Author: kono
Date: 2009-03-12 17:44:16 -0700 (Thu, 12 Mar 2009)
New Revision: 16255
Added:
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/lib/cxf-2.1.4.jar
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/lib/ebeye_cxf.jar
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/lib/ols_cxf.jar
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/lib/psicquic_cxf.jar
Removed:
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/lib/cxf-2.1.3.jar
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/lib/ebeye.jar
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/lib/intact_cxf.jar
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/lib/irefindex.jar
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/lib/mint.jar
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/lib/ols2.jar
Modified:
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/src/org/cytoscape/webservice/psicquic/ontology/OLSUtil.java
Log:
Library file renewed.
Deleted: csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/lib/cxf-2.1.3.jar
===================================================================
(Binary files differ)
Added: csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/lib/cxf-2.1.4.jar
===================================================================
(Binary files differ)
Property changes on:
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/lib/cxf-2.1.4.jar
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Deleted: csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/lib/ebeye.jar
===================================================================
(Binary files differ)
Added: csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/lib/ebeye_cxf.jar
===================================================================
(Binary files differ)
Property changes on:
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/lib/ebeye_cxf.jar
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Deleted: csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/lib/intact_cxf.jar
===================================================================
(Binary files differ)
Deleted: csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/lib/irefindex.jar
===================================================================
(Binary files differ)
Deleted: csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/lib/mint.jar
===================================================================
(Binary files differ)
Deleted: csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/lib/ols2.jar
===================================================================
(Binary files differ)
Added: csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/lib/ols_cxf.jar
===================================================================
(Binary files differ)
Property changes on:
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/lib/ols_cxf.jar
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/lib/psicquic_cxf.jar
===================================================================
(Binary files differ)
Property changes on:
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/lib/psicquic_cxf.jar
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Modified:
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/src/org/cytoscape/webservice/psicquic/ontology/OLSUtil.java
===================================================================
---
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/src/org/cytoscape/webservice/psicquic/ontology/OLSUtil.java
2009-03-12 23:23:05 UTC (rev 16254)
+++
csplugins/trunk/ucsd/kono/PSIQUICUniversalClient/src/org/cytoscape/webservice/psicquic/ontology/OLSUtil.java
2009-03-13 00:44:16 UTC (rev 16255)
@@ -1,9 +1,7 @@
package org.cytoscape.webservice.psicquic.ontology;
import java.io.IOException;
-import java.rmi.RemoteException;
import java.util.ArrayList;
-import java.util.HashMap;
import java.util.List;
import java.util.Map;
@@ -16,102 +14,100 @@
import uk.ac.ebi.ook.web.services.QueryService;
import uk.ac.ebi.ook.web.services.QueryServiceLocator;
-
-
public class OLSUtil {
-
+
// Ontology Name for PSI-MI
private static final String PSIMI = "MI";
-
+
private static final String ITR_TYPE = "MI:0190";
-
+
private static final String DB_ROOT = "MI:0444";
-
+
private static Query ols;
private static EBISearchService eport;
-
-
+
static {
QueryService locator = new QueryServiceLocator();
EBISearchService_Service ebeye = new EBISearchService_Service();
eport = ebeye.getEBISearchServiceHttpPort();
- try {
- ols = locator.getOntologyQuery();
- } catch (ServiceException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
+ try {
+ ols = locator.getOntologyQuery();
+ } catch (ServiceException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+
}
-
- }
-
+
public static List<String> keywordSearch(String key) {
int count = eport.getNumberOfResults("uniprot", key);
-
- List<String> firstResult = eport.getResultsIds("uniprot", key,
0, 100).getString();
- if(count <= 100) {
- return firstResult;
+
+ List<String> firstResult = eport.getResultsIds("uniprot", key,
0, 100)
+ .getString();
+ if (count <= 100) {
+ return firstResult;
} else {
List<String> result = new
ArrayList<String>(firstResult);
int index = 100;
- while(index<count) {
- result.addAll(eport.getResultsIds("uniprot",
key, index, 100).getString());
+ while (index < count) {
+ result.addAll(eport.getResultsIds("uniprot",
key, index, 100)
+ .getString());
index = index + 100;
}
return result;
}
}
-
public static void getOntologyList() throws IOException {
-
+
Map terms = ols.getOntologyNames();
-
- for(Object key: terms.keySet()) {
+
+ for (Object key : terms.keySet()) {
System.out.println("(key, val) = " + key + ", " +
terms.get(key));
}
-
+
ArrayOfString domain = eport.listDomains();
-
+
List<String> list = domain.getString();
- for(String d : list) {
+ for (String d : list) {
System.out.println("domain = " + d);
}
-
+
System.out.println("list size = " + terms.keySet().size());
System.out.println("V = " + ols.getVersion());
-
+
List<String> searchRes = keywordSearch("p53 human");
-
- for(String d : searchRes) {
+
+ for (String d : searchRes) {
System.out.println(d);
}
}
-
+
public static Map<String, String> getSynonymMap(List<String> idList) {
-
+
return null;
}
-
- public static Map<String, String> getAllChildren(String term) throws
IOException {
+
+ public static Map<String, String> getAllChildren(String term)
+ throws IOException {
return ols.getTermChildren(term, PSIMI, -1, null);
-
-//
-// System.out.println("========================================");
-// Map<String, String> rootTerms = ols.getTermChildren(ITR_TYPE,
PSIMI, 1, null);
-// for(String key: rootTerms.keySet()) {
-// System.out.println("(key, root val) = " + key + ", " +
rootTerms.get(key));
-// }
-
+
+ //
+ //
System.out.println("========================================");
+ // Map<String, String> rootTerms =
ols.getTermChildren(ITR_TYPE, PSIMI,
+ // 1, null);
+ // for(String key: rootTerms.keySet()) {
+ // System.out.println("(key, root val) = " + key + ", " +
+ // rootTerms.get(key));
+ // }
+
}
-
+
public static String toCanonicalName() throws IOException {
- Map<String, String> dbTerms = ols.getTermChildren(DB_ROOT,
PSIMI, -1, null);
-
-
-
+ Map<String, String> dbTerms = ols.getTermChildren(DB_ROOT,
PSIMI, -1,
+ null);
+
return null;
}
-
-
}
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