Security and workflow fixes

ucam-department-of-psychiatry / crate

Create and use de-identified research databases. Preprocess, extract text, anonymise/de-identify, link, apply natural language processing, query for research, manage consent for contact.

GNU General Public License v3.0

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Security and workflow fixes #139

Closed martinburchell closed 10 months ago

martinburchell commented 10 months ago

Some security and workflow fixes cherry-picked from therec_version_numbers and systmone_c4c_lookup branches in case it's a while before those are merged.

RudolfCardinal commented 10 months ago

Looks good! Very small thing:

Worth amalgamating the two apt-get install -y --no-install-recommends commands in crate.Dockerfile? I think this might save one Docker layer.

RudolfCardinal commented 10 months ago

I'll implement that and the other merge (https://github.com/ucam-department-of-psychiatry/crate/pull/138#issuecomment-1820672931).

RudolfCardinal commented 10 months ago

Build failed; clearly you'd thought about this more thoroughly than me! Reverted on master.

martinburchell commented 10 months ago

@RudolfCardinal yes I spent some time trying to add an inline comment to explain the two-step approach and gave up in the end.