ProteoBench is an open and collaborative platform for community-curated benchmarks for proteomics data analysis pipelines. Our goal is to allow a continuous, easy, and controlled comparison of proteomics data analysis workflows.
Describe the bug
I have an error message after pressing "I really want to upload it" with Proline data. Everything worked OK before
To Reproduce
Steps to reproduce the behavior:
upload Proline Excel file
Click on parse and bench
upload the same excel file for metadata
check that the metadata is correct and press I really want to upload it
See error:
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xad in position 41: invalid start byte
Traceback:
File "/home/ubuntu/micromamba/envs/proteobench/lib/python3.12/site-packages/streamlit/runtime/scriptrunner/script_runner.py", line 600, in _run_script
exec(code, module.__dict__)
File "/mnt/data/git/ProteoBench/webinterface/pages/DDA_Quant_ion.py", line 679, in <module>
StreamlitUI()
File "/mnt/data/git/ProteoBench/webinterface/pages/DDA_Quant_ion.py", line 56, in __init__
self._main_page()
File "/mnt/data/git/ProteoBench/webinterface/pages/DDA_Quant_ion.py", line 157, in _main_page
self._populate_results()
File "/mnt/data/git/ProteoBench/webinterface/pages/DDA_Quant_ion.py", line 217, in _populate_results
self.generate_results("", None, None, False, None)
File "/mnt/data/git/ProteoBench/webinterface/pages/DDA_Quant_ion.py", line 614, in generate_results
pr_url = self.make_submission_webinterface(params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/data/git/ProteoBench/webinterface/pages/DDA_Quant_ion.py", line 366, in make_submission_webinterface
self.ionmodule.write_intermediate_raw(
File "/home/ubuntu/micromamba/envs/proteobench/lib/python3.12/site-packages/proteobench/modules/dda_quant_base/module.py", line 217, in write_intermediate_raw
f.write(",\n".join(_file.getvalue().decode("utf-8") for _file in param_loc))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ubuntu/micromamba/envs/proteobench/lib/python3.12/site-packages/proteobench/modules/dda_quant_base/module.py", line 217, in <genexpr>
f.write(",\n".join(_file.getvalue().decode("utf-8") for _file in param_loc))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Expected behavior
the PR is sent to proteobot as it should. But instead of the error message I should get a confirmation that the PR was sent, and the link to proteobot PR (It was the PR https://github.com/Proteobot/Results_quant_ion_DDA/pull/205)
Describe the bug I have an error message after pressing "I really want to upload it" with Proline data. Everything worked OK before
To Reproduce Steps to reproduce the behavior:
Expected behavior the PR is sent to proteobot as it should. But instead of the error message I should get a confirmation that the PR was sent, and the link to proteobot PR (It was the PR https://github.com/Proteobot/Results_quant_ion_DDA/pull/205)
Screenshots