| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2023-05-16 | auth: View a collection by its ID. | Frederick Muriuki Muriithi | |
| 2023-05-15 | collections: Move code to new package. Create new collections. | Frederick Muriuki Muriithi | |
| Move the code to a new package. Enable the creation of new collection by both authenticated and anonymous users. | |||
| 2023-05-12 | auth: Provide separate endpoint for anonymous collections. | Frederick Muriuki Muriithi | |
| 2023-05-11 | auth: Fix bug with migration of user collections | Frederick Muriuki Muriithi | |
| The code, as written previously had a subtle bug - if the user created a new collection before they had tried accessing their list of collections, the older code would not have migrated the older collections. This commit fixes that by enabling the migration of older collections, whether or not the user has created a collection with their new accounts. | |||
| 2023-05-10 | auth: Add the /oauth2/user/collections/list endpoint | Frederick Muriuki Muriithi | |
| Add an endpoint to list a user's collections. This only works for logged in users. | |||
| 2023-04-27 | auth: Retrieve `system:*` privileges from resource roles | Frederick Muriuki Muriithi | |
| With the assignment of `system:*` privileges to roles, we need to check for their existence when doing authorisation. This commit provides a hack for that, seeing as user groups (and the system itself) are not treated as resources, and therefore the way to fetch the privileges is not entirely consistent. | |||
| 2023-04-27 | auth: List also the non-resource privileges the user has | Frederick Muriuki Muriithi | |
| While creating new group roles, enable the listing of non-resource privileges, e.g. `system:group:*` and `system:user:*` that the user has to allow for them to be used in role creation. | |||
| 2023-04-27 | auth: Add authorisation checks for role editting. | Frederick Muriuki Muriithi | |
| 2023-04-27 | oauth2: Provide missing `user_editable` argument. | Frederick Muriuki Muriithi | |
| 2023-04-25 | auth: bug: Provide missing `user_editable` argument. | Frederick Muriuki Muriithi | |
| 2023-04-25 | auth: provide `user_editable` flag in dictified output | Frederick Muriuki Muriithi | |
| 2023-04-25 | auth: Roles: Check for editability | Frederick 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. | |||
| 2023-04-24 | auth: Return the actual privileges for the user | Frederick 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. | |||
| 2023-04-21 | 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 | Frederick Muriuki Muriithi | |
| Fix bugs with setting up of the selected traits for use while filtering the search results. | |||
| 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`. | 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. | |||
| 2023-04-14 | auth: Add external script to search for phenotypes | Frederick 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. | |||
| 2023-04-12 | 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 | Frederick 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. | |||
| 2023-04-08 | 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 | |
| 2023-03-22 | auth: data linking: build functions to fetch unlinked phenotypes | Frederick 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. | |||
| 2023-03-22 | auth: Enable linking multiple datasets to the group at once. | Frederick Muriuki Muriithi | |
| 2023-03-20 | auth: data: Enable offset in queries | Frederick 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. | |||
| 2023-03-20 | auth: data: List Phenotypes at the trait level | Frederick Muriuki Muriithi | |
| For Phenotypes, list the Phenotype traits rather than the dataset(s). | |||
| 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 | Frederick 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. | |||
| 2023-03-14 | auth: Fix some linting and typing issues. | Frederick Muriuki Muriithi | |
| 2023-03-13 | oauth2: data: Temporarily escalate privileges to enable migration | Frederick 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. | |||
| 2023-03-13 | auth: separate user detail migration from data migration | Frederick 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. | |||
| 2023-03-10 | auth: data-migration: Fix minor bugs | Frederick Muriuki Muriithi | |
| 2023-03-09 | auth: redis data: migrate data in redis | Frederick Muriuki Muriithi | |
| Implement the code to migrate the data from redis to SQLite. | |||
| 2023-03-09 | auth: data migration: Data migration outline | Frederick Muriuki Muriithi | |
| Provide an outline of the data migration steps to be taken from some results of the experiments with the data in redis. | |||
| 2023-03-09 | auth: introspection: Protect introspection endpoint | Frederick 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. | |||
| 2023-03-07 | 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 | Frederick 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. | |||
| 2023-03-06 | 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 | |
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index : genenetwork3 | |
| GeneNetwork3 REST API for data science and machine learning |
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