Merge pull request #252 from melissalinkert/tmp-noexec-handling

Document and fail fast if tmp directory is noexec

Author: sbesson

README.md

@@ -33,6 +33,29 @@ If using features that rely on OpenCV (see the [Downsampling type](#downsampling
 
 __NOTE:__ If you are setting `jna.library.path` via the `JAVA_OPTS` environment variable, make sure the path is to the folder __containing__ the library not path to the library itself.
 
+Temporary directory usage
+=========================
+
+Beginning with 0.10.0, if the default temporary directory (usually `/tmp/`) is mounted as `noexec`, conversion will fail immediately by default.
+[CIS security benchmarks](https://www.cisecurity.org/benchmark) recommend that `/tmp/` be mounted as `noexec`; these standards are increasingly
+being adopted by major Linux distributions. For certain types of input data (e.g. NDPI, JPEG-XR compression), bioformats2raw needs
+to extract a native library from one or more jars to a temporary location. In these cases, the extracted native library must be executable in order
+to read image data.
+
+The recommended solution is to choose a different temporary directory by adding `-Djava.io.tmpdir=/path/to/alternate/tmp` to `JAVA_OPTS`.
+If multiple properties need to be set via `JAVA_OPTS`, separate them with a space, e.g. `JAVA_OPTS="-Djava.io.tmpdir/path/to/alternate/tmp -Djna.library.path=/path/to/blosc"`.
+
+If you know this issue does not affect your input data and wish to warn instead of immediately stopping conversion, the `--warn-no-exec` option can be used.
+For input data that relies on native library loading (e.g. NDPI, JPEG-XR compression), using `--warn-no-exec` instead of specifying an alternate
+temporary directory will simply cause the conversion to fail at a later point.
+
+For additional information, please see:
+
+* https://github.com/glencoesoftware/bioformats2raw/pull/252
+* https://github.com/scijava/native-lib-loader/issues/41
+* https://forum.image.sc/t/after-omero-server-upgrade-hamamatsu-ndpi-files-display-only-in-low-resolution/81868
+* https://forum.image.sc/t/bioformats-unable-to-read-czi-files-with-jpegxr-compression-on-almalinux-os-java-lang-unsatisfiedlinkerror-ome-jxrlib-jxrjni-new-decodecontext-j/82646
+
 Installation
 ============
 

src/main/java/com/glencoesoftware/bioformats2raw/Converter.java

@@ -128,6 +128,8 @@ public class Converter implements Callable<Integer> {
   private volatile Path inputPath;
   private volatile String outputLocation;
 
+  private volatile boolean warnNoExec = false;
+
   private Map<String, String> outputOptions;
   private volatile Integer pyramidResolutions;
   private volatile List<Integer> seriesList;
@@ -424,6 +426,23 @@ public void setProgressBars(boolean useProgressBars) {
     progressBars = useProgressBars;
   }
 
+  /**
+   * Configure whether to warn instead of throwing an exception
+   * if files created in the temporary directory
+   * ("java.io.tmpdir" system property) will not be executable.
+   *
+   * @param warnOnly true if a warning should be logged instead of an exception
+   */
+  @Option(
+    names = {"--warn-no-exec"},
+    description = "Warn instead of throwing an exception if " +
+                  "java.io.tmpdir is not executable",
+    defaultValue = "false"
+  )
+  public void setWarnOnNoExec(boolean warnOnly) {
+    warnNoExec = warnOnly;
+  }
+
   /**
    * Configure whether to print version information and exit
    * without converting.
@@ -966,6 +985,14 @@ public boolean getProgressBars() {
     return progressBars;
   }
 
+  /**
+   * @return true if a warning is logged instead of an exception when the tmp
+   *              directory is noexec
+   */
+  public boolean getWarnNoExec() {
+    return warnNoExec;
+  }
+
   /**
    * @return true if only version info is displayed
    */
@@ -1194,6 +1221,37 @@ public Integer call() throws Exception {
         tileWidth, tileHeight);
     }
 
+    // if the tmpdir is mounted as noexec, then any native library
+    // loading (OpenCV, turbojpeg, etc.) is expected to fail, which
+    // can cause conversion to fail with an exception that is not user friendly
+    //
+    // try to detect this case early and fail before the conversion begins,
+    // with a more informative message
+
+    // a temp file is created and set as executable
+    // in the noexec case, setting as executable is expected to silently fail
+    File tmpdirCheck = File.createTempFile("noexec-test", ".txt");
+    try {
+      // expect 'success' to be true in the noexec case, even though
+      // the file will not actually be executable
+      boolean success = tmpdirCheck.setExecutable(true);
+      if (!success || !tmpdirCheck.canExecute()) {
+        String msg = System.getProperty("java.io.tmpdir") +
+          " is noexec; fix it or specify a different java.io.tmpdir." +
+          " See https://github.com/glencoesoftware/bioformats2raw/" +
+          "blob/master/README.md#temporary-directory-usage for details";
+        if (getWarnNoExec()) {
+          LOGGER.warn(msg);
+        }
+        else {
+          throw new RuntimeException(msg);
+        }
+      }
+    }
+    finally {
+      tmpdirCheck.delete();
+    }
+
     OpenCVTools.loadOpenCV();
 
     if (progressBars) {