void fixEnsGtf(char *outName, int inCount, char *inFiles[])
/* fixEnsGtf - fix space vs. tab and start/stop codon problems in Ensemble .gtf file. */
{
FILE *f = mustOpen(outName, "w");
struct lineFile *lf;
int fileIx;
int lineSize;
char *line;
for (fileIx = 0; fileIx < inCount; ++fileIx)
{
lf = lineFileOpen(inFiles[fileIx], TRUE);
printf("Processing %s\n", lf->fileName);
while (lineFileNext(lf, &line, &lineSize))
{
fixLine(lf, line, f);
}
lineFileClose(&lf);
}
}
void printResult(QSqlQuery query)
{
int pos;
QList<TfieldDef> fields;
int ncols;
ncols = 0;
for (pos = 0; pos <= query.record().count()-1;pos++)
{
ncols++;
TfieldDef field;
field.fieldName = query.record().field(pos).name();
switch (query.record().field(pos).type())
{
case QVariant::Bool:
field.fieldType = "BOL";
break;
case QVariant::Char:
field.fieldType = "CHR";
break;
case QVariant::Date:
field.fieldType = "DAT";
break;
case QVariant::DateTime:
field.fieldType = "DTM";
break;
case QVariant::Double:
field.fieldType = "DBL";
break;
case QVariant::Int:
field.fieldType = "INT";
break;
case QVariant::String:
field.fieldType = "STR";
break;
case QVariant::Time:
field.fieldType = "TIM";
break;
case QVariant::UInt:
field.fieldType = "UIN";
break;
default:
field.fieldType = "NA";
}
fields.append(field);
}
int nrows;
nrows = 0;
while (query.next())
{
nrows++;
}
nrows++; //Heads
QVector<QVector<QString> > grid;
grid.resize(nrows);
int r;
for(r=0; r<nrows; r++)
{
grid[r].resize(ncols);
}
//Append the field names
for (pos = 0; pos <= fields.count()-1;pos++)
grid[0][pos] = fields[pos].fieldName;
for (pos = 0; pos <= fields.count()-1;pos++)
grid[0][pos] = fields[pos].fieldName;
r = 1;
query.first();
QString value;
while (query.isValid())
{
for (pos = 0; pos <= fields.count()-1;pos++)
{
if (fields[pos].fieldType == "DBL")
value = QString::number(query.value(getFieldIndex(query,fields[pos].fieldName)).toDouble(),'f',3);
else
{
if (fields[pos].fieldName != "ogc_geom")
value = query.value(getFieldIndex(query,fields[pos].fieldName)).toString().simplified();
else
value = "Geometry data";
}
grid[r][pos] = value;
}
r++;
query.next();
}
QVector< int> colSizes;
colSizes.resize(ncols);
for (pos = 0; pos <= ncols-1;pos++)
colSizes[pos] = 0;
//Get the maximum size of each column
for (pos = 0; pos <= ncols-1;pos++)
{
for(r=0; r<nrows; r++)
{
if (grid[r][pos].length() +2 > colSizes[pos])
{
colSizes[pos] = grid[r][pos].length() +2;
}
}
}
//Print the table
printf("\n");
//Print top line
for (pos=0;pos<= ncols-1;pos++)
{
printf("+");
printf(fixLine("-",colSizes[pos]).toLocal8Bit().data());
}
printf("+");
printf("\n");
//Print the columns headings
for (pos=0;pos<= ncols-1;pos++)
{
printf("+");
printf(fixString(" " + grid[0][pos] + " ",colSizes[pos]).toLocal8Bit().data());
}
printf("+");
printf("\n");
//Print separation
for (pos=0;pos<= ncols-1;pos++)
{
printf("+");
printf(fixLine("-",colSizes[pos]).toLocal8Bit().data());
}
printf("+");
printf("\n");
//Print the values
for (r=1;r<=nrows-1;r++)
{
printf("|");
for (pos=0;pos<= ncols-1;pos++)
{
printf(fixString(" " + grid[r][pos] + " ",colSizes[pos]).toLocal8Bit().data());
printf("|");
}
printf("\n");
}
//Print the end
//Print separation
for (pos=0;pos<= ncols-1;pos++)
{
printf("+");
printf(fixLine("-",colSizes[pos]).toLocal8Bit().data());
}
printf("+");
printf("\n");
}
int main(int argc, char *argv[])
{
QCoreApplication a(argc, argv);
//Command line arguments
TCLAP::CmdLine cmd("GOBLET (c) 2012, International Livestock Research Institute (ILRI) \n Developed by Carlos Quiros ([email protected])", ' ', "1.0 (Beta 1)");
//Required arguments
TCLAP::ValueArg<std::string> databaseArg("d","database","Database name",true,"","string");
TCLAP::ValueArg<std::string> calculationArg("c","calculation","Calculation to perform. For example: 'sum(DatasetA),sum(DatasetB)' ",true,"","string");
TCLAP::ValueArg<std::string> ouputArg("o","output","Output type: (h)uman readable or (c)omputer readable",true,"","string");
//Non required arguments
TCLAP::ValueArg<std::string> pathArg("a","path","Path to database. Default .",false,".","string");
TCLAP::ValueArg<std::string> hostArg("H","host","Connect to host. Default localhost",false,"localhost","string");
TCLAP::ValueArg<std::string> portArg("P","port","Port number to use. Default 3306",false,"3306","string");
TCLAP::ValueArg<std::string> userArg("u","user","User. Default empty",false,"","string");
TCLAP::ValueArg<std::string> passArg("p","password","Passwork. Default no password",false,"","string");
TCLAP::ValueArg<std::string> descArg("s","descriptions","Descriptions for the calculations separated by coma. Default value is the calculation string",false,"","string");
//Switches
TCLAP::SwitchArg remoteSwitch("r","remote","Connect to remote host", cmd, false);
cmd.add(databaseArg);
cmd.add(calculationArg);
cmd.add(ouputArg);
cmd.add(pathArg);
cmd.add(hostArg);
cmd.add(portArg);
cmd.add(userArg);
cmd.add(passArg);
cmd.add(descArg);
//Parsing the command lines
cmd.parse( argc, argv );
//Getting the variables from the command
bool remote = remoteSwitch.getValue();
QString path = QString::fromUtf8(pathArg.getValue().c_str());
QString dbName = QString::fromUtf8(databaseArg.getValue().c_str());
QString host = QString::fromUtf8(hostArg.getValue().c_str());
QString port = QString::fromUtf8(portArg.getValue().c_str());
QString userName = QString::fromUtf8(userArg.getValue().c_str());
QString password = QString::fromUtf8(passArg.getValue().c_str());
QString calculation = QString::fromUtf8(calculationArg.getValue().c_str());
QString format = QString::fromUtf8(ouputArg.getValue().c_str());
QString description = QString::fromUtf8(descArg.getValue().c_str());
myDBConn con;
QSqlDatabase mydb;
if (!remote)
{
QDir dir;
dir.setPath(path);
if (con.connectToDB(dir.absolutePath()) == 1)
{
if (!dir.cd(dbName))
{
gbtLog(QObject::tr("The database does not exists"));
con.closeConnection();
return 1;
}
mydb = QSqlDatabase::addDatabase(con.getDriver(),"connection1");
}
}
else
{
mydb = QSqlDatabase::addDatabase("QMYSQL","connection1");
mydb.setHostName(host);
mydb.setPort(port.toInt());
if (!userName.isEmpty())
mydb.setUserName(userName);
if (!password.isEmpty())
mydb.setPassword(password);
}
mydb.setDatabaseName(dbName);
if (!mydb.open())
{
gbtLog(QObject::tr("Cannot open database"));
con.closeConnection();
return 1;
}
else
{
QTime procTime;
procTime.start();
QString sql;
QSqlQuery qry(mydb);
QList <TdatasetInfo> datasets;
if (constructSQL(calculation,sql,mydb,datasets))
{
gbtLog(QObject::tr("Error in calculation."));
gbtLog(qry.lastError().databaseText());
mydb.close();
con.closeConnection();
return 1;
}
QDomDocument doc;
QDomElement root;
doc = QDomDocument("GOBLETXML");
root = doc.createElement("CalcXML");
root.setAttribute("version", "1.0");
doc.appendChild(root);
QDomElement varName;
QDomText varValue;
QList<TfieldDef> fields;
int ncols;
ncols = 0;
if (!qry.exec(sql))
{
gbtLog(QObject::tr("Cannot reset dataset."));
gbtLog(qry.lastError().databaseText());
mydb.close();
con.closeConnection();
return 1;
}
int nfields;
nfields = qry.record().count();
QString nfield;
int pos;
QStringList descriptions;
descriptions = getDescriptions(description);
if (descriptions.count() != nfields)
{
descriptions.clear();
descriptions.append("Class code");
for (pos = 1; pos <= nfields-1; pos++)
{
descriptions.append(qry.record().field(pos).name());
}
}
for (pos = 0; pos <= nfields-1;pos++)
{
ncols++;
nfield = descriptions[pos];
nfield.replace("T" + datasets[pos].code + ".",datasets[pos].name + ".");
nfield.replace(".cellvalue","");
TfieldDef field;
field.fieldName = nfield;
field.fieldDesc = nfield; //Change for description
if (pos == 0)
{
field.fieldType = "CHAR";
}
else
field.fieldType = "DEC";
fields.append(field);
}
QDomElement shapevars;
shapevars = doc.createElement("Values");
root.appendChild(shapevars);
for (pos = 0; pos <= fields.count()-1;pos++)
{
varName = doc.createElement("Field");
shapevars.appendChild(varName);
varValue = doc.createTextNode(fields[pos].fieldDesc);
varName.appendChild(varValue);
}
int nrows;
nrows = 0;
while (qry.next())
{
nrows++;
}
nrows++;
QVector<QVector<QString> > grid;
grid.resize(nrows);
int r;
for(r=0; r<nrows; r++)
{
grid[r].resize(ncols);
}
for (pos = 0; pos <= fields.count()-1;pos++)
grid[0][pos] = fields[pos].fieldDesc;
r = 1;
qry.first();
QString value;
while (qry.isValid())
{
for (pos = 0; pos <= fields.count()-1;pos++)
{
if (fields[pos].fieldType == "DEC")
value = QString::number(qry.value(pos).toDouble(),'f',3);
else
value = qry.value(pos).toString();
grid[r][pos] = value;
}
r++;
qry.next();
}
if (format == "h")
{
QVector< int> colSizes;
colSizes.resize(ncols);
for (pos = 0; pos <= ncols-1;pos++)
colSizes[pos] = 0;
//Get the maximum size of each column
for (pos = 0; pos <= ncols-1;pos++)
{
for(r=0; r<nrows; r++)
{
if (grid[r][pos].length() +2 > colSizes[pos])
{
colSizes[pos] = grid[r][pos].length() +2;
}
}
}
//Print the table
printf("\n");
//Print top line
for (pos=0;pos<= ncols-1;pos++)
{
printf("+");
printf(fixLine("-",colSizes[pos]).toLocal8Bit().data());
}
printf("+");
printf("\n");
//Print the columns headings
for (pos=0;pos<= ncols-1;pos++)
{
printf("+");
printf(fixString(" " + grid[0][pos] + " ",colSizes[pos]).toLocal8Bit().data());
}
printf("+");
printf("\n");
//Print separation
for (pos=0;pos<= ncols-1;pos++)
{
printf("+");
printf(fixLine("-",colSizes[pos]).toLocal8Bit().data());
}
printf("+");
printf("\n");
//Print the values
for (r=1;r<=nrows-1;r++)
{
printf("|");
for (pos=0;pos<= ncols-1;pos++)
{
printf(fixString(" " + grid[r][pos] + " ",colSizes[pos]).toLocal8Bit().data());
printf("|");
}
printf("\n");
}
//Print the end
//Print separation
for (pos=0;pos<= ncols-1;pos++)
{
printf("+");
printf(fixLine("-",colSizes[pos]).toLocal8Bit().data());
}
printf("+");
printf("\n");
}
else
{
QDomElement shapeData;
shapeData = doc.createElement("CalcData");
root.appendChild(shapeData);
QDomElement rowData;
QDomElement fieldData;
QDomText fieldValue;
for (r=1;r<=nrows-1;r++)
{
rowData = doc.createElement("Row");
shapeData.appendChild(rowData);
for (pos=0;pos<= ncols-1;pos++)
{
fieldData = doc.createElement("Field");
fieldData.setAttribute("Name",fields[pos].fieldDesc);
rowData.appendChild(fieldData);
fieldValue = doc.createTextNode(grid[r][pos]);
fieldData.appendChild(fieldValue);
}
}
QTextStream out(stdout);
out.setCodec("UTF-8");
doc.save(out,1,QDomNode::EncodingFromTextStream);
}
int Hours;
int Minutes;
int Seconds;
int Milliseconds;
Milliseconds = procTime.elapsed();
Hours = Milliseconds / (1000*60*60);
Minutes = (Milliseconds % (1000*60*60)) / (1000*60);
Seconds = ((Milliseconds % (1000*60*60)) % (1000*60)) / 1000;
if (format == "h")
gbtLog("Finished in " + QString::number(Hours) + " Hours," + QString::number(Minutes) + " Minutes and " + QString::number(Seconds) + " Seconds.");
mydb.close();
con.closeConnection();
return 0;
}
return 0;
}