def test_missing_parameter_value_error(self):
self.test_case.set_analysis_parameters()
self.test_case.delete_some_parameter_values()
pipeline = self.analysis.pipeline.process
pipeline.enable_all_pipeline_steps()
pipeline_tools.disable_runtime_steps_with_existing_outputs(
pipeline)
missing = pipeline_tools.nodes_with_missing_inputs(pipeline)
self.assertTrue(missing)
def _check_input_files(self, subject_ids):
subjects_with_missing_inputs = []
for subject_id in subject_ids:
analysis = self._study.analyses[subject_id]
analysis.subject = subject_id
analysis.propagate_parameters()
missing = pipeline_tools.nodes_with_missing_inputs(
analysis.pipeline)
if missing:
subject = self._study.subjects[subject_id]
subjects_with_missing_inputs.append(str(subject))
if len(subjects_with_missing_inputs) != 0:
raise MissingInputFileError("Subjects: %s" % ", ".join(subjects_with_missing_inputs))
def _create_workflow(self, subject_ids):
study_config = self._study
workflow = Workflow(
name='Morphologist UI - %s' % study_config.study_name,
jobs=[])
workflow.root_group = []
initial_vol_format = study_config.volumes_format
priority = (len(subject_ids) - 1) * 100
for subject_id in subject_ids:
analysis = self._study.analyses[subject_id]
subject = self._study.subjects[subject_id]
analysis.set_parameters(subject)
#analysis.propagate_parameters()
pipeline = analysis.pipeline
pipeline.enable_all_pipeline_steps()
# force highest priority normalization method
# FIXME: specific knowledge of Morphologist should not be used here.
pipeline.Normalization_select_Normalization_pipeline \
= 'NormalizeSPM'
pipeline_tools.disable_runtime_steps_with_existing_outputs(
pipeline)
missing = pipeline_tools.nodes_with_missing_inputs(pipeline)
if missing:
self.check_missing_models(pipeline, missing)
print('MISSING INPUTS IN NODES:', missing)
raise MissingInputFileError("subject: %s" % subject_id)
wf = pipeline_workflow.workflow_from_pipeline(
pipeline, study_config=study_config,
jobs_priority=priority)
njobs = len([j for j in wf.jobs if isinstance(j, Job)])
if njobs != 0:
priority -= 100
workflow.jobs += wf.jobs
workflow.dependencies += wf.dependencies
group = Group(wf.root_group,
name='Morphologist %s' % str(subject))
group.user_storage = subject_id
workflow.root_group.append(group) # += wf.root_group
workflow.groups += [group] + wf.groups
return workflow
