cwltool.builder

Command line builder.

Attributes

INPUT_OBJ_VOCAB

Classes

Builder

Helper class to construct a command line from a CWL CommandLineTool.

Functions

`content_limit_respected_read_bytes`(f)	Read a file as bytes, respecting the `CONTENT_LIMIT`.
`content_limit_respected_read`(f)	Read a file as a string, respecting the `CONTENT_LIMIT`.
`substitute`(value, replace)	Perform CWL SecondaryFilesDSL style substitution.

Module Contents

cwltool.builder.INPUT_OBJ_VOCAB: dict[str, str]

cwltool.builder.content_limit_respected_read_bytes(f)

Read a file as bytes, respecting the CONTENT_LIMIT.

Parameters:: f (IO[bytes]) – file handle
Returns:: the file contents
Raises:: WorkflowException – if the file is too large
Return type:: bytes

cwltool.builder.content_limit_respected_read(f)

Read a file as a string, respecting the CONTENT_LIMIT.

Parameters:: f (IO[bytes]) – file handle
Returns:: the file contents
Raises:: WorkflowException – if the file is too large
Return type:: str

cwltool.builder.substitute(value, replace)

Perform CWL SecondaryFilesDSL style substitution.

Parameters:

value (str)
replace (str)

Return type:

str

class cwltool.builder.Builder(job, files, bindings, schemaDefs, names, requirements, hints, resources, mutation_manager, formatgraph, make_fs_access, fs_access, job_script_provider, timeout, debug, js_console, force_docker_pull, loadListing, outdir, tmpdir, stagedir, cwlVersion, container_engine)

Bases: cwltool.utils.HasReqsHints

Inheritance diagram of cwltool.builder.Builder

Helper class to construct a command line from a CWL CommandLineTool.

Parameters:

job (cwltool.utils.CWLObjectType)
files (list[cwltool.utils.CWLObjectType])
bindings (list[cwltool.utils.CWLObjectType])
schemaDefs (collections.abc.MutableMapping[str, cwltool.utils.CWLObjectType])
names (schema_salad.avro.schema.Names)
requirements (list[cwltool.utils.CWLObjectType])
hints (list[cwltool.utils.CWLObjectType])
resources (dict[str, Union[int, float]])
mutation_manager (Optional[cwltool.mutation.MutationManager])
formatgraph (Optional[rdflib.Graph])
make_fs_access (type[cwltool.stdfsaccess.StdFsAccess])
fs_access (cwltool.stdfsaccess.StdFsAccess)
job_script_provider (Optional[cwltool.software_requirements.DependenciesConfiguration])
timeout (float)
debug (bool)
js_console (bool)
force_docker_pull (bool)
loadListing (cwltool.utils.LoadListingType)
outdir (str)
tmpdir (str)
stagedir (str)
cwlVersion (str)
container_engine (str)

job

files

bindings

schemaDefs

names

requirements

hints

resources

mutation_manager

formatgraph

make_fs_access

fs_access

job_script_provider

timeout

debug

js_console

force_docker_pull

loadListing

outdir

tmpdir

stagedir

cwlVersion

pathmapper: cwltool.pathmapper.PathMapper | None = None

prov_obj: cwltool.cwlprov.provenance_profile.ProvenanceProfile | None = None

find_default_container: Callable[[], str] | None = None

container_engine

build_job_script(commands)

Use the job_script_provider to turn the commands into a job script.

Parameters:: commands (list[str])
Return type:: Optional[str]

bind_input(schema, datum, discover_secondaryFiles, lead_pos=None, tail_pos=None)

Bind an input object to the command line.

Raises:

ValidationException – in the event of an invalid type union
WorkflowException – if a CWL Expression (“position”, “required”, “pattern”, “format”) evaluates to the wrong type or if a required secondary file is missing

Parameters:

schema (cwltool.utils.CWLObjectType)
datum (Union[cwltool.utils.CWLObjectType, list[cwltool.utils.CWLObjectType]])
discover_secondaryFiles (bool)
lead_pos (Optional[Union[int, list[int]]])
tail_pos (Optional[Union[str, list[int]]])

Return type:

list[collections.abc.MutableMapping[str, Union[str, list[int]]]]

tostr(value)

Represent an input parameter as a string.

Raises:: WorkflowException – if the item is a File or Directory and the “path” is missing.
Parameters:: value (Union[collections.abc.MutableMapping[str, str], Any])
Return type:: str

generate_arg(binding)

Convert an input binding to a list of command line arguments.

Parameters:: binding (cwltool.utils.CWLObjectType)
Return type:: list[str]

do_eval(ex, context=None, recursive=False, strip_whitespace=True)

Parameters:

ex (Optional[cwltool.utils.CWLOutputType])
context (Optional[Any])
recursive (bool)
strip_whitespace (bool)

Return type:

Optional[cwltool.utils.CWLOutputType]