Fix specifing dbkeys with API uploads.

Essentially a redo of changeset 83103cff8757. In order to fix uploads when now history was specified, the only available dbkey allowed was '?'. As a result of that changeset, when uploading files via the API users could only specify '?'. Now the stock dbbuilds are also available - though builds in the history are still not aviailable (TODO) and user custom builds may not be available (TODO check this).
PEP-8 fixes for test/base/twilltestcase.py.

Still hundreds of lines to fix.
PEP-8 fixes related to tool test parsing.
Refactor shared code in functional_tests.py into a method.
Small simplification to test/functional/test_toolbox.py.
Refactor tool test parsing logic out of Tool and into ToolTestBuilder.
Make formerly public methods in ToolTestBuilder private now that it does its own construction.
Refactor test data input setup logic out of TestToolBox into ToolTestBuilder.

Simplifying test_toolbox.py will hopefully make it easier to provide an alternative API driven option.
Refactor data staging and tool running logic out of test/functional/test_toolbox.py.

In a new twill specific interactor class, idea here is to proceed by implementing a matching API interactor class.
Upload a tool test's inputs in parallel.

Probably small optimization in most cases since tests generally have few inputs.
Inject master API key into functional test Galaxy.

Override or set external key with GALAXY_TEST_MASTER_API_KEY.
Break up verify_dataset_correctness in twilltestcase.py

Will want to reuse the core verification of the displayed dataset in the API driven case and will not need or be able to use the extra cruft related to checking UI, job state, etc...
Outline new API based galaxy interactor for functional tests.
Twill-less tool tests initial implementation.

Implement GalaxyInteractorApi, is working for simple tests.

Lots left to do likely - conditionals, repeats, composite uploads, pages(?).

Introduces dependency on Python requests package (needed-ish for API uploads).
Move test_toolbox's expand_grouping out into tool/test.py.

Would be good to merge these two implementations there at very least easier to reuse/test in its new home.
Simplify logic in tool test expand_grouping.
Twill-less tool tests - handle repeats and conditionals.

Expand 'inputs' tree when building tool inputs for API functional tests.

Code is in there for both flat inputs (the way the UI would submit them), and a nested tree structure. The nested tree structure will not work with the Galaxy API currently - but it is the way the API should work :).
Twill-less tool tests fix for nested input filenames.
Twill-less tool tests fix for tests with html outputs.

For example gatk_analyze_covariates.
Twill-less tool tests fix for binary data in results.

Use requests' response.content instead of response.text for reading results.

Fixes the following error 'UnicodeEncodeError: 'ascii' codec can't encode characters in position 1-3: ordinal not in range(128)' when dealing with ASN.1 binary files.