| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2023-06-30 | Edit some of the details of OAuth2 clients | Frederick Muriuki Muriithi | |
| 2023-06-30 | List all OAuth2 clients. | Frederick Muriuki Muriithi | |
| 2023-06-23 | Fetch all collections, rename variables | Frederick Muriuki Muriithi | |
| Fetch from `__REDIS_COLLECTION_KEY__` not `"collections"` to ensure all collections are retrieved correctly. Rename from `__*_DOC__` to `__REDIS_*_KEY__` to more clearly express what the variables are about. | |||
| 2023-06-20 | Fix conflicts | zsloan | |
| 2023-06-20 | Bug: Don't overwrite/delete old collections | Frederick Muriuki Muriithi | |
| 2023-06-13 | Namespace session variable | Frederick Muriuki Muriithi | |
| Extract the functions acting on the session into a separate module and namespace the session variable to prevent conflicts. | |||
| 2023-06-08 | Fix bugs with accessing/creating collections | zsloan | |
| 2023-05-29 | auth: Enable registration of OAuth2 clients | Frederick Muriuki Muriithi | |
| Add UI and code to enable the administrative user to register new OAuth2 clients that can access the API server. | |||
| 2023-05-29 | Enable Administrator login on GN3 | Frederick Muriuki Muriithi | |
| * gn3/auth/authentication/oauth2/views.py: Remove endpoint * gn3/auth/authorisation/users/admin/__init__.py: New admin module * gn3/auth/authorisation/users/admin/ui.py: New admin module * gn3/auth/authorisation/users/admin/views.py: New admin module * gn3/auth/views.py: Use new admin module * gn3/errors.py: Fix linting errors * gn3/templates/login.html: New html template * main.py: Fix linting errors | |||
| 2023-05-25 | Script to assign existing data to publicly-visible resources | Frederick Muriuki Muriithi | |
| A script to assign existing data not assigned to any group to publicly-visible resources. | |||
| 2023-05-25 | Set whether resource is publicly viewable on creation | Frederick Muriuki Muriithi | |
| 2023-05-23 | auth: Enable user masquerade | Frederick Muriuki Muriithi | |
| Enable users with the appropriate privileges to masquerade as other users by providing an endpoint that provides a new token for the "masqueradee" | |||
| 2023-05-19 | auth: Provide user and resource info in the trait data | Frederick Muriuki Muriithi | |
| Provide the user and resource_id information in each trait's authorisation details to help with linking on the UI end. | |||
| 2023-05-19 | auth: Check for json on authorisation endpoint. Add user data. | Frederick Muriuki Muriithi | |
| Ensure the authorisation endpoint expects only JSON. Add the user data to the response from the endpoint. | |||
| 2023-05-18 | auth: Rename collections | Frederick Muriuki Muriithi | |
| Enable renaming collections. | |||
| 2023-05-18 | auth: user collections: Add and/or remove traits. | Frederick Muriuki Muriithi | |
| 2023-05-17 | auth: Delete collections by ID. | Frederick Muriuki Muriithi | |
| 2023-05-17 | auth: Import/Delete Anonymous Collections | Frederick Muriuki Muriithi | |
| Add code to enable the importation/deletion of anonymous collections in the active session to the authenticated user's collections. | |||
| 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. | |||
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index : genenetwork3 | |
| GeneNetwork3 REST API for data science and machine learning |
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