Ingestion workflow example¶
1. Create a project at /api/projects
:
{
"title": "Test Project",
"description": "About Test Project ..."
}
201 Response example:
{
"identifier": "998a36b2-7251-445d-81de-01a5affc5523",
"datasets": [],
"title": "Test Project",
"description": "About Test Project ...",
"created": "2020-10-15T20:17:03.029395Z",
"updated": "2020-10-15T20:17:03.029395Z"
}
2. Create a dataset at /api/datasets
:
Add project identifier from project response.
{
"project": "998a36b2-7251-445d-81de-01a5affc5523",
"title": "Test Dataset",
"description": "About Test Dataset ...",
"data_use": {
"consent_code": {
"primary_category": {
"code": "GRU"
},
"secondary_categories": [
{
"code": "RU"
}
]
},
"data_use_requirements": [
{
"code": "COL"
}
]
}
}
201 Response example:
{
"identifier": "86766cd6-f6bd-4d09-9d8a-308df4dd1fa1",
"table_ownership": [],
"title": "Test Dataset",
"description": "About Test Dataset ...",
"contact_info": "",
"data_use": {
"consent_code": {
"primary_category": {
"code": "GRU"
},
"secondary_categories": [
{
"code": "RU"
}
]
},
"data_use_requirements": [
{
"code": "COL"
}
]
},
"linked_field_sets": [],
"version": "version_2020-10-15 20:17:52.412173+00:00",
"created": "2020-10-15T20:17:52.418029Z",
"updated": "2020-10-15T20:17:52.418029Z",
"project": "c488af39-d49b-4764-aa19-b86801220060"
}
3. Create a table ownership at /api/table_ownership
:
Generate UUID for table_id
and add dataset identifier from dataset response.
{
"table_id": "e08ff220-0f26-11eb-adc1-0242ac120002",
"service_id": "metadata_service",
"service_artifact": "metadata",
"dataset": "86766cd6-f6bd-4d09-9d8a-308df4dd1fa1"
}
201 Response example:
{
"table_id": "e08ff220-0f26-11eb-adc1-0242ac120002",
"service_id": "metadata_service",
"service_artifact": "metadata",
"dataset": "86766cd6-f6bd-4d09-9d8a-308df4dd1fa1"
}
4. Create a table at /api/tables
:
Add table_id as ownership_record
.
{
"ownership_record": "e08ff220-0f26-11eb-adc1-0242ac120002",
"name": "metadata",
"data_type": "phenopacket"
}
5. Ingest phenopackets at /private/ingest
:
Add table_id
.
Specify path to the phenopackets data.
{
"table_id": "e08ff220-0f26-11eb-adc1-0242ac120002",
"workflow_id": "phenopackets_json",
"workflow_params": {
"phenopackets_json.json_document": "path/to/phenopackets.json"
},
"workflow_outputs": {
"json_document": "path/to/phenopackets.json"
}
}