| Age | Commit message (Expand) | Author |
|---|
| 2023-06-12 | Delete unused get_trait_metadata function...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-06-08 | Fix bugs with accessing/creating collections | zsloan |
| 2023-06-08 | bug: Function expects pathlib.Path not str | Frederick Muriuki Muriithi |
| 2023-06-07 | auth: Remove "migrate-data" scope....Scope is superceded by CLI utility script.
| Frederick Muriuki Muriithi |
| 2023-06-07 | auth: Remove obsoleted scope | Frederick Muriuki Muriithi |
| 2023-06-07 | Add publication end-point...* gn3/api/metadata.py: Import get_publication_metadata
(publication): New endpoint.
* gn3/db/rdf.py (get_dataset_metadata): New function.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-06-07 | Nest duplicate entries into a list from a sparql result...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-06-07 | Remove trait_metadata endpoint...* gn3/api/metadata.py: Remove get_trait_metadata import.
(trait_metadata): Delete.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-06-06 | Pass geoSeries as a URL...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-06-06 | Rename gn:geoPlatform -> gn:geoPlatformUrl...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-06-06 | Match how dataset metadata is fetched with GN1...* gn3/db/rdf.py (sparql_query): Parse CONSTRUCTS and SELECTS
differently.
(strip_url): Rename to ...
(get_url_local_name): ... this.
(get_dataset_metadata): Fetch extra fields in RDF.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-06-06 | Replace taxon prefix with ncbiTaxon which references NCBI...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-06-06 | Rename dataset_metadata -> dataset...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-06-05 | Logging: Don't allow getting user info to stop application starting...In certain scenarios (probably due to host contamination) the effective UID of
the running application is not the expected "genenetwork" user, rather, it is
a user on the host system, which leads to the error:
KeyError: 'getpwuid(): uid not found: 1000'
This commit prevents the application from failing in such a case, but still
logs out such weirdness.
| Frederick Muriuki Muriithi |
| 2023-06-05 | Logging: Get user information. | Frederick Muriuki Muriithi |
| 2023-06-05 | Logging: Get guix profile information if present....Useful for debugging issues within the guix containers.
| Frederick Muriuki Muriithi |
| 2023-06-05 | Logging: Get info about python...This information is useful to assist with debugging issues within the guix
containers.
| Frederick Muriuki Muriithi |
| 2023-06-05 | Handle unhandled SQLite3 errors. | Frederick Muriuki Muriithi |
| 2023-06-02 | Replace SELECT with CONSTRUCT when fetching a dataset's metadata...* gn3/db/rdf.py: Importh pymonad.Nothing.
(get_dataset_metadata): Replace SELECT with CONSTRUCT.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-06-02 | Create a function for stripping the last bit from a URL...* gn3/db/rdf.py: Import unquote and urlparse.
(strip_url): New function.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-06-02 | auth: Increase limit to 100K records | Frederick Muriuki Muriithi |
| 2023-06-02 | auth: Add delay between DB inserts...Add delays to avoid overwhelming the DB server.
| Frederick Muriuki Muriithi |
| 2023-06-02 | Auth: Bug: Display all admins before taking choice | Frederick Muriuki Muriithi |
| 2023-05-31 | scripts: Write table checksums into index....* scripts/index-genenetwork (main): Write table checksums into index.
| Arun Isaac |
| 2023-05-31 | scripts: Introduce SQLTableClause....* scripts/index-genenetwork (SQLTableClause): New variable.
(genes_query, phenotypes_query): Express tables using SQLTableClause.
(serialize_sql): Serialize SQLTableClause.
| Arun Isaac |
| 2023-05-31 | scripts: Fold long lines....* scripts/index-genenetwork (write_document, index_query): Fold long lines.
| Arun Isaac |
| 2023-05-31 | scripts: Ensure only one indexing job may run at a time....* scripts/index-genenetwork (main): Ensure no other indexing job is running.
| Arun Isaac |
| 2023-05-30 | Fix linting errors and failing tests...* 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.
| Frederick Muriuki Muriithi |
| 2023-05-30 | Provide logout link. | Frederick Muriuki Muriithi |
| 2023-05-30 | Enable registering sys-admin on CLI...To ease registration of system-admin user, provide a CLI script to register
the user and mark them as sys admin in one go.
| Frederick Muriuki Muriithi |
| 2023-05-30 | auth: Change check for client secret...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.
| Frederick Muriuki Muriithi |
| 2023-05-29 | auth: Enable registration of OAuth2 clients...Add UI and code to enable the administrative user to register new OAuth2
clients that can access the API server.
| Frederick Muriuki Muriithi |
| 2023-05-29 | Enable Administrator login on GN3...* 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
| Frederick Muriuki Muriithi |
| 2023-05-29 | Move docs to Gemtext repo. | Frederick Muriuki Muriithi |
| 2023-05-27 | Document Use of OAuth2 Clients...* 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
| Frederick Muriuki Muriithi |
| 2023-05-27 | Add notes on retrieving user IDs | Frederick Muriuki Muriithi |
| 2023-05-26 | Document CLI Utility Commands...Document some CLI utility commands useful for development and for supporting
the operation of the GN3 app.
| Frederick Muriuki Muriithi |
| 2023-05-25 | Add some error checks. | Frederick Muriuki Muriithi |
| 2023-05-25 | Script to assign existing data to publicly-visible resources...A script to assign existing data not assigned to any group to publicly-visible
resources.
| Frederick Muriuki Muriithi |
| 2023-05-25 | Set whether resource is publicly viewable on creation | Frederick Muriuki Muriithi |
| 2023-05-23 | auth: Enable user masquerade...Enable users with the appropriate privileges to masquerade as other users by
providing an endpoint that provides a new token for the "masqueradee"
| Frederick Muriuki Muriithi |
| 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...Also set default value for os.environ.get("GENENETWORK_FILES")
| zsloan |
| 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 initi... | zsloan |
| 2023-05-22 | Use 'with open()' syntax...Initialize samplelist variable
| zsloan |
