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package uk.ac.ox.cs.pagoda;
import org.apache.commons.cli.*;
import org.apache.commons.io.FilenameUtils;
import uk.ac.ox.cs.pagoda.query.QueryRecord;
import uk.ac.ox.cs.pagoda.reasoner.QueryReasoner;
import uk.ac.ox.cs.pagoda.util.PagodaProperties;
import uk.ac.ox.cs.pagoda.util.Timer;
import uk.ac.ox.cs.pagoda.util.Utility;
import java.io.BufferedWriter;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.Collection;
import java.util.HashMap;
import java.util.Map;
/**
* Executable command line user interface.
*/
public class Pagoda implements Runnable {
private static final String OPTION_ONTOLOGY = "o";
private static final String OPTION_DATA = "t";
private static final String OPTION_QUERY = "q";
private static final String OPTION_ANSWER = "a";
private static final String OPTION_CLASSIFY = "c";
private static final String OPTION_HERMIT = "f";
private static final String OPTION_SKOLEM = "s";
private static final String OPTION_SKOLEM_DEPTH = "d";
private final PagodaProperties properties;
/**
* Do not use it
*/
private Pagoda() {
properties = new PagodaProperties();
}
public static void main(String... args) {
// TODO treat the mandatory options as simple args
Options options = new Options();
options.addOption(Option.builder(OPTION_ONTOLOGY)
.argName(OPTION_ONTOLOGY)
.required()
.hasArg()
.desc("The ontology path")
.build());
options.addOption(Option.builder(OPTION_DATA).argName(OPTION_DATA).hasArg().desc("The data path").build());
options.addOption(Option.builder(OPTION_QUERY)
.argName(OPTION_QUERY)
.required()
.hasArg()
.desc("The query path")
.build());
options.addOption(Option.builder(OPTION_ANSWER)
.argName(OPTION_ANSWER)
.hasArg()
.desc("The answer path")
.build());
options.addOption(Option.builder(OPTION_CLASSIFY)
.argName(OPTION_CLASSIFY)
.desc("Tell whether to classify")
.type(Boolean.class)
.build());
options.addOption(Option.builder(OPTION_HERMIT)
.argName(OPTION_HERMIT)
.desc("Tell whether to call Hermit")
.type(Boolean.class)
.build());
options.addOption(Option.builder(OPTION_SKOLEM)
.argName(OPTION_SKOLEM)
.hasArg()
.desc("Tell if and how to apply Skolemisation")
.build());
options.addOption(Option.builder(OPTION_SKOLEM_DEPTH)
.argName(OPTION_SKOLEM_DEPTH)
.hasArg()
.desc("Tell how deep to skolemise")
.build());
CommandLineParser parser = new DefaultParser();
try {
CommandLine cmd = parser.parse(options, args);
PagodaBuilder pagodaBuilder = Pagoda.builder()
.ontology(cmd.getOptionValue(OPTION_ONTOLOGY))
.query(cmd.getOptionValue(OPTION_QUERY));
if(cmd.hasOption(OPTION_DATA)) pagodaBuilder.data(cmd.getOptionValue(OPTION_DATA));
if(cmd.hasOption(OPTION_ANSWER)) pagodaBuilder.answer(cmd.getOptionValue(OPTION_ANSWER));
if(cmd.hasOption(OPTION_CLASSIFY))
pagodaBuilder.classify(Boolean.parseBoolean(cmd.getOptionValue(OPTION_CLASSIFY)));
if(cmd.hasOption(OPTION_HERMIT))
pagodaBuilder.hermit(Boolean.parseBoolean(cmd.getOptionValue(OPTION_HERMIT)));
if(cmd.hasOption(OPTION_SKOLEM))
pagodaBuilder.skolem(PagodaProperties.SkolemUpperBoundOptions.valueOf(cmd.getOptionValue(OPTION_SKOLEM)));
if(cmd.hasOption(OPTION_SKOLEM_DEPTH))
pagodaBuilder.skolemDepth(Integer.parseInt(cmd.getOptionValue(OPTION_SKOLEM_DEPTH)));
pagodaBuilder.build().run();
} catch(ParseException exp) {
HelpFormatter formatter = new HelpFormatter();
formatter.printHelp("PAGOdA", options);
Utility.logError("Parsing failed. Reason: " + exp.getMessage());
System.exit(0);
}
}
/**
* Get a builder.
*/
public static PagodaBuilder builder() {
return new PagodaBuilder();
}
@Override
public void run() {
Utility.logInfo("Ontology file: " + properties.getOntologyPath());
Utility.logInfo("Data files: " + properties.getDataPath());
Utility.logInfo("Query files: " + properties.getQueryPath());
Utility.logInfo("Answer file: " + properties.getAnswerPath());
Utility.logInfo("Skolemisation: " + properties.getSkolemUpperBound());
Utility.logInfo("Skolemisation depth: " + properties.getSkolemDepth());
QueryReasoner pagoda = null;
try {
Timer t = new Timer();
pagoda = QueryReasoner.getInstance(properties);
if(pagoda == null) return;
Utility.logInfo("Preprocessing Done in " + t.duration() + " seconds.");
if(properties.getQueryPath() != null) {
for(String queryFile : properties.getQueryPath().split(";")) {
Collection<QueryRecord> queryRecords = pagoda.getQueryManager().collectQueryRecords(queryFile);
pagoda.evaluate(queryRecords);
if(PagodaProperties.isDebuggingMode()) {
HashMap<String, Map<String, String>> statistics = new HashMap<>();
for(QueryRecord queryRecord : queryRecords) {
statistics.put(queryRecord.getQueryID(), queryRecord.getStatistics());
}
String statisticsFilename = getStatisticsFilename(properties, queryFile);
try(BufferedWriter writer = Files.newBufferedWriter(Paths.get(statisticsFilename))) {
QueryRecord.GsonCreator.getInstance().toJson(statistics, writer);
} catch(IOException e) {
Utility.logError("Unable to save statistics");
}
}
}
}
} finally {
if(pagoda != null) pagoda.dispose();
}
}
private String getStatisticsFilename(PagodaProperties properties, String queryFile) {
String statisticsFilename = "statistics";
statisticsFilename += "_" + FilenameUtils.removeExtension(FilenameUtils.getName(properties.getOntologyPath().replaceAll("_", "-")));
if(properties.getDataPath() != null)
statisticsFilename += "_" + FilenameUtils.removeExtension(FilenameUtils.getName(properties.getDataPath().replaceAll("_", "-")));
statisticsFilename += "_" + FilenameUtils.removeExtension(FilenameUtils.getName(queryFile).replaceAll("_", "-"));
statisticsFilename += "_" + ((properties.getSkolemUpperBound() == PagodaProperties.SkolemUpperBoundOptions.DISABLED)
? "" : (properties.getSkolemUpperBound() == PagodaProperties.SkolemUpperBoundOptions.BEFORE_SUMMARISATION)
? "before" : "after");
statisticsFilename += "_skd" + properties.getSkolemDepth();
statisticsFilename += "_maxtrpl" + properties.getMaxTriplesInSkolemStore();
statisticsFilename += ".json";
statisticsFilename = FilenameUtils.concat(properties.getStatisticsDir().toString(),
statisticsFilename);
return statisticsFilename;
}
/**
* Allows to set the parameters before creating a Pagoda instance.
*/
public static class PagodaBuilder {
private Pagoda instance;
private PagodaBuilder() {
instance = new Pagoda();
}
public PagodaBuilder ontology(String ontologyPath) {
if(instance == null) return null;
instance.properties.setOntologyPath(ontologyPath);
return this;
}
public PagodaBuilder ontology(Path ontologyPath) {
return ontology(ontologyPath.toString());
}
public PagodaBuilder data(String dataPath) {
if(instance == null) return null;
instance.properties.setDataPath(dataPath);
return this;
}
public PagodaBuilder data(Path dataPath) {
return data(dataPath.toString());
}
public PagodaBuilder query(String queryPath) {
if(instance == null) return null;
instance.properties.setQueryPath(queryPath);
return this;
}
public PagodaBuilder query(Path queryPath) {
return query(queryPath.toString());
}
public PagodaBuilder answer(String answerPath) {
if(instance == null) return null;
instance.properties.setAnswerPath(answerPath);
return this;
}
public PagodaBuilder answer(Path answerPath) {
return answer(answerPath.toString());
}
public PagodaBuilder classify(Boolean toClassify) {
if(instance == null) return null;
instance.properties.setToClassify(toClassify);
return this;
}
public PagodaBuilder hermit(Boolean callHermit) {
if(instance == null) return null;
instance.properties.setToCallHermiT(callHermit);
return this;
}
public PagodaBuilder skolem(PagodaProperties.SkolemUpperBoundOptions option) {
if(instance == null) return null;
instance.properties.setSkolemUpperBound(option);
return this;
}
public PagodaBuilder skolemDepth(int depth) {
if(instance == null) return null;
instance.properties.setSkolemDepth(depth);
return this;
}
public Pagoda build() {
Pagoda builtInstance = instance;
instance = null;
return builtInstance;
}
}
}
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