AssayDataHandler and AssayUpload conversion File->FileObject

checkpoint

Author: labkey-matthewb

laboratory/src/org/labkey/laboratory/LaboratoryController.java

@@ -19,6 +19,7 @@
 import jakarta.servlet.http.HttpServletResponse;
 import org.apache.commons.lang3.ArrayUtils;
 import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.vfs2.FileObject;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.NotNull;
@@ -619,8 +620,8 @@ protected File getTargetFile(String filename) throws IOException
 
             try
             {
-                File targetDirectory = AssayFileWriter.ensureUploadDirectory(getContainer());
-                return AssayFileWriter.findUniqueFileName(filename, targetDirectory);
+                FileObject targetDirectory = AssayFileWriter.ensureUploadDirectory(getContainer());
+                return AssayFileWriter.findUniqueFileName(filename, targetDirectory).getPath().toFile();
             }
             catch (ExperimentException e)
             {

laboratory/src/org/labkey/laboratory/LaboratoryServiceImpl.java

@@ -15,6 +15,7 @@
  */
 package org.labkey.laboratory;
 
+import org.apache.commons.vfs2.FileObject;
 import org.apache.logging.log4j.Logger;
 import org.apache.logging.log4j.LogManager;
 import org.jetbrains.annotations.Nullable;
@@ -196,10 +197,10 @@ public Pair<ExpExperiment, ExpRun> saveAssayBatch(List<Map<String, Object>> resu
 
         try
         {
-            File targetDirectory = AssayFileWriter.ensureUploadDirectory(ctx.getContainer());
-            File file = AssayFileWriter.findUniqueFileName(basename, targetDirectory);
+            FileObject targetDirectory = AssayFileWriter.ensureUploadDirectory(ctx.getContainer());
+            FileObject file = AssayFileWriter.findUniqueFileName(basename, targetDirectory);
 
-            return this.saveAssayBatch(results, json, file, ctx, provider, protocol);
+            return this.saveAssayBatch(results, json, file.getPath().toFile(), ctx, provider, protocol);
         }
         catch (ExperimentException e)
         {

laboratory/src/org/labkey/laboratory/assay/AssayHelper.java

@@ -15,6 +15,7 @@
  */
 package org.labkey.laboratory.assay;
 
+import org.apache.commons.vfs2.FileObject;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.Nullable;
@@ -46,6 +47,7 @@
 import org.labkey.api.exp.property.Domain;
 import org.labkey.api.exp.property.DomainKind;
 import org.labkey.api.exp.property.DomainProperty;
+import org.labkey.api.files.virtual.AuthorizedFileSystem;
 import org.labkey.api.laboratory.LaboratoryService;
 import org.labkey.api.laboratory.assay.AssayDataProvider;
 import org.labkey.api.laboratory.assay.AssayImportMethod;
@@ -88,9 +90,8 @@ public static AssayHelper get()
         return _instance;
     }
 
-    public Map<String, File> saveResultsFile(List<Map<String, Object>> results, JSONObject json, File file, AssayProvider provider, ExpProtocol protocol) throws ExperimentException, ValidationException
+    public Map<String, FileObject> saveResultsFile(List<Map<String, Object>> results, JSONObject json, File file, AssayProvider provider, ExpProtocol protocol) throws ExperimentException, ValidationException
     {
-        Map<String, File> files = new HashMap<String, File>();
         //TODO: consider adding as input??
         //files.put("RawInput", file);
 
@@ -111,7 +112,8 @@ public Map<String, File> saveResultsFile(List<Map<String, Object>> results, JSON
             throw new ExperimentException(e.getMessage());
         }
 
-        files.put(AssayDataCollector.PRIMARY_FILE, newFile);
+        Map<String, FileObject> files = new HashMap<String, FileObject>();
+        files.put(AssayDataCollector.PRIMARY_FILE, AuthorizedFileSystem.convertToFileObject(newFile));
 
         return files;
     }
@@ -209,7 +211,7 @@ public Pair<ExpExperiment, ExpRun> saveAssayBatch(List<Map<String, Object>> resu
             });
         }
 
-        Map<String, File> uploadedFiles = saveResultsFile(results, json, file, provider, protocol);
+        Map<String, FileObject> uploadedFiles = saveResultsFile(results, json, file, provider, protocol);
 
         //TODO: see AssayRunAsyncContext
         AssayRunUploadContext uploadContext = new RunUploadContext<>(protocol, provider, name, comments, runProperties, batchProperties, ctx, uploadedFiles);
@@ -243,10 +245,10 @@ private File getUniqueOutputName(File input, String extension)
         File parent = input.getParentFile();
         String basename = FileUtil.getBaseName(input);
         int suffix = 1;
-        File newFile = new File(parent,  basename + "." + extension);
+        File newFile = FileUtil.appendName(parent,  basename + "." + extension);
         while (newFile.exists())
         {
-            newFile = new File(parent,  basename + "-" + suffix + "." + extension);
+            newFile = FileUtil.appendName(parent,  basename + "-" + suffix + "." + extension);
             suffix++;
         }
         return newFile;

laboratory/src/org/labkey/laboratory/assay/RunUploadContext.java

@@ -16,6 +16,7 @@
 package org.labkey.laboratory.assay;
 
 import jakarta.servlet.http.HttpServletRequest;
+import org.apache.commons.vfs2.FileObject;
 import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.NotNull;
 import org.labkey.api.assay.AssayProvider;
@@ -33,7 +34,6 @@
 import org.labkey.api.view.ActionURL;
 import org.labkey.api.view.ViewContext;
 
-import java.io.File;
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.Map;
@@ -53,9 +53,9 @@ public class RunUploadContext<ProviderType extends AssayProvider> implements Ass
     private final ViewContext _ctx;
 
     private TransformResult _transformResult;
-    private final Map<String, File> _uploadedData;
+    private final Map<String, FileObject> _uploadedData;
 
-    public RunUploadContext(ExpProtocol protocol, ProviderType providerType, String name, String comments, Map<String, String> runProperties, Map<String, String> batchProperties, ViewContext ctx, Map<String, File> uploadedData)
+    public RunUploadContext(ExpProtocol protocol, ProviderType providerType, String name, String comments, Map<String, String> runProperties, Map<String, String> batchProperties, ViewContext ctx, Map<String, FileObject> uploadedData)
     {
         _protocol = protocol;
         _providerType = providerType;
@@ -154,7 +154,7 @@ public ActionURL getActionURL()
 
     @Override
     @NotNull
-    public Map<String, File> getUploadedData() throws ExperimentException
+    public Map<String, FileObject> getUploadedData() throws ExperimentException
     {
         return _uploadedData;
     }