FileReaderVOTable.cc
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/*
* FileReaderVOTable.cc
*
* Created on: Nov 24, 2014
* Author: AKKA
*/
#include <boost/algorithm/string/trim_all.hpp>
#include <boost/algorithm/string.hpp>
#include <boost/filesystem.hpp>
#include <libxml/xmlreader.h>
#include "TimeUtil.hh"
#include "FileReaderVOTable.hh"
namespace AMDA {
namespace LocalFileInterface {
// 32 KB is the maximum supported line size
int FileReaderVOTable::MaxLineSize = 32 * 1024;
FileReaderVOTable::FileReaderVOTable() :
_votFilePath(), _dataFloat(NULL), _dataDouble(NULL), _dataShort(NULL), _dataInt(NULL), _data(
NULL) {
}
FileReaderVOTable::~FileReaderVOTable() {
}
/**
* Parses XML file and looks for FIELD and PARAM element containing parameters informations
*/
void FileReaderVOTable::getVOTableInfo(void) {
const xmlChar *name;
const xmlChar *fieldId;
const xmlChar *fieldName;
const xmlChar *fieldXType;
const xmlChar *fieldArraySize;
const xmlChar *fieldDataType;
const xmlChar *groupId;
const xmlChar *paramName;
const xmlChar *paramSize;
const xmlChar *paramValue;
bool parsingTable = false;
bool parsingField = false;
bool parsingGroup = false;
bool parsingParam = false;
std::string crtGroupId;
// Clear current field informations
_fieldsInfo.clear();
//Clear current param informations
_paramsInfo.clear();
// created XML reader
xmlTextReaderPtr reader = xmlReaderForFile(_votFilePath.c_str(), NULL, 0);
// read xml file tag by tag
while (xmlTextReaderRead(reader) == 1) {
// -- read tag
name = xmlTextReaderConstName(reader);
if (name != NULL) {
// get tag name to easily handle it
std::string tagName = std::string((const char*) name);
if (tagName == "TABLE") {
parsingTable = !parsingTable;
}
if ((parsingTable == true) && (tagName == "GROUP")) {
// parsing group is set when we are on the start element only,
// this will prevent problems if GROUP tag ends width />
parsingGroup = (xmlTextReaderNodeType(reader) == 1);
if (parsingGroup == true) {
groupId = xmlTextReaderGetAttribute(reader,
(const xmlChar*) "ID");
if (groupId != NULL)
{
crtGroupId = std::string((const char*) groupId);
xmlFree((xmlChar *) groupId);
}
else
crtGroupId = "";
}
else
crtGroupId = "";
}
if ((parsingTable == true) && (tagName == "PARAM")) {
// parsing param is set when we are on the start element only,
// this will prevent problems if PARAM tag ends width />
parsingParam = (xmlTextReaderNodeType(reader) == 1);
if (parsingParam == true) {
// Create e new param Info
boost::shared_ptr<ParamInfo> paramInfo(new ParamInfo);
paramName = xmlTextReaderGetAttribute(reader,
(const xmlChar*) "name");
paramSize = xmlTextReaderGetAttribute(reader,
(const xmlChar*) "arraysize");
paramValue = xmlTextReaderGetAttribute(reader,
(const xmlChar*) "value");
paramInfo->setGroupId(crtGroupId);
if (paramName != NULL)
{
paramInfo->setName((const char *) paramName);
xmlFree((xmlChar *) paramName);
}
if (paramSize != NULL)
{
paramInfo->setSize((const char *) paramSize);
xmlFree((xmlChar *) paramSize);
}
if (paramValue != NULL)
{
paramInfo->setValue((const char *) paramValue);
xmlFree((xmlChar *) paramValue);
}
LOG4CXX_INFO(gLogger, "PARAM : " << tagName <<
", GROUP ID = " << paramInfo->getGroupId() <<
", name = " << paramInfo->getName() <<
", arraysize = " << paramInfo->getSize() <<
", value = " << paramInfo->getValue());
_paramsInfo.push_back(paramInfo);
}
}
if ((parsingTable == true) && (tagName == "FIELD")) {
// parsing field is set when we are on the start element only,
// this will prevent problems if FIELD tag ends width />
parsingField = (xmlTextReaderNodeType(reader) == 1);
if (parsingField == true) {
// Create e new field Info
boost::shared_ptr<FieldInfo> fieldInfo(new FieldInfo);
fieldId = xmlTextReaderGetAttribute(reader,
(const xmlChar*) "ID");
fieldName = xmlTextReaderGetAttribute(reader,
(const xmlChar*) "name");
fieldXType = xmlTextReaderGetAttribute(reader,
(const xmlChar*) "xtype");
fieldArraySize = xmlTextReaderGetAttribute(reader,
(const xmlChar*) "arraysize");
fieldDataType = xmlTextReaderGetAttribute(reader,
(const xmlChar*) "datatype");
if (fieldId != NULL)
{
fieldInfo->setId((const char *) fieldId);
xmlFree((xmlChar *) fieldId);
}
if (fieldName != NULL)
{
fieldInfo->setName((const char *) fieldName);
xmlFree((xmlChar *) fieldName);
}
if (fieldXType != NULL)
{
fieldInfo->setXtype((const char *) fieldXType);
xmlFree((xmlChar *) fieldXType);
}
if (fieldArraySize != NULL)
{
fieldInfo->setSize((const char *) fieldArraySize);
xmlFree((xmlChar *) fieldArraySize);
}
if (fieldDataType != NULL)
{
fieldInfo->setType((const char *) fieldDataType);
xmlFree((xmlChar *) fieldDataType);
}
LOG4CXX_INFO(gLogger, "FIELD : " << tagName <<
", ID = " << fieldInfo->getId() <<
", name = " << fieldInfo->getName() <<
", xtype = " << fieldInfo->getXtype() <<
", arraysize = " << fieldInfo->getSize() <<
", datatype = " << fieldInfo->getType());
_fieldsInfo.push_back(fieldInfo);
}
}
// Stop reading fields informations when data starts
if (tagName == "TABLEDATA")
break;
}
}
xmlFreeTextReader(reader);
}
/**
* Retrieve TR line position in the VOTable file where time >= timeStart
*/
int FileReaderVOTable::getStartTimePos(int timeColumn, double timeStart) {
const xmlChar *name;
bool parsingTableData = false;
bool parsingTR = false;
bool parsingTD = false;
int curTR = -1;
int curTD = -1;
// created XML reader
xmlTextReaderPtr reader = xmlReaderForFile(_votFilePath.c_str(), NULL, 0);
// read xml file tag by tag
while (xmlTextReaderRead(reader) == 1) {
// -- read tag
name = xmlTextReaderConstName(reader);
if (name != NULL) {
// get tag name to easily handle it
std::string tagName = std::string((const char*) name);
if (tagName == "TABLEDATA") {
parsingTableData = !parsingTableData;
}
// Detect start TR element
if ((parsingTableData == true) && (tagName == "TR")) {
parsingTR = !parsingTR;
// Increment TR count
// Reset TD count
if (parsingTR == true) {
curTR++;
curTD = -1;
}
}
// Detect start TD element
if ((parsingTR == true) && (tagName == "TD")) {
parsingTD = !parsingTD;
// Increment TD count
if (parsingTD == true)
curTD++;
}
// Detect TD #text element
if ((parsingTD == true) && (tagName == "#text")) {
const xmlChar *text = xmlTextReaderConstValue(reader);
// Current TD correspond with timeColumn ?
if (curTD == timeColumn) {
// Convert ISO time
double lineTime = TimeUtil::readTimeInIso((char *) text);
// Current line time is >= requested time start ?
if (lineTime >= timeStart)
{
xmlFreeTextReader(reader);
return (curTR);
}
}
}
}
}
xmlFreeTextReader(reader);
LOG4CXX_ERROR(gLogger,
"FileReaderVOTable::getFieldsStartTimePos - Cannot get record index");
return (-1);
}
std::vector<std::string> &FileReaderVOTable::split(const std::string &s, char delim, std::vector<std::string> &elems) {
std::stringstream ss(s);
std::string item;
while (std::getline(ss, item, delim)) {
if (item.empty())
continue;
elems.push_back(item);
}
return elems;
}
FileReaderStatus FileReaderVOTable::getParamPacketData(int timeColumn, int paramColumn, int recordIndex, double stopTime,
LocalParamDataPacket *packet) {
const xmlChar *name;
bool parsingTableData = false;
bool parsingTR = false;
bool parsingTD = false;
int curTR = -1;
int curTD = -1;
double lineTime = 0;
bool packetFull;
std::string columnValues;
// created XML reader
xmlTextReaderPtr reader = xmlReaderForFile(_votFilePath.c_str(), NULL, 0);
// read xml file tag by tag
while (xmlTextReaderRead(reader) == 1) {
// -- read tag
name = xmlTextReaderConstName(reader);
if (name != NULL) {
// get tag name to easily handle it
std::string tagName = std::string((const char*) name);
if (tagName == "TABLEDATA") {
parsingTableData = !parsingTableData;
}
// Detect start TR element
if ((parsingTableData == true) && (tagName == "TR")) {
parsingTR = !parsingTR;
// Increment TR count
// Reset TD count
if (parsingTR == true) {
curTR++;
curTD = -1;
}
// Detect the end of a TR element ?
// If so, and current time is not 0, write packet
if ((parsingTR == false) && (lineTime != 0)) {
std::vector<std::string> paramList;
split (columnValues, ' ', paramList);
if (((int) paramList.size()) == packet->getDimsSize()) {
// Extract values on the line depending on their type
for (int p=0;p<(int) paramList.size(); p++) {
if (packet->getType() == TYPE_FLOAT)
_dataFloat[p] = std::stof(paramList.at(p));
else if (packet->getType() == TYPE_DOUBLE)
_dataDouble[p] = std::stod(paramList.at(p));
else if (packet->getType() == TYPE_SHORT)
_dataShort[p] = (short) std::stof(paramList.at(p));
else if (packet->getType() == TYPE_INT)
_dataInt[p] = (int) std::stoi(paramList.at(p));
}
} else {
LOG4CXX_ERROR(gLogger,
"FileReaderASCII::getParamPacketData - Wrong dimension for parameter");
xmlFreeTextReader(reader);
return FRS_ERROR;
}
//add data record in the packet
if (!packet->addData(lineTime, _data, packetFull)) {
if (packetFull) {
xmlFreeTextReader(reader);
return FRS_MORE;
}
LOG4CXX_ERROR(gLogger,
"FileReaderASCII::getParamPacketData - Error to add data in packet");
xmlFreeTextReader(reader);
return FRS_ERROR;
}
}
}
// Detect start TD element
if ((parsingTR == true) && (tagName == "TD")) {
parsingTD = !parsingTD;
// Increment TD count
if (parsingTD == true)
curTD++;
}
// Wait for recordIndex TR to start extraction
if (curTR < recordIndex)
continue;
// time for the current line is greater than stopTime
// we have finished !
if (lineTime > stopTime) {
xmlFreeTextReader(reader);
return FRS_FINISH;
}
// Detect TD #text element
if ((parsingTD == true) && (tagName == "#text")) {
const xmlChar *text = xmlTextReaderConstValue(reader);
// Current TD correspond with timeColumn ?
// Yes record current time
if (curTD == timeColumn) {
lineTime = TimeUtil::readTimeInIso((char *) text);
}
// Current TD correspond with parameter columns ?
// Yes record them
if (curTD == paramColumn) {
columnValues = std::string((const char *) text);
}
}
}
}
xmlFreeTextReader(reader);
return FRS_EOF;
}
bool FileReaderVOTable::open(std::string filePath) {
// Store votTable filePath
_votFilePath = filePath;
return (boost::filesystem::exists(filePath));
}
bool FileReaderVOTable::close(void) {
return (true);
}
bool FileReaderVOTable::isOpened(void) {
return (false);
}
std::string FileReaderVOTable::getTimeParamId(void) {
LOG4CXX_DEBUG(gLogger, "FileReaderVOTable::getTimeParamId");
// Read fields informations from the VOTable file
getVOTableInfo();
for (auto fieldInfo : _fieldsInfo) {
if (fieldInfo->getXtype() == "dateTime") {
if (fieldInfo->getId().empty() == false)
return fieldInfo->getId();
else
return fieldInfo->getName();
}
}
// Time parameter id is always at the first position in text files
return std::string("");
}
bool FileReaderVOTable::getParamInfo(std::string& paramId,
LocalParamType& paramType, int& dim1Size, int& dim2Size) {
LOG4CXX_DEBUG(gLogger, "FileReaderVOTable::getParamInfo");
// Read fields informations from the VOTable file
getVOTableInfo();
for (auto fieldInfo : _fieldsInfo) {
// if Id is set check for corresponding paramId with Id, otherwise, use Name
if ((fieldInfo->getId() == paramId)
|| (fieldInfo->getName() == paramId)) {
if (fieldInfo->getType() == "float")
paramType = LocalParamType::TYPE_FLOAT;
else if (fieldInfo->getType() == "double")
paramType = LocalParamType::TYPE_DOUBLE;
else if (fieldInfo->getType() == "short")
paramType = LocalParamType::TYPE_SHORT;
else if (fieldInfo->getType() == "int")
paramType = LocalParamType::TYPE_INT;
else
// If field (data)type is not supported, suppose it's double
paramType = LocalParamType::TYPE_DOUBLE;
std::vector<std::string> dims;
boost::split(dims, fieldInfo->getSize(), boost::is_any_of("*"));
if (dims.empty())
{
dim1Size = 1;
dim2Size = 1;
}
else if (dims.size() == 1)
{
dim1Size = std::stoi(dims[0]);
dim2Size = 1;
}
else if (dims.size() == 2)
{
dim1Size = std::stoi(dims[0]);
dim2Size = std::stoi(dims[1]);
}
else
{
LOG4CXX_ERROR(gLogger, "FileReaderVOTable::getParamInfo - Unknown dimensions");
return false;
}
return true;
}
}
// Parameter types and size can't be determined by the reader
return false;
}
int FileReaderVOTable::getRecordIndex(std::string& timeId, double time) {
LOG4CXX_DEBUG(gLogger, "FileReaderVOTable::getRecordIndex");
// Read fields informations from the VOTable file
getVOTableInfo();
int timeColumn = -1;
for (int f = 0; f < (int) _fieldsInfo.size(); f++) {
if ((_fieldsInfo.at(f)->getId() == timeId)
|| (_fieldsInfo.at(f)->getName() == timeId)) {
timeColumn = f;
}
}
if (timeColumn != -1)
return getStartTimePos(timeColumn, time);
else {
LOG4CXX_ERROR(gLogger,
"FileReaderVOTable::getRecordIndex - timeColumn was not found : " << timeId);
return -1;
}
}
FileReaderStatus FileReaderVOTable::getParamPacketData(std::string& timeId,
std::string& paramId, int recordIndex, double stopTime,
LocalParamDataPacket *packet) {
LOG4CXX_DEBUG(gLogger, "FileReaderVOTable::getParamPacketData");
// Read fields informations from the VOTable file
getVOTableInfo();
int timeColumn = -1;
for (int f = 0; f < (int) _fieldsInfo.size(); f++) {
if ((_fieldsInfo.at(f)->getId() == timeId)
|| (_fieldsInfo.at(f)->getName() == timeId)) {
timeColumn = f;
}
}
if (timeColumn == -1) {
LOG4CXX_ERROR(gLogger,
"FileReaderVOTable::getParamPacketData - timeColumn was not found : " << timeId);
return FRS_ERROR;
}
int paramColumn = -1;
for (int f = 0; f < (int) _fieldsInfo.size(); f++) {
if ((_fieldsInfo.at(f)->getId() == paramId)
|| (_fieldsInfo.at(f)->getName() == paramId)) {
paramColumn = f;
}
}
// Prepare buffers used by packet->addData
if ((packet->getType() != TYPE_FLOAT) &&
(packet->getType() != TYPE_DOUBLE) &&
(packet->getType() != TYPE_SHORT) &&
(packet->getType() != TYPE_INT)) {
LOG4CXX_ERROR(gLogger,
"FileReaderVOTable::getParamPacketData - Not supported packet type");
return FRS_ERROR;
}
_dataFloat = NULL;
_dataDouble = NULL;
_dataShort = NULL;
_dataInt = NULL;
if (packet->getType() == TYPE_FLOAT) {
_dataFloat = new float[packet->getDimsSize()];
_data = _dataFloat;
} else if (packet->getType() == TYPE_DOUBLE) {
_dataDouble = new double[packet->getDimsSize()];
_data = _dataDouble;
} else if (packet->getType() == TYPE_SHORT) {
_dataShort = new short[packet->getDimsSize()];
_data = _dataShort;
} else if (packet->getType() == TYPE_INT) {
_dataInt = new int[packet->getDimsSize()];
_data = _dataInt;
}
// Get values from VOTable file by parsint it
FileReaderStatus ret = getParamPacketData(timeColumn, paramColumn,
recordIndex, stopTime, packet);
delete[] _dataFloat;
delete[] _dataDouble;
delete[] _dataShort;
delete[] _dataInt;
return ret;
}
/*
* @brief Get an information
*/
bool FileReaderVOTable::getInfo(const char* pInfoName, std::vector<double>& res)
{
res.clear();
// Read fields and params informations from the VOTable file
getVOTableInfo();
for (auto paramInfo : _paramsInfo) {
if (strcmp(paramInfo->getName().c_str(), pInfoName) == 0)
{
std::vector<std::string> valueList;
split (paramInfo->getValue(), ' ', valueList);
for (auto val : valueList)
{
res.push_back(std::stof(val));
}
return true;
}
}
return false;
}
} /* LocalFileInterface */
} /* AMDA */