See also
This code is from test/test_subpipeline.py in the Ruffus distribution
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 #!/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 test_pipeline1a = make_pipeline1(pipeline_name = "pipeline1a", starting_file_names = [tempdir + ss for ss in ("a.1", "b.1")]) test_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 test_pipeline1c = test_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") test_pipeline1c.set_output(output = []) test_pipeline1c.set_output(output = [tempdir + ss for ss in ("e.1", "f.1")]) # Join all pipeline1a-c to pipeline2 test_pipeline2 = make_pipeline2() test_pipeline2.set_input(input = [test_pipeline1a, test_pipeline1b, test_pipeline1c]) test_pipeline2.printout_graph("test.svg", "svg", [task_m_to_1]) test_pipeline2.printout(verbose = 0) test_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()