Python Code for: New Object orientated syntax for Ruffus in Version 2.6¶

#!/usr/bin/env python
from __future__ import print_function
"""


        Demonstrates the new Ruffus syntax in version 2.6
"""

import os
import sys

# add grandparent to search path for testing
grandparent_dir = os.path.abspath(os.path.join(os.path.dirname(__file__), "..", ".."))
sys.path.insert(0, grandparent_dir)

import ruffus
from ruffus import add_inputs, suffix, mkdir, regex, Pipeline, output_from, touch_file
print("\tRuffus Version = ", ruffus.__version__)

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#   imports


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import shutil


def touch (outfile):
    with open(outfile, "w"):
        pass


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#   Tasks


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tempdir = "tempdir/"
def task_originate(o):
    """
    Makes new files
    """
    touch(o)

def task_m_to_1(i, o):
    """
    Merges files together
    """
    with open(o, "w") as o_file:
        for f in sorted(i):
            with open(f) as ii:
                o_file.write(f +"=" + ii.read() + "; ")

def task_1_to_1(i, o):
    """
    1 to 1 for transform
    """
    with open(o, "w") as o_file:
        with open(i) as ii:
            o_file.write(i +"+" + ii.read())

DEBUG_do_not_define_tail_task = False
DEBUG_do_not_define_head_task = False

import unittest

#
#   Returns a fully formed sub pipeline useable as a building block
#
def make_pipeline1(pipeline_name,   # Pipelines need to have a unique name
                   starting_file_names):
    test_pipeline = Pipeline(pipeline_name)

    #   We can change the starting files later using
    #          set_input() for transform etc.
    #       or set_output() for originate
    #   But it can be more convenient to just pass this to the function making the pipeline
    #
    test_pipeline.originate(task_originate, starting_file_names)\
        .follows(mkdir(tempdir), mkdir(tempdir + "testdir", tempdir + "testdir2"))\
        .posttask(touch_file(tempdir + "testdir/whatever.txt"))
    test_pipeline.transform(task_func   = task_m_to_1,
                            name        = "add_input",
                            # Lookup Task from function name task_originate()
                            #   So long as this is unique in the pipeline
                            input       = task_originate,
                            filter      = regex(r"(.*)"),
                            add_inputs  = add_inputs(tempdir + "testdir/whatever.txt"),
                            output      = r"\1.22")
    test_pipeline.transform(task_func   = task_1_to_1,
                            name        = "22_to_33",
                            # Lookup Task from Task name
                            #   Function name is not unique in the pipeline
                            input       = output_from("add_input"),
                            filter      = suffix(".22"),
                            output      = ".33")
    tail_task = test_pipeline.transform(task_func   = task_1_to_1,
                                        name        = "33_to_44",
                                        # Ask Pipeline to lookup Task from Task name
                                        input       = test_pipeline["22_to_33"],
                                        filter      = suffix(".33"),
                                        output      = ".44")

    #   Set the tail task so that users of my sub pipeline can use it as a dependency
    #       without knowing the details of task names
    #
    #   Use Task() object directly without having to lookup
    test_pipeline.set_tail_tasks([tail_task])

    #   If we try to connect a Pipeline without tail tasks defined, we have to
    #       specify the exact task within the Pipeline.
    #   Otherwise Ruffus will not know which task we mean and throw an exception
    if DEBUG_do_not_define_tail_task:
        test_pipeline.set_tail_tasks([])

    # Set the head task so that users of my sub pipeline send input into it
    #   without knowing the details of task names
    test_pipeline.set_head_tasks([test_pipeline[task_originate]])

    return test_pipeline

#
#   Returns a fully formed sub pipeline useable as a building block
#
def make_pipeline2( pipeline_name = "pipeline2"):
    test_pipeline2 = Pipeline(pipeline_name)
    test_pipeline2.transform(task_func   = task_1_to_1,
                             # task name
                            name        = "44_to_55",
                             # placeholder: will be replaced later with set_input()
                            input       = None,
                            filter      = suffix(".44"),
                            output      = ".55")
    test_pipeline2.merge(   task_func   = task_m_to_1,
                            input       = test_pipeline2["44_to_55"],
                            output      = tempdir + "final.output",)

    # Set head and tail
    test_pipeline2.set_tail_tasks([test_pipeline2[task_m_to_1]])
    if not DEBUG_do_not_define_head_task:
        test_pipeline2.set_head_tasks([test_pipeline2["44_to_55"]])

    return test_pipeline2




#   First two pipelines are created as separate instances by the make_pipeline1 function
pipeline1a = make_pipeline1(pipeline_name = "pipeline1a", starting_file_names = [tempdir + ss for ss in ("a.1", "b.1")])
pipeline1b = make_pipeline1(pipeline_name = "pipeline1b", starting_file_names = [tempdir + ss for ss in ("c.1", "d.1")])

#   The Third pipeline is a clone of pipeline1b
pipeline1c = pipeline1b.clone(new_name = "pipeline1c")

#   Set the "originate" files for pipeline1c to ("e.1" and "f.1")
#       Otherwise they would use the original ("c.1", "d.1")
pipeline1c.set_output(output = [])
pipeline1c.set_output(output = [tempdir + ss for ss in ("e.1", "f.1")])

#   Join all pipeline1a-c to pipeline2
pipeline2 = make_pipeline2()
pipeline2.set_input(input = [pipeline1a, pipeline1b, pipeline1c])


import ruffus.cmdline as cmdline
parser = cmdline.get_argparse(description='Demonstrates the new Ruffus syntax in version 2.6')

parser.add_argument('--cleanup', "-C",
                    action="store_true",
                    help="Cleanup before and after.")


options = parser.parse_args()



#  standard python logger which can be synchronised across concurrent Ruffus tasks
logger, logger_mutex = cmdline.setup_logging (__name__, options.log_file, options.verbose)


# if we are printing only
if  not options.just_print and \
    not options.flowchart and \
    not options.touch_files_only:
    cmdline.run (options)
    sys.exit()

#
#   Cleanup beforehand
#
if options.cleanup:
    try:
        shutil.rmtree(tempdir)
    except:
        pass

#
#   Run
#
cmdline.run (options)

#
#   Cleanup Afterwards
#
if options.cleanup:
    try:
        shutil.rmtree(tempdir)
    except:
        pass