Adopt FileLike for more pipeline APIs

lincs/src/org/labkey/lincs/psp/LincsPspPipelineJob.java

@@ -12,7 +12,6 @@
 import org.labkey.api.util.FileUtil;
 import org.labkey.api.util.URLHelper;
 import org.labkey.api.view.ViewBackgroundInfo;
-import org.labkey.lincs.LincsModule;
 
 public class LincsPspPipelineJob extends PipelineJob implements LincsPspJobSupport
 {
@@ -43,7 +42,7 @@ public LincsPspPipelineJob(ViewBackgroundInfo info, PipeRoot root, ITargetedMSRu
 
         String baseLogFileName = FileUtil.makeFileNameWithTimestamp("LincsPSP_" + (_oldPspJob != null ? "rerun_" : "") + run.getBaseName().replace(" ", "_"));
 
-        LocalDirectory localDirectory = LocalDirectory.create(root, LincsModule.NAME, baseLogFileName,
+        LocalDirectory localDirectory = LocalDirectory.create(root, baseLogFileName,
                 !root.isCloudRoot() ? root.getRootPath().getAbsolutePath() : FileUtil.getTempDirectory().getPath());
         setLocalDirectory(localDirectory);
         setLogFile(localDirectory.determineLogFile());

nextflow/src/org/labkey/nextflow/NextFlowController.java

@@ -39,6 +39,7 @@
 import org.labkey.api.view.ViewBackgroundInfo;
 import org.labkey.nextflow.pipeline.NextFlowPipelineJob;
 import org.labkey.nextflow.pipeline.NextFlowProtocol;
+import org.labkey.vfs.FileLike;
 import org.springframework.validation.BindException;
 import org.springframework.validation.Errors;
 import org.springframework.web.servlet.ModelAndView;
@@ -261,17 +262,17 @@ public void validateCommand(AnalyzeForm o, Errors errors)
         @Override
         public ModelAndView getView(AnalyzeForm o, boolean b, BindException errors)
         {
-            List<File> selectedFiles = o.getValidatedFiles(getContainer(), false);
+            List<FileLike> selectedFiles = o.getValidatedFiles(getContainer(), false);
             if (selectedFiles.isEmpty())
             {
                 return new HtmlView(HtmlString.of("Couldn't find input file(s)"));
             }
             // NextFlow operates on the full directory so show the list to the user, regardless of what they selected
             // from the file listing
-            File inputDir = selectedFiles.get(0).getParentFile();
+            FileLike inputDir = selectedFiles.get(0).getParent();
 
-            File[] inputFiles = inputDir.listFiles(new PipelineProvider.FileTypesEntryFilter(NextFlowProtocol.INPUT_TYPES));
-            if (inputFiles == null || inputFiles.length == 0)
+            List<FileLike> inputFiles = inputDir.getChildren().stream().filter(new PipelineProvider.FileTypesEntryFilter(NextFlowProtocol.INPUT_TYPES)).toList();
+            if (inputFiles.isEmpty())
             {
                 return new HtmlView(HtmlString.of("Couldn't find input file(s)"));
             }
@@ -290,7 +291,7 @@ public ModelAndView getView(AnalyzeForm o, boolean b, BindException errors)
                                         INPUT(at(hidden, true, name, "launch", value, true)),
                                         Arrays.stream(o.getFile()).map(f -> INPUT(at(hidden, true, name, "file", value, f))).toList(),
                                         "Files: ",
-                                        UL(Arrays.stream(inputFiles).map(File::getName).map(DOM::LI)),
+                                        UL(inputFiles.stream().map(FileLike::getName).map(DOM::LI)),
                                         "Config: ",
                                         new SelectBuilder().name("configFile").addOptions(Arrays.stream(configFiles).filter(f -> f.isFile() && f.getName().toLowerCase().endsWith(".config")).map(File::getName).sorted(String.CASE_INSENSITIVE_ORDER).toList()).build(),
                                         DOM.BR(),
@@ -318,7 +319,7 @@ public boolean handlePost(AnalyzeForm form, BindException errors) throws Excepti
             }
             else
             {
-                List<File> inputFiles = form.getValidatedFiles(getContainer());
+                List<FileLike> inputFiles = form.getValidatedFiles(getContainer());
                 if (inputFiles.isEmpty())
                 {
                     errors.reject(ERROR_MSG, "No input files");
@@ -327,7 +328,7 @@ public boolean handlePost(AnalyzeForm form, BindException errors) throws Excepti
                 {
                     ViewBackgroundInfo info = getViewBackgroundInfo();
                     PipeRoot root = PipelineService.get().findPipelineRoot(info.getContainer());
-                    NextFlowPipelineJob job = NextFlowPipelineJob.create(info, root, configFile.toPath(), inputFiles.stream().map(File::toPath).toList());
+                    NextFlowPipelineJob job = NextFlowPipelineJob.create(info, root, configFile.toPath(), inputFiles);
                     PipelineService.get().queueJob(job);
                     LOG.info("NextFlow job queued: {}", job.getJsonJobInfo(false));
                 }

nextflow/src/org/labkey/nextflow/pipeline/NextFlowPipelineJob.java

@@ -20,7 +20,9 @@
 import org.labkey.api.util.StringUtilsLabKey;
 import org.labkey.api.util.logging.LogHelper;
 import org.labkey.api.view.ViewBackgroundInfo;
+import org.labkey.api.writer.PrintWriters;
 import org.labkey.nextflow.NextFlowManager;
+import org.labkey.vfs.FileLike;
 
 import java.io.BufferedWriter;
 import java.io.File;
@@ -35,29 +37,29 @@ public class NextFlowPipelineJob extends AbstractFileAnalysisJob
 {
     protected static final Logger LOG = LogHelper.getLogger(NextFlowPipelineJob.class, "NextFlow jobs");
 
-    private Path config;
+    private FileLike config;
 
     @SuppressWarnings("unused") // For serialization
     protected NextFlowPipelineJob()
     {}
 
-    public static NextFlowPipelineJob create(ViewBackgroundInfo info, @NotNull PipeRoot root, Path templateConfig, List<Path> inputFiles) throws IOException
+    public static NextFlowPipelineJob create(ViewBackgroundInfo info, @NotNull PipeRoot root, Path templateConfig, List<FileLike> inputFiles) throws IOException
     {
-        Path parentDir = inputFiles.get(0).getParent();
+        FileLike parentDir = inputFiles.get(0).getParent();
 
         String jobName = FileUtil.makeFileNameWithTimestamp("NextFlow");
-        Path jobDir = parentDir.resolve(jobName);
-        Path log = jobDir.resolve(jobName + ".log");
+        FileLike jobDir = parentDir.resolveChild(jobName);
+        FileLike log = jobDir.resolveChild(jobName + ".log");
         FileUtil.createDirectory(jobDir);
 
-        Path config = createConfig(templateConfig, parentDir, jobDir, info.getContainer());
+        FileLike config = createConfig(templateConfig, parentDir, jobDir, info.getContainer());
 
         return new NextFlowPipelineJob(info, root, config, inputFiles, log);
     }
 
-    public NextFlowPipelineJob(ViewBackgroundInfo info, @NotNull PipeRoot root, Path config, List<Path> inputFiles, Path log) throws IOException
+    public NextFlowPipelineJob(ViewBackgroundInfo info, @NotNull PipeRoot root, FileLike config, List<FileLike> inputFiles, FileLike log) throws IOException
     {
-        super(new NextFlowProtocol(), NextFlowPipelineProvider.NAME, info, root, config.getFileName().toString(), config, inputFiles, false, false);
+        super(new NextFlowProtocol(), NextFlowPipelineProvider.NAME, info, root, config.getName(), config, inputFiles, false);
         this.config = config;
         setLogFile(log);
     }
@@ -69,7 +71,7 @@ public JSONObject getJsonJobInfo(boolean includeInvocationCount)
         result.put("container", getContainer().getPath());
         result.put("filePath", getLogFilePath().getParent().toString());
         result.put("runName", getNextFlowRunName(includeInvocationCount));
-        result.put("configFile", getConfig().getFileName().toString());
+        result.put("configFile", getConfig().getName());
         return result;
     }
 
@@ -88,7 +90,7 @@ public ParamParser getInputParameters()
     }
 
     /** Take the template config file and substitute in the values for this job */
-    private static Path createConfig(Path configTemplate, Path parentDir, Path jobDir, Container container) throws IOException
+    private static FileLike createConfig(Path configTemplate, FileLike parentDir, FileLike jobDir, Container container) throws IOException
     {
         String template;
         try (InputStream in = Files.newInputStream(configTemplate))
@@ -104,8 +106,8 @@ private static Path createConfig(Path configTemplate, Path parentDir, Path jobDi
         uploadUrl = StringUtils.stripEnd(uploadUrl, "/");
         substitutedContent = substitutedContent.replace("${panorama.upload_url}", "panorama.upload_url = '" + uploadUrl + "'");
 
-        Path substitutedFile = jobDir.resolve(configTemplate.getFileName());
-        try (BufferedWriter writer = Files.newBufferedWriter(substitutedFile))
+        FileLike substitutedFile = jobDir.resolveChild(configTemplate.getFileName().toString());
+        try (BufferedWriter writer = new BufferedWriter(PrintWriters.getPrintWriter(substitutedFile.openOutputStream())))
         {
             writer.write(substitutedContent);
         }
@@ -115,7 +117,7 @@ private static Path createConfig(Path configTemplate, Path parentDir, Path jobDi
     @Override
     public String getDescription()
     {
-        return "NextFlow analysis of " + StringUtilsLabKey.pluralize(getInputFilePaths().size(), "file") + " using config: " + config.getFileName();
+        return "NextFlow analysis of " + StringUtilsLabKey.pluralize(getInputFilePaths().size(), "file") + " using config: " + config.getName();
     }
 
     @Override
@@ -131,7 +133,7 @@ public TaskId getTaskPipelineId()
     }
 
     @Override
-    public AbstractFileAnalysisJob createSingleFileJob(File file)
+    public AbstractFileAnalysisJob createSingleFileJob(FileLike file)
     {
         throw new UnsupportedOperationException();
     }

nextflow/src/org/labkey/nextflow/pipeline/NextFlowProtocol.java

@@ -7,8 +7,8 @@
 import org.labkey.api.pipeline.file.AbstractFileAnalysisProtocolFactory;
 import org.labkey.api.util.FileType;
 import org.labkey.api.view.ViewBackgroundInfo;
+import org.labkey.vfs.FileLike;
 
-import java.nio.file.Path;
 import java.util.List;
 import java.util.Map;
 
@@ -47,7 +47,7 @@ public NextFlowProtocol createProtocolInstance(String name, String description,
             }
 
             @Override
-            public Path getDefaultParametersFile(PipeRoot root)
+            public FileLike getDefaultParametersFile(PipeRoot root)
             {
                 return null;
             }
@@ -61,7 +61,7 @@ public String getName()
     }
 
     @Override
-    public NextFlowPipelineJob createPipelineJob(ViewBackgroundInfo info, PipeRoot root, List<Path> filesInput, Path fileParameters, @Nullable Map<String, String> variableMap)
+    public NextFlowPipelineJob createPipelineJob(ViewBackgroundInfo info, PipeRoot root, List<FileLike> filesInput, FileLike fileParameters, @Nullable Map<String, String> variableMap)
     {
         throw new UnsupportedOperationException();
     }

nextflow/src/org/labkey/nextflow/pipeline/NextFlowRunTask.java

@@ -16,6 +16,7 @@
 import org.labkey.api.util.FileType;
 import org.labkey.nextflow.NextFlowConfiguration;
 import org.labkey.nextflow.NextFlowManager;
+import org.labkey.vfs.FileLike;
 
 import java.io.BufferedReader;
 import java.io.File;
@@ -143,9 +144,9 @@ else if (Files.isDirectory(path))
         }
     }
 
-    private boolean hasAwsSection(Path configFile) throws PipelineJobException
+    private boolean hasAwsSection(FileLike configFile) throws PipelineJobException
     {
-        try (InputStream in = Files.newInputStream(configFile);
+        try (InputStream in = configFile.openInputStream();
              InputStreamReader isReader = new InputStreamReader(in, StandardCharsets.UTF_8);
              BufferedReader reader = new BufferedReader(isReader))
         {
@@ -174,7 +175,7 @@ private boolean hasAwsSection(Path configFile) throws PipelineJobException
     private @NotNull List<String> getArgs() throws PipelineJobException
     {
         NextFlowConfiguration config = NextFlowManager.get().getConfiguration();
-        Path configFile = getJob().getConfig();
+        FileLike configFile = getJob().getConfig();
 
         boolean aws = hasAwsSection(configFile);
 
@@ -194,7 +195,7 @@ private boolean hasAwsSection(Path configFile) throws PipelineJobException
             args.add(s3Path);
         }
         args.add("-c");
-        args.add(configFile.toAbsolutePath().toString());
+        args.add(configFile.toNioPathForRead().toAbsolutePath().toString());
         args.add("-name");
         args.add(getJob().getNextFlowRunName(true));
         return args;

panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicController.java

@@ -215,6 +215,8 @@
 import org.labkey.panoramapublic.view.expannotations.TargetedMSExperimentWebPart;
 import org.labkey.panoramapublic.view.expannotations.TargetedMSExperimentsWebPart;
 import org.labkey.panoramapublic.view.publish.CatalogEntryWebPart;
+import org.labkey.vfs.FileLike;
+import org.labkey.vfs.FileSystemLike;
 import org.springframework.validation.BindException;
 import org.springframework.validation.Errors;
 import org.springframework.web.servlet.ModelAndView;
@@ -1748,15 +1750,15 @@ private boolean validateAction(CopyExperimentForm form, BindException errors)
             return true;
         }
 
-        private Path getExportFilesDir(Container c)
+        private FileLike getExportFilesDir(Container c)
         {
             FileContentService fcs = FileContentService.get();
             if(fcs != null)
             {
                 Path fileRoot = fcs.getFileRootPath(c, FileContentService.ContentType.files);
                 if (fileRoot != null)
                 {
-                    return fileRoot.resolve(PipelineService.EXPORT_DIR);
+                    return FileSystemLike.wrapFile(fileRoot.resolve(PipelineService.EXPORT_DIR));
                 }
             }
             return null;
@@ -4710,7 +4712,7 @@ private static File getLocalFile(Container container, String fileName) throws Px
                 PipeRoot root = PipelineService.get().getPipelineRootSetting(container);
                 if (root != null)
                 {
-                    LocalDirectory localDirectory = LocalDirectory.create(root, PanoramaPublicModule.NAME);
+                    LocalDirectory localDirectory = LocalDirectory.create(root);
                     return new File(localDirectory.getLocalDirectoryFile(), fileName);
                 }
                 else

panoramapublic/src/org/labkey/panoramapublic/pipeline/CopyExperimentFinalTask.java

@@ -79,6 +79,7 @@
 import org.labkey.panoramapublic.query.JournalManager;
 import org.labkey.panoramapublic.query.SubmissionManager;
 import org.labkey.panoramapublic.security.PanoramaPublicSubmitterRole;
+import org.labkey.vfs.FileLike;
 
 import java.io.File;
 import java.io.IOException;
@@ -254,9 +255,9 @@ private void verifySymlinks(Container source, Container target, boolean matching
         }
     }
 
-    private void cleanupExportDirectory(User user, File directory)
+    private void cleanupExportDirectory(User user, FileLike directory)
     {
-        List<? extends ExpData> datas = ExperimentService.get().getExpDatasUnderPath(directory.toPath(), null, true);
+        List<? extends ExpData> datas = ExperimentService.get().getExpDatasUnderPath(directory.toNioPathForRead(), null, true);
         for (ExpData data : datas)
         {
             data.delete(user);

panoramapublic/src/org/labkey/panoramapublic/pipeline/CopyExperimentJobSupport.java

@@ -17,9 +17,7 @@
 
 import org.labkey.panoramapublic.model.ExperimentAnnotations;
 import org.labkey.panoramapublic.model.Journal;
-
-import java.io.File;
-import java.nio.file.Path;
+import org.labkey.vfs.FileLike;
 
 /**
  * User: vsharma
@@ -32,7 +30,7 @@ public interface CopyExperimentJobSupport
 
     Journal getJournal();
 
-    File getExportDir();
+    FileLike getExportDir();
 
     String getReviewerEmailPrefix();
 
@@ -48,5 +46,5 @@ public interface CopyExperimentJobSupport
 
     String getPreviousVersionName();
 
-    void setExportTargetPath(Path exportTargetPath);
+    void setExportTargetPath(FileLike exportTargetPath);
 }

panoramapublic/src/org/labkey/panoramapublic/pipeline/CopyExperimentPipelineJob.java

@@ -30,13 +30,12 @@
 import org.labkey.api.view.ActionURL;
 import org.labkey.api.view.NotFoundException;
 import org.labkey.api.view.ViewBackgroundInfo;
-import org.labkey.panoramapublic.PanoramaPublicModule;
 import org.labkey.panoramapublic.model.ExperimentAnnotations;
 import org.labkey.panoramapublic.model.Journal;
+import org.labkey.vfs.FileLike;
 
 import java.io.File;
 import java.io.IOException;
-import java.nio.file.Path;
 
 /**
  * User: vsharma
@@ -63,7 +62,7 @@ public class CopyExperimentPipelineJob extends PipelineJob implements CopyExperi
 
     private String _previousVersionName;
 
-    private Path _exportTargetPath;
+    private FileLike _exportTargetPath;
 
     private Container _exportSourceContainer;
 
@@ -93,7 +92,7 @@ public CopyExperimentPipelineJob(ViewBackgroundInfo info, PipeRoot root, Experim
 
         // CONSIDER: Add a static factory method to LocalDirectory instead of using the constructor.
         //           create(@NotNull PipeRoot root, @NotNull String moduleName, @NotNull String baseLogFileName, @NotNull String localDirPath, boolean temporary)
-        LocalDirectory localDirectory = new LocalDirectory(targetRoot.getContainer(), PanoramaPublicModule.NAME, root, baseLogFileName);
+        LocalDirectory localDirectory = new LocalDirectory(targetRoot.getContainer(), root, baseLogFileName);
 
         setLocalDirectory(localDirectory);
         setLogFile(localDirectory.determineLogFile());
@@ -160,9 +159,9 @@ public Journal getJournal()
     }
 
     @Override
-    public File getExportDir()
+    public FileLike getExportDir()
     {
-        return _exportTargetPath.toFile();
+        return _exportTargetPath;
     }
 
     @Override
@@ -254,7 +253,7 @@ public void setPreviousVersionName(String previousVersionName)
     }
 
     @Override
-    public void setExportTargetPath(Path exportTargetPath)
+    public void setExportTargetPath(FileLike exportTargetPath)
     {
         _exportTargetPath = exportTargetPath;
     }