owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/runner/RunEngine.java

@@ -2,24 +2,39 @@
 
 import java.io.FileNotFoundException;
 import java.io.IOException;
+import java.lang.reflect.Constructor;
 import java.util.List;
+import java.util.Map;
 
+import org.apache.jena.atlas.logging.Log;
 import org.apache.log4j.Logger;
 import org.monarchinitiative.owlsim.compute.cpt.IncoherentStateException;
+import org.monarchinitiative.owlsim.compute.matcher.MatcherMapModule;
 import org.monarchinitiative.owlsim.compute.matcher.ProfileMatcher;
+import org.monarchinitiative.owlsim.compute.matcher.impl.AbstractProfileMatcher;
+import org.monarchinitiative.owlsim.compute.matcher.impl.BayesianNetworkProfileMatcher;
 import org.monarchinitiative.owlsim.compute.matcher.impl.PhenodigmICProfileMatcher;
 import org.monarchinitiative.owlsim.io.JSONWriter;
 import org.monarchinitiative.owlsim.io.OWLLoader;
 import org.monarchinitiative.owlsim.kb.BMKnowledgeBase;
+import org.monarchinitiative.owlsim.kb.KnowledgeBaseModule;
 import org.monarchinitiative.owlsim.kb.filter.Filter;
 import org.monarchinitiative.owlsim.kb.filter.IdFilter;
 import org.monarchinitiative.owlsim.kb.filter.UnknownFilterException;
 import org.monarchinitiative.owlsim.model.match.MatchSet;
 import org.monarchinitiative.owlsim.model.match.ProfileQuery;
+import org.monarchinitiative.owlsim.model.match.impl.ProfileQueryImpl;
+import org.monarchinitiative.owlsim.model.match.impl.QueryWithNegationImpl;
 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
 
 import com.google.gson.Gson;
 import com.google.gson.GsonBuilder;
+import com.google.inject.AbstractModule;
+import com.google.inject.Guice;
+import com.google.inject.Inject;
+import com.google.inject.Injector;
+import com.google.inject.Provides;
+import com.google.inject.Singleton;
 
 /**
  * Executes a set of jobs specified by {@link RunConfiguration}
@@ -28,22 +43,39 @@
  *
  */
 public class RunEngine {
-	
+
 	//private Logger LOG = Logger.getLogger(RunEngine.class);
 
 	RunConfiguration runConfiguration;
 	MatcherModule mm = new MatcherModule();
 	ProfileMatcher profileMatcher;
 	BMKnowledgeBase kb;
+	Class[] matcherClasses = {
+			PhenodigmICProfileMatcher.class,
+			BayesianNetworkProfileMatcher.class
+	};
 
 	/**
 	 * @param runConfiguration
 	 */
-	public RunEngine(RunConfiguration runConfiguration) {
+	@Inject
+	public RunEngine(RunConfiguration runConfiguration, Map<String, ProfileMatcher> map) {
 		super();
 		this.runConfiguration = runConfiguration;
 	}
 
+	public RunConfiguration getRunConfiguration() {
+		return runConfiguration;
+	}
+
+
+
+	public void setRunConfiguration(RunConfiguration runConfiguration) {
+		this.runConfiguration = runConfiguration;
+	}
+
+
+
 	protected BMKnowledgeBase createKnowledgeBase(List<String> fns) throws OWLOntologyCreationException {
 		OWLLoader loader = null;
 		for (String fn : fns) {
@@ -58,49 +90,111 @@ protected BMKnowledgeBase createKnowledgeBase(List<String> fns) throws OWLOntolo
 		return loader.createKnowledgeBaseInterface();
 	}
 
+	public ProfileQuery createProfileQuery(Job job) {
+		ProfileQuery q = null;
+		if (job.getQueryIndividual() != null) {
+			q = profileMatcher.createProfileQuery(job.getQueryIndividual());
+		}
+		if (job.getQueryClassIds() != null) {
+			if (job.getNegatedQueryClassIds() != null) {
+				q = QueryWithNegationImpl.create(job.getQueryClassIds(), 
+						job.getNegatedQueryClassIds());
+			}
+			else {
+				q = ProfileQueryImpl.create(job.getQueryClassIds());
+			}
+		}
+
+		return q;
+	}
+
 	public void execute() throws IOException, InstantiationException, IllegalAccessException, OWLOntologyCreationException, UnknownFilterException, IncoherentStateException {
 		kb = createKnowledgeBase(runConfiguration.getOntologyInputs());
 		profileMatcher = createProfileMatcher();
 		for (PairwiseJob job : runConfiguration.getPairwiseJobs()) {
-			ProfileQuery q = profileMatcher.createProfileQuery(job.getQueryIndividual());
+			job.setId();
+			ProfileQuery q = createProfileQuery(job);
 			Filter filter = IdFilter.create(job.getTargetIndividual());
 			q.setFilter(filter);
 			//job.getTargetIndividual();
 			MatchSet mp = profileMatcher.findMatchProfile(q);
 			job.setMatchSet(mp);
 			//LOG.info(mp);
-			
+
 		}
 		for (SearchJob job : runConfiguration.getSearchJobs()) {
-			// TODO: classes
-			ProfileQuery q = profileMatcher.createProfileQuery(job.getQueryIndividual());
+			job.setId();
+			ProfileQuery q = createProfileQuery(job);
 			//job.getTargetIndividual();
 			MatchSet mp = profileMatcher.findMatchProfile(q);
 			job.setMatchSet(mp);
 			//LOG.info(mp);
-			
+
 		}
 		return;
 	}
 
+
+	/**
+	 * 
+	 * TODO: incomplete 
+	 * @return
+	 * @throws IOException
+	 * @throws InstantiationException
+	 * @throws IllegalAccessException
+	 */
 	public ProfileMatcher createProfileMatcher() throws IOException, InstantiationException, IllegalAccessException {
-		//mm.getMatchers();
-		return PhenodigmICProfileMatcher.create(kb);
+		String requestedMatcher = runConfiguration.getTool();
+		ProfileMatcher matcher = null;
+		if (requestedMatcher == null) {
+			requestedMatcher = "phenodigm";
+		}
+
+		for (int i=0; i<matcherClasses.length; i++) {
+			Class c = matcherClasses[i];
+			System.out.println(c);
+			String sn = ((ProfileMatcher) c.newInstance()).getShortName();
+
+			if (sn.equals(requestedMatcher)) {
+				Class[] args = {BMKnowledgeBase.class};
+				try {
+					Constructor constr = 
+							c.getDeclaredConstructor(args);
+						matcher = (ProfileMatcher) constr.newInstance(kb);
+				}
+				catch (Exception e) {
+					System.err.println(e.getStackTrace());
+				}
+			}
+		}
+
+		/*
+		Map<String, ProfileMatcher> mmap = mm.getMatchers();
+		for (String shortName : mmap.keySet()) {
+			if (shortName.equals(requestedMatcher)) {
+				matcher = mmap.get(shortName);
+				((AbstractProfileMatcher) matcher).setKnowledgeBase(kb);
+			}
+		}
+		 */
+		//return PhenodigmICProfileMatcher.create(kb);
+		//return matcher.getClass().create(kb);
+		return matcher;
 	}
-	
+
 	public void toJsonFile(String fn) throws FileNotFoundException {
 		JSONWriter jsonWriter = new JSONWriter(fn);
 		jsonWriter.write(runConfiguration);
 	}
 
-	
+
 	public String toJsonString() {
-		
+
 		Gson gson = new GsonBuilder().setPrettyPrinting().create();
 		return gson.toJson(runConfiguration);		
 	}
-	
-	
+
+
 	/**
 	 * 
 	 * Usage:
@@ -121,13 +215,37 @@ public static void main(String[] args) throws IOException, InstantiationExceptio
 		String outFile = args.length > 1 ? args[1] : "owlsim-output.json";
 		RunConfiguration rc = RunnerUtil.generateRunConfigurationFromJsonFile(cfgFile);
 		System.out.println(rc.getDescription());
-		RunEngine re = new RunEngine(rc);
+		Injector i = Guice.createInjector(
+				new KnowledgeBaseModule(rc.getOntologyInputs(), null),
+				new MatcherMapModule(),
+				new RunEngineConfModule(rc));
+		
+		RunEngine re = i.getInstance(RunEngine.class);
 		re.execute();
 		//LOG.info("Saving to: "+outFile);
 		re.toJsonFile(outFile);
 
 	}
 
+	static class RunEngineConfModule extends AbstractModule {
+
+		private final RunConfiguration rc;
+
+		public RunEngineConfModule(RunConfiguration rc) throws IOException {
+			this.rc = rc;
+		}
+		
+		@Provides
+		@Singleton
+		public RunConfiguration providesConf() {
+			return rc;
+		}
+
+		@Override
+		protected void configure() {
+			// empty
+		}
+	}
 }