Support bulk uploading of UKHSA surgical site infection codelists #2954
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rw251
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Is this something we will load/update in the future? If so we should probably add something to one of the docs explaining where the data came from and the exact command that we executed - especially as it's looking for multiple csvs instead of one.
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Looks good. Minor comment on docs.
Coding systems that extend the DummyCodingSystem class (OPCS4 & Readv2) don't have databases. The bulk upload script erroneously checked for presence of a database file for the requested coding system in all cases. This commit omits the check for coding systems without databases.
As part of the checking for existence of coding system database files, the bulk upload script made false assumptions regarding their path. There exists an env var - DATABASE_DIR - which controls the database file path which should be checked before assuming the default location. Ideally the coding system database paths would be pulled directly out of django.conf.settings, but this would require the full Django machinery to be instantiated for this script to run. This could be achieved by changing this ad-hoc script into a django script to be run via `runscript` but would require significant and unergonomic changes to how command-line arguments are handled.
CodelistVersions created from csv can contain additional columns beyond the default `code` and `description`. This commit supports loading of such additional columns via the bulk upload script.
Previous bulk-uploaded codelist files contained many codelists concatenated into a single file. This change allows for iteration over a set of files indicated by a glob pattern.
Fixes bug of assumed presence of optional "tag" config value.
replicate update behaviour of codelist description for methodology add tests for both
Configure column alias to allow UKHSA surgical site infection codelists to have codelist methodology set.
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For a request from @LFISHER7 routed to @opensafely-core/team-rsi
This request required some new features:
Includes a couple of drive-by bug fixes encountered in development of supporting features for this request.