| Age | Commit message (Expand) | Author |
|---|
| 2024-09-05 | Create global wiki context usable by all functions in gn3.rdf.wiki...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-09-05 | Add missing doc-strings to make pylint pass....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-09-05 | Restructure RDF module....* gn3/api/metadata.py: Import constants from gn3.db.rdf
* gn3/api/metadata_api/wiki.py: Ditto. Import
"get_wiki_entries_by_symbol" from gn3.db.rdf.wiki.
* gn3/db/constants.py: Delete file and move all constants ...
* gn3/db/rdf.py: ... and functions ...
* gn3/db/rdf/__init__.py: ... here.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-08-29 | chore: pylint docstring | John Nduli |
| 2024-08-29 | feat: add api calls to get categories and last comment | John Nduli |
| 2024-08-29 | Remove "@id" re-map in the json-ld base context....* gn3/db/constants.py [BASE_CONTEXT]: Remove "id" key.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-08-29 | Fetch the latest comment by the versionId....* gn3/db/rdf.py (get_wiki_entries_by_symbol): Update query to fetch
the latest query by the version.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-08-29 | Make fetching wiki entries by symbol case insensitive....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-08-29 | Add "created" to wiki return....* gn3/db/rdf.py (get_wiki_entries_by_symbol): Add "created" to
dictionary.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-08-26 | Fix pylint errors....* gn3/api/metadata.py: Remove duplicate imports.
* gn3/db/constants.py: Add docstring.
* gn3/db/rdf.py (get_wiki_entries_by_symbol): Remove duplicate
dictionary key.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-08-26 | If there's no data, return a 404....* gn3/api/metadata.py (get_wiki_entries): Return an empty {} when
there's no data.
* gn3/db/rdf.py (query_frame_and_compact): Delete check for empty
results. Instead just return the context as is.
(query_and_compact): Ditto.
(query_and_frame): Ditto.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-08-26 | Replace map with list comprehension....* gn3/db/rdf.py (get_wiki_entries_by_symbol): Use list comprehensions.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-08-26 | Fetch all the wiki entries by symbol....* gn3/api/metadata.py: Import "get_wiki_entries_by_symbol".
(get_gn_genewiki_entries): Rename this to...
(get_wiki_entries): this; and update the URL endpoint.
* gn3/db/rdf.py: Import constants.BASE_CONTEXT.
(get_wiki_entries_by_symbol): New function.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-08-26 | Move constants to their own file....* gn3/api/metadata.py: Move constants from here...
* gn3/db/rdf.py: ... and here, to...
* gn3/db/constants.py: ... here.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-08-26 | chore: fix pylint errors | John Nduli |
| 2024-08-26 | refactor: split out utlities into their modules and change api to use metadata | John Nduli |
| 2024-04-30 | Add an endpoint to query a dataset's git history from it's id....* gn3/api/metadata.py: Import get_history.
(view_history): New endpoint.
* gn3/db/datasets.py (get_history): New function.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-04-30 | Add a method for saving a dataset's metadata to git....* gn3/db/datasets.py (retrieve_metadata): New function.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-04-30 | Rename retrieve_dataset_metadata to retrieve_metadata....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-04-30 | Remove an f-string that doesn't have any interpolated variables....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-04-29 | Prevent error when group isn't in parents/f1s JSON file | zsloan |
| 2024-04-11 | Include parents/f1s in default samplelist + add boolean options for them | zsloan |
| 2024-02-25 | Construct genofile_path using pathlib module....* gn3/db/datasets.py: Remove os import.
(retrieve_sample_list): Replace os.path with Path.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-02-15 | Use correct names for dataset entries in json result....Since we are appending to an already flattened json-ld file, we don't
need to add the prefixes.
* gn3/api/metadata.py (DATASET_CONTEXT): Add missing "experimentType"
key.
* gn3/db/datasets.py (retrieve_dataset_metadata): Match the __subject
dict with entries from DATASET_CONTEXT.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-02-13 | Fetch extra metadata from text-files when fetching datasets....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-02-13 | Retrieve metadata from text files given a path....* gn3/db/datasets.py (retrieve_trait_dataset): New file.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 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 |
