added location feature name which fixes #2544 (#2547)

ChangeLog.md

@@ -9,6 +9,7 @@ Features
 - Added organism and species to menus [2537](https://github.com/GMOD/Apollo/pull/2537).
 - 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).
 
 Bug Fixes
 

docs/Configure.md

@@ -617,6 +617,36 @@ You should use ```tracklist=1``` to force showing the native tracklist (or use t
 
 Use ```openAnnotatorPanel=0``` to close the Annotator Panel explicitly on startup. 
 
+### Linking to annotations
+
+You can find a link to your current location by clicking the "chain link" icon in the upper, left-hand corner of the Annotator Panel.  
+
+It will provide a popup that gives you a public URL to view while not logged in and a one to use while logged in. 
+
+####Public URL
+
+<apollo server url>/<organism>/jbrowse/index.html?loc=<location>&tracks=<tracks>
+
+- `location` = <sequence name>:<fmin>..<fmax>
+- `organism` is the organism id or common name if unique.
+- `tracks` are url-encoded tracks separated by a comma
+
+Example:  
+http://demo.genomearchitect.org/Apollo2/3836/jbrowse/index.html?loc=Group1.31:287765..336436&tracks=Official%20Gene%20Set%20v3.2,GeneID
+
+####Logged in URL
+
+<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.
+- `organism` is the organism id or common name if unique.
+- `tracks` are url-encoded tracks separated by a comma
+
+Examples:
+- http://demo.genomearchitect.org/Apollo2/annotator/loadLink?loc=Group1.31:287765..336436&organism=3836&tracks=Official%20Gene%20Set%20v3.2,GeneID
+- http://demo.genomearchitect.org/Apollo2/annotator/loadLink?loc=GB51936-RA&organism=3836&tracks=Official%20Gene%20Set%20v3.2,GeneID
+- http://demo.genomearchitect.org/Apollo2/annotator/loadLink?uuid=355617c7-f8c1-4105-bb11-755cee1855df&tracks=Official%20Gene%20Set%20v3.2,GeneID
 
 ### Setting default track list behavior
 

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

@@ -66,7 +66,7 @@ class AnnotatorController {
                 clientToken = ClientTokenGenerator.generateRandomString()
                 log.debug 'generating client token on the backend: ' + clientToken
             }
-            Organism organism
+            Organism organism = null
             // check organism first
             if (params.containsKey(FeatureStringEnum.ORGANISM.value)) {
                 String organismString = params[FeatureStringEnum.ORGANISM.value]
@@ -96,7 +96,9 @@ class AnnotatorController {
             String location = params.loc
             // assume that the lookup is a symbol lookup value and not a location
             if (location) {
-                if(location.contains(':') && location.contains('..')){
+                int colonIndex = location.indexOf(':')
+                int ellipseIndex = location.indexOf('..')
+                if(colonIndex > 0 && colonIndex < ellipseIndex){
                     String[] splitString = location.split(':')
                     log.debug "splitString : ${splitString}"
                     String sequenceString = splitString[0]
@@ -116,8 +118,14 @@ class AnnotatorController {
                     log.debug "fmin ${fmin} . . fmax ${fmax} . . ${sequence}"
                     preferenceService.setCurrentSequenceLocation(sequence.name, fmin, fmax, clientToken)
                 }
-                else{
-                    searchName = location
+                else
+                if(organism && location.trim().length()>0) {
+                  def featureLocationResult = FeatureLocation.executeQuery("select fl,s from Feature f join f.featureLocations fl join fl.sequence s join s.organism o where o = :organism and f.name = :name",[organism:organism,name:location] ).first()
+                  FeatureLocation featureLocation = featureLocationResult[0]
+                  Sequence sequence = featureLocationResult[1]
+                  int fmin = featureLocation.fmin
+                  int fmax = featureLocation.fmax
+                  preferenceService.setCurrentSequenceLocation(sequence.name, fmin, fmax, clientToken)
                 }
             }
         }