Working on new table view
Merge branch 'develop' of github.com:SeqWare/seqware into feature/COURTAGEN-109_more_tables_in_portal
working on context.xml, for some reason tomcat7 thinks it's invalid
This now renders a simple study table and shows rows with samples that have workflow runs. However the code is horribly slow. I will need to either implement paging in the hibernate layer or drop the display of workflow_runs (and just provide a link).
I left off with StudyTableControllerDetails.java where I need to properly implement query based filtering/sorting.  Then I can work on paging.
I added a cancel and retry feature to the workflow run table.
Adding methods to BatchMetadataInjection... this commit probably won't be functional
Won't compile. Added samples and iuses to BatchMetadataInjection. Committing so that I can merge from develop.
Merge branch 'develop' into feature/BatchInjectTakeTwo
Corrected a missing field parameter in Metadata for IUSes (it wasn't checking for barcodes). Added functionality for adding annotations in the BatchMetadataInjection class
Modified MetadataWS so that the new methods don't err out when an object is not found. Also when annotating samples and lanes, retrieve the attributes when adding them
Added a printout statement to Metadata plugin to debug
Added annotations to Lane and Sample and added checks for nulls. Still not fully debugged
Merge branch 'develop' into feature/BatchInjectTakeTwo
Fixed a bug with adding samples wihtout interactive feedback; formatted the interactive mode so that things are easier to read; removed extraneous print statements
Lots of changes, and hopefully it works now! Added features to facilitate adding similar samples; removed extraneous println statements; created a feature to print out the dot diagram to the command line
Correct null pointer exception when no sequencer runs exist
Fixed problem with newlines in digraph
Added promptString, promptInteger, and promptBoolean to ConsoleAdapter
Not tested yet, but made the parsing code for BatchMetadataInjection BEAUTIFUL. Now it fully parses the file and prompts for values before they are created in the DB. Separated out the *Info classes from BMI to make it easier to read. BMI is now totally generic and new parsers can be added. Created a factory-like structure in BatchMetadataParser that new parsers can be built from that enforces the standard naming conventions. Can now annotate every table. Changed the calls to promptString, promptInteger, promptBoolean to use the ConsoleAdapter class. Still need to write tests