Strip .json extension from CSV filenames in json2csv (Fixes #1679)

[Mohit-Ak]

Problem

Fixes #1679.

When running plantcv-run-workflow, the CSV files it generates from the JSON
results keep the .json extension embedded in their names. For example, with a
config pointing at ./results/output_control.json, the workflow writes:

output_control.json-single-value-traits.csv
output_control.json-multi-value-traits.csv

instead of the expected output_control-single-value-traits.csv.

Root cause

In plantcv/parallel/cli.py, the JSON results filename is passed directly as the
CSV prefix:

plantcv.utils.json2csv(config.json, config.json)

json2csv then builds its outputs as csv_prefix + "-single-value-traits.csv",
so the .json extension ends up glued in front of the -single-value-traits.csv
suffix. Anyone calling json2csv directly with a .json-suffixed prefix hits the
same thing.

Fix

Strip a trailing .json extension from csv_prefix inside json2csv before the
output filenames are assembled. Doing it in json2csv covers both the automatic
workflow call and any direct call, so the whole bug class is handled in one place
rather than only patching the single reported call site.

if csv_prefix.endswith(".json"):
    csv_prefix = csv_prefix[:-len(".json")]

Testing

Added a regression test, test_json2csv_json_prefix, that calls json2csv with a
.json-suffixed prefix and asserts the output is exports-single-value-traits.csv
and not exports.json-single-value-traits.csv.

• The new test fails before the fix (writes exports.json-single-value-traits.csv)
  and passes after it.
• pytest tests/utils/ — 17 passed.
• pytest tests/parallel/ — 37 passed (this exercises the run-workflow →
  json2csv path).
• flake8 --max-line-length=127 (the repo's configured limit from
  .deepsource.toml) is clean on both changed files.

[deepsource-io]

DeepSource Code Review

We reviewed changes in 1f40fae...e892786 on this pull request. Below is the summary for the review, and you can see the individual issues we found as inline review comments.

See full review on DeepSource ↗

PR Report Card

Overall Grade

Security   Reliability   Complexity   Hygiene

Code Review Summary

Analyzer	Status	Updated (UTC)	Details
Python		Jul 10, 2026 5:02p.m.	Review ↗
Code coverage		Jul 10, 2026 5:32p.m.	Review ↗

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[nfahlgren]

@all-contributors please add @Mohit-Ak for code, testing

[allcontributors]

@nfahlgren

I've put up a pull request to add @Mohit-Ak! 🎉