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"""
A base representation of an instance of Tool Shed
"""
from typing import Optional
from bioblend.galaxyclient import GalaxyClient
from bioblend.toolshed import (
categories,
repositories,
tools,
)
class ToolShedInstance(GalaxyClient):
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 ToolShed instance, identified
by the ToolShed URL and user credentials.
After you have created a ``ToolShedInstance`` object, access various
modules via the class fields. For example, to work with repositories and
get a list of all public repositories, the following should be done::
from bioblend import toolshed
ts = toolshed.ToolShedInstance(url='https://testtoolshed.g2.bx.psu.edu')
rl = ts.repositories.get_repositories()
tools = ts.tools.search_tools('fastq')
:type url: str
:param url: A FQDN or IP for a given instance of ToolShed. For example:
https://testtoolshed.g2.bx.psu.edu . If a ToolShed instance
is served under a prefix (e.g.
http://127.0.0.1:8080/toolshed/), supply the entire URL
including the prefix (note that the prefix must end with a
slash).
:type key: str
:param key: If required, user's API key for the given instance of ToolShed,
obtained from the user preferences.
:type email: str
:param email: ToolShed e-mail address corresponding to the user.
Ignored if key is supplied directly.
:type password: str
:param password: Password of ToolShed 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.categories = categories.ToolShedCategoryClient(self)
self.repositories = repositories.ToolShedRepositoryClient(self)
self.tools = tools.ToolShedToolClient(self)
|
