cwltool.pathmapper

Module Contents

Classes

PathMapper

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

Attributes

MapperEnt

Mapper entries.
cwltool.pathmapper.MapperEnt

Mapper entries.

cwltool.pathmapper.resolved: str

The “real” path on the local file system (after resolving relative paths and traversing symlinks

cwltool.pathmapper.target: str

The path on the target file system (under stagedir)

cwltool.pathmapper.type: str

The object type. One of “File”, “Directory”, “CreateFile”, “WritableFile”, or “CreateWritableFile”.

cwltool.pathmapper.staged: bool

If the File has been staged yet

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 class: File and class: 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(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(obj, stagedir, basedir, copy=False, staged=False)
Parameters:

  • obj (cwltool.utils.CWLObjectType)

  • stagedir (str)

  • basedir (str)

  • copy (bool)

  • staged (bool)

Return type:

None

setup(referenced_files, basedir)
Parameters:

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

  • basedir (str)

Return type:

None

mapper(src)
Parameters:

src (str)

Return type:

MapperEnt

files()

Return a dictionary keys view of locations.

Return type:

KeysView[str]

items()

Return a dictionary items view.

Return type:

ItemsView[str, MapperEnt]

items_exclude_children()

Return a dictionary items view minus any entries which are children of other entries.

Return type:

ItemsView[str, MapperEnt]

reversemap(target)

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

Parameters:

target (str)

Return type:

Optional[Tuple[str, str]]

update(key, resolved, target, ctype, stage)

Update an existine entry.

Parameters:
Return type:

MapperEnt

__contains__(key)

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

Parameters:

key (str)

Return type:

bool

__iter__()

Get iterator for the maps.

Return type:

Iterator[MapperEnt]