| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2023-06-05 | Logging: Get guix profile information if present. | Frederick Muriuki Muriithi | |
| Useful for debugging issues within the guix containers. | |||
| 2023-06-05 | Logging: Get info about python | Frederick Muriuki Muriithi | |
| This information is useful to assist with debugging issues within the guix containers. | |||
| 2023-06-05 | Handle unhandled SQLite3 errors. | Frederick Muriuki Muriithi | |
| 2023-06-02 | Replace SELECT with CONSTRUCT when fetching a dataset's metadata | Munyoki Kilyungi | |
| * gn3/db/rdf.py: Importh pymonad.Nothing. (get_dataset_metadata): Replace SELECT with CONSTRUCT. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-06-02 | Create a function for stripping the last bit from a URL | Munyoki Kilyungi | |
| * gn3/db/rdf.py: Import unquote and urlparse. (strip_url): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-06-02 | auth: Increase limit to 100K records | Frederick Muriuki Muriithi | |
| 2023-06-02 | auth: Add delay between DB inserts | Frederick Muriuki Muriithi | |
| Add delays to avoid overwhelming the DB server. | |||
| 2023-06-02 | Auth: Bug: Display all admins before taking choice | Frederick Muriuki Muriithi | |
| 2023-05-31 | scripts: Write table checksums into index. | Arun Isaac | |
| * scripts/index-genenetwork (main): Write table checksums into index. | |||
| 2023-05-31 | scripts: Introduce SQLTableClause. | Arun Isaac | |
| * scripts/index-genenetwork (SQLTableClause): New variable. (genes_query, phenotypes_query): Express tables using SQLTableClause. (serialize_sql): Serialize SQLTableClause. | |||
| 2023-05-31 | scripts: Fold long lines. | Arun Isaac | |
| * scripts/index-genenetwork (write_document, index_query): Fold long lines. | |||
| 2023-05-31 | scripts: Ensure only one indexing job may run at a time. | Arun Isaac | |
| * scripts/index-genenetwork (main): Ensure no other indexing job is running. | |||
| 2023-05-30 | Fix linting errors and failing tests | Frederick Muriuki Muriithi | |
| * scripts/register_sys_admin.py: fix linting error * tests/unit/auth/fixtures/oauth2_client_fixtures.py: hash client secret in database. The code expects it hashed in the database. | |||
| 2023-05-30 | Provide logout link. | Frederick Muriuki Muriithi | |
| 2023-05-30 | Enable registering sys-admin on CLI | Frederick Muriuki Muriithi | |
| To ease registration of system-admin user, provide a CLI script to register the user and mark them as sys admin in one go. | |||
| 2023-05-30 | auth: Change check for client secret | Frederick Muriuki Muriithi | |
| We are saving the client secret in an encrypted form, meaning we have to verify that the CLIENT_SECRET that is provided is the same one as was generated at registration in a different way. Initially, I was doing a direct comparison, having saved the CLIENT_SECRET value as unencrypted plain-text. | |||
| 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 | |||
| 2023-05-29 | Move docs to Gemtext repo. | Frederick Muriuki Muriithi | |
| 2023-05-27 | Document Use of OAuth2 Clients | Frederick Muriuki Muriithi | |
| * docs/authentication_and_authorisation/oauth2_clients.md: New documentation * gn3/auth/authentication/oauth2/server.py: Raise appropriate error if no client is found. * gn3/auth/authentication/oauth2/views.py: Handle exception in the case where a UI should be presented to the user, rather than presenting the raw JSON response to the user. * gn3/errors.py: Handle any authlib OAuth2Error at the application's top-level * gn3/templates/oauth2/oauth2_error.html: Handle any authlib OAuth2Error at the application's top-level | |||
| 2023-05-27 | Add notes on retrieving user IDs | Frederick Muriuki Muriithi | |
| 2023-05-26 | Document CLI Utility Commands | Frederick Muriuki Muriithi | |
| Document some CLI utility commands useful for development and for supporting the operation of the GN3 app. | |||
| 2023-05-25 | Add some error checks. | Frederick Muriuki Muriithi | |
| 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" | |||
| 2023-05-23 | Document how to log out information in GN3 | Frederick Muriuki Muriithi | |
| 2023-05-22 | Use string literal concatenation to make genofile_path line shorter | zsloan | |
| 2023-05-22 | Fix quotes when setting genofile_path | zsloan | |
| 2023-05-22 | Fix return typing for get_trait_sample_data | zsloan | |
| 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 | |
 |
index : genenetwork3 | |
| GeneNetwork3 REST API for data science and machine learning |
| aboutsummaryrefslogtreecommitdiff |