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Provide customers with a valid JSON-file for FASTQ and RML orders #4272

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Vince-janv opened this issue Mar 7, 2025 · 2 comments
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@Vince-janv
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Description

In this ticket the customers would like guidance in how to automate their ordering for RML and FASTQ orders.

Lacking a proper auth-solution I say we exclude submission directly to the submit-order endpoint. Instead we should aim for providing clear and valid JSON example for them to replicate and be able to upload in the orderportal. Essentially describing which fields in cg.models.orders.json_sample.JsonSample need to be specified for the aforementioned order types.

Acceptance criteria

  • The customers receive an example JSON-file for FASTQ orders
  • The customers receive an example JSON-file for RML orders
  • The customer receives a description of the included fields and the values they might take
@islean islean self-assigned this Mar 13, 2025
@islean
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islean commented Mar 13, 2025

Depends on #4286.

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islean commented Mar 13, 2025

With the linked PR, the following two sample files can be uploaded:

Fastq:

{
  "comment": "",
  "customer": "custXXX",
  "name": "order-name",
  "samples": [
    {
      "application": "WGSWPFR400",
      "comment": "Free text where you can give additional info",
      "container": "Tube",
      "container_name": "name-for-your-container",
      "data_analysis":"fastq",
      "data_delivery":"fastq",
      "elution_buffer":"Tris-HCl",
      "name": "sample-1",
      "priority": "research",
      "quantity": "200",
      "require_qc_ok": true,
      "sex": "male",
      "source": "blood",
      "subject_id": "subject-id-1",
      "volume": "111",
      "well_position": ""
    },
    {
      "application": "WGSWPFR400",
      "comment": "Free text where you can give additional info",
      "container": "96 well plate",
      "container_name": "plate-name",
      "data_analysis":"fastq",
      "data_delivery":"fastq",
      "elution_buffer":"Other",
      "name": "sample-2",
      "priority": "standard",
      "quantity": "200",
      "require_qc_ok": false,
      "sex": "female",
      "source": "blood",
      "subject_id": "subject-id-2",
      "volume": "111",
      "well_position": "A:1"
    }
  ]
}

RML:

{
  "name": "order-name",
  "customer": "custXXX",
  "comment": "comment",
  "samples": [{
    "name": "rml-sample-1",
    "application": "RMLP05R800",
    "control": "",
    "data_analysis": "rml",
    "data_delivery": "fastq",
    "comment": "A:1",
    "volume": "111",
    "concentration": "10",
    "concentration_sample": "293.04000",
    "pool": "1234567",
    "rml_plate_name": "",
    "well_position_rml": "",
    "index": "NEXTflex® Unique Dual Index Barcodes 1 - 96",
    "index_number": "7",
    "priority": "standard"
  },
  {
    "name": "rml-sample-2",
    "application": "RMLP05R800",
    "control": "negative",
    "data_analysis": "rml",
    "data_delivery": "fastq",
    "comment": "C:1",
    "volume": "111",
    "concentration": "10",
    "concentration_sample": "238.38000",
    "pool": "1234567",
    "rml_plate_name": "",
    "well_position_rml": "",
    "index": "NEXTflex® Unique Dual Index Barcodes 1 - 96",
    "index_number": "31",
    "priority": "standard"
  }
]}

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