Interaction::Interaction(vector<double> const& instance,vector<bool> const& factor,
Rcpp::DataFrame const& class_data,double epsilon_cont,double epsilon_cat,int p_depth,int nb_class,double p_radius){
vector<InteractionItem> new_items(class_data.size());
Rcpp::CharacterVector names = class_data.names();
for(int i=0;i<class_data.size();++i){
vector<double> attr_data = Rcpp::as<vector<double> >(class_data[i]);
string name = Rcpp::as<string>(names[i]);
if(factor[i]){
InteractionItem item(name,instance[i],i,epsilon_cat,factor[i],attr_data);
new_items[i] = item;
}
else{
InteractionItem item(name,instance[i],i,epsilon_cont,factor[i],attr_data);
new_items[i] = item;
}
}
items = new_items;
depth = p_depth;
sims_valid = false;
vector<double> new_sims(nb_class);
sims = new_sims;
radius = p_radius;
}
bool dataframesAreEqual(Rcpp::DataFrame &a, Rcpp::DataFrame &b) {
Rcpp::NumericVector a1 = a["a"];
Rcpp::CharacterVector b1 = a["b"];
Rcpp::DoubleVector c1 = a["c"];
Rcpp::NumericVector a2 = b["a"];
Rcpp::CharacterVector b2 = b["b"];
Rcpp::DoubleVector c2 = b["c"];
if(a.size() != b.size()) {
DLOG(INFO) << "sizes different";
return false;
}
for(int i = 0; i < a1.size(); i++) {
if(a1[i] != a2[i]) {
DLOG(INFO) << a1[i] << " vs " << a2[i];
return false;
}
if(b1[i] != b2[i]) {
DLOG(INFO) << b1[i] << " vs " << b2[i];
return false;
}
if(c1[i] != c2[i]) {
DLOG(INFO) << c1[i] << " vs " << c2[i];
return false;
}
}
return true;
}
vector<double> random_instance(Rcpp::DataFrame const& x, Generator& prng){
// Select random row number
int row = prng();
vector<double> instance(x.size());
for(int i=0;i<x.size();++i){
vector<double> col = Rcpp::as<vector<double> >(x[i]);
instance[i] = col[row];
}
return instance;
}
Rcpp::StringMatrix DataFrame_to_StringMatrix( Rcpp::DataFrame df ){
Rcpp::StringVector sv = df(0);
Rcpp::StringMatrix sm(sv.size(), df.size());
sm.attr("col.names") = df.attr("col.names");
sm.attr("row.names") = df.attr("row.names");
for(int i=0; i < df.size(); i++){
sv = df(i);
for(int j=0; j < sv.size(); j++){
sm(j, i) = sv(j);
}
}
return sm;
}
bool intercrossingGenerations(Rcpp::DataFrame& pedigree, int nFounders, Rcpp::IntegerVector& mpcrossID, std::vector<int>& output)
{
#define pedFind(id) findIDInPedigree(id, pedigree)
int nFinals = mpcrossID.size();
int nPedigreeRows = pedigree.nrows();
Rcpp::IntegerVector male = Rcpp::as<Rcpp::IntegerVector>(pedigree("Male")), female = Rcpp::as<Rcpp::IntegerVector>(pedigree("Female"));
for(int finalCounter = 0; finalCounter < nFinals; finalCounter++)
{
int currentPedRow = pedFind(mpcrossID[finalCounter]);
if(currentPedRow < 0 || currentPedRow > nPedigreeRows) return false;
//Counter to stop if the loop goes too long and might be infinite
int loopCounter = 0;
//Pick the last row and proceed backwards up the pedigree until we're through all the selfing generations
while(male(currentPedRow) == female(currentPedRow))
{
int nextPedID = male(currentPedRow);
if(nextPedID < 0 || nextPedID > nPedigreeRows) return false;
currentPedRow = pedFind(nextPedID);
if(currentPedRow < 0 || currentPedRow > nPedigreeRows) return false;
loopCounter++;
if(loopCounter > 2000) return false;
}
//When we reach an NA in the pedigree the while condition will terminate, which is an error
if((male(currentPedRow) != male(currentPedRow)) || (female(currentPedRow) != female(currentPedRow)))
{
return false;
}
int ngen = 0;
while(male(currentPedRow) > 0)
{
int nextPedID = male(currentPedRow);
if(nextPedID < 0 || nextPedID > nPedigreeRows) return false;
currentPedRow = pedFind(nextPedID);
if(currentPedRow < 0 || currentPedRow > nPedigreeRows) return false;
ngen++;
if(ngen > 2000) return false;
}
//another check for NA values
if(male(currentPedRow) != male(currentPedRow))
{
return false;
}
output[finalCounter] = ngen - (int)((log(nFounders) / log(2)) + 0.5);
if(output[finalCounter] < 0) return false;
}
#undef pedFind
return true;
}
void helper(const std::string& url,
const bool dropCaches,
const std::string& objType) {
if(dropCaches) {
LOG(INFO) << "Dropping caches ...";
int res, res2;
if ((res = system ("sync")) == -1) {
throw std::runtime_error("Error running sync");
}
if ((res2 = system ("sudo sh -c 'echo 3 > /proc/sys/vm/drop_caches'")) == -1) {
throw std::runtime_error("Error dropping caches");
}
}
//std::string extension = base::utils::getExtension(url);
std::string protocol = base::utils::getProtocol(url);
std::string filename = base::utils::stripProtocol(url);
base::IFilePtr file = hdfsutils::FileFactory::makeFile(protocol, filename);
if( hdfsutils::isHdfs(protocol)) {
hdfsutils::HdfsFile *p = (hdfsutils::HdfsFile *)file.get();
base::ConfigurationMap hdfsconf;
hdfsconf["hdfsConfigurationFile"] = std::string("../ddc/test/data/server.conf");
p->configure(hdfsconf);
}
base::FileStatus status = file->stat();
base::ConfigurationMap conf;
std::string schema = "000:int64,"
"001:int64,002:int64,003:int64,004:int64,005:int64,006:int64,007:int64,008:int64,"
"009:int64,010:int64,011:int64,012:int64,013:int64,014:int64,015:int64,016:int64,"
"017:int64,018:int64,019:int64,020:int64,021:int64,022:int64,023:int64,024:int64,"
"025:int64,026:int64,027:int64,028:int64,029:int64,030:int64,031:int64,032:int64,"
"033:int64,034:int64,035:int64,036:int64,037:int64,038:int64,039:int64,040:int64,"
"041:int64,042:int64,043:int64,044:int64,045:int64,046:int64,047:int64,048:int64,"
"049:int64,050:int64,051:int64,052:int64,053:int64,054:int64,055:int64,056:int64,"
"057:int64,058:int64,059:int64,060:int64,061:int64,062:int64,063:int64,064:int64,"
"065:int64,066:int64,067:int64,068:int64,069:int64,070:int64,071:int64,072:int64,"
"073:int64,074:int64,075:int64,076:int64,077:int64,078:int64,079:int64,080:int64,"
"081:int64,082:int64,083:int64,084:int64,085:int64,086:int64,087:int64,088:int64,"
"089:int64,090:int64,091:int64,092:int64,093:int64,094:int64,095:int64,096:int64,"
"097:int64,098:int64,099:int64,100:int64,101:int64,102:int64,103:int64,104:int64,"
"105:int64,106:int64,107:int64,108:int64,109:int64,110:int64,111:int64,112:int64,"
"113:int64,114:int64,115:int64,116:int64,117:int64,118:int64,119:int64,120:int64,"
"121:int64,122:int64,123:int64,124:int64,125:int64,126:int64,127:int64";
conf["schemaUrl"] = schema;
conf["chunkStart"] = (uint64_t)0;
conf["chunkEnd"] = (uint64_t)status.length;
conf["hdfsConfigurationFile"] = std::string("../ddc/test/data/server.conf") ;
boost::shared_ptr<Rcpp::DataFrame> dfptr =
boost::any_cast<boost::shared_ptr<Rcpp::DataFrame>>(ddc_read(url,
objType,
conf));
Rcpp::DataFrame df = Rcpp::DataFrame(*(dfptr.get()));
LOG(INFO) << "Got dataframe of size " << df.size();
}
// [[Rcpp::export]]
void write_vcf_body_gz( Rcpp::DataFrame fix, Rcpp::DataFrame gt, std::string filename , int mask=0 ) {
// http://stackoverflow.com/a/5649224
// fix DataFrame
Rcpp::StringVector chrom = fix["CHROM"];
Rcpp::StringVector pos = fix["POS"];
Rcpp::StringVector id = fix["ID"];
Rcpp::StringVector ref = fix["REF"];
Rcpp::StringVector alt = fix["ALT"];
Rcpp::StringVector qual = fix["QUAL"];
Rcpp::StringVector filter = fix["FILTER"];
Rcpp::StringVector info = fix["INFO"];
// gt DataFrame
Rcpp::StringMatrix gt_cm = DataFrame_to_StringMatrix(gt);
Rcpp::StringVector column_names(gt.size());
column_names = gt.attr("names");
int i = 0;
int j = 0;
gzFile *fi = (gzFile *)gzopen(filename.c_str(),"ab");
// gzFile *fi = (gzFile *)gzopen(filename.c_str(),"abw");
for(i=0; i<chrom.size(); i++){
Rcpp::checkUserInterrupt();
if(mask == 1 && filter(i) != "PASS" ){
// Don't print variant.
} else {
std::string tmpstring;
tmpstring = chrom(i);
tmpstring = tmpstring + "\t" + pos(i) + "\t";
if(id(i) == NA_STRING){
tmpstring = tmpstring + ".";
} else {
tmpstring = tmpstring + id(i);
}
tmpstring = tmpstring + "\t" + ref(i) + "\t" + alt(i) + "\t";
if(qual(i) == NA_STRING){
tmpstring = tmpstring + "." + "\t";
} else {
tmpstring = tmpstring + qual(i) + "\t";
}
if(filter(i) == NA_STRING){
tmpstring = tmpstring + "." + "\t";
} else {
tmpstring = tmpstring + filter(i) + "\t";
}
tmpstring = tmpstring + info(i);
// gt portion
for(j=0; j<column_names.size(); j++){
if(gt_cm(i, j) == NA_STRING){
tmpstring = tmpstring + "\t" + "./.";
} else {
tmpstring = tmpstring + "\t" + gt_cm(i, j);
}
}
// gzwrite(fi,"my decompressed data",strlen("my decompressed data"));
// gzwrite(fi,"\n",strlen("\n"));
// std::string tmpstring = "test string\n";
gzwrite(fi, (char *)tmpstring.c_str(), tmpstring.size());
gzwrite(fi,"\n",strlen("\n"));
}
}
gzclose(fi);
return;
}
// [[Rcpp::export]]
void write_vcf_body( Rcpp::DataFrame fix, Rcpp::DataFrame gt, std::string filename , int mask=0 ) {
//int write_vcf_body( Rcpp::DataFrame fix, Rcpp::DataFrame gt, std::string filename , int mask=0 ) {
// fix DataFrame
Rcpp::StringVector chrom = fix["CHROM"];
Rcpp::StringVector pos = fix["POS"];
Rcpp::StringVector id = fix["ID"];
Rcpp::StringVector ref = fix["REF"];
Rcpp::StringVector alt = fix["ALT"];
Rcpp::StringVector qual = fix["QUAL"];
Rcpp::StringVector filter = fix["FILTER"];
Rcpp::StringVector info = fix["INFO"];
// gt DataFrame
Rcpp::StringMatrix gt_cm = DataFrame_to_StringMatrix(gt);
Rcpp::StringVector column_names(gt.size());
column_names = gt.attr("names");
// column_names = gt_cm.attr("col.names");
// delete gt;
int i = 0;
int j = 0;
// Uncompressed.
std::ofstream myfile;
myfile.open (filename.c_str(), std::ios::out | std::ios::app | std::ios::binary);
// gzFile *fi = (gzFile *)gzopen("file.gz","wb");
for(i=0; i<chrom.size(); i++){
Rcpp::checkUserInterrupt();
if(mask == 1 && filter(i) == "PASS" ){
// Don't print variant.
} else {
myfile << chrom(i);
myfile << "\t";
myfile << pos(i);
myfile << "\t";
if(id(i) == NA_STRING){
myfile << ".";
myfile << "\t";
} else {
myfile << id(i);
myfile << "\t";
}
myfile << ref(i);
myfile << "\t";
myfile << alt(i);
myfile << "\t";
if(qual(i) == NA_STRING){
myfile << ".";
myfile << "\t";
} else {
myfile << qual(i);
myfile << "\t";
}
if(filter(i) == NA_STRING){
myfile << ".";
myfile << "\t";
} else {
myfile << filter(i);
myfile << "\t";
}
if(info(i) == NA_STRING){
myfile << ".";
myfile << "\t";
} else {
myfile << info(i);
}
// gt region.
myfile << "\t";
myfile << gt_cm(i, 0);
for(j=1; j<column_names.size(); j++){
myfile << "\t";
myfile << gt_cm(i, j);
}
myfile << "\n";
}
}
myfile.close();
return;
}
RcppExport SEXP RXMLADiscover(SEXP handle, SEXP request, SEXP rRestrictionsString, SEXP rPropertiesString)
{
XmlaWebServiceSoapProxy service = XmlaWebServiceSoapProxy(SOAP_XML_DEFAULTNS, SOAP_XML_DEFAULTNS);
Rcpp::XPtr<XMLAHandle> ptr(handle);
const char *connectionString = ptr->connectionString;
std::string propertiesString = CHAR(STRING_ELT(rPropertiesString,0));
std::string restrictionsString = CHAR(STRING_ELT(rRestrictionsString, 0));
ns1__Session session;
std::string sessionId = ptr->sessionID;
session.SessionId = &sessionId;
service.soap_header(NULL, NULL, &session, NULL);
_ns1__Discover discover;
ns1__Restrictions restrictions;
ns1__RestrictionList restrictionList;
ns1__Properties properties;
ns1__PropertyList propertyList;
_ns1__DiscoverResponse discoverResponse;
std::string requestType = CHAR(STRING_ELT(request,0));
std::transform(requestType.begin(), requestType.end(), requestType.begin(), ::toupper);
discover.RequestType = &requestType;
discover.Restrictions = &restrictions;
restrictions.RestrictionList = &restrictionList;
discover.Properties = &properties;
properties.PropertyList = &propertyList;
if (!propertiesString.empty()) {
parseKeyValuePairs(&propertiesString, propertyList.__any);
}
if (!restrictionsString.empty()) {
parseKeyValuePairs(&restrictionsString, restrictionList.__any);
}
service.userid = ptr->userName;
service.passwd = ptr->password;
if (service.Discover(connectionString, NULL, &discover, &discoverResponse) == SOAP_OK) {
std::string rawXML = "<root xmlns=\"urn:schemas-microsoft-com:xml-analysis:rowset\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xmlns:xsd=\"http://www.w3.org/2001/XMLSchema\"><xsd:schema targetNamespace=\"urn:schemas-microsoft-com:xml-analysis:rowset\" xmlns:sql=\"urn:schemas-microsoft-com:xml-sql\" elementFormDefault=\"qualified\">";
rawXML = rawXML + discoverResponse.return_->ns2__root->xsd__schema + "</xsd:schema></root>";
char *schema = strdup(rawXML.c_str());
rapidxml::xml_document<> doc;
doc.parse<0>(schema);
// Find XML section containing column names
rapidxml::xml_node<char> *rowNode = doc.first_node()->first_node()->first_node("xsd:complexType");
while(rowNode != NULL && strcmp(rowNode->first_attribute("name")->value(), "row") != 0) {
rowNode = rowNode->next_sibling("xsd:complexType");
}
rapidxml::xml_node<char> *schemaElementNode = rowNode->first_node()->first_node();
std::vector<char *> rows = discoverResponse.return_->ns2__root->__union_ResultXmlRoot->row;
Rcpp::DataFrame resultDataFrame;
Rcpp::CharacterVector colNames;
char *colName;
while(schemaElementNode != NULL) {
colName = schemaElementNode->first_attribute("name")->value();
colNames.push_back(colName);
if (schemaElementNode->first_attribute("type") != 0) {
rowSetParseData(rows, &resultDataFrame, colName, true);
}
else {
rowSetParseData(rows, &resultDataFrame, colName, false);
}
schemaElementNode = schemaElementNode->next_sibling();
}
resultDataFrame.attr("names") = colNames;
service.destroy();
return resultDataFrame;
}
else {
std::cerr << service.fault->faultstring << std::endl;
}
service.destroy();
return Rcpp::wrap(false);
}
RcppExport SEXP RXMLAExecute(SEXP handle, SEXP query, SEXP rPropertiesString)
{
XmlaWebServiceSoapProxy service = XmlaWebServiceSoapProxy(SOAP_XML_DEFAULTNS, SOAP_XML_DEFAULTNS);
Rcpp::XPtr<XMLAHandle> ptr(handle);
const char *connectionString = ptr->connectionString;
std::string propertiesString = CHAR(STRING_ELT(rPropertiesString,0));
ns1__Session session;
std::string sessionId = ptr->sessionID;
session.SessionId = &sessionId;
service.soap_header(NULL, NULL, &session, NULL);
_ns1__Execute execute;
ns1__CommandStatement command;
ns1__Properties properties;
ns1__PropertyList propertyList;
_ns1__ExecuteResponse response;
std::string statement = CHAR(STRING_ELT(query,0));
command.Statement = &statement;
execute.Command = &command;
execute.Properties = &properties;
properties.PropertyList = &propertyList;
if (!propertiesString.empty()) {
parseKeyValuePairs(&propertiesString, propertyList.__any);
}
service.userid = ptr->userName;
service.passwd = ptr->password;
if (service.Execute(connectionString, NULL, &execute, &response) == SOAP_OK) {
// Parse MDDataSet
if (response.return_->ns4__root != NULL && response.return_->ns4__root->__union_ResultXmlRoot != NULL && response.return_->ns4__root->__union_ResultXmlRoot->Axes != NULL) {
if (response.return_->ns4__root->__union_ResultXmlRoot->Axes->Axis.size() < 3) {
std::cerr << "Error: No data on Axis1" << std::endl;
return Rcpp::wrap(false);
}
if (response.return_->ns4__root->__union_ResultXmlRoot->Axes->Axis.size() > 3) {
std::cerr << "Error: More than 2 axes not supported" << std::endl;
return Rcpp::wrap(false);
}
ns4__Axes *axes = response.return_->ns4__root->__union_ResultXmlRoot->Axes;
std::vector<ns4__Cell *> cellDataVector = response.return_->ns4__root->__union_ResultXmlRoot->CellData->Cell;
int numCols = response.return_->ns4__root->__union_ResultXmlRoot->Axes->Axis[0]->__union_Axis->Tuples->Tuple.size();
int numRows = response.return_->ns4__root->__union_ResultXmlRoot->Axes->Axis[1]->__union_Axis->Tuples->Tuple.size();
int cellDataVectorMember = 0;
Rcpp::CharacterVector colNames;
Rcpp::CharacterVector rowNames;
Rcpp::NumericMatrix resultMatrix(numRows, numCols);
for (int row = 0; row < numRows; row++) {
for (int col = 0; col < numCols; col++) {
if (cellDataVector[cellDataVectorMember]->CellOrdinal == ((row * numCols) + col)) {
resultMatrix(row, col) = *cellDataVector[cellDataVectorMember]->Value;
if (cellDataVectorMember < cellDataVector.size() - 1) {
cellDataVectorMember += 1;
}
}
else {
resultMatrix(row, col) = NA_REAL;
}
}
mdDataSetGetNames(rowNames, axes, row, true);
}
for (int col = 0; col < numCols; col++) {
mdDataSetGetNames(colNames, axes, col, false);
}
colNames.push_front("Row Names");
Rcpp::DataFrame resultDataFrame(resultMatrix);
resultDataFrame.push_front(rowNames);
resultDataFrame.attr("names") = colNames;
service.destroy();
return resultDataFrame;
}
// Parse RowSet
else if (response.return_->ns2__root != NULL
&& response.return_->ns2__root->xsd__schema != NULL
&& response.return_->ns2__root->__union_ResultXmlRoot != NULL
&& !response.return_->ns2__root->__union_ResultXmlRoot->row.empty()) {
std::string rawXML = "<root xmlns=\"urn:schemas-microsoft-com:xml-analysis:rowset\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xmlns:xsd=\"http://www.w3.org/2001/XMLSchema\"><xsd:schema targetNamespace=\"urn:schemas-microsoft-com:xml-analysis:rowset\" xmlns:sql=\"urn:schemas-microsoft-com:xml-sql\" elementFormDefault=\"qualified\">";
rawXML = rawXML + response.return_->ns2__root->xsd__schema + "</xsd:schema></root>";
char *schema = strdup(rawXML.c_str());
rapidxml::xml_document<> doc;
doc.parse<0>(schema);
// Find XML section containing column names
rapidxml::xml_node<char> *rowNode = doc.first_node()->first_node()->first_node("xsd:complexType");
while(rowNode != NULL && strcmp(rowNode->first_attribute("name")->value(), "row") != 0) {
rowNode = rowNode->next_sibling("xsd:complexType");
}
rapidxml::xml_node<char> *schemaElementNode = rowNode->first_node()->first_node();
std::vector<char *> rows = response.return_->ns2__root->__union_ResultXmlRoot->row;
Rcpp::DataFrame resultDataFrame;
Rcpp::CharacterVector colNames;
char *colName;
while(schemaElementNode != NULL) {
colName = schemaElementNode->first_attribute("name")->value();
colNames.push_back(colName);
if (schemaElementNode->first_attribute("type") != 0) {
rowSetParseData(rows, &resultDataFrame, colName, true);
}
else {
rowSetParseData(rows, &resultDataFrame, colName, false);
}
schemaElementNode = schemaElementNode->next_sibling();
}
resultDataFrame.attr("names") = colNames;
service.destroy();
return resultDataFrame;
}
service.destroy();
return Rcpp::wrap(true);
}
else {
char * errorMessage = service.fault->detail->__any;
std::cerr << errorMessage << std::endl;
}
service.destroy();
return Rcpp::wrap(false);
}