Exemplo n.º 1
0
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);
    }
}
Exemplo n.º 2
0
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");

}
Exemplo n.º 3
0
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;

}