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2023-10-27Implement "GET /metadata/publications/:name".Munyoki Kilyungi
* gn3/api/metadata.py: Delete gn3.db.rdf.get_publication_metadata. (publication): Rename this ... (publications): ... to this. Return a json-ld result. * gn3/db/rdf.py (get_publication_metadata): Delete. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Add fabio: and prism: to PREFIXES.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Implement "GET /metadata/datasets/search/:term".Munyoki Kilyungi
* gn3/api/metadata.py (search_datasets): New search endpoint with pagination. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Implement "GET /metadata/datasets/:name".Munyoki Kilyungi
* gn3/api/metadata.py: Import json, SPARQLWrapper.{JSON, JSONLD}. (dataset): Rename this to ... (datasets): ... this. Return a well formatted JSONLD result from a dataset. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Add missing dcat: prefix.Munyoki Kilyungi
2023-10-27Derive RDF_PREFIXES string from PREFIXES.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Remove get_url_local_name when processing result keys.Munyoki Kilyungi
* gn3/db/rdf.py (sparql_query): Delete "get_url_local_name". Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Simplify CONSTRUCT query when fetching a dataset's metadata.Munyoki Kilyungi
* gn3/api/metadata.py (dataset): Update docstring. * gn3/db/rdf.py (get_dataset_metadata): Simplify CONSTRUCT query. Also, now you can fetch metadata using either an accession_id or the dataset's name. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Update RDF prefixes.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-26Fix errors caught by mypy.Frederick Muriuki Muriithi
2023-10-26case-attribute: Fix linting errors.Frederick Muriuki Muriithi
2023-10-25Update __pk__Frederick Muriuki Muriithi
2023-10-25case-attribute: Implement __apply_diff__Frederick Muriuki Muriithi
Enable the "apply diff" feature which actually makes changes to the database by applying the given diff.
2023-10-25case-attribute: Bug: List ALL case-attribute valuesFrederick Muriuki Muriithi
Fix bug where only one case-attribute value was returned.
2023-10-24case-attribute: use isoformat() for datetime objects.Frederick Muriuki Muriithi
2023-10-23case-attribute: View case attribute diffFrederick Muriuki Muriithi
2023-10-19CaseAttribute: change URL, Create diff dir, fix diffFrederick Muriuki Muriithi
* Change the URL for listing an inbredset group's case-attribute diffs * Create the diff directory if it does not exist * Add `filename` to the output sent to the browser
2023-10-19Handle 404 error(s) at top level.Frederick Muriuki Muriithi
2023-10-12CaseAttributes: List diffs under reviewFrederick Muriuki Muriithi
List diffs under review for a given InbredSet. Regenerate any diff files that might be deleted while still under review.
2023-10-12CaseAttribute: Bug: Fix bugs with rejecting diffs.Frederick Muriuki Muriithi
2023-10-12CaseAttributes: Bug: Fix privileges checkFrederick Muriuki Muriithi
2023-10-12CaseAttribute: Bug: Fix query - include time_stamp.Frederick Muriuki Muriithi
2023-10-12CaseAttribute: Encode/Decode to/from JSON appropriately.Frederick Muriuki Muriithi
2023-10-12Remove unnecessary clutter.Frederick Muriuki Muriithi
2023-10-12CaseAttribute: Bug: enumerate the privileges correctly.Frederick Muriuki Muriithi
2023-10-11CaseAttribute: Reject a diff (delete file).Frederick Muriuki Muriithi
2023-10-11CaseAttribute: Load diff from file.Frederick Muriuki Muriithi
2023-10-11CaseAttribute: Save diff to db at queue time.Frederick Muriuki Muriithi
2023-10-11CaseAttribute: Save the diff to the database.Frederick Muriuki Muriithi
2023-10-10Do authorisation checks for relevant functionsFrederick Muriuki Muriithi
Add a `required_access(...)` function to be used to check that the user has the appropriate privileges to act on the case attributes.
2023-10-10Update importsFrederick Muriuki Muriithi
Update imports after removing the authentication from GN3
2023-10-10Implement some queuing logic for diffsFrederick Muriuki Muriithi
Queue the diffs into files - this might change somewhat once we verify whether case-attribute editing needs an approval step.
2023-10-10Check whether there's changes before queuing the diff.Frederick Muriuki Muriithi
2023-10-10Process Edit data. Fix bugs and typos.Frederick Muriuki Muriithi
Process the edit data into a CSV form for diff generation. Fix bug in: * processing of original data into a CSV * variable passed to DictWriter * arguments to functions
2023-10-10Retrieve InbredSet Group's samples/strainsFrederick Muriuki Muriithi
Retrieve the samples/strains that relate to a particular InbredSet group.
2023-10-10Retrieve InbredSet group details.Frederick Muriuki Muriithi
2023-10-10Clean-up original data, and case-attribute namesFrederick Muriuki Muriithi
For diff-generation purposes, this commit processes the data into a form that is useful for generation of the CSV files to be used for the diffs.
2023-10-10Implement computing of diffsFrederick Muriuki Muriithi
2023-10-10Extract fetching of case-attribute namesFrederick Muriuki Muriithi
Extract the fetching of case-attribute names into a separate function that can be used elsewhere.
2023-10-10Rename function: Make it clearer what function does.Frederick Muriuki Muriithi
2023-10-10Bug: Fix missing cursor object.Frederick Muriuki Muriithi
2023-10-10Add scaffolding for add/delete endpoints.Frederick Muriuki Muriithi
2023-10-10Add scaffolding for case-attribute editing logic.Frederick Muriuki Muriithi
2023-10-10Extract fetching of case-attributes by InbredSetIdFrederick Muriuki Muriithi
2023-10-10Editing: Retrieve case-attribute values for an InbredSet group.Frederick Muriuki Muriithi
2023-10-10Editing: Retrieve case attributes by the related InbredSetFrederick Muriuki Muriithi
2023-10-10Remove authentication from GN3Frederick Muriuki Muriithi
Authentication should be handled by the auth server (gn-auth) and thus, this commit removes code handling user authentication from the GN3 system.
2023-10-06pylint: fix variable name.Frederick Muriuki Muriithi
2023-10-06Make argument mandatoryFrederick Muriuki Muriithi
Make the `base_dir` argument mandatory to force it to be passed in from the point the function is called.
2023-10-06Get `CORRELATION_COMMAND` from current_app not `gn3.settings`Frederick Muriuki Muriithi
The default settings in `gn3.settings` are meant to be overridden thus the code should not be importing the setting from there, rather, the code should get its configurations settings from `flask.current_app.config`.
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-24 04:04:03 +0000