"""
A base representation of an instance of Galaxy
"""
import requests
import urlparse
import poster
import urllib2
import simplejson
from bioblend.galaxy import (libraries, histories, workflows, datasets, users)
[docs]class GalaxyInstance(object):
[docs] def __init__(self, url, key):
"""
A base representation of an instance of Galaxy, identified by a
URL and a user's API key.
After you have created an ``GalaxyInstance`` object, access various
modules via the class fields (see the source for the most up-to-date
list): ``libraries``, ``histories``, ``workflows``, ``datasets``,
and ``users`` are the minimum set supported. For example, to work with
histories, and get a list of all the user's histories, the following
should be done::
from bioblend import galaxy
gi = galaxy.GalaxyInstance(url='http://127.0.0.1:8000', key='your_api_key')
hl = gi.histories.get_histories()
print "List of histories:", hl
:type url: string
:param url: A FQDN or IP for a given instance of Galaxy. For example:
http://127.0.0.1:8080
:type key: string
:param key: User's API key for the given instance of Galaxy, obtained
from the user preferences.
"""
# Make sure the url scheme is defined (otherwise requests will not work)
if not urlparse.urlparse(url).scheme:
url = "http://" + url
# All of Galaxy's API's are rooted at <url>/api so make that the base url
self.base_url = url
self.url = urlparse.urljoin(url, 'api')
self.key = key
self.default_params = {'key': key}
self.json_headers = {'Content-Type': 'application/json'}
self.verify = False # Should SSL verification be done
self.libraries = libraries.LibraryClient(self)
self.histories = histories.HistoryClient(self)
self.workflows = workflows.WorkflowClient(self)
self.datasets = datasets.DatasetClient(self)
self.users = users.UserClient(self)
def _make_url(self, module, module_id=None, deleted=False, contents=False):
"""
Compose a URL based on the provided arguments.
:type module: string
:param module: The name of the base module for which to make the URL.
For example: ``libraries``, ``workflows``, ``histories``
:type module_id: string
:param module_id: The encoded ID for a specific module (eg, library ID)
:type deleted: bool
:param deleted: If ``True``, include ``deleted`` in the URL, after the module
name (eg, ``<base_url>/api/libraries/deleted``)
:type contents: bool
:param contents: If ``True``, include 'contents' in the URL, after the module ID:
``<base_url>/api/libraries/<encoded_library_id>/contents``
"""
c_url = self.url
c_url = '/'.join([c_url, module.module])
if deleted is True:
c_url = '/'.join([c_url, 'deleted'])
if module_id is not None:
c_url = '/'.join([c_url, module_id])
if contents is True:
c_url = '/'.join([c_url, 'contents'])
return c_url
[docs] def make_get_request(self, url, params=None):
"""
Make a GET request using the provided url.
If the ``params`` are not provided, use ``default_params`` class field.
If params are provided and the provided dict does not have ``key`` key,
the default ``self.key`` value will be included in what's passed to
the server via the request.
"""
if params is not None and params.get('key', False) is False:
params['key'] = self.key
else:
params = self.default_params
r = requests.get(url, verify=self.verify, params=params)
return r
[docs] def make_post_request(self, url, payload, params=None, files_attached=False):
"""
Make a POST request using the provided ``url`` and ``payload``.
The ``payload`` must be a dict that contains the request values.
The payload dict may contain file handles (in which case the files_attached
flag must be set to true).
If the ``params`` are not provided, use ``default_params`` class field.
If params are provided and the provided dict does not have ``key`` key,
the default ``self.key`` value will be included in what's passed to
the server via the request.
The return value will contain the response body as a JSON object.
"""
if params is not None and params.get('key', False) is False:
params['key'] = self.key
else:
params = self.default_params
if files_attached:
payload.update(params) # merge query string values into request body instead
poster.streaminghttp.register_openers()
datagen, headers = poster.encode.multipart_encode(payload)
request = urllib2.Request(url, datagen, headers)
fp = urllib2.urlopen(request)
return simplejson.load(fp)
else:
payload = simplejson.dumps(payload)
r = requests.post(url, data=payload, headers=self.json_headers,
verify=self.verify, params=params)
return r.json()
[docs] def make_delete_request(self, url, payload=None, params=None):
"""
Make a DELETE request using the provided ``url`` and the optional
arguments.
The ``payload`` must be a dict that can be converted into a JSON
object (via ``simplejson.dumps``)
If the ``params`` are not provided, use ``default_params`` class field.
If params are provided and the provided dict does not have ``key`` key,
the default ``self.key`` value will be included in what's passed to
the server via the request.
"""
if params is not None and params.get('key', False) is False:
params['key'] = self.key
else:
params = self.default_params
r = requests.delete(url, verify=self.verify, data=payload, params=params)
return r