rm javautil_pheno

Author: koehlers

.classpath

@@ -12,18 +12,12 @@
 		</attributes>
 	</classpathentry>
 	<classpathentry kind="var" path="M2_REPO/com/googlecode/json-simple/json-simple/1.1.1/json-simple-1.1.1.jar"/>
-	<classpathentry kind="var" path="M2_REPO/junit/junit/4.10/junit-4.10.jar" sourcepath="M2_REPO/junit/junit/4.10/junit-4.10-sources.jar">
-		<attributes>
-			<attribute name="javadoc_location" value="jar:file:/Users/sebastiankohler/.m2/repository/junit/junit/4.10/junit-4.10-javadoc.jar!/"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="var" path="M2_REPO/org/hamcrest/hamcrest-core/1.1/hamcrest-core-1.1.jar" sourcepath="M2_REPO/org/hamcrest/hamcrest-core/1.1/hamcrest-core-1.1-sources.jar"/>
+	<classpathentry kind="var" path="M2_REPO/junit/junit/4.10/junit-4.10.jar"/>
+	<classpathentry kind="var" path="M2_REPO/org/hamcrest/hamcrest-core/1.1/hamcrest-core-1.1.jar"/>
 	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry combineaccessrules="false" kind="src" path="/javautil_pheno"/>
-	<classpathentry combineaccessrules="false" kind="src" path="/ontologizer"/>
 	<classpathentry kind="output" path="target/classes"/>
 </classpath>

pom.xml

@@ -1,11 +1,19 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
 	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>phenotero</groupId>
 	<artifactId>phenotero</artifactId>
 	<version>0.0.1-SNAPSHOT</version>
 
 
+	<repositories>
+		<repository>
+			<id>compbio</id>
+			<url>http://compbio.charite.de/tl_files/maven</url>
+		</repository>
+	</repositories>
+
 	<dependencies>
 
 		<!-- https://mvnrepository.com/artifact/com.googlecode.json-simple/json-simple -->
@@ -14,7 +22,11 @@
 			<artifactId>json-simple</artifactId>
 			<version>1.1.1</version>
 		</dependency>
-
+		<dependency>
+			<groupId>ontologizer</groupId>
+			<artifactId>ontologizer</artifactId>
+			<version>0.0.3-SNAPSHOT</version>
+		</dependency>
 	</dependencies>
 
 	<build>
@@ -48,7 +60,7 @@
 					</descriptorRefs>
 					<archive>
 						<manifest>
-							<mainClass>de.phenomics.Onto2Zotero</mainClass>
+							<mainClass>de.phenomics.Obo2ZoteroJson</mainClass>
 						</manifest>
 					</archive>
 				</configuration>

src/de/phenomics/Obo2ZoteroJson.java

@@ -11,10 +11,12 @@
 import org.json.simple.JSONArray;
 import org.json.simple.JSONObject;
 
+import ontologizer.go.OBOParser;
+import ontologizer.go.OBOParserException;
 import ontologizer.go.Ontology;
 import ontologizer.go.Term;
+import ontologizer.go.TermContainer;
 import sonumina.math.graph.SlimDirectedGraphView;
-import util.OntologyUtil;
 
 /**
  * @author Sebastian Köhler (dr.sebastian.koehler@gmail.com)
@@ -39,7 +41,7 @@ public static void main(String[] args) {
 
 			// init json document
 			JSONArray jsonArrayTerms = new JSONArray();
-			Ontology ontology = OntologyUtil.parseOntology(oboFile);
+			Ontology ontology = parseOntology(oboFile);
 			SlimDirectedGraphView<Term> ontologySlim = ontology.getSlimGraphView();
 			HashSet<Term> rootChildren = new HashSet<Term>(ontologySlim.getChildren(ontology.getRootTerm()));
 
@@ -111,6 +113,28 @@ public static void main(String[] args) {
 
 	}
 
+	/**
+	 * @param oboFile
+	 * @return
+	 */
+	private static Ontology parseOntology(String oboFile) {
+		OBOParser oboParser = null;
+		oboParser = new OBOParser(oboFile, OBOParser.PARSE_DEFINITIONS | OBOParser.PARSE_XREFS);
+
+		try {
+			String parseInfo = oboParser.doParse();
+			System.out.println(parseInfo);
+
+		} catch (IOException | OBOParserException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+		// get the complete hpo
+		TermContainer termContainer = new TermContainer(oboParser.getTermMap(), oboParser.getFormatVersion(),
+				oboParser.getDataVersion());
+		return Ontology.create(termContainer);
+	}
+
 	/**
 	 * @param allSyns
 	 * @return