Update

src/ontoTool/OntologyClassGenerator.java

@@ -50,6 +50,11 @@
  */
 
 public class OntologyClassGenerator {
+	public static final String CNAME_IRI = "iri";
+	public static final String CNAME_LABEL = "label";
+	public static final String CNAME_PARENT_IRI = "parentiri";
+	public static final String CNAME_PARENT_LABEL = "parentlabel";
+
 	public static void main(String[] args) {
 		OntologyClassGeneratorOptions bean = new OntologyClassGeneratorOptions();
 	    CmdLineParser parser = new CmdLineParser(bean);
@@ -73,25 +78,28 @@ public static void main(String[] args) {
 
 		// path of input file
 		String path = config.getPath();
+
 		// tab-delimited file for conversion
 		String inputFilename = config.getInputFilename();
+
 		// ontology IRI of converted OWL file
 		String ontoIRIstr = config.getOntologyIRIstr();
+
 		// output converted OWL file name
 		String outputFilename = config.getOutputFilename();
+
 		// base URL of new term IRIs
 		String idBase = config.getIdBase();
+
 		// prefix for new term ID
 		String prefix = config.getPrefix();
+
 		// start ID number
 		int startNum = config.getStartNum();
-		// index for term label, term IRI, term parent label or IRI in the tab-delimited file
-		int iriPos = config.getIriPos();
-		int labelPos = config.getLabelPos();
-		int parentIriPos = config.getParentIriPos();
-		int parentPos = config.getParentPos();
+
 		// external ontology as reference of existing ontology class and annotation property
 		String externalOntologyFilename = config.getExternalOntologyFilename();
+
 		// labels/IRI of annotation properties that will be used in conversion
 		ArrayList<String> annotLabels = config.getAnnotLabels();
 
@@ -169,27 +177,37 @@ public static void main(String[] args) {
 
 		//annotation Property IRI and its index in the input file  
 		Hashtable<Integer, String> annotProps = new Hashtable<Integer, String>(); 				
-
-        // Find annotation property index from header of input file, any column name is not specified as
+
+		// index for term label, term IRI, term parent label or IRI in the tab-delimited file
+		int iriPos = -1;
+		int labelPos = -1;
+		int parentIriPos = -1;
+		int parentPos = -1;
+
+        // Find term and its parent IRI and label position, and annotation property index from header of input file, any column name is not specified as
         // annotation property in the setting file will be skipped
         String[] items = matrix.get(0);
-
-        for (int k = 0; k< items.length; k++) {
-        	String item = items[k].trim();
 
-        	if (item != null && !item.isEmpty() && labelIriObjects.containsKey(item.toLowerCase())) {
-         		annotProps.put(new Integer(k), labelIriObjects.get(item.toLowerCase()));
-         	}
+        for (int k = 0; k< items.length; k++) {
+        	String item = items[k];
+
+        	if (item != null && !item.isEmpty()) {
+        		if (item.toLowerCase().equals(CNAME_IRI))					iriPos = k;
+        		else if (item.toLowerCase().equals(CNAME_LABEL))			labelPos = k;
+        		else if (item.toLowerCase().equals(CNAME_PARENT_IRI))		parentIriPos = k;
+        		else if (item.toLowerCase().equals(CNAME_PARENT_LABEL))		parentPos = k;
+        		else if (labelIriObjects.containsKey(item.toLowerCase()))	annotProps.put(new Integer(k), labelIriObjects.get(item.toLowerCase()));
+        	}
 		}
 
         // create classes
 	   	for (int i = 1; i < matrix.size(); i++) {
 	   		items = matrix.get(i);
 
-	   		String termLabel = "";
-	   		String termIRIstr = "";
-	   		String parentLabel = "";
-	   		String parentIRIstr = "";
+	   		String termLabel 	= "";
+	   		String termIRIstr 	= "";
+	   		String parentLabel 	= "";
+	   		String parentIRIstr	= "";
 
 	   		// -- get term label and IRIstr --
 	   		// Term label must be provided in the input file
@@ -422,6 +440,8 @@ public static void printHashtable (Hashtable<String,String> pairs, String messag
 
 	public static String cleanString (String s) {
 		s = s.trim().replaceAll("^\"|\"$", "");	
+
+		if (s.toUpperCase().equals("NA"))	s = "";
 
 		return s;
 	}

src/ontoTool/OntologyClassGeneratorConfiguration.java

@@ -21,11 +21,6 @@ public class OntologyClassGeneratorConfiguration {
 	private String idBase = "http://purl.obolibrary.org/obo/";	// base URL of new term IRIs
 	private String prefix = "";		// prefix for new term ID
 	private int startNum = 1;		// start ID number	
-	// index for term label, term IRI, term parent label or IRI in the tab-delimited file
-	private int iriPos = -1;
-	private int labelPos = -1;
-	private int parentIriPos = -1;
-	private int parentPos = -1;
 	private String externalOntologyFilename = "";
 	private ArrayList<String> annotLabels;
 
@@ -40,10 +35,6 @@ public class OntologyClassGeneratorConfiguration {
 		this.idBase = "http://purl.obolibrary.org/obo/";
 		this.prefix = "";	
 		this.startNum = 1;	
-		this.iriPos = -1;
-		this.labelPos = -1;
-		this.parentIriPos = -1;
-		this.parentPos = -1;
 		this.externalOntologyFilename = "";
 		this.annotLabels = new ArrayList<String>();
 	}
@@ -86,18 +77,6 @@ public void parseSetting(String settingFilename) {
 								break;								
 							case "start ID":
 								setStartNum(Integer.parseInt(value));
-								break;	
-							case "term position":
-								setLabelPos(Integer.parseInt(value)-1);
-								break;	
-							case "term IRI position":
-								setIriPos(Integer.parseInt(value)-1);
-								break;	
-							case "term parent position":
-								setParentPos(Integer.parseInt(value)-1);
-								break;	
-							case "term parent IRI position":
-								setParentIriPos(Integer.parseInt(value)-1);
 								break;
 							case "external ontology file":	
 								setExternalOntologyFilename(value);
@@ -154,22 +133,6 @@ public int getStartNum () {
 		return this.startNum;
 	}
 
-	public int getIriPos () {
-		return this.iriPos;
-	}
-
-	public int getLabelPos () {
-		return this.labelPos;
-	}
-
-	public int getParentIriPos () {
-		return this.parentIriPos;
-	}
-
-	public int getParentPos () {
-		return this.parentPos;
-	}
-
 	public String getExternalOntologyFilename () {
 		return this.externalOntologyFilename;
 	}
@@ -206,23 +169,7 @@ public void setStartNum (int startNum) {
 		this.startNum = startNum;
 	}
 
-	public void setIriPos (int iriPos) {
-		this.iriPos = iriPos;
-	}
-
-	public void setLabelPos (int labelPos) {
-		this.labelPos = labelPos;
-	}
-
-	public void setParentIriPos (int parentIriPos) {
-		this.parentIriPos = parentIriPos;
-	}
-
 	public void setExternalOntologyFilename (String externalOntologyFilename) {
 		this.externalOntologyFilename = externalOntologyFilename;
 	}
-
-	public void setParentPos (int parentPos) {
-		this.parentPos = parentPos;
-	}
 }

src/ontoTool/OntologyClassGeneratorOptions.java

@@ -9,8 +9,10 @@
  */
 public class OntologyClassGeneratorOptions {
     @Option(name="-settingFilename", usage ="the configuration used to set all variables required for the OWL conversion", required = false)
-    private String settingFilename = "./test/setting.txt";
-
+    private String settingFilename = "/Users/jiezheng/Documents/VEuPathDB-git/ApiCommonData/Load/ontology/script/test-local/setting_test.txt";
+
+    //private String settingFilename = "/Users/jiezheng/Documents/ontology/DTO/proteoCommons/class/setting.txt";
+
     public String getSettingFilename () {
     	return this.settingFilename;
     }

src/owlUtil/OntologyEditor.java

@@ -12,24 +12,54 @@
 import org.semanticweb.owlapi.model.OWLAnnotationProperty;
 import org.semanticweb.owlapi.model.OWLAxiom;
 import org.semanticweb.owlapi.model.OWLClass;
+import org.semanticweb.owlapi.model.OWLClassAssertionAxiom;
 import org.semanticweb.owlapi.model.OWLDataFactory;
+import org.semanticweb.owlapi.model.OWLNamedIndividual;
+import org.semanticweb.owlapi.model.OWLObjectProperty;
+import org.semanticweb.owlapi.model.OWLObjectPropertyAssertionAxiom;
 import org.semanticweb.owlapi.model.OWLOntology;
 import org.semanticweb.owlapi.model.OWLOntologyChange;
 import org.semanticweb.owlapi.model.OWLOntologyManager;
 import org.semanticweb.owlapi.model.RemoveAxiom;
 import org.semanticweb.owlapi.search.EntitySearcher;
 import org.semanticweb.owlapi.util.OWLEntityRenamer;
+import org.semanticweb.owlapi.vocab.OWLRDFVocabulary;
 
 public class OntologyEditor {
+	// add an instance, specify its class type and add label annotation if available
+	public static void addInstance(OWLOntologyManager manager, OWLOntology ontology, String instanceIRIstr, String classIRIstr, String instanceLabel) {
+ 		// Create factory to obtain a reference to a class
+        OWLDataFactory df = manager.getOWLDataFactory();
 
-	public static void cleanEmptyAnnotationFields() {
-
-	}
-
-	public static void addAnnotations(OWLOntologyManager manager, OWLOntology ontology, String annotPropIRI, HashMap<String, String> annotationList) {
+        // Create instance
+		OWLNamedIndividual ins = df.getOWLNamedIndividual(IRI.create(instanceIRIstr));
 
+		// Add asserted class type
+        OWLClass cls = df.getOWLClass(IRI.create(classIRIstr));
+        OWLClassAssertionAxiom classTypeAxiom = df.getOWLClassAssertionAxiom(cls, ins);
+        manager.applyChange(new AddAxiom(ontology, classTypeAxiom));
+
+        // Add label if it is not null
+        if (instanceLabel.length() > 0 ) {
+    		OWLAnnotationProperty labelProp = df.getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_LABEL.getIRI());
+    		OWLAnnotation labelAnnot = df.getOWLAnnotation(labelProp, df.getOWLLiteral(instanceLabel));
+    		OWLAxiom labelAxiom = df.getOWLAnnotationAssertionAxiom(IRI.create(instanceIRIstr), labelAnnot);
+    		manager.applyChange(new AddAxiom(ontology, labelAxiom));
+        }
 	}
 
+	// add relation between two instances
+	public static void addRelation (OWLOntologyManager manager, OWLOntology ontology, String subjectIRIstr, String objectIRIstr, String objectPropIRIstr) {
+ 		// Create factory to obtain a reference to a class
+        OWLDataFactory df = manager.getOWLDataFactory();
+		OWLNamedIndividual subject = df.getOWLNamedIndividual(IRI.create(subjectIRIstr));
+		OWLNamedIndividual object = df.getOWLNamedIndividual(IRI.create(objectIRIstr));
+		OWLObjectProperty predicate = df.getOWLObjectProperty(IRI.create(objectPropIRIstr));
+		OWLObjectPropertyAssertionAxiom propAssertion = df.getOWLObjectPropertyAssertionAxiom(predicate, subject, object);
+		manager.applyChange(new AddAxiom(ontology,propAssertion));
+	}
+
+	// update annotation properties
 	public static void updateAnnotations(OWLOntologyManager manager, OWLOntology ontology, String annotPropIRI, HashMap<String, String> annotationList) {
  		// Create factory to obtain a reference to a class
         OWLDataFactory df = manager.getOWLDataFactory();
@@ -61,32 +91,6 @@ public static void updateAnnotations(OWLOntologyManager manager, OWLOntology ont
 	   	    	System.out.println(entityIRIstr + " is not in the given ontology");
 	   	    }
 	   	}
-
-
-		// go through each class in the ontology, if they are in the list for editing,
-	   	// remove any associate annotation property value(s) of the class if there are any 
-	   	// and add new annotation values to the class
-	   	/*
-	   	for (OWLClass cls : ontology.getClassesInSignature()) {	    	
-	     	String termIRIstr = cls.getIRI().toString();
-
-        	if (annotationList.containsKey(termIRIstr)) {
-        		// remove specified annotation property if it has been defined
-        		Collection<OWLAnnotation> owlAnnots = EntitySearcher.getAnnotations(cls, ontology, annotProp);
-
-        		if(!owlAnnots.isEmpty()) {
-        			for (OWLAnnotation owlAnnot : owlAnnots) {
-        				OWLAxiom ax = df.getOWLAnnotationAssertionAxiom(cls.getIRI(), owlAnnot);
-        				manager.applyChange(new RemoveAxiom(ontology, ax));
-        			}
-        		}
-
-            	OWLAnnotation newAnnot = df.getOWLAnnotation(annotProp, df.getOWLLiteral(annotationList.get(termIRIstr)));
-            	OWLAxiom ax = df.getOWLAnnotationAssertionAxiom(cls.getIRI(), newAnnot);
-            	manager.applyChange(new AddAxiom(ontology, ax));
-        	} 
-        }
-        */
 	}
 
 	// update IRIs based on mapping file

src/owlUtil/OntologyManipulator.java

@@ -2,7 +2,6 @@
 
 import org.semanticweb.owlapi.model.*;
 import org.semanticweb.owlapi.util.OWLOntologyMerger;
-import com.google.common.base.Optional;
 
 import java.io.File;
 import java.util.Set;
@@ -143,33 +142,4 @@ public static OWLOntology merge (OWLOntologyManager manager, String mergeOntURIs
 
 		return mergedOnt; 
 	}
-
-	public static OWLOntology mergeToTargetOnt (OWLOntologyManager manager, OWLOntology targetOnt, OWLOntology ont) {
-		Set<OWLAxiom> axs = ont.getAxioms();
-		for(OWLAxiom ax : axs) {
-	    	if (!targetOnt.containsAxiom(ax)) {
-	        	manager.applyChange(new AddAxiom(targetOnt, ax));
-	        }
-	    }
-
-		Optional<IRI> targetOntIRI = targetOnt.getOntologyID().getOntologyIRI();
-		Optional<IRI> ontIRI = ont.getOntologyID().getOntologyIRI();
-
-		System.out.println("All axioms in ontology " + ontIRI.toString() + " have been merged to the ontology " + targetOntIRI.toString());
-
-		return targetOnt;
-	}
-
-	public static OWLOntology setOntologyID (OWLOntologyManager manager, OWLOntology ont, String newIRIstr) {
-		String oldIRIstr = ont.getOntologyID().getOntologyIRI().toString();
-
-		if (newIRIstr.equals(oldIRIstr)) {
-			System.out.println("The new IRI: " + newIRIstr + " is same to the original one.");
-		} else {
-			SetOntologyID setOntoID =new SetOntologyID(ont,IRI.create(newIRIstr));
-			manager.applyChange(setOntoID);
-		}
-
-		return ont;
-	}
 }