source: GSEXmlParser/GSEXmlParser.cpp @ 50

#include "GSEXmlParser.h"



void   Data::Dump()

{

    LOG("Sample iid: " << iid);

    LOG("Source: " << source);

    LOG("Supplementary-Data Type: " << supp_type);

    LOG("Supplementary-Data: " << supp_data);

    LOG("\n-------- Description --------");

    for(int i = 0; i < desc.GetCount(); i++)

        LOG("   " << desc.GetKey(i) << " ..... " << desc[i]);

    LOG("-------- Description --------\n");

}



String   Data::ToXML()

{

    String descs; //descriptions

    for(int i = 0; i < desc.GetCount(); i++)

        descs << XmlTag("Description")("name", desc.GetKey(i)).Text(desc[i]);



    return XmlTag("Sample")("iid", iid)(

                     XmlTag("Source").Text(source) + 

                     XmlTag("Supplementary-Data")("type", supp_type).Text(supp_data) +

                     XmlTag("Descriptions") (descs) 

                 );

}



String Data::ToTSV()

{

  String tsv, tab, nl;

  tab = "\t";

  nl = "\n";

  tsv = source + tab + "Sample-iid" + tab + iid + nl +

        source + tab + "Supplementary-Data:" + supp_type + tab + supp_data + nl;

  for(int i = 0; i < desc.GetCount(); i++)      

      tsv += source + tab + "Description:" + desc.GetKey(i) + tab + desc[i] + nl; 

        

  return tsv;

}



void   GSEParser::Dump()

{

  LOG("\n======== GSE XML ========\n");

  for (int i=0; i < data.GetCount(); i++) {

    data[i].Dump();

  }

}



void GSEParser::LoadXML(String filename) {

  //Load XML File

    //LOG("\n---- GSE 2109 XML ----");

    

    String gse;

    /*

    Cout() << filename << "\n";

    String fn;

    fn = GetDataFile(filename);

    Cout() << fn << "\n";

    */

    gse = LoadFile(filename);

    //Cout() << gse << "\n";

    XmlNode rnode = ParseXML(gse);

    

    //Clear Data Array

    data.Clear();

    

    //Get Root Node    

    const XmlNode &xnode = rnode["MINiML"];

    

    //Save Data Array, one by one

    Vector<String> lines, des;

    String str, lstr, rstr;

    for (int i=0; i<xnode.GetCount(); i++) {

       if (xnode[i].GetTag()=="Sample") {  

          //LOG("Sample(iid):" << xnode[i].Attr("iid"));

          //LOG("Source:" << xnode[i]["Channel"]["Source"].GatherText());

          //LOG("\n-------- Description --------");

          Data d;

          d.iid = xnode[i].Attr("iid");

          d.source = xnode[i]["Channel"]["Source"].GatherText();

          d.supp_type = xnode[i]["Supplementary-Data"].Attr("type");

          d.supp_data = xnode[i]["Supplementary-Data"].GatherText();

          lines = Split(xnode[i]["Description"].GatherText(),'\n');

          for (int j=0; j<lines.GetCount(); j++) {

              if (lines[j].Find("=") > -1) {

                  des = Split(lines[j], '=');

              } else if (lines[j].Find(":") > -1) {

                  des = Split(lines[j], ':');

              }

              if (des.GetCount()>1) {

                  lstr = TrimSpace(des[0]);

                  rstr = TrimSpace(des[1]);                  

                  //LOG(lstr << ":" << rstr);

                  String& v = d.desc.GetAdd(lstr);

                  v = rstr;

              }

          }

          data.Add(d);

          //LOG("-------- Description --------\n");

       }

    }

    //    

}



String   GSEParser::ToXML()

{

  String datas; // Datas

    for (int i = 0; i < data.GetCount(); i++) {

        datas << data[i].ToXML();

    }

    return XmlHeader() + XmlTag("GSEFAMILY")(datas);

}



String   GSEParser::ToTSV()

{

  String tsv, tab; 

  tab = "\t";

  tsv = "# rowkey" + tab + "columnkey" + tab + "value\n";

  

  for (int i = 0; i < data.GetCount(); i++) {

    tsv << data[i].ToTSV();

  }

  return tsv;

}



void   GSEParser::ToMySQL(String username, String password, String db, String db_ip)

{

  //

  MySqlSession session;

  if(!session.Connect(username, password, db, db_ip)) {

    printf("Can't connect with MySql\n");

    return;

  }

  Sql sql(session);

  sql.Execute("use gse"); 

  String cmd;

  //

  Cout() << "Total Record Count:" << data.GetCount() << "\n";

  int sid;

    int did;

    String name;  

  for (int i = 0; i < data.GetCount(); i++) {   

    // check gsefamily record

    cmd = "select * from gsefamily where iid = \"" + data[i].iid + "\"";

    sql.Execute(cmd);   

    if (sql.GetRowsProcessed()>0) {

      Cout() << "Warnning: IID ["+data[i].iid+"] is exist." << "\n";      

    } else {

      // add a new gsefamily record

      cmd = "insert into gsefamily (iid,source) values (\""+data[i].iid+"\",\""+data[i].source+"\");";

      if (!sql.Execute(cmd)) {

        Cout() << "Execution Error: " << sql.GetErrorCodeString() << "  Cmd: " << sql.GetErrorStatement() << "\n";      

      }

    }

    //Cout() << "IID ["+data[i].iid+"]" << "\n";

    

    sid = 0;

    // check supplementary    

        cmd = "select sid from supplementary where type = \"" + data[i].supp_type + "\";";        

        sql.Execute(cmd);        

        if (sql.GetRowsProcessed()==0) {  

            //new a supplementary record

            cmd = "insert into supplementary (type) values (\"" + data[i].supp_type + "\");";            

            if (!sql.Execute(cmd)) {

                Cout() << "Execution Error: " << sql.GetErrorCode() << "  Cmd: " << sql.GetErrorStatement() << "\n";      

            }       

            sid = sql.GetInsertedId();     

        } else {

            if (sql.Fetch())

               sid = sql[0];

            //Cout() << "sid: " << sid << "\n";

        }

        

        //new a supplementary-map record        

        cmd = "insert into `supplementary-map` (iid,sid,value) values (\""+data[i].iid+"\",\""+AsString(sid)+"\",\""+data[i].supp_data+"\")";        

        if (!sql.Execute(cmd)) {            

            Cout() << "\nExecution Error: " << sql.GetErrorCode() << "  Cmd: " << sql.GetErrorStatement() << "\n";      

        }

                       

        //Cout() << "data[" << i << "].desc.GetCount() = " << data[i].desc.GetCount() << "\n";

        VectorMap<String, String> desc = data[i].desc;

        for (int j=0; j<desc.GetCount(); j++) {

            

      // check description

      name = desc.GetKey(j);      

          cmd = "select did from description where name = \"" + name + "\"";

          sql.Execute(cmd);

          

          did = 0;

          if (sql.GetRowsProcessed()==0) {  

              //new a description record

              cmd = "insert into description (name) values (\"" + name + "\");";

              if (!sql.Execute(cmd)) {

                  Cout() << "Execution Error: " << sql.GetErrorCodeString() << "  Cmd: " << sql.GetErrorStatement() << "\n";      

              }   

              did = sql.GetInsertedId();         

          } else {

              if (sql.Fetch())

                did = sql[0];

          }

          

          cmd = "insert into `description-map` (iid,did,value) values (\"" + data[i].iid + "\",\"" + AsString(did) + "\",\"" + desc.Get(name) + "\")";

          if (!sql.Execute(cmd)) {

              Cout() << "Execution Error: " << sql.GetErrorCodeString() << "  Cmd: " << sql.GetErrorStatement() << "\n";      

          }

                    

        }

        

  } 

}



String TrimSpace(String str) {

  while (str.StartsWith(" ") && str.GetLength()) {

    str = str.Mid(1);

  }

  while (str.EndsWith(" ") && str.GetLength()) {

    str = str.Left(str.GetLength()-1);

  }

  return str;

}



CONSOLE_APP_MAIN

{

  String in, out, fmt, user, pwd, db, ip, arg_flag;

  /*

  in = "GSE2109_family.xml";

  out = "GSEFamily.tsv";

  fmt = "tsv";

  */

  const Vector<String>& cmdline = CommandLine();

    

  for(int i = 0; i < cmdline.GetCount(); i++) {

    if (cmdline[i].StartsWith("-")){

      arg_flag = cmdline[i];      

    } else if (arg_flag.IsEqual("-i")) {

      in = cmdline[i];    

    } else if (arg_flag.IsEqual("-o")) {

      out = cmdline[i];     

    } else if (arg_flag.IsEqual("-f")) {

      fmt = cmdline[i];

    } else if (arg_flag.IsEqual("-u")) {

      user = cmdline[i];      

    } else if (arg_flag.IsEqual("-p")) {

      pwd = cmdline[i];     

    } else if (arg_flag.IsEqual("-db")) {

      db = cmdline[i];      

    } else if (arg_flag.IsEqual("-ip")) {

      ip = cmdline[i];      

    } else if (arg_flag.StartsWith("-")) {

      //Error argument

      Cout() << "Usage Error: invalid argument "<< arg_flag << "\n";

      exit(0);

    }

  }

  

  if (cmdline.GetCount()==0 || 

      ( (fmt.IsEqual("xml") || fmt.IsEqual("tsv")) && (in.IsEmpty() || out.IsEmpty() || fmt.IsEmpty()) ) ||

      ( fmt.IsEqual("mysql") && (in.IsEmpty() || user.IsEmpty() || db.IsEmpty() || ip.IsEmpty()) )

     ) {

    Cout() << "# Usage #\n";

    Cout() << "For linux:   GSEXmlParser -f (xml|tsv) -i (input file) -o (output file)\n";

    Cout() << "For windows: GSEXmlParser.exe -f (xml|tsv) -i (input file) -o (output file)\n";

    Cout() << "             GSEXmlParser.exe -f (mysql) -i (input file) -u (username) -p (password) -db (database) -ip (db host)\n";

    exit(0);  

  } 

  GSEParser parser;

  parser.LoadXML(in);

  if (fmt.IsEqual("xml"))

    SaveFile(out,parser.ToXML());

  else if (fmt.IsEqual("tsv"))  {

    SaveFile(out,parser.ToTSV());

  } else if (fmt.IsEqual("mysql")) {

    parser.ToMySQL(user,pwd,db,ip);

    Cout() << "Completed.\n";

  }

  

  

  

}