reverted unnecessary changes

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

@@ -4323,14 +4323,6 @@ define([
  var statusFlags = dojo.create("div", {'class': "status"}, statusDiv);
  var statusRadios = [];
 
- var associatedTranscriptDiv = dojo.create("div", {'class': "annotation_info_editor_section"}, content);
- var associatedTranscriptLabel = dojo.create("div", {
- innerHTML: "Transcript",
- 'class': "annotation_info_editor_label"
- }, associatedTranscriptDiv);
- var associatedTranscriptField = new dijitTextBox({'class': "annotation_editor_field"});
- dojo.place(associatedTranscriptField.domNode, associatedTranscriptDiv);
-
  var dbxrefsDiv = dojo.create("div", {'class': "annotation_info_editor_section"}, content);
  var dbxrefsLabel = dojo.create("div", {
  'class': "annotation_info_editor_section_header",
@@ -4450,7 +4442,6 @@ define([
  if (!hasWritePermission) {
  nameField.set("disabled", true);
  symbolField.set("disabled", true);
- associatedTranscriptField.set("disabled", true);
  descriptionField.set("disabled", true);
  dateCreationField.set("disabled", true);
  dateLastModifiedField.set("disabled", true);
@@ -4464,8 +4455,6 @@ define([
  dojo.attr(deleteGoIdButton, "disabled", true);
  dojo.attr(addCommentButton, "disabled", true);
  dojo.attr(deleteCommentButton, "disabled", true);
- //dojo.attr(addreplacementButton, "disabled", true);
- //dojo.attr(deletereplacementButton, "disabled", true);
  }
 
  var pubmedIdDb = "PMID";
@@ -4506,7 +4495,6 @@ define([
  initDescription(feature);
  initDates(feature);
  initStatus(feature);
- initAssociatedTranscript(feature);
  initDbxrefs(feature, config);
  initAttributes(feature, config);
  initPubmedIds(feature, config);
@@ -4651,27 +4639,6 @@ define([
  }
  };
 
- var initAssociatedTranscript = function(feature){
- // feature type
- var featureType = feature.type.name ;
- if(!JSONUtils.regulatorTypes.includes(featureType.toUpperCase())){
- dojo.style(associatedTranscriptDiv, "display", "none");
- }
- // if (feature.symbol) {
- // symbolField.set("value", feature.symbol);
- // }
- var oldAssociatedTranscript;
- dojo.connect(associatedTranscriptField, "onFocus", function () {
- oldAssociatedTranscript = associatedTranscriptField.get("value");
- });
- dojo.connect(associatedTranscriptField, "onBlur", function () {
- var newAssociatedTranscript = associatedTranscriptField.get("value");
- if (oldAssociatedTranscript != newAssociatedTranscript) {
- updateAssociatedTranscript(newAssociatedTranscript);
- }
- });
-
- };
 
  var initDbxrefs = function (feature, config) {
  if (config.hasDbxrefs) {

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

@@ -209,27 +209,6 @@ class AnnotationEditorController extends AbstractApolloController implements Ann
  }
 
 
- @RestApiMethod(description = "Set associated transcripts to a regulator type", path = "/annotationEditor/setAssociatedTranscript", verb = RestApiVerb.POST
- )
- @RestApiParams(params = [
- @RestApiParam(name = "username", type = "email", paramType = RestApiParamType.QUERY)
- , @RestApiParam(name = "password", type = "password", paramType = RestApiParamType.QUERY)
- , @RestApiParam(name = "organism", type = "string", paramType = RestApiParamType.QUERY, description = "(optional) Organism ID or common name")
- , @RestApiParam(name = "sequence", type = "string", paramType = RestApiParamType.QUERY, description = "(optional) Sequence name")
- , @RestApiParam(name = "suppressHistory", type = "boolean", paramType = RestApiParamType.QUERY, description = "Suppress the history of this operation")
- , @RestApiParam(name = "suppressEvents", type = "boolean", paramType = RestApiParamType.QUERY, description = "Suppress instant update of the user interface")
- , @RestApiParam(name = "features", type = "JSONArray", paramType = RestApiParamType.QUERY, description = "JSONArray of JSON feature objects described by https://github.com/GMOD/Apollo/blob/master/grails-app/domain/org/bbop/apollo/Feature.groovy")
- ]
- )
- def setAssociatedTranscript() {
- JSONObject inputObject = permissionService.handleInput(request, params)
- if (permissionService.hasPermissions(inputObject, PermissionEnum.WRITE)) {
- render requestHandlingService.setAssociatedTranscript(inputObject)
- } else {
- render status: HttpStatus.UNAUTHORIZED
- }
- }
-
  @RestApiMethod(description = "Add an exon", path = "/annotationEditor/addExon", verb = RestApiVerb.POST
  )
  @RestApiParams(params = [

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

@@ -581,59 +581,6 @@ class RequestHandlingService {
 
  }
 
- JSONObject setAssociatedTranscript(JSONObject inputObject){
- JSONArray features = inputObject.getJSONArray(FeatureStringEnum.FEATURES.value)
- // first feature is the transcript
- String uniqueName = features.getJSONObject(0).getString(FeatureStringEnum.UNIQUENAME.value)
- Transcript transcript = Transcript.findByUniqueName(uniqueName)
- JSONObject oldJsonObject = featureService.convertFeatureToJSON(transcript)
- Sequence sequence = permissionService.checkPermissions(inputObject, PermissionEnum.WRITE)
-
- for (int i = 1; i < features.length(); ++i) {
- JSONObject jsonExon = features.getJSONObject(i);
- // could be that this is null
- Exon gsolExon = (Terminator) featureService.convertJSONToFeature(jsonExon, sequence)
-
- featureService.updateNewGsolFeatureAttributes(gsolExon, sequence);
-
- if (gsolExon.getFmin() < 0 || gsolExon.getFmax() < 0) {
- throw new AnnotationException("Feature cannot have negative coordinates")
- }
-
- transcriptService.addExon(transcript, gsolExon, false)
-
- gsolExon.save()
- }
- featureService.removeExonOverlapsAndAdjacencies(transcript)
- transcriptService.updateGeneBoundaries(transcript)
- featureService.calculateCDS(transcript)
-
- transcript.save(flush: true)
- transcript.attach()
- nonCanonicalSplitSiteService.findNonCanonicalAcceptorDonorSpliceSites(transcript)
- transcript.save(flush: true)
-
- // TODO: one of these two versions . . .
- JSONObject newJsonObject = featureService.convertFeatureToJSON(transcript, false)
- JSONObject returnObject = createJSONFeatureContainer(newJsonObject)
-
- Gene gene = transcriptService.getGene(transcript)
-
- featureEventService.addNewFeatureEvent(FeatureOperation.ADD_EXON, gene.name, transcript.uniqueName, inputObject, oldJsonObject, newJsonObject, permissionService.getCurrentUser(inputObject))
-
- AnnotationEvent annotationEvent = new AnnotationEvent(
- features: returnObject
- , sequence: sequence
- , operation: AnnotationEvent.Operation.UPDATE
- )
-
- fireAnnotationEvent(annotationEvent)
-
- return returnObject
-
-
- }
-
  /**
  * First feature is transcript, and the rest must be exons to add
  * @param inputObject