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Save attribute datasets to the root location as a default (Resolves issue #66) #79

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Merged
ulrikpedersen merged 2 commits into from
Mar 11, 2015
Merged

Save attribute datasets to the root location as a default (Resolves issue #66) #79

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350101e
Implemented use of auto_ndattr_default tag for issue #66.
ajgdls Mar 11, 2015
3b71280
Save attribute datasets to the root location as a default (Resolve #66).
ajgdls Mar 11, 2015
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43 changes: 30 additions & 13 deletions ADApp/pluginSrc/NDFileHDF5.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -1992,27 +1992,35 @@ asynStatus NDFileHDF5::writePerformanceDataset()
}
}

if(perf_group == NULL)
{
asynPrint(this->pasynUserSelf, ASYN_TRACE_WARNING, "%s::writePerformanceDataset No default attribute group defined.\n",
driverName);
return asynError;
}

getIntegerParam(NDFileNumCaptured, &numCaptured);
dims[1] = 5;
if (numCaptured < this->numPerformancePoints) dims[0] = numCaptured;
else dims[0] = this->numPerformancePoints;

if(perf_group == NULL)
{
// Check if the auto_ndattr_default tag is true, if it is then the root group is the file
if (this->layout.getAutoNDAttrDefault()){
group_performance = this->file;
} else {
asynPrint(this->pasynUserSelf, ASYN_TRACE_WARNING, "%s::writePerformanceDataset No default attribute group defined.\n",
driverName);
return asynError;
}
} else {
group_performance = H5Gopen(this->file, perf_group->get_full_name().c_str(), H5P_DEFAULT);
}

/* Create the "timestamp" dataset */
dataspace_id = H5Screate_simple(2, dims, NULL);
group_performance = H5Gopen(this->file, perf_group->get_full_name().c_str(), H5P_DEFAULT);
dataset_id = H5Dcreate2(group_performance, "timestamp", H5T_NATIVE_DOUBLE, dataspace_id,
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (!H5Iis_valid(dataset_id)) {
asynPrint(this->pasynUserSelf, ASYN_TRACE_WARNING, "NDFileHDF5::writePerformanceDataset: unable to create \'timestamp\' dataset.");
H5Sclose(dataspace_id);
H5Gclose(group_performance);
if(perf_group != NULL){
H5Gclose(group_performance);
}
return asynError;
}
/* Write the second dataset. */
Expand All @@ -2027,7 +2035,9 @@ asynStatus NDFileHDF5::writePerformanceDataset()
H5Dclose(dataset_id);

/* Close the group. */
H5Gclose(group_performance);
if(perf_group != NULL){
H5Gclose(group_performance);
}
} else {
return asynError;
}
Expand Down Expand Up @@ -2070,8 +2080,13 @@ asynStatus NDFileHDF5::createAttributeDataset()
}
}
else {
asynPrint(this->pasynUserSelf, ASYN_TRACE_WARNING, "%s::%s No default attribute group defined.\n",
driverName, functionName);
// Check if the auto_ndattr_default tag is true, if it is then the root group is the file
if (this->layout.getAutoNDAttrDefault()){
groupDefault = this->file;
} else {
asynPrint(this->pasynUserSelf, ASYN_TRACE_WARNING, "%s::%s No default attribute group defined.\n",
driverName, functionName);
}
}

ndAttr = this->pFileAttributes->next(ndAttr); // get the first NDAttribute
Expand Down Expand Up @@ -2196,7 +2211,9 @@ asynStatus NDFileHDF5::createAttributeDataset()
}
ndAttr = this->pFileAttributes->next(ndAttr);
}
H5Gclose(groupDefault);
if(def_group != NULL){
H5Gclose(groupDefault);
}

return asynSuccess;
}
Expand Down
86 changes: 63 additions & 23 deletions ADApp/pluginSrc/NDFileHDF5LayoutXML.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -17,26 +17,28 @@
namespace hdf5
{

const std::string LayoutXML::ATTR_ELEMENT_NAME = "name";
const std::string LayoutXML::ATTR_GROUP = "group";
const std::string LayoutXML::ATTR_DATASET = "dataset";
const std::string LayoutXML::ATTR_ATTRIBUTE = "attribute";
const std::string LayoutXML::ATTR_GLOBAL = "global";
const std::string LayoutXML::ATTR_HARDLINK = "hardlink";

const std::string LayoutXML::ATTR_SOURCE = "source";
const std::string LayoutXML::ATTR_SRC_DETECTOR = "detector";
const std::string LayoutXML::ATTR_SRC_DET_DEFAULT = "det_default";
const std::string LayoutXML::ATTR_SRC_NDATTR = "ndattribute";
const std::string LayoutXML::ATTR_SRC_CONST = "constant";
const std::string LayoutXML::ATTR_SRC_CONST_VALUE = "value";
const std::string LayoutXML::ATTR_SRC_CONST_TYPE = "type";
const std::string LayoutXML::ATTR_GRP_NDATTR_DEFAULT = "ndattr_default";
const std::string LayoutXML::ATTR_SRC_WHEN = "when";
const std::string LayoutXML::ATTR_GLOBAL_NAME = "name";
const std::string LayoutXML::ATTR_GLOBAL_VALUE = "ndattribute";
const std::string LayoutXML::ATTR_HARDLINK_NAME = "name";
const std::string LayoutXML::ATTR_HARDLINK_TARGET = "target";
const std::string LayoutXML::ATTR_ELEMENT_NAME = "name";
const std::string LayoutXML::ATTR_ROOT = "hdf5_layout";
const std::string LayoutXML::ATTR_GROUP = "group";
const std::string LayoutXML::ATTR_DATASET = "dataset";
const std::string LayoutXML::ATTR_ATTRIBUTE = "attribute";
const std::string LayoutXML::ATTR_GLOBAL = "global";
const std::string LayoutXML::ATTR_HARDLINK = "hardlink";

const std::string LayoutXML::ATTR_ROOT_NDATTR_DEFAULT = "auto_ndattr_default";
const std::string LayoutXML::ATTR_SOURCE = "source";
const std::string LayoutXML::ATTR_SRC_DETECTOR = "detector";
const std::string LayoutXML::ATTR_SRC_DET_DEFAULT = "det_default";
const std::string LayoutXML::ATTR_SRC_NDATTR = "ndattribute";
const std::string LayoutXML::ATTR_SRC_CONST = "constant";
const std::string LayoutXML::ATTR_SRC_CONST_VALUE = "value";
const std::string LayoutXML::ATTR_SRC_CONST_TYPE = "type";
const std::string LayoutXML::ATTR_GRP_NDATTR_DEFAULT = "ndattr_default";
const std::string LayoutXML::ATTR_SRC_WHEN = "when";
const std::string LayoutXML::ATTR_GLOBAL_NAME = "name";
const std::string LayoutXML::ATTR_GLOBAL_VALUE = "ndattribute";
const std::string LayoutXML::ATTR_HARDLINK_NAME = "name";
const std::string LayoutXML::ATTR_HARDLINK_TARGET = "target";

const std::string LayoutXML::DEFAULT_LAYOUT = " \
<group name=\"entry\"> \
Expand Down Expand Up @@ -68,7 +70,7 @@ namespace hdf5
</group> <!-- end group data --> \
</group> <!-- end group entry --> ";

LayoutXML::LayoutXML() : ptr_tree(NULL), ptr_curr_element(NULL)
LayoutXML::LayoutXML() : auto_ndattr_default(true), ptr_tree(NULL), ptr_curr_element(NULL)
{
log = log4cxx::Logger::getLogger("LayoutXML");

Expand All @@ -89,6 +91,7 @@ namespace hdf5
int LayoutXML::load_xml()
{
int ret = 0;
auto_ndattr_default = true;
this->xmlreader = xmlReaderForMemory(DEFAULT_LAYOUT.c_str(),
(int)DEFAULT_LAYOUT.size(),
"noname.xml",
Expand Down Expand Up @@ -123,6 +126,7 @@ namespace hdf5
int LayoutXML::load_xml(const std::string& filename)
{
int ret = 0;
auto_ndattr_default = true;
// if the file name contains <?xml then load it as an xml string from memory
if (filename.find("<?xml") != std::string::npos){
this->xmlreader = xmlReaderForMemory(filename.c_str(), (int)filename.length(), NULL, NULL, 0);
Expand Down Expand Up @@ -159,6 +163,7 @@ namespace hdf5
{
int ret = 0;
int status = 0;
auto_ndattr_default = true;

// if the file name contains <?xml then load it as an xml string from memory
if (filename.find("<?xml") != std::string::npos){
Expand Down Expand Up @@ -232,6 +237,11 @@ namespace hdf5
return this->globals[name];
}

bool LayoutXML::getAutoNDAttrDefault()
{
return auto_ndattr_default;
}

/** Process one XML node and create the necessary HDF5 element if necessary
*
*/
Expand All @@ -247,13 +257,14 @@ namespace hdf5
}

std::string name((const char*)xmlname);

switch( type )
{
// Elements can be either 'group', 'dataset' or 'attribute'
case XML_READER_TYPE_ELEMENT:
//LOG4CXX_DEBUG(log, "process_node: \'" << name << "\' (" << xmlname << ")" );
if (name == LayoutXML::ATTR_GROUP){
if (name == LayoutXML::ATTR_ROOT){
ret = this->parse_root();
} else if (name == LayoutXML::ATTR_GROUP){
ret = this->new_group();
} else if (name == LayoutXML::ATTR_DATASET){
ret = this->new_dataset();
Expand Down Expand Up @@ -392,6 +403,35 @@ namespace hdf5
return ret;
}

int LayoutXML::parse_root()
{
// First check the basics, no attributes is not an error but we should return
if (! xmlTextReaderHasAttributes(this->xmlreader) ) return 0;

// Check for the auto_ndattr_default tag
xmlChar * root_auto = NULL;
root_auto = xmlTextReaderGetAttribute(this->xmlreader, (const xmlChar *)LayoutXML::ATTR_ROOT_NDATTR_DEFAULT.c_str());

// A tag has been added but it's not the one we expect, return an error
if (root_auto == NULL) return -1;

// Get the standard string representation of the tag
std::string str_root_auto((char*)root_auto);
xmlFree(root_auto);

// Now check if we have the correct string
if (str_root_auto == "false"){
// Set our flag to false and return success
auto_ndattr_default = false;
return 0;
} else if (str_root_auto == "true"){
// Do nothing but return success
return 0;
}
// Any strings other than false (or true) are not understood, return an error
return -1;
}

int LayoutXML::new_group()
{
// First check the basics
Expand Down
5 changes: 5 additions & 0 deletions ADApp/pluginSrc/NDFileHDF5LayoutXML.h
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Original file line number Diff line number Diff line change
Expand Up @@ -60,12 +60,14 @@ namespace hdf5
{
public:
static const std::string ATTR_ELEMENT_NAME;
static const std::string ATTR_ROOT;
static const std::string ATTR_GROUP;
static const std::string ATTR_DATASET;
static const std::string ATTR_ATTRIBUTE;
static const std::string ATTR_GLOBAL;
static const std::string ATTR_HARDLINK;

static const std::string ATTR_ROOT_NDATTR_DEFAULT;
static const std::string ATTR_SOURCE;
static const std::string ATTR_SRC_DETECTOR;
static const std::string ATTR_SRC_DET_DEFAULT;
Expand All @@ -92,19 +94,22 @@ namespace hdf5

Root* get_hdftree();
std::string get_global(const std::string& name);
bool getAutoNDAttrDefault();

private:
int process_node();

int process_dset_xml_attribute(DataSource& out);
int process_attribute_xml_attribute(Attribute& out);

int parse_root();
int new_group();
int new_dataset();
int new_attribute();
int new_global();
int new_hardlink();

bool auto_ndattr_default;
log4cxx::LoggerPtr log;
Root* ptr_tree;
Element *ptr_curr_element;
Expand Down