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During development, we need logging sometimes to help with troubleshooting
problems. This commit provides a module to help set up the logging in a
separate module from the app module.
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Fix bugs with setting up of the selected traits for use while filtering the
search results.
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Consistently encode all values for the top-level keys stored in redis to avoid
issues with json encode/decode
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/api/metadata.py: Import Template, sparql_query and RDF_PREFIXES.
(get_genewiki_entries): New endpoint.
* gn3/db/rdf.py: Add new constant for storing rdf prefixes.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Decouple the `gn3.db_utils` module from the global `flask.current_app` object,
ensuring that the database uri value is passed in as a required argument to
the `gn3.db_utils.database_connection` function.
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We need a search through the available phenotype traits in the database when
linking the traits to user groups. Unfortunately, the Xapian Search indexes do
not (and should not) include the internal identifiers we use to disambiguate
the traits.
On the other hand, we do not want to present the user with traits that have
already been linked to any user group within the search results.
The script in this commit, together with the modified queries for fetching the
phenotype data form a "hack" of sorts to wrap around the way the search works
while ensuring we do not present the user with "non-actionable" (linked)
traits in the search results.
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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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When a user selects some datasets and does a new search, we filter out the
selected datasets too, even though they are yet to be linked.
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Remove the deprecated function and fix a myriad of bugs that arise from
removing the function.
Issue: https://issues.genenetwork.org/issues/bugfix_coupling_current_app_and_db_utils
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There is need to run external scripts using the same configurations as the
application but without the need to couple the script to the application.
In this case, we provide the needed configuration directly in the CLI, and
modify the existing `gn3.db_utils.database_connection` function to allow it to
work coupled to the app or otherwise.
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Fix the bug where the system was trying to load a user from a non-existing
OAuth2 client, leading to an exception.
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The configuration in gn3.settings can (and does) get overwritten by values in
the environment variable `GN3_CONF` and any configurations passed in the call
to the `gn3.app.create_app` function; as such, this commit changes the
configuration used in the code to user the final configuration values that are
in the running application's `flask.current_app.config` object.
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This is an initial attempt: it does not allow a search to be carried out
across the data available in the database.
I will need to rework this, probably start from the UI and work backward.
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* gn3/db/sample_data.py: Remove 're' import.
(get_trait_csv_sample_data): Remove fetching sample data.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Enable the 'OFFSET' clause in the queries to allow for progressive fetching of
data from the database using the 'Previous' and 'Next' buttons.
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For Phenotypes, list the Phenotype traits rather than the dataset(s).
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Rework the migration trigger endpoint such that it does a bulk import of all
the resources in the redis store.
It also expects that the user that triggers the migration have the appropriate
privileges.
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The functions that fetch the unlinked data have checks to ensure they are
called by users with the appropriate privileges. This commit enables a
temporary escalation of privileges to enable fetching the data, so as to allow
successful data migration.
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Due to the fact that the data migration requires higher privileges than the
user details, separate the user details migration endpoint from the data
migrations endpoint.
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Implement the code to migrate the data from redis to SQLite.
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Provide an outline of the data migration steps to be taken from some results
of the experiments with the data in redis.
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The introspection endpoint could contain privileged information, thus requires
that the endpoint be protected. This commit ensures that a user has
authenticated to the system and that the client they are using be one of the
allowed clients.
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To avoid repeating the same thing in multiple places, leading to errors and
breakages, reuse the same basic functions for password hashing.
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Bcrypt is now somewhat vulnerable to offline cracking, so we move our password
hashing over to Argon2.
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Fetching the user by id should return the user, or raise an exception. We get
rid of the Maybe monad here since it is leading to some weird code flows -
probably the wrong monad to use here.
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