Age | Commit message (Expand) | Author |
2023-10-27 | Implement "GET /metadata/publications/:name"....* 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>
| Munyoki Kilyungi |
2023-10-27 | Add fabio: and prism: to PREFIXES....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-10-27 | Implement "GET /metadata/datasets/search/:term"....* gn3/api/metadata.py (search_datasets): New search endpoint with
pagination.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-10-27 | Implement "GET /metadata/datasets/:name"....* 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>
| Munyoki Kilyungi |
2023-10-27 | Add missing dcat: prefix. | Munyoki Kilyungi |
2023-10-27 | Derive RDF_PREFIXES string from PREFIXES....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-10-27 | Remove get_url_local_name when processing result keys....* gn3/db/rdf.py (sparql_query): Delete "get_url_local_name".
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-10-27 | Simplify CONSTRUCT query when fetching a dataset's metadata....* 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>
| Munyoki Kilyungi |
2023-10-27 | Update RDF prefixes....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
2023-10-26 | Fix errors caught by mypy. | Frederick Muriuki Muriithi |
2023-10-26 | case-attribute: Fix linting errors. | Frederick Muriuki Muriithi |
2023-10-25 | Update __pk__ | Frederick Muriuki Muriithi |
2023-10-25 | case-attribute: Implement __apply_diff__...Enable the "apply diff" feature which actually makes changes to the database
by applying the given diff.
| Frederick Muriuki Muriithi |
2023-10-25 | case-attribute: Bug: List ALL case-attribute values...Fix bug where only one case-attribute value was returned.
| Frederick Muriuki Muriithi |
2023-10-24 | case-attribute: use isoformat() for datetime objects. | Frederick Muriuki Muriithi |
2023-10-23 | case-attribute: View case attribute diff | Frederick Muriuki Muriithi |
2023-10-19 | CaseAttribute: change URL, Create diff dir, fix diff...* 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
| Frederick Muriuki Muriithi |
2023-10-19 | Handle 404 error(s) at top level. | Frederick Muriuki Muriithi |
2023-10-12 | CaseAttributes: List diffs under review...List diffs under review for a given InbredSet. Regenerate any diff files that
might be deleted while still under review.
| Frederick Muriuki Muriithi |
2023-10-12 | CaseAttribute: Bug: Fix bugs with rejecting diffs. | Frederick Muriuki Muriithi |
2023-10-12 | CaseAttributes: Bug: Fix privileges check | Frederick Muriuki Muriithi |
2023-10-12 | CaseAttribute: Bug: Fix query - include time_stamp. | Frederick Muriuki Muriithi |
2023-10-12 | CaseAttribute: Encode/Decode to/from JSON appropriately. | Frederick Muriuki Muriithi |
2023-10-12 | Remove unnecessary clutter. | Frederick Muriuki Muriithi |
2023-10-12 | CaseAttribute: Bug: enumerate the privileges correctly. | Frederick Muriuki Muriithi |
2023-10-11 | CaseAttribute: Reject a diff (delete file). | Frederick Muriuki Muriithi |
2023-10-11 | CaseAttribute: Load diff from file. | Frederick Muriuki Muriithi |
2023-10-11 | CaseAttribute: Save diff to db at queue time. | Frederick Muriuki Muriithi |
2023-10-11 | CaseAttribute: Save the diff to the database. | Frederick Muriuki Muriithi |
2023-10-10 | Do authorisation checks for relevant functions...Add a `required_access(...)` function to be used to check that the user has
the appropriate privileges to act on the case attributes.
| Frederick Muriuki Muriithi |
2023-10-10 | Update imports...Update imports after removing the authentication from GN3
| Frederick Muriuki Muriithi |
2023-10-10 | Implement some queuing logic for diffs...Queue the diffs into files - this might change somewhat once we verify whether
case-attribute editing needs an approval step.
| Frederick Muriuki Muriithi |
2023-10-10 | Check whether there's changes before queuing the diff. | Frederick Muriuki Muriithi |
2023-10-10 | Process Edit data. Fix bugs and typos....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
| Frederick Muriuki Muriithi |
2023-10-10 | Retrieve InbredSet Group's samples/strains...Retrieve the samples/strains that relate to a particular InbredSet group.
| Frederick Muriuki Muriithi |
2023-10-10 | Retrieve InbredSet group details. | Frederick Muriuki Muriithi |
2023-10-10 | Clean-up original data, and case-attribute names...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.
| Frederick Muriuki Muriithi |
2023-10-10 | Implement computing of diffs | Frederick Muriuki Muriithi |
2023-10-10 | Extract fetching of case-attribute names...Extract the fetching of case-attribute names into a separate function that can
be used elsewhere.
| Frederick Muriuki Muriithi |
2023-10-10 | Rename function: Make it clearer what function does. | Frederick Muriuki Muriithi |
2023-10-10 | Bug: Fix missing cursor object. | Frederick Muriuki Muriithi |
2023-10-10 | Add scaffolding for add/delete endpoints. | Frederick Muriuki Muriithi |
2023-10-10 | Add scaffolding for case-attribute editing logic. | Frederick Muriuki Muriithi |
2023-10-10 | Extract fetching of case-attributes by InbredSetId | Frederick Muriuki Muriithi |
2023-10-10 | Editing: Retrieve case-attribute values for an InbredSet group. | Frederick Muriuki Muriithi |
2023-10-10 | Editing: Retrieve case attributes by the related InbredSet | Frederick Muriuki Muriithi |
2023-10-10 | Remove authentication from GN3...Authentication should be handled by the auth server (gn-auth) and thus, this
commit removes code handling user authentication from the GN3 system.
| Frederick Muriuki Muriithi |
2023-10-06 | pylint: fix variable name. | Frederick Muriuki Muriithi |
2023-10-06 | Make argument mandatory...Make the `base_dir` argument mandatory to force it to be passed in from the
point the function is called.
| Frederick Muriuki Muriithi |
2023-10-06 | Get `CORRELATION_COMMAND` from current_app not `gn3.settings`...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`.
| Frederick Muriuki Muriithi |