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[HepData-svn] r1872 - trunk/hepdata-webapp/src/main/java/cedar/hepdata/formats
blackhole at projects.hepforge.org
blackhole at projects.hepforge.org
Fri Jun 19 17:09:27 BST 2015
Author: watt
Date: Fri Jun 19 17:09:27 2015
New Revision: 1872
Log:
Changes to field names in YAML formatter discussed by Mike and Eamonn
Modified:
trunk/hepdata-webapp/src/main/java/cedar/hepdata/formats/YamlFormatter.java
Modified: trunk/hepdata-webapp/src/main/java/cedar/hepdata/formats/YamlFormatter.java
==============================================================================
--- trunk/hepdata-webapp/src/main/java/cedar/hepdata/formats/YamlFormatter.java Wed Jun 17 19:35:30 2015 (r1871)
+++ trunk/hepdata-webapp/src/main/java/cedar/hepdata/formats/YamlFormatter.java Fri Jun 19 17:09:27 2015 (r1872)
@@ -6,7 +6,6 @@
import cedar.hepdata.db.*;
import cedar.hepdata.webapp.components.*;
-
import java.util.*;
import java.text.*;
import java.io.File;
@@ -18,85 +17,19 @@
public class YamlFormatter {
+
public static String format(Paper p) {
- StringBuffer s = new StringBuffer();
+ 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
+ // _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/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/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
-
-
-
+ // and now the datasets
for (Dataset ds : p.getDatasets()){
s.append("\n---\n");
@@ -105,17 +38,18 @@
s.append("additional_resources:\n");
}
for (Dataset ds : p.getDatasets()){
- s.append("---\n");
+ s.append("\n---\n");
s.append("# This is Data "+ds.getId()+"\n");
s.append(_dataYAML(ds)); // dataset information in _data
}
-// finally finish off (at present does nothing!
+ // finally finish off (at present does nothing!
s.append(_footerYAML());
-// then write it all out.
+ // then write it all out.
return s.toString();
}
+
public static String _getTimestamp(){
DateFormat dateFormat = new SimpleDateFormat("yyyyMMddHHmmss");
@@ -128,30 +62,22 @@
String s4=" ";
String sp=" - ";
StringBuffer s = new StringBuffer();
- if(p.getRedId()!=null) { s.append("durham: "+p.getRedId()+"\n"); }
+ s.append("record_ids: # optional\n");
+ if(p.getInspireId()!=null) { s.append(sp+"{type: inspire, id: "+p.getInspireId()+"}\n"); }
+ if(p.getRedId()!=null) { s.append(sp+"{type: red, id: "+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.getHaveRivet()) s.append(sp+"'http://rivet.hepforge.org/analyses#"+p.getRivetName()+"'\n");
- }
if(p.getModifications().size()>0){
s.append("modifications: # what, by whom and when encoded or changed\n");
int mcount=0;
for (Modification m : p.getModifications()){
mcount++;
if (m.getAction()!=null) {
- s.append(sp+"{ action: '"+m.getAction()+"'");
+ s.append(sp+"{action: '"+m.getAction()+"'");
} else {
- if (mcount==1) { s.append(sp+"{ action: 'Encoded'"); }
- else { s.append(sp+"{ action: 'Modified'"); }
+ if (mcount==1) { s.append(sp+"{action: 'Encoded'"); }
+ else { s.append(sp+"{action: 'Modified'"); }
}
- s.append(", date: '"+m.getComment()+"', who: '"+m.getModifier()+"' }\n");
+ s.append(", date: '"+m.getComment()+"', who: '"+m.getModifier()+"'}\n");
}
}
@@ -168,14 +94,70 @@
s.append("\n");
}
}
+
+ s.append("\nadditional_resources:\n");
+ if(p.getReferences().size()>0){
+ for (Reference r : p.getReferences()){
+ if(r.getDescription().startsWith("http")){
+ s.append(sp+"{location: '"+r.getDescription()+"', description: \"experiment TWiki page for analysis\"}\n");
+ }
+ }
+ if (p.getHaveRivet()) { s.append(sp+"{location: 'http://rivet.hepforge.org/analyses#"+p.getRivetName()+"', description: \"Rivet analysis\"}\n"); }
+ }
+
+ // 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]=""; }
+
+ for (int i=0; i<descs.length; i++){
+ for(int j=0; j<ids.length; j++){
+ 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="http://hepdata.cedar.ac.uk"+in.readLine();
+ }
+ catch (IOException e){}
+ s.append(sp+"{location: '"+link+"', description: '"+desc+"'\n");
+ }
+ }
+ }
+
+ // next the insert.html file in the resource area
+ for (int j=0; j<ids.length; j++){
+ String insertfile = "/home/hepdata/resource/" +ids[j] + "/insert.html";
+ File testinsert = new File(insertfile);
+ String insert="";
+ if(testinsert.exists()){
+ s.append(sp+"{location: 'http://hepdata.cedar.ac.uk/resource/"+ids[j]+"/insert.html', description: \"insert.html\"\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=" - ";
@@ -189,7 +171,7 @@
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")+" from: "+p.getTitle()+"\n");
s.append("label: '"+ct.replaceFirst("Location:","Data from")+"'\n");
}
}
@@ -209,34 +191,34 @@
}
s.append("keywords:\n");
if(ds.getDsReactions().size() > 0) {
- s.append(sp+"{ name: reactions, values: [");
+ 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"); }
+ if(++nr==ds.getDsReactions().size()){s.append("]}\n"); }
else {s.append(", ");}
}
}
if(ds.getDsObservables().size() > 0) {
- s.append(sp+"{ name: observables, values: [");
+ 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"); }
+ if(++no==ds.getDsObservables().size()){s.append("]}\n"); }
else {s.append(", ");}
- }
- }
+ }
+ }
if(ds.getDsPlabs().size() > 0) {
- s.append(sp+"{ name: plabs, values: [");
+ 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"); }
+ if(++np==ds.getDsPlabs().size()){s.append("]}\n"); }
else {s.append(", ");}
}
}
-
-
+
+
Double ecmlow=99999.0;
Double ecmhigh=-99999.0;
boolean haveecm=false;
@@ -256,7 +238,7 @@
if(prop.getHighValue()>ecmhigh) ecmhigh=prop.getHighValue();
haveecm=true;
}
- }
+ }
}
}
if(!haveecm){
@@ -282,14 +264,15 @@
}
if(haveecm){
- s.append(sp+"{ name: cmenergies, values: [" + ecmlow);
+ s.append(sp+"{name: cmenergies, values: [" + ecmlow);
if(!ecmlow.equals(ecmhigh)) s.append("-"+ecmhigh);
- s.append("] }\n");
+ s.append("]}\n");
}
return s.toString();
}
+
public static String _dataYAML(Dataset ds){
String s4=" ";
String sp=" - ";
@@ -299,7 +282,7 @@
String location = "";
Paper p = ds.getPaper();
- s.append("xaxes:\n");
+ s.append("independent_variables:\n");
for (XAxis xax : ds.getXAxes()){
String name=xax.getHeader();
String unit="";
@@ -310,14 +293,14 @@
s.append(sp+"header: {name: '"+name+"'");
if(!unit.equals("")){ s.append(", units: '"+unit+"'"); }
s.append("}\n");
- s.append(s4+"bins:\n");
+ s.append(s4+"values:\n");
for (Bin bin : xax.getBins()){
boolean first=true;
s.append(s4+sp+"{");
- // if(bin.getId() != null ) {
- // s.append("id: "+bin.getId());
- // first=false;
- // }
+ // if(bin.getId() != null ) {
+ // s.append("id: "+bin.getId());
+ // first=false;
+ // }
boolean asymmfocus = false;
if (bin.getLowValue() != null && bin.getHighValue() != null && bin.getFocus() != null) {
@@ -337,21 +320,21 @@
if(bin.getFocusLength()!=null) {
s.append("value: "+forms(bin.getFocus(),bin.getFocusLength()));
} else {
- s.append("value: "+bin.getFocus());
+ s.append("value: "+bin.getFocus());
}
- first=false;
+ first=false;
}
- }
- if(bin.getLowValue() != null && haswidth ) {
+ }
+ if(bin.getLowValue() != null && haswidth ) {
if(!first) { s.append(", "); }
- if(bin.getLowValueLength()!=null) {
+ if(bin.getLowValueLength()!=null) {
s.append("low: "+forms(bin.getLowValue(),bin.getLowValueLength()));
} else {
s.append("low: "+bin.getLowValue());
}
first=false;
}
- if(bin.getHighValue() != null && haswidth ) {
+ if(bin.getHighValue() != null && haswidth ) {
if(!first) {s.append(", "); }
if(bin.getHighValueLength()!=null) {
s.append("high: "+forms(bin.getHighValue(),bin.getHighValueLength()));
@@ -378,7 +361,7 @@
}
}
- s.append("yaxes:\n");
+ s.append("dependent_variables:\n");
int npoints=ds.getNumPoints();
@@ -421,8 +404,8 @@
}
if (prop.getUnit().toString().equals("") || !prop.getUnit().isDimensionless()) {
- s.append(", units: '");
- s.append(prop.getUnit().toString()+"'");
+ s.append(", units: '");
+ s.append(prop.getUnit().toString()+"'");
}
s.append("}\n");
@@ -456,46 +439,47 @@
}
}
- s.append(s4+"points:\n");
+ s.append(s4+"values:\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+"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+"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(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"));
- }
+ 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){
+ 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"));
- }
- }
+ 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=" - ";
@@ -506,38 +490,41 @@
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.getSourceType()==ErrorSource.STAT || error.getSourceType()==ErrorSource.SYS || error.getSourceType()==ErrorSource.TOTAL) {
- if(!error.getComment().equals("")) s.append(","+error.getComment());
- s.append("'");
- }
- s.append("}\n");
- return s.toString();
- }
+ }
+ 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.getSourceType()==ErrorSource.STAT || error.getSourceType()==ErrorSource.SYS || error.getSourceType()==ErrorSource.TOTAL) {
+ if(!error.getComment().equals("")) s.append(","+error.getComment());
+ s.append("'");
+ }
+ s.append("}\n");
+ return s.toString();
+ }
+
- public static String forms(Double value, int after) {
+ 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;
- }
+ 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;
+ }
+
+
}
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