#!/usr/bin/env python from __future__ import print_function """ Demonstrates the new Ruffus syntax in version 2.6 """ import os tempdir = os.path.relpath(os.path.abspath(os.path.splitext(__file__)[0])) 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 #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888 # imports #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888 import shutil def touch (outfile): with open(outfile, "w"): pass #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888 # Tasks #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888 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 (__file__, options.log_file, options.verbose) logger.debug("\tRuffus Version = " + ruffus.__version__) if options.cleanup: try: shutil.rmtree(tempdir) except: pass correct = False # if we are not printing but running if not options.just_print and \ not options.flowchart and \ not options.touch_files_only: # # Cleanup # if options.cleanup: try: shutil.rmtree(tempdir) except: pass # # Run # cmdline.run (options) # 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=; ; '.format(tempdir = tempdir) try: with open(tempdir + "/final.output") as real_output: real_output_str = real_output.read() except Exception as e: real_output_str = str(e) + "\n" if (correct_output != real_output_str): print ("_" * 80 + "\n" + " " * 25 + "Warning\n" + "_" * 80 + "\n" + "If you had run the whole of pipeline 2, " "you should have obtained:<\n\t%s>\n\n Rather than:<\n\t%s>\n\n" % (correct_output.replace("; ", ";\n\t"), real_output_str.replace("; ", ";\n\t")) + "_" * 80, "\n",) else: logger.debug("\tAll Correct.\n") correct = True # # Cleanup # if options.cleanup: try: shutil.rmtree(tempdir) except: pass else: cmdline.run (options) correct = True sys.exit(0 if correct else 1)