def get_fairshake_client(api_key=None,
username=None,
email=None,
password=None):
''' Using either the api_key directly, or with fairshake
user credentials, create an authenticated swagger client to fairshake.
'''
from pyswaggerclient import SwaggerClient
fairshake = SwaggerClient(
'https://fairshake.cloud/swagger?format=openapi', )
if not api_key:
fairshake_auth = fairshake.actions.auth_login_create.call(
data=dict({
'username': username,
'password': password,
}, **({
'email': email
} if email else {})))
api_key = fairshake_auth['key']
# FAIRshake expects a Token in the Authorization request header for
# authenticated calls
fairshake.update(headers={
'Authorization': 'Token ' + api_key,
})
return fairshake
def ask_fairsharing(doi):
from pyswaggerclient import SwaggerClient
client = SwaggerClient(
'https://fairsharing.org/api/?format=openapi',
headers={'Api-Key': os.environ.get('FAIRSHARING_API_KEY')})
results = client.actions.database_summary_list.call(doi=doi)['results']
return {
'keywords':
list(
filter(None,
[result.get('user_defined_tags') for result in results])),
'doi':
list(filter(None, [result.get('doi') for result in results])),
'name':
list(filter(None, [result.get('name') for result in results])),
'description':
list(filter(None, [result.get('description') for result in results])),
'indexed':
list(
filter(None, [('https://fairsharing.org/' +
result['bsg_id']) if result.get('bsg_id') else None
for result in results])),
'url':
list(filter(None, [result.get('homepage') for result in results])),
'license':
list(filter(None, [result.get('licence') for result in results])),
'taxonomy':
list(filter(None, [result.get('taxonomies') for result in results])),
'domain':
list(filter(None, [result.get('domains') for result in results])),
}
def get_harmonizome_client(harmonizome_spec):
''' Create a swagger client for harmonizome.
'''
harmonizome = SwaggerClient(
'https://raw.githubusercontent.com/MaayanLab/smartAPIs/master/harmonizome_smartapi.yml',
)
return harmonizome
def get_fairsharing_client(api_key):
''' Using the api_key, create an authenticated swagger client to fairsharing.
'''
# FAIRSharing expects an Api-Key in the request header for
# authenticated calls
fairsharing = SwaggerClient('https://fairsharing.org/api?format=openapi',
headers={
'Api-Key': api_key,
})
return fairsharing
def _fairsharing_client_singleton():
global client
try:
client = SwaggerClient('https://fairsharing.org/api/?format=openapi',
headers={
'Api-Key':
os.environ['FAIRSHARING_API_KEY'],
})
except Exception as e:
import traceback
traceback.print_exc()
client = False
return client
def perform(kls, inputs):
urls = inputs['target:url']
dois = [m.group(1) for m in map(url_re.match, urls) if m]
if dois:
client = SwaggerClient(
'https://fairsharing.org/api/?format=openapi',
headers={
'Api-Key':
settings.ASSESSMENT_CONFIG['fairsharing']['api-key'],
})
results = [
result for doi in dois for result in
client.actions.database_summary_list.call(doi=doi, )['results']
]
if len(results) > 1:
logging.warn(
'More than 1 DOI was identified in the fairsharing database! (%s)'
% (url))
if len(results) >= 1:
data = results[0]
else:
data = None
else:
data = None
return {
key: {
'answer': 'yes' if data.get(attr) else 'no',
'comment': data.get(attr),
}
for key, attr in metric_to_attr.items()
} if data else {key: {}
for key in metric_to_attr.keys()}
def get_dockstore_client():
''' Create a swagger client for dockstore.
'''
dockstore = SwaggerClient('https://dockstore.org/swagger.json')
return dockstore
def get_smartapi_client():
''' Create a swagger client for smartapi.
'''
smartapi = SwaggerClient('https://smart-api.info/api/metadata/27a5b60716c3a401f2c021a5b718c5b1?format=yaml')
return smartapi
https://fairsharing.github.io/FAIR-Evaluator-FrontEnd/#!/metrics
'''
import re
import json
import urllib.request
from functools import wraps
from pyswaggerclient import SwaggerClient
from fairshake_assessments.core import metric
metrics = json.load(
urllib.request.urlopen(
'https://fair-evaluator.semanticscience.org/FAIR_Evaluator/metrics.json'
))
def metric_id_to_name(id):
return re.match('^https://w3id.org/(.+)', id).group(1).replace('/', '_')
for fair_metric in metrics:
fair_metric_client = SwaggerClient(fair_metric['smarturl'])
for action in dir(fair_metric_client.actions):
if action.startswith('_'):
continue
func = getattr(fair_metric_client.actions, action).call
wrap_func = wraps(func)(
lambda content: func(content=dict(subject=content)))
globals()[metric_id_to_name(
fair_metric['@id'])] = metric(fair_metric)(wrap_func)
'$.."x-externalResources"[@."x-url"]',
'ratio': [[
'$.."x-externalResources"[@."x-type" is not None]',
'$.."x-externalResources"[@."x-description" is not None]'
], '$.."x-externalResources"[@."x-url" is not None]', 'all'],
'desc':
'x-url (smartAPI fields all described w/ x-type and x-description)',
'metric':
128,
'pattern':
re.compile(r'.+'),
},
]
SmartAPI = SwaggerClient(
'https://smart-api.info/api/metadata/27a5b60716c3a401f2c021a5b718c5b1?format=yaml'
)
def get_all(**kwargs):
n_results = 0
while True:
resp = SmartAPI.actions.query_get.call(**kwargs, **{'from': n_results})
for hit in resp['hits']:
n_results += 1
yield hit
if n_results >= resp['total']:
break
else:
resp = SmartAPI.actions.query_get.call(**kwargs)
