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Sequence collection data models without using contig alias #106

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tcezard opened this issue May 23, 2023 · 1 comment
Open

Sequence collection data models without using contig alias #106

tcezard opened this issue May 23, 2023 · 1 comment

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@tcezard
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tcezard commented May 23, 2023

What data/java model would be appropriate for storing sequence collections
We need to be able to represent all 3 levels of sequence collections:

The top level digest S3LCyI788LE6vq89Tc_LojEcsMZRixzP
The compact level

{
    "sequences": "EiYgJtUfGyad7wf5atL5OG4Fkzohp2qe",
    "lengths": "5K4odB173rjao1Cnbk5BnvLt9V7aPAa2",
    "names": "g04lKdxiYtG3dOGeUC5AdKEifw65G0Wp"
}

The canonical level

{
  "lengths": [
    "1216",
    "970",
    "1788"
  ],
  "names": [
    "A",
    "B",
    "C"
  ],
  "sequences": [
    "76f9f3315fa4b831e93c36cd88196480",
    "d5171e863a3d8f832f0559235987b1e5",
    "b9b1baaa7abf206f6b70cf31654172db"
  ]
}

Additional question: Can we add another property to a sequence collection in this datamodel

@waterflow80
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I think this response may be relevant here.
We've concluded that this proposed model needs some enhancements, because it calls for having dynamic tables, which is not supported by Spring boot (or at least not efficient at), and may raise a lot of data migration issues in the future.

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