pipeline_printout_graph_code.rst

: Python Code for Displaying the pipeline visually with pipeline_printout_graph(...) <pipeline_functions.pipeline_printout_graph>

• Manual Table of Contents <new_manual.table_of_contents>
• pipeline_printout_graph(...) <pipeline_functions.pipeline_printout_graph> syntax
• Back to : Displaying the pipeline visually <new_manual.pipeline_printout_graph>

Code

from ruffus import *
import sys

#---------------------------------------------------------------
#   create initial files
#
@originate([   ['job1.a.start', 'job1.b.start'],
               ['job2.a.start', 'job2.b.start'],
               ['job3.a.start', 'job3.b.start']    ])
def create_initial_file_pairs(output_files):
    # create both files as necessary
    for output_file in output_files:
        with open(output_file, "w") as oo: pass

#---------------------------------------------------------------
#   first task
@transform(create_initial_file_pairs, suffix(".start"), ".output.1")
def first_task(input_files, output_file):
    with open(output_file, "w"): pass


#---------------------------------------------------------------
#   second task
@transform(first_task, suffix(".output.1"), ".output.2")
def second_task(input_files, output_file):
    with open(output_file, "w"): pass

#  Print graph before running pipeline

#---------------------------------------------------------------
#
#       Show flow chart and tasks before running the pipeline
#
print "Show flow chart and tasks before running the pipeline"
pipeline_printout_graph ( open("simple_tutorial_stage5_before.png", "w"),
                         "png",
                         [second_task],
                         minimal_key_legend=True)

#---------------------------------------------------------------
#
#       Run
#
pipeline_run([second_task])


# modify job1.stage1
open("job1.a.output.1", "w").close()


#  Print graph after everything apart from ``job1.a.output.1`` is update

#---------------------------------------------------------------
#
#       Show flow chart and tasks after running the pipeline
#
print "Show flow chart and tasks after running the pipeline"
pipeline_printout_graph ( open("simple_tutorial_stage5_after.png", "w"),
                         "png",
                         [second_task],
                         no_key_legend=True)

Resulting Flowcharts

Before

After

Legend