From c7ff9222b74402e068630352ba37de0f15d07b88 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Tue, 3 Dec 2024 11:18:14 -0600
Subject: Pass the redis connection and fully qualified job id

Pass the redis connection on to the function used to build main since
it might need to use a connection to redis.

Also pass the computed fully qualified job id rather than recomputing
it every time.

Update dependent functions to take the new arguments.
---
 scripts/process_rqtl2_bundle.py | 4 ++++
 1 file changed, 4 insertions(+)

(limited to 'scripts/process_rqtl2_bundle.py')

diff --git a/scripts/process_rqtl2_bundle.py b/scripts/process_rqtl2_bundle.py
index 4efc3e0..8b7a0fb 100644
--- a/scripts/process_rqtl2_bundle.py
+++ b/scripts/process_rqtl2_bundle.py
@@ -94,7 +94,9 @@ def process_bundle(dbconn: mdb.Connection,
         if has_geno_file(thejob):
             logger.info("Processing geno files.")
             genoexit = install_genotypes(
+                rconn,
                 dbconn,
+                f"{rprefix}:{jobid}",
                 argparse.Namespace(
                     speciesid=meta["speciesid"],
                     populationid=meta["populationid"],
@@ -110,7 +112,9 @@ def process_bundle(dbconn: mdb.Connection,
 
         if has_pheno_file(thejob):
             phenoexit = install_pheno_files(
+                rconn,
                 dbconn,
+                f"{rprefix}:{jobid}",
                 argparse.Namespace(
                     speciesid=meta["speciesid"],
                     platformid=meta["platformid"],
-- 
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