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Info! If you have issues with the certificate you can perform connexions without verifing the ceriticate using the --insecure flag in curl or the parameter verify=False in the Python requests.

Launching a job

To be able to launch a job, do a POST to https://www.cancergenomeinterpreter.org/api/v1 providing your email and token:
                    
import requests
headers = {'Authorization': 'example@email.com your_token'}
payload = {'cancer_type': 'CANCER TYPE', 'title': 'Title of the run'}
r = requests.post('https://www.cancergenomeinterpreter.org/api/v1',
                headers=headers,
                files={
                        'mutations': open('/paht/to/your/mutations.ext', 'rb'),
                        'cnas': open('/paht/to/another/file.ext', 'rb'),
                        'translocations': open('/paht/to/yet/another/file.ext', 'rb')
                        },
                data=payload)
r.json()
                    
                
                    
curl --request POST \
  --url https://www.cancergenomeinterpreter.org/api/v1 \
  --header 'Authorization: example@email.com your_token' \
  -F "mutations=@/paht/to/your/file.ext" \
  -F "cnas=@/paht/to/another/file.ext" \
  -F "translocations=@/paht/to/yst/another/file.ext" \
  -F "cancer_type=CANCER TYPE" \
  -F "title=Title of the run"
                    
                
The possible parameters for a job are:
cancer_type
cancer type under analysis. This parameter is required and must be one of the values between brackets that you can find in the analysis page.
title
title for this run. This paremter is optional
cnas
file containing the CNA data. Find information about the formats in the FAQs page.
mutations
file containing the mutation data. Find information about the formats in the FAQs page.
translocations
file containing the translocation data. Find information about the formats in the FAQs page.
Note: the files (cnas, mutations and traslocations) are optional, but at least one is required.

Getting the identifiers

To get a list with the identifiers of your jobs do a GET to https://www.cancergenomeinterpreter.org/api/v1
                    
import requests
headers = {'Authorization': 'example@email.com your_token'}
r = requests.get('https://www.cancergenomeinterpreter.org/api/v1', headers=headers)
r.json()
                    
                
                    
curl --request GET \
  --url https://www.cancergenomeinterpreter.org/api/v1 \
  --header 'Authorization: example@email.com your_token'
                    
                

Accessing a job information

To get the basic information from a job https://www.cancergenomeinterpreter.org/api/v1/job_id
                    
import requests
headers = {'Authorization': 'example@email.com your_token'}
r = requests.get('https://www.cancergenomeinterpreter.org/api/v1/job_id', headers=headers)
r.json()
                    
                
                    
curl --request GET \
  --url https://www.cancergenomeinterpreter.org/api/v1/job_id \
  --header 'Authorization: example@email.com your_token'
                    
                

Actions on a job

In addition to getting the basic job information, there are a few other operations you can perform on the job data and its results. The different actions are:
download
download the job results
logs
get the logs of the job execution. It can be useful to access this information while the job is executing
To perform any of those operations, you only need to make a get indicating the action to be performed https://www.cancergenomeinterpreter.org/api/v1/job_id?action=action_to_be_performed
                    
import requests
headers = {'Authorization': 'example@email.com your_token'}
payload={'action':'logs'}
r = requests.get('https://www.cancergenomeinterpreter.org/api/v1/job_id', headers=headers, params=payload)
r.json()
                    
                
                    
curl --request GET \
  --url https://www.cancergenomeinterpreter.org/api/v1/job_id \
  --header 'Authorization: example@email.com your_token' \
  -G --data 'action=logs'
                    
                
When downloading the results, it is likely that you want to store the results file. The extension of such a file is: zip
                    
import requests
headers = {'Authorization': 'example@email.com your_token'}
payload={'action':'download'}
r = requests.get('https://www.cancergenomeinterpreter.org/api/v1/job_id', headers=headers, params=payload)
with open('file.zip', 'wb') as fd:
    fd.write(r._content)
                    
                
                    
curl --request GET \
  --url https://www.cancergenomeinterpreter.org/api/v1/job_id \
  --header 'Authorization: example@email.com your_token' \
  -G --data 'action=download' \
  -o file.zip
                    
                

Deleting a job

To be able to delete a job, do a DELETE to https://www.cancergenomeinterpreter.org/api/v1 providing the job identifier your email and token:
                    
import requests
headers = {'Authorization': 'example@email.com your_token'}
r = requests.delete('https://www.cancergenomeinterpreter.org/api/v1/job_id', headers=headers)
r.json()
                    
                
                    
curl --request DELETE \
  --url https://www.cancergenomeinterpreter.org/api/v1/jobid \
  --header 'Authorization: example@email.com your_token'
                    
                

The token in needed in any communication between the end user and the REST API.

Only registered users can request a token.