aboutsummaryrefslogtreecommitdiff
AgeCommit message (Expand)Author
2023-07-05Update test: create throw-away variable...* Commit `b529c700` changes the return value to a tuple of values rather than a single string value. Handle that in the test. Frederick Muriuki Muriithi
2023-07-04Fix minor UI bugFrederick Muriuki Muriithi
2023-07-03Spruce up UI...Make UI somewhat consistent with the GN2 UI. Frederick Muriuki Muriithi
2023-07-03Enable deletion of OAuth2 clients.Frederick Muriuki Muriithi
2023-06-30Edit some of the details of OAuth2 clientsFrederick Muriuki Muriithi
2023-06-30List all OAuth2 clients.Frederick Muriuki Muriithi
2023-06-23Fetch all collections, rename variables...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. Frederick Muriuki Muriithi
2023-06-20Fix conflictszsloan
2023-06-20Bug: Don't overwrite/delete old collectionsFrederick Muriuki Muriithi
2023-06-15Fetch genotypes from virtuoso...* gn3/api/metadata.py: Import get_genotype_metadata. (genotype): New end-point. * gn3/db/rdf.py (get_phenotype_metadata): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-06-13Namespace session variable...Extract the functions acting on the session into a separate module and namespace the session variable to prevent conflicts. Frederick Muriuki Muriithi
2023-06-12Delete unused import...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-06-12Fetch phenotypes from virtuoso...* gn3/api/metadata.py: Import get_phenotype_metadata. (phenotype): New end-point. * gn3/db/rdf.py (get_phenotype_metadata): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-06-12Correct publication function docstring...* gn3/api/metadata.py (publication): Update docstring. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-06-12Delete unused get_trait_metadata function...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-06-08Fix bugs with accessing/creating collectionszsloan
2023-06-08bug: Function expects pathlib.Path not strFrederick Muriuki Muriithi
2023-06-07auth: Remove "migrate-data" scope....Scope is superceded by CLI utility script. Frederick Muriuki Muriithi
2023-06-07auth: Remove obsoleted scopeFrederick Muriuki Muriithi
2023-06-07Add 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
2023-06-07Nest duplicate entries into a list from a sparql result...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-06-07Remove 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
2023-06-06Pass geoSeries as a URL...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-06-06Rename gn:geoPlatform -> gn:geoPlatformUrl...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-06-06Match 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
2023-06-06Replace taxon prefix with ncbiTaxon which references NCBI...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-06-06Rename dataset_metadata -> dataset...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-06-05Logging: 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
2023-06-05Logging: Get user information.Frederick Muriuki Muriithi
2023-06-05Logging: Get guix profile information if present....Useful for debugging issues within the guix containers. Frederick Muriuki Muriithi
2023-06-05Logging: Get info about python...This information is useful to assist with debugging issues within the guix containers. Frederick Muriuki Muriithi
2023-06-05Handle unhandled SQLite3 errors.Frederick Muriuki Muriithi
2023-06-02Replace 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
2023-06-02Create 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
2023-06-02auth: Increase limit to 100K recordsFrederick Muriuki Muriithi
2023-06-02auth: Add delay between DB inserts...Add delays to avoid overwhelming the DB server. Frederick Muriuki Muriithi
2023-06-02Auth: Bug: Display all admins before taking choiceFrederick Muriuki Muriithi
2023-05-31scripts: Write table checksums into index....* scripts/index-genenetwork (main): Write table checksums into index. Arun Isaac
2023-05-31scripts: Introduce SQLTableClause....* scripts/index-genenetwork (SQLTableClause): New variable. (genes_query, phenotypes_query): Express tables using SQLTableClause. (serialize_sql): Serialize SQLTableClause. Arun Isaac
2023-05-31scripts: Fold long lines....* scripts/index-genenetwork (write_document, index_query): Fold long lines. Arun Isaac
2023-05-31scripts: Ensure only one indexing job may run at a time....* scripts/index-genenetwork (main): Ensure no other indexing job is running. Arun Isaac
2023-05-30Fix 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
2023-05-30Provide logout link.Frederick Muriuki Muriithi
2023-05-30Enable 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
2023-05-30auth: 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
2023-05-29auth: 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
2023-05-29Enable 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
2023-05-29Move docs to Gemtext repo.Frederick Muriuki Muriithi
2023-05-27Document 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
2023-05-27Add notes on retrieving user IDsFrederick Muriuki Muriithi
generated by cgit v1.2.3 (git 2.46.2) at 2024-12-05 01:20:15 +0000