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2024-08-26Fix handling of sparql errors....* gn3/errors.py (handle_sparql_errors): Use the exception's class name to fetch the status code. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-08-26If 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
2024-08-26Set 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
2024-08-26Replace map with list comprehension....* gn3/db/rdf.py (get_wiki_entries_by_symbol): Use list comprehensions. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-08-26Fetch 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
2024-08-26Move 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
2024-08-26Run autopep8 against file....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-08-26chore: fix pylint errorsJohn Nduli
2024-08-26refactor: split out utlities into their modules and change api to use metadataJohn Nduli
2024-08-26refactor: clean up wiki edit implementation...* Add better error messages * Create more modular functions John Nduli
2024-08-26feat: add support for categories in edit query and clearer errorsJohn Nduli
2024-08-26feat: support for edit wiki entryJohn Nduli
2024-08-13Fix pylint errors....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-08-09Use correct stemming strategy when searching....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-08-09Add RIF/WIKI as search prefixes for XRF/XWK....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-08-01Add logging for helping with troubleshooting.Frederick Muriuki Muriithi
2024-08-01Add handler for unhandled exceptions from `gn3.oauth2` module.Frederick Muriuki Muriithi
2024-08-01Update case-attribute editing to use new authorisation.Frederick Muriuki Muriithi
2024-08-01Add `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
2024-08-01Stem 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
2024-08-01Stem 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
2024-07-08Pass output directory to R/qtl script instead of pulling it from the...environment Also fixes issue where the control marker keyword was wrong zsloan
2024-07-05fix: return query error message from xapianJohn Nduli
2024-07-03fix: use correct prefix and index key; group wiki cache queryJohn Nduli
2024-07-03feat: add wikidata prefix to search apiJohn Nduli
2024-06-26Increase 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
2024-06-14fix: typehints in index-genenetwork scriptJohn Nduli
2024-06-12refactor: add db_utils global logger that will be the defaultJohn Nduli
2024-06-12fix: use current_app's logger to log db errorsJohn Nduli
2024-06-12fix: log errors when an exception occurs due to db_utilsJohn Nduli
2024-06-01Add geneRIF prefix....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-05-20Delete 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
2024-05-20Remove unused variable....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-05-09Improve error messaging for use of invalid fahamu token.Alexander_Kabui
2024-05-01pep8 formattingAlexander_Kabui
2024-05-01Delete debug codeAlexander_Kabui
2024-05-01Debug: check for if config is loaded in gn3.Alexander_Kabui
2024-05-01Fix: fix string formatting error and remove unused imports.Alexander_Kabui
2024-05-01Refactoring... *general cleanup for debug code * improve error messaging for successful rating Alexander_Kabui
2024-05-01Debug:fix issue use current_app to fetch configAlexander_Kabui
2024-05-01Debug 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
2024-05-01Load LLM_DB_PATH as a setting.Alexander_Kabui
2024-05-01Add more error info for Database Open error raisedAlexander_Kabui
2024-04-30Add a general Exception for the /rating apiAlexander_Kabui
2024-04-30Replace SQLITE_DB_PATH with LLM_DB_PATH for llm db path.Alexander_Kabui
2024-04-30Update LLM_DB_PATH config.Alexander_Kabui
2024-04-30Add docstring to view_history function....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-04-30Use 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
2024-04-30Add 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
2024-04-30Add a method for saving a dataset's metadata to git....* gn3/db/datasets.py (retrieve_metadata): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi