def test_workflow(self):
# get settings
settings = default_preproc_settings()
settings['tmp_dir'] = tempfile.TemporaryDirectory().name
settings['output_dir'] = tempfile.TemporaryDirectory().name
gen_wf = workflow.newworkflow('test', settings)
self.assertIsInstance(gen_wf, Workflow)
def test_nodedefs(self):
# get settings
settings = default_preproc_settings()
settings['output_dir'] = tempfile.TemporaryDirectory().name
# define node object
defnodeobj = nodedefs.definednodes(settings)
# assert the instance
self.assertIsInstance(defnodeobj, nodedefs.definednodes)
def test_basenodedefs(self):
settings = default_preproc_settings()
settings['output_dir'] = tempfile.TemporaryDirectory().name
dn = basenodedefs(settings)
self.assertIsInstance(dn, basenodedefs)
dn.set_input(['test'])
self.assertIsInstance(dn.inputnode, Node)
dn.set_output(['test'])
self.assertIsInstance(dn.outputnode, Node)
dn.set_subs([('_test1', '_test2')])
dn.set_resubs([
(r'_test\d{1,3}', '_test'),
])
self.assertIsInstance(dn.datasink, Node)
import unittest
from p3.pipeline import *
from p3.settings import default_preproc_settings
from p3 import workflows
import os
import sys
import importlib
import tempfile
from nipype import Workflow
from mock import patch
from .mock_stdout import MockDevice
sys.path.append(os.path.abspath(os.path.dirname(workflows.__file__))) # set default workflows path
current_dir = os.path.dirname(os.path.abspath(os.path.realpath(__file__))) # get the current directory
# get and setup default settings
settings = default_preproc_settings()
settings['output_dir'] = tempfile.TemporaryDirectory().name
settings['tmp_dir'] = os.path.join(settings['output_dir'],'tmp')
settings['bids_dir'] = os.path.join(current_dir,'example_data')
settings['subject'] = ['01','02','03']
settings['debug'] = False
# import default workflows
imported_workflows = {}
for module in settings['workflows']:
imported_workflows[module] = importlib.import_module('{}.workflow'.format(module))
class test(unittest.TestCase):
def test_generate_subworkflows(self):
with patch('sys.stdout',new=MockDevice()) as fake_out:
# generate subworkflows
def test_workflowgnerator(self):
settings = default_preproc_settings()
settings['tmp_dir'] = tempfile.TemporaryDirectory().name
workflowgenerator('test', settings)
self.assertIsInstance(workflowgenerator.workflow, Workflow)