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2024-08-29docs: add function commentsJohn Nduli
2024-08-29feat: add api calls to get categories and last commentJohn Nduli
2024-08-29Fix minor typo.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-08-29Remove "@id" re-map in the json-ld base context.Munyoki Kilyungi
* gn3/db/constants.py [BASE_CONTEXT]: Remove "id" key. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-08-29Fetch the latest comment by the versionId.Munyoki Kilyungi
* gn3/db/rdf.py (get_wiki_entries_by_symbol): Update query to fetch the latest query by the version. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-08-29Make fetching wiki entries by symbol case insensitive.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-08-29Add "created" to wiki return.Munyoki Kilyungi
* gn3/db/rdf.py (get_wiki_entries_by_symbol): Add "created" to dictionary. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-08-29Update doc-string for "handle_sparql_errors".Munyoki Kilyungi
* gn3/errors.py (handle_sparql_errors): Correct the doc-string. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-08-29Return the correct status error code for url errors.Munyoki Kilyungi
* gn3/errors.py (url_server_error): Return a 500 http status code for URL server errors. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-08-26Fix mypy errors.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-08-26Move "GET /wiki/<symbol>" end-point to gn3.api.metadata.wiki.Munyoki Kilyungi
* 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>
2024-08-26Auto-pep8 buffer and ignore type check for payload.Munyoki Kilyungi
* gn3/api/metadata_api/wiki.py (edit_wiki): Ignore type-check for payload. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-08-26Fix pylint errors.Munyoki Kilyungi
* 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>
2024-08-26Fix handling of sparql errors.Munyoki Kilyungi
* 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>
2024-08-26If there's no data, return a 404.Munyoki Kilyungi
* 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>
2024-08-26Set correct content-header & status code for ld+json/json response.Munyoki Kilyungi
* 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>
2024-08-26Replace map with list comprehension.Munyoki Kilyungi
* gn3/db/rdf.py (get_wiki_entries_by_symbol): Use list comprehensions. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-08-26Fetch all the wiki entries by symbol.Munyoki Kilyungi
* 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>
2024-08-26Move constants to their own file.Munyoki Kilyungi
* 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>
2024-08-26Run autopep8 against file.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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 implementationJohn Nduli
* Add better error messages * Create more modular functions
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.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-08-09Use correct stemming strategy when searching.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-08-09Add RIF/WIKI as search prefixes for XRF/XWK.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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 authorisationsFrederick 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.
2024-08-01Stem 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.
2024-08-01Stem 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.
2024-07-08Pass output directory to R/qtl script instead of pulling it from thezsloan
environment Also fixes issue where the control marker keyword was wrong
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 searchzsloan
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.
2024-06-14fix: 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.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-05-20Delete 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>
2024-05-20Remove unused variable.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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
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