PXD-452 ⁃ Invalid JSON causes transaction error

[allisonheath]

Found when accidentally put "primary_diagnosis": NaN in my JSON instead of null.

Log error:

  File "/gdcapi/src/sheepdog/sheepdog/transactions/upload/__init__.py", line 39, in single_transaction_worker
    transaction.parse_doc(*doc_args)
  File "/gdcapi/src/sheepdog/sheepdog/transactions/upload/transaction.py", line 81, in parse_doc
    self.parse_entities(data)
  File "/gdcapi/src/sheepdog/sheepdog/transactions/upload/transaction.py", line 110, in parse_entities
    flag_modified(tx_log, 'canonical_json')
  File "/usr/lib/python2.7/contextlib.py", line 24, in __exit__
    self.gen.next()
  File "/gdcapi/src/sheepdog/sheepdog/transactions/transaction_base.py", line 283, in fetch_transaction_log
    .get(self.transaction_id)
  File "/usr/lib/python2.7/contextlib.py", line 24, in __exit__
    self.gen.next()
  File "/gdcapi/src/sheepdog/sheepdog/transactions/transaction_base.py", line 300, in clean_session
    yield session
  File "/usr/lib/python2.7/contextlib.py", line 24, in __exit__
    self.gen.next()
  File "/gdcapi/src/psqlgraph/psqlgraph/psqlgraph.py", line 187, in session_scope
    local.commit()
  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/orm/session.py", line 788, in commit
    self.transaction.commit()
  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/orm/session.py", line 384, in commit
    self._prepare_impl()
  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/orm/session.py", line 364, in _prepare_impl
    self.session.flush()
  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/orm/session.py", line 1985, in flush
    self._flush(objects)
  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/orm/session.py", line 2103, in _flush
    transaction.rollback(_capture_exception=True)
  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/util/langhelpers.py", line 60, in __exit__
    compat.reraise(exc_type, exc_value, exc_tb)
  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/orm/session.py", line 2067, in _flush
    flush_context.execute()
  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/orm/unitofwork.py", line 372, in execute
    rec.execute(self)
  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/orm/unitofwork.py", line 526, in execute
    uow
  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/orm/persistence.py", line 60, in save_obj
    mapper, table, update)
  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/orm/persistence.py", line 518, in _emit_update_statements
    execute(statement, params)
  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/engine/base.py", line 841, in execute
    return meth(self, multiparams, params)
  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/sql/elements.py", line 322, in _execute_on_connection
    return connection._execute_clauseelement(self, multiparams, params)
  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/engine/base.py", line 938, in _execute_clauseelement
    compiled_sql, distilled_params
  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/engine/base.py", line 1070, in _execute_context
    context)
  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/engine/base.py", line 1271, in _handle_dbapi_exception
    exc_info
  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/util/compat.py", line 199, in raise_from_cause
    reraise(type(exception), exception, tb=exc_tb)
  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/engine/base.py", line 1063, in _execute_context
    context)
  File "/usr/local/lib/python2.7/dist-packages/sqlalchemy/engine/default.py", line 442, in do_execute
    cursor.execute(statement, parameters)
DataError: (DataError) invalid input syntax for type json
LINE 1: UPDATE transaction_logs SET canonical_json='[{"type": "case"...
                                                   ^
DETAIL:  Token "NaN" is invalid.
CONTEXT:  JSON data, line 1: ..."}, "type": "diagnosis", "primary_diagnosis": NaN...

Returned back to the user is just the error:

  "transactional_errors": [
    "Internal server error. Sorry, something unexpected went wrong!"
  ],```

Would be more helpful to catch the invalid JSON and return a clearer error message.