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2024-06-12Explicitly pass sparql_uri to script.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-06-12Rework how the indexes are built.Munyoki Kilyungi
Right now, the checks are done in Guix's build expression. This moves that work to the index-genenetwork script.
2024-06-12Add method to check the validity of the tables+RDF checksums.Munyoki Kilyungi
* scripts/index-genenetwork (verify_checksums): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-06-12Generate a SHA256 checksum for the generif graph.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-06-12refactor: add db_utils global logger that will be the defaultJohn Nduli
2024-06-12fix: use current_app's logger to log db errorsJohn Nduli
2024-06-12fix: log errors when an exception occurs due to db_utilsJohn Nduli
2024-06-01Use global cache to store generif metadata.Munyoki Kilyungi
This global caches has 3,528 entries and there's no expectation for it to grow significantly. Since child processes inherit the parent’s memory, we can pass the global cache to them, reducing fetch times from 0.001s to 0.00001s, significantly boosting performance when indexing the entire database and enriching results with RDF metadata. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-06-01Add geneRIF prefix.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-06-01Add geneRIF to gene index.Munyoki Kilyungi
* scripts/index-genenetwork: Import Template, lru_cache, SPARQLWrapper, JSON (get_rif_metadata): New function. (index_rif_comments): New function. (index_genes): Add rif comments to probeset index. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-05-29Add delete functionality for gnqa history.Alexander_Kabui
2024-05-27Add regular expressions for parsing links in texts.Alexander_Kabui
2024-05-27Pylint fixes.Alexander_Kabui
2024-05-27Remove duplicate code for loading files.Alexander_Kabui
2024-05-27Delete llm obsolete unittestsAlexander_Kabui
2024-05-27Delete filter response text method and update relevant code.Alexander_Kabui
2024-05-27Update Docstrings for Api endpoints and functions.Alexander_Kabui
2024-05-24Update copyright year and email.Alexander_Kabui
2024-05-24sql: update: llm_db_update.sql: New file.Alexander_Kabui
2024-05-24Add created_at timestamp for Rating table.Alexander_Kabui
2024-05-24Add created_at timestamp to History table.Alexander_Kabui
2024-05-24Pylint fixes.Alexander_Kabui
2024-05-24Remove kwargs from LLMErrorr Exceptions and update relevant code.Alexander_Kabui
2024-05-24Initiliaze second args to LLMError as query parameter.Alexander_Kabui
2024-05-24Return first argument as error message.Alexander_Kabui
2024-05-24Remove Try/Excepts from llm api endponts.Alexander_Kabui
2024-05-24Removed status check on get_gnqa function.Alexander_Kabui
2024-05-24Check for null and empty data results and update timeout messageAlexander_Kabui
2024-05-24Pass query as an argument to api_client ask method.Alexander_Kabui
2024-05-24Initialize new class attribute self.query for to pass to LLMError.Alexander_Kabui
2024-05-24Remove try/block for get_answer/ask methods:Exception already raisedAlexander_Kabui
2024-05-24Update custom_request to raise LLMError for Exceptions.Alexander_Kabui
2024-05-24Remove redundant llm base class exception.Alexander_Kabui
2024-05-23Remove irrelevant variable assignments.Alexander_Kabui
2024-05-23rename gnqna route to search.Alexander_Kabui
2024-05-23Refactor error handling code.Alexander_Kabui
2024-05-22This commit does the following:Alexander_Kabui
* Adds a new table to store the history records. * Remove the redis dependancy.
2024-05-22Refactor error handling for llm api's.Alexander_Kabui
2024-05-22Register LLM error in app.Alexander_Kabui
* do refactoring for gn3:llm:errors
2024-05-21Remove obsolete functions.Alexander_Kabui
2024-05-21Add search gnqa history functionality.Alexander_Kabui
2024-05-20Delete 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>
2024-05-20Remove unused variable.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-05-17Add endpoint for getting prev user searchesAlexander_Kabui
2024-05-17Merge pull request #163 from genenetwork/chores/llm3-refactoringAlexander Kabui
Chores/llm3 refactoring
2024-05-17Refactor custom request codebase.Alexander_Kabui
2024-05-17Timeout code refactoring.Alexander_Kabui
2024-05-16Refactor code for http request adapters.Alexander_Kabui
2024-05-16Pylint Fixes.Alexander_Kabui
2024-05-16Init code refactoring for clients fahamu interfaceAlexander_Kabui