Improve file path validation

elisa/src/org/labkey/elisa/AbstractElisaImportHelper.java

@@ -14,8 +14,8 @@
 import org.labkey.api.exp.api.ProvenanceService;
 import org.labkey.api.exp.property.Domain;
 import org.labkey.api.exp.property.DomainProperty;
+import org.labkey.vfs.FileLike;
 
-import java.io.File;
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.Map;
@@ -26,11 +26,11 @@ public abstract class AbstractElisaImportHelper implements ElisaImportHelper
     protected AssayUploadXarContext _context;
     protected PlateBasedAssayProvider _provider;
     protected ExpProtocol _protocol;
-    protected File _dataFile;
+    protected FileLike _dataFile;
     protected Container _container;
     Map<Position, String> _specimenGroupMap;
 
-    public AbstractElisaImportHelper(AssayUploadXarContext context, PlateBasedAssayProvider provider, ExpProtocol protocol, File dataFile)
+    public AbstractElisaImportHelper(AssayUploadXarContext context, PlateBasedAssayProvider provider, ExpProtocol protocol, FileLike dataFile)
     {
         _context = context;
         _provider = provider;

elisa/src/org/labkey/elisa/ElisaDataHandler.java

@@ -107,7 +107,7 @@ protected boolean shouldAddInputMaterials()
         return true;
     }
 
-    private ElisaImportHelper getImportHelper(AssayUploadXarContext context, PlateBasedAssayProvider provider, ExpProtocol protocol, File dataFile) throws ExperimentException
+    private ElisaImportHelper getImportHelper(AssayUploadXarContext context, PlateBasedAssayProvider provider, ExpProtocol protocol, FileLike dataFile) throws ExperimentException
     {
         if (provider.getMetadataInputFormat(protocol).equals(SampleMetadataInputFormat.MANUAL))
         {
@@ -135,7 +135,7 @@ public Map<DataType, DataIteratorBuilder> getValidationDataMap(ExpData data, Fil
             Map<String, DomainProperty> sampleProperties = plateProvider.getSampleWellGroupDomain(protocol)
                     .getProperties().stream()
                     .collect(Collectors.toMap(DomainProperty::getName, dp -> dp));
-            ElisaImportHelper importHelper = getImportHelper(xarContext, plateProvider, protocol, dataFile.toNioPathForRead().toFile());
+            ElisaImportHelper importHelper = getImportHelper(xarContext, plateProvider, protocol, dataFile);
 
             for (String plateName : importHelper.getPlates())
             {
@@ -148,7 +148,7 @@ public Map<DataType, DataIteratorBuilder> getValidationDataMap(ExpData data, Fil
                         SimpleRegression regression = new SimpleRegression(true);
                         Map<String, Double> standardConcentrations = importHelper.getStandardConcentrations(plateName, analytePlateEntry.getKey());
 
-                        CurveFit standardCurve = calculateStandardCurve(run, plate, regression, standardConcentrations, runDomain);
+                        CurveFit<?> standardCurve = calculateStandardCurve(run, plate, regression, standardConcentrations, runDomain);
                         if (standardCurve != null && standardCurve.getParameters() == null)
                             throw new ExperimentException("Unable to fit the standard concentrations to a curve, please check the input data and try again");
 
@@ -321,7 +321,7 @@ private boolean isRowEmptyOrNull(Map<String, Object> row)
      * data and can be used to generate an R squared value.
      */
     @Nullable
-    private CurveFit calculateStandardCurve(ExpRun run, Plate plate, @Nullable SimpleRegression regression, Map<String, Double> standardConcentrations,
+    private CurveFit<?> calculateStandardCurve(ExpRun run, Plate plate, @Nullable SimpleRegression regression, Map<String, Double> standardConcentrations,
                                             Domain runDomain) throws ExperimentException
     {
         // compute the calibration curve, there could be multiple control groups but one contains the standards
@@ -333,7 +333,7 @@ private CurveFit calculateStandardCurve(ExpRun run, Plate plate, @Nullable Simpl
 
             for (WellGroup replicate : stdWellGroup.getOverlappingGroups(WellGroup.Type.REPLICATE))
             {
-                maxValue = replicate.getMean() > maxValue ? replicate.getMean() : maxValue;
+                maxValue = Math.max(replicate.getMean(), maxValue);
             }
 
             for (WellGroup replicate : stdWellGroup.getOverlappingGroups(WellGroup.Type.REPLICATE))
@@ -358,7 +358,7 @@ private CurveFit calculateStandardCurve(ExpRun run, Plate plate, @Nullable Simpl
 
                 // Compute curve fit parameters based on the selected curve fit (default to linear for legacy assay designs)
                 StatsService.CurveFitType curveFitType = ElisaManager.getRunCurveFitType(runDomain, run);
-                CurveFit curveFit = StatsService.get().getCurveFit(curveFitType, points.toArray(DoublePoint[]::new));
+                CurveFit<?> curveFit = StatsService.get().getCurveFit(curveFitType, points.toArray(DoublePoint[]::new));
                 curveFit.setLogXScale(false);
                 curveFit.setAssumeCurveDecreasing(false);
 

elisa/src/org/labkey/elisa/ElisaSampleFilePropertyHelper.java

@@ -16,8 +16,10 @@
 import org.labkey.api.study.assay.SampleMetadataInputFormat;
 
 import jakarta.servlet.http.HttpServletRequest;
-import java.io.File;
+import org.labkey.vfs.FileLike;
+
 import java.io.IOException;
+import java.io.InputStream;
 import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
@@ -41,13 +43,14 @@ public Map<String, Map<DomainProperty, String>> getSampleProperties(HttpServletR
         if (_sampleProperties != null)
             return _sampleProperties;
 
-        File metadataFile = getSampleMetadata(request);
+        FileLike metadataFile = getSampleMetadata(request);
         if (metadataFile == null)
             throw new ExperimentException("No metadata or data file provided");
 
         Map<String, Map<DomainProperty, String>> allProperties = new HashMap<>();
         DataLoaderFactory factory = DataLoaderService.get().findFactory(metadataFile, null);
-        try (DataLoader loader = factory.createLoader(metadataFile, true))
+        try (InputStream in = metadataFile.openInputStream();
+             DataLoader loader = factory.createLoader(in, true))
         {
             validateRequiredColumns(loader.getColumns());
 

elisa/src/org/labkey/elisa/HighThroughputImportHelper.java

@@ -21,9 +21,10 @@
 import org.labkey.api.reader.DataLoader;
 import org.labkey.api.reader.DataLoaderFactory;
 import org.labkey.api.reader.DataLoaderService;
+import org.labkey.vfs.FileLike;
 
-import java.io.File;
 import java.io.IOException;
+import java.io.InputStream;
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.List;
@@ -37,7 +38,7 @@ public class HighThroughputImportHelper extends AbstractElisaImportHelper
     private final Map<String, AnalytePlate> _plateMap = new HashMap<>();
     private Plate _plateTemplate;
 
-    public HighThroughputImportHelper(AssayUploadXarContext context, PlateBasedAssayProvider provider, ExpProtocol protocol, File dataFile) throws ExperimentException
+    public HighThroughputImportHelper(AssayUploadXarContext context, PlateBasedAssayProvider provider, ExpProtocol protocol, FileLike dataFile) throws ExperimentException
     {
         super(context, provider, protocol, dataFile);
         ensureData();
@@ -47,7 +48,8 @@ private void ensureData() throws ExperimentException
     {
         _plateTemplate = _provider.getPlate(_protocol.getContainer(), _protocol);
         DataLoaderFactory factory = DataLoaderService.get().findFactory(_dataFile, null);
-        try (DataLoader loader = factory.createLoader(_dataFile, true))
+        try (InputStream in = _dataFile.openInputStream();
+             DataLoader loader = factory.createLoader(in, true))
         {
             String signalColumnName = "Signal";
 

elisa/src/org/labkey/elisa/ManualImportHelper.java

@@ -20,6 +20,7 @@
 import org.labkey.api.exp.property.DomainProperty;
 import org.labkey.elisa.actions.ElisaRunUploadForm;
 import org.labkey.elisa.plate.BioTekPlateReader;
+import org.labkey.vfs.FileLike;
 
 import java.io.File;
 import java.util.HashMap;
@@ -32,7 +33,7 @@
  */
 public class ManualImportHelper extends AbstractElisaImportHelper
 {
-    public ManualImportHelper(AssayUploadXarContext context, PlateBasedAssayProvider provider, ExpProtocol protocol, File dataFile)
+    public ManualImportHelper(AssayUploadXarContext context, PlateBasedAssayProvider provider, ExpProtocol protocol, FileLike dataFile)
     {
         super(context, provider, protocol, dataFile);
     }

elispotassay/src/org/labkey/elispot/AbstractElispotDataHandler.java

@@ -17,6 +17,7 @@
 package org.labkey.elispot;
 
 import org.apache.logging.log4j.Logger;
+import org.jetbrains.annotations.NotNull;
 import org.labkey.api.assay.AssayUrls;
 import org.labkey.api.assay.plate.Position;
 import org.labkey.api.data.Container;
@@ -39,8 +40,8 @@
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.view.ActionURL;
 import org.labkey.api.view.ViewBackgroundInfo;
+import org.labkey.vfs.FileLike;
 
-import java.io.File;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
@@ -79,10 +80,10 @@ public interface ElispotDataFileParser
         List<Map<String, Object>> getResults() throws ExperimentException;
     }
 
-    public abstract ElispotDataFileParser getDataFileParser(ExpData data, File dataFile, ViewBackgroundInfo info, Logger log, XarContext context);
+    public abstract ElispotDataFileParser getDataFileParser(ExpData data, FileLike dataFile, ViewBackgroundInfo info, Logger log, XarContext context);
 
     @Override
-    public void importFile(ExpData data, File dataFile, ViewBackgroundInfo info, Logger log, XarContext context) throws ExperimentException
+    public void importFile(@NotNull ExpData data, @NotNull FileLike dataFile, @NotNull ViewBackgroundInfo info, @NotNull Logger log, @NotNull XarContext context) throws ExperimentException
     {
         ExpRun run = data.getRun();
 

elispotassay/src/org/labkey/elispot/ElispotDataHandler.java

@@ -89,10 +89,10 @@ public DataType getDataType()
     static class ElispotFileParser implements ElispotDataFileParser
     {
         private final ExpData _data;
-        private final File _dataFile;
+        private final FileLike _dataFile;
         private final XarContext _context;
 
-        public ElispotFileParser(ExpData data, File dataFile, XarContext context)
+        public ElispotFileParser(ExpData data, FileLike dataFile, XarContext context)
         {
             _data = data;
             _dataFile = dataFile;
@@ -199,7 +199,7 @@ else if (SPOT_SIZE_PROPERTY_NAME.equalsIgnoreCase(measurement))
     }
 
     @Override
-    public ElispotDataFileParser getDataFileParser(ExpData data, File dataFile, ViewBackgroundInfo info, Logger log, XarContext context)
+    public ElispotDataFileParser getDataFileParser(ExpData data, FileLike dataFile, ViewBackgroundInfo info, Logger log, XarContext context)
     {
         return new ElispotFileParser(data, dataFile, context);
     }
@@ -213,7 +213,7 @@ public void importTransformDataMap(ExpData data, AssayRunUploadContext<?> contex
     @Override
     public Map<DataType, DataIteratorBuilder> getValidationDataMap(ExpData data, FileLike dataFile, ViewBackgroundInfo info, Logger log, XarContext context, DataLoaderSettings settings) throws ExperimentException
     {
-        ElispotDataFileParser parser = getDataFileParser(data, dataFile.toNioPathForRead().toFile(), info, log, context);
+        ElispotDataFileParser parser = getDataFileParser(data, dataFile, info, log, context);
 
         Map<DataType, DataIteratorBuilder> datas = new HashMap<>();
         List<Map<String, Object>> rows = parser.getResults();
@@ -222,7 +222,7 @@ public Map<DataType, DataIteratorBuilder> getValidationDataMap(ExpData data, Fil
         return datas;
     }
 
-    public static Map<PlateInfo, Plate> initializePlates(ExpProtocol protocol, File dataFile, Plate template, PlateReader reader) throws ExperimentException
+    public static Map<PlateInfo, Plate> initializePlates(ExpProtocol protocol, FileLike dataFile, Plate template, PlateReader reader) throws ExperimentException
     {
         AssayProvider provider = AssayService.get().getProvider(protocol);
         Map<PlateInfo, Plate> plateMap = new HashMap<>();

elispotassay/src/org/labkey/elispot/ElispotUploadWizardAction.java

@@ -519,7 +519,7 @@ protected ExpRun finishPost(ElispotRunUploadForm form, BindException errors)
                 if (runPropMap.containsKey(ElispotAssayProvider.READER_PROPERTY_NAME))
                 {
                     reader = provider.getPlateReader(runPropMap.get(ElispotAssayProvider.READER_PROPERTY_NAME));
-                    plates = ElispotDataHandler.initializePlates(form.getProtocol(), data.get(0).getFile(), template, reader);
+                    plates = ElispotDataHandler.initializePlates(form.getProtocol(), data.get(0).getFileLike(), template, reader);
                 }
 
                 boolean subtractBackground = NumberUtils.toInt(runPropMap.get(ElispotAssayProvider.BACKGROUND_WELL_PROPERTY_NAME), 0) > 0;

elispotassay/src/org/labkey/elispot/PlateAnalytePropertyHelper.java

@@ -61,7 +61,7 @@ public PlateAnalytePropertyHelper(ElispotRunUploadForm form, List<? extends Doma
             if (runPropMap.containsKey(ElispotAssayProvider.READER_PROPERTY_NAME))
             {
                 reader = form.getProvider().getPlateReader(runPropMap.get(ElispotAssayProvider.READER_PROPERTY_NAME));
-                for (PlateUtils.GridInfo grid : reader.loadMultiGridFile(template, file.toNioPathForRead().toFile()))
+                for (PlateUtils.GridInfo grid : reader.loadMultiGridFile(template, file))
                 {
                     // attempt to parse the plate grid annotation into a PlateInfo object
                     FluorescentPlateInfo plateInfo = FluorescentPlateInfo.create(grid.getAnnotations());

elispotassay/src/org/labkey/elispot/pipeline/BackgroundSubtractionJob.java

@@ -46,6 +46,7 @@
 import org.labkey.elispot.ElispotManager;
 import org.labkey.elispot.RunDataRow;
 import org.labkey.elispot.plate.PlateInfo;
+import org.labkey.vfs.FileLike;
 
 import java.io.File;
 import java.io.IOException;
@@ -185,12 +186,12 @@ private Plate initializePlate(PlateBasedAssayProvider provider, ExpRun run, Plat
 
         if (reader != null)
         {
-            File dataFile = data.get(0).getFile();
+            FileLike dataFile = data.get(0).getFileLike();
 
             if (dataFile.exists())
             {
                 // TODO: how to handle background subtraction for fluorospot scans
-                for (Map.Entry<PlateInfo, Plate> entry : ElispotDataHandler.initializePlates(run.getProtocol(), data.get(0).getFile(), template, reader).entrySet())
+                for (Map.Entry<PlateInfo, Plate> entry : ElispotDataHandler.initializePlates(run.getProtocol(), dataFile, template, reader).entrySet())
                 {
                     if (entry.getKey().getMeasurement().equals(ElispotDataHandler.SFU_PROPERTY_NAME))
                     {

elispotassay/src/org/labkey/elispot/plate/AIDPlateReader.java

@@ -22,9 +22,10 @@
 import org.labkey.api.query.ValidationException;
 import org.labkey.api.reader.DataLoader;
 import org.labkey.api.reader.DataLoaderFactory;
+import org.labkey.vfs.FileLike;
 
-import java.io.File;
 import java.io.IOException;
+import java.io.InputStream;
 import java.util.List;
 
 /**
@@ -55,13 +56,14 @@ else if ("--".equalsIgnoreCase(token))
     }
 
     @Override
-    public double[][] loadFile(Plate template, File dataFile) throws ExperimentException
+    public double[][] loadFile(Plate template, FileLike dataFile) throws ExperimentException
     {
         String fileName = dataFile.getName().toLowerCase();
         if (fileName.endsWith(".xls") || fileName.endsWith(".xlsx"))
         {
             DataLoaderFactory factory = DataLoader.get().findFactory(dataFile, null);
-            try (DataLoader loader = factory.createLoader(dataFile, false))
+            try (InputStream in = dataFile.openInputStream();
+                DataLoader loader = factory.createLoader(in, false))
             {
                 return PlateUtils.parseGrid(dataFile, loader.load(), template.getRows(), template.getColumns(), this);
             }
@@ -77,13 +79,14 @@ public double[][] loadFile(Plate template, File dataFile) throws ExperimentExcep
     }
 
     @Override
-    public List<PlateUtils.GridInfo> loadMultiGridFile(Plate template, File dataFile) throws ExperimentException
+    public List<PlateUtils.GridInfo> loadMultiGridFile(Plate template, FileLike dataFile) throws ExperimentException
     {
         String fileName = dataFile.getName().toLowerCase();
         if (fileName.endsWith(".xls") || fileName.endsWith(".xlsx"))
         {
             DataLoaderFactory factory = DataLoader.get().findFactory(dataFile, null);
-            try (DataLoader loader = factory.createLoader(dataFile, false))
+            try (InputStream in = dataFile.openInputStream();
+                 DataLoader loader = factory.createLoader(in, false))
             {
                 return PlateUtils.parseAllGrids(dataFile, loader.load(), template.getRows(), template.getColumns(), this);
             }

flow/enginesrc/org/labkey/flow/Main.java

@@ -95,7 +95,7 @@ private static Workspace readWorkspace(File file, boolean printWarnings)
 
     private static File uniqueFile(File dir, String name)
     {
-        File file = new File(dir, name);
+        File file = FileUtil.appendName(dir, name);
         if (file.exists())
         {
             String base = name;
@@ -108,7 +108,7 @@ private static File uniqueFile(File dir, String name)
             }
 
             for (int i = 1; file.exists(); i++)
-                file = new File(dir, base + i + ext);
+                file = FileUtil.appendName(dir, base + i + ext);
         }
 
         return file;
@@ -244,7 +244,7 @@ private static void writeAnalysis(File outDir, String name, Workspace workspace,
         {
             XmlOptions options = new XmlOptions();
             options.setSavePrettyPrint();
-            doc.save(new File(outDir, name), options);
+            doc.save(FileUtil.appendName(outDir, name), options);
         }
         catch (IOException ioe)
         {

flow/enginesrc/org/labkey/flow/analysis/model/FCS.java

@@ -19,6 +19,7 @@
 import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.Logger;
 import org.apache.logging.log4j.LogManager;
+import org.labkey.api.util.FileUtil;
 import org.labkey.api.util.StringUtilsLabKey;
 
 import java.io.*;
@@ -368,7 +369,7 @@ public boolean accept(File dir, String name)
                 return ext.equals(".fcs") || ext.equals(".facs") || ext.equals(".lmd");
             }
             else
-                return isFCSFile(new File(dir,name));
+                return isFCSFile(FileUtil.appendName(dir, name));
         }
     }