FileUtil.createTempFile(File)

api/src/org/labkey/api/reports/ExternalScriptEngine.java

@@ -444,6 +444,7 @@ protected File writeScriptFile(String script, ScriptContext context, List<String
                     }
                 }
 
+                FileUtil.createTempFile(scriptFile);
                 try (PrintWriter pw = new PrintWriter(new BufferedWriter(new FileWriter(scriptFile))))
                 {
                     pw.write(script);

api/src/org/labkey/api/reports/report/ExternalScriptEngineReport.java

@@ -423,7 +423,7 @@ protected void cacheResults(ViewContext context, List<ParamReplacement> replacem
                         for (File src : param.getFiles())
                         {
                             File dst = new File(cacheDir, src.getName());
-                            if (src.exists() && dst.createNewFile())
+                            if (src.exists() && FileUtil.createTempFile(dst))
                             {
                                 FileUtil.copyFile(src, dst);
 

api/src/org/labkey/api/reports/report/ScriptReport.java

@@ -189,6 +189,7 @@ public File _createInputDataFile(@NotNull ViewContext context, ResultsFactory fa
                 try (TSVGridWriter tsv = new TSVGridWriter(srf, dataColumns))
                 {
                     tsv.setColumnHeaderType(ColumnHeaderType.Name); // CONSIDER: Use FieldKey instead
+                    FileUtil.createTempFile(resultFile);
                     tsv.write(resultFile);
                 }
             }

api/src/org/labkey/api/reports/report/python/IpynbReport.java

@@ -193,6 +193,7 @@ public HttpView<?> renderReport(ViewContext context) throws Exception
         var descriptor = getDescriptor();
         String script = descriptor.getProperty(ScriptReportDescriptor.Prop.script);
         File scriptFile = new File(workingDirectory, FileUtil.makeLegalName(descriptor.getReportName()) + ".ipynb");
+        FileUtil.createTempFile(scriptFile);
         IOUtil.copyCompletely(new StringReader(script), new FileWriter(scriptFile, StringUtilsLabKey.DEFAULT_CHARSET));
 
         Set<File> beforeExecute = new HashSet<>(FileUtils.listFiles(workingDirectory, null, true));
@@ -304,6 +305,7 @@ private static void extractTar(InputStream in, File targetDirectory) throws IOEx
                 }
                 else
                 {
+                    FileUtil.createTempFile(path);
                     try (FileOutputStream os = new FileOutputStream(path))
                     {
                         IOUtils.copy(tar, os);

api/src/org/labkey/api/reports/report/r/RserveScriptEngine.java

@@ -253,16 +253,17 @@ protected void copyWorkingDirectoryFromRemote(RConnection rconn) throws IOExcept
         File wd = getWorkingDir(getContext());
         try
         {
-            String[] names = rconn.eval("dir("+ toR(defaultIfBlank(rserveWorkingDirectory, ".")) +", all.files = TRUE, full.names = TRUE, recursive = TRUE, include.dirs = FALSE, no.. = FALSE)").asStrings();
-            for (var name : names)
+            String[] paths = rconn.eval("dir("+ toR(defaultIfBlank(rserveWorkingDirectory, ".")) +", all.files = TRUE, full.names = TRUE, recursive = TRUE, include.dirs = FALSE, no.. = FALSE)").asStrings();
+            for (var remotePath : paths)
             {
-                if ("input_data.tsv".equalsIgnoreCase(name))
+                if ("input_data.tsv".equalsIgnoreCase(remotePath))
                     continue;
-                if ("script.R".equalsIgnoreCase(name))
+                if ("script.R".equalsIgnoreCase(remotePath))
                     continue;
-                new File(wd,name).getParentFile().mkdirs();
-                try (InputStream is = rconn.openFile(name);
-                     FileOutputStream fos = new FileOutputStream(new File(wd,name)))
+                File file = new File(wd,remotePath);
+                FileUtil.createTempFile(file);
+                try (InputStream is = rconn.openFile(remotePath);
+                     FileOutputStream fos = new FileOutputStream(file))
                 {
                     IOUtil.copyCompletely(is, fos);
                 }

api/src/org/labkey/api/util/FileUtil.java

@@ -53,11 +53,15 @@
 import java.nio.CharBuffer;
 import java.nio.channels.FileChannel;
 import java.nio.channels.FileLock;
+import java.nio.file.FileSystems;
 import java.nio.file.FileVisitResult;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.StandardCopyOption;
 import java.nio.file.attribute.BasicFileAttributes;
+import java.nio.file.attribute.FileAttribute;
+import java.nio.file.attribute.PosixFilePermission;
+import java.nio.file.attribute.PosixFilePermissions;
 import java.security.DigestInputStream;
 import java.security.MessageDigest;
 import java.security.NoSuchAlgorithmException;
@@ -66,6 +70,7 @@
 import java.util.HashSet;
 import java.util.LinkedList;
 import java.util.List;
+import java.util.Set;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
@@ -1220,6 +1225,24 @@ public static File createTempFile(@Nullable String prefix, @Nullable String suff
         return path.toFile();
     }
 
+
+    private static final boolean isPosix =
+            FileSystems.getDefault().supportedFileAttributeViews().contains("posix");
+    final static private FileAttribute<?>[] tempFileAttributes = new FileAttribute[] { PosixFilePermissions.asFileAttribute(Set.of(PosixFilePermission.OWNER_READ, PosixFilePermission.OWNER_WRITE)) };
+
+    public static boolean createTempFile(File file) throws IOException
+    {
+        if (file.exists())
+            return false;
+        file.getParentFile().mkdirs();
+        if (isPosix)
+            Files.createFile(file.toPath(), tempFileAttributes);
+        else
+            Files.createFile(file.toPath());
+        return true;
+    }
+
+
     public static void deleteTempFile(File f)
     {
         if (null != f && f.isFile())