Age | Commit message (Expand) | Author |
2024-08-01 | Add `gn3.oauth2` module to handle authorisations...Add the `gn3.oauth2` which will handle the authorisations.
It is intended to eventually replace the `gn3.auth` module which is a
left over from when the authorisation server was part of GN3.
| Frederick Muriuki Muriithi |
2024-05-20 | Remove unused variable....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2024-05-01 | Load LLM_DB_PATH as a setting. | Alexander_Kabui |
2024-04-30 | Update LLM_DB_PATH config. | Alexander_Kabui |
2024-03-26 | add sqlite-db-path config | Alexander_Kabui |
2024-03-22 | use tmp for test db | Alexander_Kabui |
2024-03-22 | add gnqa db path | Alexander_Kabui |
2024-01-03 | fix fetch token error from curent app | Alexander_Kabui |
2024-01-03 | fetch auth token from current app | Alexander_Kabui |
2023-12-22 | Feature/gn llms (#140)...* add entry route for gn_llms
* add gn_llms reference doc ids
* init authorization module for gn-llm
* Add class for parsing unprocessable response
* add init config file
* add clienmodule:gn-llm fahamu interface
* Add module descriptor for client file
* reponse data handler
* add response file handler
* add processing file
* remove unnecessary files
* init code refactoring
* Restructure code to module
* refactor code:disble pylint for testing on cd | Alexander Kabui |
2023-10-10 | Do authorisation checks for relevant functions...Add a `required_access(...)` function to be used to check that the user has
the appropriate privileges to act on the case attributes.
| Frederick Muriuki Muriithi |
2023-10-06 | Settings: Add note to discourage importing directly from defaults | 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2023-06-07 | auth: Remove "migrate-data" scope....Scope is superceded by CLI utility script.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 |
2023-05-29 | 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 |
2023-04-17 | Fix typo, os.environment -> os.environ...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-04-17 | Update the default SPARQL endpoint...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-03-09 | auth: data migration: Data migration outline...Provide an outline of the data migration steps to be taken from some results
of the experiments with the data in redis.
| Frederick Muriuki Muriithi |
2023-03-09 | auth: introspection: Protect introspection endpoint...The introspection endpoint could contain privileged information, thus requires
that the endpoint be protected. This commit ensures that a user has
authenticated to the system and that the client they are using be one of the
allowed clients.
| Frederick Muriuki Muriithi |
2023-03-01 | Fetch sampledata...* gn3/api/sampledata.py (get_sampledata): New end-point.
* gn3/app.py: Register above end-point.
* gn3/settings.py: Add new conf variable for LMDB.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2022-12-22 | tests: Setup environment variables and configs...* gn3/settings.py: leave `OAUTH2_ACCESS_TOKEN_GENERATOR` in its default
setting
* tests/unit/auth/fixtures/oauth2_client_fixtures.py: setup
`AUTHLIB_INSECURE_TRANSPORT` before running the OAuth2 tests
* tests/unit/conftest.py: setup the test application's configuration correctly
for the tests.
| Frederick Muriuki Muriithi |
2022-12-22 | auth: implement OAuth2 flow....Add code to implement the OAuth2 flow.
* Add test fixtures for setting up users and OAuth2 clients
* Add tests for token generation with the "Password Grant" flow
* Fix some issues with test due to changes in the database connection's
row_factory
oauth2_auth_flow | Frederick Muriuki Muriithi |
2022-11-08 | Tests: Generalise testing 'CREATE TABLE' migrations...* gn3/settings.py: Omit trailing slash
* tests/unit/auth/test_create_table_migrations.py: Generalise testing
migrations that create tables.
* tests/unit/auth/test_create_user_credentials_table.py: delete
* tests/unit/auth/test_migration_create_users_table.py: delete
| Frederick Muriuki Muriithi |
2022-11-08 | Settings: Provide default `AUTH_DB` setting. | Frederick Muriuki Muriithi |
2022-11-03 | Add credentials checking...* gn3/auth/authentication.py: new function `credentials_in_database`
* gn3/auth/authentication/__init__.py: replace package with module
* gn3/settings.py: new `AUTH_MIGRATIONS` configuration variable
* migrations/auth/20221103_02_sGrIs-create-user-credentials-table.py: new
migration
* tests/unit/auth/test_credentials.py: test the `credentials_in_database`
function
* tests/unit/conftest.py: more test fixtures
| Frederick Muriuki Muriithi |
2022-10-26 | Add xapian database connection context manager....* gn3/settings.py (XAPIAN_DB_PATH): New variable.
* gn3/db_utils.py: Import xapian and XAPIAN_DB_PATH from gn3.settings.
(xapian_database): New function.
| Arun Isaac |
2022-07-22 | import rust_correlation when running gn3 as lib | Alexander_Kabui |
2022-07-11 | Allow CORS everywhere by default...Allow the resources (endpoints) to be accessible from anywhere on the internet
by default, while still allowing for restriction via CLI environment variable
on a case by case basis.
| Frederick Muriuki Muriithi |
2022-06-29 | new variable: CORRELATION_COMMAND | Alexander |
2022-02-21 | Fix a myriad of linter issues...* Use `with` in place of plain `open`
* Use f-strings in place of `str.format()`
* Remove string interpolation from queries - provide data as query parameters
* other minor fixes
| Frederick Muriuki Muriithi |
2022-02-08 | Use multiprocessing to speed up computation...This commit refactors the code to make it possible to use multiprocessing to
speed up the computation of the partial correlations.
The major refactor is to move the `__compute_trait_info__` function to the
top-level of the module, and provide to it all the other necessary context via
the new args.
| Frederick Muriuki Muriithi |
2021-12-02 | Implement dataset metadata API endpoint....* guix.scm: Import (gnu packages rdf).
(genenetwork3)[propagated-inputs]: Add python-sparqlwrapper.
* gn3/settings.py (SPARQL_ENDPOINT): New variable.
* gn3/api/general.py: Import datasets from gn3.db.
(dataset_metadata): New API endpoint.
* gn3/db/datasets.py: Import re, Template from string, Dict and Optional from
typing, JSON and SPARQLWrapper from SPARQLWrapper, SPARQL_ENDPOINT from
gn3.settings.
(sparql_query, dataset_metadata): New functions.
| Arun Isaac |
2021-11-20 | Merge pull request #56 from genenetwork/partial-correlations...Partial correlations | Muriithi Frederick Muriuki |
2021-11-16 | Remove sqlalchemy....* gn3/settings.py (SQLALCHEMY_TRACK_MODIFICATIONS): Delete variable.
* guix.scm (genenetwork3)[propagated-inputs]: Remove python-sqlalchemy-stubs.
* setup.py: Remove sqlalchemy-stubs from install_requires.
| Arun Isaac |
2021-11-04 | Implement `compute_partial_correlations_fast`...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Implement `compute_partial_correlations_fast` that is a partial migration of
`web.webqtl.correlation.PartialCorrDBPage.getPartialCorrelationsFast` in
GN1.
This function will probably be reworked once the dependencies are fully
migrated.
It also needs tests to be added.
| Frederick Muriuki Muriithi |
2021-11-04 | Partially implement `partial_correlation_recursive`...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/computations/partial_correlations.py: Implement one path for the
`gn3.computations.partial_correlations.partial_correlation_recursive`
function.
* gn3/settings.py: Add a setting for how many decimal places to round to
* tests/unit/computations/test_partial_correlations.py: Update test to take
the number of decimal places into consideration
Implement a single path (where the z value is a vector and not a matrix) for
the `partial_correlation_recursive` function.
| Frederick Muriuki Muriithi |
2021-11-01 | Implement `compute_partial_correlations_fast`...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Implement `compute_partial_correlations_fast` that is a partial migration of
`web.webqtl.correlation.PartialCorrDBPage.getPartialCorrelationsFast` in
GN1.
This function will probably be reworked once the dependencies are fully
migrated.
It also needs tests to be added.
| Frederick Muriuki Muriithi |
2021-10-29 | Feature/biweight reimplementation (#47)...* add biweight reimplementation with pingouin
* delete biweight scripts and tests
* add python-pingouin to guix file
* delete biweight paths
* mypy fix:pingouin mising imports
* pep8 formatting && pylint fixes | Alexander Kabui |
2021-10-19 | Fix some linting issues | Frederick Muriuki Muriithi |
2021-10-19 | Allow CORS_ORIGINS to be configurable via the environment...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/non-clustered-heatmaps-and-flipping.gmi
* gn3/app.py: setup CORS after all the configuration sources are loaded.
* gn3/settings.py: Parse CORS_ORIGINS from the environment variables.
Enable the CORS_ORIGINS configuration to be set in the environment variables
to give the application some flexibility when launching.
| Frederick Muriuki Muriithi |
2021-09-27 | fix merge conflicts | Alexander Kabui |
2021-09-20 | Enable Cross-Origin Resource Sharing...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/api/heatmaps.py: Fix bugs in data parsing
* gn3/app.py: enable CORS
* gn3/settings.py: add flask-cors configurations
* guix.scm: Add flask-cors dependency
For easier testing of the heatmaps generation feature, this commit activates
the cross-origin resource sharing for all "localhost" origins.
| Frederick Muriuki Muriithi |
2021-09-16 | Add WGCNA_SCRIT env to settings | Alexander Kabui |
2021-08-31 | Provide utilities for genotype files...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/db/genotypes.py: New module
* gn3/settings.py: Add new configuration variable
* qtlfilesexport.py: Test out new code
Add a module containing functions dealing with the genotype files.
Add a configuration variable to point to the location of the genotype files.
| Muriithi Frederick Muriuki |
2021-08-30 | Implement module for interfacing with rust-qtlreaper...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/heatmap.py: move `generate_traits_file` function to new
module
* gn3/computations/qtlreaper.py: new module to interface with the
`rust-qtlreaper` utility.
* gn3/settings.py: Provide setting for the path to the `rust-qtlreaper`
utility
* qtlfilesexport.py: Move `random_string` function to new module. Update to
use functions in new module.
Provide a module with functions to be used to interface with
`rust-qtlreaper`. This module essentially contains all the functions that
are needed to build the files needed for, and to run the qtlreaper utility.
| Muriithi Frederick Muriuki |
2021-06-23 | minor fixes for biweight script | Alexander Kabui |
2021-06-20 | merge main | Alexander Kabui |
2021-06-20 | make requested changes to biweight | Alexander Kabui |
2021-05-17 | Added RQTL_WRAPPER_CMD (which is fetched from environment) in settings.py | zsloan |
2021-05-13 | Add end-point for running an rQTL program...* gn3/api/general.py (run_r_qtl): New function.
* gn3/settings.py: New variable.
| BonfaceKilz |