Removed unused variables, improve test credential handling, refresh blob metadata on OutputStream close

Author: labkey-jeckels

src/org/labkey/targetedms/TargetedMSController.java

@@ -276,7 +276,6 @@
 import org.labkey.targetedms.view.spectrum.LibrarySpectrumMatch;
 import org.labkey.targetedms.view.spectrum.LibrarySpectrumMatchGetter;
 import org.labkey.targetedms.view.spectrum.PeptideSpectrumView;
-import org.labkey.vfs.FileLike;
 import org.springframework.validation.BindException;
 import org.springframework.validation.Errors;
 import org.springframework.web.servlet.ModelAndView;
@@ -286,7 +285,6 @@
 import java.awt.*;
 import java.awt.image.BufferedImage;
 import java.io.ByteArrayInputStream;
-import java.io.File;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.StringWriter;
@@ -3227,7 +3225,7 @@ private void addSpectrumViews(TargetedMSRun run, VBox vbox, Peptide peptide, Bin
         PipeRoot root = PipelineService.get().getPipelineRootSetting(getContainer());
         if (null != root)
         {
-            LocalDirectory localDirectory = LocalDirectory.create(root, MODULE_NAME);
+            LocalDirectory localDirectory = LocalDirectory.create(root);
             try
             {
                 List<SpeclibReaderException> specLibErrors = new ArrayList<>();
@@ -6270,7 +6268,7 @@ public boolean handlePost(ResolveConflictForm resolveConflictForm, BindException
                 PipeRoot root = PipelineService.get().getPipelineRootSetting(getContainer());
                 if (null != root)
                 {
-                    LocalDirectory localDirectory = LocalDirectory.create(root, MODULE_NAME);
+                    LocalDirectory localDirectory = LocalDirectory.create(root);
                     try
                     {
                         ChromatogramLibraryUtils.incrementLibraryRevision(getContainer(), getUser(), localDirectory);
@@ -6562,7 +6560,7 @@ public ModelAndView getView(DownloadForm form, BindException errors) throws Exce
                     PipeRoot root = PipelineService.get().getPipelineRootSetting(getContainer());
                     if (null != root)
                     {
-                        LocalDirectory localDirectory = LocalDirectory.create(root, MODULE_NAME);
+                        LocalDirectory localDirectory = LocalDirectory.create(root);
                         try
                         {
                             ChromatogramLibraryUtils.writeLibrary(container, getUser(), localDirectory, libraryRevision);

src/org/labkey/targetedms/TargetedMSManager.java

@@ -145,7 +145,6 @@
 import static org.labkey.api.targetedms.TargetedMSService.FOLDER_TYPE_PROP_NAME;
 import static org.labkey.api.targetedms.TargetedMSService.FolderType.Library;
 import static org.labkey.api.targetedms.TargetedMSService.FolderType.LibraryProtein;
-import static org.labkey.api.targetedms.TargetedMSService.MODULE_NAME;
 import static org.labkey.targetedms.TargetedMSSchema.TABLE_INSTRUMENT_NICKNAME;
 
 public class TargetedMSManager
@@ -1268,7 +1267,7 @@ public static void deleteRuns(List<Long> runIds, Container c, User user, boolean
                     PipeRoot root = PipelineService.get().getPipelineRootSetting(run.getContainer());
                     if (null != root)
                     {
-                        LocalDirectory localDirectory = LocalDirectory.create(root, MODULE_NAME);
+                        LocalDirectory localDirectory = LocalDirectory.create(root);
                         try
                         {
                             RepresentativeStateManager.setRepresentativeState(user, run.getContainer(), localDirectory, run, RunRepresentativeDataState.NotRepresentative);

src/org/labkey/targetedms/pipeline/TargetedMSImportPipelineJob.java

@@ -34,8 +34,6 @@
 
 import java.util.List;
 
-import static org.labkey.api.targetedms.TargetedMSService.MODULE_NAME;
-
 /**
  * Simple wrapper job around a {@link TargetedMSImportTask}.
  * User: vsharma
@@ -69,14 +67,14 @@ public TargetedMSImportPipelineJob(ViewBackgroundInfo info, ExpData expData, Sky
         if ((_expData.hasFileScheme() && root.isCloudRoot()) || (!_expData.hasFileScheme() && !root.isCloudRoot()))
             throw new RuntimeException("Cannot process ExpData when its schema does not match root URI scheme.");
 
-        LocalDirectory localDirectory = LocalDirectory.create(root, MODULE_NAME, baseLogFileName,
+        LocalDirectory localDirectory = LocalDirectory.create(root, baseLogFileName,
                 null != _expData.getFile() ? _expData.getFile().getParentFile().getPath() : FileUtil.getTempDirectory().getPath());
         setLocalDirectory(localDirectory);
         setLogFile(localDirectory.determineLogFile());
     }
 
     @Override
-    public TaskPipeline getTaskPipeline()
+    public TaskPipeline<?> getTaskPipeline()
     {
         return PipelineJobService.get().getTaskPipeline(new TaskId(TargetedMSImportPipelineJob.class));
     }