See also

• @mkdir in the Ruffus Manual
• @follows(mkdir(“dir”)) specifies the creation of a single directory as a task pre-requisite.
• Decorators for more decorators

@mkdir( input, filter, output )

Purpose:

• Prepares directories to receive Output files
• Used when Output path names are generated at runtime from Inputs. mkdir can make sure these runtime specified paths exist.
• Directory names are generated from Input using string substitution via formatter(), suffix() or regex().
• Behaves essentially like @transform but with its own (internal) function which does the actual work of making a directory
• Does not invoke the host task function to which it is attached
• Makes specified directories using os.makedirs
• Multiple directories can be created in a list

Note

Only missing directories are created.

In other words, the same directory can be specified multiple times safely without, for example, being recreated repeatedly.

Sometimes, for pipelines with multiple entry points, this is the only way to make sure that certain working or output directories are always created or available before the pipeline runs.

Simple Example

Creates multiple directories per job to hold the results of @transform

from ruffus import *

#   initial files
@originate([ 'A.start',
             'B.start'])
def create_initial_files(output_file):
    with open(output_file, "w") as oo: pass


# create files without making directories -> ERROR
@transform( create_initial_files,
            formatter(),
            ["{path[0]}/{basename[0]}/processed.txt",
             "{path[0]}/{basename[0]}.tmp/tmp.processed.txt"])
def create_files_without_mkdir(input_file, output_files):
    open(output_files[0], "w")
    open(output_files[1], "w")


# create files after making corresponding directories
@mkdir( create_initial_files,
        formatter(),
        ["{path[0]}/{basename[0]}",         # create directory
         "{path[0]}/{basename[0]}.tmp"])    # create directory.tmp
@transform( create_initial_files,
            formatter(),
            ["{path[0]}/{basename[0]}/processed.txt",
             "{path[0]}/{basename[0]}.tmp/tmp.processed.txt"])
def create_files_with_mkdir(input_file, output_files):
    open(output_files[0], "w")
    open(output_files[1], "w")

pipeline_run([create_files_without_mkdir])
pipeline_run([create_files_with_mkdir])

Running without making the directories first gives errors:

>>> pipeline_run([create_files_without_mkdir])
    Job  = [None -> A.start] completed
    Job  = [None -> B.start] completed
Completed Task = create_initial_files

    Traceback (most recent call last):
      File "<stdin>", line 1, in <module>
      File "/usr/local/lib/python2.7/dist-packages/ruffus/task.py", line 3738, in pipeline_run
        raise job_errors
    ruffus.ruffus_exceptions.RethrownJobError:

    Original exception:

>>> #    Exception #1
>>> #      'exceptions.IOError([Errno 2] No such file or directory: 'A/processed.txt')' raised in ...
>>> #       Task = def create_files_without_mkdir(...):
>>> #       Job  = [A.start -> [processed.txt, tmp.processed.txt]]

Running after making the directories first:

>>> pipeline_run([create_files_with_mkdir])
    Job  = [None -> A.start] completed
    Job  = [None -> B.start] completed
Completed Task = create_initial_files
    Make directories [A, A.tmp] completed
    Make directories [B, B.tmp] completed
Completed Task = (mkdir 1) before create_files_with_mkdir
    Job  = [A.start -> [processed.txt, tmp.processed.txt]] completed
    Job  = [B.start -> [processed.txt, tmp.processed.txt]] completed
Completed Task = create_files_with_mkdir

Parameters:

• input = tasks_or_file_names

  can be a:

  1. Task / list of tasks (as in the example above).

     File names are taken from the output of the specified task(s)

  2. (Nested) list of file name strings.

     File names containing *[]? will be expanded as a glob.

     E.g.:"a.*" => "a.1", "a.2"

• filter = suffix(suffix_string)

  must be wrapped in a suffix indicator object. The end of each input file name which matches suffix_string will be replaced by output.

  Input file names which do not match suffix_string will be ignored

  The non-suffix part of the match can be referred to using the r"\1" pattern. This can be useful for putting the output in different directory, for example:

  @mkdir(["1.c", "2.c"], suffix(".c"), r"my_path/\1.o")
  def compile(infile, outfile):
      pass
  

  This results in the following function calls:

  # 1.c -> my_path/1.o
  # 2.c -> my_path/2.o
  compile("1.c", "my_path/1.o")
  compile("2.c", "my_path/2.o")
  

  For convenience and visual clarity, the "\1" can be omitted from the output parameter. However, the "\1" is mandatory for string substitutions in additional parameters,

  @mkdir(["1.c", "2.c"], suffix(".c"), [r"\1.o", ".o"], "Compiling \1", "verbatim")
  def compile(infile, outfile):
      pass
  

  Results in the following function calls:

  compile("1.c", ["1.o", "1.o"], "Compiling 1", "verbatim")
  compile("2.c", ["2.o", "2.o"], "Compiling 2", "verbatim")
  

  Since r”1” is optional for the output parameter, "\1.o" and ".o" are equivalent. However, strings in other parameters which do not contain r”1” will be included verbatim, much like the string "verbatim" in the above example.

• filter = regex(matching_regex)

  is a python regular expression string, which must be wrapped in a regex indicator object See python regular expression (re) documentation for details of regular expression syntax Each output file name is created using regular expression substitution with output

• filter = formatter(...)

  a formatter indicator object containing optionally a python regular expression (re).

• output = output

  Specifies the directories to be created after string substitution