cwltool.pathmapper

Module Contents

Classes

PathMapper

Mapping of files from relative path provided in the file to a tuple.

Attributes

MapperEnt

cwltool.pathmapper.MapperEnt
class cwltool.pathmapper.PathMapper(referenced_files, basedir, stagedir, separateDirs=True)

Mapping of files from relative path provided in the file to a tuple.

(absolute local path, absolute container path)

The tao of PathMapper:

The initializer takes a list of File and Directory objects, a base directory (for resolving relative references) and a staging directory (where the files are mapped to).

The purpose of the setup method is to determine where each File or Directory should be placed on the target file system (relative to stagedir).

If separatedirs=True, unrelated files will be isolated in their own directories under stagedir. If separatedirs=False, files and directories will all be placed in stagedir (with the possibility for name collisions…)

The path map maps the “location” of the input Files and Directory objects to a tuple (resolved, target, type). The “resolved” field is the “real” path on the local file system (after resolving relative paths and traversing symlinks). The “target” is the path on the target file system (under stagedir). The type is the object type (one of File, Directory, CreateFile, WritableFile, CreateWritableFile).

The latter three (CreateFile, WritableFile, CreateWritableFile) are used by InitialWorkDirRequirement to indicate files that are generated on the fly (CreateFile and CreateWritableFile, in this case “resolved” holds the file contents instead of the path because they file doesn’t exist) or copied into the output directory so they can be opened for update (“r+” or “a”) (WritableFile and CreateWritableFile).

Parameters
  • referenced_files (List[cwltool.utils.CWLObjectType]) –

  • basedir (str) –

  • stagedir (str) –

  • separateDirs (bool) –

visitlisting(self, listing, stagedir, basedir, copy=False, staged=False)
Parameters
  • listing (List[cwltool.utils.CWLObjectType]) –

  • stagedir (str) –

  • basedir (str) –

  • copy (bool) –

  • staged (bool) –

Return type

None

visit(self, obj, stagedir, basedir, copy=False, staged=False)
Parameters
  • obj (cwltool.utils.CWLObjectType) –

  • stagedir (str) –

  • basedir (str) –

  • copy (bool) –

  • staged (bool) –

Return type

None

setup(self, referenced_files, basedir)
Parameters
  • referenced_files (List[cwltool.utils.CWLObjectType]) –

  • basedir (str) –

Return type

None

mapper(self, src)
Parameters

src (str) –

Return type

MapperEnt

files(self)
Return type

List[str]

items(self)
Return type

List[Tuple[str, MapperEnt]]

reversemap(self, target)

Find the (source, resolved_path) for the given target, if any.

Parameters

target (str) –

Return type

Optional[Tuple[str, str]]

update(self, key, resolved, target, ctype, stage)
Parameters
  • key (str) –

  • resolved (str) –

  • target (str) –

  • ctype (str) –

  • stage (bool) –

Return type

MapperEnt

__contains__(self, key)

Test for the presence of the given relative path in this mapper.

Parameters

key (str) –

Return type

bool

__iter__(self)

Get iterator for the maps.

Return type

Iterator[MapperEnt]