[svn-r29566] Merge from revise_chunks java changes in rev 29562, 29556, 29561, and add flush/refresh functions

11 files changed, 352 insertions, 10 deletions

diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java
index 7a14f8c..08589c2 100644
--- a/java/src/hdf/hdf5lib/H5.java
+++ b/java/src/hdf/hdf5lib/H5.java
@@ -2072,6 +2072,31 @@ public class H5 implements java.io.Serializable {
     public synchronized static native int H5Dwrite_VLStrings(long dataset_id, long mem_type_id, long mem_space_id,
             long file_space_id, long xfer_plist_id, Object[] buf) throws HDF5LibraryException, NullPointerException;
 
+    /**
+     * H5Dflush causes all buffers associated with a dataset to be immediately flushed to disk without removing the
+     * data from the cache.
+     *
+     * @param dset_id
+     *            IN: Identifier of the dataset to be flushed.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
+    public synchronized static native void H5Dflush(long dset_id) throws HDF5LibraryException;
+
+    /**
+     * H5Drefresh causes all buffers associated with a dataset to be cleared and immediately re-loaded with updated
+     * contents from disk. This function essentially closes the dataset, evicts all metadata associated with it
+     * from the cache, and then re-opens the dataset. The reopened dataset is automatically re-registered with the same ID.
+     *
+     * @param dset_id
+     *            IN: Identifier of the dataset to be refreshed.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
+    public synchronized static native void H5Drefresh(long dset_id) throws HDF5LibraryException;
+
     // /////// unimplemented ////////
     // H5_DLL herr_t H5Ddebug(hid_t dset_id);
     // herr_t H5Dgather(hid_t src_space_id, const void *src_buf, hid_t type_id,
@@ -3344,6 +3369,32 @@ public class H5 implements java.io.Serializable {
     private synchronized static native long _H5Gopen2(long loc_id, String name, long gapl_id)
             throws HDF5LibraryException, NullPointerException;
 
+    /**
+     * H5Gflush causes all buffers associated with a group to be immediately flushed to disk without
+     * removing the data from the cache.
+     *
+     * @param group_id
+     *            IN: Identifier of the group to be flushed.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
+    public synchronized static native void H5Gflush(long group_id) throws HDF5LibraryException;
+
+    /**
+     * H5Grefresh causes all buffers associated with a group to be cleared and immediately re-loaded
+     * with updated contents from disk. This function essentially closes the group, evicts all metadata
+     * associated with it from the cache, and then re-opens the group. The reopened group is automatically
+     * re-registered with the same ID.
+     *
+     * @param group_id
+     *            IN: Identifier of the group to be refreshed.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
+    public synchronized static native void H5Grefresh(long group_id) throws HDF5LibraryException;
+
     // ////////////////////////////////////////////////////////////
     // //
     // H5I: HDF5 1.8 Identifier Interface API Functions //
@@ -4347,6 +4398,34 @@ public class H5 implements java.io.Serializable {
     public synchronized static native long _H5Oopen_by_idx(long loc_id, String group_name,
             int idx_type, int order, long n, long lapl_id) throws HDF5LibraryException, NullPointerException;
 
+    /**
+     * H5Oflush causes all buffers associated with an object to be immediately flushed to disk without removing
+     * the data from the cache. object_id can be any named object associated with an HDF5 file including a
+     * dataset, a group, or a committed datatype.
+     *
+     * @param object_id
+     *            IN: Identifier of the object to be flushed.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
+    public synchronized static native void H5Oflush(long object_id) throws HDF5LibraryException;
+
+    /**
+     * H5Orefresh causes all buffers associated with an object to be cleared and immediately re-loaded with
+     * updated contents from disk. This function essentially closes the object, evicts all metadata associated
+     * with it from the cache, and then re-opens the object. The reopened object is automatically re-registered
+     * with the same ID. object_id can be any named object associated with an HDF5 file including a
+     * dataset, a group, or a committed datatype.
+     *
+     * @param object_id
+     *            IN: Identifier of the object to be refreshed.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
+    public synchronized static native void H5Orefresh(long object_id) throws HDF5LibraryException;
+
     // /////// unimplemented ////////
 
     // ////////////////////////////////////////////////////////////
@@ -5672,6 +5751,40 @@ public class H5 implements java.io.Serializable {
     public synchronized static native String H5Pget_mdc_log_options(long fapl_id, boolean[] mdc_log_options)
             throws HDF5LibraryException;
 
+    /**
+     * H5Pget_metadata_read_attempts retrieves the number of read attempts that is set in the file access property list plist_id.
+     *
+     * @param plist_id
+     *            IN: File access property list identifier
+     *
+     * @return The number of read attempts.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
+    public synchronized static native long H5Pget_metadata_read_attempts(long plist_id) throws HDF5LibraryException;
+
+    /**
+     * H5Pset_metadata_read_attempts sets the number of reads that the library will try when reading checksummed
+     * metadata in an HDF5 file opened with SWMR access. When reading such metadata, the library will compare the
+     * checksum computed for the metadata just read with the checksum stored within the piece of checksum. When
+     * performing SWMR operations on a file, the checksum check might fail when the library reads data on a system
+     * that is not atomic. To remedy such situations, the library will repeatedly read the piece of metadata until
+     * the check passes or finally fails the read when the allowed number of attempts is reached.
+     *
+     * @param plist_id
+     *            IN: File access property list identifier
+     * @param attempts
+     *            IN: The number of read attempts which is a value greater than 0.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
+    public synchronized static native void H5Pset_metadata_read_attempts(long plist_id, long attempts)
+            throws HDF5LibraryException;
+
     // Dataset creation property list (DCPL) routines //
 
     /**
@@ -9251,6 +9364,32 @@ public class H5 implements java.io.Serializable {
 
     private synchronized static native long _H5Tvlen_create(long base_id) throws HDF5LibraryException;
 
+    /**
+     * H5Tflush causes all buffers associated with a committed datatype to be immediately flushed to disk
+     * without removing the data from the cache.
+     *
+     * @param dtype_id
+     *            IN: Identifier of the committed datatype to be flushed.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
+    public synchronized static native void H5Tflush(long dtype_id) throws HDF5LibraryException;
+
+    /**
+     * H5Trefresh causes all buffers associated with a committed datatype to be cleared and immediately
+     * re-loaded with updated contents from disk. This function essentially closes the datatype, evicts
+     * all metadata associated with it from the cache, and then re-opens the datatype. The reopened datatype
+     * is automatically re-registered with the same ID.
+     *
+     * @param dtype_id
+     *            IN: Identifier of the committed datatype to be refreshed.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
+    public synchronized static native void H5Trefresh(long dtype_id) throws HDF5LibraryException;
+
     // /////// unimplemented ////////
 
     // H5T_conv_t H5Tfind(int src_id, int dst_id, H5T_cdata_t *pcdata);
diff --git a/java/src/jni/h5dImp.c b/java/src/jni/h5dImp.c
index f70cb5e..9e03051 100644
--- a/java/src/jni/h5dImp.c
+++ b/java/src/jni/h5dImp.c
@@ -1752,6 +1752,30 @@ Java_hdf_hdf5lib_H5_H5Diterate(JNIEnv *env, jclass clss, jbyteArray buf, jlong b
     return (jint)status;
 } /* end Java_hdf_hdf5lib_H5_H5Diterate */
 
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Dflush
+ * Signature: (J)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5Dflush(JNIEnv *env, jclass clss, jlong loc_id)
+{
+    if (H5Dflush((hid_t)loc_id) < 0)
+        h5libraryError(env);
+}
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Drefresh
+ * Signature: (J)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5Drefresh(JNIEnv *env, jclass clss, jlong loc_id)
+{
+    if (H5Drefresh((hid_t)loc_id) < 0)
+        h5libraryError(env);
+}
+
 
 #ifdef __cplusplus
 } /* end extern "C" */
diff --git a/java/src/jni/h5dImp.h b/java/src/jni/h5dImp.h
index 12078e8..0edabfc 100644
--- a/java/src/jni/h5dImp.h
+++ b/java/src/jni/h5dImp.h
@@ -312,6 +312,22 @@ JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5Dset_1extent
 JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5Diterate
   (JNIEnv*, jclass, jbyteArray, jlong, jlong, jobject, jobject);
 
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Dflush
+ * Signature: (J)V
+ */
+JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5Dflush
+  (JNIEnv*, jclass, jlong);
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Drefresh
+ * Signature: (J)V
+ */
+JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5Drefresh
+  (JNIEnv*, jclass, jlong);
+
 #ifdef __cplusplus
 } /* end extern "C" */
 #endif /* __cplusplus */
diff --git a/java/src/jni/h5gImp.c b/java/src/jni/h5gImp.c
index 632942a..eab0b02 100644
--- a/java/src/jni/h5gImp.c
+++ b/java/src/jni/h5gImp.c
@@ -251,6 +251,30 @@ Java_hdf_hdf5lib_H5_H5Gget_1info_1by_1idx(JNIEnv *env, jclass cls, jlong loc_id,
     return create_H5G_info_t(env, group_info);
 } /* end Java_hdf_hdf5lib_H5_H5Gget_1info_1by_1idx */
 
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Gflush
+ * Signature: (J)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5Gflush(JNIEnv *env, jclass clss, jlong loc_id)
+{
+    if (H5Gflush((hid_t)loc_id) < 0)
+        h5libraryError(env);
+}
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Grefresh
+ * Signature: (J)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5Grefresh(JNIEnv *env, jclass clss, jlong loc_id)
+{
+    if (H5Grefresh((hid_t)loc_id) < 0)
+        h5libraryError(env);
+}
+
 
 #ifdef __cplusplus
 } /* end extern "C" */
diff --git a/java/src/jni/h5gImp.h b/java/src/jni/h5gImp.h
index 2b9bc57..e413652 100644
--- a/java/src/jni/h5gImp.h
+++ b/java/src/jni/h5gImp.h
@@ -89,6 +89,22 @@ JNIEXPORT jobject JNICALL Java_hdf_hdf5lib_H5_H5Gget_1info_1by_1name
 JNIEXPORT jobject JNICALL Java_hdf_hdf5lib_H5_H5Gget_1info_1by_1idx
   (JNIEnv*, jclass, jlong, jstring, jint, jint, jlong, jlong);
 
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Gflush
+ * Signature: (J)V
+ */
+JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5Gflush
+  (JNIEnv*, jclass, jlong);
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Grefresh
+ * Signature: (J)V
+ */
+JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5Grefresh
+  (JNIEnv*, jclass, jlong);
+
 #ifdef __cplusplus
 } /* end extern "C" */
 #endif /* __cplusplus */
diff --git a/java/src/jni/h5oImp.c b/java/src/jni/h5oImp.c
index c38ec9a..60130fc 100644
--- a/java/src/jni/h5oImp.c
+++ b/java/src/jni/h5oImp.c
@@ -760,6 +760,30 @@ Java_hdf_hdf5lib_H5__1H5Oopen_1by_1idx(JNIEnv *env, jclass clss, jlong loc_id, j
     return (jlong)retVal;
 } /* end Java_hdf_hdf5lib_H5__1H5Oopen_1by_1idx */
 
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Oflush
+ * Signature: (J)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5Oflush(JNIEnv *env, jclass clss, jlong loc_id)
+{
+    if (H5Oflush((hid_t)loc_id) < 0)
+        h5libraryError(env);
+}
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Orefresh
+ * Signature: (J)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5Orefresh(JNIEnv *env, jclass clss, jlong loc_id)
+{
+    if (H5Orefresh((hid_t)loc_id) < 0)
+        h5libraryError(env);
+}
+
 
 #ifdef __cplusplus
 } /* end extern "C" */
diff --git a/java/src/jni/h5oImp.h b/java/src/jni/h5oImp.h
index e6889b2..a404145 100644
--- a/java/src/jni/h5oImp.h
+++ b/java/src/jni/h5oImp.h
@@ -168,6 +168,22 @@ extern "C" {
     JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5__1H5Oopen_1by_1idx
       (JNIEnv*, jclass, jlong, jstring, jint, jint, jlong, jlong);
 
+    /*
+     * Class:     hdf_hdf5lib_H5
+     * Method:    H5Oflush
+     * Signature: (J)V
+     */
+    JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5Oflush
+      (JNIEnv*, jclass, jlong);
+
+    /*
+     * Class:     hdf_hdf5lib_H5
+     * Method:    H5Orefresh
+     * Signature: (J)V
+     */
+    JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5Orefresh
+      (JNIEnv*, jclass, jlong);
+
 #ifdef __cplusplus
 } /* end extern "C" */
 #endif /* __cplusplus */
diff --git a/java/src/jni/h5pImp.c b/java/src/jni/h5pImp.c
index 8ecd81c..5181672 100644
--- a/java/src/jni/h5pImp.c
+++ b/java/src/jni/h5pImp.c
@@ -2965,16 +2965,10 @@ Java_hdf_hdf5lib_H5_H5Pset_1elink_1acc_1flags(JNIEnv *env, jclass clss, jlong la
 {
     herr_t retVal = -1;
 
-    if (((unsigned) flags != H5F_ACC_RDWR) &&
-            ((unsigned) flags != H5F_ACC_RDONLY) &&
-            ((unsigned) flags != H5F_ACC_DEFAULT)) {
-        h5badArgument(env, "H5Pset_elink_acc_flags: invalid flags value");
-    } /* end if */
-    else {
-        retVal = H5Pset_elink_acc_flags((hid_t)lapl_id, (unsigned)flags);
-        if (retVal < 0)
-            h5libraryError(env);
-    } /* end else */
+    retVal = H5Pset_elink_acc_flags((hid_t)lapl_id, (unsigned)flags);
+    if (retVal < 0)
+        h5libraryError(env);
+
     return (jint) retVal;
 } /* end Java_hdf_hdf5lib_H5_H5Pset_1elink_1acc_1flags */
 
@@ -5501,6 +5495,38 @@ Java_hdf_hdf5lib_H5_H5Piterate(JNIEnv *env, jclass clss, jlong prop_id, jintArra
     return status;
 } /* end Java_hdf_hdf5lib_H5_H5Piterate */
 
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pget_metadata_read_attempts
+ * Signature: (J)J
+ */
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_H5_H5Pget_1metadata_1read_1attempts(JNIEnv *env, jclass clss, jlong plist_id)
+{
+    unsigned attempts;
+    if (H5Pget_metadata_read_attempts((hid_t)plist_id, &attempts) < 0)
+        h5libraryError(env);
+
+    return (jlong) attempts;
+} /* end Java_hdf_hdf5lib_H5_H5Pget_1metadata_1read_1attempts */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pset_metadata_read_attempts
+ * Signature: (JJ)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5Pset_1metadata_1read_1attempts(JNIEnv *env, jclass clss, jlong plist_id, jlong attempts)
+{
+     if (attempts <= 0) {
+         h5badArgument(env, "H5Pset_metadata_read_attempts:  attempts <= 0");
+     } /* end if */
+     else {
+        if(H5Pset_metadata_read_attempts((hid_t)plist_id, (unsigned)attempts) < 0)
+            h5libraryError(env);
+     } /* end else */
+} /* end Java_hdf_hdf5lib_H5_H5Pset_1metadata_1read_1attempts */
+
 #ifdef __cplusplus
 } /* end extern "C" */
 #endif /* __cplusplus */
diff --git a/java/src/jni/h5pImp.h b/java/src/jni/h5pImp.h
index a06a64f..997a8f1 100644
--- a/java/src/jni/h5pImp.h
+++ b/java/src/jni/h5pImp.h
@@ -1329,6 +1329,23 @@ JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5Pinsert2
 JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5Piterate
   (JNIEnv*, jclass, jlong, jintArray, jobject, jobject);
 
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pget_metadata_read_attempts
+ * Signature: (J)J
+ */
+JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5_H5Pget_1metadata_1read_1attempts
+(JNIEnv *, jclass, jlong);
+
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pset_metadata_read_attempts
+ * Signature: (JJ)V
+ */
+JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5Pset_1metadata_1read_1attempts
+(JNIEnv *, jclass, jlong, jlong);
+
 
 #ifdef __cplusplus
 } /* end extern "C" */
diff --git a/java/src/jni/h5tImp.c b/java/src/jni/h5tImp.c
index 1f587de..7280aed 100644
--- a/java/src/jni/h5tImp.c
+++ b/java/src/jni/h5tImp.c
@@ -1582,6 +1582,30 @@ Java_hdf_hdf5lib_H5_H5Tconvert(JNIEnv *env, jclass clss, jlong src_id, jlong dst
     } /* end else */
 } /* end Java_hdf_hdf5lib_H5_H5Tconvert */
 
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Tflush
+ * Signature: (J)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5Tflush(JNIEnv *env, jclass clss, jlong loc_id)
+{
+    if (H5Tflush((hid_t)loc_id) < 0)
+        h5libraryError(env);
+}
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Trefresh
+ * Signature: (J)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5Trefresh(JNIEnv *env, jclass clss, jlong loc_id)
+{
+    if (H5Trefresh((hid_t)loc_id) < 0)
+        h5libraryError(env);
+}
+
 
 #ifdef __cplusplus
 } /* end extern "C" */
diff --git a/java/src/jni/h5tImp.h b/java/src/jni/h5tImp.h
index 9755a91..edaca2f 100644
--- a/java/src/jni/h5tImp.h
+++ b/java/src/jni/h5tImp.h
@@ -543,6 +543,22 @@ JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5Tget_1array_1dims2
 JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5Tconvert
   (JNIEnv *, jclass, jlong, jlong, jlong, jbyteArray, jbyteArray, jlong);
 
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Tflush
+ * Signature: (J)V
+ */
+JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5Tflush
+  (JNIEnv*, jclass, jlong);
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Trefresh
+ * Signature: (J)V
+ */
+JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5Trefresh
+  (JNIEnv*, jclass, jlong);
+
 #ifdef __cplusplus
 } /* end extern "C" */
 #endif /* __cplusplus */