This repository implements the internals of the HuBMAP data repository processing pipeline. This code is independent of the UI but works in response to requests from the data-ingest UI backend.
devtest is a mock assay for use by developers. It provides a testing tool controlled by a simple YAML file, allowing a developer to simulate execution of a full ingest pipeline without the need for real data. To do a devtest run, follow this procedure.
1) Create an input dataset, for example using the ingest UI.
Ingest operations will proceed normally from that point: 1) The state of the original dataset will change from New through Processing to QA. 2) A secondary dataset will be created, and will move through Processing to QA with an adjustable delay (see below). 3) Files specified in test.yml may be moved into the dataset directory of the secondary dataset. 4) All normal metadata will be returned, including extra metadata specified in test.yml (see below).
The format for test.yml is:
{
# the following line is required for the submission to be properly identified at assay 'devtest'
collectiontype: devtest,
# The pipeline_exec stage will delay for this many seconds before returning (default 30 seconds)
delay_sec: 120,
# If this list is present, the listed files will be copied from the submission directory to the derived dataset.
files_to_copy: ["file_068.bov", "file_068.doubles"],
# If present, the given metadata will be returned as dataset metadata for the derived dataset.
metadata_to_return: {
mymessage: 'hello world',
othermessage: 'and also this'
}
}
| API Test | |
|---|---|
| Description | Test that the API is available |
| HTTP Method | GET |
| Example URL | /api/hubmap/test |
| URL Parameters | None |
| Data Parameters | None |
| Success Response | Code: 200 Content: {"api_is_alive":true} |
| Error Responses | None |
| Get Process Strings | |
|---|---|
| Description | Get a list of valid process identifier keys |
| HTTP Method | GET |
| Example URL | /api/hubmap/get_process_strings |
| URL Parameters | None |
| Data Parameters | None |
| Success Response | Code: 200 Content: {"process_strings":[...list of keys...]} |
| Error Responses | None |
| Get Version Information | |
|---|---|
| Description | Get API version information |
| HTTP Method | GET |
| Example URL | /api/hubmap/version |
| URL Parameters | None |
| Data Parameters | None |
| Success Response | Code: 200 Content: {"api":API version, "build":build version} |
| Error Responses | None |
| Request Ingest | |
|---|---|
| Description | Cause a workflow to be applied to a dataset in the LZ. The full dataset path is computed from the data parameters. |
| HTTP Method | POST |
| Example URL | /api/hubmap/request_ingest |
| URL Parameters | None |
| Data Parameters | provider : one of a known set of providers, e.g. 'Vanderbilt' submission_id : unique identifier string for the data submission process : one of a known set of process names, e.g. 'MICROSCOPY.IMS.ALL' |
| Success Response | Code: 200 Content:{ "ingest_id":"some_unique_string", "run_id":"some_other_unique_string" } |
| Error Responses | Bad Request: Code: 400 Content strings: "Must specify provider to request data be ingested" "Must specify sample_id to request data be ingested" "Must specify process to request data be ingested" "NAME is not a known ingestion process" Unauthorized: Code: 401 Content strings: "You are not authorized to use this resource" Not Found: Code: 404 Content strings: "Resource not found" "Dag id _DAGID not found" Server Error: Code: 500 Content strings: "An unexpected problem occurred" "The request happened twice?" "Attempt to trigger run produced an error: ERROR" |