"""
A base representation of an instance of Galaxy
"""
from typing import Optional
from bioblend.galaxy import (
config,
container_resolution,
dataset_collections,
datasets,
datatypes,
folders,
forms,
ftpfiles,
genomes,
groups,
histories,
invocations,
jobs,
libraries,
quotas,
roles,
tool_data,
tool_dependencies,
tools,
toolshed,
users,
visual,
workflows,
)
from bioblend.galaxyclient import GalaxyClient
[docs]class GalaxyInstance(GalaxyClient):
[docs] def __init__(
self,
url: str,
key: Optional[str] = None,
email: Optional[str] = None,
password: Optional[str] = None,
verify: bool = True,
) -> None:
"""
A base representation of a connection to a Galaxy instance, identified
by the server URL and user credentials.
After you have created a ``GalaxyInstance`` object, access various
modules via the class fields. 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: str
:param url: A FQDN or IP for a given instance of Galaxy. For example:
http://127.0.0.1:8080 . If a Galaxy instance is served under
a prefix (e.g., http://127.0.0.1:8080/galaxy/), supply the
entire URL including the prefix (note that the prefix must
end with a slash). If a Galaxy instance has HTTP Basic
authentication with username and password, then the
credentials should be included in the URL, e.g.
http://user:pass@host:port/galaxy/
:type key: str
: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 the key will
automatically be created for the user.
:type email: str
:param email: Galaxy e-mail address corresponding to the user.
Ignored if key is supplied directly.
:type password: str
:param password: Password of Galaxy account corresponding to the above
e-mail address. Ignored if key is supplied directly.
:param verify: Whether to verify the server's TLS certificate
:type verify: bool
"""
super().__init__(url, key, email, password, verify=verify)
self.libraries = libraries.LibraryClient(self)
self.histories = histories.HistoryClient(self)
self.workflows = workflows.WorkflowClient(self)
self.invocations = invocations.InvocationClient(self)
self.datasets = datasets.DatasetClient(self)
self.dataset_collections = dataset_collections.DatasetCollectionClient(self)
self.users = users.UserClient(self)
self.genomes = genomes.GenomeClient(self)
self.tools = tools.ToolClient(self)
self.toolshed = toolshed.ToolShedClient(self)
self.toolShed = self.toolshed # historical alias
self.config = config.ConfigClient(self)
self.container_resolution = container_resolution.ContainerResolutionClient(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)
self.tool_dependencies = tool_dependencies.ToolDependenciesClient(self)
def __repr__(self) -> str:
"""
A nicer representation of this GalaxyInstance object
"""
return f"GalaxyInstance object for Galaxy at {self.base_url}"