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authorAllen Byrne <byrn@hdfgroup.org>2019-11-07 15:48:56 (GMT)
committerAllen Byrne <byrn@hdfgroup.org>2019-11-07 15:49:11 (GMT)
commit6b927a773c83bedc111dcd2ad38805f974660b15 (patch)
tree5f836ff5409d5265161b058e75f4d806c8afff1d /java/src/hdf
parent2dd5bbfe167e3e9b6b6ee657a882e24072de4aeb (diff)
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HDFFV-10876 Update h5dump and h5ls for new ref api.
Diffstat (limited to 'java/src/hdf')
-rw-r--r--java/src/hdf/hdf5lib/H5.java331
-rw-r--r--java/src/hdf/hdf5lib/HDF5Constants.java22
2 files changed, 348 insertions, 5 deletions
diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java
index 09fb223..01c18dc 100644
--- a/java/src/hdf/hdf5lib/H5.java
+++ b/java/src/hdf/hdf5lib/H5.java
@@ -1107,7 +1107,9 @@ public class H5 implements java.io.Serializable {
log.trace("H5Aread_dname_D");
status = H5Aread_double(attr_id, mem_type_id, (double[]) obj, isCriticalPinning);
}
- else if ((H5.H5Tdetect_class(mem_type_id, HDF5Constants.H5T_REFERENCE) && (is1D && (dataClass.getComponentType() == String.class))) || H5.H5Tequal(mem_type_id, HDF5Constants.H5T_STD_REF_DSETREG)) {
+ else if ((H5.H5Tdetect_class(mem_type_id, HDF5Constants.H5T_REFERENCE) &&
+ (is1D && (dataClass.getComponentType() == String.class))) ||
+ H5.H5Tequal(mem_type_id, HDF5Constants.H5T_STD_REF_DSETREG)) {
log.trace("H5Aread_reg_ref");
status = H5Aread_reg_ref(attr_id, mem_type_id, (String[]) obj);
}
@@ -2005,7 +2007,9 @@ public class H5 implements java.io.Serializable {
status = H5Dread_double(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id,
(double[]) obj, isCriticalPinning);
}
- else if ((H5.H5Tdetect_class(mem_type_id, HDF5Constants.H5T_REFERENCE) && (is1D && (dataClass.getComponentType() == String.class))) || H5.H5Tequal(mem_type_id, HDF5Constants.H5T_STD_REF_DSETREG)) {
+ else if ((H5.H5Tdetect_class(mem_type_id, HDF5Constants.H5T_REFERENCE) &&
+ (is1D && (dataClass.getComponentType() == String.class))) ||
+ H5.H5Tequal(mem_type_id, HDF5Constants.H5T_STD_REF_DSETREG)) {
log.trace("H5Dread_reg_ref");
status = H5Dread_reg_ref(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id,
(String[]) obj);
@@ -8095,6 +8099,325 @@ public class H5 implements java.io.Serializable {
// ////////////////////////////////////////////////////////////
// //
+ // H5R: HDF5 1.12 Reference API Functions //
+ // //
+ // ////////////////////////////////////////////////////////////
+
+ // Constructors //
+
+ /**
+ * H5Rcreate_object creates a reference pointing to the object named name located at loc id.
+ *
+ * @param loc_id
+ * IN: Location identifier used to locate the object being pointed to.
+ * @param name
+ * IN: Name of object at location loc_id.
+ *
+ * @return the reference (byte[]) if successful
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ * @exception NullPointerException
+ * - an input array is null.
+ * @exception IllegalArgumentException
+ * - an input array is invalid.
+ **/
+ public synchronized static native byte[] H5Rcreate_object(long loc_id, String name)
+ throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
+
+ /**
+ * H5Rcreate_region creates the reference, pointing to the region represented by
+ * space id within the object named name located at loc id.
+ *
+ * @param loc_id
+ * IN: Location identifier used to locate the object being pointed to.
+ * @param name
+ * IN: Name of object at location loc_id.
+ * @param space_id
+ * IN: Identifies the dataset region that a dataset region reference points to.
+ *
+ * @return the reference (byte[]) if successful
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ * @exception NullPointerException
+ * - an input array is null.
+ * @exception IllegalArgumentException
+ * - an input array is invalid.
+ **/
+ public synchronized static native byte[] H5Rcreate_region(long loc_id, String name, long space_id)
+ throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
+
+ /**
+ * H5Rcreate_attr creates the reference, pointing to the attribute named attr name
+ * and attached to the object named name located at loc id.
+ *
+ * @param loc_id
+ * IN: Location identifier used to locate the object being pointed to.
+ * @param name
+ * IN: Name of object at location loc_id.
+ * @param attr_name
+ * IN: Name of the attribute within the object.
+ *
+ * @return the reference (byte[]) if successful
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ * @exception NullPointerException
+ * - an input array is null.
+ * @exception IllegalArgumentException
+ * - an input array is invalid.
+ **/
+ public synchronized static native byte[] H5Rcreate_attr(long loc_id, String name, String attr_name)
+ throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
+
+ /**
+ * H5Rdestroy destroys a reference and releases resources.
+ *
+ * @param ref_ptr
+ * IN: Reference to an object, region or attribute attached to an object.
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ * @exception NullPointerException
+ * - an input array is null.
+ * @exception IllegalArgumentException
+ * - an input array is invalid.
+ **/
+ public synchronized static native void H5Rdestroy(byte[] ref_ptr)
+ throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
+
+ // Info //
+
+ /**
+ * H5Rget_type retrieves the type of a reference.
+ *
+ * @param ref_ptr
+ * IN: Reference to an object, region or attribute attached to an object.
+ *
+ * @return a valid reference type if successful; otherwise returns H5R UNKNOWN.
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ * @exception NullPointerException
+ * - an input array is null.
+ * @exception IllegalArgumentException
+ * - an input array is invalid.
+ **/
+ public synchronized static native int H5Rget_type(byte[] ref_ptr)
+ throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
+
+ /**
+ * H5Requal determines whether two references point to the same object, region or attribute.
+ *
+ * @param ref1_ptr
+ * IN: Reference to an object, region or attribute attached to an object.
+ * @param ref2_ptr
+ * IN: Reference to an object, region or attribute attached to an object.
+ *
+ * @return true if equal, else false
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ * @exception NullPointerException
+ * - an input array is null.
+ * @exception IllegalArgumentException
+ * - an input array is invalid.
+ **/
+ public synchronized static native boolean H5Requal(byte[] ref1_ptr, byte[] ref2_ptr)
+ throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
+
+ /**
+ * H5Rcopy creates a copy of an existing reference.
+ *
+ * @param src_ref_ptr
+ * IN: Reference to an object, region or attribute attached to an object.
+ *
+ * @return a valid copy of the reference (byte[]) if successful.
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ * @exception NullPointerException
+ * - an input array is null.
+ * @exception IllegalArgumentException
+ * - an input array is invalid.
+ **/
+ public synchronized static native byte[] H5Rcopy(byte[] src_ref_ptr)
+ throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
+
+ // Dereference //
+
+ /**
+ * H5Ropen_object opens that object and returns an identifier.
+ * The object opened with this function should be closed when it is no longer needed
+ * so that resource leaks will not develop. Use the appropriate close function such
+ * as H5Oclose or H5Dclose for datasets.
+ *
+ * @param ref_ptr
+ * IN: Reference to an object, region or attribute attached to an object.
+ * @param rapl_id
+ * IN: A reference access property list identifier for the reference. The access property
+ * list can be used to access external files that the reference points
+ * to (through a file access property list).
+ * @param oapl_id
+ * IN: An object access property list identifier for the reference. The access property
+ * property list must be of the same type as the object being referenced,
+ * that is a group or dataset property list.
+ *
+ * @return a valid identifier if successful
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ * @exception NullPointerException
+ * - an input array is null.
+ * @exception IllegalArgumentException
+ * - an input array is invalid.
+ **/
+ public synchronized static native long H5Ropen_object(byte[] ref_ptr, long rapl_id, long oapl_id)
+ throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
+
+ /**
+ * H5Ropen region creates a copy of the dataspace of the dataset pointed to by a region reference,
+ * ref ptr, and defines a selection matching the selection pointed to by ref ptr within the dataspace copy.
+ * Use H5Sclose to release the dataspace identifier returned by this function when the identifier is no longer needed.
+ *
+ * @param ref_ptr
+ * IN: Reference to an object, region or attribute attached to an object.
+ * @param rapl_id
+ * IN: A reference access property list identifier for the reference. The access property
+ * list can be used to access external files that the reference points
+ * to (through a file access property list).
+ * @param oapl_id
+ * IN: An object access property list identifier for the reference. The access property
+ * property list must be of the same type as the object being referenced,
+ * that is a group or dataset property list.
+ *
+ * @return a valid dataspace identifier if successful
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ * @exception NullPointerException
+ * - an input array is null.
+ * @exception IllegalArgumentException
+ * - an input array is invalid.
+ **/
+ public synchronized static native long H5Ropen_region(byte[] ref_ptr, long rapl_id, long oapl_id)
+ throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
+
+ /**
+ * H5Ropen_attr opens the attribute attached to the object and returns an identifier.
+ * The attribute opened with this function should be closed with H5Aclose when it is no longer needed
+ * so that resource leaks will not develop.
+ *
+ * @param ref_ptr
+ * IN: Reference to an object, region or attribute attached to an object.
+ * @param rapl_id
+ * IN: A reference access property list identifier for the reference. The access property
+ * list can be used to access external files that the reference points
+ * to (through a file access property list).
+ * @param aapl_id
+ * IN: An attribute access property list identifier for the reference. The access property
+ * property list must be of the same type as the object being referenced,
+ * that is a group or dataset property list.
+ *
+ * @return a valid attribute identifier if successful
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ * @exception NullPointerException
+ * - an input array is null.
+ * @exception IllegalArgumentException
+ * - an input array is invalid.
+ **/
+ public synchronized static native long H5Ropen_attr(byte[] ref_ptr, long rapl_id, long aapl_id)
+ throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
+
+ // Get type //
+
+ /**
+ * H5Rget obj type3 retrieves the type of the referenced object pointed to.
+ *
+ * @param ref_ptr
+ * IN: Reference to an object, region or attribute attached to an object.
+ * @param rapl_id
+ * IN: A reference access property list identifier for the reference. The access property
+ * list can be used to access external files that the reference points
+ * to (through a file access property list).
+ *
+ * @return Returns the object type
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ * @exception NullPointerException
+ * - array is null.
+ * @exception IllegalArgumentException
+ * - array is invalid.
+ **/
+ public synchronized static native int H5Rget_obj_type3(byte[] ref_ptr, long rapl_id)
+ throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
+
+ // Get name //
+
+ /**
+ * H5Rget_file_name retrieves the file name for the object, region or attribute reference pointed to.
+ *
+ * @param ref_ptr
+ * IN: Reference to an object, region or attribute attached to an object.
+ *
+ * @return Returns the file name of the reference
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ * @exception NullPointerException
+ * - array is null.
+ * @exception IllegalArgumentException
+ * - array is invalid.
+ **/
+ public synchronized static native String H5Rget_file_name(byte[] ref_ptr)
+ throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
+
+ /**
+ * H5Rget_obj_name retrieves the object name for the object, region or attribute reference pointed to.
+ *
+ * @param ref_ptr
+ * IN: Reference to an object, region or attribute attached to an object.
+ * @param rapl_id
+ * IN: A reference access property list identifier for the reference. The access property
+ * list can be used to access external files that the reference points
+ * to (through a file access property list).
+ *
+ * @return Returns the object name of the reference
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ * @exception NullPointerException
+ * - array is null.
+ * @exception IllegalArgumentException
+ * - array is invalid.
+ **/
+ public synchronized static native String H5Rget_obj_name(byte[] ref_ptr, long rapl_id)
+ throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
+
+ /**
+ * H5Rget_attr_name retrieves the attribute name for the object, region or attribute reference pointed to.
+ *
+ * @param ref_ptr
+ * IN: Reference to an object, region or attribute attached to an object.
+ *
+ * @return Returns the attribute name of the reference
+ *
+ * @exception HDF5LibraryException
+ * - Error from the HDF-5 Library.
+ * @exception NullPointerException
+ * - array is null.
+ * @exception IllegalArgumentException
+ * - array is invalid.
+ **/
+ public synchronized static native String H5Rget_attr_name(byte[] ref_ptr)
+ throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
+
+ // ////////////////////////////////////////////////////////////
+ // //
// H5R: HDF5 1.8 Reference API Functions //
// //
// ////////////////////////////////////////////////////////////
@@ -10328,14 +10651,12 @@ public class H5 implements java.io.Serializable {
* @param buf
* Buffer with data to be reclaimed.
*
- * @return a non-negative value if successful
- *
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - buf is null.
**/
- public synchronized static native int H5Treclaim(long type_id, long space_id, long xfer_plist_id, byte[] buf)
+ public synchronized static native void H5Treclaim(long type_id, long space_id, long xfer_plist_id, byte[] buf)
throws HDF5LibraryException, NullPointerException;
/**
diff --git a/java/src/hdf/hdf5lib/HDF5Constants.java b/java/src/hdf/hdf5lib/HDF5Constants.java
index f5be38d..4aeeb98 100644
--- a/java/src/hdf/hdf5lib/HDF5Constants.java
+++ b/java/src/hdf/hdf5lib/HDF5Constants.java
@@ -407,11 +407,18 @@ public class HDF5Constants {
public static final int H5PL_VOL_PLUGIN = H5PL_VOL_PLUGIN();
public static final int H5PL_ALL_PLUGIN = H5PL_ALL_PLUGIN();
+ public static final int H5R_ATTR = H5R_ATTR();
public static final int H5R_BADTYPE = H5R_BADTYPE();
public static final int H5R_DATASET_REGION = H5R_DATASET_REGION();
+ public static final int H5R_DATASET_REGION1 = H5R_DATASET_REGION1();
+ public static final int H5R_DATASET_REGION2 = H5R_DATASET_REGION2();
public static final int H5R_MAXTYPE = H5R_MAXTYPE();
+ public static final int H5R_REF_BUF_SIZE = H5R_REF_BUF_SIZE();
public static final int H5R_OBJ_REF_BUF_SIZE = H5R_OBJ_REF_BUF_SIZE();
public static final int H5R_OBJECT = H5R_OBJECT();
+ public static final int H5R_OBJECT1 = H5R_OBJECT1();
+ public static final int H5R_OBJECT2 = H5R_OBJECT2();
+
public static final int H5S_ALL = H5S_ALL();
public static final int H5S_MAX_RANK = H5S_MAX_RANK();
public static final int H5S_NO_CLASS = H5S_NO_CLASS();
@@ -606,6 +613,7 @@ public class HDF5Constants {
public static final long H5T_STD_I8LE = H5T_STD_I8LE();
public static final long H5T_STD_REF_DSETREG = H5T_STD_REF_DSETREG();
public static final long H5T_STD_REF_OBJ = H5T_STD_REF_OBJ();
+ public static final long H5T_STD_REF = H5T_STD_REF();
public static final long H5T_STD_U16BE = H5T_STD_U16BE();
public static final long H5T_STD_U16LE = H5T_STD_U16LE();
public static final long H5T_STD_U32BE = H5T_STD_U32BE();
@@ -1420,16 +1428,28 @@ public class HDF5Constants {
private static native final int H5PL_VOL_PLUGIN();
+ private static native final int H5R_ATTR();
+
private static native final int H5R_BADTYPE();
private static native final int H5R_DATASET_REGION();
+ private static native final int H5R_DATASET_REGION1();
+
+ private static native final int H5R_DATASET_REGION2();
+
private static native final int H5R_MAXTYPE();
+ private static native final int H5R_REF_BUF_SIZE();
+
private static native final int H5R_OBJ_REF_BUF_SIZE();
private static native final int H5R_OBJECT();
+ private static native final int H5R_OBJECT1();
+
+ private static native final int H5R_OBJECT2();
+
private static native final int H5S_ALL();
private static native final int H5S_MAX_RANK();
@@ -1818,6 +1838,8 @@ public class HDF5Constants {
private static native final long H5T_STD_REF_OBJ();
+ private static native final long H5T_STD_REF();
+
private static native final long H5T_STD_U16BE();
private static native final long H5T_STD_U16LE();