Hold GUID instead of Container (#899)

Author: labkey-adam

ms2/src/org/labkey/ms2/MS2Run.java

@@ -18,10 +18,12 @@
 
 import org.apache.logging.log4j.Logger;
 import org.labkey.api.data.Container;
+import org.labkey.api.data.ContainerManager;
 import org.labkey.api.data.SQLFragment;
 import org.labkey.api.data.SqlSelector;
 import org.labkey.api.protein.MassType;
 import org.labkey.api.query.FieldKey;
+import org.labkey.api.util.GUID;
 import org.labkey.api.util.MemTracker;
 import org.labkey.api.util.logging.LogHelper;
 import org.labkey.api.view.ViewContext;
@@ -41,7 +43,7 @@ public abstract class MS2Run implements Serializable
     protected final static String[] EMPTY_STRING_ARRAY = new String[0];
 
     protected int run;
-    protected Container container;
+    protected GUID containerId;
     protected String description;
     protected String path;
     protected String fileName;
@@ -252,13 +254,13 @@ public void setRun(int run)
 
     public Container getContainer()
     {
-        return container;
+        return ContainerManager.getForId(containerId);
     }
 
 
     public void setContainer(Container container)
     {
-        this.container = container;
+        this.containerId = container.getEntityId();
     }
 
 

ms2/src/org/labkey/ms2/pipeline/mascot/MascotRun.java

@@ -48,8 +48,7 @@ public class MascotRun extends MS2Run
     public void adjustScores(Map<String, String> map)
     {
         // Mascot exported pepXML can exclude "homologyscore"
-        if (null == map.get("homologyscore"))
-            map.put("homologyscore", "-1");
+        map.putIfAbsent("homologyscore", "-1");
         // Issue 30322 - ProteomeDiscoverer pep.xml files use a different name for the score value
         if (null == map.get("ionscore") && map.containsKey("Ions Score"))
             map.put("ionscore", map.get("Ions Score"));

nab/src/org/labkey/nab/NabAssayController.java

@@ -331,8 +331,6 @@ private DilutionAssayRun _getNabAssayRun(ExpRun run, StatsService.CurveFitType f
         return assay;
     }
 
-    private static final String LAST_NAB_RUN_KEY = NabAssayController.class.getName() + "/LastNAbRun";
-
     @RequiresPermission(ReadPermission.class)
     @ContextualRoles(RunDatasetContextualRoles.class)
     public class DetailsAction extends RunDetailsAction<RenderAssayBean>
@@ -504,12 +502,6 @@ protected DilutionAssayRun getAssayRun(ExpRun run, StatsService.CurveFitType fit
         {
             return _getNabAssayRun(run, fit, user);
         }
-
-        @Override
-        public void addNavTrail(NavTree root)
-        {
-            throw new UnsupportedOperationException();
-        }
     }
 
     public static class SampleSpreadsheetForm

nab/src/org/labkey/nab/NabAssayRun.java

@@ -42,12 +42,6 @@
 import java.util.Map;
 import java.util.Set;
 
-/*
- * User: brittp
- * Date: Dec 9, 2008
- * Time: 5:43:01 PM
- */
-
 public abstract class NabAssayRun extends DilutionAssayRun
 {
     public NabAssayRun(DilutionAssayProvider<?> provider, ExpRun run,
@@ -119,7 +113,7 @@ else if (null != dataWithHandlerType)
             if (null == outputObject)
                 throw new IllegalStateException("Expected a single data file output for this NAb run, but none matching the expected datatype found. Found a total of " + outputDatas.size());
 
-            AssayProtocolSchema schema = _provider.createProtocolSchema(_user, _run.getContainer(), _protocol, null);
+            AssayProtocolSchema schema = _provider.createProtocolSchema(getUser(), _run.getContainer(), _protocol, null);
             TableInfo virusTable = schema.createTable(DilutionManager.VIRUS_TABLE_NAME, null);
 
             Map<String, Map<PropertyDescriptor, Object>> samplePropertiesMap = getSampleProperties();

nab/src/org/labkey/nab/NabDataHandler.java

@@ -55,10 +55,6 @@
 import java.util.List;
 import java.util.Map;
 
-/**
- * User: klum
- * Date: May 15, 2009
- */
 public abstract class NabDataHandler extends DilutionDataHandler
 {
     public static final Logger LOG = LogManager.getLogger(NabDataHandler.class);
@@ -146,7 +142,7 @@ public void recalculateDilutionStats(ExpData data, ExpRun run, ExpProtocol proto
      * Calculates cutoff and AUC information from the passed in raw data and optionally saves the data to the
      * specific tables.
      *
-     * @param commitData true to persist dilution and well level data
+     * @param commitData true to persist dilution and well-level data
      * @param specimenRows if commitData is false, then specimen data will be returned in this collection
      * @param cutoffRows if commitData is false, then cutoff data will be returned in this collection
      */
@@ -268,7 +264,7 @@ public void beforeDeleteData(List<ExpData> datas, User user) throws ExperimentEx
         {
             NabManager.get().deleteRunData(datas);
         }
-        catch(SQLException e)
+        catch (SQLException e)
         {
             throw new ExperimentException(e);
         }

nab/src/org/labkey/nab/SinglePlateNabAssayRun.java

@@ -323,7 +323,7 @@ protected String getVirusName(String virusWellGroupName)
         if (!outputDatas.isEmpty())
         {
             Lsid virusLsid = DilutionDataHandler.createVirusWellGroupLsid(outputDatas.get(0), virusWellGroupName);
-            AssayProtocolSchema schema = _provider.createProtocolSchema(_user, _run.getContainer(), _protocol, null);
+            AssayProtocolSchema schema = _provider.createProtocolSchema(getUser(), _run.getContainer(), _protocol, null);
             TableInfo virusTable = schema.createTable(DilutionManager.VIRUS_TABLE_NAME, null);
             if (null != virusTable)
             {