2008-11-18 Martin Senger * Added new properties to dashboard.properties allowing to limit the list of known registries 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 was in packaging the jMoby; no change in code or behaviour) 2008-07-23 Martin Senger * Version 1.1.0 released 2008-05-23 Martin Senger * Fixed: registering data types from an XML file, in Dashboard 2008-04-20 Martin Senger * Changed CreateMobyInput client - it now requires to use the local cache. 2008-03-28 Martin Senger * Fixed a dependency for commons-collection in the project.pom. 2008-03-14 Martin Senger * Fixed a bug with missing xercesImpl classes. Putting back xercesImpl - but now with a newer version (2.7.1) 2008-03-12 Martin Senger * Version 1.0.0 released 2008-03-03 Martin Senger * Added a new method isUsingCache() to the CentralCached interface. * Fixed access to the local cache in the MoSeS service generator (the cache was not used in all circumstances). * Fixed compilation warnings for MoSeS generated data types. * Added constructors to the ExtendedServiceLocator. 2008-03-02 Martin Senger * Added: new installation task (type: ant install) - it downloads all needed librraies, builds the jMoby, fills the local cache and starts Dashboard. * Added: method MobyException.formatAndLog() * Changes in Dashboard: - Better support for configuration; it uses now also properties from the 'build.properties' file (which helps, for example, in finding the same registry local cache as the one used during the jMoby installation (ant install). - Allowing to select category when registering a new service. - The component layout in the MoSeS generators panel was slightly changed (the never-implemented flavours removed; more space for the console). - The console panels, in the append mode, now scroll better to their ends (in order to better follow what is being written there). - Fix the local class selector in the SimpleClient panel (before it suggested a file to select but in fact it was a class name that should be entered there). 2008-02-29 Martin Senger * Fixed: Calling various tasks from Dashboard sometimes caused a mysterious NullPointerException in the SimpleAnt task. This was because of a (still mysterious) bug in Ant itself. But I at least found a workaround so the bug should not occur again. * Added: New method getResource(URL url) in CentralImp class, dealing with gzipped RDF resources. 2008-02-28 Martin Senger * Fixed: the jMoby XML message parser can accept now more specialized types of members than the ones its parent was registered with 2008-02-22 Martin Senger * Change, Fixed: On various places (starting with org.biomoby.shared.Utils), starting to use Apache commons-io library (it was necessary in Utils.java because the method inputStreamToString() was broken anyway). * Added: a common parent to the command-line clients (org.biomoby.client.CmdLineHelper) - brinking more and unified features to these clients. 2008-02-14 Martin Senger * A new implementation of the CentralDigestCached classes fills much faster local caches (used also by the Dashboard). * The jMoby libraries and build files were all re-arranged in order to take advantages of the Maven technology. 2007-05-31 Martin Senger * Added: few new constants into MobyService for async services support * Added: starting to add support for the async services into MobyCmdLineClient 2007-05-29 Martin Senger * Added: new options -lt and -registry to the MobyCmdLineClient for easier selection which registry to use. * Fixed: on various place where a service was looking for, the used service pattern has now category empty (so not only services with the default 'moby' category are found). * Changed: the output list with names of found services (created by MobyCmdLineClient) contains now also service authority. * Added: MobyCmdLineClient has a new option -fc for finding services by category. 2007-05-27 Martin Senger * Added: BaseService got new methods to access HTTP headers and servlet environment of the request (getRequestLength(), getHTTPHeaders(), getServletRequest()). 2007-05-20 Martin Senger * Fixed: the date format of MobyDateTime is now fully compliant with the ISO8601. * Fixed: method ServiceException.toXML() is back as it was originally. Method ServiceException.toDOM() removed. 2007-04-18 Paul Gordon * Added support for binary data file loading, and Web image display in Seahawk & ACDServlet 2007-04-02 Paul Gordon * Added asynchronous service call support to MobyRequest, Seahawk, based on client code originally provided by Eddie Kawas. * UI updates to Seahawk for tab management and drag 'n' drop/paste functionality 2006-11-21 Martin Senger * Added 'Released-Date' tag to joMby jar files 2006-10-24 Paul Gordon * Added Seahawk (MOBY-S client) code to CVS * Added MobyServlet code 2006-10-02 Martin Senger * Added to Dashboard: 'Call RDF Agent' button * Added to Dashboard: list of well-known registries 2006-09-28 Martin Senger * Fixed CentralImpl: added XML escaping for service registration (but still not everywhere) 2006-09-27 Martin Senger * Fixed data types generator when article name of a data type member was a Java keyword. 2006-08-10 Martin Senger * Fixed (in CentralImpl.java) storing of returned RDF documents into local file. Before it had an additional RDF element. 2006-08-01 Paul Gordon * Added MobyServlet.war and documentation for it: it allows one to create MOBY Services without downloading the CVS tree, and hides many other details. 2006-07-06 Paul Gordon * de-JDOM'ed several core classes * updates to the org.biomoby.shared.data package to deal with API changes * starting to use Java 1.5 features such as Generics * added object ontology checking utilities for convenience of run-type type checking * started HTML documentation for Seahawk, a extensible MOBY GUI client program 2006-06-28 Martin Senger * Changed build.xml (slightly) to consider from now the Java 1.6 as the latest version. * Fixed (the second time) an empty error message in the Generator panel. Still not sure if it is fixed fully. 2006-06-01 Martin Senger * Fixed Dashboard renderers - reporting now correctly when generated data types are not up-to-date. 2006-05-12 Martin Senger * Added convenient methods (into MobyPackage) for evaluating exceptions. 2006-05-09 Martin Senger * Added new method setParameter() to MobyJob. * Added support for secondary parameters to BaseCmdLineClient. 2006-04-28 Martin Senger * Fixed: spinner for integer values in Service Data Input does not need to be finished by presing ENTRER 2006-04-27 Martin Senger * Fixed: lost focus in various tables stops editing (so ENTER is not enymore necessary for that) * Changed default cache directory (in order to include also curremt user name). * Added a feature to a 'pattern' in Deployment panel (Service vs. SERVICE). 2006-04-26 Martin Senger * Change build.xml - splitted to more files. 2006-04-13 Martin Senger * [Dashboard] Added line wrapping to the area for descriptions of secondary parameters. * [Dashboard] Fixed: In rare cases generator panel produced an empty error messages (and a NullPointerException message in the log file). * [Dashboard] Remember last value in the Implementation Pattern text field (Moses panel). 2006-03-10 Martin Senger * [Dashboard] Fixed cleaning of the input/output table in the service registration panel. 2006-03-03 Martin Senger * Added method extractExceptions[] to ServiceException. * Change ServiceException: now it extends MobyException. * Fixed problems with NullPoiterException when starting Dashboard (not sure if everything is fixed). 2006-02-27 Martin Senger * Fixed BaseClient - it did not use service URL fetched from a registry. 2006-02-25 Martin Senger * Added getServicesByAuthority() to CentralImpl. * Added recognition of LSIDs in MobyServices and MobyDataTypes. * Added signatureURL to a service query object. * Added get/setDescription() to MobySecondaryData; also toXML() and toString() changed. 2006-02-21 Martin Senger * Slightly changed getXXXRelationships() in CentralImpl. It uses now a newer XML request (but it should work in the same way as before). 2006-02-19 Martin Senger * Added new fields to MobyServiceLocator (timeout, sent-as-bytes). 2006-02-12 Martin Senger * Added methot getMobyTypeName() to MobyObject. 2006-02-11 Martin Senger * Added an exception to the BaseClient.getServiceLocator() - sorry this is a change that may break your code. * Added support for sending data also as byte[] into BaseClient and BaseCmdLineClient (but not to SimpleClientPanel). 2006-02-07 Martin Senger * Added method toXMLDocument() to MobyPackage (to get an XML as a DOM document and not only as a string). * Added static methods for converting pieces (MobySimple, MobyCollection, MobyDataElement, MobyJob, MobyPackage) to XML. * Added error handling to class MobyPackage (new structure of serviceNotes, changes in MobyParser). 2005-11-22 Martin Senger * Fixed getting XML parsers in CentralImpl.java in order to be thread-safe. 2005-11-12 Martin Senger * Changed MobyException to use initCause() and log.debug to better indicate what happened and where. * Fixed CentralImpl: it is not anymore vulnerable to a different types of results coming back from biomoby registry. 2005-11-10 Martin Senger * Added method getParentName() to MobyServiceType 2005-11-08 Martin Senger * Added methods getRegister[...]XML() to CentralImpl. * Changed return value of setDebug() in Central.java (now ir return the previous debug mode). 2005-11-07 Martin Senger * Change default data type in MobySecondaryData from STRING to String. 2005-11-06 Martin Senger * Added method getRegisterServiceXML() to CentralImpl. * Added test for not to duplicate same namespaces in MobyPrimaryData. * Added new class MobyPrimaryData in between MobyData and MobyPrimaryDataSimple/Set - helps better distinguished between primary and secondary data. * Added removeNamespace() to MobyPrimaryDataSimple. 2005-11-02 Martin Senger * Changed method equals() in MobyService. * Add Comparator interface/implementation to MobyService. 2005-10-26 Martin Senger * Add Comparator interface/implementtaion to MobyServiceType. * Changed slightly the output of namespaces and service types in MobyCmdLineClient (because more data is now flowing from Biomoby registers). * Add getFullNamespaces() to Central.java and its implementations. * Add Comparator interface/implementtaion to MobyNamespace. 2005-09-24 Martin Senger * Added sorting to the most of the returned results from CentralImpl. 2005-09-23 Martin Senger * Add a new method getFullNamespaces() to CentralDigest interface. * Changed some outputs of the command-line clients. * Significantly improved local caching. 2005-09-21 Martin Senger * Fixed build.xml not to produce javadoc warnings with Java 1.5 in Eclipse. 2005-09-20 Martin Senger * Fixed CentralDigestImpl - it shows now correct service type description. 2005-09-19 Martin Senger * Added caching for namespaces to CentralDigestCachedImpl 2005-09-01 Martin Senger * Fixed the Windows run...bat scripts in order to accept spaces in the file names (many double quotes added) 2005-08-31 Martin Senger * Fixed build.xml (javadoc target) to run under Windows (newlines in header and bottom caused problems). 2005-08-29 Martin Senger * Added project Moses for generating code for service providers. 2005-08-25 Martin Senger * Clean-up build.xml generally, added there new targets for samples and moses. * Changed the remote.dir for build.xml - now we are taking jmoby jars from biomoby.org/jmoby-jars/jars-archives. * Moved sources from src/Services to src/main. Space src/Services is deprecated. The exaples and tutorials are now in src/samples that is *not* compiled by default with the src/main compilation. 2005-08-21 Martin Senger * Removed packages org.biomoby.shared.dom and org.biomoby.shared.dom.wrappers (they were not in use anymore - at least I hope) 2005-08-18 Paul Gordon * Completed updated version of MobyRequest that deals with named parameters, and single anonymous parameters According to MOBY API 0.86, all parameters should be named, but this invalidates many services, so we relax the rules to allow anonymous parameters if they are unambiguous (i.e., only one of them). 2005-08-17 Martin Senger * Refactored package embl.ebi.soap into alltools2.lib (the same features but used by more projects) 2005-08-16 Martin Senger * Fixed CentralImpl - and empty registry endpoint and namespce are ignored * Fixed CentralDigestCachedImpl to ignore backup files (those ending with '~') if they appear in the cache 2005-08-14 Martin Senger * Added a static method getString() to org.biomoby.shared.data.MobyDataDateTime in order to achive the date/time string conversion features without a need to instantiate thsi object * Moved (and updated) class org.biomoby.shared.MobyObject to org.biomoby.shared.datatypes.MobyObject * Removed interface org.biomoby.shared.MobyNativeService as obsolete (and not used by anybody, at least I hope :-)) * Added method toXMLElement() to org.biomoby.shared.data.MobyProvisionInfo 2005-08-07 Paul Gordon * Added asynchronous mode to MobyRequest, so clients get callbacks when results are ready (not to be confused with asynchronous calls at the MOBY protocol level). * Web site documentation update for client/server quickstart. 2005-08-07 Martin Senger * Added methods to Central.java for getting URLs of the RDF registry resources, and for getting resources themselves. * Added new options to MobyCmdLineClient dealing with registry's endpoint and its namespace, and with getting RDF resources. 2005-07-21 Paul Gordon * Update of data instance code to fully functional status (pending minor changes to the MOBY-S API docs) * Inclusion of "quick start" guide to using the classes in org.biomoby.shared.data 2005-07-19 Martin Senger * Changed the remote repository for the third-party jar files. * Added a new option -la to the MobyCmdLineClient to list services by authorities. * Added new method getServiceNamesByAuthority() to the Central.java interface. getServiceNames() deprecated. * Default location and namespace of the Moby Central has been changed (in CentralImpl.java). 2005-05-19 Martin Senger * Updated build.xml; also separate some fragments into xmls directory. * Ant changed to its latest release. 2005-05-17 Martin Senger * Added documentation as a result of the BioMoby meeting in Vancouver, May 2005. Especially more details and hints about how to commit new code. * Added stylesheet to the documentation. 2004-12-05 Martin Senger * Updated documentation (significantly, but not yet finished). 2004-11-30 Martin Senger * Fixed CentralImpl dealing now better with 1 and 1. 2004-11-14 Martin Senger * Added MobyDigestClient for retrieving cummulative (digested) entries from registries * Added CacheRegistryClient for storing data types and service instances in a local file system 2004-11-12 Martin Senger * Added -scall for calling services (instead of a Moby Central) into the command-line client MobyCmdLineClient 2004-10-18 Martin Senger * Added general SOAP utilities in package embl.ebi.soap (the package name is consistent with other general utilities already in alltools.jar) * Added jar file with main Taverna classes (needed for generating scufl workflows). * New extension of SimpleCache: SimpleFileCache (actually it existed before but under different name). * Added finding paths between selected data types into MobyGraphs (command-line) client and GraphsServlet (servlet) client. Both these clients were also significantly changed (hopefully for better). * Added implementations of new interfaces: CentralDigestImpl.java and CentralDigestCachedImpl.java. Especially the latter one is useful allowing to cache almost full registry in your file system. * Re-implemented the caching mechanism in CentralImpl.java (using new interface SimpleCache.java). * New interface CentralDigest.java allowing to get data from Moby registry in one go. Also a new interface CentralAll.java combinaning traditional Central.java and new CentralDigest.java. * Added new methods to Central.java allowing to find what registry we are connected to. 2004-09-24 Martin Senger * Fixed signatureURL in service response object. 2004-09-23 Martin Senger * Moved constants ISA, HAS, HASA from MobyRelationship to Central (as iHAS, iHASA and iISA). 2004-09-22 Martin Senger * Fixed option -rs-out in MobyCmdLineClient. * Added a -debug option to the TestingCentral client. * Fixed TestingCentral client - it used incorectly user-defined data type in the output secondary article. * Added HAS relationship type for children of MobyDataType objects. It uses a new class MobyRelationship (meaning that methods returning children in MobyDataType got new signatures). * Changes reflecting new service registration procedure: - MobyService has new members with corresponding set/get methods for storing 'signatureURL' and a fully qualified path to the place where the service signature (an RDF document) can be stored). - CentralImpl stores retrieved RDF in a local file (read API for MobyService class, it explains what CentralImpl is doing). - command-line program MobyCmdLineClient got few new options in order to deal with 'signatureURL' (see its new help). 2004-09-03 Paul Gordon * First commit of data instance classes for base objects (Floats, Integers, Strings), and updates to Simple and Service Associated Instance objects to deal with the new object types. You can now create these objects (no XML knowledge required) for use in services, and you can create complex Moby objects using DOM fragments. Aggregation of base objects to create complex objects still needs to be implemented. 2004-07-07 Paul Gordon * Modifications to MobyRequest to handle Axis 1.1beta, and a variety of encoding schemes (base64 and XSD string) and namespaces (1999 and 2001 XSD, MOBY transport) 2004-05-20 Paul Gordon * Added full working example of service discovery and invocation in src/Client/MobyServiceInvocationExample Use that one instead of the example in this ChangeLog 2004-05-18 Martin Senger * Added a new displaying option (-on) to MobyCmdLineClient * Added a new findService() method to Central.java allowing to set also 'expandObjects' and 'expandServices' attributes. * Added/fixed MobyCmdLineClient to to able to find service by input/output. 2004-05-05 Paul Gordon * Changed MobyRequest to reflect new 0.7 API, i.e. queries and responses have the same mobyContent/mobyData envelopes. 2004-04-21 Paul Gordon * Implemented Moby data instance classes for simples, collections, secondary inputs in org.biomoby.shared.*; * Implemented namespace resolver for retrieval of MOBY attributes in DOM fragments, default namespace mapping for XPath, etc. * Implemented org.biomoby.client.MobyRequest, which handles the SOAP transactions for service invocation. Takes in Moby data objects, outputs Moby data objects e.g. // Assumes you already have a service (mobyService) and data (mobyInputData) around mobyRequest = new MobyRequest(new CentralImpl()); mobyRequest.setDebugMode(true); mobyRequest.setService(mobyService); mobyRequest.setInput((MobyDataInstance[]) mobyInputData); try{ mobyRequest.invokeService(); } catch(MobyException mobye){ System.err.println("Failure in MOBY protocol: " + mobye); } catch(SOAPException soape){ System.err.println("Failure in SOAP transaction: " + soape); } catch(NOsUccessException nse){ System.err.println("Failure in MOBY logic (input was not acceptable " + "for this service)" + nse); } 2004-04-02 Paul Gordon * Changed XML parsing to JAXP based interface that works on more platforms * Implemented Central response caching to reduce network and XML parsing loads 2004-04-02 Martin Senger * Fixed producing graphs to deal with situation that some Moby methods return simple names and some full LSIDs. * Fixed servlet producing graphs (proxy is set now correctly, cached files have no longer too long names). 2004-03-08 Martin Senger * Fixed extracting URL and emailContact from a service response object. 2004-01-15 Martin Senger * Fixed: better error reporting when am empty result is returned. 2003-11-24 Martin Senger * Added graphs of service types. * Added several new methods to Central.java dealing with relationships. Consequently MobyCmdLineClient got few new options. 2003-11-20 Martin Senger * CentralImpl.call method can deal now with results of type byte[] (base64 in the SOAP terminology). * CentralImpl sets now SOAPAction header. It was not needed when accessing the Moby Central (registry) but some users started to use CentralImpl also for calling services (by using CentralImp.call method) and that usually required a SOAPAction header. 2003-11-09 Martin Senger * Added servlet properties for HTTP proxies and path to 'dot'. 2003-11-07 Martin Senger * Added BioMoby Graphs (command-line client and a servlet-based service). 2003-10-29 Martin Senger * CentralImpl fixed to reflect the change in Moby API (a different XML tag in getDataType() method). 2003-10-17 Martin Senger * Added files searching for available connections between moby services and moby data types, and creating graphs of them. 2003-10-15 Martin Senger * Fix TestingCentral.java for properly registering ISA relationships data types. Added new undocumented command-line option - see the source code. * Fix CentralImpl.java for registration of data and service type (the ISA and HASA were still in the Boston pre-hackathon state). 2003-09-25 Martin Senger * Ant-alizing... New installation, build and distribution files. Checked that everything works fine both on Unix and on Windows. 2003-06-20 Martin Senger * Fix adding 'HASA' children into MobyDataType objects. * Method 'getDataType' added to Central.java. New command-line option '-data' in MobyCmdLineClient calls this method. * I have started recording the main changes in jMoby. But for more details and for really up-to-date list of changes consider always to look at the Moby CVS repository.