def test_pypeline__two_chained_pipelines_mock_functions__expected_correctly_value(
self):
# FIXTURE
expected = object()
test_method = Mock(return_value=expected)
sub_pipeline = Pypeline().append(test_method,
'first',
'second',
third='third').append(
test_method, something_else=True)
pipeline = Pypeline().append_context(sub_pipeline).append_context(
sub_pipeline)
# EXERCISE
result = pipeline.do()
# VERIFY
self.assertIsNone(result)
self.assertEqual(4, test_method.call_count)
# first
self.assertEqual(call('first', 'second', third='third'),
test_method.mock_calls[0])
self.assertEqual(call(expected, something_else=True),
test_method.mock_calls[1])
self.assertEqual(call('first', 'second', third='third'),
test_method.mock_calls[2])
self.assertEqual(call(expected, something_else=True),
test_method.mock_calls[3])
def test_pypeline__two_chained_simple_functions_arg_list__expected_correctly_value(
self):
# FIXTURE
pipeline = Pypeline().append(math.pow, 2, 2).append(operator.add, 5)
# EXERCISE
result = pipeline.do()
# VERIFY
self.assertEqual(9, result) # add(pow(2**2), 5)
def test_pypeline__two_chained_simple_functions_kwargs_and_arg_list__expected_correctly_value(
self):
# FIXTURE
pow = lambda x, y: math.pow(x, y) # pow take no kwarg
add = lambda a, b: operator.add(a, b) # add take no kwargs
pipeline = Pypeline().append(pow, 2, y=2).append(add, 5)
# EXERCISE
result = pipeline.do()
# VERIFY
self.assertEqual(9, result) # add(pow(2,y=2), 5)
#!/usr/bin/env python
from pypeline import Pypeline, ProcessPypeStep, PythonPypeStep
if __name__ == '__main__' :
pipeline = Pypeline(log='simple_example.log', ignore_failure=True)
steps = []
# step 1 - list the current directory
ls_fn = 'ls_out.txt'
steps.append(ProcessPypeStep('Get directory file list','ls -1d > %s'%ls_fn))
# step 2 - do a word count
wc_fn = 'wc_out.txt'
steps.append(ProcessPypeStep('Get wordcount','wc %s > %s'%(ls_fn,wc_fn)))
# step 3 - sort the file and output
steps.append(ProcessPypeStep('Sort wordcount','sort -n %s'%wc_fn))
# step 4 - cleanup files
def rm_stuff() :
import glob
from subprocess import call
txt_fns = glob.glob('*.txt')
for fn in txt_fns :
call('rm %s'%fn,shell=True)
return True
steps.append(PythonPypeStep('Cleanup',rm_stuff))
# step 5 - intentionally fail
control_fn = None
if len(args) > 3 :
control_fn = args[2]
org_settings = get_org_settings(organism)
refseq_fn = org_settings['annotation_path']
exp_fpath,exp_fname,exp_fbase,exp_fext = get_file_parts(experiment_fn)
exp_wrk_dir = os.path.abspath('.exp_%s_%s'%(exp_fbase,opts.exp_name))
if control_fn :
cnt_fpath,cnt_fname,cnt_fbase,cnt_fext = get_file_parts(control_fn)
cnt_wrk_dir = os.path.abspath('.cnt_%s_%s'%(cnt_fbase,opts.exp_name))
# the pipeline
pipeline = Pypeline()
steps = []
# split up files
calls = ["mkdir %s"%exp_wrk_dir,
"split_file.py %s --outdir=%s %s"%(opts.split_args,exp_wrk_dir,experiment_fn),]
if control_fn :
calls.extend(["mkdir %s"%cnt_wrk_dir,
"split_file.py %s --outdir=%s %s"%(opts.split_args,cnt_wrk_dir,control_fn),
])
steps.append(PPS('Split files',calls,env=os.environ))
# convert to BED format
exp_bed_fn = "%s_exp.bed"%exp_fbase
calls = ["split_qsub.py %s --ext=.bed gerald_to_bed.py --util-args=\"%s\" %s/*.[0-9][0-9][0-9][0-9]"%(opts.qsub_args,opts.bed_args,exp_wrk_dir),
org_settings = get_org_settings(organism)
refgene_fn = org_settings['refgene_anno_path']
kg_ref = org_settings['known_gene_anno_path']
kg_xref = org_settings['known_gene_xref_path']
exp_fpath,exp_fname,exp_fbase,exp_fext = get_file_parts(experiment_fn)
exp_wrk_dir = os.path.abspath('.exp_%s_%s'%(exp_fbase,opts.exp_name))
if control_fn :
cnt_fpath,cnt_fname,cnt_fbase,cnt_fext = get_file_parts(control_fn)
cnt_wrk_dir = os.path.abspath('.cnt_%s_%s'%(cnt_fbase,opts.exp_name))
# the pipeline
#log_fn = os.path.join(opts.exp_name+'_pipeline.log')
pipeline = Pypeline('Analysis pipeline for %s'%opts.exp_name)
steps = []
#if opts.parallelize :
# # split up files
# calls = ["mkdir %s"%exp_wrk_dir,
# "split_file.py %s --outdir=%s %s"%(opts.split_args,exp_wrk_dir,experiment_fn),]
# if control_fn :
# calls.extend(["mkdir %s"%cnt_wrk_dir,
# "split_file.py %s --outdir=%s %s"%(opts.split_args,cnt_wrk_dir,control_fn),
# ])
# steps.append(PPS('Split files',calls,env=os.environ))
############################################################################
# run macs