Download a FASTQ File

This example shows the REST API facilities for working with the file system.

Making the following request on the results resource,

http://myhost/rundb/api/v1/results/13?format=json

shows the path of the associated FASTQ file. The database schema includes a number of file path entries, which can all be accessed in the same way.

{
                 .
                 .
                 .
        "fastqLink": "/output/Home/Auto_B15-45_4_013/R_2010_11 ... B15-45_Au…",
                 .
                 .
                 .
}

You can get the file contents by copying the path to the URI, following the host name.

http://myhost/output/Home/Auto_B15-45_4_013/R_2010_11 ... B15-45_4.fastq

The entire sequence is shown in the following programming example.

The GET request on the results resource returns the FASTQ file path in the fastqLink field.

import requests
import simplejson as json

base_url = 'http://myhost/rundb/api/v1'
resp = requests.get('%s/results/13?format=json'%base_url, auth=('myusername', 'mypassword'))
resp_json = resp.json()

To GET the file contents, append the fastqLink value to the URI, following the host name.

resp = requests.get('http://myhost/%s'%resp_json['fastqLink'], auth=('myusername', 'mypassword'))

Display the FASTQ file path and the contents of the file.

print resp_json['fastqlink']
print resp.content