Initial support for animal aliasing in MCC.

Author: bbimber

jbrowse/src/client/JBrowse/Browser/Browser.tsx

@@ -69,13 +69,6 @@ function applyUrlParams(json, queryParam) {
             }
         }
     }
-
-    let activeTracks = queryParam.get('activeTracks')
-    if (activeTracks) {
-        activeTracks = activeTracks.split(',')
-
-        //TODO
-    }
 }
 
 function View(){
@@ -86,6 +79,15 @@ function View(){
     const [bgColor, setBgColor] = useState(null)
     const [plugins, setPlugins] = useState<PluginConstructor[]>();
     useEffect(() => {
+        let activeTracks = []
+        if (queryParam.get('activeTracks')) {
+            activeTracks = activeTracks.concat(queryParam.get('activeTracks').split(','))
+        }
+
+        if (queryParam.get('tracks')) {
+            activeTracks = activeTracks.concat(queryParam.get('tracks').split(','))
+        }
+
         Ajax.request({
             url: ActionURL.buildURL('jbrowse', 'getSession.api'),
             method: 'GET',
@@ -129,7 +131,7 @@ function View(){
                 setState("invalid");
                 console.log(res);
             },
-            params: {session: session}
+            params: {session: session, activeTracks: activeTracks.join(',')}
         });
     }, []);
 

jbrowse/src/org/labkey/jbrowse/JBrowseController.java

@@ -626,16 +626,27 @@ public void setStop(Integer stop)
 
     public static class GetSessionForm
     {
-        private String session;
+        private String _session;
+        private String _activeTracks;
 
         public String getSession()
         {
-            return session;
+            return _session;
         }
 
         public void setSession(String session)
         {
-            this.session = session;
+            _session = session;
+        }
+
+        public String getActiveTracks()
+        {
+            return _activeTracks;
+        }
+
+        public void setActiveTracks(String activeTracks)
+        {
+            _activeTracks = activeTracks;
         }
     }
 
@@ -687,7 +698,17 @@ else if (MGAP_FILTERED.equalsIgnoreCase(form.getSession()))
                     return null;
                 }
 
-                resp = db.getConfigJson(getUser(), _log);
+                List<String> additionalActiveTracks = null;
+                if (form.getActiveTracks() != null)
+                {
+                    String val = StringUtils.trimToNull(form.getActiveTracks());
+                    if (val != null)
+                    {
+                        additionalActiveTracks.addAll(Arrays.asList(val.split(",")));
+                    }
+                }
+
+                resp = db.getConfigJson(getUser(), _log, additionalActiveTracks);
             }
 
             // The rationale of this is to take the site theme, and map this to the primary site color.

jbrowse/src/org/labkey/jbrowse/model/JBrowseSession.java

@@ -2,6 +2,7 @@
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
+import org.jetbrains.annotations.Nullable;
 import org.json.JSONArray;
 import org.json.JSONObject;
 import org.labkey.api.data.CompareType;
@@ -217,7 +218,7 @@ public void ensureJsonFilesPrepared(User u, Logger log) throws PipelineJobExcept
         }
     }
 
-    public JSONObject getConfigJson(User u, Logger log) throws PipelineJobException
+    public JSONObject getConfigJson(User u, Logger log, @Nullable List<String> additionalActiveTracks) throws PipelineJobException
     {
         JSONObject ret = new JSONObject();
 
@@ -245,7 +246,7 @@ public JSONObject getConfigJson(User u, Logger log) throws PipelineJobException
         }
 
         ret.put("tracks", tracks);
-        ret.put("defaultSession", getDefaultSessionJson(visibleTracks));
+        ret.put("defaultSession", getDefaultSessionJson(visibleTracks, additionalActiveTracks));
 
         if (getJsonConfig() != null)
         {
@@ -295,7 +296,7 @@ private List<JsonFile> getGenomeTracks(User u, boolean createInDatabaseIfMissing
         return ret;
     }
 
-    public JSONObject getDefaultSessionJson(List<JsonFile> tracks)
+    public JSONObject getDefaultSessionJson(List<JsonFile> tracks, @Nullable List<String> additionalActiveTracks)
     {
         JSONObject ret = new JSONObject();
         ret.put("name", getName());
@@ -307,7 +308,8 @@ public JSONObject getDefaultSessionJson(List<JsonFile> tracks)
         JSONArray defaultTracks = new JSONArray();
         for (JsonFile jf : tracks)
         {
-            if (jf.isVisibleByDefault()) {
+            boolean visibleByDefault = jf.isVisibleByDefault() || jf.matchesTrackSelector(additionalActiveTracks);
+            if (visibleByDefault) {
                 String trackId = jf.getObjectId();
                 defaultTracks.put(new JSONObject(){{
                     put("type", jf.getTrackType());

jbrowse/src/org/labkey/jbrowse/model/JsonFile.java

@@ -525,6 +525,16 @@ private JSONObject getVcfTrack(Logger log, ExpData targetFile, ReferenceGenome r
         return ret;
     }
 
+    public boolean matchesTrackSelector(List<String> toTest)
+    {
+        if (toTest == null)
+        {
+            return false;
+        }
+
+        return toTest.contains(getObjectId()) || toTest.contains(getLabel());
+    }
+
     private JSONObject getBamTrack(Logger log, ExpData targetFile, ReferenceGenome rg)
     {
         JSONObject ret = new JSONObject();