SVN: 18677

SE-312 introducing processDataSets in Proteomics Data API. Changes in MsInjectionCopier: target file name is just data set code

SVN: 18676

SVN: 18675

change: use the more efficient way of getting the output on Unix platforms and keep the more expensive one to make it work on Windows

SVN: 18674

SVN: 18673

SVN: 18672

change: simplify reading of process output in ProcessExecutionHelper

SVN: 18671

SVN: 18670

SVN: 18669

SVN: 18668

SVN: 18667

SVN: 18666

under Unix, build the classpath on the fly to have all transformations available

SVN: 18665

SVN: 18664

fix: moving from incoming to ready-to-move when file / directory is not writable, permissions cannot be changed and incoming is remote

SVN: 18663

SVN: 18662

SVN: 18661

SVN: 18660

fix: moving from incoming to ready-to-move when file / directory is not writable and incoming is not remote

SVN: 18659

SVN: 18658

fix: ensure we correctly delete directories that are not writable but that we can set to be writable

SVN: 18657

SVN: 18656

SVN: 18655

SVN: 18654

SVN: 18653

[DMV-41] Property 'transfer-finished-executable' should not run the executable if the transfer failed

SVN: 18652

[LMS-1720] extended showing datasets indirectly connected with a sample to go through both sample and data set relationships

SVN: 18651

SVN: 18650

SVN: 18649

SVN: 18648

SVN: 18647

SVN: 18646

SVN: 18645

SVN: 18644

SVN: 18643

[LMS-1772] use cache of samples (reduces time spend on loading parents for 1000 samples with the same parent from 12s to <100ms)

SVN: 18642

SVN: 18641

SVN: 18640

SVN: 18639

SVN: 18638