2. WAVES API python samples code

These examples use coreapi package functionalities

see: http://www.coreapi.org/

2.1. Interact with services

You can interact with a WAVES API instance by using coreapi. These examples show how to get a list of services or a service details, a submission or inputs and outputs expected.

from coreapi import Client, auth
from coreapi.codecs import CoreJSONCodec, JSONCodec

decoders = [JSONCodec(), CoreJSONCodec()]
# Create a client client codecs
client = Client(decoders=decoders)
document = client.get('http://waves.demo.atgc-montpellier.fr/waves/api/schema')
# get service list - replace with actual waves-api urls
serviceList = client.action(document, ['services', 'list'])
print(serviceList)
# get service details
serviceDetails = client.action(document, ["services", "read"], params={'service_app_name': 'sample_service'})
print(serviceDetails['name'])
# get service submissions
submissions = client.action(document, ["services", "submissions_list"],
                            params={"service_app_name": 'sample_service'})
# get first submission details
sub_details = client.action(document, ["services", "submission"],
                            params={"service_app_name": "sample_service",
                                    "submission_app_name": "default"})
# get inputs / outputs
expected_inputs = sub_details['inputs']
print(expected_inputs)
expected_outputs = sub_details['outputs']
print(expected_outputs)

2.2. Authenticate with token

Some WAVES API entries require to be authenticated (jobs list, job details, job submission). Token are given by the administrator.

client = Client(decoders=decoders,
            auth=auth.TokenAuthentication(
                token="6241961ef45e4bbe7bb01a05f938ed9f0f2a3926",
                scheme="Token"))
document = client.get('http://waves.demo.atgc-montpellier.fr/waves/api/schema')
# list jobs
# get job list
job_list = client.action(document, ['jobs', 'list'])
print("job_list", job_list)
if (len(job_list) > 0):
    job_details = client.action(document, ['jobs', 'read'], params={'unique_id': job_list[0]['slug']})
    print(job_details['title'])
    print(job_details['created'])
    print(job_details['updated'])

2.3. Integrate a WAVES service form

You’ve got a website and you want your visitors could submit jobs? The better way for this is to add in your website using API. Here, you’re supposed to know there is a service named “sample_service” defined on demo WAVES instance (as you see in serviceList above).

from coreapi import Client, auth
from coreapi.codecs import CoreJSONCodec, JSONCodec, TextCodec
decoders = [JSONCodec(), CoreJSONCodec(), TextCodec()]
client = Client(decoders=decoders)
document = client.get('http://waves.demo.atgc-montpellier.fr/waves/api/schema')
wavesform = client.action(document, ['services', 'form'], params={"service_app_name": 'sample_service'}, validate=False, encoding='multipart/form-data')

Now, you just render this form into your template (ex. in a django tpl).

Warning

Don’t forget to add forms.css and services.js from your waves instance as in this sample.

{% block head %}
   {% addtoblock "waves_forms_css" %} <link rel="stylesheet" href="http://waves.demo.atgc-montpellier.fr/static/waves/css/forms.css">{% endaddtoblock %}
{% endblock %}

{% block main %}
<!-- Import the web form as is -->
{{ wavesform|safe }}
{% endblock main %}

{% block footer %}
    {% addtoblock "js" %}
        <script src="http://waves.demo.atgc-montpellier.fr/static/waves/js/services.js"></script>
    {% endaddtoblock %}
{% endblock footer %}

2.4. Create a job

It’s also possible to create a job directly from your client interface. Here we see how to create a job called “Job Name” which use a “default” submission of “sample_service” service. Inputs are defined by expected inputs of the “sample_service”. Be aware, “validate=false” is required to submit a file

# submit a job
from coreapi.utils import File
from os.path import join, dirname

with open(join(dirname(__file__), "test.fasta"), 'r') as f:
    inputs = {
        "text_input": "This is text input",
        "input_file": File("test.fasta", f)
    }
    client.action(document, ["services", "submissions", "jobs", "create"],
                  params={
                      **inputs,
                      "title": "Job Name",
                      "service_app_name": "sample_service",
                      "submission_app_name": "default"
                  }, validate=False, encoding='multipart/form-data')
job_list = client.action(document, ['jobs', 'list'])
print(job_list)