/
Owlkb.java
2011 lines (1663 loc) · 60.2 KB
/
Owlkb.java
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/*
* Owlkb 2.0, part of RICORDO.
* On the web: http://open-physiology.org
* Programmed by Sarala Wimaralatne, reprogrammed by Sam Alexander.
*
* Copyright 2014 The Farr Institute
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
import java.io.File;
import java.util.Set;
import java.util.HashSet;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import java.util.HashMap;
import org.semanticweb.elk.owlapi.ElkReasonerFactory;
import org.semanticweb.owlapi.reasoner.OWLReasoner;
import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
import org.semanticweb.owlapi.reasoner.Node;
import org.semanticweb.owlapi.reasoner.NodeSet;
import org.semanticweb.owlapi.reasoner.InferenceType;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.model.*;
import org.semanticweb.owlapi.io.FileDocumentSource;
import org.semanticweb.owlapi.io.UnparsableOntologyException;
import org.semanticweb.owlapi.io.OWLOntologyCreationIOException;
import org.semanticweb.owlapi.io.OWLOntologyInputSourceException;
import org.coode.owlapi.manchesterowlsyntax.ManchesterOWLSyntaxEditorParser;
import org.semanticweb.owlapi.util.BidirectionalShortFormProvider;
import org.semanticweb.owlapi.util.BidirectionalShortFormProviderAdapter;
import org.semanticweb.owlapi.util.AnnotationValueShortFormProvider;
import org.semanticweb.owlapi.util.OWLOntologyImportsClosureSetProvider;
import org.semanticweb.owlapi.expression.OWLEntityChecker;
import org.semanticweb.owlapi.expression.ShortFormEntityChecker;
import com.sun.net.httpserver.HttpExchange;
import com.sun.net.httpserver.HttpServer;
import com.sun.net.httpserver.Headers;
public class Owlkb
{
/*
* Variables to be specified by command-line argument.
*/
public String reasonerName; // Reasoner name. Default: "elk"
public boolean hdSave; // Whether to save changes to harddrive. Default: true
public String uclSyntax; // Endpoint for UCL syntax server. Default: null
public String kbNs; // Namespace for RICORDO_### terms. Default: "http://www.ricordo.eu/ricordo.owl"
public String kbFilename; // Name of ontology file. Default: "/home/sarala/testkb/ricordo.owl"
public boolean helpOnly; // Whether to show helpscreen and exit. Default: false
public int port; // Port number to listen on. Default: 20080
public String sparql; // URL of SPARQL endpoint
public boolean getCountsFromFeather; // For easy reversion in case SPARQL doesn't work
public String openPhactsAppId; // For querying openPHACTS API
public String openPhactsAppKey; // For querying openPHACTS API
/*
* Variables to be initialized elsewhere than the command-line
*/
OWLDataFactory df;
BidirectionalShortFormProvider shortformProvider;
BidirectionalShortFormProviderAdapter annotProvider;
OWLOntologyImportsClosureSetProvider ontSet;
Set<OWLOntology> importClosure;
OWLAnnotationProperty rdfsLabel;
public static void main(String [] args) throws Exception
{
Owlkb owlkb = new Owlkb();
owlkb.run(args);
}
/*
* Load the ontology and launch a server on user-specified port (default 20080) to serve
* the owlkb API, as described at http://www.semitrivial.com/owlkb/api.php
*/
public void run(String [] args) throws Exception
{
initOwlkb(args);
if ( helpOnly )
return;
/*
* Load the main ontology
*/
OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
logString( "Loading ontology...");
OWLOntologyLoaderConfiguration config = new OWLOntologyLoaderConfiguration(); // If the main ontology imports an RDF fragment,
config = config.setMissingOntologyHeaderStrategy(OWLOntologyLoaderConfiguration.MissingOntologyHeaderStrategy.IMPORT_GRAPH); // prevent that fragment from being saved into the ontology.
File kbFile;
OWLOntology ont;
try
{
kbFile = new File(kbFilename);
}
catch ( NullPointerException e )
{
System.out.println( "Could not load file: filename is null" );
System.out.println( "If you didn't already, try running Owlkb with command line arguments: -file <filename>" );
return;
}
catch ( Exception e )
{
System.out.println( "An unknown error occurred while trying to parse/load filename: " + kbFilename );
return;
}
ont = loadOwlkbOntology( kbFile, kbFilename, manager, config );
if ( ont == null )
return;
logString( "Ontology is loaded.");
IRI iri = manager.getOntologyDocumentIRI(ont);
/*
* Load the ontologies imported by the main ontology (e.g., the reference ontologies)
*/
importClosure = ont.getImportsClosure();
ontSet = new OWLOntologyImportsClosureSetProvider(manager, ont);
/*
* Establish infrastructure for converting long URLs to short IRIs and vice versa
* (e.g., converting between "http://purl.org/obo/owlapi/quality#PATO_0000014" and "PATO_0000014")
*/
shortformProvider = new BidirectionalShortFormProviderAdapter(manager, importClosure, new org.semanticweb.owlapi.util.SimpleShortFormProvider());
OWLEntityChecker entityChecker = new ShortFormEntityChecker(shortformProvider);
/*
* Infrastructure for searching for classes by label
*/
List<OWLAnnotationProperty> labeltypeList = new ArrayList<OWLAnnotationProperty>();
labeltypeList.add(rdfsLabel);
Map<OWLAnnotationProperty,List<String>> emptyMap = new HashMap<OWLAnnotationProperty,List<String>>();
AnnotationValueShortFormProvider preAnnotProvider = new AnnotationValueShortFormProvider(labeltypeList, emptyMap, ontSet );
annotProvider = new BidirectionalShortFormProviderAdapter(manager, importClosure, preAnnotProvider);
/*
* Initiate the reasoner
*/
logString( "Establishing "+reasonerName+" reasoner...");
OWLReasoner r;
if ( reasonerName.equals("elk") )
{
OWLReasonerFactory rf = new ElkReasonerFactory();
r = rf.createReasoner(ont);
}
else
r = new org.semanticweb.HermiT.Reasoner(ont); //Hermit reasoner
logString( "Reasoner established.");
/*
* Precompute inferences.
*/
logString( "Precomputing inferences...");
long startTime = System.nanoTime();
r.precomputeInferences(InferenceType.CLASS_HIERARCHY);
logString( "Finished precomputing inferences (took "+(System.nanoTime()-startTime)/1000000+"ms)" );
/*
* Launch HTTP server
*/
logString( "Initiating server...");
HttpServer server = HttpServer.create(new java.net.InetSocketAddress(port), 0 );
server.createContext("/subterms", new NetHandler("subterms", r, manager, ont, entityChecker, iri));
server.createContext("/siblings", new NetHandler("siblings", r, manager, ont, entityChecker, iri));
server.createContext("/parents", new NetHandler("parents", r, manager, ont, entityChecker, iri));
server.createContext("/children", new NetHandler("children", r, manager, ont, entityChecker, iri));
server.createContext("/subhierarchy", new NetHandler("subhierarchy", r, manager, ont, entityChecker, iri));
server.createContext("/apinatomy", new NetHandler("apinatomy", r, manager, ont, entityChecker, iri));
server.createContext("/eqterms", new NetHandler("eqterms", r, manager, ont, entityChecker, iri));
server.createContext("/addlabel", new NetHandler("addlabel", r, manager, ont, entityChecker, iri));
server.createContext("/terms", new NetHandler("terms", r, manager, ont, entityChecker, iri));
server.createContext("/instances", new NetHandler("instances", r, manager, ont, entityChecker, iri));
server.createContext("/labels", new NetHandler("labels", r, manager, ont, entityChecker, iri));
server.createContext("/search", new NetHandler("search", r, manager, ont, entityChecker, iri));
server.createContext("/rdfstore", new NetHandler("rdfstore", r, manager, ont, entityChecker, iri));
server.createContext("/test", new NetHandler("test", r, manager, ont, entityChecker, iri));
server.createContext("/shortestpath", new NetHandler("shortestpath", r, manager, ont, entityChecker, iri));
server.createContext("/generate-triples", new NetHandler("generate-triples", r, manager, ont, entityChecker, iri));
server.createContext("/subgraph", new NetHandler("subgraph", r, manager, ont, entityChecker, iri));
server.createContext("/similar_molecules", new NetHandler("similar_molecules", r, manager, ont, entityChecker, iri));
server.createContext("/gui", new NetHandler("gui", r, manager, ont, entityChecker, iri));
server.setExecutor(null);
server.start();
logString( "Server initiated.");
}
class NetHandler implements com.sun.net.httpserver.HttpHandler
{
String srvType;
OWLReasoner r;
OWLOntologyManager m;
OWLOntology o;
OWLEntityChecker ec;
IRI iri;
public NetHandler(String srvType, OWLReasoner r, OWLOntologyManager m, OWLOntology o, OWLEntityChecker ec, IRI iri)
{
this.srvType = srvType;
this.r = r;
this.m = m;
this.o = o;
this.ec = ec;
this.iri = iri;
}
public void handle(HttpExchange t) throws java.io.IOException
{
if ( srvType.equals("gui") )
{
sendGui(t);
return;
}
Headers requestHeaders = t.getRequestHeaders();
boolean fJson = ( requestHeaders.get("Accept") != null && requestHeaders.get("Accept").contains("application/json") );
boolean verbose = false;
boolean longURI = false;
String response;
String req = t.getRequestURI().toString().substring(2+srvType.length());
Map<String,String> args;
int qMark = req.indexOf("?");
if ( qMark != -1 )
{
String rawArgs = req.substring(qMark+1);
req = req.substring(0,qMark);
args = getArgs( rawArgs );
if ( !fJson && args.containsKey( "json" ) )
fJson = true;
if ( args.containsKey( "verbose" ) )
{
verbose = true;
fJson = true;
}
if ( args.containsKey( "longURI" ) )
longURI = true;
}
else
args = new HashMap<String,String>();
req = URLDecode(req);
if ( checkForNonEL( req, t ) )
return;
logString( "Got request: ["+req+"]" );
long startTime = System.nanoTime();
if ( srvType.equals("labels") || srvType.equals("search") )
{
boolean isLabels = srvType.equals("labels");
ArrayList<String> terms = (isLabels ? getLabels( req, o ) : SearchByLabel( req, o, verbose ));
if ( terms == null || terms.isEmpty() )
response = (isLabels ? "No class by that shortform." : "No class with that label.");
else
response = computeResponse( terms, fJson, false, verbose && !isLabels );
}
else
if ( srvType.equals("addlabel") )
response = computeAddlabelResponse( o, iri, m, req, fJson );
else
if ( srvType.equals("rdfstore") )
response = computeRdfstoreResponse( o, iri, m, ec, r, req );
else
if ( srvType.equals("apinatomy") )
{
response = computeApinatomyResponse( o, iri, m, r, req );
fJson = true;
}
else
if ( srvType.equals("generate-triples") )
{
if ( t.getRemoteAddress().getAddress().isLoopbackAddress() )
response = computeGenerateTriplesResponse( o, iri, m, r, req );
else
response = "{\"error\": \"Only requests originating from localhost can run generate-triples\"}";
fJson = true;
}
else
if ( srvType.equals("shortestpath") )
{
response = computeShortestpathResponse( o, iri, m, r, req );
fJson = true;
}
else
if ( srvType.equals("similar_molecules") )
{
response = computeSimilarMoleculesResponse( o, iri, m, r, ec, req );
fJson = true;
}
else
if ( srvType.equals("subgraph") )
{
response = computeSubgraphResponse( o, iri, m, r, req );
fJson = true;
}
else
try
{
OWLClassExpression exp;
String manchesterError = "";
if ( uclSyntax != null )
{
String lolsReply = queryURL( uclSyntax + URLEncode(req) );
if ( lolsReply == null )
{
exp = parseManchester( req, o, ec );
if ( exp == null )
manchesterError = "Could not connect to LOLS for UCL syntax parsing";
}
else
{
String error = naiveJsonParse( lolsReply, "Error" );
if ( error != null && !error.trim().equals("") )
{
manchesterError = error.trim();
exp = null;
}
else
{
String ambigs = naiveJsonParse( lolsReply, "Ambiguities", "\n [", "\n ]" );
if ( ambigs != null && !ambigs.trim().equals("") )
{
manchesterError = "{\n \"Ambiguities\":\n [\n " + ambigs.trim() + "\n ]\n}";
exp = null;
}
else
{
String uclToManchester = naiveJsonParse( lolsReply, "Result" );
if ( uclToManchester == null )
{
manchesterError = lolsReply.trim();
exp = null;
}
else
{
exp = parseManchester( uclToManchester, o, ec );
if ( exp == null )
{
String possibleError = naiveJsonParse( lolsReply, "Possible_error" );
if ( possibleError != null )
manchesterError = possibleError;
}
}
}
}
}
}
else
exp = parseManchester( req, o, ec );
if ( exp == null )
{
if ( !manchesterError.equals("") )
response = manchesterError;
else
response = "Malformed Manchester query";
}
else
{
if ( srvType.equals("subterms")
|| srvType.equals("siblings")
|| srvType.equals("parents")
|| srvType.equals("children")
|| srvType.equals("eqterms")
|| srvType.equals("instances")
|| srvType.equals("terms") )
{
ArrayList<String> terms = null;
if ( srvType.equals("subterms") )
terms = getSubTerms(exp,r,false,false,verbose);
else if ( srvType.equals("siblings") )
terms = getSiblings(exp,r,false,false,verbose);
else if ( srvType.equals("parents") )
terms = getParents(exp,r,false,false,verbose);
else if ( srvType.equals("children") )
terms = getChildren(exp,r,false,false,verbose);
else if ( srvType.equals("eqterms") )
terms = addTerm(exp,r,m,o,iri,verbose );
else if ( srvType.equals("instances") )
terms = getInstances(exp,r,verbose);
else if ( srvType.equals("terms") )
terms = getTerms(exp,r,verbose);
response = computeResponse( terms, fJson, longURI, verbose );
}
else if ( srvType.equals("subhierarchy") )
{
response = computeSubhierarchyResponse( exp, r );
}
else if ( srvType.equals("test") )
response = computeDemoResponse( exp, r, m, o, iri, startTime, fJson, verbose );
else
response = "Unrecognized request";
}
}
catch(Exception e)
{
response = "There was an error getting the results.";
}
String callback = args.get("callback"); // JSONP support
if ( callback != null )
{
String jsonpHeader = "typeof "+callback+" === 'function' && "+callback+"(\n";
response = jsonpHeader + response + ");";
}
logString( "Transmitting response..." );
sendResponse( t, response, fJson );
/*
* Measure computation time in ms.
*/
long runTime = (System.nanoTime() - startTime) / 1000000;
logString( "It took "+runTime+"ms to handle the request." );
}
}
public boolean checkForNonEL( String req, HttpExchange t )
{
/*
* To do: improve this function, which is currently just a bandaid
*/
try
{
String lower = req.toLowerCase();
if ( lower.contains(" or ") )
{
sendResponse( t, "Disjunction ('or') is forbidden because it would make the ontology non-EL.", false );
return true;
}
if ( lower.contains(" not ") || lower.substring(0,4).equals("not ") )
{
sendResponse( t, "Negation ('not') is forbidden because it would make the ontology non-EL.", false );
return true;
}
return false;
}
catch ( Exception e )
{
return false;
}
}
public void sendResponse( HttpExchange t, String response, boolean fJson ) throws java.io.IOException
{
Headers h = t.getResponseHeaders();
h.add("Cache-Control", "no-cache, no-store, must-revalidate");
h.add("Pragma", "no-cache");
h.add("Expires", "0");
if ( fJson )
h.add("Content-Type", "application/json");
t.sendResponseHeaders(200,response.getBytes().length);
java.io.OutputStream os = t.getResponseBody();
os.write(response.getBytes());
os.close();
logString( "Response transmitted.");
}
private ArrayList<String> getSubTerms(OWLClassExpression exp, OWLReasoner r, boolean longURI, boolean direct, boolean verbose )
{
ArrayList<String> idList = new ArrayList<String>();
NodeSet<OWLClass> subClasses = r.getSubClasses(exp, direct);
for ( Node<OWLClass> owlClassNode : subClasses )
classToTermlist( owlClassNode, idList, longURI, verbose );
return idList;
}
private ArrayList<String> getParents(OWLClassExpression exp, OWLReasoner r, boolean longURI, boolean direct, boolean verbose )
{
Set<Node<OWLClass>> parentNodes = r.getSuperClasses( exp, true ).getNodes();
ArrayList<String> idList = new ArrayList<String>();
for ( Node<OWLClass> n : parentNodes )
classToTermlist( n, idList, longURI, verbose );
return idList;
}
private ArrayList<String> getChildren(OWLClassExpression exp, OWLReasoner r, boolean longURI, boolean direct, boolean verbose )
{
Set<Node<OWLClass>> childNodes = r.getSubClasses( exp, true ).getNodes();
ArrayList<String> idList = new ArrayList<String>();
for ( Node<OWLClass> n : childNodes )
classToTermlist( n, idList, longURI, verbose );
return idList;
}
private ArrayList<String> getSiblings(OWLClassExpression exp, OWLReasoner r, boolean longURI, boolean direct, boolean verbose )
{
Set<Node<OWLClass>> parentNodes = r.getSuperClasses( exp, true ).getNodes();
HashSet<String> sibs = new HashSet<String>();
ArrayList<String> retVal;
if ( verbose )
retVal = new ArrayList<String>();
else
retVal = null;
for ( Node<OWLClass> pnode : parentNodes )
{
OWLClass parent = pnode.getRepresentativeElement();
NodeSet<OWLClass> childNodes = r.getSubClasses( parent, true );
String parentLabel = null, pID = null;
if ( verbose )
{
parentLabel = labelByClass(parent);
if ( parentLabel == null )
parentLabel = "null";
pID = shortUrl(parent.getIRI().toString());
}
for ( OWLClass c : childNodes.getFlattened() )
{
String sibID = shortUrl(c.getIRI().toString());
if ( sibs.contains( sibID ) )
continue;
sibs.add( sibID );
if ( verbose )
{
String label = labelByClass(c);
if ( label == null )
label = "null";
String jsObj = "{\n \"sibling\":\""+sibID+"\",\n \"label\":\""+label+"\",\n \"parent\":\""+pID+"\",\n \"parent_label\":\""+parentLabel+"\"\n}";
retVal.add(jsObj);
}
}
}
if ( verbose )
return retVal;
else
return new ArrayList<String>(sibs);
}
private ArrayList<String> getInstances(OWLClassExpression exp, OWLReasoner r, boolean verbose)
{
ArrayList<String> idList = new ArrayList<String>();
NodeSet<OWLNamedIndividual> inst = r.getInstances(exp, false);
for (Node<OWLNamedIndividual> ind : inst)
individualToTermlist( ind, idList, false, verbose );
return idList;
}
private ArrayList<String> getEquivalentTerms(OWLClassExpression exp, OWLReasoner r, boolean verbose)
{
ArrayList<String> idList = new ArrayList<String>();
Node<OWLClass> equivalentClasses = r.getEquivalentClasses(exp);
for ( OWLClass c : equivalentClasses.getEntities() )
objToTermlist( c, idList, false, verbose );
return idList;
}
public String labelByClass(OWLEntity c)
{
for ( OWLOntology imp : importClosure )
{
Set<OWLAnnotation> annots = c.getAnnotations( imp, rdfsLabel );
for ( OWLAnnotation a : annots )
{
if ( a.getValue() instanceof OWLLiteral )
return ((OWLLiteral)a.getValue()).getLiteral();
}
}
return null;
}
public ArrayList<String> getLabels(String shortform, OWLOntology o )
{
OWLEntity e = shortformProvider.getEntity(shortform);
if ( e == null )
return null;
ArrayList<String> idList = new ArrayList<String>();
Set<OWLAnnotation> annots = e.getAnnotations(o, rdfsLabel );
if ( annots.isEmpty() )
{
for ( OWLOntology imp : importClosure )
{
annots = e.getAnnotations( imp, rdfsLabel );
if ( !annots.isEmpty() )
break;
}
}
if ( annots.isEmpty() )
idList.add( "(Unlabeled class)" ); //To do: create "advanced commandline options" one of which chooses Queen's vs. American English
else
for ( OWLAnnotation a : annots )
{
if ( a.getValue() instanceof OWLLiteral )
idList.add( ((OWLLiteral)a.getValue()).getLiteral() );
}
return idList;
}
public ArrayList<String> SearchByLabel(String label, OWLOntology o, boolean verbose )
{
Set<OWLEntity> ents = annotProvider.getEntities(label);
if ( ents == null || ents.isEmpty() )
return null;
ArrayList<String> idList = new ArrayList<String>();
for ( OWLEntity e : ents )
{
if ( e.isOWLClass() && !e.asOWLClass().isAnonymous() )
objToTermlist( e, idList, false, verbose );
}
return idList;
}
public ArrayList<String> getTerms(OWLClassExpression exp, OWLReasoner r, boolean verbose)
{
ArrayList<String> idList = new ArrayList<String>();
idList.addAll(getEquivalentTerms(exp,r,verbose));
idList.addAll(getSubTerms(exp,r,false,false,verbose));
return idList;
}
public ArrayList<String> addTerm(OWLClassExpression exp, OWLReasoner r, OWLOntologyManager mgr, OWLOntology ont, IRI iri, boolean verbose )
{
ArrayList<String> idList = getEquivalentTerms(exp,r,verbose);
if(idList.isEmpty())
{
String ricordoID = String.valueOf(System.currentTimeMillis());
OWLClass newOwlClass = df.getOWLClass(IRI.create(kbNs + ricordoID));
mgr.addAxiom(ont, df.getOWLEquivalentClassesAxiom(newOwlClass, exp) );
if ( reasonerName.equals("elk") )
r.flush();
maybeSaveOntology( ont, iri, mgr );
objToTermlist( newOwlClass, idList, false, verbose );
r.precomputeInferences(InferenceType.CLASS_HIERARCHY);
}
return idList;
}
public static String shortUrl(String url)
{
int i = url.lastIndexOf("#");
if ( i != -1 )
return url.substring(i+1);
i = url.lastIndexOf("/");
int j = url.indexOf("/");
if ( i != j )
return url.substring(i+1);
return url;
}
/*
* Basic logging to stdout
*/
public static void logString( String x )
{
System.out.println( x );
}
public String computeResponse( ArrayList<String> terms, boolean fJson, boolean longURI, boolean verbose )
{
StringBuilder x = new StringBuilder();
if ( verbose )
{
boolean fFirst = false;
x.append("{\n \"results\":\n [\n " );
for ( String js : terms )
{
if ( !fFirst )
fFirst = true;
else
x.append( ",\n " );
x.append( js );
}
x.append("\n ]\n}");
return x.toString();
}
if ( fJson )
{
x.append("[\n ");
boolean fFirst = false;
for ( String termp : terms )
{
if ( !fFirst )
fFirst = true;
else
x.append(",\n ");
x.append( "\"" + (longURI ? termp : shortUrl(termp)) +"\"" );
}
x.append("]");
}
else
{
x.append("<table><tr><th>ID</th></tr>");
for ( String termp : terms )
x.append("<tr><td>" + (longURI ? termp : shortUrl(termp)) +"</td></tr>");
x.append("</table>");
}
return x.toString();
}
public void initOwlkb( String [] args )
{
df = OWLManager.getOWLDataFactory();
rdfsLabel = df.getRDFSLabel();
parseCommandlineArguments(args);
}
public void parseCommandlineArguments( String [] args )
{
reasonerName = "elk";
hdSave = true;
kbNs = "http://www.ricordo.eu/ricordo.owl#RICORDO_";
kbFilename = "/home/sarala/testkb/ricordo.owl"; // Keep this silly default for backward compatibility
sparql = null;
helpOnly = false;
port = 20080;
getCountsFromFeather = false;
openPhactsAppId = null;
openPhactsAppKey = null;
int i;
String flag;
for ( i = 0; i < args.length; i++ )
{
if ( args[i].length() > 2 && args[i].substring(0,2).equals("--") )
flag = args[i].substring(2).toLowerCase();
else if ( args[i].length() > 1 && args[i].substring(0,1).equals("-") )
flag = args[i].substring(1).toLowerCase();
else
flag = args[i].toLowerCase();
if ( flag.equals("help") || flag.equals("h") )
{
System.out.println( "Command line options are as follows:" );
System.out.println( "------------------------------------" );
System.out.println( "-file <path to file>" );
System.out.println( "(Specifies which ontology file to use)" );
System.out.println( "------------------------------------" );
System.out.println( "-port <number>" );
System.out.println( "(Specified which port the server runs on)" );
System.out.println( "(Default: 20080)" );
System.out.println( "------------------------------------" );
System.out.println( "-reasoner elk, or -reasoner hermit" );
System.out.println( "(Specifies which reasoner to use)" );
System.out.println( "(Default: elk)" );
System.out.println( "------------------------------------" );
System.out.println( "-namespace <iri>" );
System.out.println( "(Specifies namespace for ontology)" );
System.out.println( "(Default: http://www.ricordo.eu/ricordo.owl#RICORDO_)" );
System.out.println( "------------------------------------" );
System.out.println( "-save true, or -save false" );
System.out.println( "(Specifies whether owlfile changes are saved)" );
System.out.println( "(Default: true)" );
System.out.println( "------------------------------------" );
System.out.println( "-uclsyntax true, or -uclsyntax false" );
System.out.println( "(Specifies whether OWLKB understands UCL syntax)" );
System.out.println( "(Default: false)" );
System.out.println( "------------------------------------" );
System.out.println( "-sparql <url base>" );
System.out.println( "(Base of URL to use as SPARQL endpoint, to allow" );
System.out.println( " interaction with a triple store.)" );
System.out.println( "(Default: null)" );
System.out.println( "------------------------------------" );
/*
System.out.println( "-openPHACTSid <ID for openPHACTS API>" );
System.out.println( "-openPHACTSkey <App key for openPHACTS API>" );
System.out.println( "(For enabling Owlkb to query the openPHACTS" );
System.out.println( " API.)" );
System.out.println( "------------------------------------" );
*/
System.out.println( "-help" );
System.out.println( "(Displays this helpfile)" );
System.out.println( "" );
helpOnly = true;
return;
}
if ( flag.equals("port") || flag.equals("p") )
{
if ( i+1 < args.length )
{
try
{
port = Integer.parseInt(args[i+1]);
}
catch( Exception e )
{
System.out.println( "Port must be a number." );
helpOnly = true;
return;
}
System.out.println( "Owlkb will listen on port "+args[++i] );
}
else
{
System.out.println( "Which port do you want the server to listen on?" );
helpOnly = true;
return;
}
}
else if ( flag.equals("rname") || flag.equals("reasoner") )
{
if ( i+1 < args.length && (args[i+1].equals("elk") || args[i+1].equals("hermit")) )
{
reasonerName = args[++i];
System.out.println( "Using "+reasonerName+" as reasoner" );
}
else
{
System.out.println( "Valid reasoners are: ELK, HermiT" );
helpOnly = true;
return;
}
}
else if ( flag.equals("hd") || flag.equals("hd_save") || flag.equals("save") )
{
if ( i+1 < args.length && (args[i+1].equals("t") || args[i+1].equals("true")) )
hdSave = true;
else if ( i+1 < args.length && (args[i+1].equals("f") || args[i+1].equals("false")) )
{
hdSave = false;
System.out.println( "Saving changes to hard drive: disabled." );
}
else
{
System.out.println( "hd_save can be set to: true, false" );
helpOnly = true;
return;
}
i++;
}
else if ( flag.equals("openphactsid") )
{
if ( i+1 < args.length )
{
openPhactsAppId = args[i+1];
System.out.println( "Set to use "+args[i+1]+" as openPHACTS Application ID" );
}
i++;
}
else if ( flag.equals("openphactskey") )
{
if ( i+1 < args.length )
{
openPhactsAppKey = args[i+1];
System.out.println( "Set to use "+args[i+1]+" as openPHACTS Application Key" );
}
i++;
}
else if ( flag.equals( "uclsyntax" ) || flag.equals("ucl-syntax") || flag.equals("ucl_syntax") )
{
if ( i+1 < args.length && (args[i+1].equals("t") || args[i+1].equals("true")) )
{
/*
* Backwards compatibility (originally uclsyntax was a boolean and open-physiology was hardcoded as the endpoint
*/
uclSyntax = "http://open-physiology.org:5052/uclsyntax/";
System.out.println( "UCL Syntax: endpoint set to http://open-physiology.org:5052/uclsyntax/" );
}
else if ( i+1 < args.length && (args[i+1].equals("f") || args[i+1].equals("false")) )
uclSyntax = null;
else if ( i+1 < args.length )
{
uclSyntax = args[i+1];
System.out.println( "UCL Syntax: endpoint set to " + uclSyntax );
}
else
{
System.out.println( "uclsyntax can be set to: true, false" );
helpOnly = true;
return;
}
i++;
}
else if (flag.equals("kbns") || flag.equals("ns") || flag.equals("namespace") )
{
if ( i+1 < args.length )
{
System.out.println( "Using "+args[i+1]+" as ontology namespace." );
kbNs = args[++i];
}
else
{
System.out.println( "What do you want the ontology's namespace to be?" );
System.out.println( "Default: http://www.ricordo.eu/ricordo.owl#RICORDO_" );
helpOnly = true;
return;
}
}
else if ( flag.equals("sparql") )
{
if ( i+1 < args.length )
{
System.out.println( "Using "+args[i+1]+" as base of URL of SPARQL endpoint." );
sparql = args[++i];
}
else
{
System.out.println( "Specify the base of the URL of the SPARQL endpoint you want to use." );
System.out.println( "Default: null (in which case OWLKB will not interact with SPARQL)" );
helpOnly = true;
return;
}