From gss at pub.open-bio.org Thu Oct 6 13:55:16 2005 From: gss at pub.open-bio.org (Gary Schiltz) Date: Thu Oct 6 14:45:54 2005 Subject: [MOBY-guts] biomoby commit Message-ID: <200510061755.j96HtGQo009624@pub.open-bio.org> gss Thu Oct 6 13:55:16 EDT 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-serv9598/src/org/semanticmoby/graph Modified Files: MOBYMappingElement.java Log Message: Added getPropValStmt() methods moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/graph MOBYMappingElement.java,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/graph/MOBYMappingElement.java,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/graph/MOBYMappingElement.java 2005/09/14 22:06:10 1.3 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/graph/MOBYMappingElement.java 2005/10/06 17:55:16 1.4 @@ -52,6 +52,30 @@ { return propValStmts; } + + /** + * Returns the MOBYPropValStmt that represents an RDF property + */ + public MOBYPropValStmt getPropValStmt(String propURI) { + MOBYPropValStmt pvStmt = null; + for (Iterator it = propValStmts.iterator(); + it.hasNext() && (pvStmt == null);) + { + MOBYPropValStmt stmt = (MOBYPropValStmt) it.next(); + String uri = stmt.getDefiningStmt().getPredicate().getURI(); + if (uri.equals(propURI)) { + pvStmt = stmt; + } + } + return pvStmt; + } + + /** + * Returns the MOBYPropValStmt that represents a given RDF property + */ + public MOBYPropValStmt getPropValStmt(Property prop) { + return getPropValStmt(prop.getURI()); + } /** * Returns the collection of mappings that are nested within this From gss at pub.open-bio.org Thu Oct 6 13:58:10 2005 From: gss at pub.open-bio.org (Gary Schiltz) Date: Thu Oct 6 14:48:24 2005 Subject: [MOBY-guts] biomoby commit Message-ID: <200510061758.j96HwAaQ009673@pub.open-bio.org> gss Thu Oct 6 13:58:10 EDT 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-serv9648/src/org/semanticmoby/graph Modified Files: MOBYPropValStmt.java Log Message: Added another constructor moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/graph MOBYPropValStmt.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/graph/MOBYPropValStmt.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/MOBYPropValStmt.java 2005/09/14 22:06:10 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/graph/MOBYPropValStmt.java 2005/10/06 17:58:10 1.2 @@ -7,7 +7,7 @@ * of a property that is a subclass of moby:Property */ public class MOBYPropValStmt extends MOBYGraphNode -{ +{ /** * Constructs an instance from an existing model and statement; called * from parsing code @@ -18,18 +18,26 @@ } /** + * Creates an instance from scratch; the defining statement has + * the given resource as its subject, the given property as its + * predicate, and a blank node as its object. + */ + public MOBYPropValStmt(Model jenaModel, Resource subject, Property property) + { + super(jenaModel, + jenaModel.createStatement( + subject, property, jenaModel.createResource())); + } + + /** * Constructs an instance from scratch; the defining statement has * the given resource as its subject, a property with the given URI * as its predicate, and a blank node as its object. */ - public MOBYPropValStmt(Model jenaModel, Resource resource, - String propertyURI) + public MOBYPropValStmt(Model jenaModel, Resource subject, + String propertyURI) { - super(jenaModel, - jenaModel.createStatement( - resource, - jenaModel.createProperty(propertyURI), - jenaModel.createResource())); + this(jenaModel, subject, jenaModel.createProperty(propertyURI)); } /* From gss at pub.open-bio.org Thu Oct 6 13:59:43 2005 From: gss at pub.open-bio.org (Gary Schiltz) Date: Thu Oct 6 14:49:56 2005 Subject: [MOBY-guts] biomoby commit Message-ID: <200510061759.j96HxhGk009720@pub.open-bio.org> gss Thu Oct 6 13:59:43 EDT 2005 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/tools In directory pub.open-bio.org:/tmp/cvs-serv9695/src/org/semanticmoby/tools Modified Files: Util.java Log Message: Added reachableStatements() method moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/tools Util.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/tools/Util.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/tools/Util.java 2004/11/23 00:18:46 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/tools/Util.java 2005/10/06 17:59:43 1.2 @@ -43,6 +43,12 @@ return model; } + public static Model reachableStmts(Model source, Resource subject, String uri) { + Model newModel = newJenaModel(); + addReachableStmts(source, newModel, subject, uri); + return newModel; + } + public static void addReachableStmts( Model source, Model dest, Resource subject, String uri) { @@ -60,7 +66,7 @@ dest.add(dest.createStatement( stmt.getSubject(), stmt.getPredicate(), stmt.getObject())); - // If the object of the statement is a blank node or a + // If the object of the statement is a blank node, or a // resource whose URI starts with the provider URI, then // recursively add the statements that are reachable // from the object @@ -68,7 +74,10 @@ if (stmt.getObject().canAs(Resource.class)) { Resource object = (Resource) stmt.getObject().as(Resource.class); - if (object.isAnon() || (uri != null && object.getURI().startsWith(uri))) { + if ((object.isAnon()) || + (uri == null) || + (object.getURI().startsWith(uri))) + { addReachableStmts(source, dest, object, uri); } } From gss at pub.open-bio.org Thu Oct 6 14:15:05 2005 From: gss at pub.open-bio.org (Gary Schiltz) Date: Thu Oct 6 15:05:38 2005 Subject: [MOBY-guts] biomoby commit Message-ID: <200510061815.j96IF5LP009784@pub.open-bio.org> gss Thu Oct 6 14:15:05 EDT 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-serv9759/src/org/semanticmoby/parser Modified Files: Parser.java Log Message: Fixe a few more bugs moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/parser Parser.java,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/parser/Parser.java,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/parser/Parser.java 2005/09/14 22:06:10 1.3 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/parser/Parser.java 2005/10/06 18:15:05 1.4 @@ -190,9 +190,9 @@ Resource headResource = typeStmt.getSubject(); Model model = headResource.getModel(); - - // First parse the scalar properties + // First parse the literal properties + // Statement nameStmt = model.getProperty(headResource, MOBY.name); @@ -204,9 +204,12 @@ // A service can have multiple operatesOn properties, each of // which leads to a subgraph. Parse each of these subgraphs. + // Map operatesOn = new HashMap(); - StmtIterator it = - model.listStatements(headResource, MOBY.operatesOn, (RDFNode) null); + + StmtIterator it = model.listStatements( + headResource, MOBY.operatesOn, (RDFNode) null); + while (it.hasNext()) { Statement operatesOnStmt = it.nextStatement(); @@ -237,6 +240,7 @@ if (isGraph(res)) { // Throw an exception if it is also a data structure + // if (isDataStructure(res)) { throw new NonCanonicalException( @@ -245,22 +249,24 @@ } // The defining statement for the MOBYGraph instance + // Statement typeStmt = model.listStatements( res, RDF.type, MOBY.Graph).nextStatement(); - - // The statement that asserts the hasMapping property + + // Since the resource is a MOBY Graph, it should have exactly one + // hasMapping property that leads to its mapping subgraph. + // Statement hasMappingStmt = model.listStatements( res, MOBY.hasMapping, (RDFNode) null).nextStatement(); - // Since the resource is a MOBY Graph, it should have exactly one - // hasMapping property that leads to its mapping subgraph. - Resource hasMapping = getResourcePropertyValue(res, MOBY.hasMapping); + Resource hasMappingObject = (Resource) hasMappingStmt.getObject(); return new MOBYGraph(model, typeStmt, hasMappingStmt, - parseHasMapping(hasMapping)); + parseHasMapping(hasMappingObject)); } else { // Throw an exception if it is also a graph + // if (isGraph(res)) { throw new NonCanonicalException( @@ -272,6 +278,7 @@ // data structure. Iterate through the data structure elements, // parsing a mapping subgraph from each by recursively calling // this method. + // Iterator it = iteratorFor(res); List subgraphs = new ArrayList(); while (it.hasNext()) @@ -282,6 +289,7 @@ // Create and return a collection of the subgraphs; the type // of the collection depends on the type of the passed resource + // return collectionFor(res, subgraphs); } } @@ -301,6 +309,7 @@ // It is *not* legal for the object of a hasMapping to be *neither* // a Subject nor a data structure, so throw an exception if this is // the case. + // if ((! isSubject(res)) && (! isDataStructure(res))) { throw new NonCanonicalException( @@ -310,18 +319,22 @@ // Collect the properties of this subject that are // meant to be filled in by the client + // List propValStmts = mobyPropertyStatementsOf(res); // List of direct mappings, i.e. those related through hasMapping // properties. + // Map directMappings = new HashMap(); // List of nested hasMapping subgraphs + // List nestedMappings = new ArrayList(); // The statement that asserts this to be of rdf:type moby:Subject. // Since it is legal for this to not be a Subject, then the statement // can be null + // Statement typeStmt = null; if (isSubject(res)) @@ -331,14 +344,17 @@ // The resource is a MOBY Subject, so should have one or more // mapsTo properties that lead to its mapped subgraphs. + // List mapsTo = new ArrayList(); + StmtIterator it = model.listStatements(res, MOBY.mapsTo, (RDFNode) null); + while (it.hasNext()) { Statement mapsToStmt = it.nextStatement(); - Resource mapsToSubject = mapsToStmt.getResource(); - MOBYGraphNode object = parseMapsTo(mapsToSubject); + Resource mapsToObject = (Resource) mapsToStmt.getObject(); + MOBYGraphNode object = parseMapsTo(mapsToObject); directMappings.put(object, mapsToStmt); } } @@ -349,6 +365,7 @@ // nested in each element. For each element in the data structure, // recursively call this method to create a mapping subgraph, an // save the parsed object in the nestedMappings list. + // Iterator it = iteratorFor(res); while (it.hasNext()) { @@ -360,13 +377,12 @@ return new MOBYSubject(model, typeStmt, propValStmts, directMappings, collectionFor(res, nestedMappings)); } - + /** - * Parse the object of an mapsTo statement, which should be a - * Subject, a data structure, or both. If the object is a Subject, - * then it should be connected to one or more mapped subgraphs through - * mapsTo properties. If the object is a data structure, then - * each element of the data structure should be a mapped subgraph. + * 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 + * in turn be an Object, a data structure, or both. */ private MOBYObject parseMapsTo(Resource res) throws NonCanonicalException @@ -376,6 +392,7 @@ // It is *not* legal for the object of a mapsTo to be *neither* // an Object nor a data structure, so throw an exception if this is // the case. + // if ((! isObject(res)) && (! isDataStructure(res))) { throw new NonCanonicalException( @@ -385,14 +402,17 @@ // Collect the properties of this subject that are // meant to be filled in by the client + // List propValStmts = mobyPropertyStatementsOf(res); // List of nested Object subgraphs + // List nestedObjects = new ArrayList(); // The statement that asserts this to be of rdf:type moby:Object. // Since it is legal for this to not be an Object, then the statement // can be null + // Statement typeStmt = null; if (isObject(res)) @@ -407,6 +427,7 @@ // nested in each element. For each element in the data structure, // recursively call this method to create a mapping subgraph, an // save the parsed object in the nestedMappings list. + // Iterator it = iteratorFor(res); while (it.hasNext()) { @@ -418,66 +439,28 @@ return new MOBYObject(model, typeStmt, propValStmts, collectionFor(res, nestedObjects)); } - - - /** - * 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 - * in turn be an Object, a data structure, or both. - */ - /* - private MOBYObject parseMapsTo(Resource res) - { - Model model = res.getModel(); - - // Collect the properties of this object that are - // meant to be filled in by the service - List statements = mobyPropertyStatementsOf(res); - - // List of nested mapsTo statements - // - List nested = new ArrayList(); - - if (isDataStructure(res)) - { - // The resource is a data structure, so has a mapping subgraph - // nested in each element. For each element in the data structure, - // recursively call this method to create a mapping subgraph, and - // save the parsed object in the nested list. - // - Iterator it = iteratorFor(res); - while (it.hasNext()) - { - Resource r = (Resource) it.next(); - nested.add(parseMapsTo(r)); - } - } - return new MOBYObject(res, - new MOBYFixedCollection(statements, res, model), - collectionFor(res, nested), model); - } - */ /** * Return a list of statements for whom the subject is a given resource, - * whose predicate is a subproperty of moby:Property, and whose object - * is a blank node. + * whose predicate is a subproperty of moby:Property. */ private List mobyPropertyStatementsOf(Resource res) { // The statements to return + // List stmts = new ArrayList(); // Iterate over the statements whose subjects are the resource + // StmtIterator it = res.listProperties(); while (it.hasNext()) { Statement stmt = it.nextStatement(); - if (stmt.getObject().isAnon() && - !propDetector.isMOBYProperty(stmt.getPredicate())) - { - stmts.add(stmt); + Property property = stmt.getPredicate(); + + if (propDetector.isMOBYProperty(property)) { + stmts.add(new MOBYPropValStmt(res.getModel(), stmt)); + System.out.println("MOBY Property: " + property); } } return stmts; From gss at pub.open-bio.org Thu Oct 6 14:15:36 2005 From: gss at pub.open-bio.org (Gary Schiltz) Date: Thu Oct 6 15:05:59 2005 Subject: [MOBY-guts] biomoby commit Message-ID: <200510061815.j96IFasq009814@pub.open-bio.org> gss Thu Oct 6 14:15:36 EDT 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-serv9789/src/org/semanticmoby/parser Modified Files: NamespaceBasedPropertyDetector.java Log Message: Reject properties from other common namespaces besides MOBY moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/parser NamespaceBasedPropertyDetector.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/parser/NamespaceBasedPropertyDetector.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/NamespaceBasedPropertyDetector.java 2005/09/14 22:06:10 1.1 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/parser/NamespaceBasedPropertyDetector.java 2005/10/06 18:15:36 1.2 @@ -3,15 +3,24 @@ import org.semanticmoby.vocabulary.MOBY; import com.hp.hpl.jena.rdf.model.Property; +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.XSD; /** * A property value detector that does nothing more than make sure that - * the property's URI does not start with the MOBY prefix. + * the property's URI is not in any of the "standard" namespaces. */ public class NamespaceBasedPropertyDetector implements MOBYPropertyDetector { public boolean isMOBYProperty(Property prop) { - return ! prop.getURI().startsWith(MOBY.getURI()); + String uri = prop.getURI(); + return + (! uri.startsWith(MOBY.getURI())) && + (! uri.startsWith(RDF.getURI())) && + (! uri.startsWith(RDFS.getURI())) && + (! uri.startsWith(OWL.getURI())); } } \ No newline at end of file From gss at pub.open-bio.org Thu Oct 6 14:17:13 2005 From: gss at pub.open-bio.org (Gary Schiltz) Date: Thu Oct 6 15:07:29 2005 Subject: [MOBY-guts] biomoby commit Message-ID: <200510061817.j96IHDIk009865@pub.open-bio.org> gss Thu Oct 6 14:17:13 EDT 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-serv9840/src/org/semanticmoby/parser Modified Files: Parser.java Log Message: Removed some forgotten debug statements moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/parser Parser.java,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/parser/Parser.java,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/parser/Parser.java 2005/10/06 18:15:05 1.4 +++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/semanticmoby/parser/Parser.java 2005/10/06 18:17:13 1.5 @@ -460,7 +460,6 @@ if (propDetector.isMOBYProperty(property)) { stmts.add(new MOBYPropValStmt(res.getModel(), stmt)); - System.out.println("MOBY Property: " + property); } } return stmts; From senger at pub.open-bio.org Mon Oct 10 17:48:44 2005 From: senger at pub.open-bio.org (Martin Senger) Date: Mon Oct 10 18:38:34 2005 Subject: [MOBY-guts] biomoby commit Message-ID: <200510102148.j9ALmis9006629@pub.open-bio.org> senger Mon Oct 10 17:48:43 EDT 2005 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/event In directory pub.open-bio.org:/tmp/cvs-serv6611/src/main/org/biomoby/shared/event Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/event added to the repository moby-live/Java/src/main/org/biomoby/shared/event - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/event/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/event/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/event/RCS/directory,v: No such file or directory From senger at pub.open-bio.org Tue Oct 11 12:10:13 2005 From: senger at pub.open-bio.org (Martin Senger) Date: Tue Oct 11 12:59:58 2005 Subject: [MOBY-guts] biomoby commit Message-ID: <200510111610.j9BGADVC010218@pub.open-bio.org> senger Tue Oct 11 12:10:13 EDT 2005 Update of /home/repository/moby/jars-archive/current In directory pub.open-bio.org:/tmp/cvs-serv10199 Modified Files: alltools2.jar Log Message: jars-archive/current alltools2.jar,1.7,1.8 =================================================================== RCS file: /home/repository/moby/jars-archive/current/alltools2.jar,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 Binary files /home/repository/moby/jars-archive/current/alltools2.jar 2005/09/24 17:41:16 1.7 and /home/repository/moby/jars-archive/current/alltools2.jar 2005/10/11 16:10:12 1.8 differ rcsdiff: /home/repository/moby/jars-archive/current/alltools2.jar: diff failed From kawas at pub.open-bio.org Tue Oct 11 16:31:27 2005 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Oct 11 17:21:11 2005 Subject: [MOBY-guts] biomoby commit Message-ID: <200510112031.j9BKVRtA011234@pub.open-bio.org> kawas Tue Oct 11 16:31:27 EDT 2005 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/util In directory pub.open-bio.org:/tmp/cvs-serv11209/org/biomoby/client/ui/graphical/applets/util Modified Files: REGEXP.java Log Message: fixed a bug where a URI that contained a '-', ie www.my-uri.com, was rejected. moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/util REGEXP.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/util/REGEXP.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/util/REGEXP.java 2005/04/07 16:42:27 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/util/REGEXP.java 2005/10/11 20:31:27 1.2 @@ -21,7 +21,8 @@ private final static String URI = //"(^(http:\\/\\/www\\.|HTTP:\\/\\/www\\.|www\\.|http:\\/\\/|HTTP:\\/\\/)?[\\w]+\\.[\\w].*\\w$)"; //"^(([^:/?#]+):)?(//([^/?#]*))?([^?#]*)(\\?([^#]*))?(#(.*))?"; // as per rfc 2396 appendix a. - "^([\\w]+\\.[\\w]+(\\.[\\w]+)*)$"; + //"^([\\w]+\\.[\\w]+(\\.[\\w]+)*)$"; + "^([\\w]{1}[\\d\\w\\-]+\\.[\\d\\w\\-]+(\\.[\\d\\w]{2,})*)$"; private final static String URL = "(^(http:\\/\\/www\\.|HTTP:\\/\\/www\\.|http:\\/\\/|HTTP:\\/\\/)[\\w]+\\.[\\w].*(\\/\\w+(\\.{1}\\w+)*)$)"; @@ -44,7 +45,11 @@ public static boolean isValidURI(String uri) { Pattern p = Pattern.compile(URI); Matcher m = p.matcher(uri); - return m.matches(); + boolean matches = m.matches(); + p = Pattern.compile("(\\-{2,})"); + m = p.matcher(uri); + matches = matches && !m.matches(); + return matches; } /** From senger at pub.open-bio.org Wed Oct 12 07:09:15 2005 From: senger at pub.open-bio.org (Martin Senger) Date: Wed Oct 12 07:59:12 2005 Subject: [MOBY-guts] biomoby commit Message-ID: <200510121109.j9CB9FgJ013440@pub.open-bio.org> senger Wed Oct 12 07:09:15 EDT 2005 Update of /home/repository/moby/jars-archive/current In directory pub.open-bio.org:/tmp/cvs-serv13424 Added Files: log4j-1.2.12.jar Removed Files: log4j-1.2.8.jar Log Message: jars-archive/current log4j-1.2.12.jar,NONE,1.1 log4j-1.2.8.jar,1.1,NONE rcsdiff: /home/repository/moby/jars-archive/current/RCS/log4j-1.2.8.jar,v: No such file or directory From senger at pub.open-bio.org Wed Oct 12 07:17:59 2005 From: senger at pub.open-bio.org (Martin Senger) Date: Wed Oct 12 08:09:17 2005 Subject: [MOBY-guts] biomoby commit Message-ID: <200510121117.j9CBHxYk013544@pub.open-bio.org> senger Wed Oct 12 07:17:59 EDT 2005 Update of /home/repository/moby/moby-live/Java/src/Clients In directory pub.open-bio.org:/tmp/cvs-serv13525/src/Clients Modified Files: MobyDigestClient.java Log Message: moby-live/Java/src/Clients MobyDigestClient.java,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/MobyDigestClient.java,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/src/Clients/MobyDigestClient.java 2005/09/22 16:07:08 1.4 +++ /home/repository/moby/moby-live/Java/src/Clients/MobyDigestClient.java 2005/10/12 11:17:59 1.5 @@ -7,6 +7,8 @@ // import org.biomoby.shared.*; +import org.biomoby.shared.event.SimpleListener; +import org.biomoby.shared.event.Notifier; import org.biomoby.client.*; import org.tulsoft.tools.BaseCmdLine; @@ -64,8 +66,9 @@ // how much to show boolean details = cmd.hasOption ("-details"); - if (cmd.hasOption ("-verbose")) - worker.setDebug (true); + boolean verbose = (cmd.hasOption ("-v") || cmd.hasOption ("-verbose")); + if (verbose) + ((Notifier)worker).addNotificationListener (new SimpleListener()); // read (sometimes all) data types and their relationships if (cmd.hasOption ("-d")) { From senger at pub.open-bio.org Wed Oct 12 07:17:59 2005 From: senger at pub.open-bio.org (Martin Senger) Date: Wed Oct 12 08:09:27 2005 Subject: [MOBY-guts] biomoby commit Message-ID: <200510121117.j9CBHxJ9013632@pub.open-bio.org> senger Wed Oct 12 07:17:59 EDT 2005 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard In directory pub.open-bio.org:/tmp/cvs-serv13525/src/main/org/biomoby/service/dashboard Modified Files: AbstractPanel.java CommonTree.java NOTES PropertyChannel.java RegistryModel.java RegistryPanel.java Added Files: DataTypesTree.java JProgressBarWithCancel.java Log Message: moby-live/Java/src/main/org/biomoby/service/dashboard DataTypesTree.java,NONE,1.1 JProgressBarWithCancel.java,NONE,1.1 AbstractPanel.java,1.6,1.7 CommonTree.java,1.2,1.3 NOTES,1.7,1.8 PropertyChannel.java,1.1,1.2 RegistryModel.java,1.3,1.4 RegistryPanel.java,1.8,1.9 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/AbstractPanel.java,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/AbstractPanel.java 2005/09/24 17:51:51 1.6 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/AbstractPanel.java 2005/10/12 11:17:59 1.7 @@ -16,15 +16,19 @@ import javax.swing.JLabel; import javax.swing.JPanel; +import javax.swing.JScrollPane; import javax.swing.Icon; import javax.swing.JButton; import javax.swing.JCheckBox; import javax.swing.JTextField; +import javax.swing.JTextArea; import javax.swing.JComboBox; +import javax.swing.JOptionPane; import javax.swing.JFileChooser; import javax.swing.AbstractButton; import javax.swing.BorderFactory; import javax.swing.JComponent; +import javax.swing.SwingConstants; import javax.swing.border.Border; import javax.swing.border.TitledBorder; import javax.swing.border.CompoundBorder; @@ -34,6 +38,7 @@ import javax.swing.filechooser.FileFilter; import javax.swing.text.html.HTMLDocument; +import java.awt.Component; import java.awt.GridBagLayout; import java.awt.GridBagConstraints; import java.awt.Insets; @@ -84,9 +89,13 @@ protected Icon panelIcon; protected JComponent pComponent; protected static Icon confirmIcon; + protected static Icon warningIcon; // re-use "style" components protected static final Insets BREATH_TOP = new Insets (10,0,0,0); + protected static final Font MSG_AREA_FONT = new Font ("Courier", Font.PLAIN, 10); + protected static final Font TITLE_FONT = new Font ("Serif", Font.BOLD, 20); + protected static final Color TITLE_FGCOLOR = new Color (12, 55, 241); // protected PropertyChannel propertyChannel; @@ -117,8 +126,8 @@ **************************************************************************/ public JLabel getTitle() { JLabel title = new JLabel (getName(), getIcon(), JLabel.CENTER); - title.setFont (new Font ("Serif", Font.BOLD, 20)); - title.setForeground (new Color (12, 55, 241)); + title.setFont (TITLE_FONT); + title.setForeground (TITLE_FGCOLOR); return title; } @@ -269,12 +278,19 @@ } /********************************************************************* - * Create a text field (possibly with an 'initValue' with history - * taken from given 'preferenceNode'. If 'evenName' is not null - * (which means that the contens of this text filed may be of - * interest of someone outside), add an action event that will - * update the shared property storage (a global variable - * 'propertyChannel') when the text field changes its value. + * Create a text field (possibly with an 'initValue') with its + * history taken from given 'preferenceNode'.
+ * + * If 'initValue' is an empty string, the text field starts with + * an empty initial value. If the 'initValue' is null, the text + * field starts filled with the last time used value (stored in + * and taken from the 'preference node').
+ *
+ * If 'evenName' is not null (which means that the contens of this
+ * text filed may be of interest of someone outside), add an
+ * action event that will update the shared property storage
+ * (which is in a global variable 'propertyChannel') when the text
+ * field changes its value.
********************************************************************/
protected JTextFieldWithHistory createText (String initValue,
String preferenceNode,
@@ -335,4 +351,46 @@
return SwingUtils.confirm (null, msg, confirmIcon);
}
+ /*********************************************************************
+ * Display an error message.
+ ********************************************************************/
+ public static void error (Object msg) {
+ if (warningIcon == null)
+ warningIcon = SwingUtils.createIcon ("images/warningButton.gif",
+ Dashboard.class);
+ JOptionPane.showMessageDialog (null, msg, "Error message",
+ JOptionPane.PLAIN_MESSAGE, warningIcon);
+ }
+
+ /*********************************************************************
+ * Display an error message. Construct the message from
+ * 'prologue', some intermediate title, and a text area filled
+ * from the exception 'e'.
+ ********************************************************************/
+ public static void error (String prologue, Exception e) {
+
+ // slightly format message prologue
+ // TBD: HTML escape
+ prologue = prologue + "The actual error is:\n\n";
+ if (! prologue.startsWith ("";
+ prologue = prologue.replaceAll ("\n", "
\n");
+ }
+
+ // slightly format the error message
+ // TBD: make it (or part of it) red
+ String msg = e.getMessage();
+
+ JTextArea area = new JTextArea (15, 50);
+ area.setEditable (false);
+ area.setFont (MSG_AREA_FONT);
+ area.setText (msg);
+ area.setCaretPosition (0);
+
+ JPanel p = new JPanel (new GridBagLayout());
+ SwingUtils.addComponent (p, new JLabel (prologue), 0, 0, 1, 1, NONE, NWEST, 0.0, 0.0);
+ SwingUtils.addComponent (p, new JScrollPane (area), 0, 1, 1, 1, BOTH, NWEST, 1.0, 1.0);
+ error (p);
+ }
+
}
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/CommonTree.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/CommonTree.java 2005/09/24 17:51:51 1.2
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/CommonTree.java 2005/10/12 11:17:59 1.3
@@ -45,9 +45,7 @@
/**
* A common JTree re-used (and always slightly modified) by all
- * Dashboard trees.
- * - * WORK IN PROGRESS.
+ * Biomoby registry trees.
* * @author Martin Senger * @version $Id$ @@ -55,6 +53,8 @@ public class CommonTree extends JTree { + final static String RELOAD = "Reload"; + // some shared constants final static protected int SORTED_BY_NAME = 0; final static protected int SORTED_BY_AUTHORITY = 1; @@ -186,13 +186,23 @@ expand(); } })); + popup.add - (new JMenuItem (new AbstractAction ("Collaps all nodes") { + (new JMenuItem (new AbstractAction ("Collapse all nodes") { public void actionPerformed (ActionEvent e) { collapse(); } })); + popup.addSeparator(); + + popup.add + (new JMenuItem (new AbstractAction (RELOAD) { + public void actionPerformed (ActionEvent e) { + reload(); + } + })); + // add listener to this tree to bring up popup menus MouseListener popupListener = new PopupListener(); addMouseListener (popupListener); @@ -208,7 +218,22 @@ private void maybeShowPopup (MouseEvent e) { if (e.isPopupTrigger() && popup.isEnabled()) { popup.show (e.getComponent(), - e.getX(), e.getY()); + e.getX(), e.getY()); + } + } + } + + /********************************************************************* + * Enable/disable the whole popup except the 'Reload' option (that + * one remains enabled always). + ********************************************************************/ + protected void setEnabledPopup (boolean enabled) { + synchronized (popup) { + Component[] components = popup.getComponents(); + for (int i = 0; i < components.length; i++) { + if ( components[i] instanceof JMenuItem && + ! ((JMenuItem)components[i]).getText().equals (RELOAD) ) + ((JMenuItem)components[i]).setEnabled (enabled); } } } @@ -242,6 +267,14 @@ } /********************************************************************* + * Does nothing here - it is supposed to be overwritten bya + * concrete tree. + ********************************************************************/ + protected void reload() { + System.out.println ("Invoking a reload."); + } + + /********************************************************************* * Search underlying objects and highligh nodes corresponding to * the found objects. But it does nothing here - it is supposed to * be overwritten by a concrete tree. @@ -292,4 +325,11 @@ } } + /********************************************************************* + * Display an error message. + ********************************************************************/ + protected static void error (String prologue, Exception e) { + AbstractPanel.error (prologue, e); + } + } =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/NOTES,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/NOTES 2005/09/25 09:07:22 1.7 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/NOTES 2005/10/12 11:17:59 1.8 @@ -98,7 +98,6 @@ ---- -* error messages (dialog window, or a text-area window/save button, something on sterrr?) ? logging (LogPanel and/or usual logging to a file?) * communication with StatusBar (incl. progress bar, cancel button) * disabling things during a long-time operation @@ -136,6 +135,14 @@ * BUG: not sure why so many (repeated) changes from the actionlistener in JFieldTextWithHistory +? select a part of an error message and highlight it in red? + +? HELP (in a Dashboard Menu) + - helps from panels + - About + - credits + - add dynamically a URL from dashboard.properties... + TODO with views: ---------------- * change onMethods() to be protected or even private... @@ -169,6 +176,12 @@ ? improve API javadoc of all these Central*Impl ? start to work on/think of the RDF-based cache +General options (available from the menu) +--------------- +* export/import user preferences +* set-up what panels are wanted +* language ( => use proper ResourceBundler...) + Registry panel -------------- @@ -204,3 +217,5 @@ - RDF resources - Log panel - Configure a new Dashboard + +- Debugging panel (with a Memory Panel embedded; replacing current two pannels) =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/PropertyChannel.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/PropertyChannel.java 2005/09/24 17:51:51 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/PropertyChannel.java 2005/10/12 11:17:59 1.2 @@ -29,9 +29,9 @@ *
* * Obviously, there are some properties that do not make sense to be - * stored here: the short-lived properties, such as log messages, or - * progress bar change events. Such messages can be delivered in an - * ordinary way via property change listeners.
+ * stored here: the short-lived properties, such as progress bar + * change events. Such messages can be delivered in an ordinary way + * via property change listeners.
* * The panels/models are sending here properties by calling method * put. If we find, in the future, that sending properties @@ -40,7 +40,7 @@ * see any advantage of it.
* * Property names are of no interest for this class, but it is good to - * remind that the they should be defined in the class {@link + * remind that they should be defined in the class {@link * DashboardProperties}.
* @author Martin Senger
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/RegistryModel.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/RegistryModel.java 2005/09/25 09:07:22 1.3
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/RegistryModel.java 2005/10/12 11:17:59 1.4
@@ -52,14 +52,27 @@
super (support);
}
+ /**************************************************************************
+ * Return an endpoint (a stringified URL) of a default Moby
+ * registry.
+ *************************************************************************/
+ public String getDefaultRegistryEndpoint() {
+ return CentralDigestCachedImpl.DEFAULT_ENDPOINT;
+ }
+
+ /**************************************************************************
+ * Return a namespace (a URI) used by a default Moby registry.
+ *************************************************************************/
+ public String getDefaultRegistryNamespace() {
+ return CentralDigestCachedImpl.DEFAULT_NAMESPACE;
+ }
+
/*********************************************************************
*
********************************************************************/
public MobyDataType[] getDataTypesByNames()
throws MobyException {
-
- if (worker == null)
- initWorker();
+ initWorker();
MobyDataType[] dataTypes = worker.getDataTypes();
java.util.Arrays.sort (dataTypes);
@@ -72,9 +85,7 @@
public MobyDataType[] getDataTypesByAuthority()
throws MobyException {
- if (worker == null)
- initWorker();
-
+ initWorker();
MobyDataType[] dataTypes = worker.getDataTypes();
java.util.Arrays.sort
(dataTypes,
@@ -130,17 +141,40 @@
/*********************************************************************
*
********************************************************************/
- protected void initWorker()
+ protected String getCacheDir() {
+ if (worker instanceof CentralDigestCachedImpl)
+ return ((CentralDigestCachedImpl)worker).getCacheDir();
+ else
+ return null;
+ }
+
+ /*********************************************************************
+ *
+ ********************************************************************/
+ protected synchronized void initWorker()
throws MobyException {
- String registryURL = propertyChannel.getString (DP_REGISTRY_ENDPOINT);
- String registryNS = propertyChannel.getString (DP_REGISTRY_NAMESPACE);
-// String cacheDir = propertyChannel.getString (DP_CACHE_DIR);
- String cacheDir = "/home/senger/jMoby/myCache";
-// cacheDir = null;
-
- worker = new CentralDigestCachedImpl (registryURL,
- registryNS,
- cacheDir);
+ if (worker == null) {
+ String registryURL = propertyChannel.getString (DP_REGISTRY_ENDPOINT);
+ String registryNS = propertyChannel.getString (DP_REGISTRY_NAMESPACE);
+ String cacheDir = propertyChannel.getString (DP_CACHE_DIR);
+ // String cacheDir = "/home/senger/jMoby/myCache";
+ // cacheDir = null;
+
+ worker = new CentralDigestCachedImpl (registryURL,
+ registryNS,
+ cacheDir);
+ } else {
+ String maybeNewRegistryURL = propertyChannel.getString (DP_REGISTRY_ENDPOINT);
+ String maybeNewRegistryNS = propertyChannel.getString (DP_REGISTRY_NAMESPACE);
+ String maybeNewCacheDir = propertyChannel.getString (DP_CACHE_DIR);
+ if ( maybeNewRegistryURL.equals (worker.getRegistryEndpoint()) &&
+ maybeNewRegistryNS.equals (worker.getRegistryNamespace()) &&
+ maybeNewCacheDir.equals (getCacheDir()) )
+ return;
+ worker = new CentralDigestCachedImpl (maybeNewRegistryURL,
+ maybeNewRegistryNS,
+ maybeNewCacheDir);
+ }
}
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/RegistryPanel.java,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/RegistryPanel.java 2005/09/25 09:07:22 1.8
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/RegistryPanel.java 2005/10/12 11:17:59 1.9
@@ -77,6 +77,8 @@
RegistryModel registryModel;
// components that are used from more methods
+ JTextFieldWithHistory registryURL;
+ JTextFieldWithHistory registryNS;
JFileChooserWithHistory cacheDir;
JLabel labelCacheDir;
CommonConsole console;
@@ -115,9 +117,19 @@
pComponent = new JPanel (new GridBagLayout(), true);
+ // registry and cache locations (this must be created before
+ // creating various ontology trees because the trees will need
+ // to know registry and cache locations)
+ JPanel regLocation = getRegistryLocation();
+ JPanel cacheLocation = getCacheLocation();
+
+ // console panel
+ console = new CommonConsole();
+ console.setAppendMode (false);
+
// ontology trees
ServicesTree servicesTree = new ServicesTree();
- DataTypesTree dataTypesTree = new DataTypesTree();
+ DataTypesTree dataTypesTree = new DataTypesTree (registryModel, console);
dataTypesTree.update (CommonTree.SORTED_BY_NAME);
NamespacesTree namespacesTree = new NamespacesTree();
@@ -134,10 +146,6 @@
split2.setContinuousLayout (true);
split2.setOneTouchExpandable (true);
- // console panel
- console = new CommonConsole();
- console.setAppendMode (false);
-
JSplitPane split3 = new JSplitPane (JSplitPane.VERTICAL_SPLIT,
split2,
console);
@@ -145,11 +153,6 @@
split3.setContinuousLayout (true);
split3.setOneTouchExpandable (true);
-
- // registry and cache locations
- JPanel regLocation = getRegistryLocation();
- JPanel cacheLocation = getCacheLocation();
-
// put all together
SwingUtils.addComponent (pComponent, split3, 0, 0, 1, 2, BOTH, NWEST, 1.0, 1.0);
SwingUtils.addComponent (pComponent, regLocation, 1, 0, 1, 1, HORI, NWEST, 0.0, 0.0);
@@ -168,6 +171,8 @@
*
**************************************************************************/
public void onDefaults() {
+ registryURL.setText (registryModel.getDefaultRegistryEndpoint());
+ registryNS.setText (registryModel.getDefaultRegistryNamespace());
}
/**************************************************************************
@@ -202,11 +207,9 @@
**************************************************************************/
protected JPanel getRegistryLocation() {
JLabel labelRegistryURL = new JLabel("Endpoint");
- JTextFieldWithHistory registryURL =
- createText ("", "registryEndpoint", DP_REGISTRY_ENDPOINT);
+ registryURL = createText (null, "registryEndpoint", DP_REGISTRY_ENDPOINT);
JLabel labelRegistryNS = new JLabel("Namespace (URI)");
- JTextFieldWithHistory registryNS =
- createText ("", "registryNamespace", DP_REGISTRY_NAMESPACE);
+ registryNS = createText (null, "registryNamespace", DP_REGISTRY_NAMESPACE);
JButton reloadAllButton =
createButton (" Reload all ",
"Reload all ontology trees from the Biomoby registry",
@@ -307,283 +310,6 @@
}
}
- /**************************************************************************
- *
- **************************************************************************/
- class DataTypesTree extends CommonTree {
- MobyDataType[] dataTypes = null;
- int lastSorted = SORTED_BY_NAME;
- boolean hideBadGuys = false;
- boolean showMembers = false;
- JCheckBoxMenuItem hideBox;
-
- public DataTypesTree() {
- super ("DataTypes");
- createPopups ("Data Types Menu");
- }
-
- protected void createPopups (String title) {
- super.createPopups (title);
- popup.addSeparator();
- popup.add
- (new JMenuItem (new AbstractAction ("Sort by names") {
- public void actionPerformed (ActionEvent e) {
- update (lastSorted = SORTED_BY_NAME);
- hideBox.setEnabled (true);
- }
- }));
- popup.add
- (new JMenuItem (new AbstractAction ("Sort by authorities") {
- public void actionPerformed (ActionEvent e) {
- update (lastSorted = SORTED_BY_AUTHORITY);
- hideBox.setEnabled (false);
- }
- }));
- popup.addSeparator();
-
- JCheckBoxMenuItem showBox = new JCheckBoxMenuItem ("Show HAS/HASA members");
- showBox.addItemListener (new ItemListener() {
- public void itemStateChanged (ItemEvent e) {
- showMembers = (e.getStateChange() == ItemEvent.SELECTED);
- update (lastSorted);
- }
- });
- popup.add (showBox);
-
- hideBox = new JCheckBoxMenuItem ("Hide deprecated objects");
- hideBox.addItemListener (new ItemListener() {
- public void itemStateChanged (ItemEvent e) {
- hideBadGuys = (e.getStateChange() == ItemEvent.SELECTED);
- if (hideBadGuys)
- removeBadGuys();
- else
- update (lastSorted);
- }
- });
- popup.add (hideBox);
- }
-
- void update (int howSorted) {
- popup.setEnabled (false);
- final int sorted = howSorted;
- final SwingWorker worker = new SwingWorker() {
- public Object construct() {
- try {
- if (sorted == SORTED_BY_AUTHORITY)
- dataTypes = registryModel.getDataTypesByAuthority();
- else
- dataTypes = registryModel.getDataTypesByNames();
- } catch (MobyException e) {
- // TBD: what to do here?
- System.err.println ("ERROR: " + e.getMessage());
- }
- return dataTypes; // not used here
- }
-
- // runs on the event-dispatching thread.
- public void finished() {
- if (dataTypes != null) {
- if (sorted == SORTED_BY_AUTHORITY)
- onUpdateDataTreeByAuth (dataTypes);
- else
- onUpdateDataTree (dataTypes);
- popup.setEnabled (true);
- }
- }
- };
- worker.start();
- }
-
- void onUpdateDataTree (MobyDataType[] dataTypes) {
- DefaultTreeModel tModel = (DefaultTreeModel)getModel();
- DefaultMutableTreeNode root = (DefaultMutableTreeNode)tModel.getRoot();
- root.removeAllChildren(); // does not harm if no children exist
- HashMap nodes = new HashMap (dataTypes.length);
- for (int i = 0; i < dataTypes.length; i++) {
- String thisName = dataTypes[i].getName();
- DefaultMutableTreeNode thisNode = (DefaultMutableTreeNode)nodes.get (thisName);
- if (thisNode == null) {
- thisNode = new DefaultMutableTreeNode (new CommonNode (thisName));
- nodes.put (thisName, thisNode);
- }
- String[] parents = dataTypes[i].getParentNames();
- if (parents.length == 0) { // we have a top-level object
- root.add (thisNode);
- } else {
- String parentName = parents[0];
- DefaultMutableTreeNode parentNode = (DefaultMutableTreeNode)nodes.get (parentName);
- if (parentNode == null) {
- parentNode = new DefaultMutableTreeNode (new CommonNode (parentName));
- nodes.put (parentName, parentNode);
- }
- if (showMembers)
- addMembers (thisNode, dataTypes[i]);
- parentNode.add (thisNode);
- }
- }
- if (hideBadGuys)
- removeBadGuys();
- else
- tModel.reload();
- }
-
-
- void onUpdateDataTreeByAuth (MobyDataType[] dataTypes) {
- DefaultTreeModel tModel = (DefaultTreeModel)getModel();
- DefaultMutableTreeNode root = (DefaultMutableTreeNode)tModel.getRoot();
- root.removeAllChildren(); // does not harm if no children exist
- HashMap nodes = new HashMap (dataTypes.length);
- for (int i = 0; i < dataTypes.length; i++) {
- String thisName = dataTypes[i].getName();
- DefaultMutableTreeNode thisNode = (DefaultMutableTreeNode)nodes.get (thisName);
- if (thisNode == null) {
- thisNode = new DefaultMutableTreeNode (new CommonNode (thisName));
- nodes.put (thisName, thisNode);
- }
- String authority = dataTypes[i].getAuthority();
- if (UUtils.isEmpty (authority))
- authority = "
+ *
+ * @return current cache directory name
+ **************************************************************************/
+ public String getCacheDir() {
+ return cacheDir;
+ }
+
+ /**************************************************************************
* Removes object groups from the cache. If 'id' is null it
* removes the whole cache (for the Moby registry this instance as
* initiated for). Otherwise 'id' indicates what part of the cache
@@ -318,12 +327,14 @@
String typesAsXML = getDataTypeNamesAsXML();
store (dataTypesCache, LIST_FILE, typesAsXML);
Map types = createDataTypeNamesFromXML (typesAsXML);
+ fireEvent (DATA_TYPE_COUNT, new Integer (types.size()));
for (Iterator it = types.entrySet().iterator(); it.hasNext(); ) {
Map.Entry entry = (Map.Entry)it.next();
String name = (String)entry.getKey();
- messageLn ("(CDCI) Processing data type " + name + "...");
+ fireEvent (DATA_TYPE_LOADING, name);
String xml = getDataTypeAsXML (name);
store (dataTypesCache, name, xml);
+ fireEvent (DATA_TYPE_LOADED, name);
}
} catch (Exception e) {
throw new MobyException (formatException (e));
@@ -333,16 +344,17 @@
protected void fillServicesCache()
throws MobyException {
try {
- messageLn ("(CDCI) Asking for all service names...");
String byAuthorityAsXML = getServiceNamesByAuthorityAsXML();
store (servicesCache, LIST_FILE, byAuthorityAsXML);
Map authorities = createServiceNamesByAuthorityFromXML (byAuthorityAsXML);
+ fireEvent (AUTHORITY_COUNT, new Integer (authorities.size()));
for (Iterator it = authorities.entrySet().iterator(); it.hasNext(); ) {
Map.Entry entry = (Map.Entry)it.next();
String authority = (String)entry.getKey();
- messageLn ("(CDCI) Processing authority " + authority + "...");
+ fireEvent (AUTHORITY_LOADING, authority);
String xml = getServicesAsXML (new MobyService (MobyService.DUMMY_NAME, authority), null, true, true);
store (servicesCache, authority, xml);
+ fireEvent (AUTHORITY_LOADED, authority);
}
} catch (Exception e) {
throw new MobyException (formatException (e));
@@ -353,16 +365,17 @@
protected void fillServiceTypesCache()
throws MobyException {
try {
- messageLn ("(CDCI) Asking for all service type names...");
String typesAsXML = getServiceTypesAsXML();
store (serviceTypesCache, LIST_FILE, typesAsXML);
Map types = createServiceTypesFromXML (typesAsXML);
+ fireEvent (SERVICE_TYPE_COUNT, new Integer (types.size()));
for (Iterator it = types.entrySet().iterator(); it.hasNext(); ) {
Map.Entry entry = (Map.Entry)it.next();
String name = (String)entry.getKey();
- messageLn ("(CDCI) Processing service type " + name + "...");
+ fireEvent (SERVICE_TYPE_LOADING, name);
String xml = getServiceTypeRelationshipsAsXML (name, false);
store (serviceTypesCache, name, xml);
+ fireEvent (SERVICE_TYPE_LOADED, name);
}
} catch (Exception e) {
throw new MobyException (formatException (e));
@@ -373,8 +386,10 @@
protected void fillNamespacesCache()
throws MobyException {
try {
+ fireEvent (NAMESPACE_LOADING, "Loading started.");
String xml = getNamespacesAsXML();
store (namespacesCache, LIST_FILE, xml);
+ fireEvent (NAMESPACE_LOADED, "Loaded.");
} catch (Exception e) {
throw new MobyException (formatException (e));
}
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestImpl.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestImpl.java 2005/09/22 16:07:09 1.5
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestImpl.java 2005/10/12 11:17:59 1.6
@@ -7,6 +7,9 @@
package org.biomoby.client;
import org.biomoby.shared.CentralDigest;
+import org.biomoby.shared.event.Notifier;
+import org.biomoby.shared.event.NotificationEvent;
+import org.biomoby.shared.event.NotificationListener;
import org.biomoby.shared.MobyDataType;
import org.biomoby.shared.MobyException;
import org.biomoby.shared.MobyService;
@@ -30,7 +33,7 @@
public class CentralDigestImpl
extends CentralImpl
- implements CentralDigest {
+ implements CentralDigest, Notifier {
// cached (digested) Moby
protected MobyDataType[] dataTypes = new MobyDataType[] {};
@@ -75,11 +78,13 @@
try {
Vector v = new Vector();
Map types = getDataTypeNames();
+ fireEvent (DATA_TYPE_COUNT, new Integer (types.size()));
for (Iterator it = types.entrySet().iterator(); it.hasNext(); ) {
Map.Entry entry = (Map.Entry)it.next();
String name = (String)entry.getKey();
- messageLn ("(CDI) Processing data type " + name + "...");
+ fireEvent (DATA_TYPE_LOADING, name);
v.addElement (getDataType (name));
+ fireEvent (DATA_TYPE_LOADED, name, v.lastElement());
}
MobyDataType[] result = new MobyDataType [v.size()];
v.copyInto (result);
@@ -98,14 +103,16 @@
try {
Vector v = new Vector();
Map types = getServiceTypes();
+ fireEvent (SERVICE_TYPE_COUNT, new Integer (types.size()));
for (Iterator it = types.entrySet().iterator(); it.hasNext(); ) {
Map.Entry entry = (Map.Entry)it.next();
String typeName = (String)entry.getKey();
- messageLn ("(CDI) Processing service type " + typeName + "...");
+ fireEvent (SERVICE_TYPE_LOADING, typeName);
MobyServiceType serviceType = new MobyServiceType (typeName);
serviceType.setDescription ((String)entry.getValue());
serviceType.setParentNames (getServiceTypeRelationships (typeName, false));
v.addElement (serviceType);
+ fireEvent (SERVICE_TYPE_LOADED, typeName, v.lastElement());
}
MobyServiceType[] result = new MobyServiceType [v.size()];
v.copyInto (result);
@@ -130,6 +137,7 @@
throws MobyException {
try {
Map names = getNamespaces();
+ fireEvent (NAMESPACE_COUNT, new Integer (names.size()));
MobyNamespace[] result = new MobyNamespace [ names.size() ];
int i = 0;
for (Iterator it = names.entrySet().iterator(); it.hasNext(); ) {
@@ -138,6 +146,7 @@
MobyNamespace ns = new MobyNamespace (name);
ns.setDescription ((String)entry.getValue());
result[i++] = ns;
+ fireEvent (NAMESPACE_LOADED, name, ns);
}
return result;
@@ -153,18 +162,19 @@
throws MobyException {
try {
Vector v = new Vector();
- messageLn ("(CDI) Asking for all service names...");
Map authorities = getServiceNamesByAuthority();
+ fireEvent (AUTHORITY_COUNT, new Integer (authorities.size()));
for (Iterator it = authorities.entrySet().iterator(); it.hasNext(); ) {
Map.Entry entry = (Map.Entry)it.next();
String authority = (String)entry.getKey();
+ fireEvent (AUTHORITY_LOADING, authority);
String[] names = (String[])entry.getValue();
for (int i = 0; i < names.length; i++) {
- messageLn ("(CDI) Processing service " + names[i] + "...");
MobyService[] servs = findService (new MobyService (names[i], authority));
for (int j = 0; j < servs.length; j++)
v.addElement (servs[j]);
}
+ fireEvent (AUTHORITY_LOADED, authority);
}
MobyService[] result = new MobyService [v.size()];
v.copyInto (result);
@@ -186,6 +196,8 @@
buf.append (e.toString());
buf.append (DGUtils.stackTraceToString (e));
return new String (buf);
+ } else if (e instanceof MobyException) {
+ return e.getMessage();
} else {
return e.toString();
}
@@ -291,6 +303,74 @@
}
}
+ /*************************************************************************
+ *
+ * Methods implementing Notifier interface.
+ *
+ *************************************************************************/
+
+ private Vector listeners;
+
+ /*********************************************************************
+ *
+ ********************************************************************/
+ public synchronized void addNotificationListener (NotificationListener l) {
+ if (listeners == null)
+ listeners = new Vector();
+ listeners.addElement (l);
+ }
+
+ /*********************************************************************
+ *
+ ********************************************************************/
+ public void removeNotificationListener (NotificationListener l) {
+ if (listeners != null)
+ listeners.removeElement (l);
+ }
+
+ /*********************************************************************
+ *
+ ********************************************************************/
+ public NotificationListener[] getNotificationListeners() {
+ if (listeners == null)
+ return new NotificationListener[] {};
+ synchronized (listeners) {
+ NotificationListener[] result = new NotificationListener [listeners.size()];
+ listeners.copyInto (result);
+ return result;
+ }
+ }
+
+ /*********************************************************************
+ *
+ ********************************************************************/
+ protected void fireEvent (String type, Object message) {
+ fireEvent (type, message, null);
+ }
+
+ /*********************************************************************
+ *
+ ********************************************************************/
+ protected void fireEvent (String type, Object message, Object details) {
+ NotificationEvent event = null;
+ if (details == null)
+ event = new NotificationEvent (this, type, message.toString());
+ else
+ event = new NotificationEvent (this, type, message.toString(), details);
+ if (listeners != null) {
+ synchronized (listeners) {
+ for (int i = 0; i < listeners.size(); i++) {
+ NotificationListener listener = (NotificationListener)listeners.elementAt(i);
+ listener.notified (event);
+ }
+ }
+ }
+ }
+
+
+
+
+
// Work in progress - implement the methods above by getting RDF
// graphs in-one-go and parsing them. Actually ability to get such
// graphs was the main motivation for this implementation, and for
From senger at pub.open-bio.org Wed Oct 12 07:36:59 2005
From: senger at pub.open-bio.org (Martin Senger)
Date: Wed Oct 12 08:26:36 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200510121136.j9CBaxY3013784@pub.open-bio.org>
senger
Wed Oct 12 07:36:59 EDT 2005
Update of /home/repository/moby/moby-live/Java/src/Clients
In directory pub.open-bio.org:/tmp/cvs-serv13765/src/Clients
Modified Files:
UnregisterByAuthority.java
Log Message:
moby-live/Java/src/Clients UnregisterByAuthority.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/Clients/UnregisterByAuthority.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/Clients/UnregisterByAuthority.java 2005/09/04 13:45:37 1.2
+++ /home/repository/moby/moby-live/Java/src/Clients/UnregisterByAuthority.java 2005/10/12 11:36:59 1.3
@@ -6,7 +6,6 @@
// Copyright Martin Senger (martin.senger@gmail.com).
//
-import org.biomoby.shared.MobyException;
import org.biomoby.shared.MobyService;
import org.biomoby.shared.Central;
import org.biomoby.client.CentralImpl;
@@ -14,7 +13,6 @@
import org.tulsoft.tools.BaseCmdLine;
import java.util.Map;
-import java.util.Map.Entry;
import java.util.Iterator;
/**
From senger at pub.open-bio.org Wed Oct 12 07:36:59 2005
From: senger at pub.open-bio.org (Martin Senger)
Date: Wed Oct 12 08:26:37 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200510121136.j9CBaxB4013808@pub.open-bio.org>
senger
Wed Oct 12 07:36:59 EDT 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory pub.open-bio.org:/tmp/cvs-serv13765/src/main/org/biomoby/client
Modified Files:
BaseCmdLineClient.java CentralImpl.java
Log Message:
moby-live/Java/src/main/org/biomoby/client BaseCmdLineClient.java,1.3,1.4 CentralImpl.java,1.28,1.29
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/BaseCmdLineClient.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/BaseCmdLineClient.java 2005/09/22 16:07:08 1.3
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/BaseCmdLineClient.java 2005/10/12 11:36:59 1.4
@@ -27,7 +27,6 @@
import java.util.HashMap;
import java.util.Iterator;
import java.util.Map;
-import java.util.Map.Entry;
import java.util.Arrays;
import java.io.IOException;
import java.io.File;
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java,v
retrieving revision 1.28
retrieving revision 1.29
diff -u -r1.28 -r1.29
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2005/09/24 17:51:51 1.28
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2005/10/12 11:36:59 1.29
@@ -20,10 +20,8 @@
import org.biomoby.shared.MobyServiceType;
import org.biomoby.shared.NoSuccessException;
import org.biomoby.shared.PendingCurationException;
-import org.biomoby.shared.Utils;
import org.biomoby.shared.MobyResourceRef;
-import org.tulsoft.shared.UUtils;
import org.tulsoft.tools.soap.axis.AxisUtils;
import org.w3c.dom.Document;
From senger at pub.open-bio.org Wed Oct 12 07:36:59 2005
From: senger at pub.open-bio.org (Martin Senger)
Date: Wed Oct 12 08:26:37 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200510121136.j9CBaxvW013827@pub.open-bio.org>
senger
Wed Oct 12 07:36:59 EDT 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/event
In directory pub.open-bio.org:/tmp/cvs-serv13765/src/main/org/biomoby/shared/event
Modified Files:
Notifier.java
Log Message:
moby-live/Java/src/main/org/biomoby/shared/event Notifier.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/event/Notifier.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/event/Notifier.java 2005/10/12 11:17:59 1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/event/Notifier.java 2005/10/12 11:36:59 1.2
@@ -37,7 +37,7 @@
* notification events from the class that implements this
* interface.
*
- * @param the notification listener to be added
+ * @param l notification listener to be added
********************************************************************/
void addNotificationListener (NotificationListener l);
@@ -46,7 +46,7 @@
* longer receives notification events from the class that
* implements this interface.
*
- * @param the notification listener to be removed
+ * @param l notification listener to be removed
********************************************************************/
void removeNotificationListener (NotificationListener l);
From kawas at pub.open-bio.org Wed Oct 12 12:34:40 2005
From: kawas at pub.open-bio.org (Eddie Kawas)
Date: Wed Oct 12 13:24:14 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200510121634.j9CGYeI1014509@pub.open-bio.org>
kawas
Wed Oct 12 12:34:40 EDT 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv14484/org/biomoby/client/rdf/vocabulary
Modified Files:
Predicates.java
Log Message:
organized import statements
moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary Predicates.java,1.7,1.8
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java 2005/08/30 18:31:30 1.7
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/Predicates.java 2005/10/12 16:34:40 1.8
@@ -1,8 +1,4 @@
package org.biomoby.client.rdf.vocabulary;
-import java.util.Properties;
-
-import org.biomoby.registry.properties.MobyProperties;
-
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.Property;
From kawas at pub.open-bio.org Wed Oct 12 13:13:29 2005
From: kawas at pub.open-bio.org (Eddie Kawas)
Date: Wed Oct 12 14:03:04 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200510121713.j9CHDTxp014638@pub.open-bio.org>
kawas
Wed Oct 12 13:13:28 EDT 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/schema
In directory pub.open-bio.org:/tmp/cvs-serv14601/org/biomoby/shared/schema
Modified Files:
MElementHashtable.java Frame.java GenericWindowListener.java
PrimitiveVector.java
Added Files:
ServiceInstanceWSDL.java
Log Message:
organized import statements
moby-live/Java/src/main/org/biomoby/shared/schema ServiceInstanceWSDL.java,NONE,1.1 MElementHashtable.java,1.1,1.2 Frame.java,1.2,1.3 GenericWindowListener.java,1.1,1.2 PrimitiveVector.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/schema/MElementHashtable.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/schema/MElementHashtable.java 2005/08/30 18:34:11 1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/schema/MElementHashtable.java 2005/10/12 17:13:28 1.2
@@ -7,7 +7,8 @@
package org.biomoby.shared.schema;
-import java.util.*;
+import java.util.Hashtable;
+import java.util.Vector;
public class MElementHashtable
{
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/schema/Frame.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/schema/Frame.java 2005/09/06 21:29:50 1.2
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/schema/Frame.java 2005/10/12 17:13:28 1.3
@@ -29,6 +29,11 @@
*/
public class Frame extends JFrame{
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1939367498077695253L;
+
public Frame()
{
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/schema/GenericWindowListener.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/schema/GenericWindowListener.java 2005/08/30 18:34:11 1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/schema/GenericWindowListener.java 2005/10/12 17:13:28 1.2
@@ -12,7 +12,8 @@
* TODO To change the template for this generated type comment go to
* Window - Preferences - Java - Code Style - Code Templates
*/
-import java.awt.event.*;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
public class GenericWindowListener extends WindowAdapter {
public void windowClosing(WindowEvent event)
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/schema/PrimitiveVector.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/schema/PrimitiveVector.java 2005/08/30 18:34:11 1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/schema/PrimitiveVector.java 2005/10/12 17:13:28 1.2
@@ -6,7 +6,7 @@
package org.biomoby.shared.schema;
-import java.util.*;
+import java.util.Vector;
public class PrimitiveVector
{
From kawas at pub.open-bio.org Wed Oct 12 13:57:54 2005
From: kawas at pub.open-bio.org (Eddie Kawas)
Date: Wed Oct 12 14:47:29 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200510121757.j9CHvskS014779@pub.open-bio.org>
kawas
Wed Oct 12 13:57:54 EDT 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool
In directory pub.open-bio.org:/tmp/cvs-serv14742/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool
Modified Files:
ServiceFocusListener.java ServiceInstancePanelFactory.java
DescriptionWindow.java ServiceActionListener.java
Log Message:
organized import statements, removed variables that werent read, etc.
moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool ServiceFocusListener.java,1.3,1.4 ServiceInstancePanelFactory.java,1.4,1.5 DescriptionWindow.java,1.2,1.3 ServiceActionListener.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/ServiceFocusListener.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/ServiceFocusListener.java 2005/08/31 23:56:39 1.3
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/ServiceFocusListener.java 2005/10/12 17:57:54 1.4
@@ -6,7 +6,6 @@
import java.awt.event.FocusEvent;
import java.awt.event.FocusListener;
-import javax.swing.JFrame;
import javax.swing.JTextArea;
import javax.swing.JTextField;
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/ServiceInstancePanelFactory.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/ServiceInstancePanelFactory.java 2005/08/31 23:56:39 1.4
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/ServiceInstancePanelFactory.java 2005/10/12 17:57:54 1.5
@@ -28,7 +28,6 @@
import javax.swing.JTextArea;
import javax.swing.JTextField;
import javax.swing.ListSelectionModel;
-import javax.swing.text.Style;
import org.biomoby.client.ui.graphical.applets.shared.MobyTree;
import org.biomoby.client.ui.graphical.applets.util.TreeLoaderThread;
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/DescriptionWindow.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/DescriptionWindow.java 2005/09/01 00:03:56 1.2
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/DescriptionWindow.java 2005/10/12 17:57:54 1.3
@@ -21,6 +21,10 @@
*/
public class DescriptionWindow extends JDialog {
+ /**
+ *
+ */
+ private static final long serialVersionUID = -7369426386153906403L;
private javax.swing.JPanel panel = null;
private JPanel buttonpanel = null;
private JButton btnClose = null;
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/ServiceActionListener.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/ServiceActionListener.java 2005/08/31 23:56:39 1.2
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/ServiceActionListener.java 2005/10/12 17:57:54 1.3
@@ -16,7 +16,6 @@
import javax.swing.JPanel;
import org.biomoby.client.rdf.builder.ServiceInstanceRDF;
-import org.biomoby.client.ui.graphical.applets.util.REGEXP;
/**
* @author Edward Kawas Created on July 7, 2004
From kawas at pub.open-bio.org Wed Oct 12 13:57:54 2005
From: kawas at pub.open-bio.org (Eddie Kawas)
Date: Wed Oct 12 14:47:31 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200510121757.j9CHvsCM014798@pub.open-bio.org>
kawas
Wed Oct 12 13:57:54 EDT 2005
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/shared
In directory pub.open-bio.org:/tmp/cvs-serv14742/org/biomoby/client/ui/graphical/applets/shared
Modified Files:
MobyTree.java
Log Message:
organized import statements, removed variables that werent read, etc.
moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/shared MobyTree.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/shared/MobyTree.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/shared/MobyTree.java 2005/09/30 14:44:58 1.3
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/shared/MobyTree.java 2005/10/12 17:57:54 1.4
@@ -1,5 +1,7 @@
package org.biomoby.client.ui.graphical.applets.shared;
+import java.awt.BorderLayout;
+import java.awt.Dimension;
import java.awt.GridLayout;
import java.awt.Toolkit;
import java.util.ArrayList;
@@ -7,6 +9,7 @@
import java.util.HashMap;
import java.util.Iterator;
+import javax.swing.JFrame;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.JTree;
@@ -350,4 +353,21 @@
tree.clearSelection();
tree.collapseRow(0);
}
+
+ public static void main(String[] args) {
+ JFrame frame = new JFrame();
+ MobyTree tree = new MobyTree(false, "http://localhost:8080/RESOURCES/MOBY-S/Objects", "Object");
+ tree.makeObjectTree("Object");
+ tree.setPreferredSize(new Dimension(400, 400));
+ // Add button to the frame
+ frame.getContentPane().add(tree, BorderLayout.CENTER);
+
+ // Set initial size
+ int frameWidth = 300;
+ int frameHeight = 300;
+ frame.setSize(frameWidth, frameHeight);
+
+ // Show the frame
+ frame.setVisible(true);
+ }
}
From gss at pub.open-bio.org Fri Oct 14 17:29:55 2005
From: gss at pub.open-bio.org (Gary Schiltz)
Date: Fri Oct 14 18:19:16 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200510142129.j9ELTtr0025016@pub.open-bio.org>
gss
Fri Oct 14 17:29:54 EDT 2005
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/servlets
In directory pub.open-bio.org:/tmp/cvs-serv24990/src/org/semanticmoby/ref/servlets
Modified Files:
KeywordSearchServlet.java
Log Message:
Explicitly import org.semanticmoby.ref.tools.db.DBConnection to disambiguate from Jena's DBConnection class
moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/servlets KeywordSearchServlet.java,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/servlets/KeywordSearchServlet.java,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/src/org/semanticmoby/ref/servlets/KeywordSearchServlet.java 2005/10/09 01:11:21 1.5
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/src/org/semanticmoby/ref/servlets/KeywordSearchServlet.java 2005/10/14 21:29:54 1.6
@@ -9,6 +9,7 @@
import org.semanticmoby.ref.tools.*;
import org.semanticmoby.ref.tools.db.*;
+import org.semanticmoby.ref.tools.db.DBConnection;
import org.semanticmoby.tools.Util;
From gss at pub.open-bio.org Fri Oct 14 17:56:18 2005
From: gss at pub.open-bio.org (Gary Schiltz)
Date: Fri Oct 14 18:45:38 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200510142156.j9ELuI8i025115@pub.open-bio.org>
gss
Fri Oct 14 17:56:18 EDT 2005
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/build
In directory pub.open-bio.org:/tmp/cvs-serv25090/S-MOBY/ref-impl/semanticmoby.org/build
Modified Files:
build.xml
Log Message:
Removed jalopy stuff
moby-live/S-MOBY/ref-impl/semanticmoby.org/build build.xml,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/build/build.xml,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/build/build.xml 2005/10/09 01:17:49 1.6
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/build/build.xml 2005/10/14 21:56:18 1.7
@@ -140,26 +140,4 @@
We updated the BioMoby plugin so that we could add functionality that we believed was missing. In the past, users of the plugin were forced to start every Moby based workflow with the root Moby In addition, in Taverna releases prior to version 1.2, the BioMoby services were always limited to one The updated BioMoby plugin contains many new features. Some of these features include the following: To start using these new features, please follow the short tutorial below! Creating a new BioMoby scavenger has never been easier! In fact, if you are familar with Taverna, Starting from the 'Available Services' window, you will need to context click the folder labeled Performing a context click on the selected folder reveals the following menu. Notice how Upon making our selection, we will be prompted to enter certain information that will allow Taverna You may now be scratching your head, and are wondering why you have never heard of this RDF document. Once the information has been inputted into the text boxes, the Moby services and datatypes will now be available If you would like to work with your own custom Mobycentral registry and not that of the default, http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl, then it is recommended that you edit the /taverna-workbench-1.3/conf/mygrid.properties file. In this file, modify the value for the property taverna.defaultbiomoby replacing the URL with that of your custom registry. Workflow used in this tutorial may be downloaded here. Creating a workflow with the new BioMoby plugin is as easy as it was using the previous plugin. There are, of course, As an example, we will add the Moby datatype called DNASequence to our workflow. In order to do this, we must 'DNASequence' has now been added to the workflow diagram. To reveal what inputs and outputs this processor Notice how 'DNASequence' takes as input a namespace, an id, an article name, and 2 Moby datatypes: String and Our workflow diagram
-looks something like the following: A complex BioMoby datatype. 'DNASequence', and all of its subcomponents have now been added to our workflow. We will add the service 'runFasta' from the authority 'www.pcm.uam.es'. This service runs the fasta tool on the input The next thing to do is to connect the input of the 'runFasta' processor to the output of 'DNASequence'. It should be noted We are almost done! The only things that are missing now are the workflow inputs and the workflow outputs. We will create We will also create a workflow output called 'output'. This workflow output will be connected to the Once these connections have been made, you should have something similar to the image below. Note that the image is only showing So there we have a completed workflow based on BioMoby Services and datatypes. If you wish to run this The output from this data is shown below. One of the neatest things added to the plugin was the ability to obtain information regarding BioMoby datatypes. For As an example, imagine that we wanted to discover what services the Moby datatype 'Integer' feeds into. To do this, we As soon as you choose 'Moby Object Details', a pop up window appears and embedded in that window When you navigate the sub tree
- and mouse over the service name, a tool tip appears giving you the In addition, you can context click the service name, in this case
- PupaSNP,
- and a menu is shown: From this menu, you can choose to either add the selected service to the workflow or view more a more detailed The sub tree
- 'Produced by' offers similar information, except about services that produce the datatype in question. As with Moby datatypes, information about services is also available. For a particular service, we can determine Using the workflow that we created above, we can discover what inputs and outputs 'runFasta' utilize. To determine this, A pop window appears and embedded in it is a tree that has as its root the name of the Moby Similarly to the 'Moby Object Details', you can either add the input datatype to the workflow or In the future, we hope to add even more functionality to the plugin. Below are some of the features that If there are specific features that you would like us to consider, please contact the BioMoby development If you have any questions or comments, please feel free to contact Eddie Kawas @ If you have any suggestions regarding new features or you would like to report a bug, We updated the BioMoby plugin so that we could add functionality that we believed was missing. In the past, users of the plugin were forced to start every Moby based workflow with the root Moby In addition, in Taverna releases prior to version 1.2, the BioMoby services were always limited to one The updated BioMoby plugin contains many new features. Some of these features include the following: To start using these new features, please follow the short tutorial below! Creating a new BioMoby scavenger has never been easier! In fact, if you are familar with Taverna, Starting from the 'Available Services' window, you will need to context click the folder labeled Performing a context click on the selected folder reveals the following menu. Notice how Upon making our selection, we will be prompted to enter certain information that will allow Taverna You may now be scratching your head, and are wondering why you have never heard of this RDF document. Once the information has been inputted into the text boxes, the Moby services and datatypes will now be available If you would like to work with your own custom Mobycentral registry and not that of the default, http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl, then it is recommended that you edit the /taverna-workbench-1.3/conf/mygrid.properties file. In this file, modify the value for the property taverna.defaultbiomoby replacing the URL with that of your custom registry. If you would like to host your own local custom registry, please click here. Workflow used in this tutorial may be downloaded here. Creating a workflow with the new BioMoby plugin is as easy as it was using the previous plugin. There are, of course, As an example, we will add the Moby datatype called DNASequence to our workflow. In order to do this, we must 'DNASequence' has now been added to the workflow diagram. To reveal what inputs and outputs this processor Notice how 'DNASequence' takes as input a namespace, an id, an article name, and 2 Moby datatypes: String and Our workflow diagram
+
+looks something like the following: A complex BioMoby datatype. 'DNASequence', and all of its subcomponents have now been added to our workflow. We will add the service 'runFasta' from the authority 'www.pcm.uam.es'. This service runs the fasta tool on the input The next thing to do is to connect the input of the 'runFasta' processor to the output of 'DNASequence'. It should be noted We are almost done! The only things that are missing now are the workflow inputs and the workflow outputs. We will create We will also create a workflow output called 'output'. This workflow output will be connected to the Once these connections have been made, you should have something similar to the image below. Note that the image is only showing So there we have a completed workflow based on BioMoby Services and datatypes. If you wish to run this The output from this data is shown below. One of the neatest things added to the plugin was the ability to obtain information regarding BioMoby datatypes. For As an example, imagine that we wanted to discover what services the Moby datatype 'Integer' feeds into. To do this, we As soon as you choose 'Moby Object Details', a pop up window appears and embedded in that window When you navigate the sub tree
+
+ and mouse over the service name, a tool tip appears giving you the In addition, you can context click the service name, in this case
+
+ PupaSNP,
+
+ and a menu is shown: From this menu, you can choose to either add the selected service to the workflow or view more a more detailed The sub tree
+
+ 'Produced by' offers similar information, except about services that produce the datatype in question. As with Moby datatypes, information about services is also available. For a particular service, we can determine Using the workflow that we created above, we can discover what inputs and outputs 'runFasta' utilize. To determine this, A pop window appears and embedded in it is a tree that has as its root the name of the Moby Similarly to the 'Moby Object Details', you can either add the input datatype to the workflow or In the future, we hope to add even more functionality to the plugin. Below are some of the features that If there are specific features that you would like us to consider, please contact the BioMoby development If you have any questions or comments, please feel free to contact Eddie Kawas @ If you have any suggestions regarding new features or you would like to report a bug, To start using these new features, please follow the short tutorial below! Click here to download BioMoby workflows.
-Last modified: Wed Sep 21 15:27:30 2005
+Last modified: Tue Oct 18 22:04:57 2005
How to use the BioMoby plugin in Taverna 1.3
-
-
-
-
+
+
+
+
+
+
+
+
+Introduction
-
-
-
- datatype. In other words, you were able to utilize a local widget called 'create_moby_data', however,
- the Moby data really was just the root datatype in disguise.
- input and one output. This worked for many of the Moby services, but for those wishing to create a
- workflow that initally utilized a service with more inputs, that option just wasn't available.New Features
-
-
-
-
- Tutorial
-
-
- Creating a BioMoby Scavenger
-
-
-
- then adding a BioMoby scavenger is just like adding any other scavenger.
- 'Available Processors'. Below is a image illustrating the 'Available Services' window.
- we chose to add new BioMoby scavenger.
- to create our scavenger. The information that we need to provide includes the URL of the BioMoby
- central registry that we would like to use, as well as the URL of the RDF document describing the
- BioMoby datatype ontology.
- Currently, this location is undocumented in the Moby API, and the API will be supplemented with this information
- at a later time. At the time that this tutorial was written, there was only one location known for this RDF document
- and it is the default one in Taverna (shown above)
- .
- as processors in the 'Available Services' window.Creating a workflow
-
-
-
- Workflow input used in this tutorial may be downloaded here.
- a few
- differences. When creating workflows, it is no longer necessary to use the local widget 'create_moby_data'.
- When you are ready to instantiate a Moby datatype, all that is necessary is for you to choose the datatype from the list
- of 'Available Processors' under the 'Moby Objects' folder.
- navigate the datatype ontology to find DNASequence. We can find DNASequence by traversing the 'Moby Objects'
- tree in the following order:
- Object, VirtualSequence, GenericSequence, NucleotideSequence and finally DNASequence.
- Now that we have found the processor that we were looking for, let's add it to the workflow.
- utilizes, we need to ask Taverna to show us all of the ports in the workflow diagram.
- Integer. Since 'String' and 'Integer' are Moby datatypes contained within a 'DNASequence', they have been conveniently
- added to the workflow and linked appropriately.
- Next we will add a BioMoby service processor that handles our complex datatype.
- sequence
- . From the list of processors, we will navigate to www.pcm.uam.es and then choose the service that we are
- interested in, i.e. 'runFasta'.
- that there are 2 inputs to the processor 'runFasta': 'GenericSequence(_ANON_)' and 'input'. The port labelled 'input' serves to
- support workflows created prior to Taverna 1.2 and should be used when you create workflows utilizing the Local Widgets
- 'create_moby_data'.
- For our workflow, we will connect the complex datatype 'DNASequence' to the input port labeled
- 'DNASequence(sequence)' of the 'runFasta' processor.
- the following inputs:
-
-
- output port, 'FASTA_Text(_ANON_)' of the processor 'runFasta'.
- those ports that are bound to inputs or outputs.
- workflow, some suitable values for the workflow inputs are as follows:
-
- Obtaining information on a Moby datatype
-
-
-
- instance, you can find out what services a particular datatype can be used as input or output. In addition, you can find
- the descriptions of those services.
- can use our existing workflow. From the 'Advanced model explorer' window, context click on the processor called 'Integer'
- and choose 'Moby Object Details'.
- is a tree like structure. Note that this window can take up to a minute to appear depending on your
- internet connection and the data type chosen. At the root of the tree is the datatype that we chose to
- know more about, in our case
- 'Integer', and 2 sub trees labeled 'Feeds into' and 'Produced by'. In the
- 'Feeds into' sub tree, you will find out
- what BioMoby services consume the datatype in question, sorted by
- authority.
- description of the service.
- service description. Below, the window that appears upon choosing to 'Find out about PupaSNP':
- The context menu is not available for children of the 'Produced by' node. Obtaining information on a Moby service
-
-
-
- what are the inputs and outputs. And if you wish, you may add the input datatypes to the workflow.In addition,
- we can also discover what namespaces a particular input or output
- is valid in.
- we need to context click on the 'runFasta' processor from the 'Advanced model explorer', just as we had done before
- with the Moby datatype processors above, and choose 'Moby Service Details'.
- service. The children of the root node are 2 sub trees, 'Inputs' and 'Outputs'. The items under
- these sub trees simply illustrate what datatypes the service consumes and produces.
- obtain additional information on the datatype:What's Next
-
-
-
- we have thought about:
-
-
- team. Comments / Questions
-
-
-
- edward[DoT]kawas[AT]gmail[DoT]com
- please let me know.How to use the BioMoby plugin in Taverna 1.3
+
+
+
+
+
+
+
+
+
From kawas at pub.open-bio.org Wed Oct 19 18:13:11 2005
From: kawas at pub.open-bio.org (Eddie Kawas)
Date: Wed Oct 19 19:02:01 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200510192213.j9JMDBR4021823@pub.open-bio.org>
kawas
Wed Oct 19 18:13:11 EDT 2005
Update of /home/repository/moby/moby-live/Java/docs/taverna/guide
In directory pub.open-bio.org:/tmp/cvs-serv21796
Modified Files:
index.html
Added Files:
workflows.html
Log Message:
added a way to view the preconstructed workflows
moby-live/Java/docs/taverna/guide workflows.html,NONE,1.1 index.html,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/taverna/guide/index.html,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/docs/taverna/guide/index.html 2005/10/19 22:00:26 1.2
+++ /home/repository/moby/moby-live/Java/docs/taverna/guide/index.html 2005/10/19 22:13:11 1.3
@@ -61,7 +61,7 @@
Introduction
+
+
+
+
+
+
+
+ datatype. In other words, you were able to utilize a local widget called 'create_moby_data', however,
+
+ the Moby data really was just the root datatype in disguise.
+
+ input and one output. This worked for many of the Moby services, but for those wishing to create a
+
+ workflow that initally utilized a service with more inputs, that option just wasn't available.New Features
+
+
+
+
+
+
+
+
+
+ Tutorial
+
+
+
+
+
+ Creating a BioMoby Scavenger
+
+
+
+
+
+
+
+ then adding a BioMoby scavenger is just like adding any other scavenger.
+
+ 'Available Processors'. Below is a image illustrating the 'Available Services' window.
+
+ we chose to add new BioMoby scavenger.
+
+ to create our scavenger. The information that we need to provide includes the URL of the BioMoby
+
+ central registry that we would like to use, as well as the URL of the RDF document describing the
+
+ BioMoby datatype ontology.
+
+ Currently, this location is undocumented in the Moby API, and the API will be supplemented with this information
+
+ at a later time. At the time that this tutorial was written, there was only one location known for this RDF document
+
+ and it is the default one in Taverna (shown above)
+
+ .
+
+ as processors in the 'Available Services' window.Creating a workflow
+
+
+
+
+
+
+
+ Workflow input used in this tutorial may be downloaded here.
+
+ a few
+
+ differences. When creating workflows, it is no longer necessary to use the local widget 'create_moby_data'.
+
+ When you are ready to instantiate a Moby datatype, all that is necessary is for you to choose the datatype from the list
+
+ of 'Available Processors' under the 'Moby Objects' folder.
+
+ navigate the datatype ontology to find DNASequence. We can find DNASequence by traversing the 'Moby Objects'
+
+ tree in the following order:
+
+ Object, VirtualSequence, GenericSequence, NucleotideSequence and finally DNASequence.
+
+ Now that we have found the processor that we were looking for, let's add it to the workflow.
+
+ utilizes, we need to ask Taverna to show us all of the ports in the workflow diagram.
+
+ Integer. Since 'String' and 'Integer' are Moby datatypes contained within a 'DNASequence', they have been conveniently
+
+ added to the workflow and linked appropriately.
+
+ Next we will add a BioMoby service processor that handles our complex datatype.
+
+ sequence
+
+ . From the list of processors, we will navigate to www.pcm.uam.es and then choose the service that we are
+
+ interested in, i.e. 'runFasta'.
+
+ that there are 2 inputs to the processor 'runFasta': 'GenericSequence(_ANON_)' and 'input'. The port labelled 'input' serves to
+
+ support workflows created prior to Taverna 1.2 and should be used when you create workflows utilizing the Local Widgets
+
+ 'create_moby_data'.
+
+ For our workflow, we will connect the complex datatype 'DNASequence' to the input port labeled
+
+ 'DNASequence(sequence)' of the 'runFasta' processor.
+
+ the following inputs:
+
+
+
+
+
+ output port, 'FASTA_Text(_ANON_)' of the processor 'runFasta'.
+
+ those ports that are bound to inputs or outputs.
+
+ workflow, some suitable values for the workflow inputs are as follows:
+
+
+
+ Obtaining information on a Moby datatype
+
+
+
+
+
+
+
+ instance, you can find out what services a particular datatype can be used as input or output. In addition, you can find
+
+ the descriptions of those services.
+
+ can use our existing workflow. From the 'Advanced model explorer' window, context click on the processor called 'Integer'
+
+ and choose 'Moby Object Details'.
+
+ is a tree like structure. Note that this window can take up to a minute to appear depending on your
+
+ internet connection and the data type chosen. At the root of the tree is the datatype that we chose to
+
+ know more about, in our case
+
+ 'Integer', and 2 sub trees labeled 'Feeds into' and 'Produced by'. In the
+
+ 'Feeds into' sub tree, you will find out
+
+ what BioMoby services consume the datatype in question, sorted by
+
+ authority.
+
+ description of the service.
+
+ service description. Below, the window that appears upon choosing to 'Find out about PupaSNP':
+
+ The context menu is not available for children of the 'Produced by' node. Obtaining information on a Moby service
+
+
+
+
+
+
+
+ what are the inputs and outputs. And if you wish, you may add the input datatypes to the workflow.In addition,
+
+ we can also discover what namespaces a particular input or output
+
+ is valid in.
+
+ we need to context click on the 'runFasta' processor from the 'Advanced model explorer', just as we had done before
+
+ with the Moby datatype processors above, and choose 'Moby Service Details'.
+
+ service. The children of the root node are 2 sub trees, 'Inputs' and 'Outputs'. The items under
+
+ these sub trees simply illustrate what datatypes the service consumes and produces.
+
+ obtain additional information on the datatype:What's Next
+
+
+
+
+
+
+
+ we have thought about:
+
+
+
+
+
+ team. Comments / Questions
+
+
+
+
+
+
+
+ edward[DoT]kawas[AT]gmail[DoT]com
+
+ please let me know.Tutorial
From kawas at pub.open-bio.org Wed Oct 19 18:27:22 2005
From: kawas at pub.open-bio.org (Eddie Kawas)
Date: Wed Oct 19 19:16:11 2005
Subject: [MOBY-guts] biomoby commit
Message-ID: <200510192227.j9JMRMuw022280@pub.open-bio.org>
kawas
Wed Oct 19 18:27:22 EDT 2005
Update of /home/repository/moby/moby-live/Java/docs/taverna/guide
In directory pub.open-bio.org:/tmp/cvs-serv22255
Modified Files:
index.html
Log Message:
added a question/answer and modified the scavenger section.
moby-live/Java/docs/taverna/guide index.html,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/taverna/guide/index.html,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/docs/taverna/guide/index.html 2005/10/19 22:13:11 1.3
+++ /home/repository/moby/moby-live/Java/docs/taverna/guide/index.html 2005/10/19 22:27:22 1.4
@@ -10,6 +10,14 @@
- central registry that we would like to use, as well as the URL of the RDF document describing the
-
- BioMoby datatype ontology.
You may now be scratching your head, and are wondering why you have never heard of this RDF document.
-
- Currently, this location is undocumented in the Moby API, and the API will be supplemented with this information
-
- at a later time. At the time that this tutorial was written, there was only one location known for this RDF document
-
- and it is the default one in Taverna (shown above)
-
- .
Once the information has been inputted into the text boxes, the Moby services and datatypes will now be available
as processors in the 'Available Services' window.
-
If you would like to work with your own custom Mobycentral registry and not that of the default, http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl, then it is recommended that you edit the /taverna-workbench-1.3/conf/mygrid.properties file. In this file, modify the value for the property taverna.defaultbiomoby replacing the URL with that of your custom registry.
+If you would like to work with your own custom Mobycentral registry and not that of the default,
+ http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl, then it is recommended that you
+ edit the /taverna-workbench-1.3/conf/mygrid.properties file. In this file, modify the value for the
+ property taverna.defaultbiomoby replacing the URL with that of your custom registry.
If you would like to host your own local custom registry, please click here.
@@ -375,13 +375,19 @@- +Questions
++
+- How does one go about installing a local registry? +
+++To install your own registry, please go here.
+
If you have any questions or comments, please feel free to contact Eddie Kawas @
-
edward[DoT]kawas[AT]gmail[DoT]comIf you have any suggestions regarding new features or you would like to report a bug,
From kawas at pub.open-bio.org Wed Oct 19 18:34:38 2005 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Wed Oct 19 19:23:26 2005 Subject: [MOBY-guts] biomoby commit Message-ID: <200510192234.j9JMYcfH022536@pub.open-bio.org> kawas Wed Oct 19 18:34:38 EDT 2005 Update of /home/repository/moby/moby-live/Java/docs/taverna/guide In directory pub.open-bio.org:/tmp/cvs-serv22511 Modified Files: workflows.html Log Message: fixed the links - noticed that the workflows have a timestamp appended to them moby-live/Java/docs/taverna/guide workflows.html,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/taverna/guide/workflows.html,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/docs/taverna/guide/workflows.html 2005/10/19 22:13:11 1.1 +++ /home/repository/moby/moby-live/Java/docs/taverna/guide/workflows.html 2005/10/19 22:34:38 1.2 @@ -1,22 +1,24 @@ - -
please let me know.Taverna Workflows - - + +Taverna Workflows + +Taverna Workflows
-Name Last modified Size Description+ +
1 - workflow.xml 13-Oct-2005 15:26 11K - 1 - workflowInput.xml 13-Oct-2005 15:26 4.6K - 2 - blastDragonDbWor..> 13-Oct-2005 15:26 10K - 3 - cos_fixedInput.xml 13-Oct-2005 15:26 4.1K - 4 - characterizeGene..> 13-Oct-2005 15:26 7.7K +Name Last modified Size Description- +
1 - workflow.xml 13-Oct-2005 15:26 11K + 1 - workflowInput.xml 13-Oct-2005 15:26 4.6K + 2 - blastDragonDbWor..> 13-Oct-2005 15:26 10K + 3 - cos_fixedInput.xml 13-Oct-2005 15:26 4.1K + 4 - characterizeGene..> 13-Oct-2005 15:26 7.7K - 5 - BlastQueryAgains..> 13-Oct-2005 15:26 3.0K - 6 - compareKeywordAn..> 13-Oct-2005 15:26 6.2K - 7 - compareKeywordAn..> 13-Oct-2005 15:26 13K - 8 - hmm dragon workf..> 13-Oct-2005 15:26 7.1K + 5 - BlastQueryAgains..> 13-Oct-2005 15:26 3.0K + 6 - compareKeywordAn..> 13-Oct-2005 15:26 6.2K + 7 - compareKeywordAn..> 13-Oct-2005 15:26 13K + 8 - hmm dragon workf..> 13-Oct-2005 15:26 7.1K 9 - DNASequenceHolde..> 13-Oct-2005 15:26 10K readme.txt 13-Oct-2005 15:26 127 -
+