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2023-04-25auth: bug: Provide missing `user_editable` argument.Frederick Muriuki Muriithi
2023-04-25auth: provide `user_editable` flag in dictified outputFrederick Muriuki Muriithi
2023-04-25auth: Roles: Check for editabilityFrederick Muriuki Muriithi
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.
2023-04-24auth: Return the actual privileges for the userFrederick Muriuki Muriithi
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.
2023-04-21auth: Attach linked data to specific resources.Frederick Muriuki Muriithi
2023-04-21auth: Fetch user group phenotypes not attached to a resource.Frederick Muriuki Muriithi
2023-04-19oauth2: Link the phenotype traits to user groups.Frederick Muriuki Muriithi
2023-04-19Fix minor linting and typing issuesFrederick Muriuki Muriithi
2023-04-19auth: Setup selected traits correctlyFrederick Muriuki Muriithi
Fix bugs with setting up of the selected traits for use while filtering the search results.
2023-04-19auth: phenotypes - provide default empty list for selected traits.Frederick Muriuki Muriithi
2023-04-18auth: Pass `--per-page` and `--selected` options.Frederick Muriuki Muriithi
2023-04-17Hook up code to use external search script for phenotypesFrederick Muriuki Muriithi
2023-04-17auth: Delete code that is no longer usedFrederick Muriuki Muriithi
2023-04-15Decouple `gn3.db_utils` from `flask.current_app`.Frederick Muriuki Muriithi
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.
2023-04-14auth: Add external script to search for phenotypesFrederick Muriuki Muriithi
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.
2023-04-14auth: Disconnect module from flask applicationFrederick Muriuki Muriithi
To avoid application context errors in external scripts, disconnect the `gn3.auth.db` module from the `flask.current_app` dependency.
2023-04-12auth: Enable listing of unlinked genotype/mRNA group data.Frederick Muriuki Muriithi
2023-04-10Add search and link for mRNA Assay datasets.Frederick Muriuki Muriithi
2023-04-10Update expected request key.Frederick Muriuki Muriithi
2023-04-10Enable search, filtering out selected, but not linked dataFrederick Muriuki Muriithi
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.
2023-04-08auth: Link genotype datasets to groups.Frederick Muriuki Muriithi
2023-04-04auth: Search for linking genotype datasets.Frederick Muriuki Muriithi
2023-03-23auth: list the species in the database.Frederick Muriuki Muriithi
2023-03-23auth: Don't try loading the user if no client is foundFrederick Muriuki Muriithi
Fix the bug where the system was trying to load a user from a non-existing OAuth2 client, leading to an exception.
2023-03-22auth: data linking: build functions to fetch unlinked phenotypesFrederick Muriuki Muriithi
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.
2023-03-22auth: Enable linking multiple datasets to the group at once.Frederick Muriuki Muriithi
2023-03-20auth: data: Enable offset in queriesFrederick Muriuki Muriithi
Enable the 'OFFSET' clause in the queries to allow for progressive fetching of data from the database using the 'Previous' and 'Next' buttons.
2023-03-20auth: data: List Phenotypes at the trait levelFrederick Muriuki Muriithi
For Phenotypes, list the Phenotype traits rather than the dataset(s).
2023-03-18oauth2: resources: toggle whether a resource is public or notFrederick Muriuki Muriithi
2023-03-18auth: resources: Disallow duplicate resource names.Frederick Muriuki Muriithi
2023-03-15auth: Data Migrations: Rework migration triggerFrederick Muriuki Muriithi
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.
2023-03-14auth: Fix some linting and typing issues.Frederick Muriuki Muriithi
2023-03-13oauth2: data: Temporarily escalate privileges to enable migrationFrederick Muriuki Muriithi
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.
2023-03-13auth: separate user detail migration from data migrationFrederick Muriuki Muriithi
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.
2023-03-10auth: data-migration: Fix minor bugsFrederick Muriuki Muriithi
2023-03-09auth: redis data: migrate data in redisFrederick Muriuki Muriithi
Implement the code to migrate the data from redis to SQLite.
2023-03-09auth: data migration: Data migration outlineFrederick Muriuki Muriithi
Provide an outline of the data migration steps to be taken from some results of the experiments with the data in redis.
2023-03-09auth: introspection: Protect introspection endpointFrederick Muriuki Muriithi
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.
2023-03-08auth: users: Use the same basic functions for password hashingFrederick Muriuki Muriithi
To avoid repeating the same thing in multiple places, leading to errors and breakages, reuse the same basic functions for password hashing.
2023-03-08Replace Bcrypt with Argon2 for better security.Frederick Muriuki Muriithi
Bcrypt is now somewhat vulnerable to offline cracking, so we move our password hashing over to Argon2.
2023-03-07auth: group_roles: Enable addition/deletion of privilegesFrederick Muriuki Muriithi
2023-03-07auth: resources: unassign roles on resource from a user.Frederick Muriuki Muriithi
2023-03-07auth: user_by_id: Return a user or raise an exceptionFrederick Muriuki Muriithi
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.
2023-03-06auth: resources: Enable assigning a user roles on resourcesFrederick Muriuki Muriithi
2023-03-06auth: resources: Link role's group to the resource's groupFrederick Muriuki Muriithi
2023-03-06auth: resources: Get all users with access to a particular resource.Frederick Muriuki Muriithi
2023-03-03auth: Enable viewing group role details.Frederick Muriuki Muriithi
2023-03-03auth: group roles: enable creation and listing of group roles.Frederick Muriuki Muriithi
2023-03-02auth: user registration: Rework error checking. Add email validationFrederick Muriuki Muriithi
2023-02-28auth: Unlink data from resourcesdata-access-levels-endpointFrederick Muriuki Muriithi
Enable the data editor to unlink data from a particular resource.
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