genenetwork3/scripts/index-genenetwork, branch migrate-to-python3.10GeneNetwork3 REST API for data science and machine learning
http://git.genenetwork.org/genenetwork3/atom?h=migrate-to-python3.102023-05-31T19:28:46+00:00scripts: Write table checksums into index.2023-05-31T19:28:46+00:00Arun Isaac2023-05-31T18:23:17+00:00urn:sha1:78d641b1490b8b0d2b4a5437d6af90742f3011f8
* scripts/index-genenetwork (main): Write table checksums into index.
scripts: Introduce SQLTableClause.2023-05-31T18:21:14+00:00Arun Isaac2023-05-31T18:21:14+00:00urn:sha1:400cc9d9c5fa0f1db92679e7ea8d936272029e14
* scripts/index-genenetwork (SQLTableClause): New variable.
(genes_query, phenotypes_query): Express tables using SQLTableClause.
(serialize_sql): Serialize SQLTableClause.
scripts: Fold long lines.2023-05-31T14:21:30+00:00Arun Isaac2023-05-31T14:21:30+00:00urn:sha1:082e169ca6676b61935604756c0c7c63e19eeb4a
* scripts/index-genenetwork (write_document, index_query): Fold long lines.
scripts: Ensure only one indexing job may run at a time.2023-05-31T14:19:13+00:00Arun Isaac2023-05-31T14:19:13+00:00urn:sha1:7855758c7f17c32cad3c73f5a5677fb87146e32a
* scripts/index-genenetwork (main): Ensure no other indexing job is running.
Make directory at "path" and all intermediate ones.2023-05-22T07:20:57+00:00Frederick Muriuki Muriithi2023-05-22T07:19:42+00:00urn:sha1:cb52df1c320463674938462a68e0a3be4279473b
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.
Enable use of `database_connection` in scripts without current_app2023-04-05T11:51:04+00:00Frederick Muriuki Muriithi2023-04-04T07:07:03+00:00urn:sha1:3d873435f0d464864d4d691d6be4db40931fac05
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.
scripts: Fallback to 1 worker when indexing.2023-02-13T17:36:09+00:00Arun Isaac2023-02-13T17:35:13+00:00urn:sha1:283e7f08701ed80cdfeb8773df38c0c30227a10c
* scripts/index-genenetwork (worker_queue): Set default number of workers to 1
if the number of CPUs cannot be determined.
scripts: Type hint xapian indexing script.2023-02-13T17:36:09+00:00Arun Isaac2023-02-13T17:33:27+00:00urn:sha1:152d0fb36b76b7c68d8202ba3665617bad3e684b
* scripts/index-genenetwork: Import Callable, Generator, Iterable and List
from typing. Type hint all functions.
Add xapian indexing script.2022-10-18T12:15:33+00:00Arun Isaac2022-10-18T09:10:47+00:00urn:sha1:06da0390a1de5d0aa8eb6d7a0ed3120e350f8a0b
* scripts/index-genenetwork: New file.
* setup.py (install_requires): Add click, pymonad and xapian-bindings.
(scripts): Add scripts/index-genenetwork.