Source code for blend.galaxy

"""
A base representation of an instance of Galaxy
"""
import requests
from blend.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 blend 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. """ self.url = '/'.join([url, 'api']) # All of Galaxy's API's are rooted at <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): """ Make a POST request using the provided ``url`` and ``payload``. 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.post(url, data=payload, headers=self.json_headers, verify=self.verify, params=params) return r
[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