[MOBY-guts] biomoby commit
Gary Schlitz
gss at pub.open-bio.org
Wed May 19 18:26:52 UTC 2004
gss
Wed May 19 14:26:52 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets
In directory pub.open-bio.org:/tmp/cvs-serv953/src/com/acmepubs/servlets
Modified Files:
CitationSearchServlet.java
Log Message:
Incorporation of new parser
moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets CitationSearchServlet.java,1.7,1.8
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java 2004/04/02 00:03:39 1.7
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java 2004/05/19 18:26:52 1.8
@@ -2,17 +2,13 @@
import java.io.*;
import java.util.*;
-
import javax.servlet.*;
import javax.servlet.http.*;
-
-import org.go.vocabulary.Go;
-import org.smoby.tools.common.graph.MOBYGraph;
-import org.smoby.tools.common.vocabulary.MOBY;
-import org.smoby.tools.server.servlet.AbstractMobyServlet;
-import com.acmepubs.vocabulary.AcmePubs;
-
-import com.hp.hpl.jena.rdf.model.*;
+import org.go.vocabulary.*;
+import org.smoby.servlet.*;
+import org.smoby.graph.*;
+import org.smoby.vocabulary.*;
+import com.acmepubs.vocabulary.*;
/**
* This class is a concrete subclass of AbstractMobyServlet that illustrates
@@ -39,47 +35,47 @@
* a gene symbol and returning a URL for querying the
* SGD database for literature pertaining to that URL.
*/
- protected void handleRequest(MOBYGraph graph)
+ protected void handleRequest(MOBYProvider graph)
{
// Retrieve the subject of the moby:operatesOn statement (there is only
// one operatesOn statement in a valid MOBY graph)
//
- Resource mobyGraphSubject = (Resource) graph.getOperatesOnStmt().getObject();
-
- // There may be multiple moby:hasMapping statements. For each one,
- // map its geneSymbol to a literatureGuideURL
- //
- StmtIterator it = graph.getModel().listStatements(
- mobyGraphSubject, MOBY.hasMapping, (RDFNode) null);
-
- while (it.hasNext())
- {
- try
- {
- Statement hasMappingStmt = it.nextStatement();
- Resource mobySubject = (Resource) hasMappingStmt.getObject();
-
- Statement geneSymbolStmt =
- getFirstStatement(graph, mobySubject, AcmePubs.geneSymbol, null);
-
- String geneSymbol = geneSymbolStmt.getString();
-
- Statement mapsToStmt =
- getFirstStatement(graph, mobySubject, MOBY.mapsTo, null);
-
- Resource mobyObject = (Resource) mapsToStmt.getObject();
-
- Statement literatureGuideURLStmt =
- getFirstStatement(graph, mobyObject, AcmePubs.literatureGuideURL, null);
-
- String baseURI = "http://db.yeastgenome.org/cgi-bin/SGD/reference/geneinfo.pl?locus=";
- literatureGuideURLStmt.changeObject(baseURI + geneSymbol);
- }
- catch (Throwable t)
- {
- // Something went wrong, so proceed to next hasMapping statement
- }
- }
+// Resource mobyGraphSubject = (Resource) graph.getOperatesOnStmt().getObject();
+//
+// // There may be multiple moby:hasMapping statements. For each one,
+// // map its geneSymbol to a literatureGuideURL
+// //
+// StmtIterator it = graph.getModel().listStatements(
+// mobyGraphSubject, MOBY.hasMapping, (RDFNode) null);
+//
+// while (it.hasNext())
+// {
+// try
+// {
+// Statement hasMappingStmt = it.nextStatement();
+// Resource mobySubject = (Resource) hasMappingStmt.getObject();
+//
+// Statement geneSymbolStmt =
+// getFirstStatement(graph, mobySubject, AcmePubs.geneSymbol, null);
+//
+// String geneSymbol = geneSymbolStmt.getString();
+//
+// Statement mapsToStmt =
+// getFirstStatement(graph, mobySubject, MOBY.mapsTo, null);
+//
+// Resource mobyObject = (Resource) mapsToStmt.getObject();
+//
+// Statement literatureGuideURLStmt =
+// getFirstStatement(graph, mobyObject, AcmePubs.literatureGuideURL, null);
+//
+// String baseURI = "http://db.yeastgenome.org/cgi-bin/SGD/reference/geneinfo.pl?locus=";
+// literatureGuideURLStmt.changeObject(baseURI + geneSymbol);
+// }
+// catch (Throwable t)
+// {
+// // Something went wrong, so proceed to next hasMapping statement
+// }
+// }
}
/**
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