From b0e1605e985456230b9fa5c62596132b00b26cf1 Mon Sep 17 00:00:00 2001
From: labkey-matthewb <matthewb@labkey.com>
Date: Wed, 9 Oct 2024 22:47:21 -0700
Subject: [PATCH] FileSystemLike (#149)

* AssayDataHandler and AssayUpload conversion File->FileObject
checkpoint

* FileLike
---
 .../org/labkey/genotyping/HaplotypeDataCollector.java  | 10 +++++-----
 .../org/labkey/genotyping/HaplotypeDataHandler.java    |  3 +--
 2 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/genotyping/src/org/labkey/genotyping/HaplotypeDataCollector.java b/genotyping/src/org/labkey/genotyping/HaplotypeDataCollector.java
index 6b7352e9..df1b661c 100644
--- a/genotyping/src/org/labkey/genotyping/HaplotypeDataCollector.java
+++ b/genotyping/src/org/labkey/genotyping/HaplotypeDataCollector.java
@@ -24,9 +24,9 @@
 import org.labkey.api.exp.api.ExpProtocol;
 import org.labkey.api.view.HttpView;
 import org.labkey.api.view.JspView;
+import org.labkey.vfs.FileLike;
 
 import java.io.ByteArrayInputStream;
-import java.io.File;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Collections;
@@ -71,7 +71,7 @@ public String getDescription(ContextType context)
 
     @NotNull
     @Override
-    public Map<String, File> createData(ContextType context) throws IOException, ExperimentException
+    public Map<String, FileLike> createData(ContextType context) throws IOException, ExperimentException
     {
         ExpProtocol protocol = context.getProtocol();
         String data = context.getRequest().getParameter(HaplotypeAssayProvider.DATA_PROPERTY_NAME);
@@ -95,11 +95,11 @@ public Map<String, File> createData(ContextType context) throws IOException, Exp
         }
 
         // NOTE: We use a 'tmp' file extension so that DataLoaderService will sniff the file type by parsing the file's header.
-        File dir = getFileTargetDir(context);
-        File file = createFile(protocol, dir, "tmp");
+        FileLike dir = getFileTargetDir(context);
+        FileLike file = createFile(protocol, dir, "tmp");
         ByteArrayInputStream bIn = new ByteArrayInputStream(data.getBytes(context.getRequest().getCharacterEncoding()));
 
-        writeFile(bIn, file);
+        writeFile(bIn, file.toNioPathForWrite().toFile());
         return Collections.singletonMap(PRIMARY_FILE, file);
     }
 
diff --git a/genotyping/src/org/labkey/genotyping/HaplotypeDataHandler.java b/genotyping/src/org/labkey/genotyping/HaplotypeDataHandler.java
index 5b2e60fa..69b13836 100644
--- a/genotyping/src/org/labkey/genotyping/HaplotypeDataHandler.java
+++ b/genotyping/src/org/labkey/genotyping/HaplotypeDataHandler.java
@@ -16,7 +16,6 @@
 package org.labkey.genotyping;
 
 import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
 import org.jetbrains.annotations.NotNull;
 import org.junit.Assert;
 import org.junit.Test;
@@ -70,7 +69,7 @@ public DataType getDataType()
     }
 
     @Override
-    public void importFile(ExpData data, File dataFile, ViewBackgroundInfo info, Logger log, XarContext context) throws ExperimentException
+    public void importFile(@NotNull ExpData data, File dataFile, @NotNull ViewBackgroundInfo info, @NotNull Logger log, @NotNull XarContext context) throws ExperimentException
     {
         if (!dataFile.exists())
         {