| Age | Commit message (Expand) | Author |
|---|
| 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 |
| 2024-04-15 | Delete unused imports....* gn3/api/llm.py: (rate_document, logging): Remove unused imports.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-03-26 | add sqlite-db-path config | Alexander_Kabui |
| 2024-03-26 | fetch pubmed file from /gn-meta/lit | Alexander_Kabui |
| 2024-03-25 | pep8 formatting | Alexander_Kabui |
| 2024-03-25 | save db data on SQLITE_PATH file path | Alexander_Kabui |
| 2024-03-25 | fix user_id type | Alexander_Kabui |
| 2024-03-25 | enable logigng info for api <rating> | Alexander_Kabui |
| 2024-03-25 | match user id to type str | Alexander_Kabui |
| 2024-03-25 | fetch tmpdir from current app connfig | Alexander_Kabui |
| 2024-03-25 | fix db path issue for lllm | Alexander_Kabui |
| 2024-03-25 | use data dir for files | Alexander_Kabui |
| 2024-03-22 | dump gnqa rating data to db | Alexander_Kabui |
| 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 |
| 2024-01-26 | centralize common errors | Alexander_Kabui |
| 2024-01-26 | Feature/gn llm caching (#148)...* add logic for querying user gnqa search result
* add api endpoints for querying users:qnqa-search-terms,gnqa-results | Alexander Kabui |
| 2024-01-17 | Enhance error response message in API endpoint | Alexander_Kabui |
| 2024-01-17 | Refactor llms.process: Rename getGNQA to get_gnqa | Alexander_Kabui |
| 2024-01-16 | add api endpoint for rating reference documents (#146) | Alexander Kabui |
| 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 |
| 2024-01-03 | fix fetch token error from curent app | Alexander_Kabui |
| 2023-12-29 | handle exception for request error | Alexander_Kabui |
| 2023-12-22 | Feature/gn llms (#140)...* add entry route for gn_llms
* add gn_llms reference doc ids
* init authorization module for gn-llm
* Add class for parsing unprocessable response
* add init config file
* add clienmodule:gn-llm fahamu interface
* Add module descriptor for client file
* reponse data handler
* add response file handler
* add processing file
* remove unnecessary files
* init code refactoring
* Restructure code to module
* refactor code:disble pylint for testing on cd | Alexander Kabui |
| 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 |
