| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2024-06-12 | Log how long it takes to run the indexing script. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-06-12 | Check for a running process by viewing the build dir's contents. | Munyoki Kilyungi | |
| In the CI build, the actual build is run in the xapian_directory/build, which is seen as the xapian_directory in this script. The CI handles clean up WRT removing files related to the build process. * scripts/index-genenetwork (create_xapian_index): Create the xapian directory if it doesn't exist. If the xapian directory has files, exit. Create the temporary directory inside the xapian_directory. Remove "build_directory.rmdir()" Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-06-12 | Return 0 if data changes, else exit with 1. | Munyoki Kilyungi | |
| * scripts/index-genenetwork (is_data_modified): Replace click.echo with the respective sys.exit call. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-06-12 | Explicitly pass sparql_uri to script. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-06-12 | Rework 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. | |||
| 2024-06-12 | Add 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> | |||
| 2024-06-12 | Generate a SHA256 checksum for the generif graph. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-06-12 | refactor: add db_utils global logger that will be the default | John Nduli | |
| 2024-06-12 | fix: use current_app's logger to log db errors | John Nduli | |
| 2024-06-12 | fix: log errors when an exception occurs due to db_utils | John Nduli | |
| 2024-06-01 | Use 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> | |||
| 2024-06-01 | Add geneRIF prefix. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-06-01 | Add 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> | |||
| 2024-05-29 | Add delete functionality for gnqa history. | Alexander_Kabui | |
| 2024-05-27 | Add regular expressions for parsing links in texts. | Alexander_Kabui | |
| 2024-05-27 | Pylint fixes. | Alexander_Kabui | |
| 2024-05-27 | Remove duplicate code for loading files. | Alexander_Kabui | |
| 2024-05-27 | Delete llm obsolete unittests | Alexander_Kabui | |
| 2024-05-27 | Delete filter response text method and update relevant code. | Alexander_Kabui | |
| 2024-05-27 | Update Docstrings for Api endpoints and functions. | Alexander_Kabui | |
| 2024-05-24 | Update copyright year and email. | Alexander_Kabui | |
| 2024-05-24 | sql: update: llm_db_update.sql: New file. | Alexander_Kabui | |
| 2024-05-24 | Add created_at timestamp for Rating table. | Alexander_Kabui | |
| 2024-05-24 | Add created_at timestamp to History table. | Alexander_Kabui | |
| 2024-05-24 | Pylint fixes. | Alexander_Kabui | |
| 2024-05-24 | Remove kwargs from LLMErrorr Exceptions and update relevant code. | Alexander_Kabui | |
| 2024-05-24 | Initiliaze second args to LLMError as query parameter. | Alexander_Kabui | |
| 2024-05-24 | Return first argument as error message. | Alexander_Kabui | |
| 2024-05-24 | Remove Try/Excepts from llm api endponts. | Alexander_Kabui | |
| 2024-05-24 | Removed status check on get_gnqa function. | Alexander_Kabui | |
| 2024-05-24 | Check for null and empty data results and update timeout message | Alexander_Kabui | |
| 2024-05-24 | Pass query as an argument to api_client ask method. | Alexander_Kabui | |
| 2024-05-24 | Initialize new class attribute self.query for to pass to LLMError. | Alexander_Kabui | |
| 2024-05-24 | Remove try/block for get_answer/ask methods:Exception already raised | Alexander_Kabui | |
| 2024-05-24 | Update custom_request to raise LLMError for Exceptions. | Alexander_Kabui | |
| 2024-05-24 | Remove redundant llm base class exception. | Alexander_Kabui | |
| 2024-05-23 | Remove irrelevant variable assignments. | Alexander_Kabui | |
| 2024-05-23 | rename gnqna route to search. | Alexander_Kabui | |
| 2024-05-23 | Refactor error handling code. | Alexander_Kabui | |
| 2024-05-22 | This commit does the following: | Alexander_Kabui | |
| * Adds a new table to store the history records. * Remove the redis dependancy. | |||
| 2024-05-22 | Refactor error handling for llm api's. | Alexander_Kabui | |
| 2024-05-22 | Register LLM error in app. | Alexander_Kabui | |
| * do refactoring for gn3:llm:errors | |||
| 2024-05-21 | Remove obsolete functions. | Alexander_Kabui | |
| 2024-05-21 | Add search gnqa history functionality. | Alexander_Kabui | |
| 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> | |||
| 2024-05-20 | Remove unused variable. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-05-17 | Add endpoint for getting prev user searches | Alexander_Kabui | |
| 2024-05-17 | Merge pull request #163 from genenetwork/chores/llm3-refactoring | Alexander Kabui | |
| Chores/llm3 refactoring | |||
| 2024-05-17 | Refactor custom request codebase. | Alexander_Kabui | |
| 2024-05-17 | Timeout code refactoring. | Alexander_Kabui | |
 |
index : genenetwork3 | |
| GeneNetwork3 REST API for data science and machine learning |
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