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2024-09-06Modify endpoint to use query string.Alexander_Kabui
2024-09-06Merge pull request #188 from genenetwork/chores/merge-gnqa-apiAlexander Kabui
Chores/merge gnqa api
2024-09-05Fix type error.Munyoki Kilyungi
* gn3/api/metadata_api/wiki.py: Remove FIXME comment. * gn3/db/wiki.py: Fix type error. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-05Use the correct header to request json-ld data.Munyoki Kilyungi
In HTTP, we use content negotiation to server different representations of a resource to the same URI to help the user agent specify which representation is best suited for the user: <https://developer.mozilla.org/en-US/docs/Web/HTTP/Content_negotiation> The "Accept" requet HTTP indicates which content types the user is supposed to understand: <https://developer.mozilla.org/en-US/docs/Web/HTTP/Headers/Accept> * gn3/api/metadata_api/wiki.py (get_wiki_entries): Use the "Accept" header. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-05Add comment history.Munyoki Kilyungi
* 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>
2024-09-05Ignore type error and add a FIXME stub.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-09-05Restructure RDF module.Munyoki Kilyungi
* 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>
2024-09-05Sort previos records by datetime.Alexander_Kabui
2024-09-05Apply pep8 formatting.Alexander_Kabui
2024-09-05Create new endpoints for fetching user previous records.Alexander_Kabui
2024-09-03Remove unused imports.Alexander_Kabui
2024-09-03Use Jsonb for storing results.Alexander_Kabui
2024-09-02Fix spacing after punctuation.Alexander_Kabui
2024-09-02Use default datetime for table.Alexander_Kabui
2024-09-02Add spacing after punctuation.Alexander_Kabui
2024-08-30Fix merge conflict.Alexander_Kabui
2024-08-29docs: add function commentsJohn Nduli
2024-08-29feat: add api calls to get categories and last commentJohn Nduli
2024-08-29Add default timestamp and and primary key for Rating table.Alexander_Kabui
2024-08-29Fix minor typo.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-08-29Check for empty values when fetching search history.Alexander_Kabui
2024-08-29Use correct http method `Delete` for search history.Alexander_Kabui
2024-08-29Update gnqa search endpoint from POST to PUT.Alexander_Kabui
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>
2024-08-26If 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>
2024-08-26Fetch 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
2024-08-09Use 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>
2024-08-01Stem 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.
2024-06-12fix: use current_app's logger to log db errorsJohn Nduli
2024-06-01Add geneRIF prefix.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-05-29Add delete functionality for gnqa history.Alexander_Kabui
2024-05-27Update Docstrings for Api endpoints and functions.Alexander_Kabui
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