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"""
Contains interactions dealing with Galaxy dependency resolvers.
"""
from typing import (
Any,
Dict,
List,
Optional,
TYPE_CHECKING,
)
from typing_extensions import Literal
from bioblend.galaxy.client import Client
if TYPE_CHECKING:
from bioblend.galaxy import GalaxyInstance
class ToolDependenciesClient(Client):
module = "dependency_resolvers"
def __init__(self, galaxy_instance: "GalaxyInstance") -> None:
super().__init__(galaxy_instance)
def summarize_toolbox(
self,
index: Optional[int] = None,
tool_ids: Optional[List[str]] = None,
resolver_type: Optional[str] = None,
include_containers: bool = False,
container_type: Optional[str] = None,
index_by: Literal["requirements", "tools"] = "requirements",
) -> list:
"""
Summarize requirements across toolbox (for Tool Management grid).
:type index: int
:param index: index of the dependency resolver with respect to
the dependency resolvers config file
:type tool_ids: list
:param tool_ids: tool_ids to return when index_by=tools
:type resolver_type: str
:param resolver_type: restrict to specified resolver type
:type include_containers: bool
:param include_containers: include container resolvers in resolution
:type container_type: str
:param container_type: restrict to specified container type
:type index_by: str
:param index_by: By default results are grouped by requirements. Set to 'tools'
to return one entry per tool.
:rtype: list of dicts
:returns: dictified descriptions of the dependencies, with attribute
`dependency_type: None` if no match was found.
For example::
[{'requirements': [{'name': 'galaxy_sequence_utils',
'specs': [],
'type': 'package',
'version': '1.1.4'},
{'name': 'bx-python',
'specs': [],
'type': 'package',
'version': '0.8.6'}],
'status': [{'cacheable': False,
'dependency_type': None,
'exact': True,
'model_class': 'NullDependency',
'name': 'galaxy_sequence_utils',
'version': '1.1.4'},
{'cacheable': False,
'dependency_type': None,
'exact': True,
'model_class': 'NullDependency',
'name': 'bx-python',
'version': '0.8.6'}],
'tool_ids': ['vcf_to_maf_customtrack1']}]
.. note::
This method works only on Galaxy 20.01 or later and if the user is a
Galaxy admin. It relies on an experimental API particularly tied to
the GUI and therefore is subject to breaking changes.
"""
assert index_by in ["tools", "requirements"], "index_by must be one of 'tools' or 'requirements'."
params = {
"include_containers": str(include_containers),
"index_by": index_by,
}
if index:
params["index"] = str(index)
if tool_ids:
params["tool_ids"] = ",".join(tool_ids)
if resolver_type:
params["resolver_type"] = resolver_type
if container_type:
params["container_type"] = container_type
url = "/".join((self._make_url(), "toolbox"))
return self._get(url=url, params=params)
def unused_dependency_paths(self) -> List[str]:
"""
List unused dependencies
"""
url = "/".join((self._make_url(), "unused_paths"))
return self._get(url=url)
def delete_unused_dependency_paths(self, paths: List[str]) -> None:
"""
Delete unused paths
:type paths: list
:param paths: paths to delete
"""
payload: Dict[str, Any] = {"paths": paths}
url = "/".join((self._make_url(), "unused_paths"))
self._put(url=url, payload=payload)
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