| Age | Commit message (Expand) | Author |
|---|
| 2024-06-12 | Rework how the indexes are built....Right now, the checks are done in Guix's build expression. This moves
that work to the index-genenetwork script.
| Munyoki Kilyungi |
| 2024-06-12 | Add method to check the validity of the tables+RDF checksums....* scripts/index-genenetwork (verify_checksums): New function.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-06-12 | Generate a SHA256 checksum for the generif graph....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-06-01 | Use global cache to store generif metadata....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>
| Munyoki Kilyungi |
| 2024-06-01 | Add geneRIF to gene index....* 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>
| Munyoki Kilyungi |
| 2023-05-31 | scripts: Write table checksums into index....* scripts/index-genenetwork (main): Write table checksums into index.
| Arun Isaac |
| 2023-05-31 | scripts: Introduce SQLTableClause....* scripts/index-genenetwork (SQLTableClause): New variable.
(genes_query, phenotypes_query): Express tables using SQLTableClause.
(serialize_sql): Serialize SQLTableClause.
| Arun Isaac |
| 2023-05-31 | scripts: Fold long lines....* scripts/index-genenetwork (write_document, index_query): Fold long lines.
| Arun Isaac |
| 2023-05-31 | scripts: Ensure only one indexing job may run at a time....* scripts/index-genenetwork (main): Ensure no other indexing job is running.
| Arun Isaac |
| 2023-05-22 | Make directory at "path" and all intermediate ones....Make the directory at the given path, and any intermediate ones to avoid
errors in the indexing code when the directory, or its parent(s) do not exist.
| Frederick Muriuki Muriithi |
| 2023-04-05 | Enable use of `database_connection` in scripts without current_app...There is need to run external scripts using the same configurations as the
application but without the need to couple the script to the application.
In this case, we provide the needed configuration directly in the CLI, and
modify the existing `gn3.db_utils.database_connection` function to allow it to
work coupled to the app or otherwise.
| Frederick Muriuki Muriithi |
| 2023-02-13 | scripts: Fallback to 1 worker when indexing....* scripts/index-genenetwork (worker_queue): Set default number of workers to 1
if the number of CPUs cannot be determined.
| Arun Isaac |
| 2023-02-13 | scripts: Type hint xapian indexing script....* scripts/index-genenetwork: Import Callable, Generator, Iterable and List
from typing. Type hint all functions.
| Arun Isaac |
| 2022-10-18 | Add xapian indexing script....* scripts/index-genenetwork: New file.
* setup.py (install_requires): Add click, pymonad and xapian-bindings.
(scripts): Add scripts/index-genenetwork.
| Arun Isaac |
