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.. include:: ../../global.inc
.. include:: manual_chapter_numbers.inc
.. _new_manual.pipeline_printout_graph.code:
############################################################################################################################################################################################################
|new_manual.pipeline_printout_graph.chapter_num|: Python Code for Displaying the pipeline visually with :ref:`pipeline_printout_graph(...) <pipeline_functions.pipeline_printout_graph>`
############################################################################################################################################################################################################
.. seealso::
* :ref:`Manual Table of Contents <new_manual.table_of_contents>`
* :ref:`pipeline_printout_graph(...) <pipeline_functions.pipeline_printout_graph>` syntax
* Back to |new_manual.pipeline_printout_graph.chapter_num|: :ref:`Displaying the pipeline visually <new_manual.pipeline_printout_graph>`
************************************
Code
************************************
.. code-block:: python
:emphasize-lines: 28, 51
:linenos:
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
************************************
+-------------------------------------------------------------+-----------------------------------------------------------------------+
| .. image:: ../../images/simple_tutorial_stage5_before.png | .. image:: ../../images/simple_tutorial_stage5_after.png |
| :alt: Before running the pipeline | :alt: After running the pipeline |
| :scale: 95 | :scale: 95 |
| :align: center | :align: center |
| | |
| .. centered:: Before | .. centered:: After |
| | |
+-------------------------------------------------------------+-----------------------------------------------------------------------+
+-------------------------------------------------------------------------------------------------------------------------------------+
| .. image:: ../../images/tutorial_key.png |
| :alt: Legend key |
| :scale: 50 |
| :align: center |
| |
| .. centered:: Legend |
| |
+-------------------------------------------------------------------------------------------------------------------------------------+
|
