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2024-04-30Replace SQLITE_DB_PATH with LLM_DB_PATH for llm db path.Alexander_Kabui
2024-04-30Add docstring to view_history function.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-04-30Use JWT tokens from gn-auth.Munyoki Kilyungi
* 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>
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>
2024-04-30Rename retrieve_dataset_metadata to retrieve_metadata.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-04-15Delete unused imports.Munyoki Kilyungi
* gn3/api/llm.py: (rate_document, logging): Remove unused imports. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-03-26add sqlite-db-path configAlexander_Kabui
2024-03-26fetch pubmed file from /gn-meta/litAlexander_Kabui
2024-03-25pep8 formattingAlexander_Kabui
2024-03-25save db data on SQLITE_PATH file pathAlexander_Kabui
2024-03-25fix user_id typeAlexander_Kabui
2024-03-25enable logigng info for api <rating>Alexander_Kabui
2024-03-25match user id to type strAlexander_Kabui
2024-03-25fetch tmpdir from current app connfigAlexander_Kabui
2024-03-25fix db path issue for lllmAlexander_Kabui
2024-03-25use data dir for filesAlexander_Kabui
2024-03-22dump gnqa rating data to dbAlexander_Kabui
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>
2024-02-14Remove try ... except clauses around RDF endpoints.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-02-14Stem the dataset's id before constructing the path.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-02-13Use correct path for dataset metadata files.Munyoki Kilyungi
* gn3/api/metadata.py (datasets): Use "gn-docs/general/datasets". Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-02-13Update "dataset/<name>" API endpoint to fetch metadata from files.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-01-26centralize common errorsAlexander_Kabui
2024-01-26Feature/gn llm caching (#148)Alexander Kabui
* add logic for querying user gnqa search result * add api endpoints for querying users:qnqa-search-terms,gnqa-results
2024-01-17Enhance error response message in API endpointAlexander_Kabui
2024-01-17Refactor llms.process: Rename getGNQA to get_gnqaAlexander_Kabui
2024-01-16add api endpoint for rating reference documents (#146)Alexander Kabui
2024-01-10Optionally fetch dataset metadata if provided during genotype fetch.Munyoki Kilyungi
* 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>
2024-01-10Switch to gnt:belongsToSpecies in genotype queries.Munyoki Kilyungi
* gn3/api/metadata.py (genotypes): Use gnt:belongsToSpecies instead of xkos:classifiedUnder when querying for species. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-01-10Remove hard-coded dataset name.Munyoki Kilyungi
* gn3/api/metadata.py (probesets): Remove hard-coded "HC_M2_0606_P" in probeset RDF query. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-01-08Optionally fetch dataset metadata if provided during probeset fetch.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-01-06Remove extra gene metadata from query as it's un-necessary.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-01-06Add extra keys to the Probeset's json-ld context.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-01-06Refactor gene symbol handling and add references to probeset.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-01-06Use gnt:geneSymbol property to fetch genes in Probeset RDF query.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-01-03fix fetch token error from curent appAlexander_Kabui
2023-12-29handle exception for request errorAlexander_Kabui
2023-12-22Feature/gn llms (#140)Alexander Kabui
* 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
2023-12-15Update RDF ProbeSet query.Munyoki Kilyungi
* gn3/api/metadata.py (probesets): Update RDF query. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-15First frame and then compact probeset results.Munyoki Kilyungi
* 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>
2023-12-15Update ProbeSet's context.Munyoki Kilyungi
* gn3/api/metadata.py (probesets): Update context. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-15Update BASE_CONTEXT entries.Munyoki Kilyungi
* gn3/api/metadata.py: (PHENOTYPE_CONTEXT): Move "rdfs", "gnt", "gnc"... (BASE_CONTEXT): ... here. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-07Fix typo in GoTree prefix.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-07Add optional property for platform info in dataset representation.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-07Fetch normalization metadata correctly.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-07Fix typo in platform prefix.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-07Refactor metadata mappings for improved dataset representation.Munyoki Kilyungi
* 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>
2023-12-07Update phenotype queries to use gnt:belongsToGroup.Munyoki Kilyungi
* gn3/api/metadata.py (phenotypes): Use gnt:belongsToGroup instead of xkos:classifiedUnder. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-30Add a phenotype's chromosome location to the Phenotype fetch.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-30Place publication details on a sub-graph of its own.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-29 12:22:48 +0000