| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2024-06-01 | Add geneRIF prefix. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-05-20 | Delete search endpoints for datasets/publications. | Munyoki Kilyungi | |
| * gn3/api/metadata.py: Delete "query_and_frame" import. (search_datasets): Delete. (search_publications): Ditto. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-05-09 | Improve error messaging for use of invalid fahamu token. | Alexander_Kabui | |
| 2024-05-01 | pep8 formatting | Alexander_Kabui | |
| 2024-05-01 | Delete debug code | Alexander_Kabui | |
| 2024-05-01 | Debug: check for if config is loaded in gn3. | Alexander_Kabui | |
| 2024-05-01 | Fix: fix string formatting error and remove unused imports. | Alexander_Kabui | |
| 2024-05-01 | Refactoring | Alexander_Kabui | |
| *general cleanup for debug code * improve error messaging for successful rating | |||
| 2024-05-01 | Debug:fix issue use current_app to fetch config | Alexander_Kabui | |
| 2024-05-01 | Debug Process for LLM_DB_PATH | Alexander_Kabui | |
| * this commit is a debugging process for llm_path on cd * issue: writes to db but not correct path | |||
| 2024-05-01 | Add more error info for Database Open error raised | Alexander_Kabui | |
| 2024-04-30 | Add a general Exception for the /rating api | Alexander_Kabui | |
| 2024-04-30 | Replace SQLITE_DB_PATH with LLM_DB_PATH for llm db path. | Alexander_Kabui | |
| 2024-04-30 | Add docstring to view_history function. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-04-30 | Use 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> | |||
| 2024-04-30 | Add 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> | |||
| 2024-04-30 | Rename retrieve_dataset_metadata to retrieve_metadata. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-04-15 | Delete unused imports. | Munyoki Kilyungi | |
| * gn3/api/llm.py: (rate_document, logging): Remove unused imports. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 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. | 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> | |||
| 2024-02-14 | Remove try ... except clauses around RDF endpoints. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-02-14 | Stem the dataset's id before constructing the path. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-02-13 | Use 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> | |||
| 2024-02-13 | Update "dataset/<name>" API endpoint to fetch metadata from files. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-01-26 | centralize common errors | Alexander_Kabui | |
| 2024-01-26 | Feature/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 | |||
| 2024-01-17 | 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. | 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> | |||
| 2024-01-10 | Switch 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> | |||
| 2024-01-10 | Remove 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> | |||
| 2024-01-08 | Optionally fetch dataset metadata if provided during probeset fetch. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-01-06 | Remove extra gene metadata from query as it's un-necessary. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-01-06 | Add extra keys to the Probeset's json-ld context. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-01-06 | Refactor gene symbol handling and add references to probeset. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-01-06 | Use gnt:geneSymbol property to fetch genes in Probeset RDF query. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 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) | 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 | |||
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index : genenetwork3 | |
| GeneNetwork3 REST API for data science and machine learning |
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