Merge pull request #840 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to develop

* commit '17b8f0bb936633f01bf6deba247e37bcadbc6b82':
  Fix valgrind issues
  HDFFV-9724 init var to null
  HDFFV-9724 add valgrind ENV
  Fix memory leak due to addition of FORMAT check loop
  HDFFV-9724 prefix of 0 length should be null value
  HDFFV-9724 Corrected files and verified tests
  Add library INTERFACE and MPI to tools

4 files changed, 286 insertions, 2 deletions

diff --git a/java/src/jni/CMakeLists.txt b/java/src/jni/CMakeLists.txt
index 9e6c099..10d1b6d 100644
--- a/java/src/jni/CMakeLists.txt
+++ b/java/src/jni/CMakeLists.txt
@@ -51,7 +51,7 @@ set (CMAKE_INCLUDE_CURRENT_DIR_IN_INTERFACE ON)
 ########### JNI libraries always must be built shared  ###############
 add_library (${HDF5_JAVA_JNI_LIB_TARGET} SHARED ${HDF5_JAVA_JNI_CSRCS} ${HDF5_JAVA_JNI_CHDRS})
 TARGET_C_PROPERTIES (${HDF5_JAVA_JNI_LIB_TARGET} SHARED " " " ")
-target_link_libraries (${HDF5_JAVA_JNI_LIB_TARGET} ${HDF5_LIB_TARGET})
+target_link_libraries (${HDF5_JAVA_JNI_LIB_TARGET} PUBLIC ${HDF5_LIB_TARGET})
 set_target_properties (${HDF5_JAVA_JNI_LIB_TARGET} PROPERTIES FOLDER libraries/jni)
 SET_GLOBAL_VARIABLE (HDF5_LIBRARIES_TO_EXPORT "${HDF5_LIBRARIES_TO_EXPORT};${HDF5_JAVA_JNI_LIB_TARGET}")
 H5_SET_LIB_OPTIONS (${HDF5_JAVA_JNI_LIB_TARGET} ${HDF5_JAVA_JNI_LIB_NAME} SHARED ${HDF5_JAVA_PACKAGE_SOVERSION})
diff --git a/java/src/jni/h5Constants.c b/java/src/jni/h5Constants.c
index f6f8bfa..5a4b53e 100644
--- a/java/src/jni/h5Constants.c
+++ b/java/src/jni/h5Constants.c
@@ -140,6 +140,8 @@ JNIEXPORT jint JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5D_1VDS_1FIRST_1MISSING(JNIEnv *env, jclass cls) { return H5D_VDS_FIRST_MISSING; }
 JNIEXPORT jint JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5D_1VDS_1LAST_1AVAILABLE(JNIEnv *env, jclass cls) { return H5D_VDS_LAST_AVAILABLE; }
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5D_1CHUNK_1DONT_1FILTER_1PARTIAL_1CHUNKS(JNIEnv *env, jclass cls) { return H5D_CHUNK_DONT_FILTER_PARTIAL_CHUNKS; }
 
 JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5E_1ALIGNMENT(JNIEnv *env, jclass cls) { return H5E_ALIGNMENT; }
diff --git a/java/src/jni/h5pImp.c b/java/src/jni/h5pImp.c
index dcfcd82..cf27341 100644
--- a/java/src/jni/h5pImp.c
+++ b/java/src/jni/h5pImp.c
@@ -5733,6 +5733,217 @@ Java_hdf_hdf5lib_H5_H5Pset_1metadata_1read_1attempts
      } /* end else */
 } /* end Java_hdf_hdf5lib_H5_H5Pset_1metadata_1read_1attempts */
 
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pset_virtual_prefix
+ * Signature: (JLjava/lang/String;)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5Pset_1virtual_1prefix
+    (JNIEnv *env, jclass clss, jlong dapl_id, jstring prefix)
+{
+    herr_t      retVal = -1;
+    const char *aName;
+
+    PIN_JAVA_STRING(prefix, aName);
+    if (aName != NULL) {
+        retVal = H5Pset_virtual_prefix((hid_t)dapl_id, aName);
+
+        UNPIN_JAVA_STRING(prefix, aName);
+
+        if(retVal < 0)
+            h5libraryError(env);
+    }
+} /* end Java_hdf_hdf5lib_H5_H5Pset_1virtual_1prefix */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pget_virtual_prefix
+ * Signature: (J)Ljava/lang/String;
+ */
+JNIEXPORT jstring JNICALL
+Java_hdf_hdf5lib_H5_H5Pget_1virtual_1prefix
+    (JNIEnv *env, jclass clss, jlong dapl_id)
+{
+    size_t  size = 0;
+    char   *pre;
+    jlong   prefix_size = -1;
+    jstring str = NULL;
+
+    prefix_size = (jlong)H5Pget_virtual_prefix((hid_t)dapl_id, (char*)NULL, size);
+    if(prefix_size < 0) {
+        h5libraryError(env);
+    } /* end if */
+    else {
+        size = (size_t)prefix_size + 1;/* add extra space for the null terminator */
+        pre = (char*)HDmalloc(sizeof(char)*size);
+        if (pre == NULL) {
+            h5outOfMemory(env, "H5Pget_virtual_prefix:  malloc failed ");
+        } /* end if */
+        else {
+            prefix_size = (jlong)H5Pget_virtual_prefix((hid_t)dapl_id, (char*)pre, size);
+
+            if (prefix_size >= 0) {
+                str = ENVPTR->NewStringUTF(ENVPAR pre);
+                HDfree(pre);
+                if (str == NULL)
+                    h5JNIFatalError( env, "H5Pget_virtual_prefix:  return string not allocated");
+            } /* end if */
+            else {
+                HDfree(pre);
+                h5libraryError(env);
+            } /* end else */
+        } /* end else */
+    } /* end else */
+
+    return (jstring)str;
+} /* end Java_hdf_hdf5lib_H5_H5Pget_1virtual_1prefix */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pset_efile_prefix
+ * Signature: (JLjava/lang/String;)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5Pset_1efile_1prefix
+    (JNIEnv *env, jclass clss, jlong dapl_id, jstring prefix)
+{
+    herr_t      retVal = -1;
+    const char *aName;
+
+    PIN_JAVA_STRING(prefix, aName);
+    if (aName != NULL) {
+        retVal = H5Pset_efile_prefix((hid_t)dapl_id, aName);
+
+        UNPIN_JAVA_STRING(prefix, aName);
+
+        if(retVal < 0)
+            h5libraryError(env);
+    }
+} /* end Java_hdf_hdf5lib_H5_H5Pset_1efile_1prefix */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pget_efile_prefix
+ * Signature: (J)Ljava/lang/String;
+ */
+JNIEXPORT jstring JNICALL
+Java_hdf_hdf5lib_H5_H5Pget_1efile_1prefix
+    (JNIEnv *env, jclass clss, jlong dapl_id)
+{
+    size_t  size = 0;
+    char   *pre;
+    jlong   prefix_size = -1;
+    jstring str = NULL;
+
+    prefix_size = (jlong)H5Pget_efile_prefix((hid_t)dapl_id, (char*)NULL, size);
+    if(prefix_size < 0) {
+        h5libraryError(env);
+    } /* end if */
+    else {
+        size = (size_t)prefix_size + 1;/* add extra space for the null terminator */
+        pre = (char*)HDmalloc(sizeof(char)*size);
+        if (pre == NULL) {
+            h5outOfMemory(env, "H5Pget_efile_prefix:  malloc failed ");
+        } /* end if */
+        else {
+            prefix_size = (jlong)H5Pget_efile_prefix((hid_t)dapl_id, (char*)pre, size);
+
+            if (prefix_size >= 0) {
+                str = ENVPTR->NewStringUTF(ENVPAR pre);
+                HDfree(pre);
+                if (str == NULL)
+                    h5JNIFatalError( env, "H5Pget_efile_prefix:  return string not allocated");
+            } /* end if */
+            else {
+                HDfree(pre);
+                h5libraryError(env);
+            } /* end else */
+        } /* end else */
+    } /* end else */
+
+    return (jstring)str;
+} /* end Java_hdf_hdf5lib_H5_H5Pget_1efile_1prefix */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pset_evict_on_close
+ * Signature: (JZ)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5Pset_1evict_1on_1close
+    (JNIEnv *env, jclass clss, jlong fapl_id, jboolean evict_on_close)
+{
+    herr_t   retVal = -1;
+    hbool_t  evict_on_close_val;
+
+    if (evict_on_close == JNI_TRUE)
+        evict_on_close_val = TRUE;
+    else
+        evict_on_close_val = FALSE;
+
+    retVal = H5Pset_evict_on_close((hid_t)fapl_id, (hbool_t)evict_on_close_val);
+    if (retVal < 0)
+        h5libraryError(env);
+} /* end Java_hdf_hdf5lib_H5_H5Pset_1evict_1on_1close */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pget_evict_on_close
+ * Signature: (J)Z
+ */
+JNIEXPORT jboolean JNICALL
+Java_hdf_hdf5lib_H5_H5Pget_1evict_1on_1close
+    (JNIEnv *env, jclass clss, jlong fapl_id)
+{
+    hbool_t   evict_on_close_val = FALSE;
+    jboolean  bval = JNI_FALSE;
+
+    if (H5Pget_evict_on_close((hid_t)fapl_id, (hbool_t *)&evict_on_close_val) < 0) {
+        h5libraryError(env);
+    } /* end if */
+    else {
+        if (evict_on_close_val == TRUE)
+            bval =  JNI_TRUE;
+    } /* end else */
+
+    return bval;
+} /* end Java_hdf_hdf5lib_H5_H5Pget_1evict_1on_1close */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pset_chunk_opts
+ * Signature: (JI)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5Pset_1chunk_1opts
+    (JNIEnv *env, jclass clss, jlong dcpl_id, jint opts)
+{
+    herr_t   retVal = -1;
+
+    retVal = H5Pset_chunk_opts((hid_t)dcpl_id, (unsigned)opts);
+    if (retVal < 0)
+        h5libraryError(env);
+} /* end Java_hdf_hdf5lib_H5_H5Pset_1chunk_1opts */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pget_chunk_opts
+ * Signature: (J)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Pget_1chunk_1opts
+    (JNIEnv *env, jclass clss, jlong dcpl_id)
+{
+    unsigned   opts = 0;
+
+    if (H5Pget_chunk_opts((hid_t)dcpl_id, opts) < 0)
+        h5libraryError(env);
+
+    return (jint)opts;
+} /* end Java_hdf_hdf5lib_H5_H5Pget_1chunk_1opts */
+
 #ifdef __cplusplus
 } /* end extern "C" */
 #endif /* __cplusplus */
diff --git a/java/src/jni/h5pImp.h b/java/src/jni/h5pImp.h
index d413f69..1d12e3d 100644
--- a/java/src/jni/h5pImp.h
+++ b/java/src/jni/h5pImp.h
@@ -1533,7 +1533,6 @@ JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_H5_H5Pget_1metadata_1read_1attempts
 (JNIEnv *, jclass, jlong);
 
-
 /*
  * Class:     hdf_hdf5lib_H5
  * Method:    H5Pset_metadata_read_attempts
@@ -1543,6 +1542,78 @@ JNIEXPORT void JNICALL
 Java_hdf_hdf5lib_H5_H5Pset_1metadata_1read_1attempts
 (JNIEnv *, jclass, jlong, jlong);
 
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pset_virtual_prefix
+ * Signature: (JLjava/lang/String;)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5Pset_1virtual_1prefix
+(JNIEnv *, jclass, jlong, jstring);
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pget_virtual_prefix
+ * Signature: (J)Ljava/lang/String;
+ */
+JNIEXPORT jstring JNICALL
+Java_hdf_hdf5lib_H5_H5Pget_1virtual_1prefix
+(JNIEnv *, jclass, jlong);
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pset_efile_prefix
+ * Signature: (JLjava/lang/String;)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5Pset_1efile_1prefix
+(JNIEnv *, jclass, jlong, jstring);
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pget_efile_prefix
+ * Signature: (J)Ljava/lang/String;
+ */
+JNIEXPORT jstring JNICALL
+Java_hdf_hdf5lib_H5_H5Pget_1efile_1prefix
+(JNIEnv *, jclass, jlong);
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pset_evict_on_close
+ * Signature: (JZ)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5Pset_1evict_1on_1close
+(JNIEnv *, jclass, jlong, jboolean);
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pget_evict_on_close
+ * Signature: (J)Z
+ */
+JNIEXPORT jboolean JNICALL
+Java_hdf_hdf5lib_H5_H5Pget_1evict_1on_1close
+(JNIEnv *, jclass, jlong);
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pset_chunk_opts
+ * Signature: (JI)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5Pset_1chunk_1opts
+(JNIEnv *, jclass, jlong, jint);
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pget_chunk_opts
+ * Signature: (J)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Pget_1chunk_1opts
+(JNIEnv *, jclass, jlong);
+
 
 #ifdef __cplusplus
 } /* end extern "C" */