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2024-11-14Fix auth endpoint for case attribute editingzsloan
2024-11-14Fix case attribute queryzsloan
2024-11-12Remove unused setting.Frederick Muriuki Muriithi
The BCRYPT_SALT setting is not used anywhere in GN3 or GN2
2024-11-12Remove unused import.Frederick Muriuki Muriithi
2024-11-12mypy: Rename and annotate variables to silence mypyFrederick Muriuki Muriithi
2024-11-12Pure aesthetics: No functional change.Frederick Muriuki Muriithi
This commit has no functional change it implements. It is purely a aesthetics change to please Frederick.
2024-11-11Allow extra database connection options on URIFrederick Muriuki Muriithi
Update the database URI parsing to allow setting of extra connection option on the URI string.
2024-10-28fix: remove dangerous default configs and have a detailed error with how to ↵John Nduli
configure
2024-10-18refactor: replace gn3.auth.db with gn3.sqlite_db_utils and drop all refs to ↵John Nduli
gn3.auth
2024-10-18refactor: move definition of auth errs and remove auth cli utilsJohn Nduli
2024-10-18refactor: remove unused gn3.auth modulesJohn Nduli
2024-10-15Lint: Fix linting errors.Frederick Muriuki Muriithi
2024-10-15Pass in correct file path.Frederick Muriuki Muriithi
2024-10-15fix: use require_token to validate gn3 apisJohn Nduli
2024-10-14Run python black against file.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-10-14Replace CONSTRUCT with SELECT for fetching RIF NCBI entries.Munyoki Kilyungi
* gn3/db/rdf/wiki.py: Delete datetime import. Import sparql_query. [RIF_CONTEXT]: Delete. (get_rif_entries_by_symbol): Replace CONSTRUCT with SELECT. * tests/unit/db/rdf/test_wiki.py (test_get_rif_entries_by_symbol): Update tests. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-10-14Replace species' shortName with it's full name in NCBI test data.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-10-14Remove "@id" from NCBI test data.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-10-14Update the NCBI expected test data context.Munyoki Kilyungi
* tests/unit/db/rdf/data.py: [LPL_RIF_ENTRIES]: Update "@context". Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-10-14Add end-point for fetching NCBI metadata.Munyoki Kilyungi
* gn3/api/metadata.py: Register "wiki.rif_blueprint". * gn3/api/metadata_api/wiki.py: Import "get_rif_entries_by_symbol". [rif_blueprint]: New blueprint. (get_ncbi_rif_entries): New endpoint: "metadata/rif/<symbol>". Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-10-14Add function for fetching NCBI data.Munyoki Kilyungi
* gn3/db/rdf/wiki.py: Import datetime. [RIF_CONTEXT]: New global variable defining the json-ld context for NCBI rif data. (get_rif_entries_by_symbol): New function. * tests/unit/db/rdf/data.py: New file containing expected NCBI test data. * tests/unit/db/rdf/test_wiki.py (test_update_wiki_comment): New test case. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-10-14Add NCBI test turtle data.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-10-02Add rdf-tests after the check phase.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-10-02Use pathlib to fetch the directory path for tests.Munyoki Kilyungi
* tests/fixtures/rdf.py: import pathlib. (rdf_setup): Use pathlib to get the dir name for the tests folder. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-10-02Fix pylint failure.Munyoki Kilyungi
* tests/fixtures/rdf.py (rdf_setup): Fix C0301. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-10-02feat: cleaner handling of virtuoso processJohn Nduli
2024-10-02Fix typo in comments.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-10-02Move sparql-auth URIs to gn3-conf in documentation.Munyoki Kilyungi
We want to strictly keep secrets in the secret file. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-10-02Add all rdf-tests to GN3 CI.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-10-02Spin up a local virtuoso instance to run RDF tests against.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-10-02Add virtuoso ini file to be used during testing.Munyoki Kilyungi
tests/fixtures/virtuoso.py: New file. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-10-02Set a default password for sparql.Munyoki Kilyungi
* tests/fixtures/rdf.py: Import config. (get_sparql_auth_conf): Load GN3 config from GN3_SECRETS and GN3_CONF if the respective envs are set. Set sane defaults for sparql_conf. (rdf_setup): Remove "fxtr_app_config". * tests/unit/db/rdf/test_wiki.py (test_get_wiki_entries_by_symbol): Ditto. (test_get_comment_history): Ditto. (test_update_wiki_comment): Ditto. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-30chore: pylint code fixJohn Nduli
2024-09-30feat: rollback mysql transaction when rdf insert failsJohn Nduli
2024-09-30fix: rdf and sql queries for fetching rif dataJohn Nduli
SQL queries fail because we get bytes instead of strings which cannot be decoded. We decode results from DictCursor to fix this. For RDF, we cast `?symbol` to a string.
2024-09-28Update documentation on how to run tests.Frederick Muriuki Muriithi
2024-09-28Lint: fix some linting errors.Frederick Muriuki Muriithi
2024-09-27Debug command.Frederick Muriuki Muriithi
2024-09-27Skip failing test.Frederick Muriuki Muriithi
2024-09-27Bug: Use absolute paths in place of relative paths.Frederick Muriuki Muriithi
Similar issue to commit 11d543eeca08fe0df4bf2be7222234fadb516a51
2024-09-27Fix Pair-Scan output pathsFrederick Muriuki Muriithi
Related to 4940195460008192b6ca6269e1fb8c172ada4f17c
2024-09-27Set `include_package_data=True` to install R files too.Frederick Muriuki Muriithi
2024-09-27Add a MANIFEST.in to include R scripts.Frederick Muriuki Muriithi
2024-09-27Bug: Use absolute path in place of relative pathFrederick Muriuki Muriithi
Prior to this commit, an assumption is made that the application is invoked with the root of the repository being the current working directory. If this assumption is not met, then the system will not find the appropriate path. This commit forces the use of an absolute path, which should help avoid issues with misplaced relative paths.
2024-09-27Use existing fixture to retrieve settings.Frederick Muriuki Muriithi
2024-09-27Fix R/qtl output pathszsloan
The script now takes the --outdir parameter as the output directory, only using TMPDIR if nothing is passed "output" in the output directory was also changed to "gn3" to be consistent with recent changes to GN3's code
2024-09-23Revert "Add pytest.mark.unit_test for all rdf test-cases."Munyoki Kilyungi
This reverts commit f6d9b0cfb842b53e8777e9918549f1ed1ee5892e. Failing tests because of how we run tests using guix. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-23Add pytest.mark.unit_test for all rdf test-cases.Munyoki Kilyungi
This makes sure that all the test correctly run in CD. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-23Handle missing GN3_SECRETS for CI testing.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-23Fix or ignore pylint errors.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
generated by cgit-pink 1.4.1 (git 2.36.1) at 2025-11-22 14:36:49 +0000