEnum.IS_FMAX_PARTIAL.value, feature.featureLocation.isFmaxPartial.toString())
+            }
             if (writeObject.attributesToExport.contains(FeatureStringEnum.STATUS.value) && feature.getStatus() != null) {
                 attributes.put(FeatureStringEnum.STATUS.value, encodeString(feature.getStatus().value));
             }

diff --git a/src/groovy/org/bbop/apollo/history/FeatureOperation.groovy b/src/groovy/org/bbop/apollo/history/FeatureOperation.groovy
@@ -23,6 +23,7 @@ enum FeatureOperation {
   SET_TRANSLATION_ENDS,
   SET_LONGEST_ORF,
   FLIP_STRAND,
+  SET_OBSOLETE,
   REMOVE_CDS,
   SET_READTHROUGH_STOP_CODON,
   UNSET_READTHROUGH_STOP_CODON,
@@ -32,6 +33,8 @@ enum FeatureOperation {
   DISSOCIATE_TRANSCRIPT_FROM_GENE,
   ASSOCIATE_FEATURE_TO_GENE,
   DISSOCIATE_FEATURE_FROM_GENE,
+  SET_PARTIAL_FMIN,
+  SET_PARTIAL_FMAX,
 
   // structural data
   SET_SYMBOL(false),