Source code for bioblend.toolshed.categories
"""
Interaction with a Tool Shed instance categories
"""
from typing import (
Any,
Dict,
List,
TYPE_CHECKING,
)
from typing_extensions import Literal
from bioblend.galaxy.client import Client
if TYPE_CHECKING:
from bioblend.toolshed import ToolShedInstance
[docs]class ToolShedCategoryClient(Client):
module = "categories"
def __init__(self, toolshed_instance: "ToolShedInstance") -> None:
super().__init__(toolshed_instance)
[docs] def get_categories(self, deleted: bool = False) -> List[Dict[str, Any]]:
"""
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. Requires
administrator access to the Tool Shed instance.
:rtype: list
:return: A list of dictionaries containing information about
repository categories present in the Tool Shed.
For example::
[{'deleted': False,
'description': 'Tools for manipulating data',
'id': '175812cd7caaf439',
'model_class': 'Category',
'name': 'Text Manipulation',
'url': '/api/categories/175812cd7caaf439'}]
.. versionadded:: 0.5.2
"""
return self._get(deleted=deleted)
[docs] def show_category(self, category_id: str) -> Dict[str, Any]:
"""
Get details of a given category.
:type category_id: str
:param category_id: Encoded category ID
:rtype: dict
:return: details of the given category
"""
return self._get(id=category_id)
[docs] def get_repositories(
self, category_id: str, sort_key: Literal["name", "owner"] = "name", sort_order: Literal["asc", "desc"] = "asc"
) -> Dict[str, Any]:
"""
Returns a dictionary of information for a repository category including
a list of repositories belonging to the category.
:type category_id: str
:param category_id: Encoded category ID
:type sort_key: str
:param sort_key: key for sorting. Options are 'name' or 'owner' (default 'name').
:type sort_order: str
:param sort_order: ordering of sorted output. Options are 'asc' or 'desc' (default 'asc').
:rtype: dict
:return: A dict containing information about the category
including a list of repository dicts.
For example::
{'deleted': False,
'description': 'Tools for constructing and analyzing 3-dimensional shapes and '
'their properties',
'id': '589548af7e391bcf',
'model_class': 'Category',
'name': 'Constructive Solid Geometry',
'repositories': [{'create_time': '2016-08-23T18:53:23.845013',
'deleted': False,
'deprecated': False,
'description': 'Adds a surface field to a selected shape '
'based on a given mathematical expression',
'homepage_url': 'https://github.com/gregvonkuster/galaxy-csg',
'id': 'af2ccc53697b064c',
'metadata': {'0:e12b55e960de': {'changeset_revision': 'e12b55e960de',
'downloadable': True,
'has_repository_dependencies': False,
'id': 'dfe022067783215f',
'includes_datatypes': False,
'includes_tool_dependencies': False,
'includes_tools': True,
'includes_tools_for_display_in_tool_panel': True,
'includes_workflows': False,
'malicious': False,
'missing_test_components': False,
'model_class': 'RepositoryMetadata',
'numeric_revision': 0,
'repository_id': 'af2ccc53697b064c'}},
'model_class': 'Repository',
'name': 'icqsol_add_surface_field_from_expression',
'owner': 'iuc',
'private': False,
'remote_repository_url': 'https://github.com/gregvonkuster/galaxy-csg',
'times_downloaded': 152,
'type': 'unrestricted',
'user_id': 'b563abc230aa8fd0'},
# ...
],
'repository_count': 11,
'url': '/api/categories/589548af7e391bcf'}
"""
params: Dict[str, Any] = {}
if sort_key:
params.update({"sort_key": sort_key})
if sort_order:
params.update({"sort_order": sort_order})
url = self._make_url(category_id) + "/repositories"
return self._get(url=url, params=params)