This API provides endpoints to upload validate and check status of a batch.
A visual OpenAPI documentation is available at: https://qlin-me.cqgc.hsj.rtss.qc.ca
Bellow are the most used endpoints a user may want to know about.
- authentication => will grant a
token
for useremail
+password
- upload metadata => validate and save a
metadata
bybatch_id
- status of batch => summary of the current state of the batch by
batch_id
In order to use the API the user has to get a token
using the auth endpoint:
Example
curl --location 'https://qlin-me.cqgc.hsj.rtss.qc.ca/api/v1/auth/login?email=foo%40bar.com&password=<user_pwd>'
All specials characters in email or password have to be percent encoded: https://www.w3schools.com/tags/ref_urlencode.asp
OpenAPI Doc. ref. : https://qlin-me.cqgc.hsj.rtss.qc.ca/#tag/Authentication/operation/authLoginByEmailPassword
Will create or update the metadata
for the batch_id
if valid, otherwise return all the errors to the user.
curl --location 'https://qlin-me.cqgc.hsj.rtss.qc.ca/api/v1/batch/<batch_id>' \
--header 'Content-Type: application/json' \
--header 'Authorization: Bearer <token>' \
--data '{
"submissionSchema" : "CQGC_Germline",
"analyses" : [...]
}'
OpenAPI Doc. ref. : https://qlin-me.cqgc.hsj.rtss.qc.ca/#tag/Batch/operation/batchCreateUpdate
Will validate and return errors of both metadata
and cram, tsv, json, vcfs ...
files by batch_id
.
curl --location 'https://qlin-me.cqgc.hsj.rtss.qc.ca/api/v1/batch/<batch_id>/status' \
--header 'Authorization: Bearer <token>'
Note: That endpoint also works with metadata
JSON file deployed manually though aws-cli
on S3.
OpenAPI Doc. ref. : https://qlin-me.cqgc.hsj.rtss.qc.ca/#tag/Batch/operation/batchStatus