- Test for 'normalizeFile'.

SVN: 2554

- 'normalizeFile' moved from 'Parameters' to 'FileUtilities'.

SVN: 2548

Preparation phase:
1. MaterialDAO should be fetched from AbstractBusinessObject. Currently AbstractBusinessObject just calls IDAOFactory.getMaterialDAO, but in future it can decorate the DAO and fill material properties on the fly. This refactoring required moving some methods from Managers to Business Objects.
2. MaterialDAO should expose FROM and WHERE clauses of its selects - they will be used to fetch only required properties.

SVN: 2513

- improve javadoc.
- method/variable made final when possible.

SVN: 2479

- made some methods final and parameter renaming.

SVN: 2465

- build and environment info to the application log 'lims-log.txt'.

SVN: 2462

SVN: 2403

SVN: 2392

- generalize to Iterable

SVN: 2389

SVN: 2380

add:
- HCS image format to BDS library

SVN: 2377

SVN: 2374

SVN: 2363

SVN: 2360

- javadoc warnings

SVN: 2357

- improve error messages

SVN: 2356

- improve error messages

SVN: 2353

SVN: 2339

- test group 'broken'
change:
- some refactoring done in the TestNG configuration files

SVN: 2326

SVN: 2310

SVN: 2283

- 'FileComparator.BY_TYPE'
- 'CompositeComparator'

SVN: 2265

- 'FileUtilities.getRelativeFile' should work with file names (String objects) and not with File objects.

SVN: 2264

- improve unit tests

SVN: 2224

- remove class name before method call

SVN: 2222

- RenamingProcess moved to common/FileRenamingProcess
- datamover uses FileRenamingProcess

SVN: 2219

- listFiles moved from 'Utilities' to 'FileUtilities'

SVN: 2218

- IProcess, ProcessRunner and its unit test

SVN: 2186

add: a TriggeringEventEvaluator that allows to overwrite the SMTPAppender's default to only send out an email message on message of level ERROR and above
fix: ensure that NOTIFY messages of level INFO are actually sent out as an email

SVN: 2165

SVN: 2144

SVN: 2128

SVN: 2127

SVN: 2090

SVN: 2088

SVN: 2087

change: log failures in directory failures always, but start with LogCategory.OPERATION and use LogCategory.NOTIFY only when sufficiently many errors have occurred

SVN: 2080

- rename a method of TableMap

SVN: 2066

SVN: 2063

SVN: 2061

add: method ProcessResult.destroyProcess() in order to cope with an IOException under Linux when spawning processes with high frequency

SVN: 2026