Working implementation of settable experiment_spot_design and experiment_library_design.

Supporting work includes web resources for experiment_library_design, experiment_spot_design_read_spec, and experiment_spot_design (for error checking). This includes tests for those web resources and tests for modifications to the MetadataPlugin in order to access the two new fields. Modifications to Jaxb (lists of convertable classes), context, and existing experiment web resources were also made.


Former-commit-id: c99632bd82114b8dae19ee490752396907d2bb6b
SEQWARE 1579, 1724 Support creation of root samples while adding a constraint to avoid duplicate sample_hierarchy entries

Users will need to run the update script while the existing MetadataPlugin should now function correctly.


Former-commit-id: 5657e65dedcf59f979b6275370ea3bb7efc41d15
Added more explanation and a demonstrating test


Former-commit-id: 1e98d317085c135795e8f1b8adc818af55a2bb08
Make test even more explicit


Former-commit-id: d3c5e84d552f06bd2499fda8bd7e106476bb3329
SEQWARE-1682 - Test retrieval of annotations from the new study report


Former-commit-id: faf4c23cfc90a89c613c977c57537392c94548bd
Ensure that we close the Hibernate session properly


Former-commit-id: dff7ff7b2d12974aca0b5ea0ce97cb73188b15c3
Hook seqware into Maven build process and demonstrate a simple test using Maven properties to locate built script


Former-commit-id: bb8ac66df1eab00eac12c70643c755eedf4b0771
Update ubuntu_12.04_gridengine_script.sh

I think edit commands are needed since many of these are already setup by the apt-get install.  Testing now.

Former-commit-id: 2549b92a634613b4072a6186119cfd4b54785cb5
Refactoring strings into enums.

Former-commit-id: 2c5ccbcfe0ed3df0423cda64e3c91ade325bc4d1
SEQWARE-1710 - Hook the extended integration tests into the new CLI


Former-commit-id: cffd8adfb5f978f321bd731dab02335cb863912a
Appease JAXB by changing Foo.Status to FooStatus.

Former-commit-id: 59a4357873024e57c64259cf0f65b33b57ae66d3
Move SequencerRun.Status to SequencerRunStatus

Former-commit-id: 956a57a1bf1baf1340407bf599770728c5f651a0
Ensure script permissions and fix up inherited test


Former-commit-id: 42cfaccc42708e56fce13027e931cdbd48f9c6ba
I think I fixed the problem with skip-it not working, added skip-launch so you can debug configs, and modified the SGE setup process.  Need to test the latter.


Former-commit-id: a959282fb38860d34c4edda96692eae1c2198392
Tell hibernate to convert enums to strings.

Former-commit-id: 17cba9e930f6b17e469894d3a7a8a27b4f2f2f51
Fix a couple of laggard refactorings


Former-commit-id: f50850947d44171a52a3765d6afb2ba49290ac2a
Account for default behaviour of new command line

Need to direct output to files and relax the output checks


Former-commit-id: 84784832b2239f3fcdb92eca96eb069160d6a348
Move hibernate enum annotations from field to getter.

Former-commit-id: 0f0633ae32865fd1049b83abe6fb16901b28f540
Fix up format of new CLI output to match old filters


Former-commit-id: 16f66aab884f0adef0581b62db29284b2ab023f4
Use hbm mapping instead of annotations for enums.

Former-commit-id: 1448767110820838024efaae63380ff23c811752