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Run opentrons_simulate inside tempdir and use temp-copied inputs #32

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Merged
Gonza10V merged 1 commit into from
Jan 17, 2026
Merged

Run opentrons_simulate inside tempdir and use temp-copied inputs #32

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11 changes: 7 additions & 4 deletions src/buildcompiler/robotutils.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,5 @@
import sbol2
import json
import os
import shutil
import subprocess
import tempfile
Expand Down Expand Up @@ -131,11 +130,15 @@ def run_opentrons_script_with_json_to_zip(

# Run inside temp dir so relative-path outputs land in tmpdir (and get zipped)

# Run script (which has opentrons script hardcoded) using JSON file
log = subprocess.run(["opentrons_simulate", opentrons_script_path, json_file_path], capture_output=True).stdout
# Run script (which has opentrons script hardcoded) using JSON file
log = subprocess.run(
["opentrons_simulate", str(tmp_script), str(tmp_json)],
capture_output=True,
cwd=tmpdir,
Comment on lines +133 to +137
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@chatgpt-codex-connector chatgpt-codex-connector bot Jan 17, 2026

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P1 Badge Keep simulator cwd where relative inputs exist

Running opentrons_simulate with cwd=tmpdir means the protocol executes in a directory that does not contain the files/ subfolder, but the protocol script still hardcodes open("files/assemblyplan_output.json", ...) and writes output into files (see files/run_sbol2assembly_libre.py:305–311). Because only assemblyplan_output.json is copied to the tmpdir root, this change causes a FileNotFoundError (or later failure when writing the XLSX) for the standard workflow where the script expects the repo’s files/ directory. Unless you also recreate files/ inside the tempdir or adjust the protocol to use the passed JSON path, the simulator will now fail before producing a zip.

Useful? React with 👍 / 👎.

).stdout

# Save log to a file in the temporary directory
with open(os.path.join(tmpdir, "build_log.txt"), "wb") as log_file:
with open(tmpdir / "build_log.txt", "wb") as log_file:
log_file.write(log)

# Always include logs in the zip
Expand Down