Refactor JBrowse pipeline steps to allow registration on cluster startup

Author: bbimber

jbrowse/src/org/labkey/jbrowse/JBrowseModule.java

@@ -110,7 +110,10 @@ public void doStartupAfterSpringConfig(ModuleContext moduleContext)
 
         WebdavService.get().registerPreGzippedExtensions("jsonz");
         WebdavService.get().registerPreGzippedExtensions("txtz");
+    }
 
+    public static void registerPipelineSteps()
+    {
         SequencePipelineService.get().registerPipelineStep(new IndexVariantsStep.Provider());
     }
 

jbrowse/src/org/labkey/jbrowse/PipelineStartup.java

@@ -0,0 +1,24 @@
+package org.labkey.jbrowse;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
+public class PipelineStartup
+{
+    private static final Logger _log = LogManager.getLogger(PipelineStartup.class);
+    private static boolean _hasRegistered = false;
+
+    public PipelineStartup()
+    {
+        if (_hasRegistered)
+        {
+            _log.warn("JBrowse resources have already been registered, skipping");
+        }
+        else
+        {
+            _log.info("Registering JBrowse resources");
+            JBrowseModule.registerPipelineSteps();
+            _hasRegistered = true;
+        }
+    }
+}

jbrowse/webapp/WEB-INF/jbrowse/jbrowseContext.xml

@@ -31,4 +31,9 @@
             </list>
         </property>
     </bean>
+
+    <!-- This is intended to force registration of the PipelineSteps -->
+    <bean id="pipelineStartup" class="org.labkey.jbrowse.PipelineStartup">
+
+    </bean>
 </beans>

singlecell/src/org/labkey/singlecell/pipeline/singlecell/CalculateUCellScores.java

@@ -23,8 +23,8 @@ public Provider()
         {
             super("CalculateUCellScores", "Calculate UCell Scores", "Seurat", "This will generate UCell scores for a set of pre-defined gene modules", Arrays.asList(
                     SeuratToolParameter.create("storeRanks", "Store Ranks", "Passed directly to UCell::AddModuleScore_UCell.", "checkbox", new JSONObject(){{
-
-                    }}, false),
+                        put("checked", true);
+                    }}, true),
                     SeuratToolParameter.create("assayName", "Assay Name", "Passed directly to UCell::AddModuleScore_UCell.", "textfield", new JSONObject(){{
 
                     }}, "RNA"),