How to develop with jMoby
-
+
- The twelve commandments for jMoby Developers (and some good advice)
- Available APIs (more explanation coming...)
- How to develop a client talking to a BioMoby service
- How to develop a BioMoby service (coming...) From gordonp at pub.open-bio.org Thu May 12 00:58:12 2005 From: gordonp at pub.open-bio.org (Paul Gordon) Date: Thu May 12 00:36:49 2005 Subject: [MOBY-guts] biomoby commit Message-ID: <200505120458.j4C4wCYs026015@pub.open-bio.org> gordonp Thu May 12 00:58:12 EDT 2005 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data In directory pub.open-bio.org:/tmp/cvs-serv25991/main/org/biomoby/shared/data Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data added to the repository moby-live/Java/src/main/org/biomoby/shared/data - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/RCS/directory,v: No such file or directory From gordonp at pub.open-bio.org Thu May 12 00:59:49 2005 From: gordonp at pub.open-bio.org (Paul Gordon) Date: Thu May 12 00:38:19 2005 Subject: [MOBY-guts] biomoby commit Message-ID: <200505120459.j4C4xndH026055@pub.open-bio.org> gordonp Thu May 12 00:59:49 EDT 2005 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data In directory pub.open-bio.org:/tmp/cvs-serv26034 Added Files: MobyDataBytes.java MobyDataComposite.java MobyDataDateTime.java MobyDataFloat.java MobyDataInstance.java MobyDataInt.java MobyDataObject.java MobyDataObjectSet.java MobyDataSecondaryInstance.java MobyDataServiceAssocInstance.java MobyDataString.java MobyDataXref.java Log Message: Moved Data instances classes to new package, and included complete experimental instance implementations moby-live/Java/src/main/org/biomoby/shared/data MobyDataBytes.java,NONE,1.1 MobyDataComposite.java,NONE,1.1 MobyDataDateTime.java,NONE,1.1 MobyDataFloat.java,NONE,1.1 MobyDataInstance.java,NONE,1.1 MobyDataInt.java,NONE,1.1 MobyDataObject.java,NONE,1.1 MobyDataObjectSet.java,NONE,1.1 MobyDataSecondaryInstance.java,NONE,1.1 MobyDataServiceAssocInstance.java,NONE,1.1 MobyDataString.java,NONE,1.1 MobyDataXref.java,NONE,1.1 From gordonp at pub.open-bio.org Thu May 12 01:02:11 2005 From: gordonp at pub.open-bio.org (Paul Gordon) Date: Thu May 12 00:40:46 2005 Subject: [MOBY-guts] biomoby commit Message-ID: <200505120502.j4C52BwT026107@pub.open-bio.org> gordonp Thu May 12 01:02:11 EDT 2005 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared In directory pub.open-bio.org:/tmp/cvs-serv26081 Removed Files: MobyDataSecondaryInstance.java MobyDataServiceAssocInstance.java MobyDataSetInstance.java MobyDataSimpleInstance.java MobyDataString.java Log Message: Removed in favor of data instance classes in org.biomoby.shared.data moby-live/Java/src/main/org/biomoby/shared MobyDataSecondaryInstance.java,1.1,NONE MobyDataServiceAssocInstance.java,1.2,NONE MobyDataSetInstance.java,1.2,NONE MobyDataSimpleInstance.java,1.9,NONE MobyDataString.java,1.5,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/RCS/MobyDataSecondaryInstance.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/RCS/MobyDataServiceAssocInstance.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/RCS/MobyDataSetInstance.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/RCS/MobyDataSimpleInstance.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/RCS/MobyDataString.java,v: No such file or directory From gordonp at pub.open-bio.org Thu May 12 01:03:20 2005 From: gordonp at pub.open-bio.org (Paul Gordon) Date: Thu May 12 00:41:48 2005 Subject: [MOBY-guts] biomoby commit Message-ID: <200505120503.j4C53K2L026152@pub.open-bio.org> gordonp Thu May 12 01:03:20 EDT 2005 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared In directory pub.open-bio.org:/tmp/cvs-serv26126 Removed Files: MobyDataDateTime.java MobyDataFloat.java MobyDataInstance.java MobyDataInt.java MobyDataXref.java Log Message: Removed in favor of data instance classes in org.biomoby.shared.data moby-live/Java/src/main/org/biomoby/shared MobyDataDateTime.java,1.5,NONE MobyDataFloat.java,1.6,NONE MobyDataInstance.java,1.2,NONE MobyDataInt.java,1.5,NONE MobyDataXref.java,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/RCS/MobyDataDateTime.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/RCS/MobyDataFloat.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/RCS/MobyDataInstance.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/RCS/MobyDataInt.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/RCS/MobyDataXref.java,v: No such file or directory From gordonp at pub.open-bio.org Thu May 12 01:12:01 2005 From: gordonp at pub.open-bio.org (Paul Gordon) Date: Thu May 12 00:50:30 2005 Subject: [MOBY-guts] biomoby commit Message-ID: <200505120512.j4C5C1bP026223@pub.open-bio.org> gordonp Thu May 12 01:12:01 EDT 2005 Update of /home/repository/moby/moby-live/Java/src/Clients In directory pub.open-bio.org:/tmp/cvs-serv26201 Removed Files: MobyServiceInvocationExample.java Log Message: Replaced by TestRequest moby-live/Java/src/Clients MobyServiceInvocationExample.java,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/Clients/RCS/MobyServiceInvocationExample.java,v: No such file or directory From gordonp at pub.open-bio.org Thu May 12 01:13:37 2005 From: gordonp at pub.open-bio.org (Paul Gordon) Date: Thu May 12 00:52:08 2005 Subject: [MOBY-guts] biomoby commit Message-ID: <200505120513.j4C5DbYh026267@pub.open-bio.org> gordonp Thu May 12 01:13:37 EDT 2005 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory pub.open-bio.org:/tmp/cvs-serv26242 Modified Files: MobyRequest.java Log Message: Updates to deal with new data instance package moby-live/Java/src/main/org/biomoby/client MobyRequest.java,1.10,1.11 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java,v retrieving revision 1.10 retrieving revision 1.11 diff -u -r1.10 -r1.11 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java 2005/04/18 17:29:43 1.10 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java 2005/05/12 05:13:37 1.11 @@ -23,10 +23,10 @@ import org.apache.xpath.objects.XObject; import org.biomoby.shared.Central; import org.biomoby.shared.MobyData; -import org.biomoby.shared.MobyDataInstance; -import org.biomoby.shared.MobyDataSecondaryInstance; -import org.biomoby.shared.MobyDataSetInstance; -import org.biomoby.shared.MobyDataSimpleInstance; +import org.biomoby.shared.data.MobyDataInstance; +import org.biomoby.shared.data.MobyDataSecondaryInstance; +import org.biomoby.shared.data.MobyDataObjectSet; +import org.biomoby.shared.data.MobyDataObject; import org.biomoby.shared.MobyException; import org.biomoby.shared.MobyPrefixResolver; import org.biomoby.shared.MobyService; @@ -111,18 +111,24 @@ MobyPrefixResolver.XSI1999_PREFIX+ ":type, ':'), \"base64\") or starts-with(substring-after(@"+ MobyPrefixResolver.XSI2001_PREFIX+ - ":type, ':'), \"base64\")]", null, mobyPrefixResolver, XPath.SELECT); + ":type, ':'), \"base64\")]", null, + mobyPrefixResolver, XPath.SELECT); stringEncodedXPath = new XPath("//*[substring-after(@"+ MobyPrefixResolver.XSI1999_PREFIX+ ":type, ':')=\"string\" or substring-after(@"+ MobyPrefixResolver.XSI2001_PREFIX+ - ":type, ':')=\"string\"]", null, mobyPrefixResolver, XPath.SELECT); - queryResponseXPath = new XPath("//moby:mobyData | //mobyData", null, mobyPrefixResolver, XPath.SELECT); - simpleChildXPath = new XPath("moby:Simple | Simple", null, mobyPrefixResolver, XPath.SELECT); - collectionChildXPath = new XPath("moby:Collection | Collection", null, mobyPrefixResolver, XPath.SELECT); + ":type, ':')=\"string\"]", null, + mobyPrefixResolver, XPath.SELECT); + queryResponseXPath = new XPath("//moby:mobyData | //mobyData", null, + mobyPrefixResolver, XPath.SELECT); + simpleChildXPath = new XPath("moby:Simple | Simple", null, + mobyPrefixResolver, XPath.SELECT); + collectionChildXPath = new XPath("moby:Collection | Collection", null, + mobyPrefixResolver, XPath.SELECT); } catch(TransformerException te){ - debugPS.println("Syntax error encountered while compiling XPath statements for internal use (code bug?): " + te); + debugPS.println("Syntax error encountered while compiling XPath " + + "statements for internal use (code bug?): " + te); } } @@ -194,7 +200,7 @@ } /** - * Convenience method to run services that take one argument. + * Convenience method to run services that take one unnamed argument. */ public void setInput(MobyDataInstance datum) throws IllegalArgumentException{ inputData = new MobyDataInstance[1]; @@ -586,17 +592,23 @@ data[i].setXmlMode(MobyDataInstance.SERVICE_XML_MODE); } - if(data[i] instanceof MobyDataSimpleInstance){ - mobyRequest += ((MobyDataSimpleInstance) data[i]).toXML(); + if(data[i] instanceof MobyDataObject){ + // This line should be replaced with a named field + mobyRequest += "
"+ + ((MobyDataObject) data[i]).toXML()+ + " "; } - else if(data[i] instanceof MobyDataSetInstance){ - mobyRequest += ((MobyDataSetInstance) data[i]).toXML(); + else if(data[i] instanceof MobyDataObjectSet){ + mobyRequest += ((MobyDataObjectSet) data[i]).toXML(); } else{ + // Could just call toXML, but don't know if it has a Simple wrapper + // already or not, or even if it's a set. throw new MobyException("Element #" + i + " of the input data was not a " + - "MobyDataSimpleInstance or a " + - "MobyDataSetInstance (found " + data[i] + ")"); + "MobyDataObject or a " + + "MobyDataObjectSet (found " + + data[i].getClass().getName() + ")"); } // Restore the old XML mode setting if not service mode @@ -667,7 +679,7 @@ if(debug & j == 0) debugPS.println("There are " + collections.getLength() + " collections in response #" +i); - MobyDataSetInstance collection = new MobyDataSetInstance(""); + MobyDataObjectSet collection = new MobyDataObjectSet(""); // For each collection, find the simple children NodeList subsimples = null; @@ -679,13 +691,13 @@ } // And add their values to the collection - MobyDataSimpleInstance[] subout = new MobyDataSimpleInstance[subsimples.getLength()]; + MobyDataObject[] subout = new MobyDataObject[subsimples.getLength()]; for(int k = 0; k < subsimples.getLength(); k++){ if(debug && k == 0) debugPS.println("There are " + subsimples.getLength() + " simples in response #" + i + ", collection #" + j); - subout[k] = new MobyDataSimpleInstance(mobyCentral, (Element) subsimples.item(k)); + subout[k] = (MobyDataObject) MobyDataObject.createInstanceFromDOM((Element) subsimples.item(k)); } collection.setElements(subout); releaseXPath(collections.item(j)); @@ -708,7 +720,7 @@ for(int j = 0; simples != null && j < simples.getLength(); j++){ if(debug && j == 0) debugPS.println("There are " + simples.getLength() + " simples in response #" +i); - out.add(new MobyDataSimpleInstance(mobyCentral, (Element) simples.item(j))); + out.add(MobyDataObject.createInstanceFromDOM((Element) simples.item(j))); } // What we're building is a Vector, where each element represents From gordonp at pub.open-bio.org Thu May 12 01:17:59 2005 From: gordonp at pub.open-bio.org (Paul Gordon) Date: Thu May 12 00:56:29 2005 Subject: [MOBY-guts] biomoby commit Message-ID: <200505120517.j4C5HxOI026333@pub.open-bio.org> gordonp Thu May 12 01:17:58 EDT 2005 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data In directory pub.open-bio.org:/tmp/cvs-serv26312/src/main/org/biomoby/shared/data Added Files: MobyProvisionInfo.java Log Message: New class encoding the PIB moby-live/Java/src/main/org/biomoby/shared/data MobyProvisionInfo.java,NONE,1.1 From gordonp at pub.open-bio.org Thu May 12 01:19:20 2005 From: gordonp at pub.open-bio.org (Paul Gordon) Date: Thu May 12 00:57:52 2005 Subject: [MOBY-guts] biomoby commit Message-ID: <200505120519.j4C5JKmN026366@pub.open-bio.org> gordonp Thu May 12 01:19:20 EDT 2005 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder In directory pub.open-bio.org:/tmp/cvs-serv26341/src/main/org/biomoby/client/rdf/builder Modified Files: ServiceInstanceRDF.java Log Message: Updates to Eddie's code to deal with the new org.biomoby.shared.data instance class package moby-live/Java/src/main/org/biomoby/client/rdf/builder ServiceInstanceRDF.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder/ServiceInstanceRDF.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/rdf/builder/ServiceInstanceRDF.java 2005/04/07 16:42:29 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/builder/ServiceInstanceRDF.java 2005/05/12 05:19:20 1.2 @@ -15,7 +15,7 @@ import org.biomoby.registry.properties.MobyProperties; import org.biomoby.shared.Central; import org.biomoby.shared.MobyData; -import org.biomoby.shared.MobyDataSecondaryInstance; +import org.biomoby.shared.data.MobyDataSecondaryInstance; import org.biomoby.shared.MobyException; import org.biomoby.shared.MobyNamespace; import org.biomoby.shared.MobyPrimaryDataSet; From gordonp at pub.open-bio.org Thu May 12 01:19:20 2005 From: gordonp at pub.open-bio.org (Paul Gordon) Date: Thu May 12 00:57:55 2005 Subject: [MOBY-guts] biomoby commit Message-ID: <200505120519.j4C5JKSM026409@pub.open-bio.org> gordonp Thu May 12 01:19:20 EDT 2005 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared In directory pub.open-bio.org:/tmp/cvs-serv26341/src/main/org/biomoby/shared Modified Files: MobyObjectDecomposition.java MobyObjectDecompositionImpl.java Log Message: Updates to Eddie's code to deal with the new org.biomoby.shared.data instance class package moby-live/Java/src/main/org/biomoby/shared MobyObjectDecomposition.java,1.3,1.4 MobyObjectDecompositionImpl.java,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyObjectDecomposition.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/shared/MobyObjectDecomposition.java 2005/04/18 23:57:45 1.3 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyObjectDecomposition.java 2005/05/12 05:19:20 1.4 @@ -21,7 +21,7 @@ * @param object - the object to flatten into its primitives. * @return - the full decomposition of an object into its primitives. */ - public MobyDataSimpleInstance[] getFlattenedPrims(String object); + public org.biomoby.shared.data.MobyDataObject[] getFlattenedPrims(String object); /** * @@ -42,4 +42,4 @@ */ public boolean isPrimitive(String object); -} \ No newline at end of file +} =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyObjectDecompositionImpl.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/shared/MobyObjectDecompositionImpl.java 2005/04/18 23:57:45 1.3 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyObjectDecompositionImpl.java 2005/05/12 05:19:20 1.4 @@ -4,6 +4,8 @@ */ package org.biomoby.shared; +import org.biomoby.shared.data.*; + import java.io.BufferedReader; import java.io.IOException; import java.io.InputStreamReader; @@ -44,10 +46,10 @@ /* (non-Javadoc) * @see org.biomoby.client.gui.util.MobyObjectDecomposition#getFlattenedPrims(java.lang.String) */ - public final MobyDataSimpleInstance[] getFlattenedPrims(String object) { + public final MobyDataObject[] getFlattenedPrims(String object) { ArrayList list = new ArrayList(); if (isPrimitive(object)) { - return new MobyDataSimpleInstance[] {}; + return new MobyDataObject[] {}; } String lsid = "urn:lsid:biomoby.org:objectclass:" + object; String rdf = getObjectRDF(lsid); @@ -81,11 +83,11 @@ : articleNode.getTextContent(); // TODO - recurse if object is not a primitive if (isPrimitive(localName)) { - MobyDataSimpleInstance mdsi = createPrimitiveType( + MobyDataObject mdsi = createPrimitiveType( localName, articleName); list.add(mdsi); } else { - MobyDataSimpleInstance[] recurseArray = getFlattenedPrims(localName); + MobyDataObject[] recurseArray = getFlattenedPrims(localName); for (int k = 0; k < recurseArray.length; k++) { list.add(recurseArray[k]); } @@ -104,11 +106,11 @@ : articleNode.getTextContent(); // TODO - recurse if object is not a primitive if (isPrimitive(localName)) { - MobyDataSimpleInstance mdsi = createPrimitiveType( + MobyDataObject mdsi = createPrimitiveType( localName, articleName); list.add(mdsi); } else { - MobyDataSimpleInstance[] recurseArray = getFlattenedPrims(localName); + MobyDataObject[] recurseArray = getFlattenedPrims(localName); for (int k = 0; k < recurseArray.length; k++) { list.add(recurseArray[k]); } @@ -126,7 +128,7 @@ _object = _object.substring(_object.indexOf("#") + 1); } if (isPrimitive(_object) && !_object.equals("Object")) { - MobyDataSimpleInstance mdsi = new MobyDataSimpleInstance( + MobyDataObject mdsi = new MobyDataObject( _object); mdsi.setDataType(new MobyDataType(_object)); list.add(mdsi); @@ -139,7 +141,7 @@ _object = _object.substring(_object.indexOf("#") + 1); } if (isPrimitive(_object) && !_object.equals("Object")) { - MobyDataSimpleInstance mdsi = new MobyDataSimpleInstance( + MobyDataObject mdsi = new MobyDataObject( _object); mdsi.setDataType(new MobyDataType(_object)); list.add(mdsi); @@ -271,7 +273,7 @@ /* * method to create default DataTypes. */ - public final MobyDataSimpleInstance createPrimitiveType(String localName, + public final MobyDataObject createPrimitiveType(String localName, String articleName) { if (localName.equalsIgnoreCase("Float")) { return new MobyDataFloat(articleName, 0.0); @@ -280,7 +282,7 @@ } else if (localName.equalsIgnoreCase("Integer")) { return new MobyDataInt(articleName, 0); } else if (localName.equalsIgnoreCase("DateTime")) { - MobyDataSimpleInstance mdsi = new MobyDataSimpleInstance( + MobyDataObject mdsi = new MobyDataObject( articleName); mdsi.setDataType(new MobyDataType(localName)); return mdsi; @@ -289,12 +291,12 @@ return null; } - private final MobyDataSimpleInstance[] convertArrayListToMoby(ArrayList list) { + private final MobyDataObject[] convertArrayListToMoby(ArrayList list) { int size = list.size(); - MobyDataSimpleInstance[] mdsi = new MobyDataSimpleInstance[size]; + MobyDataObject[] mdsi = new MobyDataObject[size]; size = 0; for (Iterator x = list.iterator(); x.hasNext(); size++) { - mdsi[size] = (MobyDataSimpleInstance) x.next(); + mdsi[size] = (MobyDataObject) x.next(); } return mdsi; } @@ -415,4 +417,4 @@ return sb.toString(); } } -} \ No newline at end of file +} From gordonp at pub.open-bio.org Thu May 12 01:19:20 2005 From: gordonp at pub.open-bio.org (Paul Gordon) Date: Thu May 12 00:58:25 2005 Subject: [MOBY-guts] biomoby commit Message-ID: <200505120519.j4C5JKXH026385@pub.open-bio.org> gordonp Thu May 12 01:19:20 EDT 2005 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources In directory pub.open-bio.org:/tmp/cvs-serv26341/src/main/org/biomoby/client/ui/graphical/servlet/jresources Modified Files: RESOURCE.java Log Message: Updates to Eddie's code to deal with the new org.biomoby.shared.data instance class package moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources RESOURCE.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources/RESOURCE.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/servlet/jresources/RESOURCE.java 2005/04/28 18:39:40 1.2 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources/RESOURCE.java 2005/05/12 05:19:20 1.3 @@ -25,7 +25,7 @@ import org.biomoby.registry.properties.MobyProperties; import org.biomoby.shared.CentralDigest; import org.biomoby.shared.MobyData; -import org.biomoby.shared.MobyDataSecondaryInstance; +import org.biomoby.shared.data.MobyDataSecondaryInstance; import org.biomoby.shared.MobyException; import org.biomoby.shared.MobyNamespace; import org.biomoby.shared.MobyPrimaryDataSet; From gordonp at pub.open-bio.org Thu May 12 01:22:27 2005 From: gordonp at pub.open-bio.org (Paul Gordon) Date: Thu May 12 01:01:01 2005 Subject: [MOBY-guts] biomoby commit Message-ID: <200505120522.j4C5MRnU026477@pub.open-bio.org> gordonp Thu May 12 01:22:27 EDT 2005 Update of /home/repository/moby/moby-live/Java/src/Clients In directory pub.open-bio.org:/tmp/cvs-serv26456/src/Clients Added Files: TestRequest.java Log Message: Sample client demonstrating the usage of data instance classes in org.biomoby.shared.data, and the use of MobyRequest for service invocation moby-live/Java/src/Clients TestRequest.java,NONE,1.1 From kawas at pub.open-bio.org Fri May 13 15:18:19 2005 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Fri May 13 14:56:41 2005 Subject: [MOBY-guts] biomoby commit Message-ID: <200505131918.j4DJIJ9T002285@pub.open-bio.org> kawas Fri May 13 15:18:18 EDT 2005 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources In directory pub.open-bio.org:/tmp/cvs-serv2260/org/biomoby/client/ui/graphical/servlet/jresources Modified Files: RESOURCE.java Log Message: Fixed some import statements. Not sure really why I had to do this though!?! Eddie moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources RESOURCE.java,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources/RESOURCE.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/servlet/jresources/RESOURCE.java 2005/05/12 05:19:20 1.3 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/servlet/jresources/RESOURCE.java 2005/05/13 19:18:18 1.4 @@ -17,6 +17,7 @@ import javax.servlet.http.HttpServletResponse; import org.biomoby.client.CentralDigestImpl; +import org.biomoby.client.CentralImpl; import org.biomoby.client.rdf.vocabulary.MobyResources; import org.biomoby.client.rdf.vocabulary.Predicates; import org.biomoby.registry.definitions.types.JNamespaces; @@ -25,13 +26,15 @@ import org.biomoby.registry.properties.MobyProperties; import org.biomoby.shared.CentralDigest; import org.biomoby.shared.MobyData; -import org.biomoby.shared.data.MobyDataSecondaryInstance; +import org.biomoby.shared.MobyDataType; import org.biomoby.shared.MobyException; import org.biomoby.shared.MobyNamespace; import org.biomoby.shared.MobyPrimaryDataSet; import org.biomoby.shared.MobyPrimaryDataSimple; import org.biomoby.shared.MobySecondaryData; import org.biomoby.shared.MobyService; +import org.biomoby.shared.NoSuccessException; +import org.biomoby.shared.data.MobyDataSecondaryInstance; import org.w3c.rdf.model.ModelException; import com.hp.hpl.jena.rdf.model.Bag; @@ -663,6 +666,8 @@ // create the base object type "class" Resource subject = _addClassResource(model, OBJ, "Object", "a base object class consisting of a namespace and an identifier"); + model.add(model.createStatement(subject, DC.publisher, model.createLiteral("www.illuminae.com", "en"))); + model.add(model.createStatement(subject, DC.creator, model.createLiteral("markw@illuminae.com", "en"))); model.add(model.createStatement(subject, RDF.type, RDFS.Class)); for (int x = 0; x < objects.length; x++) { String[] _line = objects[x].split("\t"); @@ -679,7 +684,17 @@ Matcher m; if (obj.indexOf("(") >= 0) obj = obj.substring(0, obj.indexOf("(")); + Resource _subject = _addClassResource(model, OBJ, sub, def); + try { + //TODO make this an sql call + MobyDataType _datatype = new CentralImpl().getDataType(sub); + model.add(model.createStatement(subject, DC.publisher, model.createLiteral(_datatype.getAuthority(), "en"))); + model.add(model.createStatement(subject, DC.creator, model.createLiteral( _datatype.getEmailContact(), "en"))); + } catch (NoSuccessException e) { + // oh well, at least we tried + System.err.println(sub + " could not be augmented with its 'creator' or its 'publisher'. Oh well, at least we tried"); + } m = Pattern.compile(".*:isa$", Pattern.CASE_INSENSITIVE).matcher( pred); if (m.matches()) { @@ -921,7 +936,7 @@ } public static void main(String[] args) throws MobyException { - System.out.println(new RESOURCE().getRESOURCES("Objects")); + System.out.println(new RESOURCE().getRESOURCES("ServiceInstances")); } } From kawas at pub.open-bio.org Fri May 13 15:20:14 2005 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Fri May 13 14:58:34 2005 Subject: [MOBY-guts] biomoby commit Message-ID: <200505131920.j4DJKEjx002361@pub.open-bio.org> kawas Fri May 13 15:20:14 EDT 2005 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared In directory pub.open-bio.org:/tmp/cvs-serv2332/org/biomoby/shared Modified Files: Tag: java_1_5_compat MobyObjectDecompositionImpl.java MobyObjectDecomposition.java Log Message: Changed the import statements and references to MobyDataSimpleInstance to MobyDataObject. Seems to be the right change. Eddie moby-live/Java/src/main/org/biomoby/shared MobyObjectDecompositionImpl.java,1.1,1.1.2.1 MobyObjectDecomposition.java,1.1,1.1.2.1 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyObjectDecompositionImpl.java,v retrieving revision 1.1 retrieving revision 1.1.2.1 diff -u -r1.1 -r1.1.2.1 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyObjectDecompositionImpl.java 2005/04/07 16:37:02 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyObjectDecompositionImpl.java 2005/05/13 19:20:14 1.1.2.1 @@ -18,6 +18,7 @@ import javax.xml.parsers.DocumentBuilderFactory; import javax.xml.parsers.ParserConfigurationException; +import org.biomoby.shared.data.*; import org.biomoby.client.CentralImpl; import org.biomoby.client.ui.graphical.applets.util.PrimitiveTypes; import org.w3c.dom.Document; @@ -44,10 +45,10 @@ /* (non-Javadoc) * @see org.biomoby.client.gui.util.MobyObjectDecomposition#getFlattenedPrims(java.lang.String) */ - public final MobyDataSimpleInstance[] getFlattenedPrims(String object) { + public final MobyDataObject[] getFlattenedPrims(String object) { ArrayList list = new ArrayList(); if (isPrimitive(object)) { - return new MobyDataSimpleInstance[] {}; + return new MobyDataObject[] {}; } String lsid = "urn:lsid:biomoby.org:objectclass:" + object; String rdf = getObjectRDF(lsid); @@ -81,11 +82,11 @@ : articleNode.getTextContent(); // TODO - recurse if object is not a primitive if (isPrimitive(localName)) { - MobyDataSimpleInstance mdsi = createPrimitiveType( + MobyDataObject mdsi = createPrimitiveType( localName, articleName); list.add(mdsi); } else { - MobyDataSimpleInstance[] recurseArray = getFlattenedPrims(localName); + MobyDataObject[] recurseArray = getFlattenedPrims(localName); for (int k = 0; k < recurseArray.length; k++) { list.add(recurseArray[k]); } @@ -104,11 +105,11 @@ : articleNode.getTextContent(); // TODO - recurse if object is not a primitive if (isPrimitive(localName)) { - MobyDataSimpleInstance mdsi = createPrimitiveType( + MobyDataObject mdsi = createPrimitiveType( localName, articleName); list.add(mdsi); } else { - MobyDataSimpleInstance[] recurseArray = getFlattenedPrims(localName); + MobyDataObject[] recurseArray = getFlattenedPrims(localName); for (int k = 0; k < recurseArray.length; k++) { list.add(recurseArray[k]); } @@ -126,7 +127,7 @@ _object = _object.substring(_object.indexOf("#") + 1); } if (isPrimitive(_object) && !_object.equals("Object")) { - MobyDataSimpleInstance mdsi = new MobyDataSimpleInstance( + MobyDataObject mdsi = new MobyDataObject( _object); mdsi.setDataType(new MobyDataType(_object)); list.add(mdsi); @@ -139,7 +140,7 @@ _object = _object.substring(_object.indexOf("#") + 1); } if (isPrimitive(_object) && !_object.equals("Object")) { - MobyDataSimpleInstance mdsi = new MobyDataSimpleInstance( + MobyDataObject mdsi = new MobyDataObject( _object); mdsi.setDataType(new MobyDataType(_object)); list.add(mdsi); @@ -271,7 +272,7 @@ /* * method to create default DataTypes. */ - public final MobyDataSimpleInstance createPrimitiveType(String localName, + public final MobyDataObject createPrimitiveType(String localName, String articleName) { if (localName.equalsIgnoreCase("Float")) { return new MobyDataFloat(articleName, 0.0); @@ -280,7 +281,7 @@ } else if (localName.equalsIgnoreCase("Integer")) { return new MobyDataInt(articleName, 0); } else if (localName.equalsIgnoreCase("DateTime")) { - MobyDataSimpleInstance mdsi = new MobyDataSimpleInstance( + MobyDataObject mdsi = new MobyDataObject( articleName); mdsi.setDataType(new MobyDataType(localName)); return mdsi; @@ -289,12 +290,12 @@ return null; } - private final MobyDataSimpleInstance[] convertArrayListToMoby(ArrayList list) { + private final MobyDataObject[] convertArrayListToMoby(ArrayList list) { int size = list.size(); - MobyDataSimpleInstance[] mdsi = new MobyDataSimpleInstance[size]; + MobyDataObject[] mdsi = new MobyDataObject[size]; size = 0; for (Iterator x = list.iterator(); x.hasNext(); size++) { - mdsi[size] = (MobyDataSimpleInstance) x.next(); + mdsi[size] = (MobyDataObject) x.next(); } return mdsi; } =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyObjectDecomposition.java,v retrieving revision 1.1 retrieving revision 1.1.2.1 diff -u -r1.1 -r1.1.2.1 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyObjectDecomposition.java 2005/04/07 16:37:02 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyObjectDecomposition.java 2005/05/13 19:20:14 1.1.2.1 @@ -4,6 +4,8 @@ */ package org.biomoby.shared; +import org.biomoby.shared.data.MobyDataObject; + /** * @author Eddie Kawas @@ -21,7 +23,7 @@ * @param object - the object to flatten into its primitives. * @return - the full decomposition of an object into its primitives. */ - public MobyDataSimpleInstance[] getFlattenedPrims(String object); + public MobyDataObject[] getFlattenedPrims(String object); /** * From yanwong at pub.open-bio.org Mon May 16 08:42:01 2005 From: yanwong at pub.open-bio.org (Yan Wong) Date: Mon May 16 08:21:33 2005 Subject: [MOBY-guts] biomoby commit Message-ID: <200505161242.j4GCg1qW022091@pub.open-bio.org> yanwong Mon May 16 08:42:01 EDT 2005 Update of /home/repository/moby/moby-live/Python/bioMoby In directory pub.open-bio.org:/tmp/cvs-serv22018 Modified Files: mobyDataTypes.py Log Message: Modified the serialization/deserialization code: from bioMoby import MobyMarshaller m=MobyMarshaller() m.dumps(0) should return - Available APIs (more explanation coming...)
-
MS
+ MS
Generate a complete XML Schema for registered services. This
will allow to have complete WSDLs for BioMoby services, which will
further allow to use all existing tools using such WSDLs for
generating code and documentation.
-
MS
+ MS
Support for auto-generated clients (using the outcome of the
previous issue).
-
MS
+ MS
Similar support for BioMoby service providers - a library
helping to hide SOAP and BioMoby envelope layers so service providers
can concentrate only on the business logic.
-
MS
+ MS
More support for BioMoby complex data type in Taverna.
-
MS
+ MS
The BioMoby Graphs available directly in Taverna.
-
MS, GS
+ MS, GS
Integrate Semantic Moby services into Taverna. This will (hopefully) help to
combine S-Moby and Moby-S in the (near?) future.
@@ -77,7 +77,7 @@
individual registered services (e.g. examples of their valid inputs).
-
MS
+ MS
MobyDigestClient
(actually the classes it relies on) can be significantly optimized by
@@ -98,14 +98,14 @@
-
-
- MS
+ MS
MobyCmdLineClient
does not correctly implement its -nc and -np
options.
-
MS
+ MS
The servlet for BioMoby Graphs is still not robust
enough.
@@ -119,7 +119,7 @@
Martin Senger
-Last modified: Tue May 17 15:55:44 2005 +Last modified: Thu May 19 11:20:08 2005
-
-