| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2024-08-26 | Run autopep8 against file. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-08-26 | chore: fix pylint errors | John Nduli | |
| 2024-08-26 | refactor: split out utlities into their modules and change api to use metadata | John Nduli | |
| 2024-08-26 | refactor: clean up wiki edit implementation | John Nduli | |
| * Add better error messages * Create more modular functions | |||
| 2024-08-26 | feat: add support for categories in edit query and clearer errors | John Nduli | |
| 2024-08-26 | feat: support for edit wiki entry | John Nduli | |
| 2024-08-13 | Fix pylint errors. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-08-09 | Use correct stemming strategy when searching. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-08-09 | Add RIF/WIKI as search prefixes for XRF/XWK. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-08-01 | Add logging for helping with troubleshooting. | Frederick Muriuki Muriithi | |
| 2024-08-01 | Add handler for unhandled exceptions from `gn3.oauth2` module. | Frederick Muriuki Muriithi | |
| 2024-08-01 | Update case-attribute editing to use new authorisation. | Frederick Muriuki Muriithi | |
| 2024-08-01 | Add `gn3.oauth2` module to handle authorisations | Frederick Muriuki Muriithi | |
| 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. | |||
| 2024-08-01 | Stem group field regardless of case. | Arun Isaac | |
| * gn3/api/search.py (parse_boolean_prefixed_field): New function. (parse_query): Use parse_boolean_prefixed_field for the group field. | |||
| 2024-08-01 | Stem all the time. | Arun Isaac | |
| With the STEM_SOME, xapian does not stem query words that start with a capital letter. Hence, we switch to the STEM_ALL strategy. * gn3/api/search.py (parse_query): Set stemming strategy to STEM_ALL. | |||
| 2024-07-08 | Pass output directory to R/qtl script instead of pulling it from the | zsloan | |
| environment Also fixes issue where the control marker keyword was wrong | |||
| 2024-07-05 | fix: return query error message from xapian | John Nduli | |
| 2024-07-03 | fix: use correct prefix and index key; group wiki cache query | John Nduli | |
| 2024-07-03 | feat: add wikidata prefix to search api | John Nduli | |
| 2024-06-26 | Increase max number of results to 50000 for Xapian search | zsloan | |
| This change needs to be accompanied by a change in GN2! If it's lower than the GN2 MAX_SEARCH_RESULTS value, searches will throw an error. | |||
| 2024-06-14 | fix: typehints in index-genenetwork script | John Nduli | |
| 2024-06-12 | refactor: add db_utils global logger that will be the default | John Nduli | |
| 2024-06-12 | fix: use current_app's logger to log db errors | John Nduli | |
| 2024-06-12 | fix: log errors when an exception occurs due to db_utils | John Nduli | |
| 2024-06-01 | Add geneRIF prefix. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-05-20 | Delete search endpoints for datasets/publications. | Munyoki Kilyungi | |
| * gn3/api/metadata.py: Delete "query_and_frame" import. (search_datasets): Delete. (search_publications): Ditto. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-05-20 | Remove unused variable. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-05-09 | Improve error messaging for use of invalid fahamu token. | Alexander_Kabui | |
| 2024-05-01 | pep8 formatting | Alexander_Kabui | |
| 2024-05-01 | Delete debug code | Alexander_Kabui | |
| 2024-05-01 | Debug: check for if config is loaded in gn3. | Alexander_Kabui | |
| 2024-05-01 | Fix: fix string formatting error and remove unused imports. | Alexander_Kabui | |
| 2024-05-01 | Refactoring | Alexander_Kabui | |
| *general cleanup for debug code * improve error messaging for successful rating | |||
| 2024-05-01 | Debug:fix issue use current_app to fetch config | Alexander_Kabui | |
| 2024-05-01 | Debug Process for LLM_DB_PATH | Alexander_Kabui | |
| * this commit is a debugging process for llm_path on cd * issue: writes to db but not correct path | |||
| 2024-05-01 | Load LLM_DB_PATH as a setting. | Alexander_Kabui | |
| 2024-05-01 | Add more error info for Database Open error raised | Alexander_Kabui | |
| 2024-04-30 | Add a general Exception for the /rating api | Alexander_Kabui | |
| 2024-04-30 | Replace SQLITE_DB_PATH with LLM_DB_PATH for llm db path. | Alexander_Kabui | |
| 2024-04-30 | Update LLM_DB_PATH config. | Alexander_Kabui | |
| 2024-04-30 | Add docstring to view_history function. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-04-30 | Use JWT tokens from gn-auth. | Munyoki Kilyungi | |
| * gn3/api/metadata.py: Import time, jwt, AUthorisationError. (edit_dataset): Use JWT tokens from gn-auth and validate them. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-04-30 | Add an endpoint to query a dataset's git history from it's id. | Munyoki Kilyungi | |
| * gn3/api/metadata.py: Import get_history. (view_history): New endpoint. * gn3/db/datasets.py (get_history): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-04-30 | Add a method for saving a dataset's metadata to git. | Munyoki Kilyungi | |
| * gn3/db/datasets.py (retrieve_metadata): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-04-30 | Rename retrieve_dataset_metadata to retrieve_metadata. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-04-30 | Remove an f-string that doesn't have any interpolated variables. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-04-30 | Add command function that returns an Either monad. | Munyoki Kilyungi | |
| * gn3/commands.py: Import Either, Left, Right. (monadic_run_cmd): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-04-29 | Prevent error when group isn't in parents/f1s JSON file | zsloan | |
| 2024-04-15 | Delete unused imports. | Munyoki Kilyungi | |
| * gn3/api/llm.py: (rate_document, logging): Remove unused imports. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-04-11 | Include parents/f1s in default samplelist + add boolean options for them | zsloan | |
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index : genenetwork3 | |
| GeneNetwork3 REST API for data science and machine learning |
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