| Age | Commit message (Expand) | Author |
|---|---|---|
| 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 |
| 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 |
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index : genenetwork3 | |
| GeneNetwork3 REST API for data science and machine learning |
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