Merge branch 'master' of ssh://git@github.com/ModelSEED/Model-SEED-core.git

* 'master' of ssh://git@github.com/ModelSEED/Model-SEED-core.git:
  fixing bug where non-filename passed back in arguments for parsesbml
  Reaction, Compound, Media tests now passing
  Fix bug in FIGMODELTable
  Fixes for Import
  Renamed Reactionset.pm and Compoundset.pm to ReactionSet.pm and CompoundSet.pm.
Created ModelDriverV2.pl, which is now fully functional and includes three commands: bclist, bcprint, and bcload.
bclist is fully tested and working. Still trying to fix bcprint and bcload.
Completed implementation and testing of bcprint and bcload. The biochemistry->save() step of bc load still isn't working.
Work to get biochemistry->save() running

- Still really slow.

Conflicts:

	lib/ModelSEED/MS/Media.pm
Fixed return string bug in mdl-changedrains, works fine
Implementing model objects in new system, and enabling printing of models.
Merge branch 'master' of ssh://git@github.com/ModelSEED/Model-SEED-core.git

* 'master' of ssh://git@github.com/ModelSEED/Model-SEED-core.git:
  Work to get biochemistry->save() running
Adding biomass to getModel function. Fixed some bugs in coreAPI. Fixed bugs in model printing.
Untracked changes
Merge branch 'master' of github.com:ModelSEED/Model-SEED-core into api-work
Reverted 'bug fixes' in CoreApi from previous commit (see _processJoinedRows subroutine for documentation and an example of how to use).

Standardized joining tables to always display same columns. For example:

Reactions->{relationships}->{reactionsets}
    has both 'reaction_uuid', and 'reactionset_uuid'.

ReactionSets->{relationships}->{reactions}
    also has both 'reaction_uuid', and 'reactionset_uuid'.

While this may waste a little space, it provides consistency by keeping the structure the same as in the database.
Completing the mapping object, and enabling printing of the mapping object. Note, this code is untested.
Merge branch 'master' of ssh://git@github.com/ModelSEED/Model-SEED-core.git

* 'master' of ssh://git@github.com/ModelSEED/Model-SEED-core.git:
  Reverted 'bug fixes' in CoreApi from previous commit (see _processJoinedRows subroutine for documentation and an example of how to use).
  Untracked changes
Fixing bugs in mapping object and ModelDriver
Fixing two bugs, somehow searchnames were not being updated and the stoichiometry of balanced reactants was incorrect
Removing user as required argument to getModel
Initial revision of generatePriceData

- This package should be used to generate
  XML documents that are fed into the network
  consistency gapfilling algorithm defined
  by Nathan Price, et. al.

- Initial draft outlines the structure of the
  modulino.

- The input.xml file should now be working properly.
Removing transactions from Import
Updating Import to be able to use MySQL

- Import can now write to MySQL database.
- Changes to ModelDB to get it working with
  MySQL ( move linker-table beneath one of it's
  linked tables ).

Conflicts:

	lib/ModelSEED/Import.pm
Changes to CoreApi

- CoreApi now supports a "dsn" initialization option.
  Pass in a standard DBI configuration dsn like:
  "dbi:SQLite:path/to/filename.db" and it will connect.

- Removed the requirement that getBiochemistry, getModel
  have user passed as a parameter.