Fix mutating SQL assertion in Tool Store download

SkylineToolsStore/src/org/labkey/skylinetoolsstore/SkylineToolsStoreController.java

@@ -1088,7 +1088,12 @@ else if (toolLsid != null &&
                 // Cookie expires after 1 day
                 final int expires = 24 * 60 * 60;
 
-                SkylineToolsStoreManager.get().recordToolDownload(tool);
+                // Download counter is an incidental write on a GET action — use ignoreSqlUpdates()
+                // to avoid the dev-mode mutating SQL assertion (like auditing writes)
+                try (var ignored = SpringActionController.ignoreSqlUpdates())
+                {
+                    SkylineToolsStoreManager.get().recordToolDownload(tool);
+                }
 
                 DateFormat df = new SimpleDateFormat("EEE, dd-MMM-yyyy HH:mm:ss 'GMT'", Locale.US);
                 Calendar calendar = Calendar.getInstance();
@@ -1180,7 +1185,7 @@ public ModelAndView getView(DownloadFileForm form, BindException errors) throws
                 }
                 else
                 {
-                    PageFlowUtil.streamFile(getViewContext().getResponse(), downloadFile, true);
+                    PageFlowUtil.streamFile(getViewContext().getResponse(), downloadFile.toPath(), true);
                     return null;
                 }
             }

lincs/src/org/labkey/lincs/LincsController.java

@@ -87,6 +87,7 @@
 import org.labkey.lincs.psp.LincsPspUtil;
 import org.labkey.lincs.psp.PspEndpoint;
 import org.labkey.lincs.view.GctUtils;
+import org.labkey.vfs.FileLike;
 import org.springframework.beans.MutablePropertyValues;
 import org.springframework.validation.BindException;
 import org.springframework.validation.Errors;
@@ -144,35 +145,32 @@ public void addNavTrail(NavTree root)
         }
     }
 
-    private void copyFiles(Path gctDir, String outputFileBaseName, Path gct, File reportDir) throws IOException
+    private void copyFiles(Path gctDir, String outputFileBaseName, Path gct, FileLike reportDir) throws IOException
     {
         // reportDir is a local directory under tomcat's temp directory
-        File[] reportDirFiles = reportDir.listFiles(new FilenameFilter()
+        List<FileLike> reportDirFiles = reportDir.getChildren((f) ->
         {
-            @Override
-            public boolean accept(File dir, String name)
-            {
-                return name.toLowerCase().endsWith(".txt")
+            String name = f.getName();
+            return name.toLowerCase().endsWith(".txt")
                         || name.toLowerCase().endsWith(".gct")
                         || name.equals("script.Rout");
-            }
         });
 
         // The report should create two files: lincs.gct and lincs.processed.gct
         // Copy both to the GCT folder
-        for(File file: reportDirFiles)
+        for(FileLike file: reportDirFiles)
         {
             if(file.getName().equalsIgnoreCase("lincs.gct"))
             {
-                Files.copy(file.toPath(), gct, StandardCopyOption.REPLACE_EXISTING);
+                Files.copy(file.toNioPathForRead(), gct, StandardCopyOption.REPLACE_EXISTING);
             }
             else if(file.getName().equalsIgnoreCase("console.txt"))
             {
-                Files.copy(file.toPath(), gctDir.resolve(outputFileBaseName + ".console.txt" ), StandardCopyOption.REPLACE_EXISTING);
+                Files.copy(file.toNioPathForRead(), gctDir.resolve(outputFileBaseName + ".console.txt" ), StandardCopyOption.REPLACE_EXISTING);
             }
             else if(file.getName().equals("script.Rout"))
             {
-                Files.copy(file.toPath(), gctDir.resolve(outputFileBaseName + ".script.Rout" ), StandardCopyOption.REPLACE_EXISTING);
+                Files.copy(file.toNioPathForRead(), gctDir.resolve(outputFileBaseName + ".script.Rout" ), StandardCopyOption.REPLACE_EXISTING);
             }
         }
     }
@@ -306,11 +304,11 @@ public ApiResponse execute(GCTReportForm form, BindException errors) throws Exce
             }
             catch(Exception e)
             {
-                copyFiles(gctDir, outputFileBaseName, downloadFile, rreport.getReportDir(getContainer().getId()));
+                copyFiles(gctDir, outputFileBaseName, downloadFile, rreport.getReportDirFileLike(getContainer().getId()));
                 throw new ApiUsageException("There was an error running the GCT R script.", e);
             }
 
-            copyFiles(gctDir, outputFileBaseName, downloadFile, rreport.getReportDir(getContainer().getId()));
+            copyFiles(gctDir, outputFileBaseName, downloadFile, rreport.getReportDirFileLike(getContainer().getId()));
 
             if(!Files.exists(downloadFile))
             {

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
 {
@@ -43,8 +42,8 @@ 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,
-                !root.isCloudRoot() ? root.getRootPath().getAbsolutePath() : FileUtil.getTempDirectory().getPath());
+        LocalDirectory localDirectory = LocalDirectory.create(root, baseLogFileName,
+                !root.isCloudRoot() ? root.getRootFileLike() : FileUtil.getTempDirectoryFileLike());
         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/NextFlowModule.java

@@ -47,7 +47,7 @@ public boolean hasScripts()
     @Override
     public @Nullable Double getSchemaVersion()
     {
-        return 25.000;
+        return 26.000;
     }
 
     @Override

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

@@ -20,10 +20,11 @@
 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;
 import java.io.IOException;
 import java.io.InputStream;
 import java.nio.file.Files;
@@ -35,29 +36,29 @@ 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 +70,7 @@ 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 +89,7 @@ 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 +105,8 @@ 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 +116,7 @@ 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(getInputFiles().size(), "file") + " using config: " + config.getName();
     }
 
     @Override
@@ -131,19 +132,19 @@ public TaskId getTaskPipelineId()
     }
 
     @Override
-    public AbstractFileAnalysisJob createSingleFileJob(File file)
+    public AbstractFileAnalysisJob createSingleFileJob(FileLike file)
     {
         throw new UnsupportedOperationException();
     }
 
     @Override
-    public File findInputFile(String name)
+    public FileLike findInputFile(String name)
     {
         throw new UnsupportedOperationException();
     }
 
     @Override
-    public File findOutputFile(String name)
+    public FileLike findOutputFile(String name)
     {
         return null;
     }

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

@@ -16,9 +16,9 @@
 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;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
@@ -75,7 +75,7 @@ public NextFlowRunTask(Factory factory, PipelineJob job)
             // Need to pass to the main process directly in the future to allow concurrent execution for different users
             ProcessBuilder secretsPB = new ProcessBuilder("nextflow", "secrets", "set", "PANORAMA_API_KEY", apiKey);
             log.info("Setting secrets");
-            File dir = getJob().getLogFile().getParentFile();
+            FileLike dir = getJob().getLogFileLike().getParent();
             getJob().runSubProcess(secretsPB, dir);
 
             ProcessBuilder executionPB = new ProcessBuilder(getArgs());
@@ -84,9 +84,9 @@ public NextFlowRunTask(Factory factory, PipelineJob job)
             NextFlowPipelineJob.LOG.info("Finished executing NextFlow: {}", getJob().getJsonJobInfo(true));
 
             RecordedAction action = new RecordedAction(ACTION_NAME);
-            for (Path inputFile : getJob().getInputFilePaths())
+            for (FileLike inputFile : getJob().getInputFiles())
             {
-                action.addInput(inputFile.toFile(), SPECTRA_INPUT_ROLE);
+                action.addInput(inputFile, SPECTRA_INPUT_ROLE);
             }
             addOutputs(action, getJob().getLogFilePath().getParent().resolve("reports"), log);
             addOutputs(action, getJob().getLogFilePath().getParent().resolve("results"), log);
@@ -143,9 +143,9 @@ 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 +174,7 @@ 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 +194,7 @@ 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;