Source code for bioblend.galaxy.toolshed
"""
Interaction with a Galaxy Tool Shed.
"""
from typing import (
Any,
Dict,
List,
Optional,
TYPE_CHECKING,
)
from bioblend.galaxy.client import Client
if TYPE_CHECKING:
from bioblend.galaxy import GalaxyInstance
[docs]
class ToolShedClient(Client):
module = "tool_shed_repositories"
def __init__(self, galaxy_instance: "GalaxyInstance") -> None:
super().__init__(galaxy_instance)
[docs]
def get_repositories(self) -> List[Dict[str, Any]]:
"""
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,
'dist_to_shed': False,
'error_message': '',
'name': 'velvet_toolsuite',
'owner': 'edward-kirton',
'status': 'Installed'}]
.. versionchanged:: 0.4.1
Changed method name from ``get_tools`` to ``get_repositories`` to
better align with the Tool Shed concepts
.. seealso:: bioblend.galaxy.tools.get_tool_panel()
"""
return self._get()
[docs]
def show_repository(self, toolShed_id: str) -> Dict[str, Any]:
"""
Get details of a given Tool Shed repository as it is installed on this
Galaxy instance.
:type toolShed_id: str
:param toolShed_id: Encoded Tool Shed ID
:rtype: dict
:return: Information about the tool
For example::
{'changeset_revision': 'b17455fb6222',
'ctx_rev': '8',
'owner': 'aaron',
'status': 'Installed',
'url': '/api/tool_shed_repositories/82de4a4c7135b20a'}
.. versionchanged:: 0.4.1
Changed method name from ``show_tool`` to ``show_repository`` to
better align with the Tool Shed concepts
"""
return self._get(id=toolShed_id)
[docs]
def install_repository_revision(
self,
tool_shed_url: str,
name: str,
owner: str,
changeset_revision: str,
install_tool_dependencies: bool = False,
install_repository_dependencies: bool = False,
install_resolver_dependencies: bool = False,
tool_panel_section_id: Optional[str] = None,
new_tool_panel_section_label: Optional[str] = None,
) -> Dict[str, Any]:
"""
Install a specified repository revision from a specified Tool Shed into
this Galaxy instance. This example demonstrates installation of a repository
that contains valid tools, loading them into a section of the Galaxy tool
panel or creating a new tool panel section.
You can choose if tool dependencies or repository dependencies should be
installed through the Tool Shed,
(use ``install_tool_dependencies`` or ``install_repository_dependencies``)
or through a resolver that supports installing dependencies
(use ``install_resolver_dependencies``). Note that any combination of
the three dependency resolving variables is valid.
Installing the repository into an existing tool panel section requires
the tool panel config file (e.g., tool_conf.xml, shed_tool_conf.xml, etc)
to contain the given tool panel section:
<section id="from_test_tool_shed" name="From Test Tool Shed" version="">
</section>
:type tool_shed_url: str
:param tool_shed_url: URL of the Tool Shed from which the repository should
be installed from (e.g., ``https://testtoolshed.g2.bx.psu.edu``)
:type name: str
:param name: The name of the repository that should be installed
:type owner: str
:param owner: The name of the repository owner
:type changeset_revision: str
:param changeset_revision: The revision of the repository to be installed
:type install_tool_dependencies: bool
:param install_tool_dependencies: Whether or not to automatically handle
tool dependencies (see
https://galaxyproject.org/toolshed/tool-dependency-recipes/
for more details)
:type install_repository_dependencies: bool
:param install_repository_dependencies: Whether or not to automatically
handle repository dependencies
(see https://galaxyproject.org/toolshed/defining-repository-dependencies/
for more details)
:type install_resolver_dependencies: bool
:param install_resolver_dependencies: Whether or not to automatically
install resolver dependencies (e.g. conda).
:type tool_panel_section_id: str
:param tool_panel_section_id: The ID of the Galaxy tool panel section
where the tool should be insterted under.
Note that you should specify either this
parameter or the ``new_tool_panel_section_label``.
If both are specified, this one will take
precedence.
:type new_tool_panel_section_label: str
:param new_tool_panel_section_label: The name of a Galaxy tool panel section
that should be created and the repository
installed into.
"""
payload: Dict[str, Any] = {}
payload["tool_shed_url"] = tool_shed_url
payload["name"] = name
payload["owner"] = owner
payload["changeset_revision"] = changeset_revision
payload["install_tool_dependencies"] = install_tool_dependencies
payload["install_repository_dependencies"] = install_repository_dependencies
payload["install_resolver_dependencies"] = install_resolver_dependencies
if tool_panel_section_id:
payload["tool_panel_section_id"] = tool_panel_section_id
elif new_tool_panel_section_label:
payload["new_tool_panel_section_label"] = new_tool_panel_section_label
url = self._make_url() + "/new/install_repository_revision"
return self._post(url=url, payload=payload)
[docs]
def uninstall_repository_revision(
self, name: str, owner: str, changeset_revision: str, tool_shed_url: str, remove_from_disk: bool = True
) -> Dict[str, Any]:
"""
Uninstalls a specified repository revision from this Galaxy instance.
:type name: str
:param name: The name of the repository
:type owner: str
:param owner: The owner of the repository
:type changeset_revision: str
:param changeset_revision: The revision of the repository to uninstall
:type tool_shed_url: str
:param tool_shed_url: URL of the Tool Shed from which the repository was
installed from (e.g., ``https://testtoolshed.g2.bx.psu.edu``)
:type remove_from_disk: bool
:param remove_from_disk: whether to also remove the repository from disk
(the default) or only deactivate it
:rtype: dict
:return: If successful, a dictionary with a message noting the removal
"""
payload: Dict[str, Any] = {
"tool_shed_url": tool_shed_url,
"name": name,
"owner": owner,
"changeset_revision": changeset_revision,
"remove_from_disk": remove_from_disk,
}
return self._delete(params=payload)