Registering Schemas

Registering new Schemas

The same steps will apply when updating a previous schema.

Using the Swagger UI

Locate your endpoint of interest

From the schema dropdown, find the POST RegisterAnalysisType endpoint.

Select Try it out and input your desired values

Enter your authorization token in the authorization field and your new schema inside the request field.

Select Execute

Expected responses as well as response codes and descriptions, are conviently documented within Swagger-UI.

Verifying Schemas

To verify your schema has successfully been added, you can use the GET ListAnalysisTypes endpoint found under the Schema dropdown. If updating a pre-existing schema, use the GET GetAnalysisTypeVersion endpoint.

Using a Curl command

The following curl command makes a POST request with the required authorization tokens, headers and data:

bash

curl -X POST "https://song.virusseq-dataportal.ca/schemas" -H "accept: */*" -H "Authorization: AUTHORIZATION" -H "Content-Type: application/json" -d "{ \"name
\":\"example_demo\", \"schema\": { \"type\":\"object\", \"required\":[ \"experiment\" ], \"properties\":{ \"experiment\": { \"type\": \"object\", \"required\": [\"experiment_type\"], \"propertyNames\": { \"experiment_type\":{ \"type\":\"string\", \"enum\": [\"WGS\",\"RNA-Seq\"] }, } } } }}"

Using Python

The following script imports the necessary libraries and sends a POST request to a specified URL endpoint with a new schema. It includes authorization using a JWT or API token. If the request fails (status code is not 200), it prints an error message.

python

import json
import requests
### Verify your SONG URL either through the swagger portal or hosting terminal
url="https://song.virusseq-dataportal.ca"
### Set endpoint
endpoint="%s/schemas" % (url)
### Supply authorized JWT or API token
api_token="AUTHORIZATION"
### Format contents
headers={"accept":"*/*",
         "Authorization":"Bearer %s" % (api_token),
         "Content-Type": "application/json"
        }
### Supply schema as a json either by reading a local file or through a request
payload = new_schema
### Run POST
post_response=requests.post(endpoint, json=payload,headers=headers)
### Complain only when an attempt fails
if post_response.status_code!=200:
print("error calling patch endpoint",endpoint,post_response.status_code)

Making Schemas

Managing Schemas

Song github

Registering new Schemas