ShapeXml.java

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package cedar.hepdata.webapp;


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

import java.io.*;
import java.util.*;
import javax.servlet.*;
import javax.servlet.http.*;

import java.text.*;
import java.lang.*;

import org.exolab.castor.xml.Unmarshaller;


public class ShapeXml extends HttpServlet {

    public String getServletInfo() {
        return "Test servlet. Do not use.";
    }


    public void doGet(HttpServletRequest request, HttpServletResponse response) throws IOException, ServletException {
        response.setContentType("text/html");
        PrintWriter out = response.getWriter();

        out.println("<h1>Shape demo (XML)</h1>");
        out.println("<p>Reading in data from XML file !!!</p>");

        out.println(request.getParameter("irn"));
        String irn = request.getParameter("irn");
        int spiresid = Integer.parseInt(irn);

        String dataset = null;
        String yaxis = null;
        dataset = request.getParameter("dataset");
        yaxis = request.getParameter("yaxis");
        
        Paper p = null;
        try {
// getting from xml file
            Data data = XMLUtils.getDataFromHepML(new File("/home/whalley/hd/hepdata-migration/shapes-hepml/"+ irn + ".hep.xml"));
            if (data != null) p = data.getFirstPaper();
            if (p == null) throw new Exception("Null paper");

            this.displayHeader(p,out);
            if(dataset == null){
               this.displayDatasetError(p,out,String.valueOf(1));
            }
            else{
                this.displayDatasetError(p,out,dataset);
            }
            if(dataset == null){
                this.displayDatasets(p,out);
            }
            else if(yaxis == null){
                this.displayDataset(p,out,dataset);
            }
            else                  {
               this.displayDataset(p,out,dataset,yaxis);
            }
        } 
        catch (Exception e) {
            out.println("Exception: " + e.toString());
            out.println("<pre>");
            e.printStackTrace(out);
            out.println("</pre>");
            return;
        }
    }

    private void displayDatasets(Paper p,PrintWriter out){
        int nds = 0;
        for ( Dataset d : p.getDatasets() ) {
              nds++;
              String dataset = String.valueOf(nds);
              this.displayDataset(p,out,dataset);
        }
    }

    private void displayDataset(Paper p,PrintWriter out,String dataset){
        int ds = Integer.parseInt(dataset);
        Dataset d = p.getDataset(ds);
        int ya=0;  
        for (YAxis y : d.getYAxes()){
            ya++;
            String yaxis = String.valueOf(ya);
            this.displayDataset(p,out,dataset,yaxis);
        }
    }

    private void displayDataset(Paper p,PrintWriter out,String dataset,String yaxis){
        int ds = Integer.parseInt(dataset);
        int ya = Integer.parseInt(yaxis);
        Dataset d = p.getDataset(ds);
        YAxis y = d.getYAxis(ya);
// count the number of x and y axes and the number of bins

        int nx = d.getXAxes().size();
        int npoints = 0;
        for (XAxis x : d.getXAxes()){npoints = x.getBins().size();}
           
// counting done
// output each y axis in turn in a separate table
// first try to get the yaxis errors for this table
       for (AxisError ae : y.getErrors() ) {
            out.println("\nAxis Error");
            if (ae.getComment() != null) { out.println(ae.getComment() ); }
            if (ae.getPlus() != null) { out.println(ae.getPlus() ); }
            if (ae.getMinus() != null) { out.println(ae.getMinus() ); }
            if (ae.getSourceType() != null) { out.println(ae.getSourceType() ); }
            if (ae.getNormType() != null) { out.println(ae.getNormType() ); }
        }
       
// first the reactions for this yaxis
        out.println("<table border=1>");
        int nspan = nx+1;
        out.println("<th colspan=" + nspan + ">Dataset " + ds + " yaxis " + ya + "</th></tr><tr>");
        for ( Reaction reac : y.getReactions() ){
            out.println("<th colspan=" + nspan +">");
        
            for ( Particle part : reac.getInitialState() ){
                out.println(part.getName() + " ");
            }
            out.println("-->");
            for ( Particle part : reac.getFinalState() ){
                if (part.getMultRelation() != Relation.EQUALS) {out.println( part.getMultRelation() );}
                if (part.getMultiplicity() > 1) {out.println( part.getMultiplicity() );}
                out.println(part.getName() + " ");
            }
            out.println("</th></tr>");
        }

// next the yaxis comments (non-numerical properties!)
        for (String comment : y.getComments()){
            out.println("<tr>");
            out.println("<th colspan=" + nspan +">" + comment + "</th></tr>");
        }
// next the observable)
//             cedar.hepdata.model.Observable obs = y.getObservable();
             String sobs = y.getObservable();
             out.println("<th colspan=" + nspan + ">" + "obs:"+ sobs + "</th></tr>");
              
// next the properties
        for ( Property prop: y.getProperties() ){
            out.println("<tr>");
            out.println("<th colspan=" + nspan +">");
            out.println( prop.getName() + " : ");
            if (prop.getLowValue() != null && prop.getHighValue() != null &&
                prop.getLowValue().equals(prop.getHighValue())) {
                out.println(prop.getLowValue());
            }
            else{out.println(prop.getLowValue() + " TO " + prop.getHighValue());}
            if (!prop.getUnit().toString().equals("num")){
               out.println(" " + prop.getUnit().toString());
            }
            out.println("</th>" ) ;
        }             

// here for the headers
        out.println("<tr>");
        for (XAxis x : d.getXAxes()){
            out.println("<th>" + x.getHeader() + "</th>");
        }
        out.println("<th>" + y.getHeader() + "</th>");
        out.println("</tr>");
              
// finally the numbers themselves
// first the xaxes
        Double f = null;
        Double high = null;
        Double low = null;
        out.println("<tr>");
        for (int ix=1 ; ix<=nx; ix++){
            XAxis xaxis = d.getXAxis(ix);
            out.println("<td><pre>");
            for (int ip=1 ; ip<=npoints; ip++){
                for (Bin b : xaxis.getBins()){
                    if(b.getId() == ip) {
                        low = b.getLowValue();
                        high = b.getHighValue();
                        f = b.getFocus();
                        if(low != null){
                            out.println(forms(high,8,out) + " TO " + forms(low,8,out)); 
                        }
                        else{
                            out.println(forms(f,8,out)); 
                        }
                    }           
                }               
            }           
            out.println("</pre></td>");
        }
         
// next the yaxis
        
        StringBuffer s = new StringBuffer();
        s.append("<td><pre>");
        for (int ip=1 ; ip<=npoints; ip++){
            try {
                Point pt2 = y.getPoint(ip);
                s.append(forms(pt2.getValue(),15,out)); 
                for ( Uncertainty e : pt2.getErrors() ){
                    if( e.getPlus().equals(e.getMinus()) ) {
                        s.append(" +- " + forms(e.getPlus(),15,out) );
                    }
                    else{
                        s.append(" +" + forms(e.getPlus(),15,out) + ",-" + forms(e.getMinus(),15,out) );
                    }
                    if ( e.getNormType() == ErrorNorm.PCT ) {
                        s.append(" (" + e.getNormType().toString() + ")");
                    }
                }
                s.append("<br>");
            } 
            catch (Exception e) {
                s.append("  -  <br>");
            }
        }
        s.append("</pre></td>");
        out.println(s);
        out.println("</tr>");
        out.println("</table>");
    }

    private void displayHeader(Paper p,PrintWriter out){
        StringBuffer s = new StringBuffer();
        out.println("<pre>");
        out.println("irn = " + p.getSpiresId());
        out.println("red = " + p.getRedId());
        int icom = 0;
        for ( String comment : p.getComments() ){
            icom++;
            out.println(icom + ":" + comment);
        }
        int imod = 0;
        for ( Modification modification : p.getModifications() ){
            imod++;
            if(imod == 1){out.println("Created on " + modification.getTimestamp() + " by " + modification.getModifier());}
            else        {out.println("Modified on " + modification.getTimestamp() + " by " + modification.getModifier());}
        }
        for (String auth: p.getAuthors() ) {
            out.println("author: "  + auth);
        }
        out.println("Title:" + p.getTitle());

        out.println("Number of references are: " + p.getReferences().size()); 

        for (Reference ref : p.getReferences() ) {
            out.println("Reference:"  + ref.getDescription());
        }
        for (Experiment exp : p.getExperiments() ) {
            out.println("Experiment:"  + exp.getName());
            out.println("Laboratory:"  + exp.getLaboratory());
            out.println("InformalName:"  + exp.getInformalName());
        }
    }

    private void displayDatasetError(Paper p,PrintWriter out,String dataset){
        int ds = Integer.parseInt(dataset);
        Dataset d = p.getDataset(ds);
        for (DatasetError de : d.getErrors() ) {
            out.println("\nDataset Error");
            if (de.getComment() != null) { out.println(de.getComment() ); }
            if (de.getPlus() != null) { out.println(de.getPlus() ); }
            if (de.getMinus() != null) { out.println(de.getMinus() ); }
            if (de.getSourceType() != null) { out.println(de.getSourceType() ); }
            if (de.getNormType() != null) { out.println(de.getNormType() ); }
        }
    }
    private  String forms(Double value,PrintWriter out){
        int width = 20;
        return this.forms(value,width,out);
        
    }

    private  String forms(Double value,int width,PrintWriter out){
        int position = width/2;
        return this.forms(value,width,position,out);
    }

    private String forms(Double value,int width, int position,PrintWriter out){
        String form = "##############.###############################";
        DecimalFormat myFormatter = new DecimalFormat(form);
        String sval = myFormatter.format(value);
        String sout = " ";
        for (int i=1 ; i<width; i++){
            sout = sout.concat(" ");
        }
        int lenval = sval.length(); 
        int dotpos = sval.indexOf(".");
        String before = sval;
        String after  = "";
        if(dotpos >= 0){
            before = sval.substring(0,dotpos);
            after  = sval.substring(dotpos+1,lenval);
        }
        int lenbefore = before.length();
        int lenafter = after.length();
        int lenout = sout.length();
        StringBuffer bout = new StringBuffer(sout);
        int lstart = 1;
        int l1 = lstart+lenbefore;
        int l2 = l1;
        int l3 = l2+1;
        int l4 = l3+lenafter;
        
        bout.replace(lstart,l1,before);
        bout.replace(l2,l2,".");
        bout.replace(l3,l4,after);
        sout = bout.toString();
        
        return sout;
    } 
}

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