[Obo-svn-commit] SF.net SVN: obo:[3038] OBD-WS/trunk/src/org

[<car...@us...>]

Revision: 3038
          http://obo.svn.sourceforge.net/obo/?rev=3038&view=rev
Author:   cartik73
Date:     2010-01-15 19:46:19 +0000 (Fri, 15 Jan 2010)

Log Message:
-----------
Changed code to improve the translations of the labels of relational qualities associated with secondary entities

Modified Paths:
--------------
    OBD-WS/trunk/src/org/obd/ws/resources/PhenotypeDetailsResource.java
    OBD-WS/trunk/src/org/obd/ws/resources/PhenotypeSummaryResource.java
    OBD-WS/trunk/src/org/obd/ws/util/TaxonomyBuilder.java
    OBD-WS/trunk/src/org/phenoscape/obd/OBDQuery.java

Modified: OBD-WS/trunk/src/org/obd/ws/resources/PhenotypeDetailsResource.java
===================================================================
--- OBD-WS/trunk/src/org/obd/ws/resources/PhenotypeDetailsResource.java	2010-01-15 18:26:23 UTC (rev 3037)
+++ OBD-WS/trunk/src/org/obd/ws/resources/PhenotypeDetailsResource.java	2010-01-15 19:46:19 UTC (rev 3038)
@@ -360,7 +360,10 @@
 					String relatedEntity = phenotype.getRelatedEntity();
 					if(relatedEntityId != null && relatedEntity != null){
 						qualityObj.put("id", qualityId + "^OBO_REL:towards(" + relatedEntityId + ")");
-						qualityObj.put("name", quality + " towards " + relatedEntity);
+						if(quality.trim().endsWith("from") || quality.trim().endsWith("to") || quality.trim().endsWith("with"))
+							qualityObj.put("name", quality + " " + relatedEntity);
+						else
+							qualityObj.put("name", quality + " towards " + relatedEntity);
 					}
 					else{
 						qualityObj.put("id", qualityId);

Modified: OBD-WS/trunk/src/org/obd/ws/resources/PhenotypeSummaryResource.java
===================================================================
--- OBD-WS/trunk/src/org/obd/ws/resources/PhenotypeSummaryResource.java	2010-01-15 18:26:23 UTC (rev 3037)
+++ OBD-WS/trunk/src/org/obd/ws/resources/PhenotypeSummaryResource.java	2010-01-15 19:46:19 UTC (rev 3038)
@@ -312,8 +312,12 @@
 		Set<String> qAnnots = annots.get(2);
 		Set<String> pAnnots = annots.get(3);
 		
-		if(relatedEntityId != null && relatedEntity != null)
-			qAnnots.add(qualityId + "^OBO_REL:towards(" + relatedEntityId + ")\t" + quality + " towards " + relatedEntity);
+		if(relatedEntityId != null && relatedEntity != null){
+			if(quality.trim().endsWith("from") || quality.trim().endsWith("to") || quality.trim().endsWith("with"))
+				qAnnots.add(qualityId + "^OBO_REL:towards(" + relatedEntityId + ")\t" + quality + " " + relatedEntity);
+			else
+				qAnnots.add(qualityId + "^OBO_REL:towards(" + relatedEntityId + ")\t" + quality + " towards " + relatedEntity);
+		}
 		else if(count != null)
 			qAnnots.add(qualityId + "^PHENOSCAPE:has_count(" + count + ")\t" + quality + " of " + count);
 		else

Modified: OBD-WS/trunk/src/org/obd/ws/util/TaxonomyBuilder.java
===================================================================
--- OBD-WS/trunk/src/org/obd/ws/util/TaxonomyBuilder.java	2010-01-15 18:26:23 UTC (rev 3037)
+++ OBD-WS/trunk/src/org/obd/ws/util/TaxonomyBuilder.java	2010-01-15 19:46:19 UTC (rev 3038)
@@ -199,6 +199,7 @@
 	private List<PhenotypeDTO> consolidateReifIds(PhenotypeDTO phenotype, List<PhenotypeDTO> listOfEqcrLists, boolean isLeafNode) {
 		    for (PhenotypeDTO otherPhenotype : listOfEqcrLists) {
 			if(isPhenotypeSameAsEqcrList(phenotype, otherPhenotype)){
+				int index = listOfEqcrLists.indexOf(otherPhenotype);
 				if(isLeafNode){
 					for (String id : phenotype.getReifIds()) {
 					    otherPhenotype.addReifId(id);
@@ -214,6 +215,8 @@
 				        otherPhenotype.removeReifId(id);
 				    }
 				}
+				listOfEqcrLists.remove(index);
+				listOfEqcrLists.add(index, otherPhenotype);
 				return listOfEqcrLists;
 			}
 		}

Modified: OBD-WS/trunk/src/org/phenoscape/obd/OBDQuery.java
===================================================================
--- OBD-WS/trunk/src/org/phenoscape/obd/OBDQuery.java	2010-01-15 18:26:23 UTC (rev 3037)
+++ OBD-WS/trunk/src/org/phenoscape/obd/OBDQuery.java	2010-01-15 19:46:19 UTC (rev 3038)
@@ -75,6 +75,7 @@
         POSTCOMP_RELATIONS.put("posterior_to", "posterior to");
         POSTCOMP_RELATIONS.put("BSPO:0000099", "posterior to");
         POSTCOMP_RELATIONS.put("adjacent_to", "adjacent to");
+        POSTCOMP_RELATIONS.put("OBO_REL:adjacent_to", "adjacent to");
     }
 
 	/**
@@ -206,9 +207,12 @@
 				if(quality == null || quality.length() == 0){
 					quality = semanticLabel(qualityId);
 				}
-				if(relEntity != null)
-					quality += " towards " + relEntity; 
-				
+				if(relEntityId != null && relEntity != null){
+					if(quality.trim().endsWith("from") || quality.trim().endsWith("to") || quality.trim().endsWith("with"))
+						quality += " " + relEntity;
+					else
+						quality += " towards " + relEntity;
+				}
 				dto.setEntityId(entityId);
 				dto.setEntity(entity);
 				dto.setQualityId(qualityId);


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