Make raredisease orderable

[Vince-janv]

User story:

As a customer, I would like to be able to analyse dna samples with raredisease, so that I don't have to analyse my own FASTQ files.

Acceptance criteria:

• A customer should be able to place orders to be analysed with raredisease
• This option should only be available for dna samples
• Samples of different types (WGS and WES) should not be orderable within the same case
• The case added to status_db should have data_analysis=raredisease
• The data_delivery options exact same as mip-dna

Priority:

• raredisease will be ready for production not before august

Notes:

How will this be handled in the JSON file generated by the hospital LIMS? Ie. it needs to say raredisease instead of mip-dna if you don't want to have to change it manually in the orderportal after uploading the file. @annagellerbring @jemten

[Vince-janv]

Technical implementation

cg

• In orderform 1508 add the data_analysis option raredisease
• in cg/meta/orders add a RarediseaseSubmitter that inherits from CaseSubmitter (no extra functionality needed)
• Add entry for raredisease in cg.models.orders.constants.OrderType
• In cg/meta/orders/api.py:37 add an entry linking the aforementioned OrderType to the RarediseaseSubmitter

  clinical-genomics-ui

• In orderTypes add entry for raredisease.

  {
  text: 'To be decided by @annagellerbring  and @peterpru ',
  orderType: <new constant pointing to "raredisease">,
  applications: ['wgs', 'exo'],
  dataAnalysis: <new constant pointing to "raredisease">,
  }

• In deliveryOptions add entry for raredisease.

  raredisease: [same as mip-dna],

• The rendering and validation should be the same as for mip-dna orders

[seallard]

@Vince-janv Is this ready to be implemented?

[Vince-janv]

@Vince-janv Is this ready to be implemented?

We're waiting for a go-ahead from @peterpru when the pipeline is runnable in production