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Initial support for mzml parsing, update tester.sh #9

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merged 1 commit into from
Oct 6, 2017
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@mwes mwes commented Oct 5, 2017

This adds initial support for mzml parsing, producing the following columns as an example:

highest observed m/z ms level total ion current lowest observed m/z filename controllerType controllerNumber scan base peak intensity base peak m/z
2020.219487 1 5169367.5 346.5185385 exp1720-04-ds259269.raw 0 1 1 841227.38 371.1022651

I did some work to update tester.sh, but this somewhat for naught - the smallest .mzML file we have is 300+ MB and github complained about this. I commented out the tests for that for now (it does work) and left the other improvements in, such as implementing validate_csv and ensuring we always cleanup.

remote: Resolving deltas: 100% (5/5), completed with 5 local objects.
remote: error: GH001: Large files detected. You may want to try Git Large File Storage - https://git-lfs.github.com.
remote: error: Trace: 3d3bef7db6736aad460018767c2ca5a7
remote: error: See http://git.io/iEPt8g for more information.
remote: error: File reactors/lcms/lcms-0.1.0/localtest/exp1720-04-ds259269.mzML is 295.77 MB; this exceeds GitHub's file size limit of 100.00 M

@mwvaughn @jegentile I've already noticed that pulling the repo is taking a while with some of these large files as they build up. Very useful for local testing, but difficult when I'm on this weak airport Wifi. We'll need to think about a better longer term solution: #2

Also build.sh and push.sh were separated out.

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I'm going to accept this, then update a bit to demonstrate pulling in test data using the Agave CLI.

@mwvaughn mwvaughn merged commit 942463e into master Oct 6, 2017
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mwes commented Oct 6, 2017

Great, thanks!

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2 participants