| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2023-05-22 | Change type from 'any' to 'Any' | zsloan | |
| 2023-05-22 | Use f-string for setting genofile_path | zsloan | |
| Also set default value for os.environ.get("GENENETWORK_FILES") | |||
| 2023-05-22 | Include encoding in open statement to address pylint W1514 | zsloan | |
| 2023-05-22 | Initialize 'line'; previous pylint complained because line might not be ↵ | zsloan | |
| initialized (if the genofile was empty, for example) | |||
| 2023-05-22 | Use 'with open()' syntax | zsloan | |
| Initialize samplelist variable | |||
| 2023-05-22 | Remove unused variable this_data | zsloan | |
| 2023-05-22 | Include all samples in trait sample data | zsloan | |
| This is necessary in order to allow for editing the values of samples that don't currently have values | |||
| 2023-05-22 | Fix sample data CSV query to only fetch distinct samples | zsloan | |
| There's probably a better way to fix this query (it was previously returning each sample twice), but DISTINCT was the easiest way I could come up with | |||
| 2023-05-22 | Fix get_trait_sample_data function | zsloan | |
| 2023-05-22 | Fix retrieve_sample_list function to correctly get genofile_path | zsloan | |
| 2023-05-22 | Commit update/insert queries, since they don't seem to be executed otherwise ↵ | zsloan | |
| after the recent changes to the DB | |||
| 2023-05-22 | Add function for retrieving group name (given group ID) | zsloan | |
| 2023-05-22 | Add function for retrieving phenotype sample data as dict | zsloan | |
| 2023-05-22 | Add function for retrieving samplelist from .geno file | zsloan | |
| 2023-05-22 | Make directory at "path" and all intermediate ones. | Frederick Muriuki Muriithi | |
| Make the directory at the given path, and any intermediate ones to avoid errors in the indexing code when the directory, or its parent(s) do not exist. | |||
| 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. | |||
| 2023-05-10 | auth: Only check deliverability of emails at registration. | Frederick Muriuki Muriithi | |
| Check only that the email format is correct, but don't bother with the deliverability check during authentication. The deliverability check is done at registration. | |||
| 2023-05-09 | auth: Implement "Authorization Code Flow"auth/implement-authorization-code-flow | Frederick Muriuki Muriithi | |
| Implement the "Authorization Code Flow" for the authentication of users. * gn3/auth/authentication/oauth2/grants/authorisation_code_grant.py: query and save the authorisation code. * gn3/auth/authentication/oauth2/models/authorization_code.py: Implement the `AuthorisationCode` model * gn3/auth/authentication/oauth2/models/oauth2client.py: Fix typo * gn3/auth/authentication/oauth2/server.py: Register the `AuthorisationCodeGrant` grant with the server. * gn3/auth/authentication/oauth2/views.py: Implement `/authorise` endpoint * gn3/templates/base.html: New HTML Templates of authorisation UI * gn3/templates/common-macros.html: New HTML Templates of authorisation UI * gn3/templates/oauth2/authorise-user.html: New HTML Templates of authorisation UI * main.py: Allow both "code" and "token" response types. | |||
| 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 | logging: Set LOG LEVEL on root logger to enable logs | Frederick Muriuki Muriithi | |
| 2023-04-21 | auth: Attach linked data to specific resources. | Frederick Muriuki Muriithi | |
| 2023-04-21 | Setup module for logging | Frederick Muriuki Muriithi | |
| During development, we need logging sometimes to help with troubleshooting problems. This commit provides a module to help set up the logging in a separate module from the app module. | |||
| 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 | |
| 2023-04-18 | auth: Consistently JSON encode values. | Frederick Muriuki Muriithi | |
| Consistently encode all values for the top-level keys stored in redis to avoid issues with json encode/decode | |||
| 2023-04-17 | Fix typo, os.environment -> os.environ | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-04-17 | Update the default SPARQL endpoint | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-04-17 | Create new endpoint for fetching GeneRIF entries | Munyoki Kilyungi | |
| * gn3/api/metadata.py: Import Template, sparql_query and RDF_PREFIXES. (get_genewiki_entries): New endpoint. * gn3/db/rdf.py: Add new constant for storing rdf prefixes. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-04-17 | Hook up code to use external search script for phenotypes | Frederick Muriuki Muriithi | |
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index : genenetwork3 | |
| GeneNetwork3 REST API for data science and machine learning |
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