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#!/usr/bin/env python
from __future__ import print_function
"""
test_runtime_data.py
Tests having inputs depend on a run time parameter
(named element in the dict runtime_data passed to pipeline_run)
"""
import os
tempdir = os.path.relpath(os.path.abspath(os.path.splitext(__file__)[0])) + "/"
runtime_files = [tempdir + "a.3"]
import sys
import shutil
# 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)
# module name = script name without extension
module_name = os.path.splitext(os.path.basename(__file__))[0]
# funky code to import by file name
parent_dir = os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))
import ruffus
from ruffus import pipeline_run, pipeline_printout, Pipeline, originate, transform, suffix, follows, runtime_parameter, mkdir
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
# imports
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
import unittest
import shutil
import json
# use simplejson in place of json for python < 2.6
#try:
# import json
#except ImportError:
# import simplejson
# json = simplejson
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
# Tasks
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
#
# task1
#
@originate([tempdir + 'a.1'] + runtime_files)
def task1(outfile):
"""
First task
"""
output_text = ""
output_text += " -> " + json.dumps(outfile) + "\n"
with open(outfile, "w") as oo:
oo.write(output_text)
#
# task2
#
@transform(task1, suffix(".1"), ".2")
def task2(infile, outfile):
"""
Second task
"""
if infile:
with open(infile) as ii:
output_text = ii.read()
else:
output_text = ""
output_text += json.dumps(infile) + " -> " + json.dumps(outfile) + "\n"
with open(outfile, "w") as oo:
oo.write(output_text)
#
# task3
#
@transform(task2, suffix(".2"), ".3")
def task3(infile, outfile):
"""
Third task
"""
if infile:
with open(infile) as ii:
output_text = ii.read()
else:
output_text = ""
output_text += json.dumps(infile) + " -> " + json.dumps(outfile) + "\n"
with open(outfile, "w") as oo:
oo.write(output_text)
#
# task4
#
@follows(task3)
@transform(runtime_parameter("a"), suffix(".3"), ".4")
def task4(infile, outfile):
"""
Fourth task
"""
if infile:
with open(infile) as ii:
output_text = ii.read()
else:
output_text = ""
output_text += json.dumps(infile) + " -> " + json.dumps(outfile) + "\n"
with open(outfile, "w") as oo:
oo.write(output_text)
class Test_ruffus(unittest.TestCase):
def setUp(self):
for f in ["a.1", "a.2","a.3","a.4"]:
f = os.path.join(tempdir, f)
if os.path.exists(f):
os.unlink(f)
try:
os.makedirs(tempdir)
except:
pass
def tearDown(self):
for f in ["a.1", "a.2","a.3","a.4"]:
f = os.path.join(tempdir, f)
if os.path.exists(f):
os.unlink(f)
else:
raise Exception("%s is missing" % f)
shutil.rmtree(tempdir)
def test_ruffus (self):
pipeline_run(verbose = 0, runtime_data = {"a": runtime_files}, pipeline= "main")
def test_newstyle_ruffus (self):
test_pipeline = Pipeline("test")
test_pipeline.originate(task_func = task1,
output = [tempdir + 'a.1'] + runtime_files)
test_pipeline.transform(task2, task1, suffix(".1"), ".2")
test_pipeline.transform(task_func = task3,
input = task2,
filter = suffix(".2"),
output = ".3")
test_pipeline.transform(task_func = task4,
input = runtime_parameter("a"),
filter = suffix(".3"),
output = ".4").follows(task3)
test_pipeline.run(verbose = 0, runtime_data = {"a": runtime_files})
if __name__ == '__main__':
unittest.main()
|
