All routes require Basic access authentication over HTTPS unless otherwise noted.
All routes which receive request bodies expect a Content-Type of
application/json unless otherwise noted.
All request bodies must be encoded with UTF-8. All response bodies are encoded with UTF-8 unless explicitly declared otherwise by a Content-Type header.
All routes use standard HTTP status codes.
If the Content-Type of a 400 Bad Request response is
application/json, then the body will be a JSON object with at
least the key error. Additional keys may provide more
details.
Stores the request data as an enrollment document in a receiving area of the study database. Accepts any JSON object.
Stores the request data as presence/absence calls in a receiving area of the study database. Accepts any JSON object.
Stores the request data as a sequence read set document in a receiving area of the study database.
By convention, the body of the request should be a JSON object like the following:
{
"source": {
"sample": "20e1d4a2",
...
},
"reads": [
"https://server/path/to/reads_L001_R1_001.fastq.gz",
"https://server/path/to/reads_L001_R2_001.fastq.gz",
...
]
}
Stores the request data from a REDCap data entry trigger (DET) in a receiving area of the study database. Accepts any URL-encoded form data.
Stores the request data as a FHIR document in a receiving area of
the study database. This route expects a Content-Type of
application/fhir+json
Stores the request data as a consensus genome document in a receiving area of the study database.
Stores the request data as a manifest incident document in a receiving area of the study database. The body of the request should be a JSON document with the following format:
{
"collection": "2e99a5f3",
"failure_type": "Unused kit",
"incident_date": "2021-01-01",
"swab_type": "ans",
"corrective_action": "discarded",
"collection_matrix": "dry"
}
Retrieve metadata about an identifier id. id may be a full UUID or shortened barcode.
Retrieve metadata about all identifier sets.
Retrieve metadata about an identifier set name.
Make a new identifier set name. Idempotent if the set already exists. Optional description parameter may be provided. A use parameter is required for new sets and is optional if only updating description on an existing set.
Retrieve metadata about a sample record by sample barcode.
Retrieve metadata about a sample record by collection barcode.
Insert or update a sample record.
The body of the request should be a JSON object with the following format:
{
"sample_id": "20e1d4a2",
"collection_id": "2e99a5f3",
"sample_origin": "uw-reopening",
"collection_date": "2021-01-01",
"swab_site": "uw_club",
"clia_id": "9f8a58a6",
"received_date": "2021-01-01",
"aliquot_a":"123456789",
"aliquot_b":"987654321",
"aliquot_c":"135792468",
"aliquoted_date": "2021-01-01",
"rack_a":"TS01234567",
"rack_b":"TS07654321",
"rack_c":"TS08912345",
"rack_a_nickname":"COV2-123A",
"rack_b_nickname":"COV2-321B",
"rack_c_nickname":"COV2-213C",
"notes": "sample notes",
"swab_type": "ans",
"collection_matrix": "dry"
}
An "access_role" value is required for samples from specific projects to enable row-level security:
{
...
"access_role": "some_db_role"
...
}
Retrieve metadata about all identifier set uses.
Verify a list of barcodes and use types for each.
By convention, the body of the request should be a JSON array of objects like the following:
[
{
"barcode": "20e1d4a2",
"use": "sample"
},
...
]
These routes have been deprecated but continue to be supported (for now).
Stores the request data as an enrollment document in a receiving area of the study database. Accepts any JSON object.
Stores the request data as presence/absence calls in a receiving area of the study database. Accepts any JSON object.
Stores the request data as a sequence read set document in a receiving area of the study database.
By convention, the body of the request should be a JSON object like the following:
{
"source": {
"sample": "20e1d4a2",
...
},
"reads": [
"https://server/path/to/reads_L001_R1_001.fastq.gz",
"https://server/path/to/reads_L001_R2_001.fastq.gz",
...
]
}