def setUp(self):
self.pipeline = DummyPipeline()
tmpout = tempfile.mkstemp('.txt', prefix='capsul_test_')
os.close(tmpout[0])
os.unlink(tmpout[1])
# use a custom temporary soma-workflow dir to avoid concurrent
# access problems
tmpdb = tempfile.mkstemp('', prefix='soma_workflow')
os.close(tmpdb[0])
os.unlink(tmpdb[1])
self.soma_workflow_temp_dir = tmpdb[1]
os.mkdir(self.soma_workflow_temp_dir)
swf_conf = '[%s]\nSOMA_WORKFLOW_DIR = %s\n' \
% (socket.gethostname(), tmpdb[1])
swconfig.Configuration.search_config_path \
= staticmethod(lambda : StringIO.StringIO(swf_conf))
self.output = tmpout[1]
self.pipeline.input = '/tmp/file_in.nii'
self.pipeline.output = self.output
study_config = StudyConfig(modules=['SomaWorkflowConfig'])
study_config.input_directory = '/tmp'
study_config.somaworkflow_computing_resource = 'localhost'
study_config.somaworkflow_computing_resources_config.localhost = {
'transfer_paths': [],
}
self.study_config = study_config
def setUp(self):
study_config = StudyConfig() #modules=StudyConfig.default_modules \
#+ ['FomConfig'])
self.pipeline = DummyPipeline()
self.pipeline.set_study_config(study_config)
self.tmpdir = tempfile.mkdtemp()
self.pipeline.input = osp.join(self.tmpdir, 'file_in.nii')
self.pipeline.output1 = osp.join(self.tmpdir, '/tmp/file_out1.nii')
self.pipeline.output2 = osp.join(self.tmpdir, '/tmp/file_out2.nii')
self.pipeline.output3 = osp.join(self.tmpdir, '/tmp/file_out3.nii')
study_config.input_directory = self.tmpdir
study_config.somaworkflow_computing_resource = 'localhost'
study_config.somaworkflow_computing_resources_config.localhost = {
'transfer_paths': [study_config.input_directory],
}
self.study_config = study_config
engine = self.study_config.engine
engine.load_module('spm')
#with engine.settings as session:
#ids = [c.config_id for c in session.configs('spm', 'global')]
#for id in ids:
#session.remove_config('spm', 'global', {'config_id': id})
#session.new_config('spm', 'global',
#{'version': '12', 'standalone': True})
study_config.spm_standalone = True
study_config.spm_version = '12'
study_config.somaworkflow_keep_succeeded_workflows = False
self.exec_ids = []
def setUp(self):
self.pipeline = DummyPipeline()
self.pipeline.input = '/tmp/file_in.nii'
self.pipeline.output1 = '/tmp/file_out1.nii'
self.pipeline.output2 = '/tmp/file_out2.nii'
self.pipeline.output3 = '/tmp/file_out3.nii'
study_config = StudyConfig() #modules=StudyConfig.default_modules \
#+ ['FomConfig'])
study_config.input_directory = '/tmp'
study_config.somaworkflow_computing_resource = 'localhost'
study_config.somaworkflow_computing_resources_config.localhost = {
'transfer_paths': [study_config.input_directory],
}
self.study_config = study_config
def setUp(self):
self.pipeline = DummyPipeline()
self.pipeline.input = '/tmp/file_in.nii'
self.pipeline.output1 = '/tmp/file_out1.nii'
self.pipeline.output2 = '/tmp/file_out2.nii'
self.pipeline.output3 = '/tmp/file_out3.nii'
study_config = StudyConfig() #modules=StudyConfig.default_modules \
#+ ['FomConfig'])
study_config.input_directory = '/tmp'
study_config.somaworkflow_computing_resource = 'localhost'
study_config.somaworkflow_computing_resources_config.localhost = {
'transfer_paths': [study_config.input_directory],
}
self.study_config = study_config
def setUp(self):
self.pipeline = DummyPipeline()
tmpout = tempfile.mkstemp('.txt', prefix='capsul_test_')
os.close(tmpout[0])
os.unlink(tmpout[1])
self.output = tmpout[1]
self.pipeline.input = '/tmp/file_in.nii'
self.pipeline.output = self.output
study_config = StudyConfig(modules=['SomaWorkflowConfig'])
study_config.input_directory = '/tmp'
study_config.somaworkflow_computing_resource = 'localhost'
study_config.somaworkflow_computing_resources_config.localhost = {
'transfer_paths': [],
}
self.study_config = study_config
def setUp(self):
self.pipeline = DummyPipeline()
tmpout = tempfile.mkstemp('.txt', prefix='capsul_test_')
os.close(tmpout[0])
os.unlink(tmpout[1])
self.output = tmpout[1]
self.pipeline.input = '/tmp/file_in.nii'
self.pipeline.output = self.output
study_config = StudyConfig(modules=['SomaWorkflowConfig'])
study_config.input_directory = '/tmp'
study_config.somaworkflow_computing_resource = 'localhost'
study_config.somaworkflow_computing_resources_config.localhost = {
'transfer_paths': [],
}
self.study_config = study_config
def setUp(self):
self.pipeline = DummyPipeline()
tmpdir = tempfile.mkdtemp('capsul_output_test')
tmpout = os.path.join(tmpdir, 'capsul_test_node3_out.txt')
self.tmpdir = tmpdir
self.pipeline.input = os.path.join(tmpdir, 'file_in.nii')
with open(self.pipeline.input, 'w') as f:
print('Initial file content.', file=f)
self.pipeline.output = tmpout
study_config = StudyConfig(modules=['SomaWorkflowConfig'])
study_config.input_directory = tmpdir
study_config.somaworkflow_computing_resource = 'localhost'
study_config.somaworkflow_computing_resources_config.localhost = {
'transfer_paths': [],
}
self.study_config = study_config