2011-06-14 Martin Senger * Released version 2.3.2 2011-05-01 Mahmut Uludag * Missing getSomeResults method added to typed interface * New log file that records summary information for each job started including the IP address of the client, interface used, whether the job was successfully completed, and the time elapsed 2010-11-24 Martin Senger * Released version 2.3.1 2010-11-08 Martin Senger * Fixed uploading file in spinet: the files are now treated as with binary contents (and not blindly converted to String) * Added (to the CmdLineClient) an ability to consider an input file as binary (sending its contents as byte[] and not String) 2010-10-11 Martin Senger * Fixed problem with result containing foreign characters. Forced UTF-8 encoding. Not sure if the fix works also in Spinet for Axis1-based services. 2010-08-17 Martin Senger * Released version 2.3.0 2010-08-10 Martin Senger * Documentation: the Soaplab2 index page has now TOC at the top. * Added new input/output sequence formats (including next generation sequence formats ) to EMBOSS services. * Removed not-needed repository definitions from maven.xml. Fixed some dependencies. 2010-08-09 Martin Senger * Refactoring creation and deployment of strongly typed services. 2010-08-06 Martin Senger * Added: Documentation about 'relations' attribute in ACD files (links to EDAM ontology). 2010-08-05 Martin Senger * Fixed: the relations tags from ACD files appear now in the Soaplab's XML metadata as options named 'EDAM:XXX' with value consisting of namespace and term name; fixed for the EMBOSS 6.3.1 and also for the next EMBOSS version (where the relations tag will have different syntax) 2010-08-01 Mahmut Uludag * EMBOSS-6.3 updates for ACD changes * SAWSDL/EDAM support (help and suggestions from Hamish McWilliam) * More output types wrapped (help from Hamish McWilliam) 2010-06-15 Dietmar Sturmayr , Mahmut Uludag * Fixed: too many open files problem in SowaJob class process objects are now cleaned before the execute threads terminate, rather than leaving the cleaning job to Java garbage collection 2010-03-02 Mahmut Uludag * temporary files are saved in the relevant job directories rather than the default temporary files folder * removed some synchronized blocks or reduced their scope * destroy(jobid) function returns after making a record of the request * EMBOSS-6.2 updates for ACD changes 2009-08-14 Mahmut Uludag * removed full path information from input/output file names * fix: after terminate calls job status set to TERMINATE_BY_REQUEST * status of timed-out jobs changed to TERMINATED_BY_REQUEST 2009-08-14 Sebastien Moretti * EMBOSS tests updated for EMBOSS-6.1 * EMBOSS tests extended with new tests 2009-06-18 Mahmut Uludag * new property for customised spinet title page; spinet.welcome.msg * new property to set a limit for waitfor calls; jobs.waitfor.timeout * support for submitting jobs to LSF queues * beta version of typed interface 2009-04-22 Mahmut Uludag * use of catalina.home replaced by catalina.base suggested by José María Fernández on sourceforge tracker * new ant target (deployx) to deploy soaplab web applications using tomcat manager 2009-02-05 Mahmut Uludag, John S Robinson * Client side concurrency problems fixed - operations on the same org.apache.axis.client.Call objects are synchronized - upgraded versions of the jaxws-tools and mimepull artifacts 2008-10-23 Sebastien Moretti * Some EMBOSS ACD files that didn't have accompanying executables were disabled * EMBOSS jaspextarct program was disabled as it should normally be used by EMBOSS admins 2008-08-21 Martin Senger * Added new method getJobDir() to the Job interface 2008-05-05 Mahmut Uludag * Fixed: terminate calls was hanging occasionally or giving stream i/o errors 2008-05-04 Mahmut Uludag * Fixed (EMBOSS specific): It was not possible to specify a 'false' value for Boolean parameters with a default value 'true' 2008-05-16 Martin Senger * Released: version 2.1.1 * Changed: Replace minus characters in the job IDs to underscores. * Updated: Ant's task 'test-junit' for testing * Changed: the maven-ant library has the latest version, and, from now, it will be fetched from bio-open server 2008-04-04 Mahmut Uludag * Added: configurable jobs.timeout property which lets Soaplab terminate hanging or long running jobs automatically 2008-04-03 Mahmut Uludag * throughput of the server improved by deleting unnecessary synchronized settings in three methods; two in the PersistenceManager class, one in the FileStorage class 2008-03-31 Mahmut Uludag * Fixed: FileStorage cannot store job properties problem, Soaplab was attempting to store job properties files before the job results directory made 2008-03-30 Mahmut Uludag * Fixed: two javascript problems that break Spinet when using IE 2008-02-05 Martin Senger * Released: Version 2.1.0 [the first non-beta release] 2008-02-01 Martin Senger * Improved: Most places where the SPI mechanism is used has now a default class. Therefore, the file 'soaplab-spi-config.jar' is not anymore mandatory (which may help when Soaplab2 is used as a third-party library from a Maven repository). 2008-01-29 Mahmut Uludag * Added: - directory locks when reading and loading job properties files - better cleaning strategy for the directory locks used in FileManager - synchronization for iterations over the configuration properties - new check for testing whether a job was deleted while the JobManger iterating over the jobs list 2008-01-25 Martin Senger * Added: batch testing suites for checking services * Upgrade: dependency on Apache Commons Configuration (needed because the previous 1.3 version had bugs in properties interpolation) 2008-01-23 Martin Senger * Added: changing file permissions to become executable in the WEB-INF/run directory (see more about it in property scripts.dir) 2008-01-20 Martin Senger * Added: documentation how to create and deal with metadata * Added: Spinet web interface (shown as the "welcome page" of the Soaplab2 services) 2007-12-06 Martin Senger * Fixed: External programs started from/by Soaplab get now updated version of the environmental variable PATH (which is, for example, a requirement for such programs as EMBOSS's wossname). 2007-12-05 Martin Senger * Fixed: better support for the 'toggle' attribute in the EMBOSS ACD files (until now these parameters were displayed as simple text field, but they are now correctly shown as boolean radio buttons). 2007-12-04 Martin Senger * Fixed: Result 'report' was truncated when retrieved after a while. 2007-11-21 Martin Senger * Fixed: Soaplab2 running in Tomcat was not properly re-creating the (empty) result directory if it was removed (manually) during the Tomcat life. * Fixed: Some jobs were removed too fast; even when it was not wanted; resulting with an unexpected errors "Not Found" later 2007-11-15 Martin Senger * Added: More service properties are coming in metadata from Soaplab2 servers (version, supplier, and most importantly help_URL). 2007-11-01 Martin Senger * EMBOSS: Some administrative services disabled by default. 2007-10-28 Martin Senger * Released: 2.0.0-beta