source: trunk/FACT++/src/fits2sql.cc@ 19125

#include <boost/algorithm/string/join.hpp>
#include <boost/regex.hpp>

#include "Database.h"

#include "Time.h"
#include "Configuration.h"

#include "zfits.h"

using namespace std;

// ------------------------------------------------------------------------

struct Map : pair<string, string>
{
    Map() { }
};

std::istream &operator>>(std::istream &in, Map &m)
{
    const istreambuf_iterator<char> eos;
    string txt(istreambuf_iterator<char>(in), eos);

    const boost::regex expr("((.*)[^\\\\])/(.*)");
    boost::smatch match;
    if (!boost::regex_match(txt, match, expr))
        throw runtime_error("Could not evaluate map argument: "+txt);

    m.first  = match[1].str();
    m.second = match[3].str();

    return in;
}


void SetupConfiguration(Configuration &conf)
{
    po::options_description control("Root to SQL");
    control.add_options()
        ("uri,u",          var<string>()
#if BOOST_VERSION >= 104200
         ->required()
#endif
         , "Database link as in\n\tuser:password@server[:port]/database[/comp].")
        ("file",           var<string>("")
#if BOOST_VERSION >= 104200
         ->required()
#endif
         ,           "The root file to read from")
        ("force",          po_switch(),               "Force processing even if there is no database connection")
        ("create",         po_switch(),               "Create the database if not existing")
        ("drop",           po_switch(),               "Drop the table (implies create)")
        ("extension,e",    var<string>(""),           "Name of the fits extension (table) to convert")
        ("table",          var<string>(""),           "Name of the table to use (default is the tree name)")
        ("map",            vars<Map>(),               "A regular expression which is applied to the leaf name befoee it is used as SQL column name)")
        ("sql-type",       vars<Map>(),               "Allows to overwrite the calculated SQL type for a given column e.g. 'sql-column-name/UNSIGNED IN'")
        ("ignore",         vars<string>(),            "Ignore the given leaf, if the given regular expression matches")
        ("unsigned",       vars<string>(),            "In fits files per default columns are signed. This interpretss the column as unsigned value. Use the FITS column name.")
        ("primary",        vars<string>(),            "List of columns to be used as primary keys during table creation (in connection with --create)")
        ("first",          var<int64_t>(int64_t(0)),  "First event to start with (default: 0), mainly for test purpose")
        ("max",            var<int64_t>(int64_t(0)),  "Maximum number of events to process (0: all), mainly for test purpose")
        ("engine",         var<string>(""),           "Database engine to be used when a new table is created")
        ("row-format",     var<string>(""),           "Defines the ROW_FORMAT keyword for table creation")
        ("duplicate",      vars<string>(""),          "Specifies an assignment_list for an 'ON DUPLICATE KEY UPDATE' expression")
        ("ignore-errors",  po_switch(),               "Adds the IGNORE keyword to the INSERT query (turns errors into warnings, ignores rows with errors)")
        ;

    po::options_description debug("Debug options");
    debug.add_options()
        ("no-insert",      po_switch(),               "Does not insert any data into the table")
        ("dry-run",        po_switch(),               "Skip any query which changes the databse (might result in consecutive failures)")
        ("print-extensions", po_switch(),             "Print extensions (tables) from fits file")
        ("print-columns",  po_switch(),               "Print columns in fits table")
        ("print-insert",   po_switch(),               "Print the INSERT query (note that it contains all data)")
        ("print-create",   po_switch(),               "Print the CREATE query")
        ("verbose,v",      var<uint16_t>(1),          "Verbosity (0: quiet, 1: default, 2: more, 3, ...)")
        ;

    po::positional_options_description p;
    p.add("file", 1); // The 1st positional options (n=1)

    conf.AddOptions(control);
    conf.AddOptions(debug);
    conf.SetArgumentPositions(p);
}

void PrintUsage()
{
    cout <<
        "fits2sql - Fills the data from a fits file into a database\n"
        "\n"
        "For convenience, this documentation uses the extended version of the options, "
        "refer to the output below to get the abbreviations.\n"
        "\n"
        "This is a general purpose tool to fill the contents of a fite file into a database.\n"
        "\n"
        "Each fits file contians several table, so called extenbsions. Each tables has "
        "a number of columns compilsed from basic data types. The default extension to "
        "read from is the first one on the file but the name can be overwritten using "
        "--extension. The default table name to fill the data into is identical to "
        "the extension name. It can be overwritten using --table.\n"
        "\n"
        "The name of each column to which data is filled is obtained from "
        "the fits column names. The column names can be checked using --print-columns. "
        "Sometimes these names might not be convenient. To allow to simplify or replace "
        "column names, regular expressions (using boost's regex) can be defined to change "
        "the names. Note that these regular expressions are applied one by one on each "
        "columns's name. A valid expression could "
        "be:\n"
        "   --map=MHillas\\.f/\n"
        "which would remove all occurances of 'MHillas.f'. This option can be used more than "
        "once. They are applied in sequence. A single match does not stop the sequence.\n"
        "\n"
        "Sometimes it might also be convenient to skip a column. This can be done with "
        "the --ignore resource. If the given regular expresion yields a match, the "
        "column will be ignored. Note that the regular expression works on the raw-name "
        "of the column not the readily mapped SQL column names. Example:\n"
        "   --ignore=ThetaSq\\..*\n"
        "will skip all leaved which start with 'ThetaSq.'. This option can be used"
        "more than once.\n"
        "\n"
        "The data type of each column is kept as close as possible to the columns' data "
        "types. If for some reason this is not wanted, the data type of the SQL column "
        "can be overwritten with --sql-type sql-column/sql-ytpe, for example:\n"
        "   --sql-type=FileId/UNSIGNED INT\n"
        "while the first argument of the name of the SQL column to which the data type "
        "should be applied. The second column is the basic SQL data type. The option can "
        "be given more than once.\n"
        "\n"
        "Database interaction:\n"
        "\n"
        "To drop an existing table, --drop can be used.\n"
        "\n"
        "To create a table according to theSQL  column names and data types, --create "
        "can be used. The query used can be printed with --print-create even --create "
        "has not been specified.\n"
        "\n"
        "To choose the columns which should become primary keys, use --primary, "
        "for exmaple:\n"
        "   --primary=col1\n"
        "To define more than one column as primary key, the option can be given more than "
        "once. Note that the combination of these columns must be unique.\n"
        "\n"
        "All columns are created as NOT NULL as default. To force a database engine "
        "and/or a storage format, use --engine and --rot-format.\n"
        "\n"
        "Usually, the INSERT query would fail if the PRIMARY key exists already. "
        "This can be avoided using the 'ON DUPLICATE KEY UPDATE' directive. With the "
        "--duplicate, you can specify what should be updated in case of a duplicate key. "
        "To keep the row untouched, you can just update the primary key "
        "with the identical primary key, e.g. --duplicate='MyPrimary=VALUES(MyPrimary)'. "
        "The --duplicate resource can be specified more than once to add more expressions "
        "to the assignment_list. For more details, see the MySQL manual.\n"
        "\n"
        "Another possibility is to add the IGNORE keyword to the INSERT query by "
        "--ignore-errors, which essentially ignores all errors and turns them into "
        "warnings which are printed after the query succeeded.\n"
        "\n"
        "For debugging purpose, or to just create or drop a table, the final insert "
        "query can be skipped using --no-insert. Note that for performance reason, "
        "all data is collected in memory and a single INSERT query is issued at the "
        "end.\n"
        "\n"
        "Using a higher verbosity level (-v), an overview of the written columns or all "
        "processed leaves is printed depending on the verbosity level. The output looks "
        "like the following\n"
        "   Leaf name [root data type] (SQL name)\n"
        "for example\n"
        "   MTime.fTime.fMilliSec [Long64_t] (MilliSec)\n"
        "which means that the leaf MTime.fTime.fMilliSec is detected to be a Long64_t "
        "which is filled into a column called MilliSec. Leaves with non basic data types "
        "are ignored automatically and are marked as (-n/a-). User ignored columnd "
        "are marked as (-ignored-).\n"
        "\n"
        "If a query failed, the query is printed to stderr together with the error message. "
        "For the main INSERT query, this is only true if the verbosity level is at least 2 "
        "or the query has less than 80*25 bytes.\n"
        "\n"
        "In case of succes, 0 is returned, a value>0 otherwise.\n"
        "\n"
        "Usage: fits2sql [options] --uri URI fitsfile.fits[.gz]\n"
        "\n"
        ;
    cout << endl;
}

enum BasicType_t
{
    kNone = 0,
    kVarchar,
    kBool,
    kFloat,
    kDouble,
    kInt8,
    kUInt8,
    kInt16,
    kUInt16,
    kInt32,
    kUInt32,
    kInt64,
    kUInt64,
//    kMJD,
};

static const map<char, pair<BasicType_t, string>> ConvFits =
{
    { 'A', { kVarchar, "VARCHAR"  } },
    { 'a', { kVarchar, "VARCHAR"  } },
    { 'L', { kBool,    "BOOLEAN"  } },
    { 'l', { kBool,    "BOOLEAN"  } },
    { 'B', { kInt8,    "TINYINT"  } },
    { 'b', { kUInt8,   "TINYINT UNSIGNED"  } },
    { 'I', { kInt16,   "SMALLINT" } },
    { 'i', { kUInt16,  "SMALLINT UNSIGNED" } },
    { 'J', { kInt32,   "INT"      } },
    { 'j', { kUInt32,  "INT UNSIGNED"      } },
    { 'K', { kInt64,   "BIGINT"   } },
    { 'k', { kUInt64,  "BIGINT UNSIGNED"   } },
    { 'E', { kFloat,   "FLOAT"    } },
    { 'e', { kFloat,   "FLOAT"    } },
    { 'D', { kDouble,  "DOUBLE"   } },
    { 'd', { kDouble,  "DOUBLE"   } },
};

struct Container
{
    string branch; // fits column name
    string column; // sql  column name
    BasicType_t type;
    size_t num;
//    double offset;
    void *ptr;

    Container(const string &b, const string &c, const BasicType_t &t, const size_t &n/*, const double &offset=0*/) : branch(b), column(c), type(t), num(n), ptr(0)
    {
    }
    ~Container()
    {
    }

    string fmt(const size_t &index) const
    {
        ostringstream str;

        switch (type)
        {
        //case kVarchar: str << string(reinterpret_cast<char*>(ptr), num); break;
        case kVarchar: str << string(reinterpret_cast<char*>(ptr), num).c_str(); break;
        case kFloat:   str << setprecision(8) << reinterpret_cast<float*>(ptr)[index];  break;
//        case kMJD:     str << setprecision(16) << reinterpret_cast<double*>(ptr)[0]+offset; break;
        case kDouble:  str << setprecision(16) << reinterpret_cast<double*>(ptr)[index]; break;
        case kBool:
        case kInt8:    str << int32_t(reinterpret_cast<int8_t*>(ptr)[index]); break;
        case kUInt8:   str << uint32_t(reinterpret_cast<uint8_t*>(ptr)[index]); break;
        case kInt16:   str << reinterpret_cast<int16_t*>(ptr)[index]; break;
        case kUInt16:  str << reinterpret_cast<uint16_t*>(ptr)[index]; break;
        case kInt32:   str << reinterpret_cast<int32_t*>(ptr)[index]; break;
        case kUInt32:  str << reinterpret_cast<uint32_t*>(ptr)[index]; break;
        case kInt64:   str << reinterpret_cast<int64_t*>(ptr)[index]; break;
        case kUInt64:  str << reinterpret_cast<uint64_t*>(ptr)[index]; break;
        case kNone:
            break;
        }

        return str.str();
    }
};

int main(int argc, const char* argv[])
{
    Time start;

    Configuration conf(argv[0]);
    conf.SetPrintUsage(PrintUsage);
    SetupConfiguration(conf);

    if (!conf.DoParse(argc, argv))
        return 127;

    // ----------------------------- Evaluate options --------------------------
    const string uri             = conf.Get<string>("uri");
    const string file            = conf.Get<string>("file");
    const string extension       = conf.Get<string>("extension");
          string table           = conf.Get<string>("table");

    const uint16_t verbose       = conf.Get<uint16_t>("verbose");
    const int64_t  first         = conf.Get<int64_t>("first");
    const int64_t  max           = conf.Get<int64_t>("max");

    const bool force             = conf.Get<bool>("force");
    const bool drop              = conf.Get<bool>("drop");
    const bool create            = conf.Get<bool>("create") || drop;
    const bool noinsert          = conf.Get<bool>("no-insert");
    const bool dry_run           = conf.Get<bool>("dry-run");

    const string engine          = conf.Get<string>("engine");
    const string row_format      = conf.Get<string>("row-format");

    const bool ignore_errors     = conf.Get<bool>("ignore-errors");

    const bool print_extensions  = conf.Get<bool>("print-extensions");
    const bool print_columns     = conf.Get<bool>("print-columns");
    const bool print_create      = conf.Get<bool>("print-create");
    const bool print_insert      = conf.Get<bool>("print-insert");

    const vector<Map> mymap      = conf.Vec<Map>("map");
    const vector<Map> sqltypes   = conf.Vec<Map>("sql-type");
    const vector<string> _ignore = conf.Vec<string>("ignore");
    const vector<string> primary = conf.Vec<string>("primary");

    const vactor<string> duplicate = conf.Vec<string>("duplicate");
    const vector<string> notsigned = conf.Vec<string>("unsigned");

    // -------------------------------------------------------------------------

    if (verbose>0)
        cout << "\n-------------------------- Evaluating file -------------------------" << endl;

    zfits f(file.c_str(), extension.c_str());
    if (!f)
    {
        cerr << "Could not open file " << file << ": " << strerror(errno) << endl;
        return 1;
    }

    if (verbose>0)
        cout << "File: " << file << endl;

    if (!extension.empty() && extension!=f.Get<string>("EXTNAME"))
    {
        cerr << "Extension " << extension << " not found in file." << endl;
        return 2;
    }

    if (print_extensions)
    {
        cout << "\nTables:\n - " << boost::join(f.GetTables(), "\n - ") << '\n' << endl;
        return 3;
    }

    if (verbose>0)
        cout << "FITS extension [table]: " << f.Get<string>("EXTNAME") << endl;

    if (table.empty())
        table = f.Get<string>("EXTNAME");

    if (verbose>0)
        cout << "SQL table: " << table << endl;

//    const double mjdref = f.Get("MJDREF", double(0));

    if (print_columns)
    {
        cout << '\n';
        f.PrintColumns();
        cout << '\n';
    }

    const auto cols = f.GetColumns();

    if (verbose>0)
    {
        cout << f.GetNumRows() << " events found." << endl;
        cout << cols.size() << " columns found." << endl;
    }

    string query =
        "CREATE TABLE IF NOT EXISTS `"+table+"`\n"
        "(\n";

    vector<Container> vec;

    for (const auto &ic : cols)
    {
        const auto &col = ic.second;

        if (verbose>2)
            cout << '\n' << col.type << " " << ic.first << "[" << col.num << "]";

        string name = ic.first;

        bool found = false;
        for (auto b=_ignore.cbegin(); b!=_ignore.cend(); b++)
        {
            if (boost::regex_match(name, boost::regex(*b)))
            {
                found = true;
                if (verbose>2)
                    cout << " (-ignored-)";
                break;
            }
        }
        if (found)
            continue;

        const char tn = find(notsigned.cbegin(), notsigned.cend(), ic.first)!=notsigned.cend() ?
            tolower(col.type) : toupper(col.type);

        auto it = ConvFits.find(tn);
        if (it==ConvFits.end())
        {
            if (verbose>2)
                cout << " (-n/a-)";
            continue;
        }

        if (verbose==2)
            cout << '\n' << name << " [" << tn << "]";

        for (auto m=mymap.cbegin(); m!=mymap.cend(); m++)
            name = boost::regex_replace(name, boost::regex(m->first), m->second);

        if (verbose>1)
            cout << " (" << name << ")";

        string sqltype = it->second.second;

        for (auto m=sqltypes.cbegin(); m!=sqltypes.cend(); m++)
            if (m->first==name)
                sqltype = m->second;

        if (!vec.empty())
            query += ",\n";

        const size_t N = col.type=='A' ? 1 : col.num;
        for (int i=0; i<N; i++)
        {
            query += "   `"+name;
            if (N>1)
                query += "["+to_string(i)+"]";
            query += "` "+sqltype;
            if (col.type=='A')
                query += '('+to_string(col.num)+')';
            query += " NOT NULL COMMENT '"+ic.first;
            if (!col.unit.empty())
                query += "["+col.unit+"]";
            if (!col.comment.empty())
                query += ": "+col.comment;
            query += +"'";
            if (N>1 && i!=N-1)
                query += ",\n";
        }

        const BasicType_t bt =
            /*ic.first=="Time" && col.num==1 && col.unit=="MJD" && it->second.first==kDouble ?
            kMJD :*/ it->second.first;

        vec.emplace_back(ic.first, name, bt, col.num/*, mjdref*/);
        vec.back().ptr = f.SetPtrAddress(ic.first);
    }

    if (verbose>1)
        cout << "\n\n";
    if (verbose>0)
        cout << vec.size() << " columns setup for reading." << endl;

    // -------------------------------------------------------------------------
    // Checking for database connection

    Database connection(uri);

    try
    {
        if (!force)
            connection.connected();
    }
    catch (const exception &e)
    {
        cerr << "SQL connection failed: " << e.what() << '\n' << endl;
        return 4;
    }

    // -------------------------------------------------------------------------

    if (verbose>0)
        cout << "\n--------------------------- Database Table -------------------------" << endl;

    if (!primary.empty())
        query += ",\n   PRIMARY KEY USING BTREE (`"+boost::algorithm::join(primary, "`, `")+"`)\n";

    query +=
        ")\n"
        "DEFAULT CHARSET=latin1 COLLATE=latin1_general_ci\n";
    if (!engine.empty())
        query += "ENGINE="+engine+"\n";
    if (!row_format.empty())
        query += "ROW_FORMAT="+row_format+"\n";
    query += "COMMENT='created by "+conf.GetName()+"'\n";


    // FIXME: Can we omit the catching to be able to print the
    //        query 'autmatically'?
    try
    {
        if (drop)
        {
            // => Simple result
            if (!dry_run)
                connection.query("DROP TABLE `"+table+"`").execute();
            if (verbose>0)
                cout << "Table `" << table << "` dropped." << endl;
        }
    }
    catch (const exception &e)
    {
        cerr << "DROP TABLE `" << table << "`\n\n";
        cerr << "SQL query failed:\n" << e.what() << '\n' << endl;
        return 5;
    }

    try
    {
        if (create && !dry_run)
            connection.query(query).execute();
    }
    catch (const exception &e)
    {
        cerr << query << "\n\n";
        cerr << "SQL query failed:\n" << e.what() << '\n' << endl;
        return 6;
    }

    if (print_create)
        cout << query << endl;

    if (create && verbose>0)
        cout << "Table `" << table << "` created." << endl;

    // -------------------------------------------------------------------------

    if (verbose>0)
        cout << "\n---------------------------- Reading file --------------------------" << endl;

    //query = update ? "UPDATE" : "INSERT";
    query = "INSERT ";
    if (ignore_errors)
        query += "IGNORE ";
    query += "`"+table+"`\n"
        "(\n";

    for (auto c=vec.cbegin(); c!=vec.cend(); c++)
    {
        const size_t N = c->type==kVarchar ? 1 : c->num;
        for (int i=0; i<N; i++)
        {
            if (c!=vec.cbegin())
                query += ",\n";

            if (N==1)
                query += "   `"+c->column+"`";
            else
                query += "   `"+c->column+"["+to_string(i)+"]`";

            if (N>1 && i!=N-1)
                query += ",\n";
        }
    }

    query +=
        "\n)\n"
        "VALUES\n";

    size_t count = 0;

    const size_t num = max>0 && (max-first)<f.GetNumRows() ? (max-first) : f.GetNumRows();
    for (size_t j=first; j<num; j++)
    {
        f.GetRow(j);

        if (count>0)
            query += ",\n";

        query += "(\n";

        for (auto c=vec.cbegin(); c!=vec.cend(); c++)
        {
            const size_t N = c->type==kVarchar ? 1 : c->num;
            for (int i=0; i<N; i++)
            {
                if (c!=vec.cbegin())
                    query += ",\n";

                if (c->type==kVarchar)
                    query += "   '"+c->fmt(i)+"'";
                else
                    query += "   "+c->fmt(i);

                if (print_insert && i==0)
                    query += " /* "+c->column+" -> "+c->branch+" */";

                if (N>1 && i!=N-1)
                    query += ",\n";
            }
        }
        query += "\n)";

        count ++;
    }

    if (!duplicate.empty())
        query += "\nON DUPLICATE KEY UPDATE\n   " + boost::join(duplicate, ",\n   ");

    if (verbose>0)
        cout << count << " out of " << num << " row(s) read from file [N=" << first << ".." << num-1 << "]." << endl;

    if (count==0)
    {
        if (verbose>0)
            cout << "Total execution time: " << Time().UnixTime()-start.UnixTime() << "s\n" << endl;
        return 0;
    }

    // -------------------------------------------------------------------------

    if (verbose>0)
    {
        cout << "\n--------------------------- Inserting data -------------------------" << endl;
        cout << "Sending INSERT query (" << query.length() << " bytes)"  << endl;
    }

    try
    {
        if (!noinsert && !dry_run)
        {
            auto q = connection.query(query);
            q.execute();
            cout << q.info() << '\n' << endl;
        }
        else
            cout << "Insert query skipped!" << endl;

        if (print_insert)
            cout << query << endl;
    }
    catch (const exception &e)
    {
        if (verbose>1 || query.length()<80*25)
            cerr << query << "\n\n";
        cerr << "SQL query failed (" << query.length() << " bytes):\n" << e.what() << '\n' << endl;
        return 7;
    }

    if (verbose>0)
    {
        const auto sec = Time().UnixTime()-start.UnixTime();
        cout << "Total execution time: " << sec << "s ";
        cout << "(" << Tools::Fractional(sec/count) << "s/row)\n";

        try
        {
            const auto resw =
                connection.query("SHOW WARNINGS").store();

            for (size_t i=0; i<resw.num_rows(); i++)
            {
                const mysqlpp::Row &roww = resw[i];

                cout << roww["Level"] << '[' << roww["Code"] << "]: ";
                cout << roww["Message"] << '\n';
            }
            cout << endl;

        }
        catch (const exception &e)
        {
            cerr << "\nSHOW WARNINGS\n\n";
            cerr << "SQL query failed:\n" << e.what() << '\n' <<endl;
            return 8;
        }
    }

    return 0;
}