.. _new_syntax.worked_example.code:

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

    .. seealso::

        * :ref:`new_syntax.worked_example <new_syntax.worked_example>`

    This code is from ``test/test_subpipeline.py`` in the **Ruffus** distribution


    .. <<python

    .. code-block:: python
        :emphasize-lines: 70,76-79,86,87,94,95,101,106-107,109,112-114,118,119,125,130,132,150,154,157,158,162

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

                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__)

        #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888

        #   imports


        #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
        import shutil


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


        #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888

        #   Tasks


        #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
        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


        def run_pipeline():

            #   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])


            pipeline2.printout_graph("test.svg", "svg", [task_m_to_1])
            pipeline2.printout(verbose = 0)
            pipeline2.run(multiprocess = 10, verbose = 0)


        class Test_task(unittest.TestCase):

            def tearDown (self):
                """
                """
                try:
                    shutil.rmtree(tempdir)
                except:
                    pass


            def test_subpipelines (self):

                run_pipeline()

                # Check that the output reflecting the pipeline topology is correct.
                correct_output = 'tempdir/a.1.55=tempdir/a.1.44+tempdir/a.1.33+tempdir/a.1.22+tempdir/a.1=; tempdir/testdir/whatever.txt=; ; ' \
                                 'tempdir/b.1.55=tempdir/b.1.44+tempdir/b.1.33+tempdir/b.1.22+tempdir/b.1=; tempdir/testdir/whatever.txt=; ; ' \
                                 'tempdir/c.1.55=tempdir/c.1.44+tempdir/c.1.33+tempdir/c.1.22+tempdir/c.1=; tempdir/testdir/whatever.txt=; ; ' \
                                 'tempdir/d.1.55=tempdir/d.1.44+tempdir/d.1.33+tempdir/d.1.22+tempdir/d.1=; tempdir/testdir/whatever.txt=; ; ' \
                                 'tempdir/e.1.55=tempdir/e.1.44+tempdir/e.1.33+tempdir/e.1.22+tempdir/e.1=; tempdir/testdir/whatever.txt=; ; ' \
                                 'tempdir/f.1.55=tempdir/f.1.44+tempdir/f.1.33+tempdir/f.1.22+tempdir/f.1=; tempdir/testdir/whatever.txt=; ; '
                with open(tempdir + "final.output") as real_output:
                    real_output_str = real_output.read()
                self.assertEqual(correct_output, real_output_str)



        if __name__ == '__main__':
            unittest.main()

    ..
        python
