| Age | Commit message (Expand) | Author |
|---|
| 2023-10-27 | Fix pylint error....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-10-27 | Add functions that wrap around the common jsonld patterns....* gn3/db/rdf.py: Import jsonld.
(query_frame_and_compact, query_and_compact, query_and_frame): New
functions.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-10-27 | Break up long line....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-10-27 | Ignore construct result for mypy compliance...This commit addresses the mypy issue below by ignoring the construct
result.
```
error: Item "None" of "bytes | str | dict[Any, Any] | Graph | Document | None" has no attribute "serialize" [union-attr]
```
| Munyoki Kilyungi |
| 2023-10-27 | Abstract out (sparql) CONSTRUCT into a function....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-10-27 | Delete gn3.db.rdf.sparql_query....* gn3/api/metadata.py: Remove sparql_query import.
* gn3/db/rdf.py: Remove unused imports.
(sparql_query): Delete.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-10-27 | Delete db.rdf.get_url_local_name....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-10-27 | Implement "GET /metadata/phenotypes/:name"....* gn3/api/metadata.py: Delete gn3.db.rdf.get_phenotype_metadata.
(phenotype): Rename this to ...
(phenotypes): ... this and implement update logic.
* gn3/db/rdf.py (get_phenotype_metadata): Delete.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-10-27 | Delete get_dataset_metadata....* gn3/db/rdf.py (get_dataset_metadata): Delete.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 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/: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 |
| 2023-10-06 | 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 |
| 2023-09-21 | Fix query in update_cross_reference | zsloan |
| 2023-09-05 | Delete un-used import...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-09-05 | Fix C3001: Lambda expression assigned to a variable...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-09-05 | Remove un-necessary string concatenation...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-09-05 | Replace "escape_string" with safe-query parameters...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-09-05 | Remove type annotations for "none_case_attrs" variables...* gn3/db/sample_data.py (update_sample_data, delete_sample_data,
insert_sample_data): Remove type hints for "none_case_attrs".
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-08-24 | Change get_pheno_csv_sample_data to use group ID instead of phenotype ID | zsloan |
| 2023-08-17 | Fix query for fetching DataId when inserting ProbeSet data | zsloan |
| 2023-08-17 | Fix a couple remaining issues with function parameters | zsloan |
| 2023-08-17 | Combine pheno/mrna update functions + some other fixes | zsloan |
| 2023-08-17 | Fix queries for fetching group names | zsloan |
| 2023-08-17 | Fix fetch_trait query for phenotypes | zsloan |
| 2023-08-17 | Fix a few misnamed tables in mrna delete/insert functions | zsloan |
| 2023-08-17 | Implement ProbeSet sample data editing...Currently there's a lot of duplicated code, so I need to ask how best to simplify it later
| zsloan |
| 2023-08-17 | Fix probeset sample data and CSV sample data functions | zsloan |
| 2023-08-17 | Fix query for retrieving mrna dataset group name | zsloan |
| 2023-08-17 | Fix get_mrna_sample_data query | zsloan |
| 2023-08-17 | Fix mrna group name query | zsloan |
| 2023-08-17 | Remove Id select from probeset metadata query, since it's included in cols | zsloan |
| 2023-08-17 | Add function for retrieving mRNA Assay group name | zsloan |
| 2023-08-17 | Make several sample_data fetching functions specific to phenotype or mrna ass... | zsloan |
| 2023-08-04 | Remove the ORM-dependent `update` function. | Frederick Muriuki Muriithi |
| 2023-08-02 | Add deprecation notice to ORM-dependent `update` function...Add a deprecation notice to discourage other devs from using the deprecated
`update` function.
| Frederick Muriuki Muriithi |
| 2023-08-02 | Remove ORM-dependent `insert` function...Remove the object-relation-mapping dependent `insert` function to prevent it
being used in the code down the line.
| Frederick Muriuki Muriithi |
| 2023-08-02 | Remove ORM-dependent `fetchall` and `fetchone` functions...Remove Object-Relational Mapping dependent function, `fetchall` and `fetchone`
so as to prevent theirs use in the code moving forward.
| Frederick Muriuki Muriithi |
| 2023-07-26 | Fix variable name. | Frederick Muriuki Muriithi |
| 2023-07-26 | Remove debug statement. | Frederick Muriuki Muriithi |
| 2023-07-26 | Fetch `metadata_audit` trail with direct query functions. | Frederick Muriuki Muriithi |
| 2023-07-26 | Function to create a metadata audit trail. | Frederick Muriuki Muriithi |
| 2023-07-21 | Update a Publication in the database. | Frederick Muriuki Muriithi |
| 2023-07-21 | Fetch a publication by its PubMed ID | Frederick Muriuki Muriithi |
| 2023-07-21 | Rename function: fetch_publication ==> fetch_publication_by_id | Frederick Muriuki Muriithi |
