Index: trunk/hepdata-webapp/src/main/java/cedar/hepdata/formats/YamlFormatter.java
===================================================================
--- trunk/hepdata-webapp/src/main/java/cedar/hepdata/formats/YamlFormatter.java (revision 1863)
+++ trunk/hepdata-webapp/src/main/java/cedar/hepdata/formats/YamlFormatter.java (revision 1864)
@@ -1,489 +1,489 @@
package cedar.hepdata.formats;
import cedar.hepdata.model.*;
import cedar.hepdata.util.*;
import cedar.hepdata.xml.*;
import cedar.hepdata.db.*;
import cedar.hepdata.webapp.components.*;
import java.util.*;
import java.text.*;
import java.io.File;
import java.io.*;
import org.antlr.stringtemplate.*;
import com.Ostermiller.util.SignificantFigures;
public class YamlFormatter {
public static String format(Paper p) {
StringBuffer s = new StringBuffer();
s.append("---\n");
String s4=" ";
String sp=" - ";
if(p == null) return null;
// _header contains all the bibliographic type stuff at the beginning
s.append(_headerYAML(p));
// here we deal with the extra resource are description/line files
String[] descs = { "description1" , "description2" , "description3" , "description4" };
String[] links = { "link1" , "link2" , "link3" , "link4" };
String[] ids = new String[3];
if(p.getSpiresId() != null ) { ids[0]=p.getSpiresId().toString(); } else { ids[0]=""; }
if(p.getInspireId() != null ) { ids[1]=p.getInspireId().toString(); } else { ids[1]=""; }
if(p.getRedId() != null ) { ids[2]=p.getRedId().toString(); } else { ids[2]=""; }
boolean first=true;
for (int i=0; i<descs.length; i++){
for(int j=0; j<ids.length; j++){
- String descfile = "/home/whalley/resource/" +ids[j] + "/" + descs[i];
- String linkfile = "/home/whalley/resource/" +ids[j] + "/" + links[i];
+ String descfile = "/home/hepdata/resource/" +ids[j] + "/" + descs[i];
+ String linkfile = "/home/hepdata/resource/" +ids[j] + "/" + links[i];
File testdesc = new File(descfile);
File testlink = new File(linkfile);
String desc="";
String link="";
if(testdesc.exists() && testlink.exists() ){
try {
BufferedReader in = new BufferedReader(new FileReader(descfile));
desc=in.readLine();
}
catch (IOException e){}
try {
BufferedReader in = new BufferedReader(new FileReader(linkfile));
link=in.readLine();
}
catch (IOException e){}
if(first){
s.append("\n---\n");
// s.append("#This is Table 0\n");
s.append("name: 'Table 0'\n");
s.append("label: 'Additional resources for the whole record'\n");
s.append("additional_resources:\n");
}
first=false;
s.append(sp+"description : '"+desc+"'\n");
s.append(s4+"link : '"+link+"'\n");
}
}
}
// next the insert.html file in the resource area
first=true;
for (int j=0; j<ids.length; j++){
- String insertfile = "/home/whalley/resource/" +ids[j] + "/insert.html";
+ String insertfile = "/home/hepdata/resource/" +ids[j] + "/insert.html";
File testinsert = new File(insertfile);
String insert="";
if(testinsert.exists()){
if(first) {
s.append("---\n");
// s.append("#This is Table 0\n");
s.append("name: 'Table 0'\n");
s.append("label: 'Additional resources for the whole record'\n");
s.append("additional_resources:\n");
}
first=false;
s.append(sp+"inserthtml: '/resource/"+ids[j]+"/insert.html'\n");
}
}
// and now the datasets
for (Dataset ds : p.getDatasets()){
s.append("\n---\n");
s.append(_metadataYAML(ds)); // dataset information in _metadata
s.append("data_file: data"+ds.getId()+".yaml\n");
s.append("additional_resources:\n");
}
for (Dataset ds : p.getDatasets()){
s.append("---\n");
s.append("#This is Data "+ds.getId()+"\n");
s.append(_dataYAML(ds)); // dataset information in _data
}
// finally finish off (at present does nothing!
s.append(_footerYAML());
// then write it all out.
return s.toString();
}
public static String _getTimestamp(){
DateFormat dateFormat = new SimpleDateFormat("yyyyMMddHHmmss");
Date date = new Date();
return dateFormat.format(date);
}
public static String _headerYAML(Paper p) {
String s4=" ";
String sp=" - ";
StringBuffer s = new StringBuffer();
if(p.getRedId()!=null) { s.append("durham: "+p.getRedId()+"\n"); }
s.append("dateupdated: '"+p.getDateUpdated()+"'\n");
if(p.getReferences().size()>0){
s.append("references: # additional references (e.g. experiment TWiki page for analysis)\n");
for (Reference r : p.getReferences()){
if(r.getDescription().startsWith("http")){
s.append(sp+"'"+r.getDescription());
s.append("'\n");
}
}
}
if(p.getModifications().size()>0){
s.append("modifications: # what, by whom and when encoded or changed\n");
for (Modification m : p.getModifications()){
s.append(sp+"'"+m.getAction()+" by ");
s.append(m.getModifier()+" on ");
s.append(m.getComment());
s.append("'\n");
}
}
int count=0;
if(p.getComments().size()>0){
s.append("comment: | # preserve newlines\n");
boolean first=true;
for (String comment : p.getComments()){
if(first){
s.append(s4+"'"+comment.replaceAll("\n","\n "));
first=false;
} else {
s.append(s4+comment.replaceAll("\n","\n "));
}
if(++count==p.getComments().size()) { s.append("'"); }
s.append("\n");
}
}
return s.toString();
}
public static String _footerYAML() {
StringBuffer s = new StringBuffer();
return s.toString();
}
public static String _metadataYAML(Dataset ds){
String s4=" ";
String sp=" - ";
StringBuffer s = new StringBuffer();
int idbase=9000000;
int id=idbase+ds.getId();
String location = "";
Paper p = ds.getPaper();
s.append("name: 'Table "+ds.getId()+"'\n");
for (String ct : ds.getComments()){
if(ct.startsWith("Location:")) {
location = ct.replaceFirst("Location:","");
// s.append("label: "+ct.replaceFirst("Location:","Data from")+" from: "+p.getTitle()+"\n");
s.append("label: '"+ct.replaceFirst("Location:","Data from")+"'\n");
}
}
boolean first=true;
int count=0;
for (String ct : ds.getComments()){
count++;
if(!ct.startsWith("Location:")) {
s.append("description: |\n");
if(first){
s.append(s4+"'"+ct.replaceFirst("VERBATIM","").replaceAll(">",">").replaceAll("<","<").replaceAll("\n","\n "));
first=false;
} else {
s.append(s4+ct.replaceFirst("VERBATIM","").replaceAll(">",">").replaceAll("<","<").replaceAll("\n","\n "));
}
if(count==ds.getComments().size()-1) { s.append("'"); }
s.append("\n");
}
else{++count;}
}
s.append("keywords:\n");
if(ds.getDsReactions().size() > 0) {
s.append(sp+"{ name: reactions, values: [");
int nr=0;
for (String dsreac : ds.getDsReactions()){
s.append("'"+dsreac+"'");
if(++nr==ds.getDsReactions().size()){s.append("] }\n"); }
else {s.append(", ");}
}
}
if(ds.getDsObservables().size() > 0) {
s.append(sp+"{ name: observables, values: [");
int no=0;
for (String dsobs : ds.getDsObservables()){
s.append("'"+dsobs+"'");
if(++no==ds.getDsObservables().size()){s.append("] }\n"); }
else {s.append(", ");}
}
}
if(ds.getDsPlabs().size() > 0) {
s.append(sp+"{ name: plabs, values: [");
int np=0;
for (String dsplab : ds.getDsPlabs()){
s.append("'"+dsplab+"'");
if(++np==ds.getDsPlabs().size()){s.append("] }\n"); }
else {s.append(", ");}
}
}
return s.toString();
}
public static String _dataYAML(Dataset ds){
String s4=" ";
String sp=" - ";
StringBuffer s = new StringBuffer();
int idbase=9000000;
int id=idbase+ds.getId();
String location = "";
Paper p = ds.getPaper();
s.append("xaxes:\n");
for (XAxis xax : ds.getXAxes()){
String name=xax.getHeader();
String unit="";
if(xax.getHeader().contains(" IN ")){
name=xax.getHeader().substring(0,xax.getHeader().indexOf(" IN ")).trim();
unit=xax.getHeader().substring(xax.getHeader().indexOf(" IN ")+4).trim();
}
s.append(sp+"header: {name: '"+name+"'");
if(!unit.equals("")){ s.append(", unit: '"+unit+"'"); }
s.append("}\n");
s.append(s4+"bins:\n");
for (Bin bin : xax.getBins()){
boolean first=true;
s.append(s4+sp+"{");
// if(bin.getId() != null ) {
// s.append("id: "+bin.getId());
// first=false;
// }
boolean asymmfocus = false;
if (bin.getLowValue() != null && bin.getHighValue() != null && bin.getFocus() != null) {
double diff = bin.getFocus() - (bin.getLowValue() + bin.getHighValue()) / 2.0;
if (Math.abs(diff/bin.getFocus()) > 1E-6) { asymmfocus = true; }
}
boolean haswidth = false;
if (bin.getLowValue() != null && bin.getHighValue() != null) {
double diff = bin.getHighValue() - bin.getLowValue();
double mean = (bin.getLowValue() + bin.getHighValue()) / 2.0;
if((Math.abs(diff/mean) > 1E-6) || (mean == 0.0 && Math.abs(diff) > 1E-6)){ haswidth = true;}
}
if(bin.getFocus() != null) {
if(asymmfocus || !haswidth) {
if(!first) {s.append(", "); }
if(bin.getFocusLength()!=null) {
s.append("value: "+forms(bin.getFocus(),bin.getFocusLength()));
} else {
s.append("value: "+bin.getFocus());
}
first=false;
}
}
if(bin.getLowValue() != null && haswidth ) {
if(!first) { s.append(", "); }
if(bin.getLowValueLength()!=null) {
s.append("low: "+forms(bin.getLowValue(),bin.getLowValueLength()));
} else {
s.append("high: "+bin.getLowValue());
}
first=false;
}
if(bin.getHighValue() != null && haswidth ) {
if(!first) {s.append(", "); }
if(bin.getHighValueLength()!=null) {
s.append("high: "+forms(bin.getHighValue(),bin.getHighValueLength()));
} else {
s.append("high: "+bin.getHighValue());
}
first=false;
}
if(bin.getRelation() != null && bin.getRelation() != Relation.EQUALS ) {
if(!first) { s.append(", "); }
s.append("relation: "+bin.getRelation());
first=false;
}
if(bin.getDescription() != null ) {
if(!first) { s.append(", "); }
s.append("description: '"+bin.getDescription()+"'");
first=false;
}
if(bin.getId() < xax.getBins().size()) {
s.append("}");
}
else{s.append("}");}
s.append("\n");
}
}
s.append("yaxes:\n");
int npoints=ds.getNumPoints();
for (YAxis yax : ds.getYAxes()){
String name=yax.getHeader();
String unit="";
if(yax.getHeader().contains(" IN ")){
name=yax.getHeader().substring(0,yax.getHeader().indexOf(" IN ")).trim();
unit=yax.getHeader().substring(yax.getHeader().indexOf(" IN ")+4).trim();
}
s.append(sp+"header: {name: '"+name+"'");
if(!unit.equals("")){ s.append(", unit: '"+unit+"'"); }
s.append("}\n");
boolean first=true;
for (Property prop : yax.getProperties()){
if(first) { s.append(s4+"qualifiers:\n"); }
first=false;
s.append(s4+sp+"{type: "+prop.getName());
if(prop.getFocus()!=null || prop.getLowValue()!=null || prop.getHighValue()!=null){
s.append(", value: '");
}
if (prop.getFocus() != null){
s.append(prop.getFocus());
}
if (prop.getLowValue() != null && prop.getHighValue() != null &&
prop.getLowValue().equals(prop.getHighValue())) {
s.append(prop.getLowValue());
} else {
if(prop.getFocus() != null) { s.append(" ("); }
s.append(prop.getLowValue());
s.append("-");
s.append(prop.getHighValue());
if(prop.getFocus() != null) { s.append(")"); }
}
if(prop.getFocus()!=null || prop.getLowValue()!=null || prop.getHighValue()!=null){
s.append("'");
}
if (prop.getUnit().toString().equals("") || !prop.getUnit().isDimensionless()) {
s.append(", unit: '");
s.append(prop.getUnit().toString()+"'");
}
s.append("}\n");
}
for (String comment : yax.getComments()){
if(first) { s.append(s4+"qualifiers:\n"); }
first=false;
unit="";
String type=comment.substring(0,comment.indexOf(":")-1).trim();
String value=comment.substring(comment.indexOf(":")+1).trim();
if(type.contains(" IN ")){
unit=type.substring(type.indexOf(" IN ")+4).trim();
type=type.substring(0,type.indexOf(" IN ")).trim();
}
s.append(s4+sp+"{type: "+type);
s.append(", value: '"+ value+"'");
if(!unit.equals("")){
s.append(", unit: '"+ unit+"'");
}
s.append("}\n");
}
for(Uncertainty error : ds.getErrors()){
if(error.getPlus()==0.0){
s.append(s4+sp+"{type: sys, value: '"+error.getComment()+"'}\n");
}
}
for(Uncertainty error : yax.getErrors()){
if(error.getPlus()==0.0){
s.append(s4+sp+"{type: sys, value: '"+error.getComment()+"'}\n");
}
}
s.append(s4+"points:\n");
for (int ip=1; ip<npoints+1; ip++){
Point point = yax.getPoint(ip);
if(point==null){
// s.append(s4+sp+"id: "+ip+"\n");
// s.append(s4+s4+"value: '-'\n");
s.append(s4+sp+"value: '-'\n");
}
else{
// s.append(s4+sp+"id: "+point.getId()+"\n");
// s.append(s4+s4+"value: ");
s.append(s4+sp+"value: ");
if(point.getRelation() != Relation.EQUALS){
s.append(point.getRelation());
}
// s.append(point.getValue()+" "+point.getValueLength()+"\n");
s.append(point.getValue()+"\n");
if(point.getErrors().size()>0){
s.append(s4+s4+"errors:\n");
for(Uncertainty error : point.getErrors()){
s.append(_formatError(error,"point"));
}
}
if(yax.getErrors().size()>0){
for(Uncertainty error : yax.getErrors()){
if(error.getPlus()!=0.0) s.append(_formatError(error,"axis"));
}
}
if(ds.getErrors().size()>0){
for(Uncertainty error : ds.getErrors()){
if(error.getPlus()!=0.0) s.append(_formatError(error,"dataset"));
}
}
}
}
}
return s.toString();
}
public static String _formatError(Uncertainty error, String which) {
String s4=" ";
String sp=" - ";
StringBuffer s = new StringBuffer();
Double test = error.getMinus();
if(which.equals("point")) test=-test;
if(error.getPlus()>=0.0 && (error.getPlus().equals(test))){
s.append(s4+s4+sp+"{symerror: ");
s.append(error.getPlus());
if(error.getNormType()==ErrorNorm.PCT){ s.append("%"); }
}
else{
s.append(s4+s4+sp+"{asymerror: ");
s.append("{plus: "+error.getPlus());
if(error.getNormType()==ErrorNorm.PCT){ s.append("%"); }
s.append(", minus: "+error.getMinus());
if(error.getNormType()==ErrorNorm.PCT){ s.append("%"); }
s.append("}");
}
if(error.getSourceType()==ErrorSource.STAT) s.append(", label: stat");
else if(error.getSourceType()==ErrorSource.SYS) s.append(", label: sys");
else if(error.getSourceType()==ErrorSource.TOTAL) s.append(", label: total");
if(!error.getComment().equals("")){ s.append(","+error.getComment()); }
s.append("}\n");
return s.toString();
}
public static String forms(Double value, int after) {
String form = "0.";
for(int i=0; i<after; ++i){
form=form.concat("0");
}
DecimalFormat myFormatter = new DecimalFormat(form);
String sval = "Cannot format this";
if(value instanceof Double) {
sval = myFormatter.format(value);
}
if(sval.endsWith(".")) { sval=sval.substring(0,sval.length()-1); }
return sval;
}
}