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2024-08-29Remove "@id" re-map in the json-ld base context.Munyoki Kilyungi
* gn3/db/constants.py [BASE_CONTEXT]: Remove "id" key. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-08-29Fetch the latest comment by the versionId.Munyoki Kilyungi
* 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>
2024-08-29Make fetching wiki entries by symbol case insensitive.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-08-29Add "created" to wiki return.Munyoki Kilyungi
* gn3/db/rdf.py (get_wiki_entries_by_symbol): Add "created" to dictionary. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-08-26Fix pylint errors.Munyoki Kilyungi
* 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>
2024-08-26If there's no data, return a 404.Munyoki Kilyungi
* 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>
2024-08-26Replace map with list comprehension.Munyoki Kilyungi
* gn3/db/rdf.py (get_wiki_entries_by_symbol): Use list comprehensions. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-08-26Fetch all the wiki entries by symbol.Munyoki Kilyungi
* 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>
2024-08-26Move constants to their own file.Munyoki Kilyungi
* 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>
2024-08-26chore: fix pylint errorsJohn Nduli
2024-08-26refactor: split out utlities into their modules and change api to use metadataJohn Nduli
2024-04-30Add an endpoint to query a dataset's git history from it's id.Munyoki Kilyungi
* 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>
2024-04-30Add a method for saving a dataset's metadata to git.Munyoki Kilyungi
* gn3/db/datasets.py (retrieve_metadata): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-04-30Rename retrieve_dataset_metadata to retrieve_metadata.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-04-30Remove an f-string that doesn't have any interpolated variables.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-04-29Prevent error when group isn't in parents/f1s JSON filezsloan
2024-04-11Include parents/f1s in default samplelist + add boolean options for themzsloan
2024-02-25Construct genofile_path using pathlib module.Munyoki Kilyungi
* gn3/db/datasets.py: Remove os import. (retrieve_sample_list): Replace os.path with Path. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-02-15Use correct names for dataset entries in json result.Munyoki Kilyungi
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>
2024-02-13Fetch extra metadata from text-files when fetching datasets.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-02-13Retrieve metadata from text files given a path.Munyoki Kilyungi
* gn3/db/datasets.py (retrieve_trait_dataset): New file. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Fix pylint error.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Add functions that wrap around the common jsonld patterns.Munyoki Kilyungi
* 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>
2023-10-27Break up long line.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Ignore construct result for mypy complianceMunyoki Kilyungi
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] ```
2023-10-27Abstract out (sparql) CONSTRUCT into a function.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Delete gn3.db.rdf.sparql_query.Munyoki Kilyungi
* 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>
2023-10-27Delete db.rdf.get_url_local_name.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-10-27Implement "GET /metadata/phenotypes/:name".Munyoki Kilyungi
* 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>
2023-10-27Delete get_dataset_metadata.Munyoki Kilyungi
* gn3/db/rdf.py (get_dataset_metadata): Delete. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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/: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>
2023-10-06Make argument mandatoryFrederick Muriuki Muriithi
Make the `base_dir` argument mandatory to force it to be passed in from the point the function is called.
2023-09-21Fix query in update_cross_referencezsloan
2023-09-05Delete un-used importMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-05Fix C3001: Lambda expression assigned to a variableMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-05Remove un-necessary string concatenationMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-05Replace "escape_string" with safe-query parametersMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-05Remove type annotations for "none_case_attrs" variablesMunyoki Kilyungi
* 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>
2023-08-24Change get_pheno_csv_sample_data to use group ID instead of phenotype IDzsloan
2023-08-17Fix query for fetching DataId when inserting ProbeSet datazsloan
2023-08-17Fix a couple remaining issues with function parameterszsloan
2023-08-17Combine pheno/mrna update functions + some other fixeszsloan
2023-08-17Fix queries for fetching group nameszsloan
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-29 09:06:05 +0000