From f1d16b04536868933343f6e108553d99b5657af5 Mon Sep 17 00:00:00 2001
From: lb584 <lb584@cam.ac.uk>
Date: Fri, 29 Dec 2023 11:30:49 +0000
Subject: [PATCH] adding csvs as well as ncs for RIE files while waiting for
EPI pipeline to stop expecting csvs by default
---
coordinator/EnvSuitPipeline.py | 7 +++++++
1 file changed, 7 insertions(+)
diff --git a/coordinator/EnvSuitPipeline.py b/coordinator/EnvSuitPipeline.py
index 5fb07ec..0cc0ea8 100644
--- a/coordinator/EnvSuitPipeline.py
+++ b/coordinator/EnvSuitPipeline.py
@@ -286,6 +286,13 @@ def run_pipeline(pipeline_config, region, dateString, extracted = False, prevent
os.makedirs(strain_outPath)
shutil.copy(resultFile,strain_outFile)
+
+ # todo - Add a flad to this part of the code to enable/dosable csv writing as an option
+ resultCSVFile = envSuitPath + 'RIE.csv'
+ if os.path.isfile(resultCSVFile):
+ strain_outFile = strain_outPath + '/RIE_value.csv'
+ shutil.copy(resultCSVFile,strain_outFile)
+
logger.info(f"{strain} result successfully created and moved to {strain_outPath}/")
logger.info('SUCCESSFULLY FINISHED')
--
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