From e3e75ae0e866d3571612b4b769ae5214bf8daf67 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Wed, 3 Apr 2024 15:31:26 +0300
Subject: Reduce size of data inserted per query

Reduce the size of data inserted per query since MariDB allows a
packet with a maximum size of 1GB. This should hopefully resolve the

    …OperationalError: (2006, 'Server has gone away')

error.
---
 scripts/rqtl2/install_genotypes.py | 2 +-
 scripts/rqtl2/install_phenos.py    | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

(limited to 'scripts')

diff --git a/scripts/rqtl2/install_genotypes.py b/scripts/rqtl2/install_genotypes.py
index 709fe0f..d0731a2 100644
--- a/scripts/rqtl2/install_genotypes.py
+++ b/scripts/rqtl2/install_genotypes.py
@@ -176,7 +176,7 @@ def install_genotypes(#pylint: disable=[too-many-arguments, too-many-locals]
             cdata = rqtl2.control_data(zfile)
             genotypes = rqtl2.genotype_data(zfile)
             while True:
-                batch = tuple(take(genotypes, 5000))
+                batch = tuple(take(genotypes, 1000))
                 if len(batch) == 0:
                     logger.info("Loading Genotypes complete!")
                     logger.info(
diff --git a/scripts/rqtl2/install_phenos.py b/scripts/rqtl2/install_phenos.py
index 95745d7..b5cab8e 100644
--- a/scripts/rqtl2/install_phenos.py
+++ b/scripts/rqtl2/install_phenos.py
@@ -111,7 +111,7 @@ def install_pheno_files(#pylint: disable=[too-many-arguments, too-many-locals]
             phenorows = 0
             datarows = 0
             while True:
-                batch = tuple(take(phenodata, 5000))
+                batch = tuple(take(phenodata, 1000))
                 if len(batch) == 0:
                     logger.info("pheno data loading complete!")
                     logger.info("Inserted a total of %s new ProbeSets and %s "
-- 
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