| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2024-08-26 | Fix 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> | |||
| 2024-08-26 | If 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> | |||
| 2024-08-26 | Set 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> | |||
| 2024-08-26 | Replace 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> | |||
| 2024-08-26 | Fetch 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> | |||
| 2024-08-26 | Move 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> | |||
| 2024-08-26 | Run autopep8 against file. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 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 | John Nduli | |
| * Add better error messages * Create more modular functions | |||
| 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 | |
| 2024-08-13 | Fix pylint errors. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-08-09 | Use correct stemming strategy when searching. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-08-09 | Add RIF/WIKI as search prefixes for XRF/XWK. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-08-01 | Add logging for helping with troubleshooting. | Frederick Muriuki Muriithi | |
| 2024-08-01 | Add handler for unhandled exceptions from `gn3.oauth2` module. | Frederick Muriuki Muriithi | |
| 2024-08-01 | Update case-attribute editing to use new authorisation. | Frederick Muriuki Muriithi | |
| 2024-08-01 | Add `gn3.oauth2` module to handle authorisations | Frederick 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. | |||
| 2024-08-01 | Stem 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. | |||
| 2024-08-01 | Stem 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. | |||
| 2024-07-23 | chore: add logging info | John Nduli | |
| 2024-07-23 | chore: mypy and pylint fixes | John Nduli | |
| 2024-07-23 | fix: resolve duplicate errors when updating data | John Nduli | |
| 2024-07-23 | refactor: clean query for insert | John Nduli | |
| 2024-07-23 | refactor: clean up insert query | John Nduli | |
| 2024-07-23 | refactor: reorganize update_rif script to be more pythonic | John Nduli | |
| 2024-07-23 | chore: fix pylint errors | John Nduli | |
| 2024-07-23 | refactor: rename addRIf to update_rif_table.py | John Nduli | |
| 2024-07-12 | Rename hash_rdf_graph -> md5hash_ttl_dir. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-07-12 | Use 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> | |||
| 2024-07-12 | fix: remove .py extension for addRif to prevent pylint checks | John Nduli | |
| 2024-07-12 | refactor: fix mypy and pylint errors | John Nduli | |
| 2024-07-12 | feat: copy addRif script from genenetwork1 | John Nduli | |
| original: https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/maintainance/addRif.py Included some changes to make it python3 compatible | |||
| 2024-07-08 | Pass output directory to R/qtl script instead of pulling it from the | zsloan | |
| environment Also fixes issue where the control marker keyword was wrong | |||
| 2024-07-05 | fix: return query error message from xapian | John Nduli | |
| 2024-07-03 | Return 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> | |||
| 2024-07-03 | Generate 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> | |||
| 2024-07-03 | Add 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> | |||
| 2024-07-03 | Refactor 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> | |||
| 2024-07-03 | Use correct cache for RIF/Wiki entries. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-07-03 | feat: drop intermediate folders when running parallel xapian compact | John Nduli | |
| 2024-07-03 | feat: add support for parallel xapian compact | John Nduli | |
| 2024-07-03 | feat: index rif and wiki without positions | John Nduli | |
| 2024-07-03 | feat: drop common words when building rdf caches | John Nduli | |
| 2024-07-03 | feat: set 67 parallel processes to run in prod | John Nduli | |
| 2024-07-03 | fix: remove namespaces since child processes copy the rdf caches | 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 | |
| 2024-07-03 | feat: add wikidata indexing | John Nduli | |
 |
index : genenetwork3 | |
| GeneNetwork3 REST API for data science and machine learning |
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