galaxy.tool_util.deps.container_resolvers package

The module defines the abstract interface for resolving container images for tool execution.

class galaxy.tool_util.deps.container_resolvers.ResolutionCache(**kwds)

Bases: Bunch

Simple cache for duplicated computation created once per set of requests (likely web request in Galaxy context).

This should not be assumed to be thread safe - resolution using a given cache should all occur one resolution at a time in a single thread.

mulled_resolution_cache: Optional[Cache] = None

class galaxy.tool_util.deps.container_resolvers.ContainerResolver(app_info: AppInfo, **kwds)

Bases: Dictifiable

Description of a technique for resolving container images for tool execution.

dict_collection_visible_keys = ['resolver_type', 'can_uninstall_dependencies', 'builds_on_resolution']

can_uninstall_dependencies = False

builds_on_resolution = False

read_only = True

__init__(app_info: AppInfo, **kwds) → None

Default initializer for ContainerResolver subclasses.

abstract resolve(enabled_container_types: Container[str], tool_info: ToolInfo, **kwds) → Optional[ContainerDescription]

Find a container matching all supplied requirements for tool.

The supplied argument is a galaxy.tool_util.deps.dependencies.ToolInfo description of the tool and its requirements.

abstract property resolver_type: str

Short label for the type of container resolution.

Submodules

galaxy.tool_util.deps.container_resolvers.explicit module

This module describes the ExplicitContainerResolver ContainerResolver plugin.

class galaxy.tool_util.deps.container_resolvers.explicit.ExplicitContainerResolver(app_info: AppInfo, **kwds)

Bases: ContainerResolver

Find explicit containers referenced in the tool description (e.g. tool XML file) if present.

resolver_type = 'explicit'

resolve(enabled_container_types: Container[str], tool_info: ToolInfo, **kwds) → Optional[ContainerDescription]

Find a container explicitly mentioned in tool description.

This ignores the tool requirements and assumes the tool author crafted a correct container.

class galaxy.tool_util.deps.container_resolvers.explicit.ExplicitSingularityContainerResolver(app_info: AppInfo, **kwds)

Bases: ExplicitContainerResolver

resolver_type = 'explicit_singularity'

container_type = 'singularity'

resolve(enabled_container_types: Container[str], tool_info: ToolInfo, **kwds) → Optional[ContainerDescription]

Find a container explicitly mentioned in tool description.

This ignores the tool requirements and assumes the tool author crafted a correct container. We use singularity here to fetch docker containers, hence the container_description hack here.

class galaxy.tool_util.deps.container_resolvers.explicit.CachedExplicitSingularityContainerResolver(app_info: AppInfo, **kwargs)

Bases: CliContainerResolver

resolver_type = 'cached_explicit_singularity'

container_type = 'singularity'

cli = 'singularity'

__init__(app_info: AppInfo, **kwargs) → None

Default initializer for ContainerResolver subclasses.

resolve(enabled_container_types: Container[str], tool_info: ToolInfo, install: bool = False, **kwds) → Optional[ContainerDescription]

Find a container explicitly mentioned in tool description.

This ignores the tool requirements and assumes the tool author crafted a correct container. We use singularity here to fetch docker containers, hence the container_description hack here.

class galaxy.tool_util.deps.container_resolvers.explicit.FallbackContainerResolver(app_info: AppInfo, identifier: str = '', **kwds)

Bases: BaseAdminConfiguredContainerResolver

Specify an explicit, identified container as a Docker container resolver.

resolver_type = 'fallback'

container_type = 'docker'

__init__(app_info: AppInfo, identifier: str = '', **kwds) → None

Default initializer for ContainerResolver subclasses.

resolve(enabled_container_types: Container[str], tool_info: ToolInfo, **kwds) → Optional[ContainerDescription]

Find a container matching all supplied requirements for tool.

The supplied argument is a galaxy.tool_util.deps.dependencies.ToolInfo description of the tool and its requirements.

class galaxy.tool_util.deps.container_resolvers.explicit.FallbackSingularityContainerResolver(app_info: AppInfo, identifier: str = '', **kwds)

Bases: FallbackContainerResolver

Specify an explicit, identified container as a Singularity container resolver.

resolver_type = 'fallback_singularity'

container_type = 'singularity'

class galaxy.tool_util.deps.container_resolvers.explicit.FallbackNoRequirementsContainerResolver(app_info: AppInfo, identifier: str = '', **kwds)

Bases: FallbackContainerResolver

resolver_type = 'fallback_no_requirements'

class galaxy.tool_util.deps.container_resolvers.explicit.FallbackNoRequirementsSingularityContainerResolver(app_info: AppInfo, identifier: str = '', **kwds)

Bases: FallbackNoRequirementsContainerResolver

resolver_type = 'fallback_no_requirements_singularity'

container_type = 'singularity'

class galaxy.tool_util.deps.container_resolvers.explicit.MappingContainerResolver(app_info: AppInfo, **kwds)

Bases: BaseAdminConfiguredContainerResolver

resolver_type = 'mapping'

__init__(app_info: AppInfo, **kwds) → None

Default initializer for ContainerResolver subclasses.

resolve(enabled_container_types: Container[str], tool_info: ToolInfo, **kwds) → Optional[ContainerDescription]

Find a container matching all supplied requirements for tool.

The supplied argument is a galaxy.tool_util.deps.dependencies.ToolInfo description of the tool and its requirements.

class galaxy.tool_util.deps.container_resolvers.explicit.RequiresGalaxyEnvironmentContainerResolver(app_info: AppInfo, identifier: str = '', **kwds)

Bases: FallbackContainerResolver

resolver_type = 'requires_galaxy_environment'

class galaxy.tool_util.deps.container_resolvers.explicit.RequiresGalaxyEnvironmentSingularityContainerResolver(app_info: AppInfo, identifier: str = '', **kwds)

Bases: RequiresGalaxyEnvironmentContainerResolver

resolver_type = 'requires_galaxy_environment_singularity'

container_type = 'singularity'

galaxy.tool_util.deps.container_resolvers.mulled module

This module describes the MulledContainerResolver ContainerResolver plugin.

class galaxy.tool_util.deps.container_resolvers.mulled.CachedMulledDockerContainerResolver(app_info: AppInfo, namespace: str = 'biocontainers', hash_func: typing_extensions.Literal[v1, v2] = 'v2', **kwds)

Bases: CliContainerResolver

resolver_type = 'cached_mulled'

shell = '/bin/bash'

__init__(app_info: AppInfo, namespace: str = 'biocontainers', hash_func: typing_extensions.Literal[v1, v2] = 'v2', **kwds)

Default initializer for ContainerResolver subclasses.

resolve(enabled_container_types: Container[str], tool_info: ToolInfo, **kwds) → Optional[ContainerDescription]

Find a container matching all supplied requirements for tool.

The supplied argument is a galaxy.tool_util.deps.dependencies.ToolInfo description of the tool and its requirements.

class galaxy.tool_util.deps.container_resolvers.mulled.CachedMulledSingularityContainerResolver(app_info: AppInfo, hash_func: typing_extensions.Literal[v1, v2] = 'v2', **kwargs)

Bases: SingularityCliContainerResolver

resolver_type = 'cached_mulled_singularity'

shell = '/bin/bash'

resolve(enabled_container_types: Container[str], tool_info: ToolInfo, **kwds) → Optional[ContainerDescription]

Find a container matching all supplied requirements for tool.

The supplied argument is a galaxy.tool_util.deps.dependencies.ToolInfo description of the tool and its requirements.

class galaxy.tool_util.deps.container_resolvers.mulled.MulledDockerContainerResolver(app_info: AppInfo, namespace: str = 'biocontainers', hash_func: typing_extensions.Literal[v1, v2] = 'v2', auto_install: bool = True, **kwds)

Bases: CliContainerResolver

Look for mulled images matching tool dependencies.

resolver_type = 'mulled'

shell = '/bin/bash'

protocol: Optional[str] = None

__init__(app_info: AppInfo, namespace: str = 'biocontainers', hash_func: typing_extensions.Literal[v1, v2] = 'v2', auto_install: bool = True, **kwds) → None

Default initializer for ContainerResolver subclasses.

cached_container_description(targets: List[CondaTarget], namespace: str, hash_func: typing_extensions.Literal[v1, v2], resolution_cache: Optional[ResolutionCache] = None) → Optional[ContainerDescription]

pull(container: Container) → None

property can_list_containers: bool

resolve(enabled_container_types: Container[str], tool_info: ToolInfo, install: bool = False, session: Optional[Session] = None, **kwds) → Optional[ContainerDescription]

Find a container matching all supplied requirements for tool.

The supplied argument is a galaxy.tool_util.deps.dependencies.ToolInfo description of the tool and its requirements.

class galaxy.tool_util.deps.container_resolvers.mulled.MulledSingularityContainerResolver(app_info: AppInfo, hash_func: typing_extensions.Literal[v1, v2] = 'v2', namespace: str = 'biocontainers', auto_install: bool = True, **kwds)

Bases: SingularityCliContainerResolver, MulledDockerContainerResolver

resolver_type = 'mulled_singularity'

protocol: Optional[str] = 'docker://'

__init__(app_info: AppInfo, hash_func: typing_extensions.Literal[v1, v2] = 'v2', namespace: str = 'biocontainers', auto_install: bool = True, **kwds) → None

Default initializer for ContainerResolver subclasses.

cached_container_description(targets: List[CondaTarget], namespace: str, hash_func: typing_extensions.Literal[v1, v2], resolution_cache: Optional[ResolutionCache] = None) → Optional[ContainerDescription]

property can_list_containers: bool

pull(container: Container) → None

class galaxy.tool_util.deps.container_resolvers.mulled.BuildMulledDockerContainerResolver(app_info: AppInfo, namespace: str = 'local', hash_func: typing_extensions.Literal[v1, v2] = 'v2', auto_install: bool = True, **kwds)

Bases: CliContainerResolver

Build for Docker mulled images matching tool dependencies.

resolver_type = 'build_mulled'

shell = '/bin/bash'

builds_on_resolution = True

__init__(app_info: AppInfo, namespace: str = 'local', hash_func: typing_extensions.Literal[v1, v2] = 'v2', auto_install: bool = True, **kwds) → None

Default initializer for ContainerResolver subclasses.

resolve(enabled_container_types: Container[str], tool_info: ToolInfo, install: bool = False, **kwds) → Optional[ContainerDescription]

Find a container matching all supplied requirements for tool.

The supplied argument is a galaxy.tool_util.deps.dependencies.ToolInfo description of the tool and its requirements.

class galaxy.tool_util.deps.container_resolvers.mulled.BuildMulledSingularityContainerResolver(app_info: AppInfo, hash_func: typing_extensions.Literal[v1, v2] = 'v2', auto_install: bool = True, **kwds)

Bases: SingularityCliContainerResolver

Build for Singularity mulled images matching tool dependencies.

resolver_type = 'build_mulled_singularity'

shell = '/bin/bash'

builds_on_resolution = True

__init__(app_info: AppInfo, hash_func: typing_extensions.Literal[v1, v2] = 'v2', auto_install: bool = True, **kwds) → None

Default initializer for ContainerResolver subclasses.

resolve(enabled_container_types: Container[str], tool_info: ToolInfo, install: bool = False, **kwds) → Optional[ContainerDescription]

Find a container matching all supplied requirements for tool.

The supplied argument is a galaxy.tool_util.deps.dependencies.ToolInfo description of the tool and its requirements.