package com.github.lindenb.jvarkit.util.doid;
import java.io.BufferedReader;
import java.io.File;
import java.io.IOException;
import java.io.Reader;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import javax.xml.namespace.QName;
import javax.xml.stream.XMLEventReader;
import javax.xml.stream.XMLInputFactory;
import javax.xml.stream.XMLStreamException;
import javax.xml.stream.events.Attribute;
import javax.xml.stream.events.EndElement;
import javax.xml.stream.events.StartElement;
import javax.xml.stream.events.XMLEvent;
import com.github.lindenb.jvarkit.io.IOUtils;
public class DiseaseOntoglogyTree
{
public static final String OWL_URL="http://www.berkeleybop.org/ontologies/doid.owl";
private static final String OBO="http://purl.obolibrary.org/obo/";
private static final String RDFS="http://www.w3.org/2000/01/rdf-schema#";
private static final String OWL="http://www.w3.org/2002/07/owl#";
private static final String RDF="http://www.w3.org/1999/02/22-rdf-syntax-ns#";
private static final String OBOINOWL="http://www.geneontology.org/formats/oboInOwl#";
public static interface Term
{
public String getAcn();
public String getLabel();
public Set<Term> getParents();
public Set<Term> getChildren();
public boolean isDescendantOf(String acn);
public boolean hasDescendant(String acn);
//public Set<Term> getAllParents();
//public Set<Term> getAllChildren();
}
private DiseaseOntoglogyTree()
{
}
public int size()
{
return uri2term.size();
}
public List<? extends Term> getTerms()
{
return new ArrayList<Term>(uri2term.values());
}
public void dump()
{
for(String s: uri2term.keySet())
{
Term t=uri2term.get(s);
System.out.println(s+" "+t.getAcn()+" "+t.getLabel()+" "+t.getChildren()+" "+t.getParents());
}
}
private HashMap<String, TermImpl> uri2term=new HashMap<String, TermImpl>();
private class TermImpl implements Term
{
String accession;
String name;
Set<String> parents=new HashSet<String>();
Set<String> children=new HashSet<String>();
@Override
public String getAcn() {
return accession;
}
@Override
public String getLabel() {
return name;
}
private Set<Term> convert(Set<String> S1)
{
Set<Term> S2=new HashSet<Term>(S1.size());
for(String s:S1)
{
Term t=uri2term.get(s);
if(t==null) continue;
S2.add(t);
}
return S2;
}
@Override
public Set<Term> getChildren()
{
return convert(children);
}
@Override
public Set<Term> getParents()
{
return convert(parents);
}
/*
private void _getAllChildren(Set<String> seen)
{
for(String s:this.children)
{
TermImpl t=uri2term.get(s);
if(t==null) continue;
seen.add(s);
t._getAllChildren(seen);
}
}
private void _getAllParents(Set<String> seen)
{
for(String s:this.parents)
{
TermImpl t=uri2term.get(s);
if(t==null) continue;
seen.add(s);
t._getAllParents(seen);
}
}newChar
public Set<Term> getAllChildren()
{
Set<String> seen=new HashSet<String>();
_getAllChildren(seen);
return convert(seen);
}
//@Override
public Set<Term> getAllParents()
{
Set<String> seen=new HashSet<String>();
_getAllParents(seen);
return convert(seen);
}*/
@Override
public boolean isDescendantOf(String parentAcn)
{
if(parentAcn.equals(this.accession)) return true;
if(!parentAcn.startsWith(OBO)) parentAcn=OBO+parentAcn.replace(':', '_');
for(String p:this.parents)
{
TermImpl pNode=uri2term.get(p);
if(pNode==null || pNode==this) continue;
if(pNode.isDescendantOf(parentAcn)) return true;
}
return false;
}
@Override
public boolean hasDescendant(String descendantAcn)
{
if(descendantAcn.equals(this.accession)) return true;
if(!descendantAcn.startsWith(OBO)) descendantAcn=OBO+descendantAcn.replace(':', '_');
for(String p:this.children)
{
TermImpl pNode=uri2term.get(p);
if(pNode==null || pNode==this) continue;
if(pNode.hasDescendant(descendantAcn)) return true;
}
return false;
}
@Override
public int hashCode()
{
return accession.hashCode();
}
@Override
public boolean equals(Object obj) {
if (this == obj)
return true;
if (obj == null)
return false;
if (getClass() != obj.getClass())
return false;
TermImpl other = (TermImpl) obj;
return accession.equals(other.accession);
}
@Override
public String toString() {
return accession;
}
}
public Term getTermByAccession(String s)
{
if(!s.startsWith(OBO)) s=OBO+s.replace(':', '_');
return (Term)uri2term.get(s);
}
private static final QName rdfAbout=new QName(RDF,"about","rdf");
private static final QName rdfRsrc=new QName(RDF,"resource","rdf");
private void parseTerm(StartElement root,XMLEventReader r) throws IOException,XMLStreamException
{
Attribute aboutAtt=root.getAttributeByName(rdfAbout);
if(aboutAtt==null)
{
throw new IOException("no rdf:about");
}
TermImpl term=uri2term.get(aboutAtt.getValue());
if(term==null)
{
term=new TermImpl();
term.accession=aboutAtt.getValue();
if(term.accession.startsWith(OBO))
{
term.accession=term.accession.substring(OBO.length()).replace('_', ':');
}
term.name=term.accession;
uri2term.put(aboutAtt.getValue(),term);
}
while(r.hasNext())
{
XMLEvent evt=r.nextEvent();
if(evt.isStartElement())
{
StartElement E=evt.asStartElement();
QName qN=E.getName();
if(OBOINOWL.equals(qN.getNamespaceURI()))
{
if(qN.getLocalPart().equals("id"))
{
term.accession=r.getElementText();
}
}
else if(RDFS.equals(qN.getNamespaceURI()))
{
if(qN.getLocalPart().equals("label"))
{
term.name=r.getElementText();
}
else if(qN.getLocalPart().equals("subClassOf"))
{
Attribute rsrc=E.getAttributeByName(rdfRsrc);
if(rsrc==null) throw new IOException("att missing "+rdfRsrc+" for "+aboutAtt.getValue());
String parentUri=rsrc.getValue();
term.parents.add(parentUri);
TermImpl parentTerm=this.uri2term.get(parentUri);
if(parentTerm==null)
{
parentTerm=new TermImpl();
parentTerm.accession=parentUri;
if(parentTerm.accession.startsWith(OBO))
{
parentTerm.accession=parentTerm.accession.substring(OBO.length()).replace('_', ':');
}
parentTerm.name=parentTerm.accession;
uri2term.put(parentUri,parentTerm);
}
parentTerm.children.add(aboutAtt.getValue());
}
}
}
else if(evt.isEndElement())
{
EndElement E=evt.asEndElement();
QName qN=E.getName();
if(qN.getLocalPart().equals("Class") && OWL.equals(qN.getNamespaceURI()))
{
break;
}
}
}
}
public static DiseaseOntoglogyTree parse(Reader xmlIn) throws IOException,XMLStreamException
{
DiseaseOntoglogyTree tree=new DiseaseOntoglogyTree();
XMLInputFactory fact=XMLInputFactory.newFactory();
fact.setProperty(XMLInputFactory.IS_NAMESPACE_AWARE, Boolean.TRUE);
XMLEventReader r=fact.createXMLEventReader(xmlIn);
while(r.hasNext())
{
XMLEvent evt=r.nextEvent();
if(evt.isStartElement())
{
StartElement E=evt.asStartElement();
QName qN=E.getName();
if(qN.getLocalPart().equals("Class") && OWL.equals(qN.getNamespaceURI()))
{
tree.parseTerm(E,r);
}
}
}
r.close();
return tree;
}
public static DiseaseOntoglogyTree parse(File file) throws IOException,XMLStreamException
{
BufferedReader r=IOUtils.openFileForBufferedReading(file);
DiseaseOntoglogyTree t=parse(r);
r.close();
return t;
}
public static DiseaseOntoglogyTree parse(String uri) throws IOException,XMLStreamException
{
BufferedReader r=IOUtils.openURIForBufferedReading(uri);
DiseaseOntoglogyTree t=parse(r);
r.close();
return t;
}
}