Checklists API¶

Checklists define which metadata fields are required for sample registration. They mirror ENA metadata checklists.

List checklists¶

GET /api/v1/checklists/

curl 'http://localhost:8000/api/v1/checklists/'

Response:

[
  {"id": "ERC000011", "name": "ENA Default"},
  {"id": "ERC000020", "name": "Pathogen Clinical/Host-associated"},
  {"id": "ERC000043", "name": "Virus Pathogen"},
  {"id": "ERC000055", "name": "Farm Animal"},
  {"id": "snpchip_livestock", "name": "SNP Chip Livestock"}
]

Get checklist schema¶

GET /api/v1/checklists/{checklist_id}/schema

Returns a JSON Schema describing all fields, their types, and which are required.

curl 'http://localhost:8000/api/v1/checklists/ERC000011/schema'

Response:

{
  "id": "ERC000011",
  "name": "ENA Default",
  "required": ["organism", "tax_id"],
  "properties": {
    "organism": {"type": "string", "description": "Species name"},
    "tax_id": {"type": "integer", "description": "NCBI taxonomy ID"},
    "collection_date": {"type": "string", "format": "date"},
    "geographic_location": {"type": "string"},
    "breed": {"type": "string"},
    "host": {"type": "string"},
    "tissue": {"type": "string"},
    "developmental_stage": {"type": "string"},
    "sex": {"type": "string", "enum": ["male", "female", "unknown"]}
  }
}

Available checklists¶

ID	Name	Required Fields	Use Case
`ERC000011`	ENA Default	organism, tax_id	General-purpose genomic submissions
`ERC000020`	Pathogen Clinical/Host	organism, tax_id, isolation_source, host	Clinical pathogen samples
`ERC000043`	Virus Pathogen	organism, tax_id, strain, isolation_source	Viral genomics
`ERC000055`	Farm Animal	organism, tax_id, breed	Livestock breeding studies
`snpchip_livestock`	SNP Chip Livestock	organism, tax_id, breed	SNP genotyping arrays

How checklists are used¶

Template generation — GET /bulk-submit/template/{checklist_id} generates a TSV with all checklist fields as columns
Validation — POST /bulk-submit/validate checks required fields against the checklist
Sample creation — POST /samples/ uses checklist_id to tag the sample