ConstructQueryPaper.java

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package cedar.hepdata.webapp.pages;

import cedar.hepdata.model.*;
import cedar.hepdata.xml.*;
import cedar.hepdata.db.*;

import org.apache.tapestry5.annotations.*;
import org.apache.tapestry5.ioc.annotations.*;
import org.apache.tapestry5.services.*;

import org.hibernate.*;
import org.hibernate.criterion.*;
import java.util.*;


public class ConstructQueryPaper{

    public static Query QueryString(String queryString, String flag,  org.hibernate.Session _session){
//
//start by removing the FIND at the beginning of the query if it is present
       int ix = -1; 
       if(queryString.toUpperCase().startsWith("F ") ||
          queryString.toUpperCase().startsWith("FI ") ||
          queryString.toUpperCase().startsWith("FIN ") ||
          queryString.toUpperCase().startsWith("FIND ")){
          ix = queryString.indexOf(" ");
       }
       
// deal with > and < with no spacings, taking care of the reaction --> 
       queryString=queryString.replaceAll("<"," < ");
       queryString=queryString.replaceAll(">"," > ");
       queryString=queryString.replaceAll("- >","->");
       
       
// these next lines are for the special queries on on event shapes etc... 
       if( queryString.toUpperCase().equals("EVENTSHAPES") ){
          return EventShapes(flag,_session);
       }
       else if( queryString.toUpperCase().equals("EVENTSHAPESEE") ){
          return EventShapesEE(flag,_session);
       }
       else if( queryString.toUpperCase().equals("EVENTSHAPESNOTEE") ){
          return EventShapesNotEE(flag,_session);
       }
       else if( queryString.toUpperCase().equals("JETPRODUCTION") ){
          return JetProduction(flag,_session);
       }
       else if( queryString.toUpperCase().equals("JETPRODUCTIONEE") ){
          return JetProductionEE(flag,_session);
       }
       else if( queryString.toUpperCase().equals("JETPRODUCTIONNOTEE") ){
          return JetProductionNotEE(flag,_session);
       }
       System.out.println("query: " + queryString);
//
      
       String words[] = queryString.substring(ix+1).toUpperCase().split("\\s+AND\\s+");
       String reaction = null;
       String observable = null;
       String sqrts = null;
       String spiresid = null;
       String redid = null;
       String experiment = null;
       String author = null;
       String reference = null;
       String date = null;
       String datetype = "=";
       System.out.println(queryString);
       for (int i=0; i<words.length; i++){
           String parts[] = words[i].split("\\s+");
           if( parts[0].equals("RE") || parts[0].equals("REAC") || parts[0].equals("REACTION") ) { 
               reaction = parts[1];
               for (int j=2; j<parts.length; j++){
                   if(parts[j].equals("HADRONS")){parts[j] = "2HADRON";}
                   if(parts[j].equals("JETS")){parts[j] = "2JET";}
                   reaction = reaction.concat(" " + parts[j]);
               }
           }
           if(parts[0].equals("OBS")) {observable = parts[1];}
           if(parts[0].equals("IRN")) {spiresid = parts[1];}
           if(parts[0].equals("RED")) {redid = parts[1];}
           if(parts[0].equals("EXP") || parts[0].equals("DE") || parts[0].equals("CN")) {experiment = parts[1];}
           if(parts[0].equals("AUTH") || parts[0].equals("A") || parts[0].equals("AUTHOR") ) {author = parts[1];}
           if(parts[0].equals("SQRTS") || parts[0].equals("ECM")) {sqrts = parts[1];}
           if(parts[0].equals("REF") || parts[0].equals("R") ) {
               reference = parts[1];
               for (int j=2; j<parts.length; j++){
                   reference = reference.concat(" " + parts[j]);
               }
           }
           if(parts[0].equals("DATE") || parts[0].equals("YEAR") || parts[0].equals("D") ) {
               int next = 1;
               if(parts[1].equals("<") || 
                  parts[1].equals(">") ){
                  datetype=parts[1];
                  next=2;
               }
               date = parts[next];
               for (int j=next+1; j<parts.length; j++){
                   date = date.concat(" " + parts[j]);
               }
           System.out.println(datetype);
           }
           if(parts[0].equals("FSP")){
               if(parts[1].equals("HADRONS")){parts[1] = "2HADRON";}
               if(parts[1].equals("JETS")){parts[1] = "2JET";}
               reaction = "--> " + parts[1];
           }
            if(parts[0].equals("FS")){
               if(parts[1].equals("HADRONS")){parts[1] = "2HADRON";}
               if(parts[1].equals("JETS")){parts[1] = "2JET";}
               reaction = "--> " + parts[1];
               for (int j=2; j<parts.length; j++){
                   if(parts[j].equals("HADRONS")){parts[j] = "2HADRON";}
                   if(parts[j].equals("JETS")){parts[j] = "2JET";}
                   reaction = reaction.concat(" " + parts[j]);
               }
           }
          if(parts[0].equals("BEAM") || parts[0].equals("TARG")){
               reaction = parts[1];
           }
       }
       if(spiresid != null) { return SpiresId(spiresid,flag,_session);}
       else if(redid != null) { return RedId(redid,flag,_session);}
       else if(author != null) { return Author(author,flag,_session);}
       else if(experiment != null) {
           if(date  != null){
               if(reaction != null || observable != null || sqrts != null){
                  return Physics(experiment,date,datetype,reaction,observable,sqrts,flag,_session);
               }
               else{
                  System.out.println("calling ExperimentDate" + experiment + date);
                  return ExperimentDate(experiment,date,datetype,flag,_session);
               }
           }
           else{
               if(reaction != null || observable != null || sqrts != null){
                  return Physics(experiment,date,datetype,reaction,observable,sqrts,flag,_session); 
               }
               else{
                   return Experiment(experiment,flag,_session);
               }
           }
       }
       else if(date != null) { 
            if(experiment !=null) {   
               if(reaction != null || observable != null || sqrts != null){
                  return Physics(experiment,date,datetype,reaction,observable,sqrts,flag,_session);
               }
               else{
                  System.out.println("calling ExperimentDate" + experiment + date);
                  return ExperimentDate(experiment,date,datetype,flag,_session);
               }
           }
           else{
               if(reaction != null || observable != null || sqrts != null){
                  return Physics(experiment,date,datetype,reaction,observable,sqrts,flag,_session); 
               }
               else{
                   return Date(date,datetype,flag,_session);
               }
           }
       }
       else if(reference != null) { return Reference(reference,flag,_session);}
       else{ return Physics(experiment,date,datetype,reaction,observable,sqrts,flag,_session); }
    }
    public static Query EventShapes(String flag,org.hibernate.Session _session){
       Query q=null;         
       StringBuffer b = new StringBuffer();
           
       if (flag.equals("count")){
           b.append("select count(distinct p.PAPER_ID) from Papers p");
       }
       else{
           b.append("select distinct {p.*} from Papers {p}");
       }
       b.append(",Datasets ds");
       b.append(",DsObservables dsobs");

       b.append(" where (dsobs.DsObservables like 'dsig/dcol%'");
       b.append(" or dsobs.DsObservables like 'dn/dcol%')");
       b.append(" and dsobs.DATASET_ID=ds.DATASET_ID");
       
       b.append(" and p.PAPER_ID=ds._paper_PAPER_ID");
       b.append(" order by p.SpiresId desc");

       if(flag.equals("count")){
           q = _session.createSQLQuery(b.toString());
       }
       else{
           q = _session.createSQLQuery(b.toString()).addEntity("p",Paper.class);
       }
       System.out.println(q.toString());
       return q;
    }
    public static Query EventShapesEE(String flag,org.hibernate.Session _session){
       System.out.println("using Special");
       Query q=null;         
       StringBuffer b = new StringBuffer();
           
       if (flag.equals("count")){
           b.append("select count(distinct p.PAPER_ID) from Papers p");
       }
       else{
           b.append("select distinct {p.*} from Papers {p}");
       }
       b.append(",Datasets ds");
       b.append(",DsObservables dsobs");
       b.append(",DsReactions dsreac");

       b.append(" where (dsobs.DsObservables like 'dsig/dcol%'");
       b.append(" or dsobs.DsObservables like 'dn/dcol%')");
       b.append(" and dsobs.DATASET_ID=ds.DATASET_ID");

       b.append(" and dsreac.DsReactions like 'E+ E-%'");
       b.append(" and dsreac.DATASET_ID=ds.DATASET_ID"); 

       b.append(" and p.PAPER_ID=ds._paper_PAPER_ID");
       b.append(" order by p.SpiresId desc");

       if(flag.equals("count")){
           q = _session.createSQLQuery(b.toString());
       }
       else{
           q = _session.createSQLQuery(b.toString()).addEntity("p",Paper.class);
       }
       System.out.println(q.toString());
       return q;
    }
    public static Query EventShapesNotEE(String flag,org.hibernate.Session _session){
       System.out.println("using Special");
       Query q=null;         
       StringBuffer b = new StringBuffer();
           
       if (flag.equals("count")){
           b.append("select count(distinct p.PAPER_ID) from Papers p");
       }
       else{
           b.append("select distinct {p.*} from Papers {p}");
       }
       b.append(",Datasets ds");
       b.append(", DsObservables dsobs");
       b.append(", DsReactions dsreac");

       b.append(" where (dsobs.DsObservables like 'dsig/dcol%'");
       b.append(" or dsobs.DsObservables like 'dn/dcol%')");
       b.append(" and dsobs.DATASET_ID=ds.DATASET_ID");

       b.append(" and dsreac.DsReactions not like 'E+ E-%'");
       b.append(" and dsreac.DATASET_ID=ds.DATASET_ID"); 
       
       b.append(" and p.PAPER_ID=ds._paper_PAPER_ID");
       b.append(" order by p.SpiresId desc");

       if(flag.equals("count")){
           q = _session.createSQLQuery(b.toString());
       }
       else{
           q = _session.createSQLQuery(b.toString()).addEntity("p",Paper.class);
       }
       System.out.println(q.toString());
       return q;
    }
    public static Query JetProduction(String flag,org.hibernate.Session _session){
       System.out.println("using Special");
       Query q=null;         
       StringBuffer b = new StringBuffer();
           
       if (flag.equals("count")){
           b.append("select count(distinct p.PAPER_ID) from Papers p");
       }
       else{
           b.append("select distinct {p.*} from Papers {p}");
       }
       b.append(",Datasets ds");
       b.append(",YAxes ya");
       b.append(",AxisReactions ar");
       b.append(",FinalStates fs");

       b.append(" where fs.ParticleName like 'JET'");
       b.append(" and fs.REACTION_ID=ar.REACTION_ID");
       b.append(" and ar._yAxis_AXIS_ID=ya.AXIS_ID");
       b.append(" and ya._dataset_DATASET_ID=ds.DATASET_ID");
       
       b.append(" and p.PAPER_ID=ds._paper_PAPER_ID");
       b.append(" order by p.SpiresId desc");

       if(flag.equals("count")){
           q = _session.createSQLQuery(b.toString());
       }
       else{
           q = _session.createSQLQuery(b.toString()).addEntity("p",Paper.class);
       }
       System.out.println(q.toString());
       return q;
    }
    public static Query JetProductionEE(String flag,org.hibernate.Session _session){
       System.out.println("using Special");
       Query q=null;         
       StringBuffer b = new StringBuffer();
           
       if (flag.equals("count")){
           b.append("select count(distinct p.PAPER_ID) from Papers p");
       }
       else{
           b.append("select distinct {p.*} from Papers {p}");
       }
       b.append(",Datasets ds");
       b.append(",YAxes ya");
       b.append(",AxisReactions ar");
       b.append(",FinalStates fs");
       b.append(", DsReactions dsreac");

       b.append(" where dsreac.DsReactions like 'E+ E-%'");
       b.append(" and dsreac.DATASET_ID=ds.DATASET_ID"); 

       b.append(" and fs.ParticleName like 'JET'");
       b.append(" and fs.REACTION_ID=ar.REACTION_ID");
       b.append(" and ar._yAxis_AXIS_ID=ya.AXIS_ID");
       b.append(" and ya._dataset_DATASET_ID=ds.DATASET_ID");
       
       b.append(" and p.PAPER_ID=ds._paper_PAPER_ID");
       b.append(" order by p.SpiresId desc");

       if(flag.equals("count")){
           q = _session.createSQLQuery(b.toString());
       }
       else{
           q = _session.createSQLQuery(b.toString()).addEntity("p",Paper.class);
       }
       System.out.println(q.toString());
       return q;
    }
    public static Query JetProductionNotEE(String flag,org.hibernate.Session _session){
       System.out.println("using Special");
       Query q=null;         
       StringBuffer b = new StringBuffer();
           
       if (flag.equals("count")){
           b.append("select count(distinct p.PAPER_ID) from Papers p");
       }
       else{
           b.append("select distinct {p.*} from Papers {p}");
       }
       b.append(",Datasets ds");
       b.append(",YAxes ya");
       b.append(",AxisReactions ar");
       b.append(",FinalStates fs");
       b.append(", DsReactions dsreac");

       b.append(" where dsreac.DsReactions not like 'E+ E-%'");
       b.append(" and dsreac.DATASET_ID=ds.DATASET_ID"); 

       b.append(" and fs.ParticleName like 'JET'");
       b.append(" and fs.REACTION_ID=ar.REACTION_ID");
       b.append(" and ar._yAxis_AXIS_ID=ya.AXIS_ID");
       b.append(" and ya._dataset_DATASET_ID=ds.DATASET_ID");
       
       b.append(" and p.PAPER_ID=ds._paper_PAPER_ID");
       b.append(" order by p.SpiresId desc");

       if(flag.equals("count")){
           q = _session.createSQLQuery(b.toString());
       }
       else{
           q = _session.createSQLQuery(b.toString()).addEntity("p",Paper.class);
       }
       System.out.println(q.toString());
       return q;
    }
    public static Query Experiment(String experiment,String flag,org.hibernate.Session _session){
       System.out.println("using Experiment");
       String theExp=experiment;
       Query q=null;         
       StringBuffer b = new StringBuffer();
           
       if (flag.equals("count")){
           b.append("select count(distinct p) from Paper p");
       }
       else{
           b.append("select distinct p from Paper p");
       }
       b.append(" join p._experiments exp");
       b.append(" where (exp._name like '%");
       b.append(experiment);
       b.append("%'");
       b.append(" or exp._informalName like '%");
       b.append(experiment);
       b.append("%')");
       b.append(" order by p._spiresId desc");
       q = _session.createQuery(b.toString());
       System.out.println(q.toString());
//       q.setString("exp",theExp);
       
       return q;
    }
    public static Query ExperimentDate(String experiment,String date,String datetype,String flag,org.hibernate.Session _session){
       System.out.println("using ExperimentDate");
       String theDate=date;
       String theExp=experiment;
       Query q=null;         
       StringBuffer b = new StringBuffer();
           
       if (flag.equals("count")){
           b.append("select count(distinct p) from Paper p");
       }
       else{
           b.append("select distinct p from Paper p");
       }
       b.append(" join p._experiments exp");
       b.append(" join p._references ref");
       b.append(" where (exp._name like '%");
       b.append(experiment);
       b.append("%'");
       b.append(" or exp._informalName like '%");
       b.append(experiment);
       b.append("%')");

       if(datetype.equals("=")){
           b.append(" and ref._date like '%");
           b.append(date);
           b.append("'");
       }
       else{
           b.append(" and ref._date " + datetype);
           b.append(date);
           b.append(" and ref._date not like ''");
       }   
       b.append(" order by p._spiresId desc");

       q = _session.createQuery(b.toString());
       System.out.println(q.toString());
//       q.setString("date",theDate);
       
       return q;
    }
    public static Query Reference(String reference,String flag,  org.hibernate.Session _session){
       System.out.println("using Reference");
       String theRef=reference;
       Query q=null;         
       StringBuffer b = new StringBuffer();
           
       if (flag.equals("count")){
           b.append("select count(distinct p) from Paper p");
       }
       else{
           b.append("select distinct p from Paper p");
       }
       b.append(" join p._references ref");
       b.append(" where ref._description like '");
       b.append(reference);
       b.append("'");
       b.append(" order by p._spiresId desc");
       q = _session.createQuery(b.toString());
//       q.setString("ref",theRef);
       
       return q;
    }
    public static Query Date(String date,String datetype,String flag,  org.hibernate.Session _session){
       System.out.println("using Date");
       String theDate=date;
       Query q=null;         
       StringBuffer b = new StringBuffer();
           
       if (flag.equals("count")){
           b.append("select count(distinct p) from Paper p");
       }
       else{
           b.append("select distinct p from Paper p");
       }
       b.append(" join p._references ref");
       if(datetype.equals("=")){
           b.append(" where ref._date like '%");
           b.append(date);
           b.append("'");
        }
        else{
           b.append(" where ref._date " + datetype);
           b.append(date);
           b.append(" and ref._date not like ''");
        }   
       b.append(" order by p._spiresId desc");
       q = _session.createQuery(b.toString());
//       q.setString("date",theDate);
       
       return q;
    }
    public static Query SpiresId(String spiresid,String flag,  org.hibernate.Session _session){
       System.out.println("using SpiresId");
       String theIrn=spiresid;
       Query q=null;         
       StringBuffer b = new StringBuffer();
           
       if (flag.equals("count")){
           b.append("select count(distinct p) from Paper p");
       }
       else{
           b.append("select distinct p from Paper p");
       }
       b.append(" where p._spiresId like '");
       b.append(spiresid);
       b.append("' order by p._spiresId desc");
       q = _session.createQuery(b.toString());
//       q.setString("exp",theExp);
       
       return q;
    }
    public static Query RedId(String redid,String flag,  org.hibernate.Session _session){
       System.out.println("using RedId");
       Query q=null;         
       StringBuffer b = new StringBuffer();
           
       if (flag.equals("count")){
           b.append("select count(distinct p) from Paper p");
       }
       else{
           b.append("select distinct p from Paper p");
       }
       b.append(" where p._redId like '");
       b.append(redid);
       b.append("' order by p._spiresId desc");
       q = _session.createQuery(b.toString());
       
       return q;
    }
    public static Query Author(String author,String flag,  org.hibernate.Session _session){
       String theAuth=author;
       Query q=null;         
       StringBuffer b = new StringBuffer();
           
       if (flag.equals("count")){
           b.append("select count(p.HepdataId) from Papers p, PaperAuthors pa");
       }
       else{
           b.append("select * from Papers p, PaperAuthors pa");
      }
       b.append(" where p.PAPER_ID=pa.PAPER_ID");
       b.append(" and pa.element like '");
       b.append(author);
       b.append("' order by p.SpiresId desc");
       if(flag.equals("count")){
           q = _session.createSQLQuery(b.toString());
       }
       else{
           q = _session.createSQLQuery(b.toString()).addEntity("p",Paper.class);
       }
       return q;
    }

    public static Query Physics(String experiment, String date, String datetype, String reaction, String observable, String sqrts, String flag, org.hibernate.Session _session){
       System.out.println("using Physics");

        List <String> isp = new ArrayList();
        List  <String> fsp = new ArrayList();
        List <String>  mfsp = new ArrayList();
        List <String>  misp = new ArrayList();
        
        System.out.println("Here we are in Papers");
        System.out.println("sorting reaction: " + reaction);
        if( reaction != null && !reaction.equals("") && !reaction.equals("null")) {
            String is = getInitialState(reaction);
            java.util.StringTokenizer stis = new java.util.StringTokenizer(is);
            String st = "";
            while(stis.hasMoreTokens()){
                st = stis.nextToken();
                if(st.matches("^[A-Za-z].*")){
                    if(isp.isEmpty()){
                        isp.add(st);
                        misp.add("1");
                    }
                    else{
                        int isize = isp.size();
                        for (int i=0; i<isize; i++){
                            if(isp.get(i).equals(st)){
                                int n = Integer.parseInt(misp.get(i));
                                n += 1;
                                misp.set(i,Integer.toString(n));
                            }
                            else{
                                isp.add(st);
                                misp.add("1");
                            }
                        }
                    }   
                }
                else{
                    isp.add(st.substring(1));
                    misp.add(st.substring(0,1));
                }
//             isp.add(stis.nextToken());
            }
            String fs = getFinalState(reaction);
            java.util.StringTokenizer stfs = new java.util.StringTokenizer(fs);
            while(stfs.hasMoreTokens()){
                st = stfs.nextToken();
                if(st.matches("^[A-Za-z].*")){
                    if(fsp.isEmpty()){
                        fsp.add(st);
                        mfsp.add("1");
                    }
                    else{
                        int fsize = fsp.size();
                        for (int i=0; i<fsize; i++){
                            if(fsp.get(i).equals(st)){
                                int n = Integer.parseInt(mfsp.get(i));
                                n += 1;
                                mfsp.set(i,Integer.toString(n));
                            }
                            else{
                                fsp.add(st);
                                mfsp.add("1");
                            }
                        }
                    }   
                }
                else{
                    fsp.add(st.substring(1));
                    mfsp.add(st.substring(0,1));
                }
            }
        }
        String theObs = "";
        if ( observable != null && !observable.equals("") && !observable.equals("null") ) { theObs  = observable;  }
        
        String theSqrtsLo = "";
        System.out.println("sqrts is: " + sqrts);
        if ( sqrts != null && !sqrts.equals("") && !sqrts.equals("null")) { theSqrtsLo  = sqrts; System.out.println(sqrts); }

        Query q = null;

        // the string buffer way!!
        StringBuffer b = new StringBuffer();

        if(isp.size() > 0){
//select...
            System.out.println("we have an intial state " + isp + "/" + misp);
            System.out.println("and final state " + fsp + "/" + mfsp );
            System.out.println("and observable " + observable);
            if (flag.equals("count")){
                b.append("select count(distinct pbeam) from Paper pbeam");
            }
            else{
                b.append("select distinct pbeam from Paper pbeam");
            }
//joins....
            if(experiment != null) {b.append(" join pbeam._experiments exp");}
            if(date       != null) {b.append(" join pbeam._references ref");}
            b.append(" join pbeam._datasets dsbeam");
            b.append(" join dsbeam._yAxes yabeam");
            b.append(" join yabeam._reactions yrbeam");
            b.append(" join yrbeam._initialState beam"); 
            if (isp.size() > 1){ 
                b.append(",Paper ptarg");
                b.append(" join ptarg._datasets dstarg");
                b.append(" join dstarg._yAxes yatarg");
                b.append(" join yatarg._reactions yrtarg");
                b.append(" join yrtarg._initialState targ"); 
            }
            for (int i = 1 ; i <= fsp.size(); i++){ 
               b.append(",Paper pfsp"+i);
               b.append(" join pfsp"+i+"._datasets dsfsp"+i); 
               b.append(" join dsfsp"+i+"._yAxes yafsp"+i);
               b.append(" join yafsp"+i+"._reactions yrfsp"+i);
               b.append(" join yrfsp"+i+"._finalState fsp"+i);
            }
            if( theSqrtsLo != null && !theSqrtsLo.equals("") && !theSqrtsLo.equals("null") ){
               b.append(",Paper pprop");
               b.append(" join pprop._datasets dsprop");
               b.append(" join dsprop._yAxes yaprop");
               b.append(" join yaprop._properties prop");
            }
//where...
            b.append(" where beam.name like :beampart and beam.multiplicity=:beammult");
            if(experiment != null){       
                b.append(" and (exp._name like '%");
                b.append(experiment);
                b.append("%'");
                b.append(" or exp._informalName like '%");
                b.append(experiment);
                b.append("%')");
            }
            if(date != null){
                if(datetype.equals("=")){       
                    b.append(" and ref._date like '%");
                    b.append(date);
                    b.append("'");}
                else{
                    b.append(" and ref._date " + datetype);
                    b.append(date);
                    b.append(" and ref._date not like ''");
                }
            }
            if (isp.size() > 1){ 
                b.append(" and targ.name=:targpart");  
                b.append(" and yrbeam = yrtarg");
            } 
            for (int i = 1 ; i <= fsp.size(); i++){ 
               b.append(" and fsp"+i+".name like :fsp"+i+"part and fsp"+i+".multiplicity=:fsp"+i+"mult");
               b.append(" and yrbeam = yrfsp"+i);
            }
            if ( theObs != null && !theObs.equals("") && !theObs.equals("null") ) { b.append(" and yabeam._observable like:observable"); } 
            if ( theSqrtsLo != null && !theSqrtsLo.equals("") && !theSqrtsLo.equals("null") ){
                b.append(" and yabeam = yaprop");
                b.append(" and prop._name like 'sqrts' and prop._lowValue>:sqrtslo");
            }
// sort 
            b.append(" order by pbeam._spiresId desc");
//create query
//make substitutions
            q = _session.createQuery(b.toString());
            q.setString("beampart",isp.get(0));
            q.setString("beammult",misp.get(0));
            if (isp.size() > 1)  {q.setString( "targpart",isp.get(1)); }
            for (int i = 1 ; i <= fsp.size(); i++){
                q.setString( "fsp"+i+"part",fsp.get(i-1));
                q.setString( "fsp"+i+"mult",mfsp.get(i-1)); 
            }
//            System.out.println(q.toString());
            if ( theObs != null && !theObs.equals("") && !theObs.equals("null") ) {q.setString( "observable",theObs); }
            if ( theSqrtsLo != null && !theSqrtsLo.equals("") && !theSqrtsLo.equals("null") ) {q.setString( "sqrtslo",theSqrtsLo); }
        }

        // no inital state so next assuming we have a fsp
        else if(fsp.size() > 0) {
//select(no initialstate)...
            if (flag.equals("count")){
                b.append("select count(distinct pfsp1) from Paper pfsp1");
            }
            else{
                b.append("select distinct pfsp1 from Paper pfsp1");
            }
//joins(no initialstate)...
            if(experiment != null) {b.append(" join pfsp1._experiments exp");}
            if(date       != null) {b.append(" join pfsp1._references ref");}
            b.append(" join pfsp1._datasets dsfsp1");
            b.append(" join dsfsp1._yAxes yafsp1");
            b.append(" join yafsp1._reactions yrfsp1");
            b.append(" join yrfsp1._finalState fsp1"); 
            for (int i = 2 ; i <= fsp.size(); i++){ 
               b.append(",Paper pfsp"+i);
               b.append(" join pfsp"+i+"._datasets dsfsp"+i);
               b.append(" join dsfsp"+i+"._yAxes yafsp"+i);
               b.append(" join yafsp"+i+"._reactions yrfsp"+i);
               b.append(" join yrfsp"+i+"._finalState fsp"+i);
            }
            if ( theSqrtsLo != null && !theSqrtsLo.equals("") && !theSqrtsLo.equals("null") ) {
               b.append(",Paper pprop");
               b.append(" join pprop._datasets dsprop");
               b.append(" join dsprop._yAxes yaprop");
               b.append(" join yaprop._properties prop");
            }  
//where(no initialstate)...
            b.append(" where fsp1.name like :fsp1part and fsp1.multiplicity=:fsp1mult"); 
            if(experiment != null){       
                b.append(" and (exp._name like '%");
                b.append(experiment);
                b.append("%'");
                b.append(" or exp._informalName like '%");
                b.append(experiment);
                b.append("%')");
            }
            if(date != null){       
                if(datetype.equals("=")){       
                    b.append(" and ref._date like '%");
                    b.append(date);
                    b.append("'");}
                else{
                    b.append(" and ref._date " + datetype);
                    b.append(date);
                    b.append(" and ref._date not like ''");
                }
            }
            for (int i = 2 ; i <= fsp.size(); i++){ 
               b.append(" and fsp"+i+".name like :fsp"+i+"part and fsp"+i+".multiplicity=:fsp"+i+"mult");
               b.append(" and yrfsp1 = yrfsp"+i);
            }
            if ( theObs != null && !theObs.equals("") && !theObs.equals("null") ) { b.append(" and yafsp1._observable like:observable"); } 
            if ( theSqrtsLo != null && !theSqrtsLo.equals("") && !theSqrtsLo.equals("null") ) {
                b.append(" and yafsp1 = yaprop");
                b.append(" and prop._name like 'sqrts' and prop._lowValue>:sqrtslo");
            }
            b.append(" order by pfsp1._spiresId desc");
//create query...
            q = _session.createQuery(b.toString());
//make substitutions...
            for (int i = 1 ; i <= fsp.size(); i++){
              q.setString("fsp"+i+"part",fsp.get(i-1)); 
              q.setString("fsp"+i+"mult",mfsp.get(i-1)); 
            }
            if ( theObs != null && !theObs.equals("") && !theObs.equals("null") ) {q.setString("observable",theObs);}
            if ( theSqrtsLo != null && !theSqrtsLo.equals("") && !theSqrtsLo.equals("null") ) {q.setString( "sqrtslo",theSqrtsLo); }
        }
// OK no reaction  .. so do we have an observable?
        else if ( theObs != null && !theObs.equals("") && !theObs.equals("null") ) {
//> here we have no reaction but an observable
            if (flag.equals("count")){
                b.append("select count(distinct pobs) from Paper pobs");
            }
            else{
                b.append("select distinct pobs from Paper pobs");
            }
            if(experiment != null) {b.append(" join pobs._experiments exp");}
            if(date       != null) {b.append(" join pobs._references ref");}
            b.append(" join pobs._datasets dsobs join dsobs._yAxes yaobs"); 
            if ( theSqrtsLo != null && !theSqrtsLo.equals("") && !theSqrtsLo.equals("null") ) {
               b.append(",Paper pprop");
               b.append(" join pprop._datasets dsprop");
               b.append(" join dsprop._yAxes yaprop");
               b.append(" join yaprop._properties prop");
            }  
            b.append(" where yaobs._observable like:observable");  
            if(experiment != null){       
                b.append(" and (exp._name like '%");
                b.append(experiment);
                b.append("%'");
                b.append(" or exp._informalName like '%");
                b.append(experiment);
                b.append("%')");
            }
            if(date != null){       
                if(datetype.equals("=")){       
                    b.append(" and ref._date like '%");
                    b.append(date);
                    b.append("'");}
                else{
                    b.append(" and ref._date " + datetype);
                    b.append(date);
                    b.append(" and ref._date not like ''");
                }
            }
            if ( theSqrtsLo != null && !theSqrtsLo.equals("") && !theSqrtsLo.equals("null") ) {
                b.append(" and yaobs = yaprop");
                b.append(" and prop._name like 'sqrts' and prop._lowValue>:sqrtslo");
            }
            b.append(" order by pobs._spiresId desc");
            q = _session.createQuery(b.toString());
            q.setString("observable",theObs);
            if ( theSqrtsLo != null && !theSqrtsLo.equals("") && !theSqrtsLo.equals("null") ) {q.setString( "sqrtslo",theSqrtsLo); }
        }

// here if sqrtslo on its own ! just to test 
        else if ( theSqrtsLo != null && !theSqrtsLo.equals("") && !theSqrtsLo.equals("null") ) {
            if (flag.equals("count")){
                b.append("select count(distinct pprop) from Paper pprop");
            }
            else{
                b.append("select distinct pprop from Paper pprop");
            }
            if(experiment != null) {b.append(" join pprop._experiments exp");}
            if(date       != null) {b.append(" join pprop._references ref");}
            b.append(" join pprop._datasets dsprop");
            b.append(" join dsprop._yAxes yaprop");
            b.append(" join yaprop._properties prop");

            b.append(" where prop._name like 'sqrts' and prop._lowValue>:sqrtslo");
            if(experiment != null){       
                b.append(" and (exp._name like '%");
                b.append(experiment);
                b.append("%'");
                b.append(" or exp._informalName like '%");
                b.append(experiment);
                b.append("%')");
            }
            if(date != null){       
                if(datetype.equals("=")){       
                    b.append(" and ref._date like '%");
                    b.append(date);
                    b.append("'");}
                else{
                    b.append(" and ref._date " + datetype);
                    b.append(date);
                    b.append(" and ref._date not like ''");
                }
            }
            b.append(" order by pprop._spiresId desc");
            q = _session.createQuery(b.toString());
            q.setString("sqrtslo",theSqrtsLo);
        }
// nothing left so must want everything !!
        else{
            if (flag.equals("count")){
                b.append("select count(distinct pa) from Paper pa");
            }
            else{
                b.append("select distinct pa from Paper pa");
            }
            b.append(" order by pa._spiresId desc");
            q = _session.createQuery(b.toString());
        }

        System.out.println(q.toString());
        return q;

    }

    private static String getInitialState(String r){
        String is="";
        int ipos = r.indexOf("-->");
        if(ipos > -1 ){ is = r.substring(0,ipos); }
        else { is = r; }
        return is.trim();
    }
    private static String getFinalState(String r){
        String fs="";
        int ipos = r.indexOf("-->");
        if(ipos > -1) {fs = r.substring(ipos+3);}
        return fs.trim();
    }
}

---