/*
* Class: hdf_hdf5lib_H5
* Method: H5Iget_name
* Signature: (J)Ljava/lang/String;
*/
JNIEXPORT jstring JNICALL
Java_hdf_hdf5lib_H5_H5Iget_1name
(JNIEnv *env, jclass clss, jlong obj_id)
{
char *aName;
jstring str = NULL;
ssize_t buf_size;
/* get the length of the name */
buf_size = H5Iget_name((hid_t)obj_id, NULL, 0);
if (buf_size <= 0) {
h5badArgument(env, "H5Iget_name: buf_size <= 0");
} /* end if */
else {
buf_size++; /* add extra space for the null terminator */
aName = (char*)HDmalloc(sizeof(char) * (size_t)buf_size);
if (aName == NULL) {
h5outOfMemory(env, "H5Iget_name: malloc failed");
} /* end if */
else {
buf_size = H5Iget_name((hid_t)obj_id, aName, (size_t)buf_size);
if (buf_size < 0) {
h5libraryError(env);
} /* end if */
else {
str = ENVPTR->NewStringUTF(ENVPAR aName);
}
HDfree(aName);
}
}
return str;
} /* end Java_hdf_hdf5lib_H5_H5Iget_1name */
void NSDFWriter::createEventMap()
{
herr_t status;
hid_t eventMapContainer = require_group(filehandle_, MAPEVENTSRC);
// Open the container for the event maps
// Create the Datasets themselves (one for each field - each row
// for one object).
for (map< string, vector < string > >::iterator ii = classFieldToEventSrc_.begin();
ii != classFieldToEventSrc_.end();
++ii){
vector < string > pathTokens;
tokenize(ii->first, "/", pathTokens);
string className = pathTokens[0];
string fieldName = pathTokens[1];
hid_t classGroup = require_group(eventMapContainer, className);
hid_t strtype = H5Tcopy(H5T_C_S1);
status = H5Tset_size(strtype, H5T_VARIABLE);
// create file space
hid_t ftype = H5Tcreate(H5T_COMPOUND, sizeof(hvl_t) +sizeof(hobj_ref_t));
status = H5Tinsert(ftype, "source", 0, strtype);
status = H5Tinsert(ftype, "data", sizeof(hvl_t), H5T_STD_REF_OBJ);
hsize_t dims[1] = {ii->second.size()};
hid_t space = H5Screate_simple(1, dims, NULL);
// The dataset for mapping is named after the field
hid_t ds = H5Dcreate2(classGroup, fieldName.c_str(), ftype, space,
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
status = H5Sclose(space);
map_type * buf = (map_type*)calloc(ii->second.size(), sizeof(map_type));
// Populate the buffer entries with source uid and data
// reference
for (unsigned int jj = 0; jj < ii->second.size(); ++jj){
buf->source = ii->second[jj].c_str();
char * dsname = (char*)calloc(256, sizeof(char));
ssize_t size = H5Iget_name(classFieldToEvent_[ii->first][jj], dsname, 255);
if (size > 255){
free(dsname);
dsname = (char*)calloc(size, sizeof(char));
size = H5Iget_name(classFieldToEvent_[ii->first][jj], dsname, 255);
}
status = H5Rcreate(&(buf->data), filehandle_, dsname, H5R_OBJECT, -1);
free(dsname);
assert(status >= 0);
}
// create memory space
hid_t memtype = H5Tcreate(H5T_COMPOUND, sizeof(map_type));
status = H5Tinsert(memtype, "source",
HOFFSET(map_type, source), strtype);
status = H5Tinsert(memtype, "data",
HOFFSET(map_type, data), H5T_STD_REF_OBJ);
status = H5Dwrite(ds, memtype, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
free(buf);
status = H5Tclose(strtype);
status = H5Tclose(ftype);
status = H5Tclose(memtype);
status = H5Dclose(ds);
}
}
/****if* H5If/h5iget_name_c
* NAME
* h5iget_name_c
* PURPOSE
* Call H5Iget_name to get object's name
* INPUTS
* obj_id - object identifier
* buf_size - size of the buffer
* OUTPUTS
* buf - buffer to hold the name
* RETURNS
* length of the name on success, -1 on failure
* AUTHOR
* Elena Pourmal
* Wednesday, March 12, 2003
* HISTORY
*
* Changed the size of c_buf_size to c_buf_size + 1, which
* fixes the problem of truncating the string by 1 if the
* exact size of the string (buf_size) is passed in.
* M. Scot Breitenfeld, April 21, 2008
* SOURCE
*/
int_f
h5iget_name_c(hid_t_f *obj_id, _fcd buf, size_t_f *buf_size, size_t_f *name_size)
/******/
{
int ret_value = -1;
hid_t c_obj_id;
ssize_t c_size;
size_t c_buf_size;
char *c_buf =NULL;
/*
* Allocate buffer to hold name of an object
*/
c_buf_size = (size_t)*buf_size +1;
c_buf = (char *)HDmalloc(c_buf_size);
if (c_buf == NULL) return ret_value;
/*
* Call H5IAget_name function
*/
c_obj_id = (hid_t)*obj_id;
c_size = H5Iget_name(c_obj_id, c_buf, c_buf_size);
if (c_size < 0) goto DONE;
/*
* Convert C name to FORTRAN and place it in the given buffer
*/
HD5packFstring(c_buf, _fcdtocp(buf), c_buf_size-1);
*name_size = (size_t_f)c_size;
ret_value = 0;
DONE:
HDfree(c_buf);
return ret_value;
}
herr_t alien_visitor(hid_t did, unsigned dim, hid_t dsid,
void *visitor_data)
{
char name1[NC_MAX_NAME];
H5G_stat_t statbuf;
HDF5_OBJID_T *objid = visitor_data;
/* This should get "/var1", the name of the dataset that the scale
* is attached to. */
if (H5Iget_name(did, name1, NC_MAX_NAME) < 0) ERR;
if (strcmp(&name1[1], VAR1_NAME)) ERR;
/*printf("visiting did 0x%x dim %d dsid 0x%x name of did %s \n",
did, dim, dsid, name1);*/
/* Get more info on the dimscale object.*/
if (H5Gget_objinfo(dsid, ".", 1, &statbuf) < 0) ERR;
objid->fileno[0] = statbuf.fileno[0];
objid->objno[0] = statbuf.objno[0];
objid->fileno[1] = statbuf.fileno[1];
objid->objno[1] = statbuf.objno[1];
/*printf("for dsid: statbuf.fileno = %d statbuf.objno = %d\n",
statbuf.fileno, statbuf.objno);*/
if (H5Gget_objinfo(did, ".", 1, &statbuf) < 0) ERR;
/*printf("for did: statbuf.fileno = %d statbuf.objno = %d\n",
statbuf.fileno, statbuf.objno);*/
return 0;
}
/*
* Class: hdf_hdf5lib_H5
* Method: H5Iget_name_long
* Signature: (JLjava/lang/String;J)J
*/
JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5_H5Iget_1name_1long
(JNIEnv *env, jclass clss, jlong obj_id, jobjectArray name, jlong buf_size)
{
char *aName;
jstring str;
hssize_t size = -1;
long bs;
bs = (long)buf_size;
if (bs <= 0) {
h5badArgument(env, "H5Iget_name: buf_size <= 0");
} /* end if */
else {
aName = (char*)HDmalloc(sizeof(char) * (size_t)bs);
if (aName == NULL) {
h5outOfMemory(env, "H5Iget_name: malloc failed");
} /* end if */
else {
size = H5Iget_name((hid_t)obj_id, aName, (size_t)buf_size);
if (size < 0) {
h5libraryError(env);
} /* end if */
else {
str = ENVPTR->NewStringUTF(ENVPAR aName);
ENVPTR->SetObjectArrayElement(ENVPAR name, 0, str);
}
HDfree(aName);
}
}
return (jlong)size;
} /* end Java_hdf_hdf5lib_H5_H5Iget_1name */
//--------------------------------------------------------------------------
// Function: H5Object::getObjName
///\brief Returns the name of this object as an \a H5std_string.
///\return Name of the object
///\exception H5::Exception
// Programmer Binh-Minh Ribler - Mar, 2014
// Modification
//--------------------------------------------------------------------------
H5std_string H5Object::getObjName() const
{
H5std_string obj_name(""); // object name to return
// Preliminary call to get the size of the object name
ssize_t name_size = H5Iget_name(getId(), NULL, static_cast<size_t>(0));
// If H5Iget_name failed, throw exception
if (name_size < 0)
{
throw Exception(inMemFunc("getObjName"), "H5Iget_name failed");
}
else if (name_size == 0)
{
throw Exception(inMemFunc("getObjName"), "Object must have a name, but name length is 0");
}
// Object's name exists, retrieve it
else if (name_size > 0)
{
char* name_C = new char[name_size+1]; // temporary C-string
HDmemset(name_C, 0, name_size+1); // clear buffer
// Use overloaded function
name_size = getObjName(name_C, name_size+1);
// Convert the C object name to return
obj_name = name_C;
// Clean up resource
delete []name_C;
}
// Return object's name
return(obj_name);
}
/*-------------------------------------------------------------*/
static void validateFloat3Attribute(pNXVcontext self,
hid_t dpField, char *name)
{
hid_t attID, attType, attSpace;
H5T_class_t h5class;
hsize_t dims[2], maxDims[2];
char fname[512];
memset(fname,0,sizeof(fname));
H5Iget_name(dpField,fname,sizeof(fname));
if(!H5LTfind_attribute(dpField,name)){
NXVsetLog(self,"sev","error");
NXVprintLog(self,"message",
"Missing attribute %s on %s",
name, fname);
NXVlog(self);
self->errCount++;
} else {
attID = H5Aopen(dpField,name,H5P_DEFAULT);
assert(attID >= 0);
attType = H5Aget_type(attID);
assert(attType >= 0);
h5class = H5Tget_class(attType);
if(h5class != H5T_FLOAT){
NXVsetLog(self,"sev","error");
NXVprintLog(self,"message",
"%s attribute on %s is of wrong type, expected float",
name, fname);
NXVlog(self);
self->errCount++;
} else {
attSpace = H5Aget_space(attID);
if(H5Sget_simple_extent_ndims(attSpace) != 1){
NXVsetLog(self,"sev","error");
NXVprintLog(self,"message",
"%s attribute on %s is of wrong rank, expected 1",
name, fname);
NXVlog(self);
self->errCount++;
} else {
H5Sget_simple_extent_dims(attSpace,dims,maxDims);
if(dims[0] != 3){
NXVsetLog(self,"sev","error");
NXVprintLog(self,"message",
"%s attribute on %s is of wrong size, expected 3",
name, fname);
NXVlog(self);
self->errCount++;
}
}
H5Sclose(attSpace);
}
H5Tclose(attType);
H5Aclose(attID);
}
}
/*--------------------------------------------------------------
This validates the lesser depends_on chain fields like
vector, offset and transformation_type
----------------------------------------------------------------*/
static void validateDependsOnAttributes(pNXVcontext self,hid_t dpField)
{
char fname[512], transData[512];
hid_t attID, attType, attSpace;
H5T_class_t h5class;
memset(fname,0,sizeof(fname));
memset(transData,0,sizeof(transData));
H5Iget_name(dpField,fname,sizeof(fname));
/*
deal with transformation_type
*/
if(!H5LTfind_attribute(dpField,"transformation_type")){
NXVsetLog(self,"sev","error");
NXVprintLog(self,"message",
"Missing attribute transformation_type on %s",
fname);
NXVlog(self);
self->errCount++;
} else {
attID = H5Aopen(dpField,"transformation_type",H5P_DEFAULT);
assert(attID >= 0);
attType = H5Aget_type(attID);
assert(attType >= 0);
h5class = H5Tget_class(attType);
if(h5class != H5T_STRING){
NXVsetLog(self,"sev","error");
NXVprintLog(self,"message",
"transformation_type on %s is of wrong type, expected string",
fname);
NXVlog(self);
self->errCount++;
} else {
H5NXget_attribute_string(self->fileID, fname,
"transformation_type",transData);
if(strcmp(transData,"translation") != 0
&& strcmp(transData,"rotation") != 0){
NXVsetLog(self,"sev","error");
NXVprintLog(self,"message",
"transformation_type on %s contains bad data: %s",
fname,
"expected rotation or translation");
NXVlog(self);
self->errCount++;
}
}
H5Tclose(attType);
H5Aclose(attID);
}
validateFloat3Attribute(self,dpField,"offset");
validateFloat3Attribute(self,dpField,"vector");
}
herr_t alien_visitor(hid_t did, unsigned dim, hid_t dsid,
void *visitor_data)
{
char name1[STR_LEN], name2[STR_LEN];
H5G_stat_t statbuf;
(*(hid_t *)visitor_data) = dsid;
if (H5Iget_name(did, name1, STR_LEN) < 0) ERR;
if (H5Iget_name(dsid, name2, STR_LEN) < 0) ERR;
/* printf("visiting did 0x%x dim %d dsid 0x%x name of did %s \n", */
/* did, dim, dsid, name1); */
/* printf("name of dsid: %s\n", name2); */
if (H5Gget_objinfo(did, ".", 1, &statbuf) < 0) ERR;
/* printf("statbuf.fileno = %d statbuf.objno = %d\n",
statbuf.fileno, statbuf.objno);*/
return 0;
}
/*--------------------------------------------------------------*/
static void validateDependsOn(pNXVcontext self, hid_t groupID,
hid_t fieldID)
{
char fname[512], dpData[1024];
hid_t h5type, dpfieldID;
H5T_class_t h5class;
memset(fname,0,sizeof(fname));
memset(dpData,0,sizeof(dpData));
H5Iget_name(fieldID,fname,sizeof(fname));
NXVsetLog(self,"dataPath",fname);
NXVsetLog(self,"sev","debug");
NXVprintLog(self,"message","Validating depends_on chain starting at %s",
fname);
NXVlog(self);
/*
test that the depends_on field is of the right type
*/
h5type = H5Dget_type(fieldID);
h5class = H5Tget_class(h5type);
H5Tclose(h5type);
if(h5class != H5T_STRING){
NXVsetLog(self,"sev","error");
NXVsetLog(self,"message",
"depends_on field is of wrong type, expect string");
NXVlog(self);
self->errCount++;
return;
}
/*
read the field
*/
H5LTread_dataset_string(groupID,"depends_on",dpData);
/*
find the field and start iterating through the chain
*/
dpfieldID = findDependentField(self,fieldID,dpData);
if(dpfieldID < 0){
NXVsetLog(self,"sev","error");
NXVprintLog(self,"message",
"Cannot even find the starting point of the depends_on chain, %s",
dpData);
NXVlog(self);
self->errCount++;
return;
} else {
validateDependsOnField(self,groupID,dpfieldID);
H5Dclose(dpfieldID);
}
}
/*-------------------------------------------------------------*/
static hid_t findDependentField(pNXVcontext self,
hid_t inFieldID,char *dpData)
{
char *pPtr;
hid_t fieldID, groupID;
char fname[512], newPath[1024], groupName[1024];
/*
get at enclosing group
*/
memset(groupName,0,sizeof(groupName));
H5Iget_name(inFieldID,groupName,sizeof(groupName));
pPtr = strrchr(groupName,'/');
*pPtr = '\0';
pPtr = NULL;
pPtr = strchr(dpData,'/');
if(pPtr != NULL){
if(pPtr == dpData){
/* absolute path */
if(H5LTpath_valid(self->fileID,dpData,1)){
fieldID = H5Oopen(self->fileID,dpData,H5P_DEFAULT);
return fieldID;
} else {
return -1;
}
} else {
/* relative path further along the path */
snprintf(newPath,sizeof(newPath), "%s/%s", groupName, dpData);
if(H5LTpath_valid(self->fileID,newPath,1)){
fieldID = H5Oopen(self->fileID,newPath,H5P_DEFAULT);
return fieldID;
} else {
return -1;
}
}
} else {
/* path within the group */
groupID = H5Oopen(self->fileID, groupName,H5P_DEFAULT);
if(H5LTfind_dataset(groupID,dpData)){
fieldID = H5Dopen(groupID,dpData,H5P_DEFAULT);
H5Oclose(groupID);
return fieldID;
} else {
H5Oclose(groupID);
return -1;
}
}
return -1;
}
//--------------------------------------------------------------------------
// Function: getObjName
///\brief Given an id, returns the type of the object.
///\return The name of the object
// Programmer Binh-Minh Ribler - Mar, 2014
//--------------------------------------------------------------------------
ssize_t H5Object::getObjName(char *obj_name, size_t buf_size) const
{
// H5Iget_name will get buf_size-1 chars of the name to null terminate it
ssize_t name_size = H5Iget_name(getId(), obj_name, buf_size);
// If H5Iget_name returns a negative value, raise an exception
if (name_size < 0)
{
throw Exception(inMemFunc("getObjName"), "H5Iget_name failed");
}
else if (name_size == 0)
{
throw Exception(inMemFunc("getObjName"), "Object must have a name, but name length is 0");
}
// Return length of the name
return(name_size);
}
CXI_Data_Reference * cxi_create_data_link(CXI_Entry * entry, CXI_Dataset * data){
if(!entry || ! data){
return NULL;
}
if(entry->handle <= 0 || data->handle <= 0){
return NULL;
}
CXI_Data * root_data = calloc(sizeof(CXI_Data),1);
CXI_Data_Reference * data_ref = cxi_create_data(entry->handle,root_data);
if(!data_ref) return NULL;
char path[1024];
if(H5Iget_name(data->handle, path, 1024) <= 0){
return NULL;
}
if(H5Lcreate_soft(path, root_data->handle, "data", H5P_DEFAULT, H5P_DEFAULT) < 0){
return NULL;
}
return data_ref;
}
herr_t alien_visitor2(hid_t did, unsigned dim, hid_t dsid, void *visitor_data)
{
char name1[NC_MAX_NAME];
H5G_stat_t statbuf;
HDF5_OBJID_T *objid = visitor_data;
if (H5Iget_name(did, name1, NC_MAX_NAME) < 0) ERR;
/*printf("visiting did 0x%x dim %d dsid 0x%x name of did %s \n",
did, dim, dsid, name1); */
/* Get obj id of the dimscale object. THis will be used later to
* match dimensions to dimscales. */
if (H5Gget_objinfo(dsid, ".", 1, &statbuf) < 0) ERR;
objid->fileno[0] = statbuf.fileno[0];
objid->objno[0] = statbuf.objno[0];
objid->fileno[1] = statbuf.fileno[1];
objid->objno[1] = statbuf.objno[1];
return 0;
}
herr_t alien_visitor(hid_t did, unsigned dim, hid_t dsid,
void *visitor_data)
{
char name1[STR_LEN];
H5G_stat_t statbuf;
HDF5_OBJID_T *objid = visitor_data;
/* This should get "/var1", the name of the dataset that the scale
* is attached to. */
if (H5Iget_name(did, name1, STR_LEN) < 0) ERR;
if (strcmp(&name1[1], VAR1_NAME)) ERR;
/* Get more info on the dimscale object.*/
if (H5Gget_objinfo(dsid, ".", 1, &statbuf) < 0) ERR;
objid->fileno[0] = statbuf.fileno[0];
objid->objno[0] = statbuf.objno[0];
objid->fileno[1] = statbuf.fileno[1];
objid->objno[1] = statbuf.objno[1];
return 0;
}
/*-------------------------------------------------------------------------
* Function: toomany
*
* Purpose: Build a file with too many symbolic links
*
* Return: Success: 0
*
* Failure: -1
*
* Programmer: Quincey Koziol
* Tuesday, August 9, 2005
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static int
toomany(hid_t fapl)
{
hid_t fid = (-1); /* File ID */
hid_t gid = (-1); /* Group ID */
hid_t gid2 = (-1); /* Datatype ID */
char objname[NAME_BUF_SIZE]; /* Object name */
ssize_t name_len; /* Length of object name */
char filename[NAME_BUF_SIZE];
TESTING("too many links");
/* Make certain test is valid */
/* XXX: should probably make a "generic" test that creates the proper
* # of links based on this value - QAK
*/
HDassert(H5G_NLINKS == 16);
/* Create files */
h5_fixname(FILENAME[1], fapl, filename, sizeof filename);
if((fid=H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl))<0) TEST_ERROR;
/* Create group with short name in file (used as target for hard links) */
if((gid=H5Gcreate (fid, "final", (size_t)0))<0) TEST_ERROR;
/* Create chain of hard links to existing object (no limit on #) */
if(H5Glink2(fid, "final", H5G_LINK_HARD, fid, "hard1") < 0) TEST_ERROR;
if(H5Glink2(fid, "hard1", H5G_LINK_HARD, fid, "hard2") < 0) TEST_ERROR;
if(H5Glink2(fid, "hard2", H5G_LINK_HARD, fid, "hard3") < 0) TEST_ERROR;
if(H5Glink2(fid, "hard3", H5G_LINK_HARD, fid, "hard4") < 0) TEST_ERROR;
if(H5Glink2(fid, "hard4", H5G_LINK_HARD, fid, "hard5") < 0) TEST_ERROR;
if(H5Glink2(fid, "hard5", H5G_LINK_HARD, fid, "hard6") < 0) TEST_ERROR;
if(H5Glink2(fid, "hard6", H5G_LINK_HARD, fid, "hard7") < 0) TEST_ERROR;
if(H5Glink2(fid, "hard7", H5G_LINK_HARD, fid, "hard8") < 0) TEST_ERROR;
if(H5Glink2(fid, "hard8", H5G_LINK_HARD, fid, "hard9") < 0) TEST_ERROR;
if(H5Glink2(fid, "hard9", H5G_LINK_HARD, fid, "hard10") < 0) TEST_ERROR;
if(H5Glink2(fid, "hard10", H5G_LINK_HARD, fid, "hard11") < 0) TEST_ERROR;
if(H5Glink2(fid, "hard11", H5G_LINK_HARD, fid, "hard12") < 0) TEST_ERROR;
if(H5Glink2(fid, "hard12", H5G_LINK_HARD, fid, "hard13") < 0) TEST_ERROR;
if(H5Glink2(fid, "hard13", H5G_LINK_HARD, fid, "hard14") < 0) TEST_ERROR;
if(H5Glink2(fid, "hard14", H5G_LINK_HARD, fid, "hard15") < 0) TEST_ERROR;
if(H5Glink2(fid, "hard15", H5G_LINK_HARD, fid, "hard16") < 0) TEST_ERROR;
if(H5Glink2(fid, "hard16", H5G_LINK_HARD, fid, "hard17") < 0) TEST_ERROR;
if(H5Glink2(fid, "hard17", H5G_LINK_HARD, fid, "hard18") < 0) TEST_ERROR;
if(H5Glink2(fid, "hard18", H5G_LINK_HARD, fid, "hard19") < 0) TEST_ERROR;
if(H5Glink2(fid, "hard19", H5G_LINK_HARD, fid, "hard20") < 0) TEST_ERROR;
if(H5Glink2(fid, "hard20", H5G_LINK_HARD, fid, "hard21") < 0) TEST_ERROR;
/* Create chain of soft links to existing object (limited) */
if(H5Glink2(fid, "final", H5G_LINK_SOFT, fid, "soft1") < 0) TEST_ERROR;
if(H5Glink2(fid, "soft1", H5G_LINK_SOFT, fid, "soft2") < 0) TEST_ERROR;
if(H5Glink2(fid, "soft2", H5G_LINK_SOFT, fid, "soft3") < 0) TEST_ERROR;
if(H5Glink2(fid, "soft3", H5G_LINK_SOFT, fid, "soft4") < 0) TEST_ERROR;
if(H5Glink2(fid, "soft4", H5G_LINK_SOFT, fid, "soft5") < 0) TEST_ERROR;
if(H5Glink2(fid, "soft5", H5G_LINK_SOFT, fid, "soft6") < 0) TEST_ERROR;
if(H5Glink2(fid, "soft6", H5G_LINK_SOFT, fid, "soft7") < 0) TEST_ERROR;
if(H5Glink2(fid, "soft7", H5G_LINK_SOFT, fid, "soft8") < 0) TEST_ERROR;
if(H5Glink2(fid, "soft8", H5G_LINK_SOFT, fid, "soft9") < 0) TEST_ERROR;
if(H5Glink2(fid, "soft9", H5G_LINK_SOFT, fid, "soft10") < 0) TEST_ERROR;
if(H5Glink2(fid, "soft10", H5G_LINK_SOFT, fid, "soft11") < 0) TEST_ERROR;
if(H5Glink2(fid, "soft11", H5G_LINK_SOFT, fid, "soft12") < 0) TEST_ERROR;
if(H5Glink2(fid, "soft12", H5G_LINK_SOFT, fid, "soft13") < 0) TEST_ERROR;
if(H5Glink2(fid, "soft13", H5G_LINK_SOFT, fid, "soft14") < 0) TEST_ERROR;
if(H5Glink2(fid, "soft14", H5G_LINK_SOFT, fid, "soft15") < 0) TEST_ERROR;
if(H5Glink2(fid, "soft15", H5G_LINK_SOFT, fid, "soft16") < 0) TEST_ERROR;
if(H5Glink2(fid, "soft16", H5G_LINK_SOFT, fid, "soft17") < 0) TEST_ERROR;
/* Close objects */
if(H5Gclose(gid)<0) TEST_ERROR;
if(H5Fclose(fid)<0) TEST_ERROR;
/* Open file */
if((fid=H5Fopen(filename, H5F_ACC_RDWR, fapl))<0) TEST_ERROR;
/* Open object through last hard link */
if((gid = H5Gopen(fid, "hard21")) < 0) TEST_ERROR;
/* Check name */
if((name_len = H5Iget_name( gid, objname, (size_t)NAME_BUF_SIZE )) < 0) TEST_ERROR
if(HDstrcmp(objname, "/hard21")) TEST_ERROR
/* Create object in hard-linked group */
if((gid2 = H5Gcreate(gid, "new_hard", (size_t)0)) < 0) TEST_ERROR
/* Close group in hard-linked group */
if(H5Gclose(gid2) < 0) TEST_ERROR
/* Close hard-linked object */
if(H5Gclose(gid) < 0) TEST_ERROR;
/* Open object through too deep soft link */
H5E_BEGIN_TRY {
gid = H5Gopen(fid, "soft17");
} H5E_END_TRY;
if (gid >= 0) {
H5_FAILED();
puts(" Should have failed for sequence of too many nested links.");
goto error;
}
/* Open object through lesser soft link */
if((gid = H5Gopen(fid, "soft16")) < 0) TEST_ERROR;
/* Check name */
if((name_len = H5Iget_name( gid, objname, (size_t)NAME_BUF_SIZE )) < 0) TEST_ERROR
if(HDstrcmp(objname, "/soft16")) TEST_ERROR
/* Create object in external file */
if((gid2 = H5Gcreate(gid, "new_soft", (size_t)0)) < 0) TEST_ERROR
/* Close group in external file */
if(H5Gclose(gid2) < 0) TEST_ERROR
/* Close external object */
if(H5Gclose(gid) < 0) TEST_ERROR;
/* Close first file */
if(H5Fclose(fid)<0) TEST_ERROR;
PASSED();
return 0;
error:
H5E_BEGIN_TRY {
H5Gclose (gid2);
H5Gclose (gid);
H5Fclose (fid);
} H5E_END_TRY;
return -1;
} /* end toomany() */
int
main (void)
{
hid_t file, space, dset, obj, attr; /* Handles */
herr_t status;
hsize_t dims[1] = {DIM0};
hobj_ref_t wdata[DIM0], /* Write buffer */
*rdata; /* Read buffer */
H5G_obj_t objtype;
ssize_t size;
char *name;
int ndims,
i;
/*
* Create a new file using the default properties.
*/
file = H5Fcreate (FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/*
* Create a dataset with a scalar dataspace.
*/
space = H5Screate (H5S_SCALAR);
obj = H5Dcreate (file, "DS2", H5T_STD_I32LE, space, H5P_DEFAULT);
status = H5Dclose (obj);
status = H5Sclose (space);
/*
* Create a group.
*/
obj = H5Gcreate (file, "G1", H5P_DEFAULT);
status = H5Gclose (obj);
/*
* Create references to the previously created objects. Passing -1
* as space_id causes this parameter to be ignored. Other values
* besides valid dataspaces result in an error.
*/
status = H5Rcreate (&wdata[0], file, "G1", H5R_OBJECT, -1);
status = H5Rcreate (&wdata[1], file, "DS2", H5R_OBJECT, -1);
/*
* Create dataset with a scalar dataspace to serve as the parent
* for the attribute.
*/
space = H5Screate (H5S_SCALAR);
dset = H5Dcreate (file, DATASET, H5T_STD_I32LE, space, H5P_DEFAULT);
status = H5Sclose (space);
/*
* Create dataspace. Setting maximum size to NULL sets the maximum
* size to be the current size.
*/
space = H5Screate_simple (1, dims, NULL);
/*
* Create the attribute and write the object references to it.
*/
attr = H5Acreate (dset, ATTRIBUTE, H5T_STD_REF_OBJ, space, H5P_DEFAULT);
status = H5Awrite (attr, H5T_STD_REF_OBJ, wdata);
/*
* Close and release resources.
*/
status = H5Aclose (attr);
status = H5Dclose (dset);
status = H5Sclose (space);
status = H5Fclose (file);
/*
* Now we begin the read section of this example. Here we assume
* the attribute has the same name and rank, but can have any size.
* Therefore we must allocate a new array to read in data using
* malloc().
*/
/*
* Open file, dataset, and attribute.
*/
file = H5Fopen (FILE, H5F_ACC_RDONLY, H5P_DEFAULT);
dset = H5Dopen (file, DATASET);
attr = H5Aopen_name (dset, ATTRIBUTE);
/*
* Get dataspace and allocate memory for read buffer.
*/
space = H5Aget_space (attr);
ndims = H5Sget_simple_extent_dims (space, dims, NULL);
rdata = (hobj_ref_t *) malloc (dims[0] * sizeof (hobj_ref_t));
/*
* Read the data.
*/
status = H5Aread (attr, H5T_STD_REF_OBJ, rdata);
/*
* Output the data to the screen.
*/
for (i=0; i<dims[0]; i++) {
printf ("%s[%d]:\n ->", ATTRIBUTE, i);
/*
* Open the referenced object, get its name and type.
*/
obj = H5Rdereference (dset, H5R_OBJECT, &rdata[i]);
objtype = H5Rget_obj_type (dset, H5R_OBJECT, &rdata[i]);
/*
* Get the length of the name, allocate space, then retrieve
* the name.
*/
size = 1 + H5Iget_name (obj, NULL, 0);
if (size > 1) {
name = (char *) malloc (size);
size = 1 + H5Iget_name (obj, name, size);
}
/*
* Print the object type and close the object.
*/
switch (objtype) {
case H5G_GROUP:
printf ("Group");
status = H5Gclose (obj);
break;
case H5G_DATASET:
printf ("Dataset");
status = H5Dclose (obj);
break;
case H5G_TYPE:
printf ("Named Datatype");
status = H5Tclose (obj);
}
/*
* Print the name and deallocate space for the name.
*/
if (size > 1) {
printf (": %s", name);
free (name);
}
printf ("\n");
}
/*
* Close and release resources.
*/
free (rdata);
status = H5Aclose (attr);
status = H5Dclose (dset);
status = H5Sclose (space);
status = H5Fclose (file);
return 0;
}
SWIGEXPORT hid_t JNICALL Java_permafrost_hdf_libhdf_ObjectLibExtensionJNI_JHOopen_1by_1idx(
JNIEnv *jenv,
jclass jcls,
jint loc_id,
jstring group_name,
jint idx_type,
jint order,
jlong n,
jint lapl_id,
jintArray type,
jobjectArray name
) {
jint sz = 0;
char* pGroupName = NULL;
hid_t obj_id = -1;
jint jiType;
char* pName = NULL;
char* tmpName = NULL;
const int szName = 64;
int lenName = 0;
jstring jname;
if (!group_name) {
SWIG_JavaThrowException(jenv, SWIG_JavaIllegalArgumentException, "Null group name.");
return (-1);
} else if (!type) {
SWIG_JavaThrowException(jenv, SWIG_JavaIllegalArgumentException, "Null type array.");
return (-1);
} else if (!name) {
SWIG_JavaThrowException(jenv, SWIG_JavaIllegalArgumentException, "Null object name array.");
return (-1);
}
sz = (*jenv)->GetArrayLength(jenv, type);
if (sz < 1) {
SWIG_JavaThrowException(jenv, SWIG_JavaIllegalArgumentException, "Zero-length type array.");
return (-1);
}
sz = (*jenv)->GetArrayLength(jenv, name);
if (sz < 1) {
SWIG_JavaThrowException(jenv, SWIG_JavaIllegalArgumentException, "Zero-length object name array.");
return (-1);
}
pGroupName = (char *)(*jenv)->GetStringUTFChars(jenv, group_name, 0);
if (!pGroupName) return -1;
obj_id = H5Oopen_by_idx(
(hid_t)loc_id,
pGroupName,
(H5_index_t) idx_type,
(H5_iter_order_t) order,
(hsize_t) n,
(hid_t) lapl_id
);
if (pGroupName) (*jenv)->ReleaseStringUTFChars(jenv, group_name, (const char *) pGroupName);
if (obj_id <= 0) return (obj_id);
jiType = (jint) H5Iget_type(obj_id);
(*jenv)->SetIntArrayRegion(jenv, type, 0, 1, &jiType);
pName = (char*) calloc(szName, sizeof(char));
lenName = H5Iget_name(obj_id, pName, szName-1);
if (lenName >= szName) {
char* tmpName = (char*) realloc(pName, sizeof(char)*lenName+1);
if (!tmpName) {
free(pName);
pName = NULL;
H5Oclose(loc_id);
return (-1);
}
pName = tmpName;
lenName = H5Iget_name(obj_id, pName, lenName);
}
jname = (*jenv)->NewStringUTF(jenv, pName);
(*jenv)->SetObjectArrayElement(jenv, name, 0, jname);
free(pName);
return (obj_id);
}
/*--------------------------------------------------------------*/
static void validateLink(pNXVcontext self, hid_t groupID,
xmlChar *name, xmlChar *target)
{
hid_t objID;
herr_t att;
char linkTarget[512], dataPath[512];
char nxdlPath[512], curPath[512];
/*
set our path for correct error printing
*/
snprintf(nxdlPath,sizeof(nxdlPath),"%s/%s", self->nxdlPath,
(char *)name);
NXVsetLog(self,"nxdlPath",nxdlPath);
H5Iget_name(groupID,curPath,sizeof(curPath));
snprintf(dataPath,sizeof(dataPath),"%s/%s", curPath,
(char *)name);
NXVsetLog(self,"dataPath",dataPath);
/*
log what we are doing
*/
NXVsetLog(self,"sev","debug");
NXVprintLog(self,"message","Validating link %s at %s",
(char *)name, (char *)target);
NXVlog(self);
/*
now we really validate
*/
if(H5LTpath_valid(groupID,(char *)name, 1)){
/*
The positive test means that the link exists and is pointing to
a valid HDF5 object. This is alread good.
*/
objID = H5Oopen(groupID,(char *)name,H5P_DEFAULT);
assert(objID >= 0); /* we just tested for existence, didn't we? */
memset(linkTarget,0,sizeof(linkTarget));
att = H5NXget_attribute_string(groupID,(char *)name,"target",linkTarget);
if(att < 0){
NXVsetLog(self,"sev","error");
H5Iget_name(objID,dataPath,sizeof(dataPath));
NXVsetLog(self,"dataPath",dataPath);
NXVsetLog(self,"message","Link is missing required attribute target");
NXVlog(self);
self->errCount++;
} else {
/*
test that the target attribute really points to something
real. It could be that the link was done right but the
target attribute set sloppily.
*/
if(!H5LTpath_valid(self->fileID,linkTarget,1)){
NXVsetLog(self,"sev","error");
H5Iget_name(objID,dataPath,sizeof(dataPath));
NXVsetLog(self,"dataPath",dataPath);
NXVprintLog(self,"message","Link target %s is invalid",
linkTarget);
NXVlog(self);
self->errCount++;
} else {
validateLinkTarget(self,target,linkTarget);
}
}
H5Oclose(objID);
} else {
NXVsetLog(self,"sev","error");
NXVprintLog(self,"message",
"Required link %s missing or not pointing to an HDF5 object",
(char *)name);
NXVlog(self);
self->errCount++;
}
}
static void validateGroupAttributes(pNXVcontext self,
hid_t groupID, xmlNodePtr groupNode)
{
xmlNodePtr cur;
xmlChar *type, *name;
herr_t attID;
char data[512], gname[512];
memset(data,0,sizeof(data));
memset(gname,0,sizeof(gname));
H5Iget_name(groupID,gname,sizeof(gname));
type = xmlGetProp(groupNode,(xmlChar *)"type");
attID = H5NXget_attribute_string(groupID,gname,"NX_class",data);
if(attID < 0){
NXVsetLog(self,"sev","error");
NXVsetLog(self,"message","Required group attribute NX_class missing");
NXVlog(self);
self->errCount++;
} else {
if(strcmp(data,(char *)type) != 0){
/*
accept NXsubentry if NXentry is asked for
*/
if(!(strcmp((char *)type,"NXentry") == 0 &&
strcmp(data,"NXsubentry") == 0)){
NXVsetLog(self,"sev","error");
NXVprintLog(self,"message","Wrong group type, expected %s, got %s",
(char *)type, data);
NXVlog(self);
self->errCount++;
}
}
}
xmlFree(type);
/*
search attribute child nodes
*/
cur = groupNode->xmlChildrenNode;
while(cur != NULL){
if(xmlStrcmp(cur->name, (xmlChar *)"attribute") == 0){
name = xmlGetProp(cur,(xmlChar *)"name");
if(!H5LTfind_attribute(groupID,(char *)name)){
NXVsetLog(self,"sev","error");
NXVprintLog(self,"message","Required group attribute %s missing",
name);
NXVlog(self);
self->errCount++;
} else {
/*
TODO validate attribute data.
As we do not use group attributes heavily, deferred for
now
*/
}
xmlFree(name);
}
cur = cur->next;
}
}
hid_t dat1Reopen( hid_t file_id, unsigned int flags, hid_t fapl,
int *status ){
/* Local Variables; */
HDSLoc **loc;
HDSLoc **loclist;
char **paths;
char file[EMS__SZMSG+1];
char path[EMS__SZMSG+1];
hid_t *file_ids;
hid_t id;
int *isgroup;
int iloc;
int nlev;
int nloc;
ssize_t size;
/* Return immediately if an error has already occurred. */
if( *status != SAI__OK ) return file_id;
/* Get a list of any active locators associated with the file. Also get a
list of file_ids for the same file that have associated locators. */
hds1GetLocators( file_id, &nloc, &loclist, &file_ids, status );
/* Check that none of the locators are mapped. */
if( *status == SAI__OK ) {
loc = loclist;
for( iloc = 0; iloc < nloc; iloc++,loc++ ) {
if( (*loc)->regpntr ) {
hdsTrace( (*loc), &nlev, path, file, status, sizeof(path), sizeof(file) );
*status = DAT__PRMAP;
emsRepf( " ", "hdsOpen: Cannot re-open '%s' in read-write mode "
"since '%s' is currently mapped.", status, file, path );
break;
}
}
}
/* Store the path to the HDF5 object associated with each active locator,
and also a flag indicating if the HDF5 object is a group or dataset.
Then close the HDF5 objects. */
paths = MEM_CALLOC( nloc, sizeof( *paths ) );
isgroup = MEM_CALLOC( nloc, sizeof( *isgroup ) );
if( paths && isgroup && *status == SAI__OK ) {
loc = loclist;
for( iloc = 0; iloc < nloc; iloc++,loc++ ) {
if( (*loc)->group_id ) {
isgroup[ iloc ] = 1;
id = (*loc)->group_id;
} else {
isgroup[ iloc ] = 0;
id = (*loc)->dataset_id;
}
if( id ) {
size = H5Iget_name( id, NULL, 0 );
paths[ iloc ] = MEM_CALLOC( size + 1, 1 );
H5Iget_name( id, paths[ iloc ], size + 1 );
} else {
hdsTrace( (*loc), &nlev, path, file, status, sizeof(path), sizeof(file) );
*status = DAT__FATAL;
emsRepf( " ", "hdsOpen: Locator for '%s.%s' has no group or "
"dataset so cannot be reopened.", status, file, path );
break;
}
if( H5Oclose( id ) < 0 ) {
hdsTrace( (*loc), &nlev, path, file, status, sizeof(path), sizeof(file) );
*status = DAT__FATAL;
dat1H5EtoEMS( status );
emsRepf( " ", "hdsOpen: Failed to close HDF5 object for '%s.%s'.",
status, file, path );
break;
}
}
}
/* Get the path for the file. */
H5Fget_name( file_id, path, sizeof(path) );
/* Close all HDF5 file_ids associated with file. */
if( *status == SAI__OK ) {
int this_closed = 0;
int i = -1;
while( file_ids[ ++i ] ) {
if( file_ids[ i ] == file_id ) this_closed = 1;
if( H5Fclose( file_ids[ i ] ) < 0 ) {
*status = DAT__FATAL;
dat1H5EtoEMS( status );
emsRepf( " ", "hdsOpen: Failed to close file '%s' prior to "
"re-opening it.", status, path );
break;
}
}
/* Close the supplied file_id if it has not already been closed. */
if( !this_closed ) {
if( H5Fclose( file_id ) < 0 ) {
*status = DAT__FATAL;
dat1H5EtoEMS( status );
emsRepf( " ", "hdsOpen: Failed to close file '%s' prior to "
"re-opening it.", status, path );
}
}
}
/* Re-open it. */
if( *status == SAI__OK ) {
file_id = H5Fopen( path, flags, fapl );
if( file_id < 0 ) {
*status = DAT__FATAL;
dat1H5EtoEMS( status );
emsRepf( " ", "hdsOpen: Failed to reopen file '%s'.",
status, path );
}
}
/* Update the file, group and dataset id in each locator. */
if( *status == SAI__OK ) {
loc = loclist;
for( iloc = 0; iloc < nloc; iloc++,loc++ ) {
hds1SetFileId( (*loc), file_id, status );
if( isgroup[ iloc ] ) {
(*loc)->group_id = H5Gopen2( file_id, paths[ iloc ], H5P_DEFAULT );
} else {
(*loc)->dataset_id = H5Dopen2( file_id, paths[ iloc ], H5P_DEFAULT );
}
}
}
/* Free resources. */
if( paths ) {
for( iloc = 0; iloc < nloc; iloc++ ) {
MEM_FREE( paths[ iloc ] );
}
MEM_FREE( paths );
}
if( isgroup ) MEM_FREE( isgroup );
if( loclist ) MEM_FREE( loclist );
if( file_ids ) MEM_FREE( file_ids );
/* Return the new file id. */
return file_id;
}
/* Test basic functionality of registering and deleting types and IDs */
static int basic_id_test(void)
{
H5I_type_t myType = H5I_BADID;
hid_t arrayID = H5I_INVALID_HID;
void* testObj = NULL;
void* testPtr = NULL;
char nameString[10];
hid_t testID;
ssize_t testSize = -1;
herr_t err;
int num_ref;
hsize_t num_members;
/* Try to register an ID with ficticious types */
H5E_BEGIN_TRY
arrayID = H5Iregister((H5I_type_t) 420, testObj);
H5E_END_TRY
VERIFY(arrayID, H5I_INVALID_HID, "H5Iregister");
if(arrayID != H5I_INVALID_HID)
goto out;
H5E_BEGIN_TRY
arrayID = H5Iregister((H5I_type_t) -1, testObj);
H5E_END_TRY
VERIFY(arrayID, H5I_INVALID_HID, "H5Iregister");
if(arrayID != H5I_INVALID_HID)
goto out;
/* Try to access IDs with ficticious types */
H5E_BEGIN_TRY
testPtr = H5Iobject_verify((hid_t)100, (H5I_type_t) 0);
H5E_END_TRY
VERIFY(testPtr, NULL, "H5Iobject_verify");
if(testPtr != NULL)
goto out;
H5E_BEGIN_TRY
testPtr = H5Iobject_verify((hid_t)700, (H5I_type_t) 700);
H5E_END_TRY
VERIFY(testPtr, NULL, "H5Iobject_verify");
if(testPtr != NULL)
goto out;
/* Register a type */
myType = H5Iregister_type((size_t)64, 0, (H5I_free_t) free );
CHECK(myType, H5I_BADID, "H5Iregister_type");
if(myType == H5I_BADID)
goto out;
/* Register an ID and retrieve the object it points to.
* Once the ID has been registered, testObj will be freed when
* its ID type is destroyed. */
testObj = HDmalloc(7 * sizeof(int));
arrayID = H5Iregister(myType, testObj);
CHECK(arrayID, H5I_INVALID_HID, "H5Iregister");
if(arrayID == H5I_INVALID_HID)
{
HDfree(testObj);
goto out;
}
testPtr = (int *) H5Iobject_verify(arrayID, myType);
VERIFY(testPtr, testObj, "H5Iobject_verify");
if(testPtr != testObj)
goto out;
/* Ensure that H5Iget_file_id and H5Iget_name() fail, since this
* is an hid_t for the wrong kind of object */
H5E_BEGIN_TRY
testID = H5Iget_file_id(arrayID);
H5E_END_TRY
VERIFY(testID, H5I_INVALID_HID, "H5Iget_file_id");
if(testID != H5I_INVALID_HID)
goto out;
H5E_BEGIN_TRY
testSize = H5Iget_name(arrayID, nameString, (size_t)9);
H5E_END_TRY
VERIFY(testSize, -1, "H5Iget_name");
if(testSize != -1)
goto out;
/* Make sure H5Iremove_verify catches objects of the wrong type */
H5E_BEGIN_TRY
testPtr = (int*) H5Iremove_verify(arrayID, (H5I_type_t) 0);
H5E_END_TRY
VERIFY(testPtr, NULL, "H5Iremove_verify");
if(testPtr != NULL)
goto out;
H5E_BEGIN_TRY
testPtr = (int*) H5Iremove_verify(arrayID, (H5I_type_t) ((int) myType-1));
H5E_END_TRY
VERIFY(testPtr, NULL, "H5Iremove_verify");
if(testPtr != NULL)
goto out;
/* Remove an ID and make sure we can't access it */
testPtr = (int*) H5Iremove_verify(arrayID, myType);
CHECK(testPtr, NULL, "H5Iremove_verify");
if(testPtr == NULL)
goto out;
H5E_BEGIN_TRY
testPtr = (int*) H5Iobject_verify(arrayID, myType);
H5E_END_TRY
VERIFY(testPtr, NULL, "H5Iobject_verify");
if(testPtr != NULL)
goto out;
/* Delete the type and make sure we can't access objects within it */
arrayID = H5Iregister(myType, testObj);
err = H5Idestroy_type(myType);
VERIFY(err, 0, "H5Idestroy_type");
if( err != 0)
goto out;
VERIFY(H5Itype_exists(myType), 0, "H5Itype_exists");
if(H5Itype_exists(myType) != 0)
goto out;
H5E_BEGIN_TRY
VERIFY(H5Inmembers(myType, NULL), -1, "H5Inmembers");
if(H5Inmembers(myType, NULL) != -1)
goto out;
H5E_END_TRY
/* Register another type and another object in that type */
myType = H5Iregister_type((size_t)64, 0, (H5I_free_t) free );
CHECK(myType, H5I_BADID, "H5Iregister_type");
if(myType == H5I_BADID)
goto out;
/* The memory that testObj pointed to should already have been
* freed when the previous type was destroyed. Allocate new
* memory for it.
*/
testObj = HDmalloc(7 * sizeof(int));
arrayID = H5Iregister(myType, testObj);
CHECK(arrayID, H5I_INVALID_HID, "H5Iregister");
if(arrayID == H5I_INVALID_HID)
{
HDfree(testObj);
goto out;
}
err = H5Inmembers(myType, &num_members);
CHECK(err, -1, "H5Inmembers");
if (err < 0)
goto out;
VERIFY(num_members, 1, "H5Inmembers");
if(num_members != 1)
goto out;
/* Increment references to type and ensure that dec_type_ref
doesn't destroy the type */
num_ref = H5Iinc_type_ref(myType);
VERIFY(num_ref, 2, "H5Iinc_type_ref");
if( num_ref != 2)
goto out;
num_ref = H5Idec_type_ref(myType);
VERIFY(num_ref, 1, "H5Idec_type_ref");
if(num_ref != 1)
goto out;
err = H5Inmembers(myType, &num_members);
CHECK(err, -1, "H5Inmembers");
if (err < 0)
goto out;
VERIFY(num_members, 1, "H5Inmembers");
if(num_members != 1)
goto out;
/* This call to dec_type_ref should destroy the type */
num_ref = H5Idec_type_ref(myType);
VERIFY(num_ref, 0, "H5Idec_type_ref");
if(num_ref != 0)
goto out;
VERIFY(H5Itype_exists(myType), 0, "H5Itype_exists");
if (H5Itype_exists(myType) != 0)
goto out;
H5E_BEGIN_TRY
err = H5Inmembers(myType, &num_members);
if(err >= 0)
goto out;
H5E_END_TRY
return 0;
out:
/* Clean up type if it has been allocated and free memory used
* by testObj */
if(myType >= 0)
H5Idestroy_type(myType);
return -1;
}
int main(void)
{
hid_t file_id; /* file identifier */
hid_t space_id; /* dataspace identifiers */
hid_t spacer_id;
hid_t dsetv_id; /*dataset identifiers*/
hid_t dsetr_id;
hsize_t dims[2] = {2,9};
hsize_t dimsr[1] = {2};
int rank = 2;
int rankr =1;
herr_t status;
hdset_reg_ref_t ref[2];
hdset_reg_ref_t ref_out[2];
int data[2][9] = {{1,1,2,3,3,4,5,5,6},{1,2,2,3,4,4,5,6,6}};
int data_out[2][9] = {{0,0,0,0,0,0,0,0,0},{0,0,0,0,0,0,0,0,0}};
hsize_t start[2];
hsize_t count[2];
hsize_t coord[2][3] = {{0, 0, 1}, {6, 0, 8}};
unsigned num_points = 3;
int i, j;
size_t name_size1, name_size2;
char buf1[10], buf2[10];
/*
* Create file with default file access and file creation properties.
*/
file_id = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/*
* Create dataspace for datasets.
*/
space_id = H5Screate_simple(rank, dims, NULL);
spacer_id = H5Screate_simple(rankr, dimsr, NULL);
/*
* Create integer dataset.
*/
dsetv_id = H5Dcreate2(file_id, dsetnamev, H5T_NATIVE_INT, space_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
/*
* Write data to the dataset.
*/
status = H5Dwrite(dsetv_id, H5T_NATIVE_INT, H5S_ALL , H5S_ALL, H5P_DEFAULT,data);
status = H5Dclose(dsetv_id);
/*
* Dataset with references.
*/
dsetr_id = H5Dcreate2(file_id, dsetnamer, H5T_STD_REF_DSETREG, spacer_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
/*
* Create a reference to the hyperslab.
*/
start[0] = 0;
start[1] = 3;
count[0] = 2;
count[1] = 3;
status = H5Sselect_hyperslab(space_id, H5S_SELECT_SET, start, NULL, count, NULL);
status = H5Rcreate(&ref[0], file_id, dsetnamev, H5R_DATASET_REGION, space_id);
/*
* Create a reference to elements selection.
*/
status = H5Sselect_none(space_id);
status = H5Sselect_elements(space_id, H5S_SELECT_SET, num_points, (const hsize_t *)coord);
status = H5Rcreate(&ref[1], file_id, dsetnamev, H5R_DATASET_REGION, space_id);
/*
* Write dataset with the references.
*/
status = H5Dwrite(dsetr_id, H5T_STD_REF_DSETREG, H5S_ALL, H5S_ALL, H5P_DEFAULT,ref);
/*
* Close all objects.
*/
status = H5Sclose(space_id);
status = H5Sclose(spacer_id);
status = H5Dclose(dsetr_id);
status = H5Fclose(file_id);
/*
* Reopen the file to read selections back.
*/
file_id = H5Fopen(filename, H5F_ACC_RDWR, H5P_DEFAULT);
/*
* Reopen the dataset with object references and read references
* to the buffer.
*/
dsetr_id = H5Dopen2(file_id, dsetnamer, H5P_DEFAULT);
status = H5Dread(dsetr_id, H5T_STD_REF_DSETREG, H5S_ALL, H5S_ALL,
H5P_DEFAULT, ref_out);
/*
* Dereference the first reference.
*/
dsetv_id = H5Rdereference2(dsetr_id, H5P_DEFAULT, H5R_DATASET_REGION, &ref_out[0]);
/*
* Get name of the dataset the first region reference points to
* using H5Rget_name
*/
name_size1 = H5Rget_name(dsetr_id, H5R_DATASET_REGION, &ref_out[0], (char*)buf1, 10);
printf(" Dataset's name (returned by H5Rget_name) the reference points to is %s, name length is %d\n", buf1, (int)name_size1);
/*
* Get name of the dataset the first region reference points to
* using H5Iget_name
*/
name_size2 = H5Iget_name(dsetv_id, (char*)buf2, 10);
printf(" Dataset's name (returned by H5Iget_name) the reference points to is %s, name length is %d\n", buf2, (int)name_size2);
space_id = H5Rget_region(dsetr_id, H5R_DATASET_REGION,&ref_out[0]);
/*
* Read and display hyperslab selection from the dataset.
*/
status = H5Dread(dsetv_id, H5T_NATIVE_INT, H5S_ALL, space_id,
H5P_DEFAULT, data_out);
printf("Selected hyperslab: ");
for (i = 0; i <= 1; i++)
{
printf("\n");
for (j = 0; j <= 8; j++)
printf("%d ", data_out[i][j]);
}
printf("\n");
/*
* Close dataspace and the dataset.
*/
status = H5Sclose(space_id);
status = H5Dclose(dsetv_id);
/*
* Initialize data_out array again to get point selection.
*/
for (i = 0; i <= 1; i++)
for (j = 0; j <= 8; j++)
data_out[i][j] = 0;
/*
* Dereference the second reference.
*/
dsetv_id = H5Rdereference2(dsetr_id, H5P_DEFAULT, H5R_DATASET_REGION, &ref_out[1]);
space_id = H5Rget_region(dsetv_id, H5R_DATASET_REGION,&ref_out[1]);
/*
* Read selected data from the dataset.
*/
status = H5Dread(dsetv_id, H5T_NATIVE_INT, H5S_ALL, space_id,
H5P_DEFAULT, data_out);
printf("Selected points: ");
for (i = 0; i <= 1; i++)
{
printf("\n");
for (j = 0; j <= 8; j++)
printf("%d ", data_out[i][j]);
}
printf("\n");
/*
* Close dataspace and the dataset.
*/
status = H5Sclose(space_id);
status = H5Dclose(dsetv_id);
status = H5Dclose(dsetr_id);
status = H5Fclose(file_id);
return 0;
}
/*--------------------------------------------------------------*/
static void validateDependsOnField(pNXVcontext self,
hid_t groupID,hid_t dpFieldID)
{
char fname[512], transData[512];
hid_t attID, attType, attSpace, dpField;
H5T_class_t h5class;
memset(fname,0,sizeof(fname));
memset(transData,0,sizeof(transData));
H5Iget_name(dpFieldID,fname,sizeof(fname));
NXVsetLog(self,"dataPath", fname);
NXVsetLog(self,"sev","debug");
NXVprintLog(self,"message","Validating depends_on element %s", fname);
NXVlog(self);
/*
validate the simple ones
*/
validateDependsOnAttributes(self,dpFieldID);
/*
follow the depends_on chain
*/
if(!H5LTfind_attribute(dpFieldID,"depends_on")){
NXVsetLog(self,"sev","error");
NXVprintLog(self,"message",
"Missing attribute depends_on on %s",
fname);
NXVlog(self);
self->errCount++;
} else {
attID = H5Aopen(dpFieldID,"depends_on",H5P_DEFAULT);
assert(attID >= 0);
attType = H5Aget_type(attID);
assert(attType >= 0);
h5class = H5Tget_class(attType);
if(h5class != H5T_STRING){
NXVsetLog(self,"sev","error");
NXVprintLog(self,"message",
"depends_onattribute on %s is of wrong type, expected string",
fname);
NXVlog(self);
self->errCount++;
} else {
H5NXget_attribute_string(self->fileID, fname,
"depends_on",transData);
if(strcmp(transData,".") == 0){
H5Dclose(dpFieldID);
return;
} else {
dpField = findDependentField(self,dpFieldID,transData);
if(dpField < 0){
NXVsetLog(self,"sev","error");
NXVprintLog(self,"message","Dependency chain broken at %s, %s %s",
fname, transData, "pointing nowhere (nirvana?)");
NXVlog(self);
self->errCount++;
} else {
validateDependsOnField(self,groupID,dpField);
H5Dclose(dpField);
}
}
}
}
}
//-*****************************************************************************
ArImpl::~ArImpl()
{
m_data.reset();
if ( m_file >= 0 )
{
int dsetCount = H5Fget_obj_count( m_file,
H5F_OBJ_LOCAL | H5F_OBJ_DATASET);
int grpCount = H5Fget_obj_count( m_file,
H5F_OBJ_LOCAL | H5F_OBJ_GROUP );
int dtypCount = H5Fget_obj_count( m_file,
H5F_OBJ_LOCAL | H5F_OBJ_DATATYPE );
int attrCount = H5Fget_obj_count( m_file,
H5F_OBJ_LOCAL | H5F_OBJ_ATTR );
int objCount = dsetCount + grpCount + dtypCount + attrCount;
if ( objCount != 0 )
{
std::stringstream strm;
strm << "Open HDF5 handles detected during reading:" << std::endl
<< "DataSets: " << dsetCount
<< ", Groups: " << grpCount
<< ", DataTypes: " << dtypCount
<< ", Attributes: " << attrCount;
std::vector< hid_t > objList;
// when getting the name corresponding to a hid_t, the get_name
// functions always append a NULL character, which we strip off
// when injecting into out stream.
std::string name;
if ( dsetCount > 0 )
{
strm << std::endl << "DataSets: " << std::endl;
objList.resize( dsetCount );
H5Fget_obj_ids( m_file, H5F_OBJ_LOCAL | H5F_OBJ_DATASET,
dsetCount, &objList.front() );
for ( int i = 0; i < dsetCount; ++i )
{
int strLen = H5Iget_name( objList[i], NULL, 0 ) + 1;
name.resize( strLen );
H5Iget_name( objList[i], &(name[0]), strLen );
strm << name.substr(0, name.size() - 1) << std::endl;
}
}
if ( grpCount > 0 )
{
strm << std::endl << std::endl << "Groups:" << std::endl;
objList.resize( grpCount );
H5Fget_obj_ids( m_file, H5F_OBJ_LOCAL | H5F_OBJ_GROUP,
grpCount, &objList.front() );
for ( int i = 0; i < grpCount; ++i )
{
int strLen = H5Iget_name( objList[i], NULL, 0 ) + 1;
name.resize( strLen );
H5Iget_name( objList[i], &(name[0]), strLen );
strm << std::endl << name.substr(0, name.size() - 1);
}
}
if ( attrCount > 0 )
{
strm << std::endl << std::endl << "Attrs:" << std::endl;
objList.resize( attrCount );
H5Fget_obj_ids( m_file, H5F_OBJ_LOCAL | H5F_OBJ_ATTR,
attrCount, &objList.front() );
for ( int i = 0; i < attrCount; ++i )
{
int strLen = H5Aget_name( objList[i], 0, NULL ) + 1;
name.resize( strLen );
H5Aget_name( objList[i], strLen, &(name[0]) );
strm << std::endl << name.substr(0, name.size() - 1);
}
}
// just for formatting purposes
if ( dtypCount > 0 )
{
strm << std::endl;
}
m_file = -1;
ABCA_THROW( strm.str() );
}
H5Fclose( m_file );
m_file = -1;
}
}
int
main (void)
{
hid_t file, space, memspace, dset, dset2, attr;
/* Handles */
herr_t status;
hsize_t dims[1] = {DIM0},
dims2[2] = {DS2DIM0, DS2DIM1},
coords[4][2] = { {0, 1},
{2, 11},
{1, 0},
{2, 4} },
start[2] = {0, 0},
stride[2] = {2, 11},
count[2] = {2, 2},
block[2] = {1, 3};
hssize_t npoints;
hdset_reg_ref_t wdata[DIM0], /* Write buffer */
*rdata; /* Read buffer */
ssize_t size;
char wdata2[DS2DIM0][DS2DIM1] = {"The quick brown",
"fox jumps over ",
"the 5 lazy dogs"},
*rdata2,
*name;
int ndims,
i;
/*
* Create a new file using the default properties.
*/
file = H5Fcreate (FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/*
* Create a dataset with character data.
*/
space = H5Screate_simple (2, dims2, NULL);
dset2 = H5Dcreate (file, DATASET2, H5T_STD_I8LE, space, H5P_DEFAULT,
H5P_DEFAULT, H5P_DEFAULT);
status = H5Dwrite (dset2, H5T_NATIVE_CHAR, H5S_ALL, H5S_ALL, H5P_DEFAULT,
wdata2);
/*
* Create reference to a list of elements in dset2.
*/
status = H5Sselect_elements (space, H5S_SELECT_SET, 4, coords[0]);
status = H5Rcreate (&wdata[0], file, DATASET2, H5R_DATASET_REGION, space);
/*
* Create reference to a hyperslab in dset2, close dataspace.
*/
status = H5Sselect_hyperslab (space, H5S_SELECT_SET, start, stride, count,
block);
status = H5Rcreate (&wdata[1], file, DATASET2, H5R_DATASET_REGION, space);
status = H5Sclose (space);
/*
* Create dataset with a null dataspace to serve as the parent for
* the attribute.
*/
space = H5Screate (H5S_NULL);
dset = H5Dcreate (file, DATASET, H5T_STD_I32LE, space, H5P_DEFAULT,
H5P_DEFAULT, H5P_DEFAULT);
status = H5Sclose (space);
/*
* Create dataspace. Setting maximum size to NULL sets the maximum
* size to be the current size.
*/
space = H5Screate_simple (1, dims, NULL);
/*
* Create the attribute and write the region references to it.
*/
attr = H5Acreate (dset, ATTRIBUTE, H5T_STD_REF_DSETREG, space, H5P_DEFAULT,
H5P_DEFAULT);
status = H5Awrite (attr, H5T_STD_REF_DSETREG, wdata);
/*
* Close and release resources.
*/
status = H5Aclose (attr);
status = H5Dclose (dset);
status = H5Dclose (dset2);
status = H5Sclose (space);
status = H5Fclose (file);
/*
* Now we begin the read section of this example. Here we assume
* the attribute has the same name and rank, but can have any size.
* Therefore we must allocate a new array to read in data using
* malloc().
*/
/*
* Open file, dataset, and attribute.
*/
file = H5Fopen (FILE, H5F_ACC_RDONLY, H5P_DEFAULT);
dset = H5Dopen (file, DATASET, H5P_DEFAULT);
attr = H5Aopen (dset, ATTRIBUTE, H5P_DEFAULT);
/*
* Get dataspace and allocate memory for read buffer.
*/
space = H5Aget_space (attr);
ndims = H5Sget_simple_extent_dims (space, dims, NULL);
rdata = (hdset_reg_ref_t *) malloc (dims[0] * sizeof (hdset_reg_ref_t));
status = H5Sclose (space);
/*
* Read the data.
*/
status = H5Aread (attr, H5T_STD_REF_DSETREG, rdata);
/*
* Output the data to the screen.
*/
for (i=0; i<dims[0]; i++) {
printf ("%s[%d]:\n ->", ATTRIBUTE, i);
/*
* Open the referenced object, retrieve its region as a
* dataspace selection.
*/
dset2 = H5Rdereference (dset, H5P_DEFAULT, H5R_DATASET_REGION, &rdata[i]);
space = H5Rget_region (dset, H5R_DATASET_REGION, &rdata[i]);
/*
* Get the length of the object's name, allocate space, then
* retrieve the name.
*/
size = 1 + H5Iget_name (dset2, NULL, 0);
name = (char *) malloc (size);
size = H5Iget_name (dset2, name, size);
/*
* Allocate space for the read buffer. We will only allocate
* enough space for the selection, plus a null terminator. The
* read buffer will be 1-dimensional.
*/
npoints = H5Sget_select_npoints (space);
rdata2 = (char *) malloc (npoints + 1);
/*
* Read the dataset region, and add a null terminator so we can
* print it as a string.
*/
memspace = H5Screate_simple (1, (hsize_t *) &npoints, NULL);
status = H5Dread (dset2, H5T_NATIVE_CHAR, memspace, space, H5P_DEFAULT,
rdata2);
rdata2[npoints] = '\0';
/*
* Print the name and region data, close and release resources.
*/
printf (" %s: %s\n", name, rdata2);
free (rdata2);
free (name);
status = H5Sclose (space);
status = H5Sclose (memspace);
status = H5Dclose (dset2);
}
/*
* Close and release resources.
*/
free (rdata);
status = H5Aclose (attr);
status = H5Dclose (dset);
status = H5Fclose (file);
return 0;
}
std::string HdfGroup::name() const
{
char name[HDF_MAX_NAME];
H5Iget_name( d->id, name, HDF_MAX_NAME );
return std::string( name );
}
/*--------------------------------------------------------------*/
int NXVvalidateGroup(pNXVcontext self, hid_t groupID,
xmlNodePtr groupNode)
{
hash_table namesSeen, baseNames;
xmlNodePtr cur = NULL;
xmlChar *name = NULL, *myClass = NULL;
xmlChar *target = NULL;
hid_t childID;
char fName[256], childName[512], nxdlChildPath[512], childPath[512];
char mynxdlPath[512];
char *savedNXDLPath, *pPtr;
SecondPassData spd;
hsize_t idx = 0;
/*
manage nxdlPath, xmlGetNodePath does not work
*/
savedNXDLPath = self->nxdlPath;
myClass = xmlGetProp(groupNode,(xmlChar *)"type");
if(self->nxdlPath == NULL) {
snprintf(mynxdlPath,sizeof(mynxdlPath),"/%s", (char *) myClass);
} else {
snprintf(mynxdlPath,sizeof(mynxdlPath),"%s/%s",
self->nxdlPath, (char *) myClass);
}
self->nxdlPath = mynxdlPath;
/*
tell what we are doing
*/
H5Iget_name(groupID,fName,sizeof(fName));
NXVsetLog(self,"sev","debug");
NXVsetLog(self,"message","Validating group");
NXVsetLog(self,"nxdlPath",self->nxdlPath);
NXVsetLog(self,"dataPath",fName);
NXVlog(self);
validateGroupAttributes(self, groupID, groupNode);
hash_construct_table(&namesSeen,100);
/* first pass */
cur = groupNode->xmlChildrenNode;
while(cur != NULL){
if(xmlStrcmp(cur->name,(xmlChar *) "group") == 0){
childID = findGroup(self, groupID, cur);
if(childID >= 0){
H5Iget_name(childID, childName,sizeof(childName));
/*
we have to get at the HDF5 name. There may be no
name in the NXDL, but a suitable group has been found
by NXclass.
*/
pPtr = strrchr(childName,'/');
if(pPtr != NULL){
hash_insert(pPtr+1,strdup(""),&namesSeen);
} else {
hash_insert(childName,strdup(""),&namesSeen);
}
NXVvalidateGroup(self,childID,cur);
} else {
name = xmlGetProp(cur,(xmlChar *)"type");
snprintf(nxdlChildPath,sizeof(nxdlChildPath),"%s/%s",
self->nxdlPath, (char *)name);
xmlFree(name);
NXVsetLog(self,"dataPath",fName);
NXVsetLog(self,"nxdlPath", nxdlChildPath);
if(!isOptional(cur)){
NXVsetLog(self,"sev","error");
NXVsetLog(self,"message","Required group missing");
NXVlog(self);
self->errCount++;
} else {
NXVsetLog(self,"sev","warnopt");
NXVsetLog(self,"message","Optional group missing");
NXVlog(self);
}
}
}
if(xmlStrcmp(cur->name,(xmlChar *) "field") == 0){
name = xmlGetProp(cur,(xmlChar *)"name");
if(H5LTfind_dataset(groupID,(char *)name) ) {
childID = H5Dopen(groupID,(char *)name,H5P_DEFAULT);
} else {
childID = -1;
}
snprintf(childPath,sizeof(childPath),"%s/%s",
fName,name);
if(childID < 0){
NXVsetLog(self,"dataPath",childPath);
snprintf(nxdlChildPath,sizeof(nxdlChildPath),
"%s/%s", self->nxdlPath, name);
NXVsetLog(self,"nxdlPath", nxdlChildPath);
if(!isOptional(cur)){
NXVsetLog(self,"sev","error");
NXVsetLog(self,"message","Required field missing");
NXVlog(self);
self->errCount++;
} else {
NXVsetLog(self,"sev","warnopt");
NXVsetLog(self,"message","Optional field missing");
NXVlog(self);
}
} else {
if(xmlStrcmp(name,(xmlChar *)"depends_on") == 0){
/*
This must b validated from the field level. As
it might point to fields which are not in the
application definition
*/
validateDependsOn(self,groupID,childID);
} else {
NXVvalidateField(self,childID, cur);
}
hash_insert((char *)name,strdup(""),&namesSeen);
}
xmlFree(name);
}
if(xmlStrcmp(cur->name,(xmlChar *) "link") == 0){
name = xmlGetProp(cur,(xmlChar *)"name");
target = xmlGetProp(cur,(xmlChar *)"target");
hash_insert((char *)name,strdup(""),&namesSeen);
validateLink(self,groupID,name, target);
xmlFree(name);
xmlFree(target);
}
cur = cur->next;
}
/*
Second pass: search the HDF5 group for additional
stuff which have not checked yet. Most of the hard work
is in the SecondPassIterator.
*/
hash_construct_table(&baseNames,100);
NXVloadBaseClass(self,&baseNames,(char *)myClass);
spd.baseNames = &baseNames;
spd.namesSeen = &namesSeen;
spd.self = self;
NXVsetLog(self,"nxdlPath", mynxdlPath);
H5Literate(groupID, H5_INDEX_NAME, H5_ITER_INC, &idx,
SecondPassIterator, &spd);
/*
clean up
*/
hash_free_table(&namesSeen,free);
hash_free_table(&baseNames,free);
xmlFree(myClass);
/*
restore my paths...
*/
self->nxdlPath = savedNXDLPath;
return 0;
}
/*--------------------------------------------------------------*/
static herr_t SecondPassIterator(hid_t g_id,
const char *name,
const H5L_info_t *info, void *op_data)
{
SecondPassData *spd = (SecondPassData *)op_data;
H5O_info_t obj_info;
hid_t attID, groupID, dataID;
char nxClass[512], fname[512];
/*
have we seen that yet?
*/
if(hash_lookup((char *)name,spd->namesSeen) != NULL){
return 0;
}
/*
Nope, we will have to warn...
*/
H5Oget_info_by_name(g_id, name, &obj_info,H5P_DEFAULT);
if(obj_info.type == H5O_TYPE_GROUP){
groupID = H5Gopen(g_id,name,H5P_DEFAULT);
H5Iget_name(groupID, fname,sizeof(fname));
NXVsetLog(spd->self,"dataPath",fname);
if(H5LTfind_attribute(groupID,"NX_class") == 1){
memset(nxClass,0,sizeof(nxClass));
H5NXget_attribute_string(g_id,name,
"NX_class", nxClass);
if(hash_lookup(nxClass,spd->baseNames) == NULL){
NXVsetLog(spd->self,"sev","warnundef");
NXVprintLog(spd->self,"message","Unknown group %s of class %s found",
name, nxClass);
NXVlog(spd->self);
spd->self->warnCount++;
} else {
NXVsetLog(spd->self,"sev","warnbase");
NXVprintLog(spd->self,"message",
"Additional base class group %s of type %s found",
name, nxClass);
NXVlog(spd->self);
spd->self->warnCount++;
}
} else {
NXVsetLog(spd->self,"sev","warnundef");
NXVprintLog(spd->self,"message",
"Additional non NeXus group %s found",
name);
NXVlog(spd->self);
spd->self->warnCount++;
}
H5Gclose(groupID);
} else if (obj_info.type == H5O_TYPE_DATASET) {
dataID = H5Dopen(g_id,name,H5P_DEFAULT);
H5Iget_name(dataID, fname,sizeof(fname));
H5Dclose(dataID);
NXVsetLog(spd->self,"dataPath",fname);
if(hash_lookup((char *)name,spd->baseNames) == NULL){
NXVsetLog(spd->self,"sev","warnundef");
NXVprintLog(spd->self,"message","Unknown dataset %s found",
name);
NXVlog(spd->self);
spd->self->warnCount++;
} else {
NXVsetLog(spd->self,"sev","warnbase");
NXVprintLog(spd->self,"message","Additional base class dataset %s found",
name);
NXVlog(spd->self);
spd->self->warnCount++;
}
}
return 0;
}
