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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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In certain scenarios (probably due to host contamination) the effective UID of
the running application is not the expected "genenetwork" user, rather, it is
a user on the host system, which leads to the error:
KeyError: 'getpwuid(): uid not found: 1000'
This commit prevents the application from failing in such a case, but still
logs out such weirdness.
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To avoid application context errors in external scripts, disconnect the
`gn3.auth.db` module from the `flask.current_app` dependency.
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Enable the FOREIGN KEY constraints for the connections to the database to help
with queries that would otherwise lead to data corruption.
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* gn3/auth/db.py: For easier setting up of objects after querying, set the
default row_factory object that allows indexing by database field name.
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* gn3/auth/authorisation/privileges.py: Set id to UUID type
* gn3/auth/authorisation/roles.py: fix parameters to types that sqlite3
supports
* gn3/auth/db.py: add logging for errors and re-raise the exception
* tests/unit/auth/test_roles.py: fix test
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