| Age | Commit message (Expand) | Author |
|---|
| 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...The Name is generally used as the identifier, while the FullName can container spaces which can cause problems
| zsloan |
| 2024-06-18 | Revert "Set the file path for the logger."...This reverts commit b21102bc4ad3678173e7c94d3e66333ec7c1d40a.
| Munyoki Kilyungi |
| 2024-06-18 | refactor: drop global variables | John Nduli |
| 2024-06-17 | Check table names in Xapian; if not, default to "-1"....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>
| Munyoki Kilyungi |
| 2024-06-17 | Fetch distinct comments....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 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....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-06-12 | Set the file path for the logger....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-06-12 | Change the date format for the logger....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-06-12 | Log how long it takes to run the indexing script....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-06-12 | Check for a running process by viewing the build dir's contents....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>
| Munyoki Kilyungi |
| 2024-06-12 | Return 0 if data changes, else exit with 1....* scripts/index-genenetwork (is_data_modified): Replace click.echo
with the respective sys.exit call.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2024-06-12 | Explicitly pass sparql_uri to script....Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 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 |
