Adopt FileLike for more pipeline APIs (#576)

labkey-jeckels · web-flow · commit b2bd997b7126 · 2025-11-04T17:48:16.000-08:00
diff --git a/lincs/src/org/labkey/lincs/psp/LincsPspPipelineJob.java b/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());
diff --git a/nextflow/src/org/labkey/nextflow/NextFlowController.java b/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));
                 }
diff --git a/nextflow/src/org/labkey/nextflow/pipeline/NextFlowPipelineJob.java b/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();
     }
diff --git a/nextflow/src/org/labkey/nextflow/pipeline/NextFlowProtocol.java b/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();
     }
diff --git a/nextflow/src/org/labkey/nextflow/pipeline/NextFlowRunTask.java b/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;
diff --git a/panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicController.java b/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
diff --git a/panoramapublic/src/org/labkey/panoramapublic/pipeline/CopyExperimentFinalTask.java b/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);
diff --git a/panoramapublic/src/org/labkey/panoramapublic/pipeline/CopyExperimentJobSupport.java b/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);
 }
diff --git a/panoramapublic/src/org/labkey/panoramapublic/pipeline/CopyExperimentPipelineJob.java b/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;
     }
diff --git a/panoramapublic/src/org/labkey/panoramapublic/pipeline/ExperimentExportTask.java b/panoramapublic/src/org/labkey/panoramapublic/pipeline/ExperimentExportTask.java
diff --git a/panoramapublic/src/org/labkey/panoramapublic/pipeline/ExperimentImportTask.java b/panoramapublic/src/org/labkey/panoramapublic/pipeline/ExperimentImportTask.java
diff --git a/panoramapublic/src/org/labkey/panoramapublic/pipeline/PostPanoramaPublicMessageJob.java b/panoramapublic/src/org/labkey/panoramapublic/pipeline/PostPanoramaPublicMessageJob.java
diff --git a/panoramapublic/src/org/labkey/panoramapublic/pipeline/PrivateDataReminderJob.java b/panoramapublic/src/org/labkey/panoramapublic/pipeline/PrivateDataReminderJob.java

Original file line number	Diff line number	Diff line change
`@@ -39,6 +39,7 @@`
`39`	`39`	`import org.labkey.api.view.ViewBackgroundInfo;`
`40`	`40`	`import org.labkey.nextflow.pipeline.NextFlowPipelineJob;`
`41`	`41`	`import org.labkey.nextflow.pipeline.NextFlowProtocol;`
	`42`	`+import org.labkey.vfs.FileLike;`
`42`	`43`	`import org.springframework.validation.BindException;`
`43`	`44`	`import org.springframework.validation.Errors;`
`44`	`45`	`import org.springframework.web.servlet.ModelAndView;`
`@@ -261,17 +262,17 @@ public void validateCommand(AnalyzeForm o, Errors errors)`
`261`	`262`	`@Override`
`262`	`263`	`public ModelAndView getView(AnalyzeForm o, boolean b, BindException errors)`
`263`	`264`	`{`
`264`		`- List<File> selectedFiles = o.getValidatedFiles(getContainer(), false);`
	`265`	`+ List<FileLike> selectedFiles = o.getValidatedFiles(getContainer(), false);`
`265`	`266`	`if (selectedFiles.isEmpty())`
`266`	`267`	`{`
`267`	`268`	`return new HtmlView(HtmlString.of("Couldn't find input file(s)"));`
`268`	`269`	`}`
`269`	`270`	`// NextFlow operates on the full directory so show the list to the user, regardless of what they selected`
`270`	`271`	`// from the file listing`
`271`		`- File inputDir = selectedFiles.get(0).getParentFile();`
	`272`	`+ FileLike inputDir = selectedFiles.get(0).getParent();`
`272`	`273`
`273`		`- File[] inputFiles = inputDir.listFiles(new PipelineProvider.FileTypesEntryFilter(NextFlowProtocol.INPUT_TYPES));`
`274`		`- if (inputFiles == null \|\| inputFiles.length == 0)`
	`274`	`+ List<FileLike> inputFiles = inputDir.getChildren().stream().filter(new PipelineProvider.FileTypesEntryFilter(NextFlowProtocol.INPUT_TYPES)).toList();`
	`275`	`+ if (inputFiles.isEmpty())`
`275`	`276`	`{`
`276`	`277`	`return new HtmlView(HtmlString.of("Couldn't find input file(s)"));`
`277`	`278`	`}`
`@@ -290,7 +291,7 @@ public ModelAndView getView(AnalyzeForm o, boolean b, BindException errors)`
`290`	`291`	`INPUT(at(hidden, true, name, "launch", value, true)),`
`291`	`292`	`Arrays.stream(o.getFile()).map(f -> INPUT(at(hidden, true, name, "file", value, f))).toList(),`
`292`	`293`	`"Files: ",`
`293`		`- UL(Arrays.stream(inputFiles).map(File::getName).map(DOM::LI)),`
	`294`	`+ UL(inputFiles.stream().map(FileLike::getName).map(DOM::LI)),`
`294`	`295`	`"Config: ",`
`295`	`296`	`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(),`
`296`	`297`	`DOM.BR(),`
`@@ -318,7 +319,7 @@ public boolean handlePost(AnalyzeForm form, BindException errors) throws Excepti`
`318`	`319`	`}`
`319`	`320`	`else`
`320`	`321`	`{`
`321`		`- List<File> inputFiles = form.getValidatedFiles(getContainer());`
	`322`	`+ List<FileLike> inputFiles = form.getValidatedFiles(getContainer());`
`322`	`323`	`if (inputFiles.isEmpty())`
`323`	`324`	`{`
`324`	`325`	`errors.reject(ERROR_MSG, "No input files");`
`@@ -327,7 +328,7 @@ public boolean handlePost(AnalyzeForm form, BindException errors) throws Excepti`
`327`	`328`	`{`
`328`	`329`	`ViewBackgroundInfo info = getViewBackgroundInfo();`
`329`	`330`	`PipeRoot root = PipelineService.get().findPipelineRoot(info.getContainer());`
`330`		`- NextFlowPipelineJob job = NextFlowPipelineJob.create(info, root, configFile.toPath(), inputFiles.stream().map(File::toPath).toList());`
	`331`	`+ NextFlowPipelineJob job = NextFlowPipelineJob.create(info, root, configFile.toPath(), inputFiles);`
`331`	`332`	`PipelineService.get().queueJob(job);`
`332`	`333`	`LOG.info("NextFlow job queued: {}", job.getJsonJobInfo(false));`
`333`	`334`	`}`
Original file line number	Diff line number	Diff line change
`@@ -20,7 +20,9 @@`
`20`	`20`	`import org.labkey.api.util.StringUtilsLabKey;`
`21`	`21`	`import org.labkey.api.util.logging.LogHelper;`
`22`	`22`	`import org.labkey.api.view.ViewBackgroundInfo;`
	`23`	`+import org.labkey.api.writer.PrintWriters;`
`23`	`24`	`import org.labkey.nextflow.NextFlowManager;`
	`25`	`+import org.labkey.vfs.FileLike;`
`24`	`26`
`25`	`27`	`import java.io.BufferedWriter;`
`26`	`28`	`import java.io.File;`
`@@ -35,29 +37,29 @@ public class NextFlowPipelineJob extends AbstractFileAnalysisJob`
`35`	`37`	`{`
`36`	`38`	`protected static final Logger LOG = LogHelper.getLogger(NextFlowPipelineJob.class, "NextFlow jobs");`
`37`	`39`
`38`		`- private Path config;`
	`40`	`+ private FileLike config;`
`39`	`41`
`40`	`42`	`@SuppressWarnings("unused") // For serialization`
`41`	`43`	`protected NextFlowPipelineJob()`
`42`	`44`	`{}`
`43`	`45`
`44`		`- public static NextFlowPipelineJob create(ViewBackgroundInfo info, @NotNull PipeRoot root, Path templateConfig, List<Path> inputFiles) throws IOException`
	`46`	`+ public static NextFlowPipelineJob create(ViewBackgroundInfo info, @NotNull PipeRoot root, Path templateConfig, List<FileLike> inputFiles) throws IOException`
`45`	`47`	`{`
`46`		`- Path parentDir = inputFiles.get(0).getParent();`
	`48`	`+ FileLike parentDir = inputFiles.get(0).getParent();`
`47`	`49`
`48`	`50`	`String jobName = FileUtil.makeFileNameWithTimestamp("NextFlow");`
`49`		`- Path jobDir = parentDir.resolve(jobName);`
`50`		`- Path log = jobDir.resolve(jobName + ".log");`
	`51`	`+ FileLike jobDir = parentDir.resolveChild(jobName);`
	`52`	`+ FileLike log = jobDir.resolveChild(jobName + ".log");`
`51`	`53`	`FileUtil.createDirectory(jobDir);`
`52`	`54`
`53`		`- Path config = createConfig(templateConfig, parentDir, jobDir, info.getContainer());`
	`55`	`+ FileLike config = createConfig(templateConfig, parentDir, jobDir, info.getContainer());`
`54`	`56`
`55`	`57`	`return new NextFlowPipelineJob(info, root, config, inputFiles, log);`
`56`	`58`	`}`
`57`	`59`
`58`		`- public NextFlowPipelineJob(ViewBackgroundInfo info, @NotNull PipeRoot root, Path config, List<Path> inputFiles, Path log) throws IOException`
	`60`	`+ public NextFlowPipelineJob(ViewBackgroundInfo info, @NotNull PipeRoot root, FileLike config, List<FileLike> inputFiles, FileLike log) throws IOException`
`59`	`61`	`{`
`60`		`- super(new NextFlowProtocol(), NextFlowPipelineProvider.NAME, info, root, config.getFileName().toString(), config, inputFiles, false, false);`
	`62`	`+ super(new NextFlowProtocol(), NextFlowPipelineProvider.NAME, info, root, config.getName(), config, inputFiles, false);`
`61`	`63`	`this.config = config;`
`62`	`64`	`setLogFile(log);`
`63`	`65`	`}`
`@@ -69,7 +71,7 @@ public JSONObject getJsonJobInfo(boolean includeInvocationCount)`
`69`	`71`	`result.put("container", getContainer().getPath());`
`70`	`72`	`result.put("filePath", getLogFilePath().getParent().toString());`
`71`	`73`	`result.put("runName", getNextFlowRunName(includeInvocationCount));`
`72`		`- result.put("configFile", getConfig().getFileName().toString());`
	`74`	`+ result.put("configFile", getConfig().getName());`
`73`	`75`	`return result;`
`74`	`76`	`}`
`75`	`77`
`@@ -88,7 +90,7 @@ public ParamParser getInputParameters()`
`88`	`90`	`}`
`89`	`91`
`90`	`92`	`/** Take the template config file and substitute in the values for this job */`
`91`		`- private static Path createConfig(Path configTemplate, Path parentDir, Path jobDir, Container container) throws IOException`
	`93`	`+ private static FileLike createConfig(Path configTemplate, FileLike parentDir, FileLike jobDir, Container container) throws IOException`
`92`	`94`	`{`
`93`	`95`	`String template;`
`94`	`96`	`try (InputStream in = Files.newInputStream(configTemplate))`
`@@ -104,8 +106,8 @@ private static Path createConfig(Path configTemplate, Path parentDir, Path jobDi`
`104`	`106`	`uploadUrl = StringUtils.stripEnd(uploadUrl, "/");`
`105`	`107`	`substitutedContent = substitutedContent.replace("${panorama.upload_url}", "panorama.upload_url = '" + uploadUrl + "'");`
`106`	`108`
`107`		`- Path substitutedFile = jobDir.resolve(configTemplate.getFileName());`
`108`		`- try (BufferedWriter writer = Files.newBufferedWriter(substitutedFile))`
	`109`	`+ FileLike substitutedFile = jobDir.resolveChild(configTemplate.getFileName().toString());`
	`110`	`+ try (BufferedWriter writer = new BufferedWriter(PrintWriters.getPrintWriter(substitutedFile.openOutputStream())))`
`109`	`111`	`{`
`110`	`112`	`writer.write(substitutedContent);`
`111`	`113`	`}`
`@@ -115,7 +117,7 @@ private static Path createConfig(Path configTemplate, Path parentDir, Path jobDi`
`115`	`117`	`@Override`
`116`	`118`	`public String getDescription()`
`117`	`119`	`{`
`118`		`- return "NextFlow analysis of " + StringUtilsLabKey.pluralize(getInputFilePaths().size(), "file") + " using config: " + config.getFileName();`
	`120`	`+ return "NextFlow analysis of " + StringUtilsLabKey.pluralize(getInputFilePaths().size(), "file") + " using config: " + config.getName();`
`119`	`121`	`}`
`120`	`122`
`121`	`123`	`@Override`
`@@ -131,7 +133,7 @@ public TaskId getTaskPipelineId()`
`131`	`133`	`}`
`132`	`134`
`133`	`135`	`@Override`
`134`		`- public AbstractFileAnalysisJob createSingleFileJob(File file)`
	`136`	`+ public AbstractFileAnalysisJob createSingleFileJob(FileLike file)`
`135`	`137`	`{`
`136`	`138`	`throw new UnsupportedOperationException();`
`137`	`139`	`}`
Original file line number	Diff line number	Diff line change
`@@ -7,8 +7,8 @@`
`7`	`7`	`import org.labkey.api.pipeline.file.AbstractFileAnalysisProtocolFactory;`
`8`	`8`	`import org.labkey.api.util.FileType;`
`9`	`9`	`import org.labkey.api.view.ViewBackgroundInfo;`
	`10`	`+import org.labkey.vfs.FileLike;`
`10`	`11`
`11`		`-import java.nio.file.Path;`
`12`	`12`	`import java.util.List;`
`13`	`13`	`import java.util.Map;`
`14`	`14`
`@@ -47,7 +47,7 @@ public NextFlowProtocol createProtocolInstance(String name, String description,`
`47`	`47`	`}`
`48`	`48`
`49`	`49`	`@Override`
`50`		`- public Path getDefaultParametersFile(PipeRoot root)`
	`50`	`+ public FileLike getDefaultParametersFile(PipeRoot root)`
`51`	`51`	`{`
`52`	`52`	`return null;`
`53`	`53`	`}`
`@@ -61,7 +61,7 @@ public String getName()`
`61`	`61`	`}`
`62`	`62`
`63`	`63`	`@Override`
`64`		`- public NextFlowPipelineJob createPipelineJob(ViewBackgroundInfo info, PipeRoot root, List<Path> filesInput, Path fileParameters, @Nullable Map<String, String> variableMap)`
	`64`	`+ public NextFlowPipelineJob createPipelineJob(ViewBackgroundInfo info, PipeRoot root, List<FileLike> filesInput, FileLike fileParameters, @Nullable Map<String, String> variableMap)`
`65`	`65`	`{`
`66`	`66`	`throw new UnsupportedOperationException();`
`67`	`67`	`}`
Original file line number	Diff line number	Diff line change
`@@ -16,6 +16,7 @@`
`16`	`16`	`import org.labkey.api.util.FileType;`
`17`	`17`	`import org.labkey.nextflow.NextFlowConfiguration;`
`18`	`18`	`import org.labkey.nextflow.NextFlowManager;`
	`19`	`+import org.labkey.vfs.FileLike;`
`19`	`20`
`20`	`21`	`import java.io.BufferedReader;`
`21`	`22`	`import java.io.File;`
`@@ -143,9 +144,9 @@ else if (Files.isDirectory(path))`
`143`	`144`	`}`
`144`	`145`	`}`
`145`	`146`
`146`		`- private boolean hasAwsSection(Path configFile) throws PipelineJobException`
	`147`	`+ private boolean hasAwsSection(FileLike configFile) throws PipelineJobException`
`147`	`148`	`{`
`148`		`- try (InputStream in = Files.newInputStream(configFile);`
	`149`	`+ try (InputStream in = configFile.openInputStream();`
`149`	`150`	`InputStreamReader isReader = new InputStreamReader(in, StandardCharsets.UTF_8);`
`150`	`151`	`BufferedReader reader = new BufferedReader(isReader))`
`151`	`152`	`{`
`@@ -174,7 +175,7 @@ private boolean hasAwsSection(Path configFile) throws PipelineJobException`
`174`	`175`	`private @NotNull List<String> getArgs() throws PipelineJobException`
`175`	`176`	`{`
`176`	`177`	`NextFlowConfiguration config = NextFlowManager.get().getConfiguration();`
`177`		`- Path configFile = getJob().getConfig();`
	`178`	`+ FileLike configFile = getJob().getConfig();`
`178`	`179`
`179`	`180`	`boolean aws = hasAwsSection(configFile);`
`180`	`181`
`@@ -194,7 +195,7 @@ private boolean hasAwsSection(Path configFile) throws PipelineJobException`
`194`	`195`	`args.add(s3Path);`
`195`	`196`	`}`
`196`	`197`	`args.add("-c");`
`197`		`- args.add(configFile.toAbsolutePath().toString());`
	`198`	`+ args.add(configFile.toNioPathForRead().toAbsolutePath().toString());`
`198`	`199`	`args.add("-name");`
`199`	`200`	`args.add(getJob().getNextFlowRunName(true));`
`200`	`201`	`return args;`
Original file line number	Diff line number	Diff line change
`@@ -215,6 +215,8 @@`
`215`	`215`	`import org.labkey.panoramapublic.view.expannotations.TargetedMSExperimentWebPart;`
`216`	`216`	`import org.labkey.panoramapublic.view.expannotations.TargetedMSExperimentsWebPart;`
`217`	`217`	`import org.labkey.panoramapublic.view.publish.CatalogEntryWebPart;`
	`218`	`+import org.labkey.vfs.FileLike;`
	`219`	`+import org.labkey.vfs.FileSystemLike;`
`218`	`220`	`import org.springframework.validation.BindException;`
`219`	`221`	`import org.springframework.validation.Errors;`
`220`	`222`	`import org.springframework.web.servlet.ModelAndView;`
`@@ -1748,15 +1750,15 @@ private boolean validateAction(CopyExperimentForm form, BindException errors)`
`1748`	`1750`	`return true;`
`1749`	`1751`	`}`
`1750`	`1752`
`1751`		`- private Path getExportFilesDir(Container c)`
	`1753`	`+ private FileLike getExportFilesDir(Container c)`
`1752`	`1754`	`{`
`1753`	`1755`	`FileContentService fcs = FileContentService.get();`
`1754`	`1756`	`if(fcs != null)`
`1755`	`1757`	`{`
`1756`	`1758`	`Path fileRoot = fcs.getFileRootPath(c, FileContentService.ContentType.files);`
`1757`	`1759`	`if (fileRoot != null)`
`1758`	`1760`	`{`
`1759`		`- return fileRoot.resolve(PipelineService.EXPORT_DIR);`
	`1761`	`+ return FileSystemLike.wrapFile(fileRoot.resolve(PipelineService.EXPORT_DIR));`
`1760`	`1762`	`}`
`1761`	`1763`	`}`
`1762`	`1764`	`return null;`
`@@ -4710,7 +4712,7 @@ private static File getLocalFile(Container container, String fileName) throws Px`
`4710`	`4712`	`PipeRoot root = PipelineService.get().getPipelineRootSetting(container);`
`4711`	`4713`	`if (root != null)`
`4712`	`4714`	`{`
`4713`		`- LocalDirectory localDirectory = LocalDirectory.create(root, PanoramaPublicModule.NAME);`
	`4715`	`+ LocalDirectory localDirectory = LocalDirectory.create(root);`
`4714`	`4716`	`return new File(localDirectory.getLocalDirectoryFile(), fileName);`
`4715`	`4717`	`}`
`4716`	`4718`	`else`
Original file line number	Diff line number	Diff line change
`@@ -79,6 +79,7 @@`
`79`	`79`	`import org.labkey.panoramapublic.query.JournalManager;`
`80`	`80`	`import org.labkey.panoramapublic.query.SubmissionManager;`
`81`	`81`	`import org.labkey.panoramapublic.security.PanoramaPublicSubmitterRole;`
	`82`	`+import org.labkey.vfs.FileLike;`
`82`	`83`
`83`	`84`	`import java.io.File;`
`84`	`85`	`import java.io.IOException;`
`@@ -254,9 +255,9 @@ private void verifySymlinks(Container source, Container target, boolean matching`
`254`	`255`	`}`
`255`	`256`	`}`
`256`	`257`
`257`		`- private void cleanupExportDirectory(User user, File directory)`
	`258`	`+ private void cleanupExportDirectory(User user, FileLike directory)`
`258`	`259`	`{`
`259`		`- List<? extends ExpData> datas = ExperimentService.get().getExpDatasUnderPath(directory.toPath(), null, true);`
	`260`	`+ List<? extends ExpData> datas = ExperimentService.get().getExpDatasUnderPath(directory.toNioPathForRead(), null, true);`
`260`	`261`	`for (ExpData data : datas)`
`261`	`262`	`{`
`262`	`263`	`data.delete(user);`