Continue adopting FileLike instead of File or Path (#186)

Author: labkey-jeckels

genotyping/src/org/labkey/genotyping/sequences/AlleleFastaLoader.java

@@ -19,6 +19,7 @@
 import org.junit.BeforeClass;
 import org.junit.Test;
 import org.junit.experimental.categories.Category;
+import org.labkey.api.util.FileUtil;
 import org.labkey.test.BaseWebDriverTest;
 import org.labkey.test.Locator;
 import org.labkey.test.categories.CustomModules;
@@ -118,7 +119,7 @@ private void receiveDataFromGalaxyServer()
         String analysisFolder = "analysis_" + getRunNumber();
         for (String file: filesToCopy)
         {
-            copyFile(new File(getPipelineLoc(), file), new File(getPipelineLoc(), analysisFolder + "/" + file));
+            copyFile(FileUtil.appendName(getPipelineLoc(), file), FileUtil.appendName(FileUtil.appendName(getPipelineLoc(), analysisFolder), file));
         }
         refresh();
         waitForPipelineJobsToComplete(++pipelineJobCount, "Import genotyping analysis", false);

genotyping/test/src/org/labkey/test/tests/GenotypingTest.java

@@ -19,6 +19,7 @@
 import org.junit.BeforeClass;
 import org.junit.Test;
 import org.junit.experimental.categories.Category;
+import org.labkey.api.util.FileUtil;
 import org.labkey.serverapi.reader.Readers;
 import org.labkey.test.BaseWebDriverTest;
 import org.labkey.test.Locator;
@@ -90,7 +91,7 @@ public void testSteps() throws Exception
     //https://docs.google.com/a/labkey.com/file/d/0B45Fm0-0-NLtdmpDR1hKaW5jSWc/edit
     private void verifyCleanIlluminaSampleSheets()
     {
-        importFolderFromZip(new File(getPipelineLoc(), "genoCleanSamples.folder.zip"), true, 2);
+        importFolderFromZip(FileUtil.appendName(getPipelineLoc(), "genoCleanSamples.folder.zip"), true, 2);
         goToProjectHome();
         click(Locator.linkWithText("Samples"));
         waitForText("SIVkcol2");