[svn-r30075] Description:

    Bring object/dataset/group/named datatype features from revise_chunks
branch to trunk.  Also CMake support for h5format_convert and a bunch of
misc. cleanups.

Tested on:
    MacOSX/64 10.11.5 (amazon) w/serial, parallel & production
    (h5committest forthcoming)

14 files changed, 332 insertions, 1 deletions

diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java
index e7f5fe8..e555a4f 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,
@@ -3289,6 +3314,32 @@ 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 //
@@ -4290,6 +4341,34 @@ 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 ////////
 
     // ////////////////////////////////////////////////////////////
@@ -9155,6 +9234,32 @@ 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 330752b..9bcbd5f 100644
--- a/java/src/jni/h5dImp.c
+++ b/java/src/jni/h5dImp.c
@@ -1779,6 +1779,33 @@ Java_hdf_hdf5lib_H5_H5Diterate
     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 a44d465..2a91334 100644
--- a/java/src/jni/h5dImp.h
+++ b/java/src/jni/h5dImp.h
@@ -348,6 +348,24 @@ 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 649ddde1..a2c0de0 100644
--- a/java/src/jni/h5gImp.c
+++ b/java/src/jni/h5gImp.c
@@ -260,6 +260,33 @@ Java_hdf_hdf5lib_H5_H5Gget_1info_1by_1idx
     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);
+} /* end Java_hdf_hdf5lib_H5_H5Gflush */
+
+/*
+ * 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);
+} /* end Java_hdf_hdf5lib_H5_H5Grefresh */
+
+
 
 #ifdef __cplusplus
 } /* end extern "C" */
diff --git a/java/src/jni/h5gImp.h b/java/src/jni/h5gImp.h
index 05c1e39..3113689 100644
--- a/java/src/jni/h5gImp.h
+++ b/java/src/jni/h5gImp.h
@@ -97,6 +97,24 @@ 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 21723b8..872bb4c 100644
--- a/java/src/jni/h5oImp.c
+++ b/java/src/jni/h5oImp.c
@@ -779,6 +779,33 @@ Java_hdf_hdf5lib_H5__1H5Oopen_1by_1idx
     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);
+} /* end Java_hdf_hdf5lib_H5_H5Oflush */
+
+/*
+ * 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);
+} /* end Java_hdf_hdf5lib_H5_H5Orefresh */
+
+
 
 #ifdef __cplusplus
 } /* end extern "C" */
diff --git a/java/src/jni/h5oImp.h b/java/src/jni/h5oImp.h
index 29e08e9..293dc2e 100644
--- a/java/src/jni/h5oImp.h
+++ b/java/src/jni/h5oImp.h
@@ -186,6 +186,24 @@ 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/h5tImp.c b/java/src/jni/h5tImp.c
index dc052bc..55e16f8 100644
--- a/java/src/jni/h5tImp.c
+++ b/java/src/jni/h5tImp.c
@@ -1640,6 +1640,31 @@ Java_hdf_hdf5lib_H5_H5Tconvert
     } /* 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 9e6779d..e614082 100644
--- a/java/src/jni/h5tImp.h
+++ b/java/src/jni/h5tImp.h
@@ -608,6 +608,24 @@ 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 */
diff --git a/java/test/JUnit-interface.txt b/java/test/JUnit-interface.txt
index 12e67ad..cbd93e0 100644
--- a/java/test/JUnit-interface.txt
+++ b/java/test/JUnit-interface.txt
@@ -105,7 +105,9 @@ JUnit version 4.11
 .testH5Gcreate_null
 .testH5Gget_info_by_idx_fileid
 .testH5Gclose_invalid
+.testH5Gflush_invalid
 .testH5Gopen_invalid
+.testH5Grefresh_invalid
 .testH5Gget_info_invalid
 .testH5Gcreate_invalid
 .testH5Gcreate_exists
@@ -232,9 +234,11 @@ JUnit version 4.11
 .testH5Tget_nmembers_invalid
 .testH5Tarray_create_value_null
 .testH5Tset_size_invalid
+.testH5Tflush_invalid
 .testH5Tenum_insert_invalid
 .testH5Tget_array_dims_null
 .testH5Tget_member_index_null
+.testH5Trefresh_invalid
 .testH5Tset_sign_invalid
 .testH5Tenum_insert_name_null
 .testH5Tequal_not
@@ -270,6 +274,8 @@ JUnit version 4.11
 .testH5Dvlen_reclaim_invalid
 .testH5Dopen_invalid
 .testH5Dclose_invalid
+.testH5Dflush_invalid
+.testH5Drefresh_invalid
 .testH5Dget_storage_size_invalid
 .testH5Dget_space_invalid
 .testH5Dopen_null
@@ -564,7 +570,9 @@ JUnit version 4.11
 .testH5Oset_comment_by_name_invalid
 .testH5Oopen_null
 .testH5Oclose_invalid
+.testH5Oflush_invalid
 .testH5Oget_comment_by_name_invalid
+.testH5Orefresh_invalid
 .testH5Ocopy_null_dest
 .testH5Olink_invalid
 .testH5Oget_info_by_idx_invalid
@@ -626,7 +634,7 @@ JUnit version 4.11
 
 Time:  XXXX
 
-OK (624 tests)
+OK (632 tests)
 
 HDF5-DIAG: Error detected in HDF5 (version (number)) thread (IDs):
   #000: (file name) line (number) in H5Fopen(): can't set access and transfer property lists
diff --git a/java/test/TestH5Dparams.java b/java/test/TestH5Dparams.java
index f056027..2cdd121 100644
--- a/java/test/TestH5Dparams.java
+++ b/java/test/TestH5Dparams.java
@@ -131,4 +131,14 @@ public class TestH5Dparams {
         H5.H5Dget_storage_size(-1);
     }
 
+    @Test(expected = HDF5LibraryException.class)
+    public void testH5Dflush_invalid() throws Throwable {
+        H5.H5Dflush(-1);
+    }
+
+    @Test(expected = HDF5LibraryException.class)
+    public void testH5Drefresh_invalid() throws Throwable {
+        H5.H5Drefresh(-1);
+    }
+
 }
diff --git a/java/test/TestH5Gbasic.java b/java/test/TestH5Gbasic.java
index 70acef4..b049e15 100644
--- a/java/test/TestH5Gbasic.java
+++ b/java/test/TestH5Gbasic.java
@@ -368,4 +368,14 @@ public class TestH5Gbasic {
         assertNotNull(info);
     }
 
+    @Test(expected = HDF5LibraryException.class)
+    public void testH5Gflush_invalid() throws Throwable {
+        H5.H5Gflush(-1);
+    }
+
+    @Test(expected = HDF5LibraryException.class)
+    public void testH5Grefresh_invalid() throws Throwable {
+        H5.H5Grefresh(-1);
+    }
+
 }
diff --git a/java/test/TestH5Oparams.java b/java/test/TestH5Oparams.java
index ced66f5..9398940 100644
--- a/java/test/TestH5Oparams.java
+++ b/java/test/TestH5Oparams.java
@@ -151,4 +151,14 @@ public class TestH5Oparams {
         H5.H5Oget_comment_by_name(-1, null, -1);
     }
 
+    @Test(expected = HDF5LibraryException.class)
+    public void testH5Oflush_invalid() throws Throwable {
+        H5.H5Oflush(-1);
+    }
+
+    @Test(expected = HDF5LibraryException.class)
+    public void testH5Orefresh_invalid() throws Throwable {
+        H5.H5Orefresh(-1);
+    }
+
 }
diff --git a/java/test/TestH5Tparams.java b/java/test/TestH5Tparams.java
index 15cc6af..4ebeea7 100644
--- a/java/test/TestH5Tparams.java
+++ b/java/test/TestH5Tparams.java
@@ -386,4 +386,14 @@ public class TestH5Tparams {
         H5.H5Tget_native_type(-1);
     }
 
+    @Test(expected = HDF5LibraryException.class)
+    public void testH5Tflush_invalid() throws Throwable {
+        H5.H5Tflush(-1);
+    }
+
+    @Test(expected = HDF5LibraryException.class)
+    public void testH5Trefresh_invalid() throws Throwable {
+        H5.H5Trefresh(-1);
+    }
+
 }