| Age | Commit message (Expand) | Author |
|---|
| 2024-09-27 | Skip failing test. | Frederick Muriuki Muriithi |
| 2024-09-27 | Bug: Use absolute paths in place of relative paths....Similar issue to commit 11d543eeca08fe0df4bf2be7222234fadb516a51
| Frederick Muriuki Muriithi |
| 2024-09-27 | Fix Pair-Scan output paths...Related to 4940195460008192b6ca6269e1fb8c172ada4f17c
| Frederick Muriuki Muriithi |
| 2024-09-27 | Set `include_package_data=True` to install R files too. | Frederick Muriuki Muriithi |
| 2024-09-27 | Add a MANIFEST.in to include R scripts. | Frederick Muriuki Muriithi |
| 2024-09-27 | Bug: Use absolute path in place of relative path...Prior to this commit, an assumption is made that the application is
invoked with the root of the repository being the current working
directory. If this assumption is not met, then the system will not
find the appropriate path.
This commit forces the use of an absolute path, which should help
avoid issues with misplaced relative paths.
| Frederick Muriuki Muriithi |
| 2024-09-27 | Use existing fixture to retrieve settings. | Frederick Muriuki Muriithi |
| 2024-09-27 | Fix R/qtl output paths...The script now takes the --outdir parameter as the output directory, only using TMPDIR if nothing is passed
"output" in the output directory was also changed to "gn3" to be consistent with recent changes to GN3's code
| zsloan |
| 2024-09-23 | Revert "Add pytest.mark.unit_test for all rdf test-cases."...This reverts commit f6d9b0cfb842b53e8777e9918549f1ed1ee5892e. Failing
tests because of how we run tests using guix.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-09-23 | Add pytest.mark.unit_test for all rdf test-cases....This makes sure that all the test correctly run in CD.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-09-23 | Handle missing GN3_SECRETS for CI testing....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-09-23 | Fix or ignore pylint errors....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 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 | Add section on setting up virtuoso locally....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-09-23 | Update docs to use default virtuoso ports....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-09-23 | Update docs on how to use SPARQL default ports....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 | Load GN3_SECRETS after loading GN3_CONF settings....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-09-23 | Remove dead comment....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-09-23 | Make sure the the test graph is empty before running rdf tests....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-09-23 | Update docs to highlight sparql conf params in SECRETS file....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 test fixtures to set-up a test named graph....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-09-23 | Add RDF test cases....* pytest.ini: Add rdf pytest marker.
* tests/test_data/ttl-files/test-data.ttl: New file with turtle test
data for RIF editing.
* tests/unit/db/rdf/test_wiki.py (test_sanitize_result): New test
case.
(test_get_comment_history): Ditto.
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 docs with extra conf vars for updating virtuoso....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 |
