Secure your code as it's written. Use Snyk Code to scan source code in minutes - no build needed - and fix issues immediately.
def test_set_retry_delay(self):
self.gi.get_retry_delay = 5
self.assertEqual(5, Client.get_retry_delay())
"""
Contains possible interactions with the Galaxy Workflows
"""
import json
import os
from bioblend.galaxy.client import Client
class WorkflowClient(Client):
def __init__(self, galaxy_instance):
self.module = 'workflows'
super(WorkflowClient, self).__init__(galaxy_instance)
# the 'deleted' option is not available for workflows
def get_workflows(self, workflow_id=None, name=None, published=False):
"""
Get all workflows or filter the specific one(s) via the provided ``name``
or ``workflow_id``. Provide only one argument, ``name`` or ``workflow_id``,
but not both.
:type workflow_id: str
:param workflow_id: Encoded workflow ID (incompatible with ``name``)
:type name: str
:param name: Filter by name of workflow (incompatible with
"""
Interaction with a Tool Shed instance tools
"""
from bioblend.galaxy.client import Client
class ToolShedToolClient(Client):
def __init__(self, toolshed_instance):
self.module = 'tools'
super().__init__(toolshed_instance)
def search_tools(self, q, page=1, page_size=10):
"""
Search for tools in a Galaxy Tool Shed.
:type q: str
:param q: query string for searching purposes
:type page: int
:param page: page requested
:type page_size: int
"""
Contains possible interaction dealing with Galaxy users.
Most of these methods must be executed by a registered Galaxy admin user.
"""
from bioblend.galaxy.client import Client
class UserClient(Client):
def __init__(self, galaxy_instance):
self.module = 'users'
super().__init__(galaxy_instance)
def get_users(self, deleted=False, f_email=None, f_name=None, f_any=None):
"""
Get a list of all registered users. If ``deleted`` is set to ``True``,
get a list of deleted users.
:type deleted: bool
:param deleted: Whether to include deleted users
:type f_email: str
:param f_email: filter for user emails. The filter will be active for
Contains possible interactions with the Galaxy Data Libraries
"""
import logging
import time
from bioblend.galaxy.client import Client
from bioblend.galaxy.datasets import (
DatasetTimeoutException,
TERMINAL_STATES,
)
from bioblend.util import attach_file
log = logging.getLogger(__name__)
class LibraryClient(Client):
def __init__(self, galaxy_instance):
self.module = 'libraries'
super().__init__(galaxy_instance)
def create_library(self, name, description=None, synopsis=None):
"""
Create a data library with the properties defined in the arguments.
:type name: str
:param name: Name of the new data library
:type description: str
:param description: Optional data library description
:type synopsis: str
def _get_extra_files(self, dataset_details):
extra_files_url = "%s/%s/contents/%s/extra_files" % (
self._user_gi._make_url(self._user_gi.histories), self._history_id, dataset_details["id"]
)
extra_files = Client._get(self._user_gi.jobs, url=extra_files_url)
return extra_files
"""
Interaction with a Tool Shed instance categories
"""
from bioblend.galaxy.client import Client
class ToolShedCategoryClient(Client):
def __init__(self, toolshed_instance):
self.module = 'categories'
super().__init__(toolshed_instance)
def get_categories(self, deleted=False):
"""
Returns a list of dictionaries that contain descriptions of the
repository categories found on the given Tool Shed instance.
:type deleted: bool
:param deleted: whether to show deleted categories
:rtype: list
:return: A list of dictionaries containing information about
repository categories present in the Tool Shed.
"""
Interaction with a Galaxy Tool Shed.
"""
from bioblend.galaxy.client import Client
class ToolShedClient(Client):
def __init__(self, galaxy_instance):
self.module = 'tool_shed_repositories'
super().__init__(galaxy_instance)
def get_repositories(self):
"""
Get the list of all installed Tool Shed repositories on this Galaxy instance.
:rtype: list
:return: a list of dictionaries containing information about
repositories present in the Tool Shed.
For example::
[{'changeset_revision': '4afe13ac23b6',
'deleted': False,
"""
Contains possible interactions with the Galaxy Forms
"""
from bioblend.galaxy.client import Client
class FormsClient(Client):
def __init__(self, galaxy_instance):
self.module = 'forms'
super().__init__(galaxy_instance)
def get_forms(self):
"""
Get the list of all forms.
:rtype: list
:return: Displays a collection (list) of forms.
For example::
[{'id': 'f2db41e1fa331b3e',
'model_class': 'FormDefinition',
'name': 'First form',
"""
Contains possible interactions with the Galaxy visualization
"""
from bioblend.galaxy.client import Client
class VisualClient(Client):
def __init__(self, galaxy_instance):
self.module = 'visualizations'
super().__init__(galaxy_instance)
def get_visualizations(self):
"""
Get the list of all visualizations.
:rtype: list
:return: A list of dicts with details on individual visualizations.
For example::
[{'dbkey': 'eschColi_K12',
'id': 'df1c7c96fc427c2d',
'title': 'AVTest1',