| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2024-07-03 | Refactor how the generif md5 sum is calculated and stored in XAPIAN. | Munyoki Kilyungi | |
| * scripts/index-genenetwork (hash_generif_graph): Build the generif checksum by directly building it from the file. (is_data_modified): Update how generif-checksums are verified. (create_xapian_index): Update how generif-checksums are stored in XAPIAN. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-07-03 | Use correct cache for RIF/Wiki entries. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-07-03 | feat: drop intermediate folders when running parallel xapian compact | John Nduli | |
| 2024-07-03 | feat: add support for parallel xapian compact | John Nduli | |
| 2024-07-03 | feat: index rif and wiki without positions | John Nduli | |
| 2024-07-03 | feat: drop common words when building rdf caches | John Nduli | |
| 2024-07-03 | feat: set 67 parallel processes to run in prod | John Nduli | |
| 2024-07-03 | fix: remove namespaces since child processes copy the rdf caches | John Nduli | |
| 2024-07-03 | fix: use correct prefix and index key; group wiki cache query | John Nduli | |
| 2024-07-03 | feat: add wikidata indexing | John Nduli | |
| 2024-07-03 | feat: add global wikicache | John Nduli | |
| 2024-07-03 | feat: add sparql query to get wikidata | John Nduli | |
| 2024-06-24 | Use dataset Name instead of FullName for indexing | zsloan | |
| The Name is generally used as the identifier, while the FullName can container spaces which can cause problems | |||
| 2024-06-18 | Revert "Set the file path for the logger." | Munyoki Kilyungi | |
| This reverts commit b21102bc4ad3678173e7c94d3e66333ec7c1d40a. | |||
| 2024-06-18 | refactor: drop global variables | John Nduli | |
| 2024-06-17 | Check table names in Xapian; if not, default to "-1". | Munyoki Kilyungi | |
| Without this check, there will always be an error when this script is run with the "is-data-modified" flag should there be no database in the XAPIAN_DIRECTORY. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-06-17 | Fetch distinct comments. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-06-14 | fix: typehints in index-genenetwork script | John Nduli | |
| 2024-06-14 | fix: fix incorrect parameters in index_query function | John Nduli | |
| 2024-06-12 | Move the generated xapian files to the correct directory. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-06-12 | Set the file path for the logger. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-06-12 | Change the date format for the logger. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 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> | |||
| 2024-06-01 | 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 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> | |||
| 2024-03-18 | pep8 formatting | Alexander_Kabui | |
| 2024-03-18 | pep8 formatting | Alexander_Kabui | |
| 2024-03-15 | add pubmed metadata | Alexander_Kabui | |
| 2024-03-13 | Add documentation on what the script is for and does. | Frederick Muriuki Muriithi | |
| 2024-03-13 | Remove debug prints in the script | Frederick Muriuki Muriithi | |
| 2024-03-12 | Commit migration script for CaseAttribute* tables | Frederick Muriuki Muriithi | |
| 2023-12-05 | Move script to gn-auth | Frederick Muriuki Muriithi | |
| The script is not used in GN3. | |||
| 2023-11-02 | Make scripts directory a package to eliminate path issues. | Frederick Muriuki Muriithi | |
| 2023-10-27 | Make scripts/ a module since it referenced in argparse_actions.py. | Munyoki Kilyungi | |
| * scripts/__init__.py: New file. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-10-10 | Remove authentication from GN3 | Frederick Muriuki Muriithi | |
| Authentication should be handled by the auth server (gn-auth) and thus, this commit removes code handling user authentication from the GN3 system. | |||
| 2023-08-02 | Use correct variable | Frederick Muriuki Muriithi | |
| After copying the calls to assign appropriate roles to the admin in the script, I forgot to update the variable name. This commit fixes that. | |||
| 2023-08-02 | Fix module name. | Frederick Muriuki Muriithi | |
| 2023-08-02 | Assign `group-leader` role to the admin for automatic group. | Frederick Muriuki Muriithi | |
| 2023-06-02 | auth: Increase limit to 100K records | Frederick Muriuki Muriithi | |
| 2023-06-02 | auth: Add delay between DB inserts | Frederick Muriuki Muriithi | |
| Add delays to avoid overwhelming the DB server. | |||
| 2023-06-02 | Auth: Bug: Display all admins before taking choice | Frederick Muriuki Muriithi | |
| 2023-05-31 | scripts: Write table checksums into index. | Arun Isaac | |
| * scripts/index-genenetwork (main): Write table checksums into index. | |||
| 2023-05-31 | scripts: Introduce SQLTableClause. | Arun Isaac | |
| * scripts/index-genenetwork (SQLTableClause): New variable. (genes_query, phenotypes_query): Express tables using SQLTableClause. (serialize_sql): Serialize SQLTableClause. | |||
| 2023-05-31 | scripts: Fold long lines. | Arun Isaac | |
| * scripts/index-genenetwork (write_document, index_query): Fold long lines. | |||
 |
index : genenetwork3 | |
| GeneNetwork3 REST API for data science and machine learning |
| aboutsummaryrefslogtreecommitdiff |