SVN: 34127

SVN: 34031

SSDM-1930: Introducing MonitoredIOStreamCopier with unit tests and use it in multi data set archiving.

SVN: 34030

SSDM-1794: Refactoring package structure of jython and jython27 in common. Removing some duplicated classes.

SVN: 33994

SSDM-1768: monitoring based on rsync progress output if --progress option added to property extra-rsync-params

SVN: 33966

SSDM-1768 ProcessExecutor, IPathCopier and RsyncCopier extended to allow to monitor stdout and stderr during processing.

SVN: 33962

SVN: 33835

SVN: 33824

SVN: 33353

SVN: 33190

SVN: 33107

SVN: 33074

SVN: 33072

SVN: 33068

SVN: 33065

SSDM-1290 - CKAN - publication webapp bugfixing - added caching of mesh terms in an http session - fix tests

SVN: 32987

SVN: 32600

SSDM-946: - Introducing IntensityRescaling.IImageToPixelsConverter in order to handle BioFormat Index16ColorModel in ImageUtil.rescale() if highQuality8Bit is set. This improves conversion of 12/16-bit images to 8-bit images for Nikon ND2 files considerable. It is also used when thumbnails are created.
- ImageChannelUtils: User defined image re-scaling is always done on 8-bit images.
- ImageChannelUtils: Many refactorings to make code better readable.
- System tests adapted and modified.

SVN: 32547

SSDM-773: Handle 12-bit microscopy images correctly in order to allow useful user defined transformation.

SVN: 32471

SSDM-864: Further refactoring of IntensityRescaling and included classes. MixColors.mixImages: White point calculation removed because IntensityRescaling.computeLevels() will be used in ImageChannelsUtils.mergeChannels(). ImageChannelsUtils refactored and improved (bugs fixed). New system tests: Simple16BitImageDropboxTest and PlatonicPlateImageDropboxTest.

SVN: 32447

SSDM-864: MixColors: Log time needed for mixing. IntensityRescaling refactored in order to remove code duplications. New tests added to IntensityRecsalingTest.

SVN: 32443

Fixed a failing uniprot test (data returned by http://www.uniprot.org/uniprot/?query=accession:p12345&format=tab&columns=id,entry%20name,existence,genes,last-modified,length,sequence,reviewed,version has changed on 03.09.2014)

SVN: 32420

SVN: 32394

SVN: 32393

SVN: 32391

SSDM-802: Extending AbstractScreeningSystemTestCase with helper classes for checking reference images with images loaded from image download servlet.

SVN: 32390

SSDM-85: FastaUtilities with a method to determine whether a string is a sequence of nucleic acid codes or amino acid codes.

SVN: 31436

SVN: 29963

SVN: 29893

SVN: 29791

SVN: 29790

SVN: 29788

SVN: 29787

SP-864 / BIS-531 : Novartis, BSSE#1029353 - Too many open files error - fix dependencies + initial unit tests of releasing resources in python scripts

SVN: 29775

SVN: 29772

SVN: 29730

SVN: 29729

SVN: 29712

SVN: 29685

SVN: 29683