fixes #2601 when complete (#2617)

* fixes #2601 when complete * added reasonable UI * kind of validating * added example * works, but only for the first anntation * fixed compilation errors * fixed empty references and withOrFrom * added * updated * server code working * updated rest doc and added reload * fixed messages * fixed messages * fixed null references * fixed formatting * fixed deletions * removed consol logs * updated REST api * added changelog * fixed calls to clear
GMOD · May 10, 2021 · 9016b45 · 9016b45
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commit 9016b45
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diff --git a/ChangeLog.md b/ChangeLog.md
@@ -1,4 +1,10 @@
 
+### 2.6.5
+
+Features
+
+- Added method to upload bulk functional annotations from JSON in the interface [2617](https://github.com/GMOD/Apollo/pull/2617).
+
 
 ## 2.6.4 
 

diff --git a/grails-app/controllers/org/bbop/apollo/AnnotatorController.groovy b/grails-app/controllers/org/bbop/apollo/AnnotatorController.groovy
@@ -4,6 +4,8 @@ import grails.converters.JSON
 import grails.transaction.NotTransactional
 import grails.transaction.Transactional
 import org.bbop.apollo.event.AnnotationEvent
+import org.bbop.apollo.geneProduct.GeneProduct
+import org.bbop.apollo.go.GoAnnotation
 import org.bbop.apollo.gwt.shared.ClientTokenGenerator
 import org.bbop.apollo.gwt.shared.FeatureStringEnum
 import org.bbop.apollo.gwt.shared.GlobalPermissionEnum
@@ -21,6 +23,8 @@ import org.restapidoc.pojo.RestApiParamType
 import org.restapidoc.pojo.RestApiVerb
 import org.springframework.http.HttpStatus
 
+import static org.springframework.http.HttpStatus.UNAUTHORIZED
+
 /**
  * This is server-side code supporting the high-level functionality of the GWT AnnotatorPanel class.
  */
@@ -1067,6 +1071,124 @@ class AnnotatorController {
         exportService.export(params.format, response.outputStream, annotatorGroupList, fields, labels, formatters, parameters)
     }
 
+
+    @RestApiMethod(description = "Get annotators report for group", path = "/group/getAnnotatorsReportForGroup", verb = RestApiVerb.POST)
+    @RestApiParams(params = [
+            @RestApiParam(name = "username", type = "email", paramType = RestApiParamType.QUERY)
+            , @RestApiParam(name = "password", type = "password", paramType = RestApiParamType.QUERY)
+            , @RestApiParam(name = "data", type = "json strong", paramType = RestApiParamType.QUERY, description = "JSON of go annotations, gene products , and provenance to be added at once (see upload annotations in interface)")
+    ]
+    )
+    def addFunctionalAnnotations(){
+        JSONObject dataObject = permissionService.handleInput(request, params)
+        println "input data object ${dataObject as JSON}"
+        if(!permissionService.checkLoginGlobalAndLocalPermissions(dataObject,GlobalPermissionEnum.USER,PermissionEnum.WRITE)){
+            render status : UNAUTHORIZED
+            return
+        }
+        User user = permissionService.getCurrentUser(dataObject)
+        Feature feature = null
+//        JSONObject originalFeatureJsonObject = null
+
+        List<GoAnnotation> goAnnotationList = []
+        List<GeneProduct> geneProductArrayList = []
+        List<Provenance> provenanceArrayList = []
+
+        JSONArray goArray = dataObject.getJSONArray(FeatureStringEnum.GO_ANNOTATIONS.value)
+        for(JSONObject object in goArray){
+            if(feature==null){
+                feature = Feature.findByUniqueName(object.feature)
+//                originalFeatureJsonObject = featureService.convertFeatureToJSON(feature)
+            }
+            GoAnnotation goAnnotation = new GoAnnotation()
+            goAnnotation.feature = feature
+            goAnnotation.aspect = object.aspect
+            goAnnotation.goRef = object.goTerm
+            goAnnotation.geneProductRelationshipRef = object.geneRelationship
+            goAnnotation.evidenceRef = object.evidenceCode
+            goAnnotation.goRefLabel = object.goTermLabel
+            goAnnotation.evidenceRefLabel = object.evidenceCodeLabel
+            goAnnotation.negate = object.negate ?: false
+            goAnnotation.withOrFromArray = object.withOrFrom
+            goAnnotation.notesArray = object.notes
+            goAnnotation.reference = object.reference
+            goAnnotation.lastUpdated = new Date()
+            goAnnotation.dateCreated = new Date()
+            goAnnotation.addToOwners(user)
+            feature.addToGoAnnotations(goAnnotation)
+            goAnnotation.save(failOnError: true)
+            goAnnotationList.add(goAnnotation)
+        }
+
+        JSONArray geneProductArray = dataObject.getJSONArray(FeatureStringEnum.GENE_PRODUCT.value)
+        for(JSONObject object in geneProductArray){
+            if(feature==null){
+                feature = Feature.findByUniqueName(object.feature)
+//                originalFeatureJsonObject = featureService.convertFeatureToJSON(feature)
+            }
+            GeneProduct geneProduct = new GeneProduct()
+            geneProduct.feature = feature
+            geneProduct.productName = object.productName
+            geneProduct.evidenceRef = object.evidenceCode
+            geneProduct.evidenceRefLabel = object.evidenceCodeLabel
+            geneProduct.alternate = object.alternate ?: false
+            geneProduct.withOrFromArray = object.withOrFrom
+            geneProduct.notesArray = object.notes
+            geneProduct.reference = object.reference
+            geneProduct.lastUpdated = new Date()
+            geneProduct.dateCreated = new Date()
+            geneProduct.addToOwners(user)
+            feature.addToGeneProducts(geneProduct)
+            geneProduct.save(failOnError: true)
+            GeneProductName.findOrSaveByName(geneProduct.productName)
+            geneProductArrayList.add(geneProduct)
+        }
+
+        JSONArray provenanceArray = dataObject.getJSONArray(FeatureStringEnum.PROVENANCE.value)
+        for(JSONObject object in provenanceArray){
+            if(feature==null){
+                feature = Feature.findByUniqueName(object.feature)
+//                originalFeatureJsonObject = featureService.convertFeatureToJSON(feature)
+            }
+            Provenance provenance = new Provenance()
+            provenance.feature = feature
+            provenance.field = object.field
+            provenance.evidenceRef = object.evidenceCode
+            provenance.evidenceRefLabel = object.evidenceCodeLabel
+            provenance.withOrFromArray = object.withOrFrom
+            provenance.notesArray = object.notes
+            provenance.reference = object.reference
+            provenance.lastUpdated = new Date()
+            provenance.dateCreated = new Date()
+            provenance.addToOwners(user)
+            feature.addToProvenances(provenance)
+            provenance.save(failOnError: true)
+            provenanceArrayList.add(provenance)
+        }
+
+
+//        JSONArray oldFeaturesJsonArray = new JSONArray()
+//        oldFeaturesJsonArray.add(originalFeatureJsonObject)
+//        JSONArray newFeaturesJsonArray = new JSONArray()
+//        JSONObject currentFeatureJsonObject = featureService.convertFeatureToJSON(feature)
+//        newFeaturesJsonArray.add(currentFeatureJsonObject)
+//        featureEventService.addNewFeatureEvent(FeatureOperation.ADD_BULK_FUNCTIONAL_ANNOTATIONS,
+//                feature.name,
+//                feature.uniqueName,
+//                dataObject,
+//                oldFeaturesJsonArray,
+//                newFeaturesJsonArray,
+//                user)
+
+        if(feature==null){
+            render new JSONObject() as JSON
+            return
+        }
+        render feature as JSON
+    }
+
+
+
     @RestApiMethod(description = "Get annotators report for group", path = "/group/getAnnotatorsReportForGroup", verb = RestApiVerb.POST)
     @RestApiParams(params = [
             @RestApiParam(name = "username", type = "email", paramType = RestApiParamType.QUERY)

diff --git a/grails-app/controllers/org/bbop/apollo/GoAnnotationController.groovy b/grails-app/controllers/org/bbop/apollo/GoAnnotationController.groovy
@@ -84,7 +84,7 @@ class GoAnnotationController {
       return
     }
     User user = permissionService.getCurrentUser(dataObject)
-      GoAnnotation goAnnotation = new GoAnnotation()
+    GoAnnotation goAnnotation = new GoAnnotation()
     Feature feature = Feature.findByUniqueName(dataObject.feature)
 
     JSONObject originalFeatureJsonObject = featureService.convertFeatureToJSON(feature)

diff --git a/grails-app/services/org/bbop/apollo/RequestHandlingService.groovy b/grails-app/services/org/bbop/apollo/RequestHandlingService.groovy
@@ -2181,9 +2181,13 @@ class RequestHandlingService {
                   provenanceService.deleteAnnotationFromFeature(transcript)
                   geneProductService.deleteAnnotationFromFeature(transcript)
 
-                  goAnnotationService.removeGoAnnotationsFromFeature(transcript)
-                  provenanceService.removeProvenancesFromFeature(transcript)
-                  geneProductService.removeGeneProductsFromFeature(transcript)
+                  transcript?.goAnnotations?.clear()
+                  transcript?.geneProducts?.clear()
+                  transcript?.provenances?.clear()
+
+//                  goAnnotationService.removeGoAnnotationsFromFeature(transcript)
+//                  provenanceService.removeProvenancesFromFeature(transcript)
+//                  geneProductService.removeGeneProductsFromFeature(transcript)
 
                   featureRelationshipService.removeFeatureRelationship(gene, transcript)
                   featureRelationshipService.deleteFeatureAndChildren(transcript)

diff --git a/src/groovy/org/bbop/apollo/history/FeatureOperation.groovy b/src/groovy/org/bbop/apollo/history/FeatureOperation.groovy
@@ -59,6 +59,7 @@ enum FeatureOperation {
   REMOVE_GO_ANNOTATION(false),
   UPDATE_GO_ANNOTATION(false),
   ADD_GO_ANNOTATION(false),
+  ADD_BULK_FUNCTIONAL_ANNOTATIONS(false),
 
   REMOVE_GENE_PRODUCT(false),
   UPDATE_GENE_PRODUCT(false),

diff --git a/src/gwt/org/bbop/apollo/gwt/client/ExportPanel.java b/src/gwt/org/bbop/apollo/gwt/client/ExportPanel.java
@@ -267,7 +267,6 @@ public void showExportStatus(String exportStatus) {
     public Div parseStatus(String status) {
         Div div = new Div();
         JSONObject jsonObject = JSONParser.parseStrict(status).isObject();
-        GWT.log(jsonObject.toString());
         for(String key : jsonObject.keySet()) {
             div.add(new Paragraph(key + ": " + jsonObject.get(key).toString().replaceAll("\"", "")));
         }

diff --git a/src/gwt/org/bbop/apollo/gwt/client/GeneDetailPanel.java b/src/gwt/org/bbop/apollo/gwt/client/GeneDetailPanel.java
@@ -79,6 +79,8 @@ interface AnnotationDetailPanelUiBinder extends UiBinder<Widget, GeneDetailPanel
     InlineCheckBox partialMax;
     @UiField
     InlineCheckBox obsoleteButton;
+    @UiField
+    Button uploadAnnotationButton;
 
     private SuggestedNameOracle suggestedNameOracle = new SuggestedNameOracle();
 
@@ -101,6 +103,11 @@ private void handleNameChange() {
         updateGene();
     }
 
+    @UiHandler("uploadAnnotationButton")
+    void uploadAnnotation(ClickEvent clickEvent){
+        new UploadDialog(internalAnnotationInfo) ;
+    }
+
     @UiHandler("symbolField")
     void handleSymbolChange(ChangeEvent e) {
         String updatedName = symbolField.getText();

diff --git a/src/gwt/org/bbop/apollo/gwt/client/GeneDetailPanel.ui.xml b/src/gwt/org/bbop/apollo/gwt/client/GeneDetailPanel.ui.xml
@@ -65,6 +65,7 @@
                 <b:Button ui:field="syncNameButton" icon="REFRESH" enabled="false" text="Sync name with transcript"
                           addStyleNames="{style.action-buttons}"/>
                 <b:InlineCheckBox ui:field="obsoleteButton">Obsolete</b:InlineCheckBox>
+                <b:Button ui:field="uploadAnnotationButton" icon="UPLOAD">Annotations</b:Button>
                 <b:Button type="DANGER" icon="TRASH_O" title="Go To" iconSize="LARGE"
                           text="Delete" pull="RIGHT"
                           ui:field="deleteAnnotation" enabled="false"

diff --git a/src/gwt/org/bbop/apollo/gwt/client/ProvenancePanel.java b/src/gwt/org/bbop/apollo/gwt/client/ProvenancePanel.java
@@ -476,11 +476,6 @@ private List<String> getNoteList() {
     return noteList;
   }
 
-//    @UiHandler("referenceValidateButton")
-//    public void validateReference(ClickEvent clickEvent) {
-//        GWT.log("not sure what to do here ");
-//    }
-
   @UiHandler("cancelNewProvenance")
   public void cancelNewProvenanceButton(ClickEvent e) {
     clearModal();

diff --git a/src/gwt/org/bbop/apollo/gwt/client/TranscriptDetailPanel.java b/src/gwt/org/bbop/apollo/gwt/client/TranscriptDetailPanel.java
@@ -75,6 +75,8 @@ interface AnnotationDetailPanelUiBinder extends UiBinder<Widget, TranscriptDetai
     InlineCheckBox partialMax;
     @UiField
     InlineCheckBox obsoleteButton;
+    @UiField
+    Button uploadAnnotationButton;
 
     private Boolean editable = false;
 
@@ -195,6 +197,11 @@ public void onError(Request request, Throwable exception) {
 
     }
 
+    @UiHandler("uploadAnnotationButton")
+    void uploadAnnotation(ClickEvent clickEvent){
+       new UploadDialog(internalAnnotationInfo) ;
+    }
+
     @UiHandler("annotationIdButton")
     void getAnnotationInfo(ClickEvent clickEvent) {
       new LinkDialog("UniqueName: "+internalAnnotationInfo.getUniqueName(),"Link to: "+MainPanel.getInstance().generateApolloLink(internalAnnotationInfo.getUniqueName()),true);

diff --git a/src/gwt/org/bbop/apollo/gwt/client/TranscriptDetailPanel.ui.xml b/src/gwt/org/bbop/apollo/gwt/client/TranscriptDetailPanel.ui.xml
@@ -61,6 +61,7 @@
                 <b:Button ui:field="syncNameButton" icon="REFRESH" enabled="true" text="Sync name with gene"
                           addStyleNames="{style.action-buttons}"/>
                 <b:InlineCheckBox ui:field="obsoleteButton">Obsolete</b:InlineCheckBox>
+                <b:Button ui:field="uploadAnnotationButton" icon="UPLOAD">Annotations</b:Button>
                 <b:Button type="DANGER" icon="TRASH_O" title="Go To" iconSize="LARGE"
                           text="Delete" pull="RIGHT"
                           ui:field="deleteAnnotation" enabled="true"