cwltool.builder

Module Contents

Classes

Builder

Base class for get_requirement().

Functions

content_limit_respected_read_bytes(f)

content_limit_respected_read(f)

substitute(value, replace)

formatSubclassOf(fmt, cls, ontology, visited)

Determine if fmt is a subclass of cls.

check_format(actual_file, input_formats, ontology)

Confirm that the format present is valid for the allowed formats.

Attributes

INPUT_OBJ_VOCAB

cwltool.builder.INPUT_OBJ_VOCAB :Dict[str, str]
cwltool.builder.content_limit_respected_read_bytes(f)
Parameters

f (IO[bytes]) –

Return type

bytes

cwltool.builder.content_limit_respected_read(f)
Parameters

f (IO[bytes]) –

Return type

str

cwltool.builder.substitute(value, replace)
Parameters
  • value (str) –

  • replace (str) –

Return type

str

cwltool.builder.formatSubclassOf(fmt, cls, ontology, visited)

Determine if fmt is a subclass of cls.

Parameters
  • fmt (str) –

  • cls (str) –

  • ontology (Optional[rdflib.Graph]) –

  • visited (Set[str]) –

Return type

bool

cwltool.builder.check_format(actual_file, input_formats, ontology)

Confirm that the format present is valid for the allowed formats.

Parameters
  • actual_file (Union[cwltool.utils.CWLObjectType, List[cwltool.utils.CWLObjectType]]) –

  • input_formats (Union[List[str], str]) –

  • ontology (Optional[rdflib.Graph]) –

Return type

None

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

Base class for get_requirement().

Parameters
  • job (cwltool.utils.CWLObjectType) –

  • files (List[cwltool.utils.CWLObjectType]) –

  • bindings (List[cwltool.utils.CWLObjectType]) –

  • schemaDefs (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 (typing_extensions.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 (str) –

  • outdir (str) –

  • tmpdir (str) –

  • stagedir (str) –

  • cwlVersion (str) –

  • container_engine (str) –

build_job_script(self, commands)
Parameters

commands (List[str]) –

Return type

Optional[str]

bind_input(self, schema, datum, discover_secondaryFiles, lead_pos=None, tail_pos=None)
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[MutableMapping[str, Union[str, List[int]]]]

tostr(self, value)
Parameters

value (Union[MutableMapping[str, str], Any]) –

Return type

str

generate_arg(self, binding)
Parameters

binding (cwltool.utils.CWLObjectType) –

Return type

List[str]

do_eval(self, 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]