\n";
$message .= "$default\n";
$message .= "$datatype\n";
From mwilkinson at pub.open-bio.org Wed Mar 16 15:05:46 2005
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Wed Mar 16 14:50:24 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200503162005.j2GK5k0Q010412@pub.open-bio.org>
mwilkinson
Wed Mar 16 15:05:46 EST 2005
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv10393/MOBY/Client
Modified Files:
Central.pm
Log Message:
removing the code that calls the RDF builder just for the moment. it needs to be parameterized first.
moby-live/Perl/MOBY/Client Central.pm,1.92,1.93
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v
retrieving revision 1.92
retrieving revision 1.93
diff -u -r1.92 -r1.93
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2005/03/16 19:14:15 1.92
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2005/03/16 20:05:46 1.93
@@ -980,16 +980,18 @@
# return ( $self->parseRegXML( $return ) );
#_______call a new version RDFbuilder (by Eddie Kawas) _________________________________________
my $reg = $self->parseRegXML( $return );
- if ($reg->success == 1){
- require LWP::UserAgent;
-
- my $ua = LWP::UserAgent->new;
- my $url='http://mobycentral.cbr.nrc.ca:8090/DemoServlet/forms/getSignatureResponse?domain='.$authURI.'&serviceName='.$name;
-
- my $response = $ua->get($url);
- my $rdf = $response->content;
- print "$rdf\n";
-}
+
+# if ($reg->success == 1){
+# require LWP::UserAgent;
+#
+# my $ua = LWP::UserAgent->new;
+# my $url='http://mobycentral.cbr.nrc.ca:8090/DemoServlet/forms/getSignatureResponse?domain='.$authURI.'&serviceName='.$name;
+#
+# my $response = $ua->get($url);
+# my $rdf = $response->content;
+# print "$rdf\n";
+#}
+
return $reg;
#_______________________________________________________________________________________________
From mwilkinson at pub.open-bio.org Wed Mar 16 17:30:31 2005
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Wed Mar 16 17:15:09 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200503162230.j2GMUVii010922@pub.open-bio.org>
mwilkinson
Wed Mar 16 17:30:31 EST 2005
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv10903/MOBY
Modified Files:
CommonSubs.pm
Log Message:
altered getNodeContentWithArticle so that you can get the text content of the root node by leaving off the articleName argument. This is very useful... honest...
moby-live/Perl/MOBY CommonSubs.pm,1.63,1.64
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.63
retrieving revision 1.64
diff -u -r1.63 -r1.64
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2005/03/14 18:30:57 1.63
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2005/03/16 22:30:31 1.64
@@ -1158,11 +1158,15 @@
be the entire mobyData block.
$tagname - the tagname (effectively from the Object type ontology),
or "Parameter" if you are trying to get secondaries
- $articleName - the articleName that we are searching for
+ $articleName - the articleName that we are searching for.
+ to get the content of the primary object, leave
+ this field blank!
+
+ returns : an ARRAY of the stringified text content for each
+ node that matched the tagname/articleName specified; one
+ array element for each matching node. Newlines are NOT considered
+ new nodes (as they are in normal XML).
- returns : an array of the stringified text content for each
- node that matched the tagname/articleName specified.
- note that each line of content is an element of the string.
notes : This was written for the purpose of getting the values of
String, Integer, Float, Date_Time, and other such primitives.
For example, in the following XML:
@@ -1221,9 +1225,9 @@
foreach my $article(@articles){
my ($type, $DOM) = @{$article};
if ($type == SECONDARY){
- $cutoff = getNodeContentsWithArticle($DOM, "Parameter", "cutoff");
+ ($cutoff) = getNodeContentsWithArticle($DOM, "Parameter", "cutoff");
} else {
- $sequences = getNodeContentWithArticle($DOM, "String", "SequenceString");
+ @sequences = getNodeContentWithArticle($DOM, "String", "SequenceString");
}
}
}
@@ -1245,11 +1249,24 @@
my @contents;
return () unless ref( $node ) =~ /XML::LibXML/;
return () unless $element;
- return () unless $articleName;
+
+ unless ($articleName){ # the request is for root node if no articleName
+ my $resp;
+ foreach my $child($node->childNodes){
+ next unless ($child->nodeType == TEXT_NODE || $child->nodeType == CDATA_SECTION_NODE);
+ $resp .= $child->nodeValue;
+ }
+ push @contents, $resp;
+ return @contents;
+ }
+
my $nodes = $node->getElementsByTagName( $element );
unless ( $nodes->get_node( 1 ) ) {
$nodes = $node->getElementsByTagName( "moby:$element" );
}
+
+
+ # if there is an articleName, then get that specific node
for ( 1 .. $nodes->size() ) {
my $child = $nodes->get_node( $_ );
if (
From gss at pub.open-bio.org Mon Mar 21 16:29:44 2005
From: gss at pub.open-bio.org (Gary Schiltz)
Date: Mon Mar 21 16:14:37 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200503212129.j2LLTiqW008258@pub.open-bio.org>
gss
Mon Mar 21 16:29:44 EST 2005
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/graph
In directory pub.open-bio.org:/tmp/cvs-serv8173/src/org/semanticmoby/graph
Modified Files:
MOBYEnumeration.java MOBYCollection.java
MOBYSingleElement.java MOBYFixedCollection.java
MOBYProviderSet.java MOBYSubject.java MOBYDescriptor.java
MOBYProvider.java MOBYDocument.java MOBYOntology.java
MOBYGraphNode.java MOBYObject.java MOBYMappingElement.java
MOBYOrderedCollection.java MOBYUnorderedCollection.java
MOBYResizableCollection.java
Log Message:
Major cleanup of graph classes
moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/graph MOBYEnumeration.java,1.1,1.2 MOBYCollection.java,1.1,1.2 MOBYSingleElement.java,1.1,1.2 MOBYFixedCollection.java,1.1,1.2 MOBYProviderSet.java,1.1,1.2 MOBYSubject.java,1.1,1.2 MOBYDescriptor.java,1.1,1.2 MOBYProvider.java,1.1,1.2 MOBYDocument.java,1.1,1.2 MOBYOntology.java,1.1,1.2 MOBYGraphNode.java,1.1,1.2 MOBYObject.java,1.1,1.2 MOBYMappingElement.java,1.1,1.2 MOBYOrderedCollection.java,1.1,1.2 MOBYUnorderedCollection.java,1.1,1.2 MOBYResizableCollection.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/graph/MOBYEnumeration.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/MOBYEnumeration.java 2004/11/23 00:18:46 1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/graph/MOBYEnumeration.java 2005/03/21 21:29:44 1.2
@@ -1,19 +1,38 @@
package org.semanticmoby.graph;
import java.util.*;
+
import com.hp.hpl.jena.rdf.model.*;
/**
- * A class representing a resizable collection of objects, in
- * which the order of the elements is not defined; the intention is
- * for the elements to represent possible choices for a value.
+ * 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; the intention is for the elements
+ * to represent possible choices for a value; corresponds to an
+ * RDF Alt.
*/
public class MOBYEnumeration extends MOBYUnorderedCollection
{
- public MOBYEnumeration(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 MOBYEnumeration(Resource resource,
+ Model underlyingJenaModel)
{
- super(resource, elements, underlying);
+ super(null, resource, underlyingJenaModel);
}
- public boolean isEnumeration() { return true; }
+ /**
+ * 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 MOBYEnumeration(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/MOBYCollection.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/MOBYCollection.java 2004/11/23 00:18:46 1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/graph/MOBYCollection.java 2005/03/21 21:29:44 1.2
@@ -1,24 +1,34 @@
package org.semanticmoby.graph;
-import com.hp.hpl.jena.rdf.model.*;
import java.util.*;
+import com.hp.hpl.jena.rdf.model.*;
+
/**
- * A common abstract class for collections, both fixed sized and resizeable,
- * of elements in MOBY graphs.
+ * A common abstract class for collections, both fixed sized and
+ * resizeable, of elements in MOBY graphs.
*/
public abstract class MOBYCollection extends MOBYGraphNode
{
+ /**
+ * A list to hold the elements of the collection
+ */
protected List elements = new ArrayList();
-
- public MOBYCollection(Resource resource, List elements, Model underlying)
+
+ /**
+ * Create an instance with the initial list of elements
+ * @param initialElements the initial elements
+ */
+ public MOBYCollection(List initialElements, Resource resource,
+ Model model)
{
- super(resource, underlying);
- for (Iterator it = elements.iterator(); it.hasNext();) {
- this.elements.add(it.next());
+ super(resource, model);
+
+ if (initialElements != null) {
+ elements.addAll(initialElements);
}
}
-
+
/**
* Return the size of the collection.
*/
@@ -36,15 +46,18 @@
}
/**
- * Return whether or not the collection is fixed in size
+ * Return whether or not this object is a collection.
*/
- public abstract boolean isFixedSized();
+ public boolean isCollection()
+ {
+ return true;
+ }
/**
- * Return whether or not the collection is resizable
+ * Return whether or not this object is a singular element.
*/
- public abstract boolean isResizable();
-
- public boolean isSingular() { return false; }
- public boolean isCollection() { return true; }
+ public boolean isSingular()
+ {
+ return false;
+ }
}
\ No newline at end of file
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/graph/MOBYSingleElement.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/MOBYSingleElement.java 2004/11/23 00:18:46 1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/graph/MOBYSingleElement.java 2005/03/21 21:29:44 1.2
@@ -18,6 +18,19 @@
super(resource, underlying);
}
- public boolean isSingular() { return true; }
- public boolean isCollection() { return false; }
+ /**
+ * Return whether or not this object is a collection.
+ */
+ public boolean isCollection()
+ {
+ return false;
+ }
+
+ /**
+ * Return whether or not this object is a singular element.
+ */
+ public boolean isSingular()
+ {
+ return true;
+ }
}
\ No newline at end of file
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/graph/MOBYFixedCollection.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/MOBYFixedCollection.java 2004/11/23 00:18:46 1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/graph/MOBYFixedCollection.java 2005/03/21 21:29:44 1.2
@@ -1,20 +1,34 @@
package org.semanticmoby.graph;
import java.util.*;
+
import com.hp.hpl.jena.rdf.model.*;
/**
- * A class representing unordered, fixed sized collection
- * of objects.
+ * A class for holding an ordered, fixed sized collection
+ * of objects; corresponds to an RDF List.
*/
public class MOBYFixedCollection extends MOBYCollection
{
+ /**
+ * Create an instance with the initial list of elements
+ * @param initialElements the initial elements
+ * @param resource the resource node that represents this collection
+ * @param model the Jena model from which this is derived
+ */
+ public MOBYFixedCollection(List initialElements, Resource resource,
+ Model model)
+ {
+ super(initialElements, resource, model);
+ }
- public MOBYFixedCollection(Resource resource, List elements, Model underlying)
+ /**
+ * 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)
{
- super(resource, elements, underlying);
+ return elements.get(index);
}
-
- public boolean isResizable() { return false; }
- public boolean isFixedSized() { return true; }
}
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/graph/MOBYProviderSet.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/MOBYProviderSet.java 2004/11/23 00:18:46 1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/graph/MOBYProviderSet.java 2005/03/21 21:29:44 1.2
@@ -46,7 +46,7 @@
for (Iterator it = providers.iterator(); it.hasNext();)
{
MOBYProvider provider = (MOBYProvider) it.next();
- Model underlying = provider.getUnderlying();
+ Model underlying = provider.getModel();
merged.add(underlying);
merged.setNsPrefixes(underlying.getNsPrefixMap());
}
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/graph/MOBYSubject.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/MOBYSubject.java 2004/11/23 00:18:46 1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/graph/MOBYSubject.java 2005/03/21 21:29:44 1.2
@@ -15,7 +15,7 @@
* subject of one or more moby:mapsTo properties. The collection of
* objects of each of these properties is returned by getDirectMappings().
*
- * 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 @@
-
+
-
+
@@ -15,8 +15,7 @@
-
-
+
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.project,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.project 2004/11/04 22:31:36 1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.project 2005/03/21 21:40:30 1.3
@@ -1,6 +1,6 @@
- www.semanticmoby.org
+ semanticmoby.org
@@ -26,22 +26,17 @@
- de.bb.bje.eclipse.IncrementalJspBuilder
-
-
-
-
- com.genuitec.eclipse.ast.deploy.core.DeploymentBuilder
+ com.ibm.etools.validation.validationbuilder
- com.ibm.etools.validation.validationbuilder
+ com.ibm.sse.model.structuredbuilder
- com.ibm.sse.model.structuredbuilder
+ com.genuitec.eclipse.ast.deploy.core.DeploymentBuilder
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.mymetadata,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/.mymetadata 2004/11/04 22:31:36 1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/.mymetadata 2005/03/21 21:40:30 1.4
@@ -1,11 +1,11 @@
+ j2ee-spec="1.4"
+ archive="semanticmoby.org.war">
From gss at pub.open-bio.org Mon Mar 21 16:41:58 2005
From: gss at pub.open-bio.org (Gary Schiltz)
Date: Mon Mar 21 16:26:00 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200503212141.j2LLfw0I009218@pub.open-bio.org>
gss
Mon Mar 21 16:41:58 EST 2005
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/proxies
In directory pub.open-bio.org:/tmp/cvs-serv9194/WebRoot/examples/proxies
Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/proxies added to the repository
moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/proxies - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/proxies/RCS/-,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/proxies/RCS/New,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/examples/proxies/RCS/directory,v: No such file or directory
From gss at pub.open-bio.org Mon Mar 21 16:42:01 2005
From: gss at pub.open-bio.org (Gary Schiltz)
Date: Mon Mar 21 16:26:09 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200503212142.j2LLg19i009260@pub.open-bio.org>
gss
Mon Mar 21 16:42:01 EST 2005
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images
In directory pub.open-bio.org:/tmp/cvs-serv9239/WebRoot/images
Added Files:
search.gif rdf-logo.gif smoby-small.gif cshl-logo.gif
help1.gif nsf-logo.gif smoby-medium.gif ncgr-logo.gif
pinstripe.gif
Log Message:
Misc
moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images search.gif,NONE,1.1 rdf-logo.gif,NONE,1.1 smoby-small.gif,NONE,1.1 cshl-logo.gif,NONE,1.1 help1.gif,NONE,1.1 nsf-logo.gif,NONE,1.1 smoby-medium.gif,NONE,1.1 ncgr-logo.gif,NONE,1.1 pinstripe.gif,NONE,1.1
From gss at pub.open-bio.org Mon Mar 21 16:42:01 2005
From: gss at pub.open-bio.org (Gary Schiltz)
Date: Mon Mar 21 16:26:13 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200503212142.j2LLg1ao009300@pub.open-bio.org>
gss
Mon Mar 21 16:42:01 EST 2005
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools
In directory pub.open-bio.org:/tmp/cvs-serv9239/src/org/semanticmoby/ref/tools
Modified Files:
KeywordFinder.java MOBYProperties.java DiscoveryQuery.java
InvocationBroker.java URIInvestigator.java KeywordQuery.java
Log Message:
Misc
moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools KeywordFinder.java,1.1,1.2 MOBYProperties.java,1.1,1.2 DiscoveryQuery.java,1.1,1.2 InvocationBroker.java,1.1,1.2 URIInvestigator.java,1.1,1.2 KeywordQuery.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/KeywordFinder.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/semanticmoby.org/src/org/semanticmoby/ref/tools/KeywordFinder.java 2004/11/22 22:58:40 1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/KeywordFinder.java 2005/03/21 21:42:01 1.2
@@ -7,9 +7,7 @@
import java.util.*;
import com.hp.hpl.jena.rdf.model.*;
import com.hp.hpl.jena.shared.*;
-import com.hp.hpl.jena.vocabulary.OWL;
-import com.hp.hpl.jena.vocabulary.RDF;
-import com.hp.hpl.jena.vocabulary.RDFS;
+import com.hp.hpl.jena.vocabulary.*;
public class KeywordFinder
{
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/MOBYProperties.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/semanticmoby.org/src/org/semanticmoby/ref/tools/MOBYProperties.java 2004/11/22 22:58:40 1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/MOBYProperties.java 2005/03/21 21:42:01 1.2
@@ -5,7 +5,6 @@
import javax.servlet.ServletContext;
-
/**
* This abstract class contains a set of static methods for retrieving
* properties that are stored in the S-MOBY properties file.
@@ -13,10 +12,9 @@
public abstract class MOBYProperties
{
/**
- * The name of the S-MOBY properties file. The file itself should
- * exist in some directory in the Java class path.
+ * The path to the S-MOBY properties file.
*/
- private static String PROP_FILE_NAME = "smoby.properties";
+ private static String PROP_FILE_NAME = "/WEB-INF/smoby.properties";
/**
* A static Properties object for accessing the properties file.
@@ -67,12 +65,12 @@
if (props == null) // Only try to read it once
{
props = new Properties();
- InputStream is = context.getResourceAsStream(PROP_FILE_NAME);
- if (is == null) {
+ String path = context.getRealPath(PROP_FILE_NAME);
+ if (path == null) {
throw new FileNotFoundException(
"Properties file \"" + PROP_FILE_NAME + "\" not found");
}
- props.load(is);
+ props.load(new FileInputStream(path));
}
}
}
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/DiscoveryQuery.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/semanticmoby.org/src/org/semanticmoby/ref/tools/DiscoveryQuery.java 2004/11/22 22:58:40 1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/DiscoveryQuery.java 2005/03/21 21:42:01 1.2
@@ -110,7 +110,7 @@
Model dbModel = null;
try
{
- Model queryModel = ((MOBYProvider) queryProvider).getUnderlying();
+ Model queryModel = ((MOBYProvider) queryProvider).getModel();
String queryString = buildQueryString(queryModel);
StorageManager manager = new StorageManager();
dbModel = manager.openDBModel();
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/InvocationBroker.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/semanticmoby.org/src/org/semanticmoby/ref/tools/InvocationBroker.java 2004/11/22 22:58:40 1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/InvocationBroker.java 2005/03/21 21:42:01 1.2
@@ -7,7 +7,6 @@
import javax.servlet.http.*;
import org.apache.commons.httpclient.*;
import org.semanticmoby.graph.*;
-import org.semanticmoby.graph.tools.*;
import org.semanticmoby.http.*;
import org.semanticmoby.parser.*;
import org.semanticmoby.vocabulary.MOBY;
@@ -59,14 +58,14 @@
private String rdfxmlString(MOBYProvider provider)
{
StringWriter writer = new StringWriter();
- provider.getUnderlying().write(writer);
+ provider.getModel().write(writer);
return writer.toString();
}
private String n3String(MOBYProvider provider)
{
StringWriter writer = new StringWriter();
- provider.getUnderlying().write(writer, "N3");
+ provider.getModel().write(writer, "N3");
return writer.toString();
}
@@ -247,7 +246,7 @@
private String getInputURI(MOBYProvider provider)
{
try {
- Model model = provider.getUnderlying();
+ Model model = provider.getModel();
Statement stmt = model.listStatements(
provider.getResource(), MOBY.inputURI,
(String) null).nextStatement();
@@ -260,7 +259,7 @@
private String getOutputURI(MOBYProvider provider)
{
try {
- Model model = provider.getUnderlying();
+ Model model = provider.getModel();
Statement stmt = model.listStatements(
provider.getResource(), MOBY.outputURI,
(String) null).nextStatement();
@@ -295,26 +294,6 @@
private boolean requiresInputs(MOBYProvider provider)
{
- MOBYProviderTraverser traverser = new MOBYProviderTraverser();
- try {
- traverser.traverse(provider,
- new MOBYProviderVisitorAdapter(){
- public void visitSubjectPropValStmtEnd(
- MOBYPropertyValueStatement stmt)
- throws MOBYProviderTraversalException
- {
- if (stmt.getValue().isResource()) {
- MOBYResource res = (MOBYResource) stmt.getValue();
- if (res.isBlank()) {
- throw new MOBYProviderTraversalException();
- }
- }
- }
- },
- true);
- } catch (MOBYProviderTraversalException e) {
- return true;
- }
- return false;
+ return getInputURI(provider) != null;
}
}
\ No newline at end of file
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/URIInvestigator.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/semanticmoby.org/src/org/semanticmoby/ref/tools/URIInvestigator.java 2004/11/22 22:58:40 1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/URIInvestigator.java 2005/03/21 21:42:01 1.2
@@ -247,7 +247,9 @@
Parser parser = Parser.forInputStream(in, Parser.LANGUAGE_RDF_XML);
provider = parser.parseProvider();
}
- catch (Throwable t) {}
+ catch (Throwable t) {
+ System.err.println("Parse error: " + t);
+ }
// De-register the provider, printing a removal message if
// a provider couldn't be parsed
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/KeywordQuery.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/semanticmoby.org/src/org/semanticmoby/ref/tools/KeywordQuery.java 2004/11/22 22:58:40 1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/KeywordQuery.java 2005/03/21 21:42:01 1.2
@@ -26,6 +26,7 @@
}
public List findMatchingProviders()
+ throws Exception
{
List matching = new ArrayList();
@@ -53,10 +54,12 @@
catch (StorageException e)
{
System.err.println(e);
+ throw e;
}
catch (SQLException e)
{
System.err.println(e);
+ throw e;
}
return matching;
From gss at pub.open-bio.org Mon Mar 21 16:42:02 2005
From: gss at pub.open-bio.org (Gary Schiltz)
Date: Mon Mar 21 16:26:14 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200503212142.j2LLg2iw009371@pub.open-bio.org>
gss
Mon Mar 21 16:42:02 EST 2005
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/db
In directory pub.open-bio.org:/tmp/cvs-serv9239/src/org/semanticmoby/ref/tools/db
Modified Files:
StorageManager.java
Log Message:
Misc
moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/db StorageManager.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/db/StorageManager.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/semanticmoby.org/src/org/semanticmoby/ref/tools/db/StorageManager.java 2004/11/22 22:58:41 1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/tools/db/StorageManager.java 2005/03/21 21:42:02 1.2
@@ -59,7 +59,7 @@
public void registerProvider(MOBYProvider provider, Date lastModifiedDate)
throws StorageException
{
- Model model = ((MOBYProvider) provider).getUnderlying();
+ Model model = ((MOBYProvider) provider).getModel();
Model dbModel = null;
String uriString = provider.getResource().getURI();
Resource uri = model.createResource(uriString);
From gss at pub.open-bio.org Mon Mar 21 16:42:02 2005
From: gss at pub.open-bio.org (Gary Schiltz)
Date: Mon Mar 21 16:26:16 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200503212142.j2LLg2NM009349@pub.open-bio.org>
gss
Mon Mar 21 16:42:02 EST 2005
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv9239/WebRoot
Modified Files:
index.html help.html
Log Message:
Misc
moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot index.html,1.5,1.6 help.html,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/index.html,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/index.html 2004/11/23 00:20:02 1.5
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/index.html 2005/03/21 21:42:01 1.6
@@ -3,118 +3,71 @@
Semantic MOBY
-
-
-Semantic MOBY
-
-
-
-
+
-
-
-
-
-
-
-
-About Semantic MOBY Help on Searching
+About Semantic MOBY
+Help on Searching
+
+
+Developers: see the JavaDoc for the Semantic MOBY API!
-
-
-
-
|
-
+ href="http://www.cshl.edu" target="_blank">
|
-
+ href="http://www.ncgr.org" target="_blank">
|
+ href="http://www.nsf.gov" target="_blank">
-
CSHL |
-
NCGR |
-
NSF |
-
-
- |
-
-
-
-
-
+
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/help.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/help.html 2004/07/21 22:35:25 1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/help.html 2005/03/21 21:42:01 1.4
@@ -3,43 +3,44 @@
Semantic MOBY Search Help
+
-Semantic
-MOBY
Search Help
+
Semantic MOBY maintains a searchable repository of descriptions of
-providers of services that are available on the web. At the heart
-of these descriptions is the notion that providers map one type
+Service Providers that are available on the web. At the heart
+of these descriptions is the notion that providers transform one type
of thing (the Subject) to another (the Object), or
vice versa.
-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
-- Keywords are not case sensitive, so
HELLO
means the
-same thing as hello
as does HeLlO
.
+ - Keywords are not case sensitive, so
PANEL
means the
+same thing as panel
as does PaNeL
.
- The wildcard character (
*
) 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
.
- Multiple words enclosed in double quotes are considered to be a
single keyword. For example, the quoted string
"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.
- Multiple keywords may be typed in one of the fields; this means to
search for any of the keywords in that field. For example,
@@ -50,7 +51,9 @@
match keywords for all the fields will match. For example,
typing
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.
+
+