| Age | Commit message (Expand) | Author |
|---|
| 2023-04-25 | auth: Roles: Check for editability...Some roles should not be user-editable, and as such, we need to check before
allowing any edits on such roles. This commit makes that possible.
| Frederick Muriuki Muriithi |
| 2023-04-24 | auth: Return the actual privileges for the user...Previously, the `oauth2/data/authorisation` endpoint was returning hard-coded
values for the privileges assigned to the user for each resource. In this
change, we rework to return the actual privileges for the user.
| Frederick Muriuki Muriithi |
| 2023-04-21 | auth: Attach linked data to specific resources. | Frederick Muriuki Muriithi |
| 2023-04-21 | auth: Fetch user group phenotypes not attached to a resource. | Frederick Muriuki Muriithi |
| 2023-04-19 | oauth2: Link the phenotype traits to user groups. | Frederick Muriuki Muriithi |
| 2023-04-19 | Fix minor linting and typing issues | Frederick Muriuki Muriithi |
| 2023-04-19 | auth: Setup selected traits correctly...Fix bugs with setting up of the selected traits for use while filtering the
search results.
| Frederick Muriuki Muriithi |
| 2023-04-19 | auth: phenotypes - provide default empty list for selected traits. | Frederick Muriuki Muriithi |
| 2023-04-18 | auth: Pass `--per-page` and `--selected` options. | Frederick Muriuki Muriithi |
| 2023-04-17 | Hook up code to use external search script for phenotypes | Frederick Muriuki Muriithi |
| 2023-04-17 | auth: Delete code that is no longer used | Frederick Muriuki Muriithi |
| 2023-04-15 | Decouple `gn3.db_utils` from `flask.current_app`....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.
| Frederick Muriuki Muriithi |
| 2023-04-14 | auth: Add external script to search for phenotypes...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.
| Frederick Muriuki Muriithi |
| 2023-04-14 | auth: Disconnect module from flask application...To avoid application context errors in external scripts, disconnect the
`gn3.auth.db` module from the `flask.current_app` dependency.
| Frederick Muriuki Muriithi |
| 2023-04-12 | auth: Enable listing of unlinked genotype/mRNA group data. | Frederick Muriuki Muriithi |
| 2023-04-10 | Add search and link for mRNA Assay datasets. | Frederick Muriuki Muriithi |
| 2023-04-10 | Update expected request key. | Frederick Muriuki Muriithi |
| 2023-04-10 | Enable search, filtering out selected, but not linked data...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.
| Frederick Muriuki Muriithi |
| 2023-04-08 | auth: Link genotype datasets to groups. | Frederick Muriuki Muriithi |
| 2023-04-04 | auth: Search for linking genotype datasets. | Frederick Muriuki Muriithi |
| 2023-03-23 | auth: list the species in the database. | Frederick Muriuki Muriithi |
| 2023-03-23 | auth: Don't try loading the user if no client is found...Fix the bug where the system was trying to load a user from a non-existing
OAuth2 client, leading to an exception.
| Frederick Muriuki Muriithi |
| 2023-03-22 | auth: data linking: build functions to fetch unlinked phenotypes...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.
| Frederick Muriuki Muriithi |
| 2023-03-22 | auth: Enable linking multiple datasets to the group at once. | Frederick Muriuki Muriithi |
| 2023-03-20 | auth: data: Enable offset in queries...Enable the 'OFFSET' clause in the queries to allow for progressive fetching of
data from the database using the 'Previous' and 'Next' buttons.
| Frederick Muriuki Muriithi |
| 2023-03-20 | auth: data: List Phenotypes at the trait level...For Phenotypes, list the Phenotype traits rather than the dataset(s).
| Frederick Muriuki Muriithi |
| 2023-03-18 | oauth2: resources: toggle whether a resource is public or not | Frederick Muriuki Muriithi |
| 2023-03-18 | auth: resources: Disallow duplicate resource names. | Frederick Muriuki Muriithi |
| 2023-03-15 | auth: Data Migrations: Rework migration trigger...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.
| Frederick Muriuki Muriithi |
| 2023-03-14 | auth: Fix some linting and typing issues. | Frederick Muriuki Muriithi |
| 2023-03-13 | oauth2: data: Temporarily escalate privileges to enable migration...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.
| Frederick Muriuki Muriithi |
| 2023-03-13 | auth: separate user detail migration from data migration...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.
| Frederick Muriuki Muriithi |
| 2023-03-10 | auth: data-migration: Fix minor bugs | Frederick Muriuki Muriithi |
| 2023-03-09 | auth: redis data: migrate data in redis...Implement the code to migrate the data from redis to SQLite.
| Frederick Muriuki Muriithi |
| 2023-03-09 | auth: data migration: Data migration outline...Provide an outline of the data migration steps to be taken from some results
of the experiments with the data in redis.
| Frederick Muriuki Muriithi |
| 2023-03-09 | auth: introspection: Protect introspection endpoint...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.
| Frederick Muriuki Muriithi |
| 2023-03-08 | auth: users: Use the same basic functions for password hashing...To avoid repeating the same thing in multiple places, leading to errors and
breakages, reuse the same basic functions for password hashing.
| Frederick Muriuki Muriithi |
| 2023-03-08 | Replace Bcrypt with Argon2 for better security....Bcrypt is now somewhat vulnerable to offline cracking, so we move our password
hashing over to Argon2.
| Frederick Muriuki Muriithi |
| 2023-03-07 | auth: group_roles: Enable addition/deletion of privileges | Frederick Muriuki Muriithi |
| 2023-03-07 | auth: resources: unassign roles on resource from a user. | Frederick Muriuki Muriithi |
| 2023-03-07 | auth: user_by_id: Return a user or raise an exception...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.
| Frederick Muriuki Muriithi |
| 2023-03-06 | auth: resources: Enable assigning a user roles on resources | Frederick Muriuki Muriithi |
| 2023-03-06 | auth: resources: Link role's group to the resource's group | Frederick Muriuki Muriithi |
| 2023-03-06 | auth: resources: Get all users with access to a particular resource. | Frederick Muriuki Muriithi |
| 2023-03-03 | auth: Enable viewing group role details. | Frederick Muriuki Muriithi |
| 2023-03-03 | auth: group roles: enable creation and listing of group roles. | Frederick Muriuki Muriithi |
| 2023-03-02 | auth: user registration: Rework error checking. Add email validation | Frederick Muriuki Muriithi |
| 2023-02-28 | auth: Unlink data from resources...Enable the data editor to unlink data from a particular resource.
data-access-levels-endpoint | Frederick Muriuki Muriithi |
| 2023-02-28 | auth: Unlink data from resources...Enable the data editor to unlink data from a particular resource.
| Frederick Muriuki Muriithi |
| 2023-02-27 | auth: Endpoint to get access levels for data...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.
| Frederick Muriuki Muriithi |
