Fix for Github issue 98

[ehenneken]

This PR provides a fix for #98 . Since the exception also occurs on the /parse endpoint, this PR also provides a solution for this case. In the case of the /parse endpoint, the output has been augmented to include a rejected entry in the JSON that will list all reference strings that could not be processed (because of an exception). The crf.py module has been updated to throw an exception with a specific error text to indicate that it was the collection of tagged token that threw the exception.

Unittests have been added to cover the changes.

[Thomas-S-Allen]

Line 463 in referencesrv/views.py could append an empty list to the response. Could replace with:

response = {'parsed': results}
if rejected:
    response['rejected'] = rejected

Note that this would require line 819 in referencesrv/tests/unittests/test_referencesrv_parser.py to revert back to its previous state.

Line 833 in referencesrv/tests/unittests/test_referencesrv_parser.py: replace with with mock.patch.object(self.current_app.client, 'get') as get_mock: because it is mocking the SOLR call - solrquery.py line 55 uses response = client().get(...)

Line 315 in referencesrv/parser/crf.py: can make the exception causality chain more explicit by changing raise Exception('Failed to generate tagged tokens: {0}'.format(err)) to raise Exception('Failed to generate tagged tokens: {0}'.format(err)) from err

Also, for .gitignore should .DS_Store be kept for Mac users?

For the unit tests, can further ensure a graceful response by adding self.assertEqual(r.status_code, 200) before line 827 and 842

There are a couple of pre-existing items, the first is a bug:

Line 229 in referencesrv/views.py - raise "Not Resolved" should raise an exception object not a string: raise ValueError("Not Resolved")

Lines 201-216 have duplicate exception blocks, the first excepts specific errors, the second is generic

[Thomas-S-Allen]

Looks good to merge.