cwltool.builder
Command line builder.
Module Contents
Classes
Helper class to construct a command line from a CWL CommandLineTool. |
Functions
Read a file as bytes, respecting the |
|
Read a file as a string, respecting the |
|
|
Perform CWL SecondaryFilesDSL style substitution. |
Attributes
- 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:
- 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:
- cwltool.builder.substitute(value, replace)
Perform CWL SecondaryFilesDSL style substitution.
- 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
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 (MutableMapping[str, cwltool.utils.CWLObjectType]) –
names (schema_salad.avro.schema.Names) –
requirements (List[cwltool.utils.CWLObjectType]) –
hints (List[cwltool.utils.CWLObjectType]) –
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) –
- 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:
- Return type:
- 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:
- Return type: