Adopt FileLike for more pipeline APIs

src/org/labkey/targetedms/TargetedMSController.java

@@ -285,7 +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;
@@ -3226,7 +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<>();
@@ -3936,18 +3935,6 @@ public void setPeptideRepresentative(String[] peptideRepresentative)
         {
             _peptideRepresentative = peptideRepresentative;
         }
-
-        @Override
-        public List<File> getValidatedFiles(Container c)
-        {
-            List<File> files = super.getValidatedFiles(c);
-            List<File> resolvedFiles = new ArrayList<>(files.size());
-            for(File file: files)
-            {
-                resolvedFiles.add(FileUtil.resolveFile(file));  // Strips out ".." and "." from the path
-            }
-            return resolvedFiles;
-        }
     }
 
     @RequiresPermission(InsertPermission.class)
@@ -6281,7 +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);
@@ -6573,7 +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

@@ -116,6 +116,7 @@
 import org.labkey.targetedms.query.PeptideManager;
 import org.labkey.targetedms.query.PrecursorManager;
 import org.labkey.targetedms.query.RepresentativeStateManager;
+import org.labkey.vfs.FileLike;
 
 import java.io.IOException;
 import java.net.URI;
@@ -144,7 +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
@@ -707,7 +707,7 @@ public static Long addRunToQueue(ViewBackgroundInfo info,
             XarSource source = new AbstractFileXarSource("Wrap Targeted MS Run", container, user)
             {
                 @Override
-                public Path getLogFilePath()
+                public FileLike getLogFilePath()
                 {
                     throw new UnsupportedOperationException();
                 }
@@ -1308,7 +1308,7 @@ 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/ChromatogramCrawlerJob.java

@@ -42,7 +42,7 @@ protected ChromatogramCrawlerJob()
     public ChromatogramCrawlerJob(ViewBackgroundInfo info, @NotNull PipeRoot root)
     {
         super(TargetedMSPipelineProvider.name, info, root);
-        setLogFile(root.getRootFileLike().resolveChild(FileUtil.makeFileNameWithTimestamp("ChromatogramCrawl", "log")).toNioPathForWrite());
+        setLogFile(root.getRootFileLike().resolveChild(FileUtil.makeFileNameWithTimestamp("ChromatogramCrawl", "log")));
 
         getLogger().info("Description of key statuses:");
         for (Chromatogram.SourceStatus value : Chromatogram.SourceStatus.values())

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));
     }

src/org/labkey/targetedms/view/confirmImport.jsp

@@ -18,6 +18,7 @@
 <%@ page import="org.labkey.api.view.ActionURL"%>
 <%@ page import="org.labkey.api.view.HttpView"%>
 <%@ page import="org.labkey.targetedms.TargetedMSController" %>
+<%@ page import="org.labkey.vfs.FileLike" %>
 <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %>
 <%@ page extends="org.labkey.api.jsp.JspBase" %>
 <%
@@ -51,7 +52,7 @@
     </tr>
     <labkey:form action="<%=targetURL%>" method="POST">
         <input type="hidden" name="path" value="<%= h(form.getPath() )%>" />
-        <% for (java.io.File file : form.getValidatedFiles(getContainer()))
+        <% for (FileLike file : form.getValidatedFiles(getContainer()))
         { %>
             <tr style="border:1px solid;">
                 <td>

test/src/org/labkey/test/components/targetedms/TargetedMSRunsTable.java

@@ -69,7 +69,7 @@ public void deleteRun(String documentName)
         if (rowIndex < 0)
             fail("Unable to find checkbox for non-existent file: " + documentName);
         checkCheckbox(rowIndex);
-        clickHeaderButtonByText("Delete");
+        clickHeaderButton("Delete");
         getWrapper().clickButton("Confirm Delete");
     }
 
@@ -90,7 +90,7 @@ public void openDialogForDocuments(String buttonText, List<String> documentNames
             checkCheckbox(rowIndex);
         }
 
-        clickHeaderButtonByText(buttonText);
+        clickHeaderButton(buttonText);
     }
 
     public void showAllVersions()

test/src/org/labkey/test/tests/targetedms/TargetedMSLinkVersionsTest.java

@@ -84,7 +84,7 @@ private void deleteExistingQCRuns()
 
         if (hasRunsToDelete)
         {
-            table.clickHeaderButtonByText("Delete");
+            table.clickHeaderButton("Delete");
             clickButton("Confirm Delete");
         }
     }