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[HepData-svn] r1856 - trunk/hepdata-webapp/src/main/java/cedar/hepdata/formats
blackhole at projects.hepforge.org
blackhole at projects.hepforge.org
Wed Apr 22 12:34:55 BST 2015
Author: whalley
Date: Wed Apr 22 12:34:55 2015
New Revision: 1856
Log:
first go at yaml formatter
Added:
trunk/hepdata-webapp/src/main/java/cedar/hepdata/formats/YamlFormatter.java
Added: trunk/hepdata-webapp/src/main/java/cedar/hepdata/formats/YamlFormatter.java
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ trunk/hepdata-webapp/src/main/java/cedar/hepdata/formats/YamlFormatter.java Wed Apr 22 12:34:55 2015 (r1856)
@@ -0,0 +1,239 @@
+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();
+ String s4=" ";
+ String sp=" - ";
+ if(p == null) return null;
+
+// _headerXML contains all the bibliographic type stuff at the beginning
+
+ s.append(_headerXML(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("extras:\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("inserts:\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
+
+ }
+
+// finally finish off (at present does nothing!
+ s.append(_footerXML());
+
+// 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 _headerXML(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");
+ }
+ }
+ if(p.getReferences().size()>0){
+ s.append("references:\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(p.getModifications().size()>0){
+ s.append("modifications:\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("collaboration: "+p.getInformalName()+"\n");
+ s.append("experiment: "+p.getExperimentName()+"\n");
+ if(p.getComments().size()>0){
+ s.append("comments:\n");
+ for (String comment : p.getComments()){
+ s.append(sp+"comment: "+comment+"\n");
+ }
+ }
+ return s.toString();
+ }
+
+ public static String _footerXML() {
+ StringBuffer s = new StringBuffer();
+ return s.toString();
+ }
+
+ public static String _metadataXML(Dataset ds){
+ String s4=" ";
+ String sp=" - ";
+ StringBuffer s = new StringBuffer();
+ int idbase=9000000;
+ int id=idbase+ds.getId();
+ String location = "";
+ Paper p = ds.getPaper();
+
+ 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");
+ }
+ }
+
+ for (String ct : ds.getComments()){
+ if(!ct.startsWith("Location:")) {
+ s.append(s4+"comment: "+ct.replaceFirst("VERBATIM","").replaceAll(">",">").replaceAll("<","<")+"\n");
+ }
+ }
+
+ 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(s4+"xaxes:\n");
+ for (XAxis xax : ds.getXAxes()){
+ s.append(s4+sp+"xheader: "+xax.getHeader()+"\n");
+ s.append(s4+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("}");}
+ else{s.append("}");}
+ s.append("\n");
+ }
+ }
+
+ s.append(s4+"yaxes:\n");
+ for (YAxis yax : ds.getYAxes()){
+ s.append(s4+sp+"yheader: "+yax.getHeader()+"\n");
+ boolean first=true;
+ for (Property prop : yax.getProperties()){
+ if(first) { s.append(s4+s4+"qualifiers:\n"); }
+ first=false;
+ s.append(s4+s4+sp+"qualifier: "+prop.getFull()+"\n");
+ }
+ for (String comment : yax.getComments()){
+ if(first) { s.append(s4+s4+"qualifiers:\n"); }
+ first=false;
+ s.append(s4+s4+sp+"qualifier: "+comment+"\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");
+ }
+ }
+ }
+ }
+ return s.toString();
+ }
+}
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