forked from galaxyproject/bioblend
/
__init__.py
91 lines (75 loc) · 3.56 KB
/
__init__.py
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"""
A base representation of an instance of Galaxy
"""
from bioblend.galaxy.client import Client
from bioblend.galaxy import (libraries, histories, workflows, datasets, users,
genomes, tools, toolshed, config, visual, quotas,
groups, datatypes, jobs, forms, ftpfiles, folders,
roles, tool_data)
from bioblend.galaxyclient import GalaxyClient
class GalaxyInstance(GalaxyClient):
def __init__(self, url, key=None, email=None, password=None):
"""
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()
: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. If a key is not supplied, an
email address and password must be and key will
automatically be created for the user.
:type email: string
:param email: Galaxy e-mail address corresponding to the user.
Ignored if key is supplied directly.
:type password: string
:param password: Password of Galaxy account corresponding to the above
e-mail address. Ignored if key is supplied directly.
"""
super(GalaxyInstance, self).__init__(url, key, email, password)
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)
self.genomes = genomes.GenomeClient(self)
self.tools = tools.ToolClient(self)
self.toolShed = toolshed.ToolShedClient(self)
self.config = config.ConfigClient(self)
self.visual = visual.VisualClient(self)
self.quotas = quotas.QuotaClient(self)
self.groups = groups.GroupsClient(self)
self.roles = roles.RolesClient(self)
self.datatypes = datatypes.DatatypesClient(self)
self.jobs = jobs.JobsClient(self)
self.forms = forms.FormsClient(self)
self.ftpfiles = ftpfiles.FTPFilesClient(self)
self.tool_data = tool_data.ToolDataClient(self)
self.folders = folders.FoldersClient(self)
@property
def max_get_attempts(self):
return Client.max_get_retries()
@max_get_attempts.setter
def max_get_attempts(self, v):
Client.set_max_get_retries(v)
@property
def get_retry_delay(self):
return Client.get_retry_delay()
@get_retry_delay.setter
def get_retry_delay(self, v):
Client.set_get_retry_delay(v)
def __repr__(self):
"""
A nicer representation of this GalaxyInstance object
"""
return "GalaxyInstance object for Galaxy at {0}".format(self.base_url)