+
Generated: ${TODAY_LONG}]]>
- * As an RDF data structure, this can have one or more elements, each
+ * As an RDF data structure, it can have one or more elements, each
* of which can itself be either a moby:Subject, an RDF data structure,
* or both. This collection of elements is returned by getNestedMappings().
*/
@@ -36,10 +36,11 @@
}
/**
- * Return a resizable, unordered collection of the MOBYNode instances,
- * which are objects of mapsTo statements, whose subjects are this.
+ * Return the collection of direct mappings, i.e. moby:mapsTo statements
+ * whose subject is this.
*/
- public MOBYUnorderedCollection getDirectMappings() {
+ public MOBYUnorderedCollection getDirectMappings()
+ {
return directMappings;
}
}
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/graph/MOBYDescriptor.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/semanticmoby/graph/MOBYDescriptor.java 2004/11/23 00:18:46 1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/graph/MOBYDescriptor.java 2005/03/21 21:29:44 1.2
@@ -3,18 +3,20 @@
import com.hp.hpl.jena.rdf.model.*;
/**
- * The MOBYDescriptor class represents things that are available
- * at a URI.
+ * The MOBYDescriptor class represents things that are also
+ * represented as a Jena Model
*/
public abstract class MOBYDescriptor
{
- protected Model underlying;
protected Resource resource;
+ protected Model model;
- public MOBYDescriptor(Resource resource, Model underlying)
+ public MOBYDescriptor() {}
+
+ public MOBYDescriptor(Resource resource, Model model)
{
this.resource = resource;
- this.underlying = underlying;
+ this.model = model;
}
/**
@@ -28,9 +30,9 @@
/**
* Return the underlying Jena model
*/
- public Model getUnderlying()
+ public Model getModel()
{
- return underlying;
+ return model;
}
/**
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/graph/MOBYProvider.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/semanticmoby/graph/MOBYProvider.java 2004/11/23 00:18:46 1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/graph/MOBYProvider.java 2005/03/21 21:29:44 1.2
@@ -1,7 +1,12 @@
package org.semanticmoby.graph;
import java.io.*;
+
+import org.semanticmoby.tools.Util;
+import org.semanticmoby.vocabulary.MOBY;
+
import com.hp.hpl.jena.rdf.model.*;
+import com.hp.hpl.jena.vocabulary.RDF;
/**
* The Provider class represents a resource that provides a
@@ -9,19 +14,76 @@
*/
public class MOBYProvider extends MOBYDocument
{
- private String name;
- private String oneLineDescription;
- private String moreInfoURI;
+ /**
+ * The statement that asserts this provider is a moby:Provider
+ */
+ private Statement providerStmt;
+
+ /**
+ * The name of the provider; stored in MOBY.name property
+ */
+ private Statement nameStmt;
+
+ /**
+ * A one line description of the provider; stored in the
+ * MOBY.oneLineDescription property
+ */
+ private Statement oneLineDescriptionStmt;
+
+ /**
+ * A URI at which more information can be retrieved about the
+ * provider; stored in the MOBY.moreInfoURI property
+ */
+ private Statement aboutURIStmt;
+
+ /**
+ * An unordered collection of operatesOn subgraphs. Each
+ * subgraph is itself either a MOBYGraph, or a MOBYCollection
+ */
private MOBYUnorderedCollection operatesOn;
- public MOBYProvider(Resource resource, String name, String oneLineDescription,
- String moreInfoURI, MOBYUnorderedCollection operatesOn,
- Model underlying)
+ /**
+ * Constructor for building an instance from scratch (i.e. not one
+ * being parsed from a model).
+ */
+ public MOBYProvider(String uri, String name, String oneLineDescription,
+ String aboutURI)
+ {
+ // Create a model and resource within the model to represent the
+ // URI at which the model is located
+ //
+ this.model = Util.newJenaModel();
+ this.resource = model.createResource(uri);
+
+ // Assert that the provider is a moby:Provider
+ //
+ model.add(providerStmt = model.createStatement(
+ resource, RDF.type, MOBY.Provider));
+
+ // Save the literal properties by creating the corresponding
+ // statements and adding them to the model
+ //
+ model.add(nameStmt = model.createStatement(
+ resource, MOBY.name, name));
+
+ model.add(oneLineDescriptionStmt = model.createStatement(
+ resource, MOBY.oneLineDescription, oneLineDescription));
+
+ model.add(aboutURIStmt = model.createStatement(
+ resource, MOBY.aboutURI, aboutURI));
+ }
+
+ public MOBYProvider(Resource resource,
+ Statement nameStmt,
+ Statement oneLineDescriptionStmt,
+ Statement aboutURIStmt,
+ MOBYUnorderedCollection operatesOn,
+ Model underlying)
{
super(resource, underlying);
- this.name = name;
- this.oneLineDescription = oneLineDescription;
- this.moreInfoURI = moreInfoURI;
+ this.nameStmt = nameStmt;
+ this.oneLineDescriptionStmt = oneLineDescriptionStmt;
+ this.aboutURIStmt = aboutURIStmt;
this.operatesOn = operatesOn;
}
@@ -30,7 +92,11 @@
*/
public String getName()
{
- return name;
+ try {
+ return nameStmt.getObject().toString();
+ } catch (NullPointerException e) {
+ return "";
+ }
}
/**
@@ -38,16 +104,24 @@
*/
public String getOneLineDescription()
{
- return oneLineDescription;
+ try {
+ return oneLineDescriptionStmt.getObject().toString();
+ } catch (NullPointerException e) {
+ return "";
+ }
}
/**
* Return a URI that can be accessed to obtain more information
* about the provider.
*/
- public String getMoreInfoURI()
+ public String getAboutURI()
{
- return moreInfoURI;
+ try {
+ return aboutURIStmt.getObject().toString();
+ } catch (NullPointerException e) {
+ return "";
+ }
}
/**
@@ -63,11 +137,11 @@
{
StringBuffer sb = new StringBuffer();
sb.append("Provider [name=\"");
- sb.append(name);
+ sb.append(getName());
sb.append("\", oneLineDescription=\"");
- sb.append(oneLineDescription);
- sb.append("\", moreInfoURI=");
- sb.append(moreInfoURI);
+ sb.append(getOneLineDescription());
+ sb.append("\", aboutURI=");
+ sb.append(getAboutURI());
sb.append("\"]");
return sb.toString();
@@ -79,6 +153,11 @@
*/
public void serialize(OutputStream out)
{
- underlying.write(out);
+ model.write(out);
+ }
+
+ public void serializeAsN3(OutputStream out)
+ {
+ model.write(out, "N3");
}
}
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/graph/MOBYDocument.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/semanticmoby/graph/MOBYDocument.java 2004/11/23 00:18:46 1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/graph/MOBYDocument.java 2005/03/21 21:29:44 1.2
@@ -8,8 +8,10 @@
*/
public abstract class MOBYDocument extends MOBYDescriptor
{
- public MOBYDocument(Resource resource, Model underlying)
+ public MOBYDocument() {}
+
+ public MOBYDocument(Resource resource, Model model)
{
- super(resource, underlying);
+ super(resource, model);
}
}
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/graph/MOBYOntology.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/semanticmoby/graph/MOBYOntology.java 2004/11/23 00:18:46 1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/graph/MOBYOntology.java 2005/03/21 21:29:44 1.2
@@ -8,7 +8,7 @@
*/
public class MOBYOntology extends MOBYDocument
{
- public MOBYOntology(Resource resource, Model underlying) {
- super(resource, underlying);
+ public MOBYOntology(Resource resource, Model model) {
+ super(resource, model);
}
}
\ No newline at end of file
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/graph/MOBYGraphNode.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/semanticmoby/graph/MOBYGraphNode.java 2004/11/23 00:18:46 1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/graph/MOBYGraphNode.java 2005/03/21 21:29:44 1.2
@@ -8,9 +8,9 @@
*/
public abstract class MOBYGraphNode extends MOBYDescriptor
{
- public MOBYGraphNode(Resource resource, Model underlying)
+ public MOBYGraphNode(Resource resource, Model model)
{
- super(resource, underlying);
+ super(resource, model);
}
/**
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/graph/MOBYObject.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/semanticmoby/graph/MOBYObject.java 2004/11/23 00:18:46 1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/graph/MOBYObject.java 2005/03/21 21:29:44 1.2
@@ -1,5 +1,6 @@
package org.semanticmoby.graph;
+
import com.hp.hpl.jena.rdf.model.*;
/**
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/graph/MOBYMappingElement.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/semanticmoby/graph/MOBYMappingElement.java 2004/11/23 00:18:46 1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/graph/MOBYMappingElement.java 2005/03/21 21:29:44 1.2
@@ -1,5 +1,6 @@
package org.semanticmoby.graph;
+
import com.hp.hpl.jena.rdf.model.*;
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/graph/MOBYOrderedCollection.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/semanticmoby/graph/MOBYOrderedCollection.java 2004/11/23 00:18:46 1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/graph/MOBYOrderedCollection.java 2005/03/21 21:29:44 1.2
@@ -1,22 +1,58 @@
package org.semanticmoby.graph;
import java.util.*;
+
import com.hp.hpl.jena.rdf.model.*;
+/**
+ * A class representing collections that can be resized (i.e.
+ * elements added to or removed from), in which the order of
+ * the elements is defined; corresponds to an RDF Seq
+ */
public class MOBYOrderedCollection extends MOBYResizableCollection
{
- public MOBYOrderedCollection(Resource resource, List elements, Model underlying)
+ /**
+ * Create an instance with no elements
+ * @param resource the resource node that represents this collection
+ * @param underlyingJenaModel the Jena model from which this is stored
+ */
+ public MOBYOrderedCollection(Resource resource,
+ Model underlyingJenaModel)
{
- super(resource, elements, underlying);
+ super(null, resource, underlyingJenaModel);
+ }
+
+ /**
+ * Create an instance with the initial list of elements
+ * @param initialElements the initial elements
+ * @param resource the resource node that represents this collection
+ * @param underlyingJenaModel the Jena model from which this is stored
+ */
+ public MOBYOrderedCollection(List initialElements, Resource resource,
+ Model underlyingJenaModel)
+ {
+ super(initialElements, resource, underlyingJenaModel);
}
- public boolean isOrdered() { return true; }
-
/**
- * Return the object at a given zero-based index.
+ * Return the element at the given index
+ * @param index the zero-based index of the element to retrieve
+ * @return the element
*/
public Object get(int index)
{
return elements.get(index);
}
+
+ /**
+ * Add the given element to the collection so that its new
+ * zero-based index is given index
+ * @param index the zero-based index at which the new element
+ * should be added
+ * @param elementToAdd the element to add
+ */
+ public void add(int index, Object elementToAdd)
+ {
+ elements.add(index, elementToAdd);
+ }
}
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/graph/MOBYUnorderedCollection.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/semanticmoby/graph/MOBYUnorderedCollection.java 2004/11/23 00:18:46 1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/graph/MOBYUnorderedCollection.java 2005/03/21 21:29:44 1.2
@@ -2,27 +2,35 @@
import java.util.*;
-import org.semanticmoby.graph.*;
-
-import com.hp.hpl.jena.rdf.model.Model;
-import com.hp.hpl.jena.rdf.model.Resource;
+import com.hp.hpl.jena.rdf.model.*;
/**
- * A class representing resizable collection of objects, in
- * which the order of the elements is not defined.
+ * A class representing collections that can be resized (i.e.
+ * elements added to or removed from), in which the order of
+ * the elements is not defined; corresponds to an RDF Bag
*/
public class MOBYUnorderedCollection extends MOBYResizableCollection
{
- public MOBYUnorderedCollection(Resource resource, List elements, Model underlying)
+ /**
+ * Create an instance with no elements
+ * @param resource the resource node that represents this collection
+ * @param underlyingJenaModel the Jena model from which this is stored
+ */
+ public MOBYUnorderedCollection(Resource resource,
+ Model underlyingJenaModel)
{
- super(resource, elements, underlying);
+ super(null, resource, underlyingJenaModel);
}
- public boolean isOrdered() { return false; }
-
/**
- * Return whether or not the elements of this collection represent
- * choices (i.e. elements of an enumeration of possible values).
+ * Create an instance with the initial list of elements
+ * @param initialElements the initial elements
+ * @param resource the resource node that represents this collection
+ * @param underlyingJenaModel the Jena model from which this is stored
*/
- public boolean isEnumeration() { return false; }
+ public MOBYUnorderedCollection(List initialElements, Resource resource,
+ Model underlyingJenaModel)
+ {
+ super(initialElements, resource, underlyingJenaModel);
+ }
}
\ No newline at end of file
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/graph/MOBYResizableCollection.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/semanticmoby/graph/MOBYResizableCollection.java 2004/11/23 00:18:46 1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/graph/MOBYResizableCollection.java 2005/03/21 21:29:44 1.2
@@ -2,10 +2,7 @@
import java.util.*;
-import org.semanticmoby.graph.*;
-
-import com.hp.hpl.jena.rdf.model.Model;
-import com.hp.hpl.jena.rdf.model.Resource;
+import com.hp.hpl.jena.rdf.model.*;
/**
* A class representing collections that can be resized (i.e.
@@ -14,16 +11,51 @@
*/
public abstract class MOBYResizableCollection extends MOBYCollection
{
- public MOBYResizableCollection(Resource resource, List elements, Model underlying)
+ /**
+ * Create an instance with no elements
+ * @param resource the resource node that represents this collection
+ * @param model the Jena model from which this is derived
+ */
+ public MOBYResizableCollection(Resource resource, Model model)
{
- super(resource, elements, underlying);
+ super(null, resource, model);
}
-
+
/**
- * Return whether or not this collection is ordered.
+ * Create an instance with the initial list of elements
+ * @param initialElements the initial elements
+ * @param resource the resource node that represents this collection
+ * @param underlyingJenaModel the Jena model from which this is stored
*/
- public abstract boolean isOrdered();
+ public MOBYResizableCollection(List initialElements, Resource resource,
+ Model underlyingJenaModel)
+ {
+ super(initialElements, resource, underlyingJenaModel);
+ }
- public boolean isResizable() { return true; }
- public boolean isFixedSized() { return false; }
+ /**
+ * Add an element to the collection
+ * @param elementToAdd the element to add to the collection
+ */
+ public void add(Object elementToAdd)
+ {
+ elements.add(elementToAdd);
+ }
+
+ /**
+ * Remove an element from the collection
+ * @param elementToRemove the element to remove
+ */
+ public void remove(Object elementToRemove)
+ {
+ elements.remove(elementToRemove);
+ }
+
+ /**
+ * Remove all the elements from the collection
+ */
+ public void clear()
+ {
+ elements.clear();
+ }
}
From gss at pub.open-bio.org Mon Mar 21 16:30:18 2005
From: gss at pub.open-bio.org (Gary Schiltz)
Date: Mon Mar 21 16:14:39 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200503212130.j2LLUIHF008307@pub.open-bio.org>
gss
Mon Mar 21 16:30:18 EST 2005
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/graph/tools
In directory pub.open-bio.org:/tmp/cvs-serv8280/src/org/semanticmoby/graph/tools
Removed Files:
package.html MOBYProviderTraverser.java
MOBYProviderVisitor.java MOBYProviderXMLGenerator.java
MOBYProviderTraversalException.java
MOBYProviderVisitorAdapter.java
Log Message:
Package no longer needed
moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/graph/tools package.html,1.1,NONE MOBYProviderTraverser.java,1.1,NONE MOBYProviderVisitor.java,1.1,NONE MOBYProviderXMLGenerator.java,1.1,NONE MOBYProviderTraversalException.java,1.1,NONE MOBYProviderVisitorAdapter.java,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/graph/tools/RCS/package.html,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/graph/tools/RCS/MOBYProviderTraverser.java,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/graph/tools/RCS/MOBYProviderVisitor.java,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/graph/tools/RCS/MOBYProviderXMLGenerator.java,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/graph/tools/RCS/MOBYProviderTraversalException.java,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/graph/tools/RCS/MOBYProviderVisitorAdapter.java,v: No such file or directory
From gss at pub.open-bio.org Mon Mar 21 16:31:14 2005
From: gss at pub.open-bio.org (Gary Schiltz)
Date: Mon Mar 21 16:15:23 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200503212131.j2LLVEDa008358@pub.open-bio.org>
gss
Mon Mar 21 16:31:14 EST 2005
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core
In directory pub.open-bio.org:/tmp/cvs-serv8336
Removed Files:
build.xml
Log Message:
Moved to build subdirectory
moby-live/S-MOBY/ref-impl/core build.xml,1.4,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/RCS/build.xml,v: No such file or directory
From gss at pub.open-bio.org Mon Mar 21 16:31:29 2005
From: gss at pub.open-bio.org (Gary Schiltz)
Date: Mon Mar 21 16:16:01 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200503212131.j2LLVTMe008387@pub.open-bio.org>
gss
Mon Mar 21 16:31:29 EST 2005
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/build
In directory pub.open-bio.org:/tmp/cvs-serv8363/build
Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/build added to the repository
moby-live/S-MOBY/ref-impl/core/build - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/build/RCS/-,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/build/RCS/New,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/build/RCS/directory,v: No such file or directory
From gss at pub.open-bio.org Mon Mar 21 16:31:31 2005
From: gss at pub.open-bio.org (Gary Schiltz)
Date: Mon Mar 21 16:16:01 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200503212131.j2LLVVTC008421@pub.open-bio.org>
gss
Mon Mar 21 16:31:31 EST 2005
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/build
In directory pub.open-bio.org:/tmp/cvs-serv8400/build
Added Files:
build.xml .cvsignore
Log Message:
New build subdirectory
moby-live/S-MOBY/ref-impl/core/build build.xml,NONE,1.1 .cvsignore,NONE,1.1
From gss at pub.open-bio.org Mon Mar 21 16:32:02 2005
From: gss at pub.open-bio.org (Gary Schiltz)
Date: Mon Mar 21 16:16:10 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200503212132.j2LLW2LU008451@pub.open-bio.org>
gss
Mon Mar 21 16:32:01 EST 2005
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core
In directory pub.open-bio.org:/tmp/cvs-serv8426
Modified Files:
.cvsignore
Log Message:
Changed to reflect new build structure
moby-live/S-MOBY/ref-impl/core .cvsignore,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.cvsignore,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/.cvsignore 2004/06/14 16:24:12 1.6
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.cvsignore 2005/03/21 21:32:01 1.7
@@ -1,4 +1,3 @@
-build
-smoby.jar
+classes
.classpath
.project
From gss at pub.open-bio.org Mon Mar 21 16:32:38 2005
From: gss at pub.open-bio.org (Gary Schiltz)
Date: Mon Mar 21 16:17:24 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200503212132.j2LLWc3v008490@pub.open-bio.org>
gss
Mon Mar 21 16:32:38 EST 2005
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/parser
In directory pub.open-bio.org:/tmp/cvs-serv8465/src/org/semanticmoby/parser
Modified Files:
Parser.java
Log Message:
Fixed to use new org.semanticmoby.graph.* signatures
moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/parser Parser.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/parser/Parser.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/semanticmoby/parser/Parser.java 2004/11/23 00:18:46 1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/parser/Parser.java 2005/03/21 21:32:38 1.2
@@ -5,17 +5,16 @@
import java.util.*;
import org.semanticmoby.graph.*;
-import org.semanticmoby.parser.*;
-import org.semanticmoby.tools.ModelRetriever;
-import org.semanticmoby.tools.Util;
+import org.semanticmoby.tools.*;
import org.semanticmoby.vocabulary.*;
import com.hp.hpl.jena.rdf.model.*;
import com.hp.hpl.jena.vocabulary.*;
/**
- * This class is used to parse OWL models, stored as Jena2 models, into
- * objects that implement interfaces from the org.semanticmoby.graph package.
+ * This class is used to parse RDF models, stored as Jena2 models, into
+ * objects that implement interfaces from the org.semanticmoby.graph
+ * package.
*/
public class Parser
{
@@ -186,7 +185,7 @@
// Create and return an unordered collection of the parsed providers
//
- return new MOBYUnorderedCollection(null, providers, null);
+ return new MOBYUnorderedCollection(providers, null, null);
}
/**
@@ -199,9 +198,9 @@
// First parse the scalar properties name, oneLineDescription, and aboutURI
//
- String name = getDataPropertyValue(provider, MOBY.name);
- String oneLiner = getDataPropertyValue(provider, MOBY.oneLineDescription);
- String aboutURI = getDataPropertyValue(provider, MOBY.aboutURI);
+ Statement nameStmt = model.getProperty(provider, MOBY.name);
+ Statement oneLineDescriptionStmt = model.getProperty(provider, MOBY.oneLineDescription);
+ Statement aboutURIStmt = model.getProperty(provider, MOBY.aboutURI);
// A provider can have multiple operatesOn properties, each of
// which leads to a subgraph. Parse each of these subgraphs.
@@ -219,8 +218,8 @@
// oneLineDescription, aboutURI, and collection of operatesOn subgraphs
//
return new MOBYProvider(
- provider, name, oneLiner, aboutURI,
- new MOBYUnorderedCollection(provider, operatesOn, model),
+ provider, nameStmt, oneLineDescriptionStmt, aboutURIStmt,
+ new MOBYUnorderedCollection(operatesOn, provider, model),
model);
}
@@ -326,16 +325,16 @@
// Create and return a Subject to describe this hasMapping subgraph
//
return new MOBYSubject(res,
- new MOBYFixedCollection(res, statements, model),
- new MOBYUnorderedCollection(res, directMappings, model),
+ new MOBYFixedCollection(statements, res, model),
+ new MOBYUnorderedCollection(directMappings, res, model),
collectionFor(res, nestedMappings),
model);
}
/**
- * Parse the object of a mapsTo statement, which should be a
- * Subject, a data structure, or both. If the object is a data
+ * Parse the object of a mapsTo statement, which should be an
+ * Object, a data structure, or both. If the object is a data
* structure, then each element of the data structure should
* be a mapped subgraph.
*/
@@ -370,7 +369,7 @@
//
Model model = res.getModel();
return new MOBYObject(res,
- new MOBYFixedCollection(res, statements, model),
+ new MOBYFixedCollection(statements, res, model),
collectionFor(res, nested), model);
}
@@ -462,12 +461,6 @@
model.contains(p, RDFS.subPropertyOf, MOBY.Property);
}
- private String getDataPropertyValue(Resource subject, Property property)
- {
- Statement s = subject.getModel().getProperty(subject, property);
- return (s == null) ? null : s.getObject().toString();
- }
-
private Resource getResourcePropertyValue(Resource subject, Property property)
{
Statement s = subject.getModel().getProperty(subject, property);
@@ -500,13 +493,13 @@
private MOBYCollection collectionFor(Resource res, List elements)
{
if (isList(res)) {
- return new MOBYFixedCollection(res, elements, res.getModel());
+ return new MOBYFixedCollection(elements, res, res.getModel());
} else if (isBag(res)) {
- return new MOBYUnorderedCollection(res, elements, res.getModel());
+ return new MOBYUnorderedCollection(elements, res, res.getModel());
} else if (isSeq(res)) {
- return new MOBYOrderedCollection(res, elements, res.getModel());
+ return new MOBYOrderedCollection(elements, res, res.getModel());
} else if (isAlt(res)) {
- return new MOBYEnumeration(res, elements, res.getModel());
+ return new MOBYEnumeration(elements, res, res.getModel());
} else {
return null;
}
From gss at pub.open-bio.org Mon Mar 21 16:33:19 2005
From: gss at pub.open-bio.org (Gary Schiltz)
Date: Mon Mar 21 16:19:30 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200503212133.j2LLXJJV008537@pub.open-bio.org>
gss
Mon Mar 21 16:33:19 EST 2005
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv8495/archive/WebRoot
Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/WebRoot added to the repository
moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/WebRoot - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/WebRoot/RCS/-,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/WebRoot/RCS/New,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/WebRoot/RCS/directory,v: No such file or directory
From gss at pub.open-bio.org Mon Mar 21 16:33:24 2005
From: gss at pub.open-bio.org (Gary Schiltz)
Date: Mon Mar 21 16:19:31 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200503212133.j2LLXOdN008750@pub.open-bio.org>
gss
Mon Mar 21 16:33:24 EST 2005
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/WebRoot/meeting
In directory pub.open-bio.org:/tmp/cvs-serv8729/archive/WebRoot/meeting
Added Files:
missing-fields.jsp registration-confirmation.jsp
registration-form.html lodging.html index.html shuttles.html
Log Message:
Archived a few things
moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/WebRoot/meeting missing-fields.jsp,NONE,1.1 registration-confirmation.jsp,NONE,1.1 registration-form.html,NONE,1.1 lodging.html,NONE,1.1 index.html,NONE,1.1 shuttles.html,NONE,1.1
From gss at pub.open-bio.org Mon Mar 21 16:33:20 2005
From: gss at pub.open-bio.org (Gary Schiltz)
Date: Mon Mar 21 16:19:33 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200503212133.j2LLXK26008637@pub.open-bio.org>
gss
Mon Mar 21 16:33:20 EST 2005
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/src/org/semanticmoby
In directory pub.open-bio.org:/tmp/cvs-serv8495/archive/src/org/semanticmoby
Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/src/org/semanticmoby added to the repository
moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/src/org/semanticmoby - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/src/org/semanticmoby/RCS/-,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/src/org/semanticmoby/RCS/New,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/src/org/semanticmoby/RCS/directory,v: No such file or directory
From gss at pub.open-bio.org Mon Mar 21 16:33:24 2005
From: gss at pub.open-bio.org (Gary Schiltz)
Date: Mon Mar 21 16:19:33 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200503212133.j2LLXOON008796@pub.open-bio.org>
gss
Mon Mar 21 16:33:24 EST 2005
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/WebRoot/meeting/images
In directory pub.open-bio.org:/tmp/cvs-serv8729/archive/WebRoot/meeting/images
Added Files:
moby.png ncgr.png
Log Message:
Archived a few things
moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/WebRoot/meeting/images moby.png,NONE,1.1 ncgr.png,NONE,1.1
From gss at pub.open-bio.org Mon Mar 21 16:33:24 2005
From: gss at pub.open-bio.org (Gary Schiltz)
Date: Mon Mar 21 16:19:34 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200503212133.j2LLXOMM008765@pub.open-bio.org>
gss
Mon Mar 21 16:33:24 EST 2005
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/src/org/semanticmoby/graph/tools
In directory pub.open-bio.org:/tmp/cvs-serv8729/archive/src/org/semanticmoby/graph/tools
Added Files:
MOBYProviderTraversalException.java MOBYProviderVisitor.java
package.html MOBYProviderTraverser.java
MOBYProviderVisitorAdapter.java MOBYProviderXMLGenerator.java
Log Message:
Archived a few things
moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/src/org/semanticmoby/graph/tools MOBYProviderTraversalException.java,NONE,1.1 MOBYProviderVisitor.java,NONE,1.1 package.html,NONE,1.1 MOBYProviderTraverser.java,NONE,1.1 MOBYProviderVisitorAdapter.java,NONE,1.1 MOBYProviderXMLGenerator.java,NONE,1.1
From gss at pub.open-bio.org Mon Mar 21 16:33:24 2005
From: gss at pub.open-bio.org (Gary Schiltz)
Date: Mon Mar 21 16:19:34 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200503212133.j2LLXORn008814@pub.open-bio.org>
gss
Mon Mar 21 16:33:24 EST 2005
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv8729/archive/WebRoot
Added Files:
index.html
Log Message:
Archived a few things
moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/WebRoot index.html,NONE,1.1
From gss at pub.open-bio.org Mon Mar 21 16:33:20 2005
From: gss at pub.open-bio.org (Gary Schiltz)
Date: Mon Mar 21 16:19:35 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200503212133.j2LLXK2b008596@pub.open-bio.org>
gss
Mon Mar 21 16:33:19 EST 2005
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/src
In directory pub.open-bio.org:/tmp/cvs-serv8495/archive/src
Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/src added to the repository
moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/src - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/src/RCS/-,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/src/RCS/New,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/src/RCS/directory,v: No such file or directory
From gss at pub.open-bio.org Mon Mar 21 16:33:20 2005
From: gss at pub.open-bio.org (Gary Schiltz)
Date: Mon Mar 21 16:19:36 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200503212133.j2LLXKBQ008617@pub.open-bio.org>
gss
Mon Mar 21 16:33:20 EST 2005
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/src/org
In directory pub.open-bio.org:/tmp/cvs-serv8495/archive/src/org
Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/src/org added to the repository
moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/src/org - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/src/org/RCS/-,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/src/org/RCS/New,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/src/org/RCS/directory,v: No such file or directory
From gss at pub.open-bio.org Mon Mar 21 16:33:24 2005
From: gss at pub.open-bio.org (Gary Schiltz)
Date: Mon Mar 21 16:19:37 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200503212133.j2LLXOGc008781@pub.open-bio.org>
gss
Mon Mar 21 16:33:24 EST 2005
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/src/org/semanticmoby/meeting
In directory pub.open-bio.org:/tmp/cvs-serv8729/archive/src/org/semanticmoby/meeting
Added Files:
MeetingRegistrationServlet.java
Log Message:
Archived a few things
moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/src/org/semanticmoby/meeting MeetingRegistrationServlet.java,NONE,1.1
From gss at pub.open-bio.org Mon Mar 21 16:33:20 2005
From: gss at pub.open-bio.org (Gary Schiltz)
Date: Mon Mar 21 16:19:41 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200503212133.j2LLXKWA008659@pub.open-bio.org>
gss
Mon Mar 21 16:33:20 EST 2005
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/src/org/semanticmoby/graph
In directory pub.open-bio.org:/tmp/cvs-serv8495/archive/src/org/semanticmoby/graph
Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/src/org/semanticmoby/graph added to the repository
moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/src/org/semanticmoby/graph - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/src/org/semanticmoby/graph/RCS/-,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/src/org/semanticmoby/graph/RCS/New,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/src/org/semanticmoby/graph/RCS/directory,v: No such file or directory
From gss at pub.open-bio.org Mon Mar 21 16:33:19 2005
From: gss at pub.open-bio.org (Gary Schiltz)
Date: Mon Mar 21 16:21:33 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200503212133.j2LLXJFL008519@pub.open-bio.org>
gss
Mon Mar 21 16:33:19 EST 2005
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive
In directory pub.open-bio.org:/tmp/cvs-serv8495/archive
Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive added to the repository
moby-live/S-MOBY/ref-impl/semanticmoby.org/archive - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/RCS/-,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/RCS/New,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/RCS/directory,v: No such file or directory
From gss at pub.open-bio.org Mon Mar 21 16:33:19 2005
From: gss at pub.open-bio.org (Gary Schiltz)
Date: Mon Mar 21 16:21:33 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200503212133.j2LLXJqj008555@pub.open-bio.org>
gss
Mon Mar 21 16:33:19 EST 2005
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/WebRoot/meeting
In directory pub.open-bio.org:/tmp/cvs-serv8495/archive/WebRoot/meeting
Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/WebRoot/meeting added to the repository
moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/WebRoot/meeting - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/WebRoot/meeting/RCS/-,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/WebRoot/meeting/RCS/New,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/WebRoot/meeting/RCS/directory,v: No such file or directory
From gss at pub.open-bio.org Mon Mar 21 16:33:20 2005
From: gss at pub.open-bio.org (Gary Schiltz)
Date: Mon Mar 21 16:21:35 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200503212133.j2LLXKGC008575@pub.open-bio.org>
gss
Mon Mar 21 16:33:19 EST 2005
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/WebRoot/meeting/images
In directory pub.open-bio.org:/tmp/cvs-serv8495/archive/WebRoot/meeting/images
Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/WebRoot/meeting/images added to the repository
moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/WebRoot/meeting/images - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/WebRoot/meeting/images/RCS/-,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/WebRoot/meeting/images/RCS/New,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/WebRoot/meeting/images/RCS/directory,v: No such file or directory
From gss at pub.open-bio.org Mon Mar 21 16:33:20 2005
From: gss at pub.open-bio.org (Gary Schiltz)
Date: Mon Mar 21 16:21:36 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200503212133.j2LLXKHf008682@pub.open-bio.org>
gss
Mon Mar 21 16:33:20 EST 2005
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/src/org/semanticmoby/graph/tools
In directory pub.open-bio.org:/tmp/cvs-serv8495/archive/src/org/semanticmoby/graph/tools
Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/src/org/semanticmoby/graph/tools added to the repository
moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/src/org/semanticmoby/graph/tools - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/src/org/semanticmoby/graph/tools/RCS/-,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/src/org/semanticmoby/graph/tools/RCS/New,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/src/org/semanticmoby/graph/tools/RCS/directory,v: No such file or directory
From gss at pub.open-bio.org Mon Mar 21 16:33:20 2005
From: gss at pub.open-bio.org (Gary Schiltz)
Date: Mon Mar 21 16:21:36 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200503212133.j2LLXKmu008700@pub.open-bio.org>
gss
Mon Mar 21 16:33:20 EST 2005
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/src/org/semanticmoby/meeting
In directory pub.open-bio.org:/tmp/cvs-serv8495/archive/src/org/semanticmoby/meeting
Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/src/org/semanticmoby/meeting added to the repository
moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/src/org/semanticmoby/meeting - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/src/org/semanticmoby/meeting/RCS/-,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/src/org/semanticmoby/meeting/RCS/New,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/archive/src/org/semanticmoby/meeting/RCS/directory,v: No such file or directory
From gss at pub.open-bio.org Mon Mar 21 16:39:19 2005
From: gss at pub.open-bio.org (Gary Schiltz)
Date: Mon Mar 21 16:23:23 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200503212139.j2LLdJes008975@pub.open-bio.org>
gss
Mon Mar 21 16:39:19 EST 2005
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/resources
In directory pub.open-bio.org:/tmp/cvs-serv8951/resources
Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/resources added to the repository
moby-live/S-MOBY/ref-impl/semanticmoby.org/resources - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/resources/RCS/-,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/resources/RCS/New,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/resources/RCS/directory,v: No such file or directory
From gss at pub.open-bio.org Mon Mar 21 16:39:19 2005
From: gss at pub.open-bio.org (Gary Schiltz)
Date: Mon Mar 21 16:23:23 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200503212139.j2LLdJp1008994@pub.open-bio.org>
gss
Mon Mar 21 16:39:19 EST 2005
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/resources/Photoshop Files
In directory pub.open-bio.org:/tmp/cvs-serv8951/resources/Photoshop Files
Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/resources/Photoshop Files added to the repository
moby-live/S-MOBY/ref-impl/semanticmoby.org/resources/Photoshop Files - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/resources/Photoshop/RCS/Files,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/resources/Photoshop/RCS/-,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/resources/Photoshop/RCS/New,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/resources/Photoshop/RCS/directory,v: No such file or directory
From gss at pub.open-bio.org Mon Mar 21 16:39:26 2005
From: gss at pub.open-bio.org (Gary Schiltz)
Date: Mon Mar 21 16:23:28 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200503212139.j2LLdQko009055@pub.open-bio.org>
gss
Mon Mar 21 16:39:26 EST 2005
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/resources
In directory pub.open-bio.org:/tmp/cvs-serv9018/resources
Added Files:
moby_keyword.sql web.xml
Log Message:
Initial version
moby-live/S-MOBY/ref-impl/semanticmoby.org/resources moby_keyword.sql,NONE,1.1 web.xml,NONE,1.1
From gss at pub.open-bio.org Mon Mar 21 16:39:26 2005
From: gss at pub.open-bio.org (Gary Schiltz)
Date: Mon Mar 21 16:23:29 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200503212139.j2LLdQsv009040@pub.open-bio.org>
gss
Mon Mar 21 16:39:25 EST 2005
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/resources/Photoshop Files
In directory pub.open-bio.org:/tmp/cvs-serv9018/resources/Photoshop Files
Added Files:
smoby-medium.psd ncgr-logo.psd rdf-logo.png smoby-small.psd
rdf-logo.psd nsf-logo.psd search.psd
Log Message:
Initial version
moby-live/S-MOBY/ref-impl/semanticmoby.org/resources/Photoshop Files smoby-medium.psd,NONE,1.1 ncgr-logo.psd,NONE,1.1 rdf-logo.png,NONE,1.1 smoby-small.psd,NONE,1.1 rdf-logo.psd,NONE,1.1 nsf-logo.psd,NONE,1.1 search.psd,NONE,1.1
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/resources/Photoshop/RCS/Files,v: No such file or directory
From gss at pub.open-bio.org Mon Mar 21 16:39:58 2005
From: gss at pub.open-bio.org (Gary Schiltz)
Date: Mon Mar 21 16:24:02 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200503212139.j2LLdwfp009087@pub.open-bio.org>
gss
Mon Mar 21 16:39:58 EST 2005
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/build
In directory pub.open-bio.org:/tmp/cvs-serv9063/build
Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/build added to the repository
moby-live/S-MOBY/ref-impl/semanticmoby.org/build - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/build/RCS/-,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/build/RCS/New,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/build/RCS/directory,v: No such file or directory
From gss at pub.open-bio.org Mon Mar 21 16:40:00 2005
From: gss at pub.open-bio.org (Gary Schiltz)
Date: Mon Mar 21 16:24:03 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200503212140.j2LLe0Sx009126@pub.open-bio.org>
gss
Mon Mar 21 16:40:00 EST 2005
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/build
In directory pub.open-bio.org:/tmp/cvs-serv9105/build
Added Files:
build.xml .cvsignore
Log Message:
Initial version
moby-live/S-MOBY/ref-impl/semanticmoby.org/build build.xml,NONE,1.1 .cvsignore,NONE,1.1
From gss at pub.open-bio.org Mon Mar 21 16:40:31 2005
From: gss at pub.open-bio.org (Gary Schiltz)
Date: Mon Mar 21 16:24:35 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200503212140.j2LLeVr9009172@pub.open-bio.org>
gss
Mon Mar 21 16:40:31 EST 2005
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org
In directory pub.open-bio.org:/tmp/cvs-serv9139
Modified Files:
.classpath .project .mymetadata
Log Message:
Misc
moby-live/S-MOBY/ref-impl/semanticmoby.org .classpath,1.3,1.4 .project,1.2,1.3 .mymetadata,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.classpath,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/.classpath 2004/11/23 00:20:01 1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.classpath 2005/03/21 21:40:30 1.4
@@ -2,11 +2,11 @@
Semantic MOBY
-
-
-
-
-
-
- MOBY Autumn 2004 Meeting
-
- November 20-21 — Santa Fe, New Mexico
-
- Register Now!
-
+
-About Semantic MOBY Help on Searching
+About Semantic MOBY
+Help on Searching
+
+
+Developers: see the JavaDoc for the Semantic MOBY API!
-
-
-
- CSHL
-
NCGR
-
NSF
-
-
-
-Semantic
-MOBY
Search Help
-Providers, as well as subjects and objects, are
-classified using web-accessible definitions (ontologies), and these definitions
+Providers, as well as subjects and objects, are classified using
+web-accessible definitions (ontologies), and these definitions
have keywords associated with them. For example, the following shows
-a query for providers whose definitions include the keyword "hello":
+a query for providers whose subjects are members of any class that
+has the keyword "panel" associated with it:
.
+
.
Search hints
-
+
+
HELLO means the
-same thing as hello as does HeLlO.
+PANEL means the
+same thing as panel as does PaNeL.
*) can be used at the end of a keyword
to match keywords that start with the characters before the wildcard.
-For example, he* will match hello as well
-as help.
+For example, pan* will match panel as well
+as panini.
"gene symbol"
-is considered to be a single keyword composed of 11 characters, including a space.
-The wildcard character is interpreted literally (i.e. as the '*'
-character) if it appears within a quoted string.
+is considered to be a single keyword composed of 11 characters, including
+a space. The wildcard character is interpreted literally (i.e. as the
+'*' character) if it appears within a quoted string.
fat sugar into the Subject field, and
"weight gain" into the Object field will search for
-providers that map either fat or sugar to weight gain.
+providers that map either fat or sugar to weight gain.