obo-svn-commit

[<cmu...@us...>]

Revision: 1422
          http://obo.svn.sourceforge.net/obo/?rev=1422&view=rev
Author:   cmungall
Date:     2008-01-28 16:54:04 -0800 (Mon, 28 Jan 2008)

Log Message:
-----------


Modified Paths:
--------------
    obdapi/trunk/OBDAPI/src/org/obd/parser/ZFINGenotypePhenotypeParser.java

Added Paths:
-----------
    obdapi/trunk/OBDAPI/src/org/obd/parser/ZFINGenotypePhenotypeOBOParser.java

Added: obdapi/trunk/OBDAPI/src/org/obd/parser/ZFINGenotypePhenotypeOBOParser.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/parser/ZFINGenotypePhenotypeOBOParser.java	                        (rev 0)
+++ obdapi/trunk/OBDAPI/src/org/obd/parser/ZFINGenotypePhenotypeOBOParser.java	2008-01-29 00:54:04 UTC (rev 1422)
@@ -0,0 +1,170 @@
+package org.obd.parser;
+
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+
+import org.obd.model.CompositionalDescription;
+import org.obd.model.LinkStatement;
+import org.obd.model.Node;
+import org.obd.model.Statement;
+import org.obd.model.CompositionalDescription.Predicate;
+import org.obd.model.Node.Metatype;
+import org.obd.query.ComparisonQueryTerm.Operator;
+
+/**
+ * 
+ * @author cjm
+ * 
+ * TODO: DRY - see also ZFINGenotypePhenotypeParser
+ *
+ */
+public class ZFINGenotypePhenotypeOBOParser extends TabularInfoParser {
+
+	protected String src = "ZFIN";
+	private String taxId = "NCBITax:7955";
+	protected String defaultURL = 
+		"http://zfin.org/data_transfer/Downloads/pheno_obo.txt";
+	
+
+	public ZFINGenotypePhenotypeOBOParser() {
+		super();
+	}
+
+	public ZFINGenotypePhenotypeOBOParser(String path) {
+		super(path);
+	}
+	
+	public String createId(String local) {
+		return "ZFIN:"+local;
+	}
+
+
+	public void parseColVals(String[] colVals) throws Exception {
+		index();
+		if (colVals.length < 6) {
+			throw new Exception("not enough vals: "+currentLine);
+		}
+		int n = 0;
+		String gtId = colVals[n++];
+		String gtLabel = colVals[n++];
+		
+		String startId = colVals[n++];
+		//String startLabel = colVals[3];
+		String endId = colVals[n++];
+		//String endLabel = colVals[5];
+		String entityId = colVals[n++];
+		//String entityLabel = colVals[7];
+		String qualityId = colVals[n++];
+		//String qualityLabel = colVals[9];
+		String ab = colVals[12];
+		String pubId = colVals[13];
+
+		Node gtNode = addNode(gtId);
+		gtNode.setLabel(gtLabel);		
+		
+		HashSet<LinkStatement> diffs = new HashSet<LinkStatement>();
+		if (startId != null && !startId.equals("ZFS:0000000")) {
+			LinkStatement d = new LinkStatement();
+			d.setRelationId("OBO_REL:starts_during");
+			d.setTargetId(entityId);
+			diffs.add(d);
+		}
+		if (endId != null && !endId.equals("ZFS:0000000")) {
+			LinkStatement d = new LinkStatement();
+			d.setRelationId("OBO_REL:ends_during");
+			d.setTargetId(entityId);
+			diffs.add(d);
+		}
+		if (entityId != null) {
+			LinkStatement d = new LinkStatement();
+			d.setRelationId("OBO_REL:inheres_in");
+			d.setTargetId(entityId);
+			diffs.add(d);
+		}
+		else {
+			return; 
+		}
+		if (qualityId != null) {
+			CompositionalDescription desc = new CompositionalDescription(qualityId, diffs);
+
+			String phenoId = desc.generateId();
+			desc.setId(phenoId);
+			graph.addStatements(desc);
+
+
+			LinkStatement annot = new LinkStatement();
+			annot.setNodeId(gtId);
+			annot.setRelationId("OBO_REL:influences");
+			
+			LinkStatement pubLink = new LinkStatement();
+			pubLink.setRelationId("oban:has_data_source");
+			pubLink.setTargetId(pubId);
+			annot.addSubStatement(pubLink);
+			
+			LinkStatement abLink = new LinkStatement();
+			pubLink.setRelationId("oban:assigned_by");
+			pubLink.setTargetId("ZFIN");
+			annot.addSubStatement(abLink);
+			
+			annot.setTargetId(phenoId);
+			annot.setSourceId(src);
+			this.addStatement(annot);
+		}
+		else {
+			warn("cannot find quality");
+		}
+		
+	}
+	
+	public Node addNode(String id) {
+		Node node = super.addNode(id);
+		node.setMetatype(Metatype.CLASS);
+		node.setSourceId(src);
+		addInOrganismLink(id, taxId, src);	
+		return node;
+	}
+
+	public String lookup(String id) {
+		return lookup(id,null);
+	}
+	
+	public String lookup(String id, String label) {
+		if (id != null) {
+			if (termIndex.containsKey(id))
+				return termIndex.get(id);
+			if (termIndex.containsKey(createId(id)))
+				return termIndex.get(createId(id));
+		}
+		if (label != null)
+			if (termIndex.containsKey(label))
+				return termIndex.get(label);
+		return null;
+	}
+
+	Map <String,String> termIndex = new HashMap<String,String>();
+	boolean isIndexed = false;
+	public void index() {
+		if (isIndexed)
+			return;
+		for (Node n : shard.getNodes()) {
+			String nid = n.getId();
+			termIndex.put(n.getLabel(), nid);
+			//System.out.println("indexing: "+n.getLabel()+" "+nid);
+			for (Statement s : shard.getStatementsForNode(nid)) {
+				if (s instanceof LinkStatement) {
+					LinkStatement ls = (LinkStatement)s;
+					if (ls.isXref()) {
+						termIndex.put(ls.getTargetId(), nid);
+					}
+				}
+			}
+			// TODO: xrefs
+		}
+		System.err.println("index size="+termIndex.size());
+		isIndexed = true;
+	}
+	
+	
+}

Modified: obdapi/trunk/OBDAPI/src/org/obd/parser/ZFINGenotypePhenotypeParser.java
===================================================================
--- obdapi/trunk/OBDAPI/src/org/obd/parser/ZFINGenotypePhenotypeParser.java	2008-01-28 23:54:26 UTC (rev 1421)
+++ obdapi/trunk/OBDAPI/src/org/obd/parser/ZFINGenotypePhenotypeParser.java	2008-01-29 00:54:04 UTC (rev 1422)
@@ -18,7 +18,11 @@
 
 	protected String src = "ZFIN";
 	private String taxId = "NCBITax:7955";
+	
+	protected String defaultURL = 
+		"http://zfin.org/data_transfer/Downloads/phenotype.txt";
 
+
 	public ZFINGenotypePhenotypeParser() {
 		super();
 	}


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