Allen Institute Mock LIMS implementation

Tested on Python 3.8 with Flask 1.1.2

Getting Started

1. Download source

   git clone https://github.com/KitwareMedical/AllenInstituteMockLIMS
   cd AllenInstituteMockLIMS

2. Create virtual environment

   python3 -m venv venv
   . venv/bin/activate

3. Install requirements

   pip install -r requirements.txt

4. Start the flask application

   python -m flask run

Endpoints:

Fetch Specimen Metadata

GET /specimen_metadata/view

Returns json metadata of a specimen based on the kind of metadata.

Query Parameters

Parameter	Type	Description
specimen_id	integer	Unique id property of the Specimen entry in the LIMS that the metadata is associated with
kind	string	The kind of metadata that is to be retrieved (eg. "IVSCC cell locations")
version_number (opt.)	integer	The version of the metadata, which may be defined by the kind of metadata

Response

Success 200

{
  "version_number": 2,
  "data": {"foo": "bar"}
}

Error

Status Code	Body
500	{ "status": 500, "message": "Something went wrong" }
404	{ "status": 404, "message": "Record not found" }
400	{ "status": 400, "message": "Param foo is missing" }

Sample Call

Request:

GET /specimen_metadata/view?specimen_id=1234&kind=IVSCC%20cell%20locations

Response:

{
  "version_number": 2,
  "data": {"foo": "bar"}
}

Notes

If version_number is not specified, then the current version will be returned

Store Specimen Metadata

POST /specimen_metadata/store

Stores json metadata of a specimen based on the kind of metadata.

URL Params

None. If URL params are provided, the request will be rejected with code 400

POST body

Required:

Value	Type	Description
specimen_id	integer	Unique id property of the Specimen entry in the LIMS that the metadata is associated with
kind	string	The kind of metadata that is to be retrieved (eg. "IVSCC cell locations")
data	object	The metadata to be stored. This should be a vaid JSON object

Example Body:

{
    "specimen_id": 1234,
    "kind": "IVSCC cell locations",
    "data": {"foo": "bar"}
}

Headers

Header	Value
Content-Type	application/json

Response

Success 200

{
  "id": 1234,
  "version_number": 2
}

Error

Status Code	Body
500	{"status": 500, "message": "Something went wrong"}
404	{"status": 404, "message": "Record not found"}
400	{"status": 400, "message": "Param foo is missing"}

Sample Call

Request:

POST /specimen_metadata/store

{
  "specimen_id": 1234,
  "kind": "IVSCC cell locations",
  "data": {"foo": "bar"}
}

Response:

{
  "id": 1234,
  "version_number": 2
}