Adopt FileLike for more pipeline APIs

SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceJob.java

@@ -161,10 +161,9 @@ protected void addCustomParams(JSONObject params)
         params.put("labkeyFolderPath", getContainer().isWorkbook() ? getContainer().getParent().getPath() : getContainer().getPath());
     }
 
-    private Path _getLogFile()
+    private FileLike _getLogFile()
     {
-        var file = FileUtil.findUniqueFileName((FileUtil.makeLegalName(_jobName) + ".log"), getDataDirectoryFileObject());
-        return file.toNioPathForWrite();
+        return FileUtil.findUniqueFileName((FileUtil.makeLegalName(_jobName) + ".log"), getDataDirectoryFileObject());
     }
 
     @Override
@@ -342,9 +341,9 @@ public String getBaseNameForFileType(FileType fileType)
     }
 
     @Override
-    public File getDataDirectory()
+    public FileLike getDataDirectoryFileLike()
     {
-        return _webserverJobDir.toNioPathForWrite().toFile();
+        return _webserverJobDir;
     }
 
     public FileLike getDataDirectoryFileObject()
@@ -397,13 +396,6 @@ public File getParametersFile()
         return FileUtil.appendName(dir.toNioPathForWrite().toFile(),_folderPrefix + ".json");
     }
 
-    @Nullable
-    @Override
-    public File getJobInfoFile()
-    {
-        return FileUtil.appendName(_webserverJobDir.toNioPathForWrite().toFile(), FileUtil.makeLegalName(_jobName) + ".job.json");
-    }
-
     @Override
     public FileType.gzSupportLevel getGZPreference()
     {

SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/VariantProcessingJob.java

@@ -37,6 +37,8 @@
 import org.labkey.api.writer.PrintWriters;
 import org.labkey.sequenceanalysis.util.ScatterGatherUtils;
 import org.labkey.sequenceanalysis.util.SequenceUtil;
+import org.labkey.vfs.FileLike;
+import org.labkey.vfs.FileSystemLike;
 
 import java.io.File;
 import java.io.IOException;
@@ -408,9 +410,9 @@ public void intervalSerializeTest() throws Exception
         {
             VariantProcessingJob job1 = new VariantProcessingJob(){
                 @Override
-                public File getDataDirectory()
+                public FileLike getDataDirectoryFileLike()
                 {
-                    return new File(System.getProperty("java.io.tmpdir"));
+                    return FileSystemLike.wrapFile(new File(System.getProperty("java.io.tmpdir")));
                 }
             };
 

SequenceAnalysis/test/src/org/labkey/test/tests/external/labModules/SequenceTest.java

@@ -23,6 +23,7 @@
 import org.junit.Assert;
 import org.junit.Test;
 import org.junit.experimental.categories.Category;
+import org.labkey.api.util.FileUtil;
 import org.labkey.remoteapi.CommandException;
 import org.labkey.remoteapi.Connection;
 import org.labkey.remoteapi.query.Filter;
@@ -295,13 +296,22 @@ private void createIlluminaSampleSheet()
         assertTextPresent(fileSearcher, prop_name + "," + prop_value);
 
         File fileRoot = TestFileUtils.getDefaultFileRoot(getProjectName());
-        File importTemplate = new File(fileRoot, ILLUMINA_CSV);
+        File importTemplate = FileUtil.appendName(fileRoot, ILLUMINA_CSV);
         if (importTemplate.exists())
             importTemplate.delete();
 
 
         //NOTE: use the text generated directly using JS
-        TestFileUtils.saveFile(importTemplate.getParentFile(), importTemplate.getName(), outputTable);
+        File tsvFile = FileUtil.appendName(importTemplate.getParentFile(), importTemplate.getName());
+
+        try
+        {
+            TestFileUtils.writeFile(tsvFile, outputTable);
+        }
+        catch (IOException e)
+        {
+            e.printStackTrace(System.err);
+        }
         goToProjectHome();
     }
 
@@ -330,7 +340,7 @@ private void importIlluminaTest() throws Exception
         File fileRoot = TestFileUtils.getDefaultFileRoot(getProjectName());
         for (String fn : Arrays.asList("Illumina-F.fastq.gz", "Illumina-R.fastq.gz", "SkipMe.fastq.gz"))
         {
-            File target = new File(fileRoot, fn);
+            File target = FileUtil.appendName(fileRoot, fn);
             if (target.exists())
             {
                 target.delete();
@@ -749,7 +759,7 @@ private void alignmentImportPanelTest(boolean sequencePipelineEnabled) throws Ex
         File fileRoot = TestFileUtils.getDefaultFileRoot(getProjectName());
         log("file root: " + fileRoot.getPath());
 
-        File inputBam = new File(fileRoot, "test.bam");
+        File inputBam = FileUtil.appendName(fileRoot, "test.bam");
         File inputBamIdx = new File(inputBam.getPath() + ".bai");
         if (inputBam.exists())
         {
@@ -763,8 +773,8 @@ private void alignmentImportPanelTest(boolean sequencePipelineEnabled) throws Ex
             inputBamIdx.delete();
         }
 
-        FileUtils.copyFile(new File(_sampleData, "test.bam"), inputBam);
-        FileUtils.copyFile(new File(_sampleData, "test.bam.bai"), inputBamIdx);
+        FileUtils.copyFile(FileUtil.appendName(_sampleData, "test.bam"), inputBam);
+        FileUtils.copyFile(FileUtil.appendName(_sampleData, "test.bam.bai"), inputBamIdx);
 
         _helper.initiatePipelineJob(_alignmentImportPipelineName, List.of(inputBam.getName()), getProjectName());
         waitForText("Job Name");

Studies/src/org/labkey/studies/StudiesServiceImpl.java

@@ -25,12 +25,12 @@
 import org.labkey.api.util.Path;
 import org.labkey.api.util.logging.LogHelper;
 import org.labkey.studies.query.StudiesTableCustomizer;
+import org.labkey.vfs.FileLike;
 
 import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStream;
-import java.nio.file.Files;
 import java.sql.SQLException;
 import java.util.HashMap;
 import java.util.List;
@@ -56,28 +56,28 @@ public void importFolderDefinition(Container container, User user, Module m, Pat
     {
         Resource root = m.getModuleResource(sourceFolderDirPath);
         PipeRoot pipeRoot = PipelineService.get().findPipelineRoot(container);
-        java.nio.file.Path pipeRootPath = pipeRoot.getRootNioPath();
+        FileLike pipeRootPath = pipeRoot.getRootFileLike();
 
-        java.nio.file.Path folderXmlPath;
+        FileLike folderXmlPath;
 
-        if (root instanceof DirectoryResource && ((DirectoryResource)root).getDir().equals(pipeRootPath.toFile()))
+        if (root instanceof DirectoryResource dir && dir.getDir().equals(pipeRootPath.toNioPathForRead().toFile()))
         {
             // The pipeline root is already pointed at the folder definition, like it might be on a dev machine.
             // No need to copy, especially since copying can cause infinite recursion when the paths are nested
-            folderXmlPath = pipeRootPath.resolve("folder.xml");
+            folderXmlPath = pipeRootPath.resolveChild("folder.xml");
         }
         else
         {
-            java.nio.file.Path folderPath = pipeRootPath.resolve("moduleFolderImport");
-            folderXmlPath = folderPath.resolve("folder.xml");
-            if (Files.exists(folderPath))
+            FileLike folderPath = pipeRootPath.resolveChild("moduleFolderImport");
+            folderXmlPath = folderPath.resolveChild("folder.xml");
+            if (folderPath.exists())
             {
                 FileUtil.deleteDir(folderPath);
             }
             copyResourceToPath(root, folderPath);
         }
 
-        if (!Files.exists(folderXmlPath))
+        if (!folderXmlPath.exists())
         {
             throw new FileNotFoundException("Couldn't find an extracted " + folderXmlPath);
         }
@@ -87,21 +87,21 @@ public void importFolderDefinition(Container container, User user, Module m, Pat
         PipelineService.get().runFolderImportJob(container, user, null, folderXmlPath, "folder.xml", pipeRoot, options);
     }
 
-    private void copyResourceToPath(Resource resource, java.nio.file.Path target) throws IOException
+    private void copyResourceToPath(Resource resource, FileLike target) throws IOException
     {
         if (resource.isCollection())
         {
-            Files.createDirectory(target);
+            FileUtil.createDirectory(target);
             for (Resource child : resource.list())
             {
-                java.nio.file.Path childTarget = target.resolve(child.getName());
+                FileLike childTarget = target.resolveChild(child.getName());
                 copyResourceToPath(child, childTarget);
             }
         }
         else
         {
             try (InputStream in = resource.getInputStream();
-                 OutputStream out = Files.newOutputStream(target))
+                 OutputStream out = target.openOutputStream())
             {
                 FileUtil.copyData(in, out);
             }