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galaxy.tool_util.cwl package

galaxy.tool_util.cwl.tool_proxy(tool_path=None, tool_object=None, strict_cwl_validation=True, tool_directory=None, uuid=None) → ToolProxy

Provide a proxy object to cwltool data structures to just grab relevant data.

galaxy.tool_util.cwl.tool_proxy_from_persistent_representation(persisted_tool, strict_cwl_validation=True, tool_directory=None) → ToolProxy

Load a ToolProxy from a previously persisted representation.

galaxy.tool_util.cwl.workflow_proxy(workflow_path, strict_cwl_validation=True) → WorkflowProxy

galaxy.tool_util.cwl.handle_outputs(job_directory=None)

galaxy.tool_util.cwl.to_cwl_job(tool, param_dict, local_working_directory)

tool is Galaxy’s representation of the tool and param_dict is the parameter dictionary with wrapped values.

galaxy.tool_util.cwl.to_galaxy_parameters(tool, as_dict)

Tool is Galaxy’s representation of the tool and as_dict is a Galaxified representation of the input json (no paths, HDA references for instance).

galaxy.tool_util.cwl.needs_shell_quoting(string, pos=0, endpos=9223372036854775807)

Scan through string looking for a match, and return a corresponding match object instance.

Return None if no position in the string matches.

Submodules

galaxy.tool_util.cwl.cwltool_deps module

Logic for dealing with cwltool as an optional dependency.

Use this as the import interface for cwltool and just call ensure_cwltool_available() before using any of the imported functionality at runtime.

class galaxy.tool_util.cwl.cwltool_deps.CommentedMap(*args: Any, **kw: Any)

Bases: ordereddict, CommentedBase

__init__(*args: Any, **kw: Any) → None

update([E, ]**F) → None.  Update D from dict/iterable E and F.

If E is present and has a .keys() method, then does: for k in E: D[k] = E[k] If E is present and lacks a .keys() method, then does: for k, v in E: D[k] = v In either case, this is followed by: for k in F: D[k] = F[k]

insert(pos: Any, key: Any, value: Any, comment: Optional[Any] = None) → None

insert key value into given position attach comment if provided

mlget(key: Any, default: Any = None, list_ok: Any = False) → Any

multi-level get that expects dicts within dicts

get(key: Any, default: Any = None) → Any

Return the value for key if key is in the dictionary, else default.

non_merged_items() → Any

keys() → a set-like object providing a view on D's keys

values() → an object providing a view on D's values

items() → a set-like object providing a view on D's items

property merge

copy() → a shallow copy of od

add_referent(cm: Any) → None

add_yaml_merge(value: Any) → None

update_key_value(key: Any) → None

galaxy.tool_util.cwl.cwltool_deps.default_loader(fetcher_constructor: Optional[Callable[[Dict[str, Union[str, Graph, bool]], Session], Fetcher]] = None, enable_dev: bool = False, doc_cache: bool = True) → Loader

galaxy.tool_util.cwl.cwltool_deps.ensure_cwltool_available()

Assert optional dependencies proxied via this module are available at runtime.

Throw an ImportError with a description of the problem if they do not exist.

galaxy.tool_util.cwl.cwltool_deps.getdefault(val: Any, default: Any) → Any

class galaxy.tool_util.cwl.cwltool_deps.LoadingContext(kwargs: Optional[Dict[str, Any]] = None)

Bases: ContextBase

__init__(kwargs: Optional[Dict[str, Any]] = None) → None

Initialize the LoadingContext from the kwargs.

copy() → LoadingContext

galaxy.tool_util.cwl.cwltool_deps.needs_shell_quoting(string, pos=0, endpos=9223372036854775807)

Scan through string looking for a match, and return a corresponding match object instance.

Return None if no position in the string matches.

galaxy.tool_util.cwl.cwltool_deps.normalizeFilesDirs(job: Optional[Union[MutableSequence[MutableMapping[str, Any]], MutableMapping[str, Any], DirectoryType]]) → None

galaxy.tool_util.cwl.cwltool_deps.relink_initialworkdir(pathmapper: PathMapper, host_outdir: str, container_outdir: str, inplace_update: bool = False) → None

galaxy.tool_util.cwl.cwltool_deps.resolve_and_validate_document(loadingContext: LoadingContext, workflowobj: Union[CommentedMap, CommentedSeq], uri: str, preprocess_only: bool = False, skip_schemas: Optional[bool] = None) → Tuple[LoadingContext, str]

Validate a CWL document.

class galaxy.tool_util.cwl.cwltool_deps.RuntimeContext(kwargs: Optional[Dict[str, Any]] = None)

Bases: ContextBase

__init__(kwargs: Optional[Dict[str, Any]] = None) → None

Initialize the RuntimeContext from the kwargs.

get_outdir() → str

Return self.outdir or create one with self.tmp_outdir_prefix.

get_tmpdir() → str

Return self.tmpdir or create one with self.tmpdir_prefix.

get_stagedir() → str

Return self.stagedir or create one with self.tmpdir_prefix.

create_tmpdir() → str

Create a temporary directory that respects self.tmpdir_prefix.

create_outdir() → str

Create a temporary directory that respects self.tmp_outdir_prefix.

copy() → RuntimeContext

class galaxy.tool_util.cwl.cwltool_deps.StdFsAccess(basedir: str)

Bases: object

Local filesystem implementation.

__init__(basedir: str) → None

Perform operations with respect to a base directory.

glob(pattern: str) → List[str]

open(fn: str, mode: str) → IO[Any]

exists(fn: str) → bool

size(fn: str) → int

isfile(fn: str) → bool

isdir(fn: str) → bool

listdir(fn: str) → List[str]

join(path: str, *paths: str) → str

realpath(path: str) → str

galaxy.tool_util.cwl.cwltool_deps.visit_class(rec: Any, cls: Iterable[Any], op: Callable[[...], Any]) → None

Apply a function to with “class” in cls.

galaxy.tool_util.cwl.cwltool_deps.yaml_no_ts()

galaxy.tool_util.cwl.parser module

This module provides proxy objects around objects from the common workflow language reference implementation library cwltool. These proxies adapt cwltool to Galaxy features and abstract the library away from the rest of the framework.

galaxy.tool_util.cwl.parser.tool_proxy(tool_path=None, tool_object=None, strict_cwl_validation=True, tool_directory=None, uuid=None) → ToolProxy

Provide a proxy object to cwltool data structures to just grab relevant data.

galaxy.tool_util.cwl.parser.load_job_proxy(job_directory, strict_cwl_validation=True) → JobProxy

galaxy.tool_util.cwl.representation module

This module is responsible for converting between Galaxy’s tool input description and the CWL description for a job json.

class galaxy.tool_util.cwl.representation.INPUT_TYPE(value)

Bases: str, Enum

An enumeration.

DATA = 'data'

INTEGER = 'integer'

FLOAT = 'float'

TEXT = 'text'

BOOLEAN = 'boolean'

SELECT = 'select'

FIELD = 'field'

CONDITIONAL = 'conditional'

DATA_COLLECTION = 'data_collection'

class galaxy.tool_util.cwl.representation.TypeRepresentation(name, galaxy_param_type, label, collection_type)

Bases: tuple

property name

Alias for field number 0

property galaxy_param_type

Alias for field number 1

property label

Alias for field number 2

property collection_type

Alias for field number 3

property uses_param

galaxy.tool_util.cwl.representation.type_representation_from_name(type_representation_name)

galaxy.tool_util.cwl.representation.type_descriptions_for_field_types(field_types)

galaxy.tool_util.cwl.representation.dataset_wrapper_to_file_json(inputs_dir, dataset_wrapper)

galaxy.tool_util.cwl.representation.dataset_wrapper_to_directory_json(inputs_dir, dataset_wrapper)

galaxy.tool_util.cwl.representation.collection_wrapper_to_array(inputs_dir, wrapped_value)

galaxy.tool_util.cwl.representation.collection_wrapper_to_record(inputs_dir, wrapped_value)

galaxy.tool_util.cwl.representation.to_cwl_job(tool, param_dict, local_working_directory)

tool is Galaxy’s representation of the tool and param_dict is the parameter dictionary with wrapped values.

galaxy.tool_util.cwl.representation.to_galaxy_parameters(tool, as_dict)

Tool is Galaxy’s representation of the tool and as_dict is a Galaxified representation of the input json (no paths, HDA references for instance).

galaxy.tool_util.cwl.representation.field_to_field_type(field)

galaxy.tool_util.cwl.runnable module

Lighter-weight variant of Planemo runnable outputs.

galaxy.tool_util.cwl.runnable.get_outputs(path)

class galaxy.tool_util.cwl.runnable.CwlWorkflowOutput(label)

Bases: object

__init__(label)

get_id()

class galaxy.tool_util.cwl.runnable.ToolOutput(tool_output)

Bases: object

__init__(tool_output)

get_id()

galaxy.tool_util.cwl.runtime_actions module

galaxy.tool_util.cwl.runtime_actions.handle_outputs(job_directory=None)

galaxy.tool_util.cwl.schema module

Abstraction around cwltool and related libraries for loading a CWL artifact.

class galaxy.tool_util.cwl.schema.RawProcessReference(loading_context, process_object, uri)

Bases: tuple

property loading_context

Alias for field number 0

property process_object

Alias for field number 1

property uri

Alias for field number 2

class galaxy.tool_util.cwl.schema.ResolvedProcessDefinition(loading_context, uri, raw_process_reference)

Bases: tuple

property loading_context

Alias for field number 0

property uri

Alias for field number 1

property raw_process_reference

Alias for field number 2

class galaxy.tool_util.cwl.schema.SchemaLoader(strict=True, validate=True)

Bases: object

__init__(strict=True, validate=True)

property raw_document_loader

loading_context()

raw_process_reference(path, loading_context=None)

raw_process_reference_for_object(process_object, uri=None, loading_context=None)

process_definition(raw_process_reference: RawProcessReference) → ResolvedProcessDefinition

tool(**kwds)

galaxy.tool_util.cwl.util module

Client-centric CWL-related utilities.

Used to share code between the Galaxy test framework and other Galaxy CWL clients (e.g. Planemo).

galaxy.tool_util.cwl.util.set_basename_and_derived_properties(properties, basename)

class galaxy.tool_util.cwl.util.OutputPropertiesType(**kwargs)

Bases: dict

class: str

location: Optional[str]

path: Optional[str]

listing: Optional[List[Any]]

basename: Optional[str]

nameroot: Optional[str]

nameext: Optional[str]

secondaryFiles: List[Any]

checksum: str

size: int

galaxy.tool_util.cwl.util.output_properties(path: Optional[str] = None, content: Optional[bytes] = None, basename=None, pseudo_location=False) → OutputPropertiesType

galaxy.tool_util.cwl.util.abs_path_or_uri(path_or_uri: str, relative_to: str) → str

Return the absolute path if this isn’t a URI, otherwise keep the URI the same.

galaxy.tool_util.cwl.util.abs_path(path_or_uri: str, relative_to: str) → str

Return the absolute path if this is a file:// URI or a local path.

galaxy.tool_util.cwl.util.path_or_uri_to_uri(path_or_uri: str) → str

galaxy.tool_util.cwl.util.galactic_job_json(job: Dict[str, Any], test_data_directory: str, upload_func: Callable[[UploadTarget], Dict[str, Any]], collection_create_func: Callable[[List[Dict[str, Any]], str], Dict[str, Any]], tool_or_workflow: typing_extensions.Literal[tool, workflow] = 'workflow') → Tuple[Dict[str, Any], List[Dict[str, Any]]]

Adapt a CWL job object to the Galaxy API.

CWL derived tools in Galaxy can consume a job description sort of like CWL job objects via the API but paths need to be replaced with datasets and records and arrays with collection references. This function will stage files and modify the job description to adapt to these changes for Galaxy.

class galaxy.tool_util.cwl.util.UploadTarget

Bases: object

class galaxy.tool_util.cwl.util.FileLiteralTarget(contents: str, **kwargs)

Bases: UploadTarget

__init__(contents: str, **kwargs) → None

class galaxy.tool_util.cwl.util.FileUploadTarget(path: Optional[str], secondary_files: Optional[str] = None, composite_data: Optional[List[str]] = None, **kwargs)

Bases: UploadTarget

__init__(path: Optional[str], secondary_files: Optional[str] = None, composite_data: Optional[List[str]] = None, **kwargs) → None

class galaxy.tool_util.cwl.util.ObjectUploadTarget(the_object: Any)

Bases: UploadTarget

__init__(the_object: Any) → None

class galaxy.tool_util.cwl.util.DirectoryUploadTarget(tar_path: str)

Bases: UploadTarget

__init__(tar_path: str) → None

class galaxy.tool_util.cwl.util.GalaxyOutput(history_id, history_content_type, history_content_id, metadata)

Bases: tuple

property history_content_id

Alias for field number 2

property history_content_type

Alias for field number 1

property history_id

Alias for field number 0

property metadata

Alias for field number 3

galaxy.tool_util.cwl.util.tool_response_to_output(tool_response, history_id, output_name)

galaxy.tool_util.cwl.util.invocation_to_output(invocation, history_id, output_name)

galaxy.tool_util.cwl.util.output_to_cwl_json(galaxy_output, get_metadata, get_dataset, get_extra_files, pseudo_location=False)

Convert objects in a Galaxy history into a CWL object.

Useful in running conformance tests and implementing the cwl-runner interface via Galaxy.

galaxy.tool_util.cwl.util.download_output(galaxy_output, get_metadata, get_dataset, get_extra_files, output_path)

galaxy.tool_util.cwl.util.guess_artifact_type(path)