From a281939a68a0ecfe299f2e68c411ebc9ff1e1469 Mon Sep 17 00:00:00 2001
From: Josh Sumner <51797700+joshqsumner@users.noreply.github.com>
Date: Tue, 21 Jan 2025 14:31:31 -0600
Subject: [PATCH 1/2] adding json2csv to run-workflow
---
plantcv/parallel/cli.py | 10 ++++++++++
1 file changed, 10 insertions(+)
diff --git a/plantcv/parallel/cli.py b/plantcv/parallel/cli.py
index 834724c85..bec7670b6 100644
--- a/plantcv/parallel/cli.py
+++ b/plantcv/parallel/cli.py
@@ -5,6 +5,7 @@
import time
import datetime
import plantcv.parallel
+import plantcv.utils
import tempfile
import shutil
@@ -119,6 +120,15 @@ def main():
print(f"Processing results took {process_results_clock_time} seconds.", file=sys.stderr)
###########################################
+ # Convert json results to csv files
+ ###########################################
+ # Convert results start time
+ process_results_start_time = time.time()
+ print("Converting json to csv... ", file=sys.stderr)
+ plantcv.utils.json2csv(config.json, config.json)
+ print(f"Processing results took {process_results_clock_time} seconds.", file=sys.stderr)
+ ###########################################
+
# Cleanup
if config.cleanup is True:
shutil.rmtree(config.tmp_dir)
From 9c5b6a297653ea285009c395f2f101712f5f2012 Mon Sep 17 00:00:00 2001
From: Josh Sumner <51797700+joshqsumner@users.noreply.github.com>
Date: Wed, 22 Jan 2025 15:13:22 -0600
Subject: [PATCH 2/2] fixing time tracking
---
plantcv/parallel/cli.py | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/plantcv/parallel/cli.py b/plantcv/parallel/cli.py
index bec7670b6..919ca9a55 100644
--- a/plantcv/parallel/cli.py
+++ b/plantcv/parallel/cli.py
@@ -123,10 +123,11 @@ def main():
# Convert json results to csv files
###########################################
# Convert results start time
- process_results_start_time = time.time()
+ convert_results_start_time = time.time()
print("Converting json to csv... ", file=sys.stderr)
plantcv.utils.json2csv(config.json, config.json)
- print(f"Processing results took {process_results_clock_time} seconds.", file=sys.stderr)
+ convert_results_clock_time = time.time() - convert_results_start_time
+ print(f"Processing results took {convert_results_clock_time} seconds.", file=sys.stderr)
###########################################
# Cleanup