meek0/clin-qlin-me

Qlin-Me

Introduction

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

Step by step

Bellow are the most used endpoints a user may want to know about.

• authentication => will grant a token for user email + password
• upload metadata => validate and save a metadata by batch_id
• status of batch => summary of the current state of the batch by batch_id

Authentication

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

Upload metadata

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

Status of a batch

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