Error with Rust mzml library

[ypriverol]

@RalfG I found this error with the rust library:

pyo3_runtime.PanicException: Expected a dateTime value conforming to ISO 8601 standard: ParseError(TooShort)
thread '<unnamed>' panicked at /opt/conda/conda-bld/ms2rescore-rs_1737374122806/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/mzdata-0.39.0/src/io/mzml/reading_shared.rs:886:74:
Expected a dateTime value conforming to ISO 8601 standard: ParseError(TooShort)
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace
Process SpawnPoolWorker-4:
Traceback (most recent call last):
  File "/usr/local/lib/python3.11/multiprocessing/process.py", line 314, in _bootstrap
    self.run()
  File "/usr/local/lib/python3.11/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/usr/local/lib/python3.11/multiprocessing/pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
                    ^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.11/site-packages/ms2pip/core.py", line 911, in _process_spectra
    for spectrum in read_spectrum_file(spec_file):
  File "/usr/local/lib/python3.11/site-packages/ms2pip/spectrum_input.py", line 33, in read_spectrum_file
    spectra = get_ms2_spectra(str(spectrum_file))
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
pyo3_runtime.PanicException: Expected a dateTime value conforming to ISO 8601 standard: ParseError(TooShort)
thread '<unnamed>' panicked at /opt/conda/conda-bld/ms2rescore-rs_1737374122806/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/mzdata-0.39.0/src/io/mzml/reading_shared.rs:886:74:
Expected a dateTime value conforming to ISO 8601 standard: ParseError(TooShort)
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace
Process SpawnPoolWorker-3:
Traceback (most recent call last):
  File "/usr/local/lib/python3.11/multiprocessing/process.py", line 314, in _bootstrap
    self.run()
  File "/usr/local/lib/python3.11/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/usr/local/lib/python3.11/multiprocessing/pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
                    ^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.11/site-packages/ms2pip/core.py", line 911, in _process_spectra
    for spectrum in read_spectrum_file(spec_file):
  File "/usr/local/lib/python3.11/site-packages/ms2pip/spectrum_input.py", line 33, in read_spectrum_file
    spectra = get_ms2_spectra(str(spectrum_file))

mzml: https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/quantms-benchmark/01321_E03_P013560_B00_N21_R1.mzML

[ypriverol]

Can we have a method the allows an external library to pass the psm with the spectra instead of relying in this function get_ms2_spectra(str(spectrum_file)) I have found multiple errors with it in production. I fix some of them but It would be nice if we can have the possibility to load the spectra.

[jonasscheid]

@RalfG running into the same issue with 3.1.4. Would CompOmics/ms2rescore-rs#4 solve this issue?

[steffenlem]

I have also come across this issue. In my tests, v3.0.3 still worked fine, but v3.1.1 & v3.1.4 both throw the error described above

[RalfG]

Thanks for reporting everyone! And thanks for fixing in CompOmics/ms2rescore-rs#4, @mobiusklein.

@ypriverol Unfortunately in the current structure of MS²Rescore, each feature generator reads the spectrum files itself. For instance, the MS²PIP feature generator is only passed the PSMList and the configuration which points to the spectrum files. If you find other issues in spectrum reading, do let us know!

[RalfG]

Should be fixed with ms2rescore-rs v0.4.2: https://pypi.org/project/ms2rescore-rs/0.4.2/. Let me know if it worked, @ypriverol.