| Age | Commit message (Expand) | Author |
|---|
| 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 |
| 2024-03-25 | pep8 formatting | Alexander_Kabui |
| 2024-03-25 | save db data on SQLITE_PATH file path | Alexander_Kabui |
| 2024-03-25 | fix user_id type | Alexander_Kabui |
| 2024-03-25 | enable logigng info for api <rating> | Alexander_Kabui |
| 2024-03-25 | match user id to type str | Alexander_Kabui |
| 2024-03-25 | fetch tmpdir from current app connfig | Alexander_Kabui |
| 2024-03-25 | fix db path issue for lllm | Alexander_Kabui |
| 2024-03-25 | use data dir for files | Alexander_Kabui |
| 2024-03-22 | dump gnqa rating data to db | Alexander_Kabui |
| 2024-02-15 | Use correct names for dataset entries in json result.•••Since we are appending to an already flattened json-ld file, we don't
need to add the prefixes.
* gn3/api/metadata.py (DATASET_CONTEXT): Add missing "experimentType"
key.
* gn3/db/datasets.py (retrieve_dataset_metadata): Match the __subject
dict with entries from DATASET_CONTEXT.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
