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", ... ] }