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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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* gn3/api/sampledata.py (get_sampledata): New end-point.
* gn3/app.py: Register above end-point.
* gn3/settings.py: Add new conf variable for LMDB.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/db/matrix.py (get_total_versions, get_nth_matrix,
get_current_matrix): Open lmdb in readonly mode.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/api/metadata.py (dataset_metadata): New function and endpoint.
(jsonify_dataset_metadata): Rename to dataset_metadata.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/db/rdf.py (get_dataset_metadata): New function.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Enable the data editor to unlink data from a particular resource.
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Enable the data editor to unlink data from a particular resource.
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When the endpoint is accessed with a list of traits, it should/will respond
with the access privileges for each of the traits attached for the active
user.
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In order for the group leaders (and other resource creators) to be able to
link data to the resources, the data needs to be first linked to the relevant
group.
This commit enables the system admin to link the data in MySQL to the groups.
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Load the data that is attached to a particular resource together with the
resource.
List any unlinked data: useful when linking data to resources.
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When user has no roles assigned, return an empty tuple rather than
pymonad.maybe.Nothing to ease maintenance.
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