Setup script changes and misc bug fixes

[jeremyestein]

Setup script changes for validation (including fixing #25 )

Design doc update.

Miscellaneous fixes that were needed to process the HL7 dump file during validation. Mostly parsing error handling.

[github-actions]

PR checklist

Default guide for a PR (if multiple PRs for the work, only keep one version of it and link to it on the other PRs)

• From the UCLH data science desktop, a validation run has been set off
• load times
  in UCL teams has been populated with the run information
• During the run, glowroot has been checked for any queries which are taking a substantial proportion of the
  total processing time. This can be useful to identify indexes that are required.
• After the run, look for any unexpected errors in the etl_per_message_logging table, the error_search.sql file
  on the shared drive can be used for this \\sharefs6\UCLH6\EMAP\Shared\EmapSqlScripts\devops\error_search.sql.
  Create an issue if you find an unexpected exception and is not related to the changes you've made, otherwise
  fix them!
• After the run, populate the end time in
  load times
• Let Aasiyah know about the completed validation and give her information on the changes and where to start
  with the validation
• Check validation report and give any feedback to Aasiyah if there are any changes needed on her side,
  iterate on getting the validation to match at least 99% (validation and emap code).

[t-young31]

not looked at the Java but the Python changes LGTM 🚀

[t-young31]

perhaps this should be

if self.args.use_hoover and "hoover" not in self.global_config["repositories"]:
    raise ValueError("hoover missing from repositories in global config")

[jeremyestein]

Ah yes, that avoids failing silently if the user asked for hoover

[t-young31]

🙃

Probably best to change the type of start_time to datetime.datetime then

Suggested change

	"""Time elapsed since the runner started"""
	return timedelta(seconds=time() - self.start_time)
	"""Time elapsed since the runner started"""
	assert self.start_time is not None
	return datetime.now() - self.start_time

?

[jeremyestein]

Since start_time isn't needed outside that method I've turned it into a local. And it should be a monotonic clock to ignore system time jumps.