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Update snappy-java and migrate mjson to org.json to address CVEs #1670

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merged 6 commits into from
Aug 1, 2023

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bbimber
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@bbimber bbimber commented Jun 25, 2023

There are CVEs reported for mjson, which does not appear to be an actively maintained project:

https://nvd.nist.gov/vuln/detail/CVE-2023-34611
bolerio/mjson#40

and also snappy-java:

https://nvd.nist.gov/vuln/detail/CVE-2023-34453
https://nvd.nist.gov/vuln/detail/CVE-2023-34455

the latest snappy-java has been patched.

This PR does two things:

  • It updates to the latest snappy-java
  • It migrates from mjson (which appears to be a dead project) to org.json. From what I can tell mjson wasnt being used for anything other than pretty basic JSON object manipulation. In theory these should function about the same.

@lbergelson
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@bbimber Thank you!

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Thank you @bbimber

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bbimber commented Jul 31, 2023

@lbergelson were there any other changes you needed on this? Also, and this isnt urgent, but is there a defined release schedule on htsjdk? Thanks.

@lbergelson lbergelson merged commit 44817ee into samtools:master Aug 1, 2023
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@lbergelson
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Ack, I had it set to rebase instead of squash. Sorry for commit spam.

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Thanks for doing this. I was thinking of doing a release very soon.

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