make mstoolkit (more) thread safe

[rickhelmus]

Hello,

I was hoping to use mstoolkit in a multi-threaded (with a private MSReader object per thread), but ran into issues. So far, I noticed the following needs to be changed:

• Use strtok_s() (Windows) or strtok_r() instead of strtok(), as the latter uses a static buffer and is therefore not thread safe. See e.g. https://stackoverflow.com/a/54702249
• The lLastScanIndex variable defined in mzParser.h is static. Moving this to a member variable of RAMPFILE seems like a proper solution.

So far, I quickly patched the above changes, and things seem OK. But at the moment I am also only using just the mzML part of the library. If more issues will arise, I will update this issue again.

Thanks,
Rick

edit1: I made the issue more generic for threading after noticing more issues.

[mhoopmann]

Hi Rick,
Yes, I should make MSToolkit more thread safe. I can implement changes where you suggest and look for others as well.
Cheers,
Mike

[fabianegli]

To use more modern C++ language features (for better and easier programming using threads) it would also be nice to update the standard version against which MSToolkit is compiled. I made experiments with C++17 and this worked for me, but required an update to the zlib library from version 1.2.11 to 1.3.1. This issue surfaced while working on fixing an issue in Comet: UWPR/Comet#92

If you would like I'd be happy to make a PR for the zlib update change.

The new version also compiles on a MacOS which might lead to MSToolkit also supporting this platform.

[mhoopmann]

I have no problem with that. We go on holiday for the rest of the week in a few hours, so I'll make this a priority next week. Because the work involves coordinating with Jimmy, it's easiest if I do the upgrade. I'm happy to do the work.

[mhoopmann]

The upgrade to zlib 1.3.1 is complete, sitting in the dev-2.1 branch. Also, I updated VS to use v143 (VS2022) by default now. Still behind the latest, but that's for legacy purposes with some other tools.

Please keep me posted if any other thread issues arise.

[fabianegli]

The Linux build was not successful yet, #36 should fix it and adds capabilites to the Makefile so the build works on MacOS.