SSDM-5132: Fixing bug in DirectoryScannedStore by logging error twice:: one for notification (has no stack trace) and one for the log file with stack trace.

SVN: 38653

SVN: 38652

SVN: 38578

SVN: 38577

SVN: 37929

SVN: 37927

SSDM-4843 : Common file operations used to make local move operations on DSS to use Java 7 ATOMIC_MOVE

SVN: 37907

SVN: 37899

SVN: 37898

SVN: 37689

New constructor introduce for JythonEvaluatorSpringComponent in order to make it usable in unit tests.

SVN: 37522

- new maintenance task that marks new, scheduled, running executions as failed after server restart
- fix a maintenance task that marks execution information (core, summary, details) as timeout_pending to mark it only if it is still available but not, for instance, already timed_out

SVN: 37460

SVN: 37389

SSDM-4379: move IOptionalSTackTraceLoggingException and InvalidSessionException from commonbase to common.

SVN: 37388

SVN: 37387

SSDM-4379: move StringUtils, AlternativeStringFilter and tests classes from commonbase to common. modify IdentitySet to be conform with Java 6

SVN: 37386

SVN: 37377

SSDM-4379: remove all classes from 'common' which also in 'commonbase'. Adapt build script in common. Make some changes needed in datamover and screening

SVN: 37369

SVN: 37359

SVN: 37343

SVN: 37342

SVN: 37340

SVN: 37175

SSDM-3895: Explicitely specify by a property whether proteomics/screening application contexts are needed.

SVN: 36912

SVN: 36904

SVN: 36841

SSDM-3745: Jython27: Execute everything with the right context class loader otherwise python xml module wouldn't work

SVN: 36769

SSDM-3745: JythonEvaluatorSpringComponent refactored. Subclass DataStoreServerJythonEvaluatorSpringComponent introduced which gets the Jython27EvaluatorFactory instance from Jython27FactoriesProvider by using Jython27ClassLoader for loading. Also in JythonTopLevelDataSetHandlerV2 Jython27InterpreterFactory is provided by Jython27FactoriesProvider. jython27 JAR not added to classpath in datastore_server.sh

SVN: 36768

SVN: 36762

SVN: 36761

SVN: 36758

SSDM-3745: introducing IJythonInterpreter.isNextCommand() in order to run master data registration for jython 2.5 or 2.7. Some JythonUtils method are inlined.

SVN: 36750

SSDM-3745: Disable not-used jython lib. MasterDataRegistrationScriptRunner uses configured jython version. IJythonInterpreter extended.

SVN: 36747

SVN: 36556

SVN: 36551

SVN: 36341

SVN: 36312

SVN: 36309

SVN: 36307

SDDM-3507: Setting idle timeout of HttpClient and request brake tests in projects gradle-datastore_server and gradle-openbis-oai-pmh. Thus, no idle timeout is set for HttpClient and instead of idle timeout the total time out is set for requests as it was before check-in r35963 for SSDM-3386.

SVN: 36304