FileSystemLike and FileLike interfaces

(it compiles)

Author: labkey-matthewb

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

@@ -19,7 +19,6 @@
 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;
@@ -89,6 +88,7 @@
 import org.labkey.api.view.template.ClientDependency;
 import org.labkey.laboratory.assay.AssayHelper;
 import org.labkey.laboratory.query.WorkbookModel;
+import org.labkey.vfs.FileLike;
 import org.springframework.validation.BindException;
 import org.springframework.validation.Errors;
 import org.springframework.web.servlet.ModelAndView;
@@ -620,8 +620,8 @@ protected File getTargetFile(String filename) throws IOException
 
             try
             {
-                FileObject targetDirectory = AssayFileWriter.ensureUploadDirectory(getContainer());
-                return AssayFileWriter.findUniqueFileName(filename, targetDirectory).getPath().toFile();
+                FileLike targetDirectory = AssayFileWriter.ensureUploadDirectory(getContainer());
+                return AssayFileWriter.findUniqueFileName(filename, targetDirectory).toNioPathForWrite().toFile();
             }
             catch (ExperimentException e)
             {

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

@@ -15,7 +15,6 @@
  */
 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;
@@ -56,6 +55,7 @@
 import org.labkey.laboratory.assay.AssayHelper;
 import org.labkey.laboratory.query.DefaultAssayCustomizer;
 import org.labkey.laboratory.query.LaboratoryTableCustomizer;
+import org.labkey.vfs.FileLike;
 
 import java.io.File;
 import java.lang.reflect.InvocationTargetException;
@@ -197,10 +197,10 @@ public Pair<ExpExperiment, ExpRun> saveAssayBatch(List<Map<String, Object>> resu
 
         try
         {
-            FileObject targetDirectory = AssayFileWriter.ensureUploadDirectory(ctx.getContainer());
-            FileObject file = AssayFileWriter.findUniqueFileName(basename, targetDirectory);
+            FileLike targetDirectory = AssayFileWriter.ensureUploadDirectory(ctx.getContainer());
+            FileLike file = AssayFileWriter.findUniqueFileName(basename, targetDirectory);
 
-            return this.saveAssayBatch(results, json, file.getPath().toFile(), ctx, provider, protocol);
+            return this.saveAssayBatch(results, json, file.toNioPathForRead().toFile(), ctx, provider, protocol);
         }
         catch (ExperimentException e)
         {

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

@@ -15,7 +15,6 @@
  */
 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;
@@ -47,7 +46,6 @@
 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;
@@ -60,6 +58,8 @@
 import org.labkey.api.view.ViewContext;
 import org.labkey.laboratory.LaboratoryController;
 import org.labkey.laboratory.LaboratorySchema;
+import org.labkey.vfs.FileLike;
+import org.labkey.vfs.FileSystemLike;
 
 import java.beans.Introspector;
 import java.io.File;
@@ -90,7 +90,7 @@ public static AssayHelper get()
         return _instance;
     }
 
-    public Map<String, FileObject> saveResultsFile(List<Map<String, Object>> results, JSONObject json, File file, AssayProvider provider, ExpProtocol protocol) throws ExperimentException, ValidationException
+    public Map<String, FileLike> saveResultsFile(List<Map<String, Object>> results, JSONObject json, File file, AssayProvider provider, ExpProtocol protocol) throws ExperimentException, ValidationException
     {
         //TODO: consider adding as input??
         //files.put("RawInput", file);
@@ -112,9 +112,8 @@ public Map<String, FileObject> saveResultsFile(List<Map<String, Object>> results
             throw new ExperimentException(e.getMessage());
         }
 
-        Map<String, FileObject> files = new HashMap<String, FileObject>();
-        files.put(AssayDataCollector.PRIMARY_FILE, AuthorizedFileSystem.convertToFileObject(newFile));
-
+        Map<String, FileLike> files = new HashMap<String, FileLike>();
+        files.put(AssayDataCollector.PRIMARY_FILE, FileSystemLike.wrapFile(newFile));
         return files;
     }
 
@@ -211,7 +210,7 @@ public Pair<ExpExperiment, ExpRun> saveAssayBatch(List<Map<String, Object>> resu
             });
         }
 
-        Map<String, FileObject> uploadedFiles = saveResultsFile(results, json, file, provider, protocol);
+        Map<String, FileLike> uploadedFiles = saveResultsFile(results, json, file, provider, protocol);
 
         //TODO: see AssayRunAsyncContext
         AssayRunUploadContext uploadContext = new RunUploadContext<>(protocol, provider, name, comments, runProperties, batchProperties, ctx, uploadedFiles);

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

@@ -16,7 +16,6 @@
 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;
@@ -33,6 +32,7 @@
 import org.labkey.api.security.User;
 import org.labkey.api.view.ActionURL;
 import org.labkey.api.view.ViewContext;
+import org.labkey.vfs.FileLike;
 
 import java.util.Collections;
 import java.util.HashMap;
@@ -53,9 +53,9 @@ public class RunUploadContext<ProviderType extends AssayProvider> implements Ass
     private final ViewContext _ctx;
 
     private TransformResult _transformResult;
-    private final Map<String, FileObject> _uploadedData;
+    private final Map<String, FileLike> _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)
+    public RunUploadContext(ExpProtocol protocol, ProviderType providerType, String name, String comments, Map<String, String> runProperties, Map<String, String> batchProperties, ViewContext ctx, Map<String, FileLike> uploadedData)
     {
         _protocol = protocol;
         _providerType = providerType;
@@ -154,7 +154,7 @@ public ActionURL getActionURL()
 
     @Override
     @NotNull
-    public Map<String, FileObject> getUploadedData() throws ExperimentException
+    public Map<String, FileLike> getUploadedData() throws ExperimentException
     {
         return _uploadedData;
     }