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2024-01-06Add extra keys to the Probeset's json-ld context....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-01-06Refactor gene symbol handling and add references to probeset....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-01-06Use gnt:geneSymbol property to fetch genes in Probeset RDF query....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2024-01-05http request header fixesAlexander_Kabui
2024-01-05max delay timeAlexander_Kabui
2024-01-05increase number of retriesAlexander_Kabui
2024-01-03fix fetch token error from curent appAlexander_Kabui
2024-01-03pylint fixesAlexander_Kabui
2024-01-03fetch auth token from current appAlexander_Kabui
2024-01-03load gn3 secret fileAlexander_Kabui
2024-01-03Delete obsolete Guix system definition....* guix-system.scm: Delete file. Arun Isaac
2024-01-03Do not log user information....* gn3/app.py (create_app): Do not log user information. Arun Isaac
2023-12-29handle exception for request errorAlexander_Kabui
2023-12-29fix mypy issuesAlexander_Kabui
2023-12-22Feature/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 cdAlexander Kabui
2023-12-22setup.py: Find packages automatically using find_packages.Arun Isaac
2023-12-19README: Replace pylint and mypy CI badges with all-tests CI badge.Arun Isaac
2023-12-19guix: Add genenetwork3-all-tests....* .guix/genenetwork3-package.scm: Import python-pylint from (gnu packages check) and python-mypy from (gnu packages python-check). (genenetwork3-all-tests): New variable. Arun Isaac
2023-12-15Update RDF ProbeSet query....* gn3/api/metadata.py (probesets): Update RDF query. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-12-15First 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
2023-12-15Update ProbeSet's context....* gn3/api/metadata.py (probesets): Update context. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-12-15Update 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
2023-12-07Fix typo in GoTree prefix....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-12-07Add optional property for platform info in dataset representation....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-12-07Fetch normalization metadata correctly....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-12-07Fix typo in platform prefix....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-12-07Refactor 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
2023-12-07Update 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
2023-12-05Move script to gn-auth...The script is not used in GN3. Frederick Muriuki Muriithi
2023-11-30Add a phenotype's chromosome location to the Phenotype fetch....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-11-30Place publication details on a sub-graph of its own....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-11-30Replace LRS with lodScore....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-11-27Remove unused variable "args"....* gn3/api/metadata.py (phenotypes): Delete "args". Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-11-27Attach 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
2023-11-27Use "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
2023-11-27Construct a more semantic graph for phenotypes....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-11-27Remove 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
2023-11-27Replace "ex:" prefix with a semantic prefix when fetching phenotype....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-11-27Add "gnt:abbreviation" and "ex:inbredSet" to PHENOTYPE_CONTEXT....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-11-27Add "ex:species" to phenotypes json-ld context....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-11-27Return 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
2023-11-27Add ex:pages and ex:hits to the search context....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-11-27First 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
2023-11-27Add "inbredSet" to the dataset's search context....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-11-27Fetch a dataset's contributors in RDF....* gn3/api/metadata.py (DATASET_CONTEXT): Add key for "contributors." (datasets): Fetch a dataset's contributors. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-11-27Fetch dataset specifics in RDF....* gn3/api/metadata.py (DATASET_CONTEXT): Add key for "specifics". (datasets): Fetch a dataset's specifics. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-11-02Make scripts directory a package to eliminate path issues.Frederick Muriuki Muriithi
2023-11-02Remove files depending on yoyo-migrations.Frederick Muriuki Muriithi
2023-10-30Use correct upstream guix-bioinformatics channel....* .guix-channel: Use git.genenetwork.org instead of gitlab. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-10-28Revert "Roll back to python 3.9 in .guix-channel"...This reverts commit 38b2241d31fdbc4f239eae2b3e3b1a8e31a2f4c6. Arun Isaac
generated by cgit v1.2.3 (git 2.46.2) at 2024-12-04 15:16:17 +0000