| Age | Commit message (Expand) | Author |
|---|---|---|
| 2024-09-05 | Add comment history....* gn3/api/metadata_api/wiki.py: Import get_comment_history. (get_history): New end-point. * gn3/db/rdf/wiki.py: (get_comment_history): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-05 | Ignore type error and add a FIXME stub....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-05 | Restructure RDF module....* gn3/api/metadata.py: Import constants from gn3.db.rdf * gn3/api/metadata_api/wiki.py: Ditto. Import "get_wiki_entries_by_symbol" from gn3.db.rdf.wiki. * gn3/db/constants.py: Delete file and move all constants ... * gn3/db/rdf.py: ... and functions ... * gn3/db/rdf/__init__.py: ... here. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-08-29 | docs: add function comments | John Nduli |
| 2024-08-29 | feat: add api calls to get categories and last comment | John Nduli |
| 2024-08-29 | Fix minor typo....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-08-26 | Fix mypy errors....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-08-26 | Move "GET /wiki/<symbol>" end-point to gn3.api.metadata.wiki....* gn3/api/metadata.py (get_wiki_entries): Move this... * gn3/api/metadata_api/wiki.py (edit_wiki): ... here. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-08-26 | Auto-pep8 buffer and ignore type check for payload....* gn3/api/metadata_api/wiki.py (edit_wiki): Ignore type-check for payload. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-08-26 | Fix pylint errors....* gn3/api/metadata.py: Remove duplicate imports. * gn3/db/constants.py: Add docstring. * gn3/db/rdf.py (get_wiki_entries_by_symbol): Remove duplicate dictionary key. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-08-26 | If there's no data, return a 404....* gn3/api/metadata.py (get_wiki_entries): Return an empty {} when there's no data. * gn3/db/rdf.py (query_frame_and_compact): Delete check for empty results. Instead just return the context as is. (query_and_compact): Ditto. (query_and_frame): Ditto. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-08-26 | Set correct content-header & status code for ld+json/json response....* gn3/api/metadata.py: Import jsonify, make_response. (get_wiki_entries): Set a 404 status code when a response is empty. Set correct Content-Type header for ld+json. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-08-26 | Fetch all the wiki entries by symbol....* gn3/api/metadata.py: Import "get_wiki_entries_by_symbol". (get_gn_genewiki_entries): Rename this to... (get_wiki_entries): this; and update the URL endpoint. * gn3/db/rdf.py: Import constants.BASE_CONTEXT. (get_wiki_entries_by_symbol): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-08-26 | Move constants to their own file....* gn3/api/metadata.py: Move constants from here... * gn3/db/rdf.py: ... and here, to... * gn3/db/constants.py: ... here. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-08-26 | Run autopep8 against file....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 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...* Add better error messages * Create more modular functions | John Nduli |
| 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 |
| 2024-08-09 | Use correct stemming strategy when searching....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-08-09 | Add RIF/WIKI as search prefixes for XRF/XWK....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-08-01 | Stem group field regardless of case....* gn3/api/search.py (parse_boolean_prefixed_field): New function. (parse_query): Use parse_boolean_prefixed_field for the group field. | Arun Isaac |
| 2024-08-01 | Stem all the time....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. | Arun Isaac |
| 2024-07-08 | Pass output directory to R/qtl script instead of pulling it from the...environment Also fixes issue where the control marker keyword was wrong | zsloan |
| 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...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. | zsloan |
| 2024-06-12 | fix: use current_app's logger to log db errors | John Nduli |
| 2024-06-01 | Add geneRIF prefix....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-05-20 | Delete search endpoints for datasets/publications....* gn3/api/metadata.py: Delete "query_and_frame" import. (search_datasets): Delete. (search_publications): Ditto. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 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... *general cleanup for debug code * improve error messaging for successful rating | Alexander_Kabui |
| 2024-05-01 | Debug:fix issue use current_app to fetch config | Alexander_Kabui |
| 2024-05-01 | Debug Process for LLM_DB_PATH... * this commit is a debugging process for llm_path on cd * issue: writes to db but not correct path | 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 | Add docstring to view_history function....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-04-30 | Use JWT tokens from gn-auth....* 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> | Munyoki Kilyungi |
| 2024-04-30 | Add an endpoint to query a dataset's git history from it's id....* 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> | Munyoki Kilyungi |
| 2024-04-30 | Rename retrieve_dataset_metadata to retrieve_metadata....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-04-15 | Delete unused imports....* gn3/api/llm.py: (rate_document, logging): Remove unused imports. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-03-26 | add sqlite-db-path config | Alexander_Kabui |
| 2024-03-26 | fetch pubmed file from /gn-meta/lit | Alexander_Kabui |
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index : genenetwork3 | |
| GeneNetwork3 REST API for data science and machine learning |
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