| Age | Commit message (Expand) | Author |
|---|
| 2024-08-26 | Move "GET /wiki/<symbol>" end-point to gn3.api.metadata.wiki....* gn3/api/metadata.py (get_wiki_entries): Move this...
* gn3/api/metadata_api/wiki.py (edit_wiki): ... here.
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 | Set correct content-header & status code for ld+json/json response....* gn3/api/metadata.py: Import jsonify, make_response.
(get_wiki_entries): Set a 404 status code when a response is empty.
Set correct Content-Type header for ld+json.
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 | Run autopep8 against file....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-08-26 | refactor: split out utlities into their modules and change api to use metadata | John Nduli |
| 2024-05-20 | Delete search endpoints for datasets/publications....* gn3/api/metadata.py: Delete "query_and_frame" import.
(search_datasets): Delete.
(search_publications): Ditto.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-04-30 | Add docstring to view_history function....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-04-30 | Use JWT tokens from gn-auth....* gn3/api/metadata.py: Import time, jwt, AUthorisationError.
(edit_dataset): Use JWT tokens from gn-auth and validate them.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 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 | Rename retrieve_dataset_metadata to retrieve_metadata....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 |
| 2024-02-14 | Remove try ... except clauses around RDF endpoints....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-02-14 | Stem the dataset's id before constructing the path....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-02-13 | Use correct path for dataset metadata files....* gn3/api/metadata.py (datasets): Use "gn-docs/general/datasets".
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-02-13 | Update "dataset/<name>" API endpoint to fetch metadata from files....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-01-10 | Optionally fetch dataset metadata if provided during genotype fetch....* gn3/api/metadata.py (genotypes): If a dataset name is provided fetch
the group it belongs to and the dataset's full and short name.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-01-10 | Switch to gnt:belongsToSpecies in genotype queries....* gn3/api/metadata.py (genotypes): Use gnt:belongsToSpecies instead of
xkos:classifiedUnder when querying for species.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-01-10 | Remove hard-coded dataset name....* gn3/api/metadata.py (probesets): Remove hard-coded "HC_M2_0606_P" in
probeset RDF query.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-01-08 | Optionally fetch dataset metadata if provided during probeset fetch....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-01-06 | Remove extra gene metadata from query as it's un-necessary....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-01-06 | Add extra keys to the Probeset's json-ld context....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-01-06 | Refactor gene symbol handling and add references to probeset....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-01-06 | Use gnt:geneSymbol property to fetch genes in Probeset RDF query....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-12-15 | Update RDF ProbeSet query....* gn3/api/metadata.py (probesets): Update RDF query.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-12-15 | First frame and then compact probeset results....* gn3/api/metadata.py: Reshape the data in a nice way by first framing
and compacting the json-ld result.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-12-15 | Update ProbeSet's context....* gn3/api/metadata.py (probesets): Update context.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-12-15 | Update BASE_CONTEXT entries....* gn3/api/metadata.py: (PHENOTYPE_CONTEXT): Move "rdfs", "gnt",
"gnc"...
(BASE_CONTEXT): ... here.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-12-07 | Fix typo in GoTree prefix....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-12-07 | Add optional property for platform info in dataset representation....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-12-07 | Fetch normalization metadata correctly....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-12-07 | Fix typo in platform prefix....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-12-07 | Refactor metadata mappings for improved dataset representation....* gn3/api/metadata.py: (DATASET_CONTEXT): Remove "ex:" prefixes. Add
new prefixes for citation, platform, GoTree, tissueInfo, contactWebUrl
and contactName.
(datasets): Update query.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-12-07 | Update phenotype queries to use gnt:belongsToGroup....* gn3/api/metadata.py (phenotypes): Use gnt:belongsToGroup instead of xkos:classifiedUnder.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-11-30 | Add a phenotype's chromosome location to the Phenotype fetch....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-11-30 | Place publication details on a sub-graph of its own....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-11-30 | Replace LRS with lodScore....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-11-27 | Remove unused variable "args"....* gn3/api/metadata.py (phenotypes): Delete "args".
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-11-27 | Attach phenotype endpoints to one function....* gn3/api/metadata.py (phenotypes): Add "/phenotypes/<group>/<name>"
to this endpoint.
(fetch_phenotype_by_group): Delete.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-11-27 | Use "dcat:Dataset" when framing when fetching phenotypes....* gn3/api/metadata.py (phenotypes): Filter for "dcat:Dataset" in
json-ld context.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-11-27 | Construct a more semantic graph for phenotypes....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-11-27 | Remove unused argument during template substitution....* gn3/api/metadata.py (phenotypes): Delete "name" from template
substitution.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-11-27 | Replace "ex:" prefix with a semantic prefix when fetching phenotype....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-11-27 | Add "gnt:abbreviation" and "ex:inbredSet" to PHENOTYPE_CONTEXT....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-11-27 | Add "ex:species" to phenotypes json-ld context....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-11-27 | Return distinct results after a dataset search....* gn3/api/metadata.py (search_datasets): Return distinct search
results.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-11-27 | Add ex:pages and ex:hits to the search context....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-11-27 | First fram and compact the jsonld results during dataset search....* gn3/api/metadata.py (search_datasets): Replace query_and_frame with
query_frame_and_compact.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
