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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.
2024-07-23chore: add logging infoJohn Nduli
2024-07-23chore: mypy and pylint fixesJohn Nduli
2024-07-23fix: resolve duplicate errors when updating dataJohn Nduli
2024-07-23refactor: clean query for insertJohn Nduli
2024-07-23refactor: clean up insert queryJohn Nduli
2024-07-23refactor: reorganize update_rif script to be more pythonicJohn Nduli
2024-07-23chore: fix pylint errorsJohn Nduli
2024-07-23refactor: rename addRIf to update_rif_table.pyJohn Nduli
2024-07-12Rename hash_rdf_graph -> md5hash_ttl_dir.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-07-12Use correct ttl-dir path when generating checksums.Munyoki Kilyungi
* scripts/index-genenetwork (is_data_modified): Provide directory instead of specific ttl file. (create_xapian_index): Ditto. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-07-12fix: remove .py extension for addRif to prevent pylint checksJohn Nduli
2024-07-12refactor: fix mypy and pylint errorsJohn Nduli
2024-07-12feat: copy addRif script from genenetwork1John Nduli
original: https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/maintainance/addRif.py Included some changes to make it python3 compatible
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
2024-07-03Return a "-1" if the turtle directory does not exist.Munyoki Kilyungi
* scripts/index-genenetwork (hash_rdf_graph): Remove check for the turtle directory. (is_data_modified): Ditto. (create_xapian_index): Ditto. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-07-03Generate a checksum for all the ttl files.Munyoki Kilyungi
* scripts/index-genenetwork (hash_generif_graph): Rename to hash_rdf_graph. Generate a checksum of all the turtle files inside the ttl directory that's the basis for the GN virtuoso graph. (create_xapian_index): Rename hash_generif_graph -> hash_rdf_graph. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-07-03Add type-hints to hash_generif_graph.Munyoki Kilyungi
* scripts/index-genenetwork (hash_generif_graph): Add proper type hints. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-07-03Refactor how the generif md5 sum is calculated and stored in XAPIAN.Munyoki Kilyungi
* scripts/index-genenetwork (hash_generif_graph): Build the generif checksum by directly building it from the file. (is_data_modified): Update how generif-checksums are verified. (create_xapian_index): Update how generif-checksums are stored in XAPIAN. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-07-03Use correct cache for RIF/Wiki entries.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-07-03feat: drop intermediate folders when running parallel xapian compactJohn Nduli
2024-07-03feat: add support for parallel xapian compactJohn Nduli
2024-07-03feat: index rif and wiki without positionsJohn Nduli
2024-07-03feat: drop common words when building rdf cachesJohn Nduli
2024-07-03feat: set 67 parallel processes to run in prodJohn Nduli
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 21:38:24 +0000