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Figure out azure authentication in tests #8612

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lbergelson opened this issue Dec 9, 2023 · 0 comments
Open

Figure out azure authentication in tests #8612

lbergelson opened this issue Dec 9, 2023 · 0 comments
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azure tests

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@lbergelson
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We need a way to read files from azure in our tests. This means one of:

  1. adding a service account (or whatever the azure equivalent is) and the ability to generate SAS tokens
  2. finding a way to make a SAS token that has a very long expiration time
lbergelson added a commit that referenced this issue Dec 9, 2023
@lbergelson @nalinigans
Allow GenomicsDBImport to connect to az:// files without interference (…
2ad4a3e 
…#8438)

* GATK's lack of support for az:// URIs means that although GenomicsDB can
  natively read them, parts of the java code crash when interacting with them
* Adding --avoid-nio and --header arguments
  These allow disabling all of the java interaction with the az:// links
  and simply passing  them through to genomicsdb
  This disables some safeguards but allows operating on files in azur
* Update GenomicsDB version to 1.5.1 for azure improved support

* There are no direct tests on azure since we do not yet have any infrastructure
  to generate the necessary tokens, there is a disabled test which requires
  #8612 before we can enable it.

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Co-authored-by: Nalini Ganapati <[email protected]>
Co-authored-by: Nalini Ganapati <[email protected]>
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