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"""
Contains interactions dealing with Galaxy container resolvers.
Works only with Galaxy > 22.01
"""
from typing import (
List,
Optional,
)
from bioblend.galaxy.client import Client
class ContainerResolutionClient(Client):
module = "container_resolvers"
def get_container_resolvers(self) -> list:
"""
List container resolvers
:rtype: list
return: List of container resolvers
For example:
[{'builds_on_resolution': False,
'can_uninstall_dependencies': False,
'model_class': 'CachedExplicitSingularityContainerResolver',
'resolver_type': 'cached_explicit_singularity'},
{'builds_on_resolution': False,
'can_uninstall_dependencies': False,
'model_class': 'CachedMulledSingularityContainerResolver',
'resolver_type': 'cached_mulled_singularity'},
{'builds_on_resolution': False,
'can_uninstall_dependencies': False,
'model_class': 'MulledSingularityContainerResolver',
'resolver_type': 'mulled_singularity'}] {'builds_on_resolution': False,
"""
url = self._make_url()
return self._get(url=url)
def show_container_resolver(self, index: int) -> dict:
"""
Show container resolver
:type index: int
:param index: index of the dependency resolver with respect to
the dependency resolvers config file
:rtype: dict
return: Dict of properties of a given container resolver
{'builds_on_resolution': False,
'can_uninstall_dependencies': False,
'model_class': 'CachedMulledSingularityContainerResolver',
'resolver_type': 'cached_mulled_singularity'}
"""
url = f"{self._make_url()}/{index}"
return self._get(url=url)
def resolve(
self,
tool_id: str,
index: Optional[int] = None,
resolver_type: Optional[str] = None,
container_type: Optional[str] = None,
requirements_only: bool = False,
install: bool = False,
) -> dict:
"""
Resolve described requirement against specified container resolvers.
:type index: int
:param index: index of the dependency resolver with respect to
the dependency resolvers config file
:type tool_id: str
:param tool_id: tool id to resolve against containers
:type resolver_type: str
:param resolver_type: restrict to specified resolver type
:type container_type: str
:param container_type: restrict to specified container type
:type requirements_only: bool
:param requirements_only: ignore tool containers, properties - just search based on tool requirements set to True to mimic default behavior of tool dependency API.
:type install: bool
:param install: allow installation of new containers (for build_mulled containers) the way job resolution will operate, defaults to False
:rtype: dict
For example:
{
'requirements': [{'name': 'pyarrow', 'specs': [], 'type': 'package', 'version': '4.0.1'}],
'status': {
'cacheable': False,
'container_description': {'identifier': 'quay.io/biocontainers/pyarrow:4.0.1', 'resolve_dependencies': False, 'shell': '/bin/bash', 'type': 'docker'},
'container_resolver': {'builds_on_resolution': False, 'can_uninstall_dependencies': False, 'model_class': 'MulledDockerContainerResolver', 'resolver_type': 'mulled'},
'dependency_type': 'docker',
...
},
'tool_id': 'CONVERTER_parquet_to_csv'
}
"""
params = {}
if tool_id:
params["tool_id"] = tool_id
if resolver_type:
params["resolver_type"] = resolver_type
if container_type:
params["container_type"] = container_type
params["requirements_only"] = str(requirements_only)
params["install"] = str(install)
if index is not None:
url = "/".join((self._make_url(), str(index), "resolve"))
else:
url = "/".join((self._make_url(), "resolve"))
return self._get(url=url, params=params)
def resolve_toolbox(
self,
index: Optional[int] = None,
tool_ids: Optional[List[str]] = None,
resolver_type: Optional[str] = None,
container_type: Optional[str] = None,
requirements_only: bool = False,
install: bool = False,
) -> list:
"""
Apply resolve() to each tool in the toolbox and return the results as a list.
See documentation for resolve() for a description of parameters that can be
consumed and a description of the resulting items.
: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 filter toolbox on
:type resolver_type: str
:param resolver_type: restrict to specified resolver type
:type container_type: str
:param container_type: restrict to specified container type
:type requirements_only: bool
:param requirements_only: ignore tool containers, properties - just search based on tool requirements set to True to mimic default behavior of tool dependency API.
:type install: bool
:param install: allow installation of new containers (for build_mulled containers) the way job resolution will operate, defaults to False
:rtype: list
For example::
[{'tool_id': 'upload1', 'status': {'model_class': 'NullDependency', 'dependency_type': None, 'exact': True, 'name': None, 'version': None, 'cacheable': False}, 'requirements': []}, ...]
"""
params = {}
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
params["requirements_only"] = str(requirements_only)
params["install"] = str(install)
if index is not None:
url = "/".join((self._make_url(), str(index), "toolbox"))
else:
url = "/".join((self._make_url(), "toolbox"))
return self._get(url=url, params=params)
def resolve_toolbox_with_install(
self,
index: Optional[int] = None,
tool_ids: Optional[List[str]] = None,
resolver_type: Optional[str] = None,
container_type: Optional[str] = None,
requirements_only: bool = False,
) -> list:
"""
Do the resolution of dependencies like resolve_toolbox(), but allow building and installing new containers.
: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 filter toolbox on
:type resolver_type: str
:param resolver_type: restrict to specified resolver type
:type container_type: str
:param container_type: restrict to specified container type
:type requirements_only: bool
:param requirements_only: ignore tool containers, properties - just search based on tool requirements set to True to mimic default behavior of tool dependency API.
:rtype: list of dicts
:returns: dictified descriptions of the dependencies, with attribute
`dependency_type: None` if no match was found.
For example::
[{'requirements': [{'name': 'canu',
'specs': [],
'type': 'package',
'version': '2.2'}],
'status': {'cacheable': False,
'container_description': {'identifier': 'docker://quay.io/biocontainers/canu:2.2--ha47f30e_0',
'resolve_dependencies': False,
'shell': '/bin/bash',
'type': 'singularity'},
'container_resolver': {'builds_on_resolution': False,
'can_uninstall_dependencies': False,
'model_class': 'MulledSingularityContainerResolver',
'resolver_type': 'mulled_singularity'},
'dependency_type': 'singularity',
'environment_path': 'docker://quay.io/biocontainers/canu:2.2--ha47f30e_0',
'exact': True,
'model_class': 'ContainerDependency',
'name': None,
'version': None},
'tool_id': 'toolshed.g2.bx.psu.edu/repos/bgruening/canu/canu/2.2+galaxy0'}]
"""
params = {}
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
params["requirements_only"] = str(requirements_only)
if index is not None:
url = "/".join((self._make_url(), str(index), "toolbox", "install"))
else:
url = "/".join((self._make_url(), "toolbox", "install"))
return self._post(url=url, payload=params)
|
