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[HepData-svn] r1863 - trunk/hepdata-webapp/src/main/java/cedar/hepdata/formats
blackhole at projects.hepforge.org
blackhole at projects.hepforge.org
Wed Jun 10 13:49:11 BST 2015
Author: whalley
Date: Wed Jun 10 13:49:11 2015
New Revision: 1863
Log:
almost complete rewrite
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 3 18:34:31 2015 (r1862)
+++ trunk/hepdata-webapp/src/main/java/cedar/hepdata/formats/YamlFormatter.java Wed Jun 10 13:49:11 2015 (r1863)
@@ -20,13 +20,14 @@
public static String format(Paper p) {
StringBuffer s = new StringBuffer();
+ s.append("---\n");
String s4=" ";
String sp=" - ";
if(p == null) return null;
-// _headerXML contains all the bibliographic type stuff at the beginning
+// _header contains all the bibliographic type stuff at the beginning
- s.append(_headerXML(p));
+ s.append(_headerYAML(p));
// here we deal with the extra resource are description/line files
@@ -36,12 +37,12 @@
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];
+ String descfile = "/home/whalley/resource/" +ids[j] + "/" + descs[i];
+ String linkfile = "/home/whalley/resource/" +ids[j] + "/" + links[i];
File testdesc = new File(descfile);
File testlink = new File(linkfile);
String desc="";
@@ -57,39 +58,60 @@
link=in.readLine();
}
catch (IOException e){}
- if(first){ s.append("extras:\n"); }
+ 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");
+ 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("inserts:\n"); }
- first=false;
- s.append(sp+"inserthtml: /resource/"+ids[j]+"insert.html\n");
- }
- }
+ first=true;
+ for (int j=0; j<ids.length; j++){
+ String insertfile = "/home/whalley/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()){
- if(ds.getId() == 1) { s.append("datasets:\n"); } // first dataset, start the array
- s.append(_metadataXML(ds)); // dataset information in _metadataXML
+
+ 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(_footerXML());
+ s.append(_footerYAML());
// then write it all out.
return s.toString();
@@ -102,60 +124,55 @@
}
- public static String _headerXML(Paper p) {
+ public static String _headerYAML(Paper p) {
String s4=" ";
String sp=" - ";
StringBuffer s = new StringBuffer();
- s.append("inspireid: "+p.getInspireId()+"\n");
- if(p.getSpiresId()!=null) { s.append("spires: "+p.getSpiresId()+"\n"); }
- if(p.getArchive()!=null) { s.append("archive: "+p.getArchive().replaceAll("ARXIV","arXiv")+"\n"); }
if(p.getRedId()!=null) { s.append("durham: "+p.getRedId()+"\n"); }
- if(p.getCdsId()!=null) { s.append("cds: "+p.getCdsId()+"\n"); }
- s.append("dateupdated: "+p.getDateUpdated()+"\n");
- if(p.getTitle()!=null) { s.append("title: "+p.getTitle()+"\n"); }
- if(p.getAuthors().size()>0){
- s.append("authors:\n");
- for (String author : p.getAuthors()){
- s.append(sp+"author: "+author+"\n");
- }
- }
+ s.append("dateupdated: '"+p.getDateUpdated()+"'\n");
if(p.getReferences().size()>0){
- s.append("references:\n");
+ s.append("references: # additional references (e.g. experiment TWiki page for analysis)\n");
for (Reference r : p.getReferences()){
- s.append(sp+"{description: "+r.getDescription()+", ");
- s.append("date: "+r.getDate()+", ");
- s.append("type: "+r.getType()+"}");
- s.append("\n");
+ if(r.getDescription().startsWith("http")){
+ s.append(sp+"'"+r.getDescription());
+ s.append("'\n");
+ }
}
}
if(p.getModifications().size()>0){
- s.append("modifications:\n");
+ s.append("modifications: # what, by whom and when encoded or changed\n");
for (Modification m : p.getModifications()){
- s.append(sp+"{action: "+m.getAction()+", ");
- s.append("modifier: "+m.getModifier()+", ");
- s.append("date: "+m.getComment()+"}");
- s.append("\n");
+ s.append(sp+"'"+m.getAction()+" by ");
+ s.append(m.getModifier()+" on ");
+ s.append(m.getComment());
+ s.append("'\n");
}
}
-
- s.append("collaboration: "+p.getInformalName()+"\n");
- s.append("experiment: "+p.getExperimentName()+"\n");
+ int count=0;
if(p.getComments().size()>0){
- s.append("comments:\n");
- for (String comment : p.getComments()){
- s.append(sp+"comment: "+comment+"\n");
+ 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 _footerXML() {
+ public static String _footerYAML() {
StringBuffer s = new StringBuffer();
return s.toString();
}
- public static String _metadataXML(Dataset ds){
+ public static String _metadataYAML(Dataset ds){
String s4=" ";
String sp=" - ";
StringBuffer s = new StringBuffer();
@@ -164,76 +181,309 @@
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(sp+"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");
}
}
+ boolean first=true;
+ int count=0;
for (String ct : ds.getComments()){
+ count++;
if(!ct.startsWith("Location:")) {
- s.append(s4+"comment: "+ct.replaceFirst("VERBATIM","").replaceAll(">",">").replaceAll("<","<")+"\n");
+ 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;}
}
-
- for (String dsreac : ds.getDsReactions()){
- s.append(s4+"reackey: "+dsreac+"\n");
- }
- for (String dsobs : ds.getDsObservables()){
- s.append(s4+"obskey: "+dsobs+"\n");
- }
- for (String dsplab : ds.getDsPlabs()){
- s.append(s4+"plabkey: \""+dsplab+"\n");
+ 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(", ");}
+ }
}
- s.append(s4+"xaxes:\n");
+ 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()){
- s.append(s4+sp+"xheader: "+xax.getHeader()+"\n");
- s.append(s4+s4+"bins:\n");
+ 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()){
- s.append(s4+s4+sp+"{id: "+bin.getId()+", ");
- if(bin.getDescription() != null ) { s.append("description: "+bin.getDescription()+", "); }
- s.append("relation: "+bin.getRelation()+", ");
- s.append("focus: "+bin.getFocus()+", ");
- s.append("high: "+bin.getHighValue()+", ");
- s.append("low: "+bin.getLowValue()+"");
- if(bin.getId() < xax.getBins().size()) {s.append("}");}
+ 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(s4+"yaxes:\n");
+ s.append("yaxes:\n");
+
+ int npoints=ds.getNumPoints();
+
for (YAxis yax : ds.getYAxes()){
- s.append(s4+sp+"yheader: "+yax.getHeader()+"\n");
+ 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+s4+"qualifiers:\n"); }
+ if(first) { s.append(s4+"qualifiers:\n"); }
first=false;
- s.append(s4+s4+sp+"qualifier: "+prop.getFull()+"\n");
+
+ 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+s4+"qualifiers:\n"); }
+ if(first) { s.append(s4+"qualifiers:\n"); }
first=false;
- s.append(s4+s4+sp+"qualifier: "+comment+"\n");
+ 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");
+ }
}
- s.append(s4+s4+"points:\n");
- for (Point point : yax.getPoints()){
- s.append(s4+s4+sp+"id: "+point.getId()+"\n");
- s.append(s4+s4+s4+"value: "+point.getValue()+"\n");
- if(point.getErrors().size()>0){
- s.append(s4+s4+s4+"errors:\n");
- for(PointError error : point.getErrors()){
- s.append(s4+s4+s4+sp+"{plus: "+error.getPlus()+", ");
- s.append("minus: \""+error.getMinus()+", ");
- s.append("norm: "+error.getNormType()+", ");
- s.append("type: "+error.getSourceType()+", ");
- s.append("comment: "+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;
+ }
}
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