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<#-- @formatter:off -->
import requests
import json
import urllib
import os
try:
from urllib.parse import quote_plus
except ImportError:
# Python 2
from urllib import quote_plus
class Session():
'''Representation of a session with the MOLGENIS REST API.
Usage:
>>> session = molgenis.Session('http://localhost:8080/api/')
>>> session.login('user', 'password')
>>> session.get('Person')
'''
def __init__(self, url="http://localhost:8080/api/"):
'''Constructs a new Session.
Args:
url -- URL of the REST API. Should be of form 'http[s]://[:port]/api/'
Examples:
>>> connection = molgenis.Session('http://localhost:8080/api/')
'''
self.url = url
self.session = requests.Session()
def login(self, username, password):
'''Logs in a user and stores the acquired session token in this Session object.
Args:
username -- username for a registered molgenis user
password -- password for the user
'''
self.session.cookies.clear()
response = self.session.post(self.url + "v1/login",
data=json.dumps({"username": username, "password": password}),
headers={"Content-Type": "application/json"})
if response.status_code == 200:
self.token = response.json()["token"]
response.raise_for_status()
return response
def logout(self):
'''Logs out the current session token.'''
response = self.session.post(self.url + "v1/logout",
headers=self._get_token_header())
if response.status_code == 200:
self.token = None
self.session.cookies.clear()
response.raise_for_status()
return response
def getById(self, entity, id, attributes=None, expand=None):
'''Retrieves a single entity row from an entity repository.
Args:
entity -- fully qualified name of the entity
id -- the value for the idAttribute of the entity
attributes -- The list of attributes to retrieve
expand -- the attributes to expand
Examples:
session.get('Person', 'John')
'''
response = self.session.get(self.url + "v1/" + quote_plus(entity) + '/' + quote_plus(id),
headers=self._get_token_header(),
params={"attributes": attributes, "expand": expand})
if response.status_code == 200:
return response.json()
response.raise_for_status()
return response
def get(self, entity, q=None, attributes=None, expand=None, num=100, start=0, sortColumn=None, sortOrder=None):
'''Retrieves entity rows from an entity repository.
Args:
entity -- fully qualified name of the entity
q -- query in json form, see the MOLGENIS REST API v1 documentation for details
attributes -- The list of attributes to retrieve
expand -- the attributes to expand
num -- the amount of entity rows to retrieve
start -- the index of the first row to retrieve (zero indexed)
sortColumn -- the attribute to sort on
sortOrder -- the order to sort in
Examples:
session.get('Person')
'''
if q:
response = self.session.post(self.url + "v1/" + quote_plus(entity),
headers=self._get_token_header_with_content_type(),
params={"_method": "GET"},
data=json.dumps(
{"q": q, "attributes": attributes, "expand": expand, "num": num,
"start": start,
"sortColumn": sortColumn, "sortOrder": sortOrder}))
else:
response = self.session.get(self.url + "v1/" + quote_plus(entity),
headers=self._get_token_header(),
params={"attributes": attributes, "expand": expand, "num": num, "start": start,
"sortColumn": sortColumn, "sortOrder":
sortOrder})
if response.status_code == 200:
return response.json()["items"]
response.raise_for_status()
return response
def add(self, entity, data={}, files={}, **kwargs):
'''Adds a single entity row to an entity repository.
Args:
entity -- fully qualified name of the entity
files -- dictionary containing file attribute values for the entity row.
The dictionary should for each file attribute map the attribute name to a tuple containing the file name and an
input stream.
data -- dictionary mapping attribute name to non-file attribute value for the entity row, gets merged with the
kwargs argument
**kwargs -- keyword arguments get merged with the data argument
Examples:
>>> session.add('Person', firstName='Jan', lastName='Klaassen')
>>> session.add('Person', {'firstName': 'Jan', 'lastName':'Klaassen'})
You can have multiple file type attributes.
>>> session.add('Plot', files={'image': ('expression.jpg', open('~/first-plot.jpg','rb')),
'image2': ('expression-large.jpg', open('/Users/me/second-plot.jpg', 'rb'))},
data={'name':'IBD-plot'})
'''
response = self.session.post(self.url + "v1/" + quote_plus(entity),
headers=self._get_token_header(),
data=self._merge_two_dicts(data, kwargs),
files=files)
if response.status_code == 201:
return response.headers["Location"].split("/")[-1]
response.raise_for_status()
return response
def add_all(self, entity, entities):
'''Adds multiple entity rows to an entity repository.'''
response = self.session.post(self.url + "v2/" + quote_plus(entity),
headers=self._get_token_header_with_content_type(),
data=json.dumps({"entities": entities}))
if response.status_code == 201:
return [resource["href"].split("/")[-1] for resource in response.json()["resources"]]
response.raise_for_status()
return response
def update_one(self, entity, id, attr, value):
'''Updates one attribute of a given entity in a table with a given value'''
response = self.session.put(self.url + "v1/" + quote_plus(entity) + "/" + id + "/" + attr,
headers=self._get_token_header_with_content_type(),
data=json.dumps(value))
response.raise_for_status()
return response
def delete(self, entity, id):
'''Deletes a single entity row from an entity repository.'''
response = self.session.delete(self.url + "v1/" + quote_plus(entity) + "/" + quote_plus(id), headers=
self._get_token_header())
response.raise_for_status()
return response
def delete_list(self, entity, entities):
'''Deletes multiple entity rows to an entity repository, given a list of id's.'''
response = self.session.delete(self.url + "v2/" + quote_plus(entity),
headers=self._get_token_header_with_content_type(),
data=json.dumps({"entityIds": entities}))
response.raise_for_status()
return response
def get_entity_meta_data(self, entity):
'''Retrieves the metadata for an entity repository.'''
response = self.session.get(self.url + "v1/" + quote_plus(entity) + "/meta?expand=attributes", headers=
self._get_token_header())
response.raise_for_status()
return response.json()
def get_attribute_meta_data(self, entity, attribute):
'''Retrieves the metadata for a single attribute of an entity repository.'''
response = self.session.get(self.url + "v1/" + quote_plus(entity) + "/meta/" + quote_plus(attribute), headers=
self._get_token_header())
response.raise_for_status()
return response.json()
def upload_zip(self, meta_data_zip):
'''Uploads a given zip with data and metadata'''
header = self._get_token_header()
files = {'file': open(os.path.abspath(meta_data_zip), 'rb')}
url = self.url.strip('/api/') + '/plugin/importwizard/importFile'
response = requests.post(url, headers=header, files=files)
if response.status_code == 201:
return response.content.decode("utf-8")
response.raise_for_status()
return response
def _get_token_header(self):
'''Creates an 'x-molgenis-token' header for the current session.'''
try:
return {"x-molgenis-token": self.token}
except AttributeError:
return {}
def _get_token_header_with_content_type(self):
'''Creates an 'x-molgenis-token' header for the current session and a 'Content-Type: application/json' header'''
headers = self._get_token_header()
headers.update({"Content-Type": "application/json"})
return headers
@staticmethod
def _merge_two_dicts(x, y):
'''Given two dicts, merge them into a new dict as a shallow copy.'''
z = x.copy()
z.update(y)
return z
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