Manual sync with develop (#95)

Brings all features from develop. Note that RELEASE.txt has not been
updated (will be done in a future PR).

7 files changed, 185 insertions, 11 deletions

diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java
index 3c5a124..1c37839 100644
--- a/java/src/hdf/hdf5lib/H5.java
+++ b/java/src/hdf/hdf5lib/H5.java
@@ -8518,6 +8518,55 @@ public class H5 implements java.io.Serializable {
     public synchronized static native void H5Pset_evict_on_close(long fapl_id, boolean evict_on_close)
             throws HDF5LibraryException;
 
+    /**
+     * H5Pget_use_file_locking retrieves whether we are using file locking.
+     *
+     * @param fapl_id
+     *            IN: File access property list identifier
+     *
+     * @return indication if file locking is used.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
+    public synchronized static native boolean H5Pget_use_file_locking(long fapl_id)
+            throws HDF5LibraryException;
+
+    /**
+     * H5Pget_use_file_locking retrieves whether we ignore file locks when they are disabled.
+     *
+     * @param fapl_id
+     *            IN: File access property list identifier
+     *
+     * @return indication if file locking is ignored.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
+    public synchronized static native boolean H5Pget_ignore_disabled_file_locking(long fapl_id)
+            throws HDF5LibraryException;
+
+    /**
+     * H5Pset_file_locking sets parameters related to file locking.
+     *
+     * @param fapl_id
+     *            IN: File access property list identifier
+     *
+     * @param use_file_locking
+     *            IN: Whether the library will use file locking when opening files (mainly for SWMR semantics).
+     *
+     * @param ignore_when_disabled
+     *            IN: Whether file locking will be ignored when disabled on a file system (useful for Lustre).
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
+    public synchronized static native void H5Pset_file_locking(long fapl_id, boolean use_file_locking, boolean ignore_when_disabled)
+            throws HDF5LibraryException;
+
     //  /////  unimplemented /////
     // herr_t H5Pset_vol(hid_t plist_id, hid_t new_vol_id, const void *new_vol_info);
     // herr_t H5Pget_vol_id(hid_t plist_id, hid_t *vol_id);
diff --git a/java/src/hdf/hdf5lib/HDF5Constants.java b/java/src/hdf/hdf5lib/HDF5Constants.java
index 2241238..a4f17e6 100644
--- a/java/src/hdf/hdf5lib/HDF5Constants.java
+++ b/java/src/hdf/hdf5lib/HDF5Constants.java
@@ -215,8 +215,8 @@ public class HDF5Constants {
     public static final long H5E_CANTLOAD = H5E_CANTLOAD();
     /** Minor error codes - Resource errors - Unable to lock object */
     public static final long H5E_CANTLOCK = H5E_CANTLOCK();
-//    /** Minor error codes - File accessibility errors  Unable to lock file */
-//    public static final long H5E_CANTLOCKFILE = H5E_CANTLOCKFILE();
+    /** Minor error codes - File accessibility errors  Unable to lock file */
+    public static final long H5E_CANTLOCKFILE = H5E_CANTLOCKFILE();
     /** Minor error codes - Cache related errors - Unable to mark a pinned entry as clean */
     public static final long H5E_CANTMARKCLEAN = H5E_CANTMARKCLEAN();
     /** Minor error codes - Cache related errors - Unable to mark a pinned entry as dirty */
@@ -289,8 +289,8 @@ public class HDF5Constants {
     public static final long H5E_CANTUNDEPEND = H5E_CANTUNDEPEND();
     /** Minor error codes - Resource errors - Unable to unlock object */
     public static final long H5E_CANTUNLOCK = H5E_CANTUNLOCK();
-//    /** Minor error codes - File accessibility errors  Unable to unlock file */
-//    public static final long H5E_CANTUNLOCKFILE = H5E_CANTUNLOCKFILE();
+    /** Minor error codes - File accessibility errors  Unable to unlock file */
+    public static final long H5E_CANTUNLOCKFILE = H5E_CANTUNLOCKFILE();
     /** Minor error codes - Cache related errors - Unable to un-pin cache entry */
     public static final long H5E_CANTUNPIN = H5E_CANTUNPIN();
     /** Minor error codes - Cache related errors - Unable to unprotect metadata */
@@ -1262,7 +1262,7 @@ public class HDF5Constants {
 
     private static native final long H5E_CANTLOCK();
 
-//    private static native final long H5E_CANTLOCKFILE();
+    private static native final long H5E_CANTLOCKFILE();
 
     private static native final long H5E_CANTMARKCLEAN();
 
@@ -1336,7 +1336,7 @@ public class HDF5Constants {
 
     private static native final long H5E_CANTUNLOCK();
 
-//    private static native final long H5E_CANTUNLOCKFILE();
+    private static native final long H5E_CANTUNLOCKFILE();
 
     private static native final long H5E_CANTUNPIN();
 
diff --git a/java/src/jni/h5Constants.c b/java/src/jni/h5Constants.c
index ade28e8..66ce8cc 100644
--- a/java/src/jni/h5Constants.c
+++ b/java/src/jni/h5Constants.c
@@ -594,13 +594,11 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTLOCK(JNIEnv *env, jclass cls)
 {
     return H5E_CANTLOCK;
 }
-/*
 JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTLOCKFILE(JNIEnv *env, jclass cls)
 {
     return H5E_CANTLOCKFILE;
 }
-*/
 JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTMARKCLEAN(JNIEnv *env, jclass cls)
 {
@@ -781,13 +779,11 @@ Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTUNLOCK(JNIEnv *env, jclass cls)
 {
     return H5E_CANTUNLOCK;
 }
-/*
 JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTUNLOCKFILE(JNIEnv *env, jclass cls)
 {
     return H5E_CANTUNLOCKFILE;
 }
-*/
 JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1CANTUNPIN(JNIEnv *env, jclass cls)
 {
diff --git a/java/src/jni/h5pFAPLImp.c b/java/src/jni/h5pFAPLImp.c
index bbeddaf..0077df4 100644
--- a/java/src/jni/h5pFAPLImp.c
+++ b/java/src/jni/h5pFAPLImp.c
@@ -1364,6 +1364,76 @@ done:
 
 /*
  * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pset_file_locking
+ * Signature: (JZZ)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5Pset_1file_1locking(JNIEnv *env, jclass clss, jlong fapl_id, jboolean use_file_locking,
+                                          jboolean ignore_when_disabled)
+{
+    hbool_t use_file_locking_val     = TRUE;
+    hbool_t ignore_when_disabled_val = TRUE;
+
+    UNUSED(clss);
+
+    use_file_locking_val     = (use_file_locking == JNI_TRUE) ? TRUE : FALSE;
+    ignore_when_disabled_val = (ignore_when_disabled == JNI_TRUE) ? TRUE : FALSE;
+
+    if (H5Pset_file_locking((hid_t)fapl_id, use_file_locking_val, ignore_when_disabled_val) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+done:
+    return;
+} /* end Java_hdf_hdf5lib_H5_H5Pset_1file_1locking */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pget_use_file_locking
+ * Signature: (J)Z
+ */
+JNIEXPORT jboolean JNICALL
+Java_hdf_hdf5lib_H5_H5Pget_1use_1file_1locking(JNIEnv *env, jclass clss, jlong fapl_id)
+{
+    hbool_t  use_file_locking_val = TRUE;
+    hbool_t  unused               = TRUE;
+    jboolean bval                 = JNI_FALSE;
+
+    UNUSED(clss);
+
+    if (H5Pget_file_locking((hid_t)fapl_id, &use_file_locking_val, &unused) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+    bval = (use_file_locking_val == TRUE) ? JNI_TRUE : JNI_FALSE;
+
+done:
+    return bval;
+} /* end Java_hdf_hdf5lib_H5_H5Pget_1use_1file_1locking */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pget_ignore_disabled_file_locking
+ * Signature: (J)Z
+ */
+JNIEXPORT jboolean JNICALL
+Java_hdf_hdf5lib_H5_H5Pget_1ignore_1disabled_1file_1locking(JNIEnv *env, jclass clss, jlong fapl_id)
+{
+    hbool_t  ignore_when_disabled_val = TRUE;
+    hbool_t  unused                   = TRUE;
+    jboolean bval                     = JNI_FALSE;
+
+    UNUSED(clss);
+
+    if (H5Pget_file_locking((hid_t)fapl_id, &unused, &ignore_when_disabled_val) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+    bval = (ignore_when_disabled_val == TRUE) ? JNI_TRUE : JNI_FALSE;
+
+done:
+    return bval;
+} /* end Java_hdf_hdf5lib_H5_H5Pget_1ignore_1disabled_1file_1locking */
+
+/*
+ * Class:     hdf_hdf5lib_H5
  * Method:    H5Pset_metadata_read_attempts
  * Signature: (JJ)V
  */
diff --git a/java/src/jni/h5pFAPLImp.h b/java/src/jni/h5pFAPLImp.h
index 8c9d7ab..780ebc4 100644
--- a/java/src/jni/h5pFAPLImp.h
+++ b/java/src/jni/h5pFAPLImp.h
@@ -331,6 +331,32 @@ JNIEXPORT jboolean JNICALL Java_hdf_hdf5lib_H5_H5Pget_1evict_1on_1close(JNIEnv *
 
 /*
  * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pset_file_locking
+ * Signature: (JZZ)V
+ */
+JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5Pset_1file_1locking(JNIEnv *env, jclass clss, jlong fapl_id,
+                                                                 jboolean use_file_locking,
+                                                                 jboolean ignore_when_disabled);
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pget_use_file_locking
+ * Signature: (J)Z
+ */
+JNIEXPORT jboolean JNICALL Java_hdf_hdf5lib_H5_H5Pget_1use_1file_1locking(JNIEnv *env, jclass clss,
+                                                                          jlong fapl_id);
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pget_ignore_disabled_file_locking
+ * Signature: (J)Z
+ */
+JNIEXPORT jboolean JNICALL Java_hdf_hdf5lib_H5_H5Pget_1ignore_1disabled_1file_1locking(JNIEnv *env,
+                                                                                       jclass  clss,
+                                                                                       jlong   fapl_id);
+
+/*
+ * Class:     hdf_hdf5lib_H5
  * Method:    H5Pset_metadata_read_attempts
  * Signature: (JJ)V
  */
diff --git a/java/test/TestH5Pfapl.java b/java/test/TestH5Pfapl.java
index 10a79dd..4233580 100644
--- a/java/test/TestH5Pfapl.java
+++ b/java/test/TestH5Pfapl.java
@@ -1398,4 +1398,36 @@ public class TestH5Pfapl {
             fail("H5P_evict_on_close: " + err);
         }
     }
+
+    @Test
+    public void testH5P_file_locking() {
+        boolean use_file_locking = false;
+        boolean ignore_disabled_file_locking = false;
+        try {
+            // false values (usually not the default)
+            H5.H5Pset_file_locking(fapl_id, false, false);
+            use_file_locking = H5.H5Pget_use_file_locking(fapl_id);
+            ignore_disabled_file_locking = H5.H5Pget_ignore_disabled_file_locking(fapl_id);
+            assertFalse("H5P_file_locking", use_file_locking);
+            assertFalse("H5P_file_locking", ignore_disabled_file_locking);
+
+            // true values (typically the default)
+            H5.H5Pset_file_locking(fapl_id, true, true);
+            use_file_locking = H5.H5Pget_use_file_locking(fapl_id);
+            ignore_disabled_file_locking = H5.H5Pget_ignore_disabled_file_locking(fapl_id);
+            assertTrue("H5P_file_locking", use_file_locking);
+            assertTrue("H5P_file_locking", ignore_disabled_file_locking);
+        }
+        catch (HDF5PropertyListInterfaceException err) {
+            // parallel is not supported
+            if (err.getMinorErrorNumber() != HDF5Constants.H5E_UNSUPPORTED) {
+                err.printStackTrace();
+                fail("H5P_test_file_locking: " + err);
+            }
+        }
+        catch (Throwable err) {
+            err.printStackTrace();
+            fail("H5P_test_file_locking: " + err);
+        }
+    }
 }
diff --git a/java/test/testfiles/JUnit-TestH5Pfapl.txt b/java/test/testfiles/JUnit-TestH5Pfapl.txt
index c4f37d0..c34ac1c 100644
--- a/java/test/testfiles/JUnit-TestH5Pfapl.txt
+++ b/java/test/testfiles/JUnit-TestH5Pfapl.txt
@@ -28,6 +28,7 @@ JUnit version 4.11
 .testH5Pset_elink_fapl
 .testH5P_hyper_vector_size
 .testH5P_gc_references
+.testH5P_file_locking
 .testH5P_family_offset
 .testH5P_fapl_core
 .testH5P_fapl_muti
@@ -37,5 +38,5 @@ JUnit version 4.11
 
 Time:  XXXX
 
-OK (35 tests)
+OK (36 tests)