added a lookup for uuid in loc (#2549)

* added a lookup for uuid in loc

* updated

* made ids linkable

Author: nathandunn

ChangeLog.md

@@ -10,6 +10,7 @@ Features
 - Added UUID lookup and link [2539](https://github.com/GMOD/Apollo/pull/2539/).
 - Added status filter for recent annotations [2543](https://github.com/GMOD/Apollo/pull/2543/).
 - Add feature name `loc` to loadLink [2544](https://github.com/GMOD/Apollo/issues/2544).
+- `loc` loadLink now supports UUID and ID popup provides link [2549](https://github.com/GMOD/Apollo/issues/2549).
 
 Bug Fixes
 
@@ -18,6 +19,7 @@ Bug Fixes
 - Now able to resize terminators by dragging  [2521](https://github.com/GMOD/Apollo/issues/2521).
 - Added missing GO annotations [2535](https://github.com/GMOD/Apollo/pull/2535).
 - findAllOrganism webserver failed when user is not an admin and no session is present [2540](https://github.com/GMOD/Apollo/issues/2540).
+- Provide minor UI and bug fixes [2548](https://github.com/GMOD/Apollo/pull/2548).
 
 Infrastructure Changes
 

docs/Configure.md

@@ -638,8 +638,7 @@ http://demo.genomearchitect.org/Apollo2/3836/jbrowse/index.html?loc=Group1.31:28
 
 <apollo server url>/<organism>/annotator/loadLink?loc=<location>&organism=<organism>&tracks=<tracks>
 
-- `location` = <sequence name>:<fmin>..<fmax>  it can also be the annotated feature name as well
-- `uuid` = The uniquename of the feature.  It replaces the feature and does not require an organism argument.   It is used inplace of the `loc` option.
+- `location` = <sequence name>:<fmin>..<fmax>  it can also be the annotated feature `name` if an organims is provided or the `uniqueName` (see the ID in the annotation detail window), which is typically a UUID and does not require an organism.
 - `organism` is the organism id or common name if unique.
 - `tracks` are url-encoded tracks separated by a comma
 

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

@@ -85,7 +85,14 @@ class AnnotatorController {
                 organism = featureLocation.sequence.organism
             }
 
-            if (!allowedOrganisms.contains(organism)) {
+          if (Feature.countByUniqueName(params.loc)>0) {
+            Feature feature = Feature.findByUniqueName(params.loc)
+            FeatureLocation featureLocation = feature.featureLocation
+            params.loc = featureLocation.sequence.name + ":" + featureLocation.fmin + ".." + featureLocation.fmax
+            organism = featureLocation.sequence.organism
+          }
+
+          if (!allowedOrganisms.contains(organism)) {
                 log.error("Can not load organism ${organism?.commonName} so loading ${allowedOrganisms.first().commonName} instead.")
                 params.loc = null
                 organism = allowedOrganisms.first()
@@ -94,10 +101,12 @@ class AnnotatorController {
             log.debug "loading organism: ${organism}"
             preferenceService.setCurrentOrganism(permissionService.currentUser, organism, clientToken)
             String location = params.loc
-            // assume that the lookup is a symbol lookup value and not a location
+
+          // assume that the lookup is a symbol lookup value and not a location
             if (location) {
                 int colonIndex = location.indexOf(':')
                 int ellipseIndex = location.indexOf('..')
+
                 if(colonIndex > 0 && colonIndex < ellipseIndex){
                     String[] splitString = location.split(':')
                     log.debug "splitString : ${splitString}"
@@ -127,6 +136,9 @@ class AnnotatorController {
                   int fmax = featureLocation.fmax
                   preferenceService.setCurrentSequenceLocation(sequence.name, fmin, fmax, clientToken)
                 }
+              else{
+                  log.error("Failed to process load process loadLink string")
+                }
             }
         }
 

src/gwt/org/bbop/apollo/gwt/client/AnnotatorPanel.java

@@ -1034,8 +1034,7 @@ public void updateStatus(ChangeEvent changeEvent){
 
   @UiHandler(value = {"annotationLinkButton"})
   public void showAnnotationLink(ClickEvent clickEvent){
-    String url = MainPanel.getInstance().generateApolloUrl(selectedAnnotationInfo.getUniqueName());
-    String link = "<a href='"+url+"'>"+url+"</a>";
+    String link =MainPanel.getInstance().generateApolloLink(selectedAnnotationInfo.getUniqueName());
     new LinkDialog("Link to '"+selectedAnnotationInfo.getName()+"'",link,true);
   }
 

src/gwt/org/bbop/apollo/gwt/client/GeneDetailPanel.java

@@ -267,7 +267,7 @@ public void updateData(AnnotationInfo annotationInfo) {
 
     @UiHandler("annotationIdButton")
     void getAnnotationInfo(ClickEvent clickEvent) {
-        Bootbox.alert(internalAnnotationInfo.getUniqueName());
+        new LinkDialog("UniqueName: "+internalAnnotationInfo.getUniqueName(),"Link to: "+MainPanel.getInstance().generateApolloLink(internalAnnotationInfo.getUniqueName()),true);
     }
 
     @UiHandler("gotoAnnotation")

src/gwt/org/bbop/apollo/gwt/client/MainPanel.java

@@ -953,6 +953,11 @@ public String generateApolloUrl() {
         return generateApolloUrl(null);
     }
 
+  public String generateApolloLink(String uuid) {
+    String url = generateApolloUrl(uuid);
+    return "<a href='"+url+"'>"+url+"</a>";
+  }
+
     public String generateApolloUrl(String uuid) {
         String url = Annotator.getRootUrl();
         url += "annotator/loadLink";
@@ -964,7 +969,7 @@ public String generateApolloUrl(String uuid) {
           }
         }
         else{
-          url += "?uuid="+uuid;
+          url += "?loc="+uuid;
         }
         url += "&organism=" + currentOrganism.getId();
         url += "&tracks=";

src/gwt/org/bbop/apollo/gwt/client/RepeatRegionDetailPanel.java

@@ -32,7 +32,7 @@
  */
 public class RepeatRegionDetailPanel extends Composite {
     private AnnotationInfo internalAnnotationInfo;
-   
+
     interface AnnotationDetailPanelUiBinder extends UiBinder<Widget, RepeatRegionDetailPanel> {
     }
 
@@ -74,7 +74,7 @@ public RepeatRegionDetailPanel() {
 
     @UiHandler("annotationIdButton")
     void getAnnotationInfo(ClickEvent clickEvent) {
-        Bootbox.alert(internalAnnotationInfo.getUniqueName());
+      new LinkDialog("UniqueName: "+internalAnnotationInfo.getUniqueName(),"Link to: "+MainPanel.getInstance().generateApolloLink(internalAnnotationInfo.getUniqueName()),true);
     }
 
     @UiHandler("gotoAnnotation")
@@ -184,7 +184,7 @@ void handleNameChange(ChangeEvent e) {
         internalAnnotationInfo.setName(updatedName);
         updateEntity();
     }
-    
+
     @UiHandler("descriptionField")
     void handleDescriptionChange(ChangeEvent e) {
         String updatedDescription = descriptionField.getText();
@@ -204,7 +204,7 @@ private void enableFields(boolean enabled) {
         descriptionField.setEnabled(enabled);
         synonymsField.setEnabled(enabled);
     }
-    
+
     private void updateEntity() {
         final AnnotationInfo updatedInfo = this.internalAnnotationInfo;
         enableFields(false);
@@ -227,7 +227,7 @@ public void onError(Request request, Throwable exception) {
         data.put(FeatureStringEnum.ORGANISM.getValue(),new JSONString(MainPanel.getInstance().getCurrentOrganism().getId()));
         RestService.sendRequest(requestCallback, "annotator/updateFeature/", data);
     }
-    
+
     public void updateData(AnnotationInfo annotationInfo) {
         GWT.log("Updating entity");
         this.internalAnnotationInfo = annotationInfo;
@@ -305,4 +305,4 @@ public void setEditable(boolean editable) {
         synonymsField.setEnabled(editable);
         deleteAnnotation.setEnabled(editable);
     }
-}
+}

src/gwt/org/bbop/apollo/gwt/client/TranscriptDetailPanel.java

@@ -159,7 +159,7 @@ public void callback(boolean result) {
 
     @UiHandler("annotationIdButton")
     void getAnnotationInfo(ClickEvent clickEvent) {
-        Bootbox.alert(internalAnnotationInfo.getUniqueName());
+      new LinkDialog("UniqueName: "+internalAnnotationInfo.getUniqueName(),"Link to: "+MainPanel.getInstance().generateApolloLink(internalAnnotationInfo.getUniqueName()),true);
     }
 
     @UiHandler("gotoAnnotation")

src/gwt/org/bbop/apollo/gwt/client/VariantDetailPanel.java

@@ -155,7 +155,7 @@ public void callback(boolean result) {
 
     @UiHandler("annotationIdButton")
     void getAnnotationInfo(ClickEvent clickEvent) {
-        Bootbox.alert(internalAnnotationInfo.getUniqueName());
+      new LinkDialog("UniqueName: "+internalAnnotationInfo.getUniqueName(),"Link to: "+MainPanel.getInstance().generateApolloLink(internalAnnotationInfo.getUniqueName()),true);
     }
 
     @UiHandler("gotoAnnotation")
@@ -315,4 +315,4 @@ public void onError(Request request, Throwable exception) {
     public static boolean isValidDNA(String bases) {
         return bases.matches("^[ATCGN]+$");
     }
-}
+}