| Age | Commit message (Expand) | Author |
|---|---|---|
| 2024-09-23 | Revert "Remove one-line if/else statement."...This reverts commit 0d15840913c9cc401d1e74295aa5e17e34f2987b. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-23 | Remove one-line if/else statement....* gn3/db/rdf/wiki.py (__sanitize_result): When fetching pubmed_ids and categories, default to [] if the key misses, and remove the subsequent one-line if/else statement. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-23 | Use correct object modifier for a label when inserting a comment....* gn3/db/rdf/wiki.py (update_wiki_comment) [query]: Replace "rdf:label" with "rdfs:label". Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-23 | Update docstring for "update_wiki_comment"....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-23 | Use correct object modifier in triple when fetching comment history....* gn3/db/rdf/wiki.py (get_comment_history) [query]: Replace ?symbolName with ?symbolName. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-23 | Use correct modifier when getting species name in SPARQL....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-23 | Remove dead variable from RDF query....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-23 | Alphabetically sort the categories and pubmed_ids array....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-23 | Remove un-necessary triple in comment history RDF query....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-19 | Use correct return type....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-19 | Remove extraneous keyword....* gn3/api/metadata_api/wiki.py (edit_wiki): Remove comment_id from args---it's already in the insert_dict. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-18 | Pass in insert_dict instead of payload in "get_wiki_entries"....* gn3/api/metadata_api/wiki.py (edit_wiki) [insert_dict]: Add species, categories fields. [update_wiki_comment]: Pass in insert_dict, and get rid of redundant keys. Directly pass in sparql_auth's conf params instead of a dict. * gn3/db/rdf/wiki.py (get_next_comment_version): Get rid of redundant params. Use fields directly from insert_dict. Directly pass in sparql_auth's conf params instead of a dict. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-18 | Pass in the createtime as an arg when inserting into RDF graph....* gn3/api/metadata_api/wiki.py (edit_wiki): Pass in the createtime as an arg. * gn3/db/rdf/wiki.py: Remove un-used imports. (update_wiki_comment): Use passed in "created" arg in the createtime field. This makes sure that the SQL/RDF timestamps match. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-18 | Get the next versionId from SQL....* gn3/api/metadata_api/wiki.py (edit_wiki): Get the next version Id from SQL * gn3/db/rdf/wiki.py (get_next_comment_version): Delete. (update_wiki_comment): Provide the next_version id as an extra arg. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-18 | Update "POST /wiki/comment_id/edit" to have RDF edits....* gn3/api/metadata_api/wiki.py: Import update_wiki_comment. (edit_wiki): Update wiki in RDF. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-18 | Fix typo....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-18 | Add method that inserts new RIF comments....* gn3/db/rdf/wiki.py: Import datetime, update_rdf. (update_wiki_comment): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-18 | Fetch symbol by it's name....The RDF ttl files were updated to have: comment gnt:symbol "name" . instead of: comment gnt:symbol symbolQname . * gn3/db/rdf/wiki.py (get_wiki_entries_by_symbol): Fetch symbol using it's string literal name. (get_comment_history): Ditto. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-18 | Fetch the next comment version in RDF....* gn3/db/rdf/wiki.py (get_next_comment_version): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-18 | Rename sparql_construct_query -> sparql_query....* gn3/db/rdf/__init__.py (sparql_construct_query): Rename to... (sparql_query): ... this. Extend function to be able to return JSQN for SELECT queries. (query_frame_and_compact): Ditto. (query_and_compact): Ditto. (query_and_frame): Ditto. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-18 | Add new method for updating RDF Graph content....* gn3/db/rdf/__init__.py: Import POST, DIGEST, JSON. (update_rdf): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-18 | Run python-black against file....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-17 | Fix C0411/C0412 pylint errors in gn3.api.metadata.api.wiki....* gn3/api/metadata_api/wiki.py: Re-order imports to fix pylint errors. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-17 | fix: error when result dict contains None | John Nduli |
| 2024-09-17 | feat: require auth for edit api call | John Nduli |
| 2024-09-12 | Fix pylint errors....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2024-09-12 | feat: pick results from sqlite3 if they were stored | John Nduli |
| 2024-09-12 | Initialise the package to ensure setuptools finds it. | Frederick Muriuki Muriithi |
| 2024-09-12 | BugFix: assign value and use variable. | Frederick Muriuki Muriithi |
| 2024-09-12 | Fix failing tests after merging in Pjotr's pull request. | Frederick Muriuki Muriithi |
| 2024-09-12 | Gracefully print out debug messages even outside app context...The flask.current_app object depends on the application context existing. In the case that no such context existing, then we still log out information, gracefully with this commit. | Frederick Muriuki Muriithi |
| 2024-09-12 | From gn3 only use TMPDIR/gn3 paths | Pjotr Prins |
| 2024-09-12 | Make sure dir exists before running R/qtl | Pjotr Prins |
| 2024-09-12 | Replace TMPDIR/output with TMPDIR/gn3 so it is clear where it comes from | Pjotr Prins |
| 2024-09-12 | Modify script paths so they can be edited in Guix | Pjotr Prins |
| 2024-09-12 | rqtl_wrapper: minor fixes | Pjotr Prins |
| 2024-09-12 | Mistake using envvar | Pjotr Prins |
| 2024-09-12 | Make sure TMPDIR directories exist! | Pjotr Prins |
| 2024-09-12 | Getting Rqtl to run on fallback | Pjotr Prins |
| 2024-09-12 | assert_paths_exist: make throw_error optional | Pjotr Prins |
| 2024-09-12 | gn3/errors.py: add stack trace to error log | Pjotr Prins |
| 2024-09-12 | Move assert_paths_exist into fs_helpers | Pjotr Prins |
| 2024-09-12 | Change behavior of do_paths_exist to actually throw useful error | Pjotr Prins |
| 2024-09-12 | Getting Rqtl to run on fallback | Pjotr Prins |
| 2024-09-12 | assert_paths_exist: make throw_error optional | Pjotr Prins |
| 2024-09-12 | Move assert_paths_exist into fs_helpers | Pjotr Prins |
| 2024-09-12 | Change behavior of do_paths_exist to actually throw useful error | Pjotr Prins |
| 2024-09-12 | Make the gnqa search endpoint a get request. | Alexander_Kabui |
| 2024-09-11 | Minor typo fix. | Alexander_Kabui |
| 2024-09-11 | Update docs on use for custom request when query fahamu Api. | Alexander_Kabui |
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