From nopushneva at pub.open-bio.org Mon Nov 1 14:16:32 2004
From: nopushneva at pub.open-bio.org (Nina Opushneva)
Date: Mon Nov 1 13:45:49 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200411011916.iA1JGWsC017573@pub.open-bio.org>
nopushneva
Mon Nov 1 14:16:28 EST 2004
Update of /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/lib
In directory pub.open-bio.org:/tmp/cvs-serv17507
Added Files:
activation.jar commons-logging.jar icu4j.jar
jakarta-oro-2.0.5.jar jdom.jar jena.jar junit.jar
log4j-1.2.4.jar mail.jar rdf-api-2001-01-19.jar xercesImpl.jar
xml-apis.jar
Log Message:
The temporary restore
moby-live/Agents/MOBY-S/RDFAgent/lib activation.jar,1.2,1.3 commons-logging.jar,1.2,1.3 icu4j.jar,1.2,1.3 jakarta-oro-2.0.5.jar,1.2,1.3 jdom.jar,1.2,1.3 jena.jar,1.2,1.3 junit.jar,1.2,1.3 log4j-1.2.4.jar,NONE,1.1 mail.jar,1.2,1.3 rdf-api-2001-01-19.jar,1.2,1.3 xercesImpl.jar,1.2,1.3 xml-apis.jar,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/lib/activation.jar,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
Binary files /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/lib/activation.jar 2004/10/19 00:10:04 1.2 and /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/lib/activation.jar 2004/11/01 19:16:26 1.3 differ
rcsdiff: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/lib/activation.jar: diff failed
===================================================================
RCS file: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/lib/commons-logging.jar,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/lib/icu4j.jar,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/lib/jakarta-oro-2.0.5.jar,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/lib/jdom.jar,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
Binary files /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/lib/jdom.jar 2004/10/19 00:10:05 1.2 and /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/lib/jdom.jar 2004/11/01 19:16:26 1.3 differ
rcsdiff: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/lib/jdom.jar: diff failed
===================================================================
RCS file: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/lib/jena.jar,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/lib/junit.jar,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/lib/mail.jar,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/lib/rdf-api-2001-01-19.jar,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/lib/xercesImpl.jar,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Agents/MOBY-S/RDFAgent/lib/xml-apis.jar,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
From nopushneva at pub.open-bio.org Mon Nov 1 14:21:42 2004
From: nopushneva at pub.open-bio.org (Nina Opushneva)
Date: Mon Nov 1 13:50:58 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200411011921.iA1JLgjh017640@pub.open-bio.org>
nopushneva
Mon Nov 1 14:21:42 EST 2004
Update of /home/repository/moby/moby-live/Java
In directory pub.open-bio.org:/tmp/cvs-serv17614
Modified Files:
build.xml
Log Message:
add target for building RDFagent files
moby-live/Java build.xml,1.8,1.9
===================================================================
RCS file: /home/repository/moby/moby-live/Java/build.xml,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Java/build.xml 2004/10/18 14:35:05 1.8
+++ /home/repository/moby/moby-live/Java/build.xml 2004/11/01 19:21:42 1.9
@@ -31,7 +31,7 @@
-
+
@@ -42,6 +42,7 @@
+
@@ -65,7 +66,8 @@
-
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@@ -176,6 +180,7 @@
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-
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@@ -431,8 +459,53 @@
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From gss at pub.open-bio.org Thu Nov 4 17:21:20 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Nov 4 16:50:18 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200411042221.iA4MLKue031258@pub.open-bio.org>
gss
Thu Nov 4 17:21:20 EST 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/tools
In directory pub.open-bio.org:/tmp/cvs-serv31225/src/org/smoby/graph/tools
Modified Files:
MOBYProviderXMLGenerator.java MOBYProviderVisitor.java
MOBYProviderTraverser.java
Added Files:
MOBYProviderVisitorAdapter.java
Log Message:
Experimental package
moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/tools MOBYProviderVisitorAdapter.java,NONE,1.1 MOBYProviderXMLGenerator.java,1.1,1.2 MOBYProviderVisitor.java,1.1,1.2 MOBYProviderTraverser.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/tools/MOBYProviderXMLGenerator.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/tools/MOBYProviderXMLGenerator.java 2004/07/29 23:34:45 1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/tools/MOBYProviderXMLGenerator.java 2004/11/04 22:21:19 1.2
@@ -1,6 +1,7 @@
package org.smoby.graph.tools;
import org.smoby.graph.*;
+
import java.io.*;
public class MOBYProviderXMLGenerator implements MOBYProviderVisitor
@@ -45,11 +46,11 @@
}
public boolean visitGraphBegin(MOBYGraph graph) {
- return start("graph", null, false);
+ return start("moby-graph", null, false);
}
public void visitGraphEnd(MOBYGraph graph) {
- end("graph");
+ end("moby-graph");
}
public boolean visitHasMappingBegin(MOBYGraphNode graphNode) {
@@ -159,4 +160,18 @@
{
currentIndent -= 4;
}
+
+ public boolean visitSubjectPropValStmtsBegin(MOBYCollection stmts) throws MOBYProviderTraversalException {
+ return false;
+ }
+
+ public void visitSubjectPropValStmtsEnd(MOBYCollection stmts) throws MOBYProviderTraversalException {
+ }
+
+ public boolean visitSubjectPropValStmtBegin(MOBYPropertyValueStatement stmt) throws MOBYProviderTraversalException {
+ return false;
+ }
+
+ public void visitSubjectPropValStmtEnd(MOBYPropertyValueStatement stmt) throws MOBYProviderTraversalException {
+ }
}
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/tools/MOBYProviderVisitor.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/tools/MOBYProviderVisitor.java 2004/07/29 23:34:45 1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/tools/MOBYProviderVisitor.java 2004/11/04 22:21:19 1.2
@@ -8,41 +8,48 @@
//
public boolean visitProviderBegin(MOBYProvider provider)
throws MOBYProviderTraversalException;
- public void visitProviderEnd(MOBYProvider provider);
+ public void visitProviderEnd(MOBYProvider provider)
+ throws MOBYProviderTraversalException;
// Visitation of the collection of things the provider operates on
//
public boolean visitOperatesOnBegin(MOBYCollection subgraphs)
throws MOBYProviderTraversalException;
- public void visitOperatesOnEnd(MOBYCollection subgraphs);
+ public void visitOperatesOnEnd(MOBYCollection subgraphs)
+ throws MOBYProviderTraversalException;
// Visitation of an operatesOn subgraph
//
public boolean visitGraphBegin(MOBYGraph graph)
throws MOBYProviderTraversalException;
- public void visitGraphEnd(MOBYGraph graph);
+ public void visitGraphEnd(MOBYGraph graph)
+ throws MOBYProviderTraversalException;
// Visitation of a hasMapping
//
public boolean visitHasMappingBegin(MOBYGraphNode graphNode)
throws MOBYProviderTraversalException;
- public void visitHasMappingEnd(MOBYGraphNode graphNode);
+ public void visitHasMappingEnd(MOBYGraphNode graphNode)
+ throws MOBYProviderTraversalException;
// Visitation of a subject
//
public boolean visitSubjectBegin(MOBYSubject subject)
throws MOBYProviderTraversalException;
- public void visitSubjectEnd(MOBYSubject subject);
+ public void visitSubjectEnd(MOBYSubject subject)
+ throws MOBYProviderTraversalException;
// Visitation of a set of property value statements
//
- public boolean visitPropValStmtsBegin(MOBYCollection stmts)
+ public boolean visitSubjectPropValStmtsBegin(MOBYCollection stmts)
+ throws MOBYProviderTraversalException;
+ public void visitSubjectPropValStmtsEnd(MOBYCollection stmts)
throws MOBYProviderTraversalException;
- public void visitPropValStmtsEnd(MOBYCollection stmts);
// Visitation of a given property value statement
//
- public boolean visitPropValStmtBegin(MOBYPropertyValueStatement stmt)
+ public boolean visitSubjectPropValStmtBegin(MOBYPropertyValueStatement stmt)
+ throws MOBYProviderTraversalException;
+ public void visitSubjectPropValStmtEnd(MOBYPropertyValueStatement stmt)
throws MOBYProviderTraversalException;
- public void visitPropValStmtEnd(MOBYPropertyValueStatement stmt);
}
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/tools/MOBYProviderTraverser.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/tools/MOBYProviderTraverser.java 2004/07/29 23:34:45 1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/tools/MOBYProviderTraverser.java 2004/11/04 22:21:19 1.2
@@ -7,6 +7,13 @@
public class MOBYProviderTraverser
{
+ public void traverse(MOBYProvider provider, MOBYProviderVisitor visitor)
+ {
+ try {
+ traverse(provider, visitor, false);
+ } catch (MOBYProviderTraversalException e) {}
+ }
+
/**
* Traverse the given provider, visiting its components with the
* given visitor.
@@ -16,7 +23,9 @@
* @return whether or not the visitor said to stop before the
* entire provider graph was traversed
*/
- private void traverse(MOBYProvider provider, MOBYProviderVisitor visitor)
+ public void traverse(MOBYProvider provider, MOBYProviderVisitor visitor,
+ boolean rethrowExceptions)
+ throws MOBYProviderTraversalException
{
try
{
@@ -54,7 +63,12 @@
}
// Visitors indicate that traversal should stop by throwing
// provider traversal exceptions.
- catch (MOBYProviderTraversalException e) {}
+ catch (MOBYProviderTraversalException e)
+ {
+ if (rethrowExceptions) {
+ throw e;
+ }
+ }
}
/**
@@ -96,7 +110,7 @@
if (keepGoing)
{
MOBYCollection coll = subject.getPropertyValueStatements();
- keepGoing = visitor.visitPropValStmtsBegin(coll);
+ keepGoing = visitor.visitSubjectPropValStmtsBegin(coll);
if (keepGoing)
{
Iterator it = subject.getPropertyValueStatements().iterator();
@@ -104,12 +118,12 @@
{
MOBYPropertyValueStatement stmt =
(MOBYPropertyValueStatement) it.next();
- if (visitor.visitPropValStmtBegin(stmt)) {
- visitor.visitPropValStmtEnd(stmt);
+ if (visitor.visitSubjectPropValStmtBegin(stmt)) {
+ visitor.visitSubjectPropValStmtEnd(stmt);
}
}
}
- visitor.visitPropValStmtsEnd(coll);
+ visitor.visitSubjectPropValStmtsEnd(coll);
}
if (keepGoing)
@@ -140,15 +154,15 @@
return keepGoing;
}
- public static void main(String[] args) throws Exception
- {
- File f = new File("get-individuals.n3");
- Parser parser = Parser.forN3File(f);
- MOBYProvider provider = parser.parseProvider();
-
- MOBYProviderTraverser traverser = new MOBYProviderTraverser();
- MOBYProviderXMLGenerator printer = new MOBYProviderXMLGenerator();
-
- traverser.traverse(provider, printer);
- }
+// public static void main(String[] args) throws Exception
+// {
+// File f = new File("get-individuals.n3");
+// Parser parser = Parser.forN3File(f);
+// MOBYProvider provider = parser.parseProvider();
+//
+// MOBYProviderTraverser traverser = new MOBYProviderTraverser();
+// MOBYProviderXMLGenerator printer = new MOBYProviderXMLGenerator();
+//
+// traverser.traverse(provider, printer);
+// }
}
From gss at pub.open-bio.org Thu Nov 4 17:22:29 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Nov 4 16:51:24 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200411042222.iA4MMT1F031299@pub.open-bio.org>
gss
Thu Nov 4 17:22:29 EST 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/http
In directory pub.open-bio.org:/tmp/cvs-serv31274/src/org/smoby/http
Modified Files:
HTTPRequest.java
Log Message:
Misc fixes
moby-live/S-MOBY/ref-impl/core/src/org/smoby/http HTTPRequest.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/http/HTTPRequest.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/http/HTTPRequest.java 2004/05/24 22:05:35 1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/http/HTTPRequest.java 2004/11/04 22:22:29 1.2
@@ -16,18 +16,21 @@
public class HTTPRequest
{
/**
- * Constant meaning to use HTTP GET as the method for communicating
- * with the registration server.
+ * Constant meaning to use HTTP GET as the method
*/
public final static int HTTP_GET = 0;
/**
- * Constant meaning to use HTTP POST as the method for communicating
- * with the registration server.
+ * Constant meaning to use HTTP POST as the method
*/
public final static int HTTP_POST = 1;
/**
+ * Constant meaning to use HTTP HEAD as the method
+ */
+ public final static int HTTP_HEAD = 2;
+
+ /**
* The URL of the server to be contacted
*/
private String serverURL = null;
@@ -63,6 +66,11 @@
return new HTTPRequest(serverURL, HTTP_POST);
}
+ public static HTTPRequest newHeadRequest(String uri)
+ {
+ return new HTTPRequest(uri, HTTP_HEAD);
+ }
+
public void addParameter(String paramName, String paramValue)
{
params.add(new NameValuePair(paramName, paramValue));
@@ -97,20 +105,27 @@
{
HttpMethod methodObject = null;
- if (method == HTTP_GET) {
- methodObject = new GetMethod(getURLString());
- }
- else if (method == HTTP_POST)
- {
- methodObject = new PostMethod(getURLString());
- NameValuePair[] paramArray = new NameValuePair[params.size()];
- Iterator it = params.iterator();
- for (int i = 0; i < paramArray.length; i++)
- {
- paramArray[i] = (NameValuePair) it.next();
- }
- ((PostMethod) methodObject).setRequestBody(paramArray);
- }
+ switch (method)
+ {
+ case HTTP_GET :
+ methodObject = new GetMethod(getURLString());
+ break;
+
+ case HTTP_POST :
+ methodObject = new PostMethod(getURLString());
+ NameValuePair[] paramArray = new NameValuePair[params.size()];
+ Iterator it = params.iterator();
+ for (int i = 0; i < paramArray.length; i++)
+ {
+ paramArray[i] = (NameValuePair) it.next();
+ }
+ ((PostMethod) methodObject).setRequestBody(paramArray);
+ break;
+
+ case HTTP_HEAD :
+ methodObject = new HeadMethod(getURLString());
+ break;
+ }
// Add request headers to the method
//
@@ -136,8 +151,8 @@
try {
methodObject.getResponseBodyAsString();
- } catch (IOException e) {
- throw new HTTPException("Couldn't get response body", e);
+ } catch (Throwable t) {
+ throw new HTTPException("Couldn't get response body", t);
}
methodObject.releaseConnection();
From gss at pub.open-bio.org Thu Nov 4 17:23:10 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Nov 4 16:52:06 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200411042223.iA4MNAFp031337@pub.open-bio.org>
gss
Thu Nov 4 17:23:10 EST 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser
In directory pub.open-bio.org:/tmp/cvs-serv31312/src/org/smoby/parser
Modified Files:
Parser.java
Log Message:
Misc
moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser Parser.java,1.7,1.8
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.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/core/src/org/smoby/parser/Parser.java 2004/07/29 23:35:09 1.7
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/Parser.java 2004/11/04 22:23:10 1.8
@@ -34,6 +34,12 @@
* plus all statements that are reachable from it.
*/
private List subModels = new ArrayList();
+
+ /**
+ * A map relating a property's URI to an Inference model derived from
+ * its base model
+ */
+ private Map cachedPropertyModels = new HashMap();
/**
* Create and return a parser for parsing an N3 file
@@ -426,13 +432,20 @@
*/
private InfModel getPropertyModel(Property p)
{
- Model model = ModelRetriever.retrieveModel(p.getURI());
+ InfModel cachedModel = (InfModel)
+ cachedPropertyModels.get(p.getURI());
- if (model == null) {
- return null;
- } else {
- return ModelFactory.createRDFSModel(model);
+ if (cachedModel == null)
+ {
+ Model model = ModelRetriever.retrieveModel(p.getURI());
+
+ if (model != null)
+ {
+ cachedModel = ModelFactory.createRDFSModel(model);
+ cachedPropertyModels.put(p.getURI(), cachedModel);
+ }
}
+ return cachedModel;
}
/**
From gss at pub.open-bio.org Thu Nov 4 17:23:34 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Nov 4 16:52:30 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200411042223.iA4MNYSr031375@pub.open-bio.org>
gss
Thu Nov 4 17:23:33 EST 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/servlet
In directory pub.open-bio.org:/tmp/cvs-serv31350/src/org/smoby/servlet
Modified Files:
AbstractMobyServlet.java
Log Message:
Misc
moby-live/S-MOBY/ref-impl/core/src/org/smoby/servlet AbstractMobyServlet.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/servlet/AbstractMobyServlet.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/servlet/AbstractMobyServlet.java 2004/05/24 22:05:34 1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/servlet/AbstractMobyServlet.java 2004/11/04 22:23:33 1.2
@@ -100,10 +100,11 @@
try
{
- // Read the invocation graph from the "graph" parameter
- // and parse it into a MOBYGraph object
+ // Read the invocation graph from the MOBY.GRAPH_PARAMETER_NAME
+ // parameter and parse it into a MOBYGraph object
//
- String graphString = ParamReader.getParameter("graph", request);
+ String graphString = ParamReader.getParameter(
+ MOBY.GRAPH_PARAMETER_NAME, request);
Parser parser = Parser.forString(
graphString, Parser.LANGUAGE_RDF_XML);
MOBYProvider provider = parser.parseProvider();
From gss at pub.open-bio.org Thu Nov 4 17:25:30 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Nov 4 16:54:24 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200411042225.iA4MPUr5031418@pub.open-bio.org>
gss
Thu Nov 4 17:25:30 EST 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv31393/src/org/smoby/vocabulary
Modified Files:
MOBY.java
Log Message:
Added properties for inputURI and outputURI
moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary MOBY.java,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/MOBY.java,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/MOBY.java 2004/07/19 21:22:09 1.6
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/MOBY.java 2004/11/04 22:25:30 1.7
@@ -7,6 +7,14 @@
{
public final static String IF_MODIFIED_HEADER = "If-Modified-Since";
public final static String LAST_MODIFIED_HEADER = "Last-Modified";
+
+ /**
+ * When doing an HTTP POST to a Semantic MOBY provider (i.e.
+ * engaging the provider), the graph that the provider is to
+ * operate on is stored in a parameter with this name, whose
+ * value is a serialized RDF/XML graph.
+ */
+ public final static String GRAPH_PARAMETER_NAME = "graph";
public static String getURI()
{
@@ -31,6 +39,8 @@
public static final Property name = property(getURI(), "name");
public static final Property oneLineDescription = property(getURI(), "oneLineDescription");
public static final Property aboutURI = property(getURI(), "aboutURI");
+ public static final Property inputURI = property(getURI(), "inputURI");
+ public static final Property outputURI = property(getURI(), "outputURI");
public static final Property operatesOn = property(getURI(), "operatesOn");
public static final Property hasMapping = property(getURI(), "hasMapping");
public static final Property mapsTo = property(getURI(), "mapsTo");
From gss at pub.open-bio.org Thu Nov 4 17:26:48 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Nov 4 16:55:43 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200411042226.iA4MQmeQ031460@pub.open-bio.org>
gss
Thu Nov 4 17:26:48 EST 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/jsp
In directory pub.open-bio.org:/tmp/cvs-serv31436/WebRoot/jsp
Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/jsp added to the repository
moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/jsp - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/jsp/RCS/-,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/jsp/RCS/New,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/jsp/RCS/directory,v: No such file or directory
From gss at pub.open-bio.org Thu Nov 4 17:26:49 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Nov 4 16:55:46 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200411042226.iA4MQnG3031494@pub.open-bio.org>
gss
Thu Nov 4 17:26:49 EST 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/jsp
In directory pub.open-bio.org:/tmp/cvs-serv31473/WebRoot/jsp
Added Files:
display.jsp display-redirector.jsp
Log Message:
Utility JSPs
moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/jsp display.jsp,NONE,1.1 display-redirector.jsp,NONE,1.1
From gss at pub.open-bio.org Thu Nov 4 17:27:42 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu Nov 4 16:56:37 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200411042227.iA4MRgnl031548@pub.open-bio.org>
gss
Thu Nov 4 17:27:42 EST 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv31523/WebRoot
Modified Files:
index.html
Log Message:
Added text to enter * for all providers
moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot index.html,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/index.html,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/index.html 2004/07/21 22:35:25 1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/index.html 2004/11/04 22:27:42 1.4
@@ -24,7 +24,11 @@
Type any terms into the boxes above and press Search
-(for example type 'hello' (without quotes) into the Provider box)
+(for example type 'hello' (without quotes) into the Provider field,
+
+or to see all providers, type just an asterisk (*) into the
+
+Provider field and leave the other fields blank)