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tech debt: wire Transfer_VIGAS, VIGASP_ID, and NIRD upload paths from SampleSheet instead of test values #205

Description

@georgemarselis-nvi

Currently both the IRIDA upload target and the NIRD tarball destination are
sidelined to test values pending resolution of upstream dependencies.

VIGASP (IRIDA):

  • Transfer_VIGAS field controls whether a sample is uploaded to VIGASP
  • VIGASP_ID field specifies the target IRIDA project ID per sample
  • currently sidelined to project 154 for testing

NIRD:

  • tarballs currently go to test location
  • production NIRD path not wired from SampleSheet
  • QC tarball destination unresolved - production upload of QC tarballs not
    yet decided

Required behaviour:

  • both VIGASP_ID and NIRD upload path read from SampleSheet per sample
  • upload state machine and NIRD transport receive paths from sample metadata,
    not from constants
  • QC tarball handling must be resolved before NIRD paths can go to production

Blocked by: #195 (SampleSheet-with-path-names fallback removal) - once
ShinyLIMS is the source of truth for paths, both VIGASP_ID and NIRD paths
should come from ShinyLIMS via the same mechanism.

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