From gordonp at dev.open-bio.org Thu Oct 16 13:38:22 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Thu, 16 Oct 2008 13:38:22 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200810161738.m9GHcM60022387@dev.open-bio.org> gordonp Thu Oct 16 13:38:21 EDT 2008 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv22355 Added Files: vectorstrip.acd Log Message: File referenced by the ACDServlet tutorial moby-live/Java/docs vectorstrip.acd,NONE,1.1 From gordonp at dev.open-bio.org Thu Oct 16 13:44:44 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Thu, 16 Oct 2008 13:44:44 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200810161744.m9GHiiSY022454@dev.open-bio.org> gordonp Thu Oct 16 13:44:43 EDT 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test In directory dev.open-bio.org:/tmp/cvs-serv22418 Modified Files: KEGG.wsdl Log Message: Change of returned Moby object from GeneId to KEGG_GENES moby-live/Java/src/main/ca/ucalgary/services/util/test KEGG.wsdl,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/KEGG.wsdl,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/KEGG.wsdl 2008/06/30 17:42:29 1.2 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/KEGG.wsdl 2008/10/16 17:44:43 1.3 @@ -496,8 +496,8 @@ The fact that the output's type is an Array in XML Schema means that it will implicitly be wrapped as a Moby "Collection" of GeneIds. --> + sawsdl:modelReference="urn:lsid:biomoby.org:namespacetype:KEGG_GENES" + sawsdl:liftingSchemaMapping="urn:lsid:bioxml.info:mobyLiftingSchemaMapping:string2KEGG_GENES"/> From kawas at dev.open-bio.org Tue Oct 21 12:34:30 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 21 Oct 2008 12:34:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200810211634.m9LGYUvU021295@dev.open-bio.org> kawas Tue Oct 21 12:34:29 EDT 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared In directory dev.open-bio.org:/tmp/cvs-serv21264/src/main/org/biomoby/shared Added Files: MobyUnitTest.java Log Message: committing a (slightly revised) class created by wendy that is used to store unit test information for any given service. moby-live/Java/src/main/org/biomoby/shared MobyUnitTest.java,NONE,1.1 From kawas at dev.open-bio.org Tue Oct 21 12:36:09 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 21 Oct 2008 12:36:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200810211636.m9LGa9qr021391@dev.open-bio.org> kawas Tue Oct 21 12:36:09 EDT 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary In directory dev.open-bio.org:/tmp/cvs-serv21356/src/main/org/biomoby/client/rdf/vocabulary Modified Files: FetaVocabulary.java Log Message: committing revisons to the vocab that contain predicates for unit testing moby services. moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary FetaVocabulary.java,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/FetaVocabulary.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/rdf/vocabulary/FetaVocabulary.java 2006/07/13 18:35:01 1.3 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/rdf/vocabulary/FetaVocabulary.java 2008/10/21 16:36:09 1.4 @@ -3,7 +3,8 @@ package org.biomoby.client.rdf.vocabulary; import com.hp.hpl.jena.rdf.model.*; /** - * @author Eddie + * @author Eddie Kawas + * @author Wendy Alexander *

created Nov 10, 2005 *

This class encapsulates the vocabulary needed to interact with the myGrid ontology. */ @@ -73,6 +74,14 @@ public static final Resource operation; public static final Resource organisation; public static final Resource parameter; + + // unit test predicates + public static final Property hasUnitTest; + public static final Resource unitTest; + public static final Property exampleInput; + public static final Property validOutputXML; + public static final Property validXPath; + public static final Property validREGEX; static { @@ -133,5 +142,13 @@ simpleParameter = m_model.createResource(getURI() + "simpleParameter"); collectionParameter = m_model.createResource(getURI() + "collectionParameter"); secondaryParameter = m_model.createResource(getURI() + "secondaryParameter"); + + //unit test predicates + hasUnitTest = m_model.createProperty(getURI() + "hasUnitTest"); + unitTest = m_model.createResource(getURI() + "unitTest"); + exampleInput = m_model.createProperty(getURI() + "exampleInput"); + validOutputXML = m_model.createProperty(getURI() + "validOutputXML"); + validREGEX = m_model.createProperty(getURI() + "validREGEX"); + validXPath = m_model.createProperty(getURI() + "validXPath"); } } From kawas at dev.open-bio.org Tue Oct 21 12:38:45 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 21 Oct 2008 12:38:45 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200810211638.m9LGcjjL021469@dev.open-bio.org> kawas Tue Oct 21 12:38:44 EDT 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared In directory dev.open-bio.org:/tmp/cvs-serv21434/src/main/org/biomoby/shared Modified Files: MobyService.java Log Message: committing additions to the class that augment MobyService with unit testing code moby-live/Java/src/main/org/biomoby/shared MobyService.java,1.24,1.25 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyService.java,v retrieving revision 1.24 retrieving revision 1.25 diff -u -r1.24 -r1.25 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyService.java 2008/03/02 12:45:26 1.24 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyService.java 2008/10/21 16:38:44 1.25 @@ -52,6 +52,8 @@ protected String id = null; protected String lsid = null; protected MobyServiceType serviceType; + // moby unit test object + protected MobyUnitTest unitTest = null; public static final int UNCHECKED = 0; public static final int DEAD= 1; @@ -144,6 +146,8 @@ clone.setSignatureURL(getSignatureURL()); clone.setPathToRDF(getPathToRDF()); clone.setRDF(getRDF()); + clone.setUnitTest(getUnitTest()); + clone.serviceStatus = serviceStatus; clone.statusChecks = statusChecks; for(MobyPrimaryData primary: getPrimaryInputs()){ @@ -265,6 +269,24 @@ } /** + * + * @return the MobyUnitTest object associated with this service + */ + public MobyUnitTest getUnitTest() { + return unitTest; + } + + /** + * + * @param unitTest + * the MobyUnitTest object to associate with this service + */ + public void setUnitTest(MobyUnitTest unitTest) { + if (unitTest != null) + this.unitTest = unitTest; + } + + /** * Return a URL where this service is being served from. It is a * URL where the clients of this service are going when they want * to use it.

@@ -482,6 +504,13 @@ buf.append ("Signature URL: " + signatureURL + "\n"); buf.append ("Path to RDF: " + pathToRDF + "\n"); if (id != null) buf.append ("ID: " + id + "\n"); + + // print unitTest information for this service + if (unitTest != null) { + buf.append(unitTest.toString()); + } else { + buf.append("Unit Test: None available\n"); + } buf.append ("Primary inputs:\n"); for (Enumeration en = primaryInputs.elements(); en.hasMoreElements(); ) From kawas at dev.open-bio.org Tue Oct 21 12:41:23 2008 From: kawas at dev.open-bio.org (Eddie Kawas) Date: Tue, 21 Oct 2008 12:41:23 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200810211641.m9LGfNGx021546@dev.open-bio.org> kawas Tue Oct 21 12:41:22 EDT 2008 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended In directory dev.open-bio.org:/tmp/cvs-serv21511/src/main/org/biomoby/shared/extended Modified Files: ServiceInstanceParser.java Log Message: committing additions to the class that augment this class with the ability to parse and set unit testing data for a service moby-live/Java/src/main/org/biomoby/shared/extended ServiceInstanceParser.java,1.24,1.25 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java,v retrieving revision 1.24 retrieving revision 1.25 diff -u -r1.24 -r1.25 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java 2008/02/28 17:00:12 1.24 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java 2008/10/21 16:41:22 1.25 @@ -18,6 +18,7 @@ import org.biomoby.shared.MobySecondaryData; import org.biomoby.shared.MobyService; import org.biomoby.shared.MobyServiceType; +import org.biomoby.shared.MobyUnitTest; import org.biomoby.shared.Utils; import com.hp.hpl.jena.rdf.model.Model; @@ -35,7 +36,10 @@ /** * - * @author Eddie created Oct 18, 2005 This class parses the RDF document that + * @author Eddie Kawas + * @author Wendy Alexander + * + * created Oct 18, 2005 This class parses the RDF document that * describes the service instance ontology. *

* An example of how to use this class is below: @@ -247,6 +251,21 @@ } } } + + // get/set the unit test information for the service + if (hoResource.hasProperty(FetaVocabulary.hasUnitTest)) { + Resource utResource = hoResource.getProperty(FetaVocabulary.hasUnitTest).getResource(); + MobyUnitTest mut = new MobyUnitTest(); + if (utResource.hasProperty(FetaVocabulary.exampleInput)) + mut.setExampleInput(utResource.getProperty(FetaVocabulary.exampleInput).getObject().toString()); + if (utResource.hasProperty(FetaVocabulary.validOutputXML)) + mut.setValidOutputXML(utResource.getProperty(FetaVocabulary.validOutputXML).getObject().toString()); + if (utResource.hasProperty(FetaVocabulary.validXPath)) + mut.setValidXPath(utResource.getProperty(FetaVocabulary.validXPath).getObject().toString()); + if (utResource.hasProperty(FetaVocabulary.validREGEX)) + mut.setValidREGEX(utResource.getProperty(FetaVocabulary.validREGEX).getObject().toString()); + service.setUnitTest(mut); + } } From senger at dev.open-bio.org Thu Oct 23 20:36:27 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 23 Oct 2008 20:36:27 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200810240036.m9O0aRtu030851@dev.open-bio.org> senger Thu Oct 23 20:36:27 EDT 2008 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv30832/docs Modified Files: index.html Added Files: LICENSE Log Message: added licensing into the documentation moby-live/Java/docs LICENSE,NONE,1.1 index.html,1.33,1.34 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/index.html,v retrieving revision 1.33 retrieving revision 1.34 diff -u -r1.33 -r1.34 --- /home/repository/moby/moby-live/Java/docs/index.html 2008/05/21 19:18:22 1.33 +++ /home/repository/moby/moby-live/Java/docs/index.html 2008/10/24 00:36:27 1.34 @@ -73,6 +73,12 @@

What license jMoby uses:
+ + Unless individual jMoby parts define it differently, the code is + licensed under the Apache + License.
+
How to get jMoby
@@ -225,7 +231,7 @@

Martin Senger
-Last modified: Sat Mar 8 20:32:22 2008 +Last modified: Fri Oct 24 08:34:57 2008
From senger at dev.open-bio.org Thu Oct 23 21:41:37 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Thu, 23 Oct 2008 21:41:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200810240141.m9O1fbkT030935@dev.open-bio.org> senger Thu Oct 23 21:41:37 EDT 2008 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv30916/xmls Modified Files: install.xml Log Message: fixed ant install to clean also generated datatypes and skeletons moby-live/Java/xmls install.xml,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/install.xml,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Java/xmls/install.xml 2008/03/02 16:05:01 1.5 +++ /home/repository/moby/moby-live/Java/xmls/install.xml 2008/10/24 01:41:37 1.6 @@ -72,6 +72,8 @@ + + From senger at dev.open-bio.org Sat Oct 25 10:28:19 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 25 Oct 2008 10:28:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200810251428.m9PESJNc004231@dev.open-bio.org> senger Sat Oct 25 10:28:18 EDT 2008 Update of /home/repository/moby/moby-live/Java In directory dev.open-bio.org:/tmp/cvs-serv4212 Modified Files: build.xml Log Message: fix properties in jar file issue moby-live/Java build.xml,1.74,1.75 =================================================================== RCS file: /home/repository/moby/moby-live/Java/build.xml,v retrieving revision 1.74 retrieving revision 1.75 diff -u -r1.74 -r1.75 --- /home/repository/moby/moby-live/Java/build.xml 2008/08/13 19:41:04 1.74 +++ /home/repository/moby/moby-live/Java/build.xml 2008/10/25 14:28:18 1.75 @@ -442,7 +442,7 @@ + excludes="*.properties org/biomoby/service/dashboard/** org/biomoby/client/ui/** ca/** org/biomoby/registry/sync/** org/biomoby/registry/rdfagent/** org/biomoby/registry/Central/** org/biomoby/registry/definitions/** **/test/**"/> From senger at dev.open-bio.org Sat Oct 25 10:28:19 2008 From: senger at dev.open-bio.org (Martin Senger) Date: Sat, 25 Oct 2008 10:28:19 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200810251428.m9PESJRj004249@dev.open-bio.org> senger Sat Oct 25 10:28:18 EDT 2008 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv4212/docs Modified Files: ChangeLog Log Message: fix properties in jar file issue moby-live/Java/docs ChangeLog,1.92,1.93 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v retrieving revision 1.92 retrieving revision 1.93 diff -u -r1.92 -r1.93 --- /home/repository/moby/moby-live/Java/docs/ChangeLog 2008/08/13 19:41:04 1.92 +++ /home/repository/moby/moby-live/Java/docs/ChangeLog 2008/10/25 14:28:18 1.93 @@ -1,3 +1,8 @@ +2008-10-25 Martin Senger + + * Fixed: Ant's task creating jMoby jar file now does not include + there log4j.properties. + 2008-08-13 Martin Senger * Version 1.1.1 released (the only changed from the previous one From gordonp at dev.open-bio.org Wed Oct 29 15:53:03 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 29 Oct 2008 15:53:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200810291953.m9TJr3tV009906@dev.open-bio.org> gordonp Wed Oct 29 15:53:03 EDT 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test In directory dev.open-bio.org:/tmp/cvs-serv9870/src/main/ca/ucalgary/services/util/test Modified Files: KEGG.wsdl Log Message: Changed contact info to proxy provider, not original service provider moby-live/Java/src/main/ca/ucalgary/services/util/test KEGG.wsdl,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/KEGG.wsdl,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/KEGG.wsdl 2008/10/16 17:44:43 1.3 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/KEGG.wsdl 2008/10/29 19:53:02 1.4 @@ -933,7 +933,7 @@ xmlns:moby="http://www.biomoby.org/moby" moby:serviceName="getGenesByECNumber" moby:serviceAuthority="genome.jp" - moby:serviceContact="ktym at hgc.jp" + moby:serviceContact="gordonp at ucalgary.ca" moby:serviceDesc="Retrieves the list of genes in a given organism that are annotated as having a particular EC (enzyme) number"/> From gordonp at dev.open-bio.org Wed Oct 29 22:03:00 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 29 Oct 2008 22:03:00 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200810300203.m9U230Ae010298@dev.open-bio.org> gordonp Wed Oct 29 22:02:59 EDT 2008 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv10262/docs Modified Files: index.html Added Files: sawsdlServlet.html Log Message: Updates to introduce SAWSDL-based services moby-live/Java/docs sawsdlServlet.html,NONE,1.1 index.html,1.34,1.35 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/index.html,v retrieving revision 1.34 retrieving revision 1.35 diff -u -r1.34 -r1.35 --- /home/repository/moby/moby-live/Java/docs/index.html 2008/10/24 00:36:27 1.34 +++ /home/repository/moby/moby-live/Java/docs/index.html 2008/10/30 02:02:59 1.35 @@ -180,8 +180,9 @@ service, an alternate mechanism for the Extremely Lazy, Complete Idiots, Dummies, etc. (a.k.a. "MobyServlet")
A note on using secondary articles with MobyServlet +
How to wrap an EMBOSS/ACD program as a Moby service
How to wrap an EMBOSS/ACD program as a Moby service +border=0/>How to wrap an exisitng Web Service as a Moby service (using SAWSDL)
The org.biomoby.shared.data package "In Anger": creating data instances

> serviceInputs; private Map> serviceInputFormats; private Map> serviceSecondaries; + private Map> serviceSecondaryFormats; private Map> serviceOutputs; private Map> serviceOutputFormats; private Map> fixedParams; @@ -36,6 +37,7 @@ serviceOutputs = new HashMap>(); fixedParams = new HashMap>(); serviceInputFormats = new HashMap>(); + serviceSecondaryFormats = new HashMap>(); serviceOutputFormats = new HashMap>(); } @@ -102,10 +104,23 @@ return serviceInputs.get(currentService); } + public void setSecondaryInputFormats(Map specs){ + serviceSecondaryFormats.put(currentService, specs); + } + + public Map getSecondaryInputFormats(){ + return serviceSecondaryFormats.get(currentService); + } + public void setPrimaryInputFormats(Map specs){ serviceInputFormats.put(currentService, specs); } + /** + * Note that the string values for the formats are specialized for the + * various LegacyService child classes, as they will all have their own naming scheme for legacy + * formats. + */ public Map getPrimaryInputFormats(){ return serviceInputFormats.get(currentService); } =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/SourceMap.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/SourceMap.java 2008/06/30 17:42:29 1.1 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/SourceMap.java 2008/10/30 02:33:24 1.2 @@ -4,23 +4,21 @@ import java.io.*; import java.util.*; -import java.util.concurrent.ConcurrentHashMap; -import java.util.concurrent.ConcurrentMap; /** * Converts a Map of Strings into a Source for the Java SOAP libraries. * The Map should be of the form (SOAP input param name -> XML Schema Instance data). */ -public class SourceMap extends javax.xml.transform.stream.StreamSource implements ConcurrentMap{ +public class SourceMap extends javax.xml.transform.stream.StreamSource implements Map{ - private ConcurrentHashMap members; + private TreeMap members; private QName messageName; /** * @param msgName the name of the operation message (WSDL 1.1) or operation element (WSDL 2.0) that is being encapsulated */ public SourceMap(QName msgName){ - members = new ConcurrentHashMap(); + members = new TreeMap(); messageName = msgName; } @@ -38,7 +36,7 @@ xmlContents.append("\n"); xmlContents.append(""); - // Serialize map members NOTE: not correct yet! + // Serialize map members for(String value: values()){ xmlContents.append(value); } @@ -140,41 +138,5 @@ public int size(){ return members.size(); } - - /* - * If the field with a given name is not yet associated with any value, associate it with the given value. - * Note that this operation is atomic for data integrity purposes in multi-threaded apps. - */ - public String putIfAbsent(String key, String value){ - return members.putIfAbsent(key, value); - } - - /* - * Removes the field with the given name only if it currently has the given value. - * Note that this operation is atomic for data integrity purposes in multi-threaded apps. - * - * @return true if the replacement operation caused a change in the object value - */ - public boolean remove(Object key, Object value){ - return members.remove(key, value); - } - - /* - * Replaces the field with the given name only if the field already exists in the composite. - * Note that this operation is atomic for data integrity purposes in multi-threaded apps. - */ - public String replace(String fieldName, String value){ - return members.replace(fieldName, value); - } - - /* - * Replaces the field with the given name only if it currently has a given value - * Note that this operation is atomic for data integrity purposes in multi-threaded apps. - * - * @return true if the replacement operation caused a change in the object value - */ - public boolean replace(String fieldName, String oldValue, String newValue){ - return members.replace(fieldName, oldValue, newValue); - } } =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/WSDLConfig.java,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/WSDLConfig.java 2008/07/03 16:29:25 1.4 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/WSDLConfig.java 2008/10/30 02:33:24 1.5 @@ -138,6 +138,7 @@ NodeList partElements = messageElement.getElementsByTagNameNS(MobyPrefixResolver.WSDL_NAMESPACE, "part"); Map inputs = new HashMap(); Map inputMappings = new HashMap(); + Map secondaryMappings = new HashMap(); Map inputTypes = new HashMap(); Map secondaryInputs = new HashMap(); Map outputs = new HashMap(); @@ -177,6 +178,7 @@ "' is not a properly formed Moby primary or secondary param LSID as required"); } secondaryInputs.put(partName, mobyParam); + secondaryMappings.put(partName, schemaMapping); } else{ inputs.put(partName, mobyParam); @@ -200,6 +202,7 @@ setPrimaryInputFormats(inputMappings); setInputXSDTypes(inputTypes); setSecondaryInputs(secondaryInputs); + setSecondaryInputFormats(secondaryMappings); } else{ // it's output setPrimaryOutputs(outputs); @@ -216,25 +219,31 @@ (!dataTypeLSIDFields[3].equals("objectclass") && !dataTypeLSIDFields[3].equals("namespacetype"))){ return null; } - // Special case, if the LSID is a namespace, spec out a base object in the given namespace - if(dataTypeLSIDFields[3].equals("namespacetype")){ - return paramName+":"+MobyTags.MOBYOBJECT+":"+dataTypeLSIDFields[4]; - } - else{ - // Deal with the case where the output XSD data type is an array: - // implicitly make the return data type Collection(Thing) - - // See if the name is namespace qualified, and separate the local part if so - String nsURI = ""; - if(paramXSDType.contains(":")){ - String nsPrefix = paramXSDType.substring(0, paramXSDType.indexOf(":")); //XML NS prefix - paramXSDType = paramXSDType.substring(paramXSDType.indexOf(":")+1); //local part - nsURI = element.lookupNamespaceURI(nsPrefix); //prefix->URI + // Deal with the case where the output XSD data type is an array: + // implicitly make the return data type Collection(Thing) + + // See if the name is namespace qualified, and separate the local part if so + String nsURI = ""; + if(paramXSDType.contains(":")){ + String nsPrefix = paramXSDType.substring(0, paramXSDType.indexOf(":")); //XML NS prefix + paramXSDType = paramXSDType.substring(paramXSDType.indexOf(":")+1); //local part + nsURI = element.lookupNamespaceURI(nsPrefix); //prefix->URI + } + Element schemaDataTypeElement = isBasicType(paramXSDType) ? null : + getSchemaElement(element.getOwnerDocument(), nsURI, paramXSDType); + if(getArrayType(schemaDataTypeElement) != null){ + // Special case, if the LSID is a namespace, spec out a base object in the given namespace + if(dataTypeLSIDFields[3].equals("namespacetype")){ + return paramName+":Collection("+MobyTags.MOBYOBJECT+"):"+dataTypeLSIDFields[4]; } - Element schemaDataTypeElement = getSchemaElement(element.getOwnerDocument(), nsURI, paramXSDType); - if(getArrayType(schemaDataTypeElement) != null){ + else{ return paramName+":Collection("+dataTypeLSIDFields[4]+")"; } + } + else{ + if(dataTypeLSIDFields[3].equals("namespacetype")){ + return paramName+":"+MobyTags.MOBYOBJECT+":"+dataTypeLSIDFields[4]; + } else{ return paramName+":"+dataTypeLSIDFields[4]; } @@ -242,6 +251,10 @@ } + private boolean isBasicType(String xsdType){ + return "string".equals(xsdType); //TODO: fill out list + } + public String wsdlParam2MobySecondaryParam(Element partElement, String paramName, String paramXSDType, String dataTypeLSID) throws Exception{ String[] dataTypeLSIDFields = dataTypeLSID.split(":"); @@ -252,6 +265,7 @@ } // the format for secondaries is "name:type:defaultValue:[min,max]", where [min,max] can be an enumeration as well String restrictionsSpec = getSecondaryParamRestrictions(partElement); + //System.err.println("Full secondary spec is " + paramName+":"+dataTypeLSIDFields[4]+":"+restrictionsSpec); return paramName+":"+dataTypeLSIDFields[4]+":"+restrictionsSpec; } @@ -478,6 +492,9 @@ // // // + if(schemaDefElement == null){ + return null; + } NodeList contentElements = schemaDefElement.getElementsByTagNameNS(MobyPrefixResolver.XSD_NAMESPACE, "complexContent"); if(contentElements.getLength() == 1){ @@ -538,6 +555,31 @@ nsUri + " does not exist"); } + public static Element renameSoapArrayElements(Element arrayElement, String newName, Document owner){ + NodeList arrayElements = arrayElement.getChildNodes(); + Element renamedArray = owner.createElement("soap-array"); + for(int j = 0; j < arrayElements.getLength(); j++){ + if(!(arrayElements.item(j) instanceof Element)){ + continue; + } + // For XPath rules to work properly, we need to rename the items + // in the array to the parent name + Element renamedArrayItem = owner.createElement(newName); + // clone the old element attributes and children into the new one + Element oldElement = (Element) arrayElements.item(j); + NamedNodeMap attrs = oldElement.getAttributes(); + for(int k = 0; k < attrs.getLength(); k++){ + renamedArrayItem.setAttributeNodeNS((Attr) attrs.item(k).cloneNode(true)); + } + NodeList children = oldElement.getChildNodes(); + for(int k = 0; k < children.getLength(); k++){ + renamedArrayItem.appendChild(children.item(k).cloneNode(true)); + } + renamedArray.appendChild(renamedArrayItem); + } + return renamedArray; + } + protected String convertSourceToMobySecondaryValues(Source source, URL liftingSchema, boolean arrayRule) throws Exception{ // The source will contain an XML document, lets convert it to a string of the form val1,val2,val3 using a stylesheet TransformerFactory transformerFactory = TransformerFactory.newInstance(); @@ -560,8 +602,22 @@ if(!(source instanceof StreamSource)){ StringWriter verbatim = new StringWriter(); transformerFactory.newTransformer().transform(source, new StreamResult(verbatim)); - //System.err.println("Verbatim source is:\n" + verbatim); - source = new StreamSource(new StringReader(verbatim.toString())); + // Need to compensate for the fact that some XSLT transformers don't copy over the + // namespace declaration properly, so declare it manually for xsi if that's the case + // otherwise you get a parsing error later on when trying to do the + // xml schema -> moby xml transformation. Ditto with soap encoding. + String verb = verbatim.toString(); + if(verb.indexOf(" xmlns:xsi") == -1 && + verb.indexOf(" xsi:") != -1){ + verb = verb.replaceFirst(" xsi:", + " xmlns:xsi=\""+MobyPrefixResolver.XSI_NAMESPACE2001+"\" xsi:"); + } + if(verb.indexOf(" xmlns:SOAP-ENC") == -1 && + verb.indexOf(" SOAP-ENC:") != -1){ + verb = verb.replaceFirst(" SOAP-ENC:", + " xmlns:SOAP-ENC=\""+MobyPrefixResolver.SOAP_ENC_NAMESPACE+"\" SOAP-ENC:"); + } + source = new StreamSource(new StringReader(verb)); } Document arrayDoc = null; @@ -572,10 +628,16 @@ arrayDoc = docBuilder.parse(new org.xml.sax.InputSource(((StreamSource) source).getReader())); } else{ - throw new Exception("Neither the InputStream or Reader was available from " + + throw new Exception("Neither an InputStream nor a Reader was available from " + "the StreamSource, cannot process the source"); } - NodeList arrayElements = arrayDoc.getElementsByTagName("item"); + Element arrayElement = (Element) arrayDoc.getDocumentElement().getFirstChild(); + String dataTypeAttr = arrayElement.getAttributeNS(MobyPrefixResolver.SOAP_ENC_NAMESPACE, "arrayType"); + String dataType = dataTypeAttr.replaceFirst("^.*:([^\\[]+).*", "$1"); + //System.err.println("Array Data Type for secondary source is " + dataType); + // for RPC-encoded data, rename item tags to real data type name + Element renamedArray = renameSoapArrayElements(arrayElement, dataType, arrayDoc); + NodeList arrayElements = renamedArray.getElementsByTagName(dataType); for(int i = 0; i < arrayElements.getLength(); i++){ if(i != 0){ stringWriter.write(','); //join values with a comma @@ -587,7 +649,7 @@ else{ transformer.transform(source, new StreamResult(stringWriter)); } - //System.err.println("Response payload:\n"+stringWriter.toString()); + //System.err.println("Response payload for secondary param:\n"+stringWriter.toString()); return stringWriter.toString(); } From gordonp at dev.open-bio.org Wed Oct 29 22:33:24 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 29 Oct 2008 22:33:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200810300233.m9U2XOCa010626@dev.open-bio.org> gordonp Wed Oct 29 22:33:24 EDT 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services In directory dev.open-bio.org:/tmp/cvs-serv10500/src/main/ca/ucalgary/seahawk/services Modified Files: MobyClient.java TextClient.java Log Message: Updates related to SAWSDL wrapping Web Service implementation moby-live/Java/src/main/ca/ucalgary/seahawk/services MobyClient.java,1.20,1.21 TextClient.java,1.5,1.6 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/MobyClient.java,v retrieving revision 1.20 retrieving revision 1.21 diff -u -r1.20 -r1.21 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/MobyClient.java 2008/01/14 23:00:44 1.20 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/MobyClient.java 2008/10/30 02:33:24 1.21 @@ -93,12 +93,8 @@ */ public MobyClient(Registry reg) throws MobyException{ registry = reg; - if(reg != null && reg.getEndpoint() != null){ - c = new CentralCachedCallsImpl(reg.getEndpoint()); - } - else{ - c = new CentralCachedCallsImpl(); - } + c = CentralImpl.getDefaultCentral(registry); + xpathMap = new HashMap(); urlRegexMap = new HashMap(); regexMap = new HashMap(); @@ -328,6 +324,8 @@ } } // for each ruleset + + // TODO: add warning if no rules at all were added (the file may not be a MOB rules file!) } public boolean isPrefixRule(Element e){ @@ -634,6 +632,57 @@ } /** + * Create a MOBY data instance from a DOM by applying the rules of the given MobyClient. + * The creation of a single object or collection is done according to the dataTemplate provided. + * + * @throws MobyServiceException NOTE: these are just warning level exceptions about collection-simple casting that you can add to the service response, or ignore if you like + */ + public MobyDataInstance getMobyObject(Node n, MobyPrimaryData dataTemplate) + throws Exception, MobyServiceException{ + Vector results = new Vector(); + + for(MobyDataObject resultPart: getMobyObjects(n)){ //TODO: , dataTemplate.getDataType())){ + results.add(resultPart); + } + + if(results.isEmpty()){ + throw new Exception("No MOB rules could be applied to the input data"); + } + else if(results.size() > 1){ + if(dataTemplate instanceof MobyPrimaryDataSimple){ + // In this case, eliminate any higher-up objects that + // have the exact same contents as the same members who are their + // subtypes, as these are superfluous. + + System.err.println("Multiple Moby objects were found in the text data, " + + "but the request was to return a simple. " + + "Only the first value in the collection has been returned."); + for(MobyDataObject result: results){ + System.err.println("Found object: " + result.getDataType().getName()); + } + // TODO: should we instead return the one deepest in the hierarchy (or with the most members)? + return results.elementAt(0); + } + else{ + MobyDataObjectSet resultSet = new MobyDataObjectSet(dataTemplate.getName()); + resultSet.addAll(results); + return resultSet; + } + } + // One result + else{ + if(dataTemplate instanceof MobyPrimaryDataSimple){ + return results.elementAt(0); + } + else{ // Collection of 1 + MobyDataObjectSet resultSet = new MobyDataObjectSet(dataTemplate.getName()); + resultSet.add(results.elementAt(0)); + return resultSet; + } + } + } + + /** * Create a MOBY data instance from a map of name->bytes[] by applying the rules of the given MobyClient. * The creation of a single object or collection is done according to the dataTemplate provided. * @@ -643,7 +692,6 @@ throws Exception, MobyServiceException{ Vector results = new Vector(); - // System.err.println("Data has " + resultParts.size() + " parts"); // The output parameter *potentially* has multiple parts // (e.g. multiple .png files from EMBOSS's "banana" program) // hence the nested for loops (part iteration, followed by created-object iteration) =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/TextClient.java,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/TextClient.java 2007/08/01 18:14:33 1.5 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/services/TextClient.java 2008/10/30 02:33:24 1.6 @@ -30,7 +30,8 @@ private TransformerFactory transFactory; private DocumentBuilder docBuilder; - private Map> typeTemplates; + private Map> typeTemplates; //mobytype -> Vector(xsltrule1, xsltrule2,...) + private Map> typeNsRestrictions; //mobytype -> Vector(mobynamespace1, ...) private Map templateMode; public TextClient() throws Exception{ @@ -45,10 +46,14 @@ moby2textConverters = new Vector(); typeTemplates = new HashMap>(); + typeNsRestrictions = new HashMap>(); templateMode = new HashMap(); } - public synchronized void addMappingsFromURL(URL xsltURL) throws Exception{ + /** + * @return the data format the xslt creates (the last template mode attribute in the file) + */ + public synchronized String addMappingsFromURL(URL xsltURL) throws Exception{ StreamSource stylesheet = new StreamSource(xsltURL.toString()); // Prepend to list, so later rules can override ones specified earlier moby2textConverters.insertElementAt(transFactory.newTransformer(stylesheet), 0); @@ -64,8 +69,10 @@ + xsltURL + " (empty or malformed document?)"); } + String mode = null; // returned in the end + // Lines look something like below - // + // NodeList templates = xsltDOMRoot.getElementsByTagNameNS(XSLT_NS, "template"); for(int i = 0; i < templates.getLength(); i++){ Element template = (Element) templates.item(i); @@ -73,17 +80,21 @@ continue; } String templateName = template.getAttribute("name"); - templateMode.put(templateName, template.getAttribute("mode")); + String m = template.getAttribute("mode"); + if(m != null && m.trim().length() > 0){ + mode = template.getAttribute("mode"); + } + templateMode.put(templateName, m); //System.err.println("Processing template " + templateName + ", mode " + template.getAttribute("mode")); // Keep track of the list of templates using the given MOBY object type String[] templateNameParts = templateName.split("\\."); - if(templateNameParts.length == 1){ - System.err.println("Ignoring template without \"DataType#1\" format for its name attribute (" + - templateName); - continue; - } + // if(templateNameParts.length == 1){ +// System.err.println("Ignoring template without \"DataType.1\" format for its name attribute (" + +// templateName); +// continue; +// } if(templateNameParts[0].startsWith("Collection-")){ if(templateNameParts[0].length() == 11){ @@ -94,20 +105,41 @@ } // See if the type exists in the ontology + // TODO: add support for registry spec via LSID in mode (how to deal with colons?) MobyDataType type = MobyDataType.getDataType(templateNameParts[0], SeahawkOptions.getRegistry()); + MobyNamespace ns = null; //no ns restriction by default if(type == null){ - System.err.println("Ignoring template whose name attribute (" + templateName + - ") uses a non-existent datatype (" + templateNameParts[0] + ")"); - continue; + // See if there is a namespace restriction e.g. Object-EC + if(templateNameParts[0].contains("-") && !templateNameParts[0].endsWith("-")){ + // Assumes no dashes in the namespace label itself + String namespace = templateNameParts[0].substring(templateNameParts[0].lastIndexOf("-")+1); + //System.err.println("Found a dash in "+templateNameParts[0] + ", assuming ns is " + namespace); + ns = MobyNamespace.getNamespace(namespace, SeahawkOptions.getRegistry()); + // If it can be parsed as a real namespace, treat the stuff before the "-NS" as the data type + if(ns != null){ + templateNameParts[0] = templateNameParts[0].substring(0, templateNameParts[0].lastIndexOf("-")); + type = MobyDataType.getDataType(templateNameParts[0], SeahawkOptions.getRegistry()); + } + //System.err.println("Resolved ns is " + type); + } + if(type == null){ + System.err.println("Ignoring template whose name attribute (" + templateName + + ") uses a non-existent datatype (" + templateNameParts[0] + ")"); + continue; + } } if(!typeTemplates.containsKey(templateNameParts[0])){ typeTemplates.put(templateNameParts[0], new Vector()); + typeNsRestrictions.put(templateNameParts[0], new Vector()); } // Later templates have higher priority than earlier declarations typeTemplates.get(templateNameParts[0]).insertElementAt(templateName, 0); - + typeNsRestrictions.get(templateNameParts[0]).insertElementAt(ns, 0); } + + //System.err.println("Mode returned by " + xsltURL + " is " + mode); + return mode; // return the last mode value in the file (useful when mapping XSLT -> data format) } /** @@ -127,8 +159,13 @@ type != null; type = type.getParent()){ if(typeTemplates.containsKey(type.getName())){ - for(String templateName: typeTemplates.get(type.getName())){ - if(textType.equals(templateMode.get(templateName))){ + // These two vectors should be of the same length! + Vector templateNames = typeTemplates.get(type.getName()); + Vector nsRestrictions = typeNsRestrictions.get(type.getName()); + for(int i = 0; i < templateNames.size(); i++){ + String templateName = templateNames.elementAt(i); + // the template input moby datatype is the same type as we have an instance of + if(textType.equals(templateMode.get(templateName))){ // Input Moby type and output text type match: does set-ness? if(dataTemplate instanceof MobyPrimaryDataSet){ if(templateName.startsWith("Collection-")){ @@ -140,6 +177,15 @@ return true; } } + // Is there a namespace restriction on the transformation rule? + MobyNamespace ns = nsRestrictions.elementAt(i); + if(ns != null){ + for(MobyNamespace n: dataTemplate.getNamespaces()){ + if(ns.equals(n)){ + return true; + } + } + } } } } @@ -154,6 +200,8 @@ * try representing the data in simpler top level objects until we get a rule * that produces something. * + * @param mobyData must be an instance of a MobyPrimaryData that will be transformed + * * @return null if the moby data or target text type is null, null if data is not primary, null if no templates apply, or a string representing the transformation if successful */ public String getText(MobyDataInstance mobyData, String targetTextType) throws Exception{ @@ -163,11 +211,60 @@ // Spaces are not allowed in mode names targetTextType = targetTextType.replace(' ', '-'); + if(!(mobyData instanceof MobyPrimaryData)){ + throw new IllegalArgumentException("Require a MobyPrimaryData instance for arg 0 but " + + "was passed a "+mobyData.getClass().getName() + " instead."); + } + Vector candidateTypes = new Vector(); for(MobyDataType type = ((MobyPrimaryData) mobyData).getDataType(); type != null; type = type.getParent()){ if(typeTemplates.containsKey(type.getName())){ + // These two vectors should be of the same length! + Vector templateNames = typeTemplates.get(type.getName()); + Vector nsRestrictions = typeNsRestrictions.get(type.getName()); + for(int i = 0; i < templateNames.size(); i++){ + String templateName = templateNames.elementAt(i); + // the template input moby datatype is the same type as we have an instance of + if(targetTextType.equals(templateMode.get(templateName))){ + // Is there a namespace restriction on the transformation rule? + MobyNamespace ns = nsRestrictions.elementAt(i); + if(ns != null){ + boolean nsMatch = false; + for(MobyNamespace n: ((MobyPrimaryData) mobyData).getNamespaces()){ + if(ns.equals(n)){ + nsMatch = true; + break; + } + } + if(!nsMatch){ + continue; // ns doesn't match, don't bother checking set-ness + } + } + + // Input Moby type and output text type match, we'll try the template here + if(mobyData instanceof MobyPrimaryDataSet){ + if(templateName.startsWith("Collection-")){ + candidateTypes.add(type); + break; + } + } + else{ + if(!templateName.startsWith("Collection-")){ + candidateTypes.add(type); + break; + } + } + } + } + } + } + + for(MobyDataType type = ((MobyPrimaryData) mobyData).getDataType(); + type != null; + type = type.getParent()){ + if(typeTemplates.containsKey(type.getName())){ for(String templateName: typeTemplates.get(type.getName())){ if(targetTextType.equals(templateMode.get(templateName))){ // Input Moby type and output text type match, we'll try the template here From gordonp at dev.open-bio.org Wed Oct 29 22:33:25 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 29 Oct 2008 22:33:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200810300233.m9U2XPIp010730@dev.open-bio.org> gordonp Wed Oct 29 22:33:25 EDT 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test In directory dev.open-bio.org:/tmp/cvs-serv10500/src/main/ca/ucalgary/services/util/test Modified Files: WSDLConfigTestCase.java Log Message: Updates related to SAWSDL wrapping Web Service implementation moby-live/Java/src/main/ca/ucalgary/services/util/test WSDLConfigTestCase.java,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/WSDLConfigTestCase.java,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/WSDLConfigTestCase.java 2008/07/03 16:29:26 1.3 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/util/test/WSDLConfigTestCase.java 2008/10/30 02:33:25 1.4 @@ -39,9 +39,9 @@ private final static int NUM_OUTPUTS = 1; private final static String OUTPUT_NAME1 = "return"; - private final static String OUTPUT_TYPE1 = "return:Collection(GeneId)"; //should be collection due to XSD array type of return + private final static String OUTPUT_TYPE1 = "return:Collection(Object):KEGG_GENES"; //should be collection due to XSD array type of return private final static String OUTPUT_XSDTYPE1 = "typens:ArrayOfstring"; - private final static String OUTPUT_SCHEMA_MAPPING1 = "urn:lsid:bioxml.info:mobyLiftingSchemaMapping:string2GeneId"; + private final static String OUTPUT_SCHEMA_MAPPING1 = "urn:lsid:bioxml.info:mobyLiftingSchemaMapping:string2KEGG_GENES"; private final static String SOAP_SERVICE_NAME = "KEGG"; private final static String SOAP_SERVICE_URI = "SOAP/KEGG"; From gordonp at dev.open-bio.org Wed Oct 29 22:33:24 2008 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 29 Oct 2008 22:33:24 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200810300233.m9U2XOOw010600@dev.open-bio.org> gordonp Wed Oct 29 22:33:24 EDT 2008 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources In directory dev.open-bio.org:/tmp/cvs-serv10500/src/main/ca/ucalgary/seahawk/resources Modified Files: mobyBuilderRules.xml Log Message: Updates related to SAWSDL wrapping Web Service implementation moby-live/Java/src/main/ca/ucalgary/seahawk/resources mobyBuilderRules.xml,1.7,1.8 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources/mobyBuilderRules.xml,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources/mobyBuilderRules.xml 2008/01/30 00:04:06 1.7 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/resources/mobyBuilderRules.xml 2008/10/30 02:33:24 1.8 @@ -103,6 +103,14 @@ + +