def test_03_visit_special(self):
"""
This test tries to visit special files.
These can be copies from already loaded files, DICOM with missing fields, etc.
"""
# Create a simple provenance
provenance_id = files_recording.create_provenance('TEST_DATA2',
db_url=DB_URL)
assert_equal(
self.db_conn.db_session.query(self.db_conn.Provenance).count(), 3)
# Visit various files
files_recording.visit('./data/any/',
provenance_id,
'SPECIAL',
1,
db_url=DB_URL)
assert_equal(
self.db_conn.db_session.query(self.db_conn.DataFile).count(), 8)
# A few more things to check
assert_equal(
self.db_conn.db_session.query(
self.db_conn.DataFile).filter_by(type='DICOM').count(), 4)
assert_equal(
self.db_conn.db_session.query(
self.db_conn.DataFile).filter_by(type='NIFTI').count(), 3)
assert_equal(
self.db_conn.db_session.query(
self.db_conn.DataFile).filter_by(is_copy=True).count(), 1)
def test_01_visit(self):
"""
This is a basic use case.
First, we want to visit a DICOM data-set after the 'ACQUISITION' process. Then, we want to visit a NIFTI
data-set generated from the previous DICOM files after the 'DICOM2NIFTI' process.
"""
# Create a simple provenance
provenance_id = files_recording.create_provenance('TEST_DATA',
db_url=DB_URL)
assert_equal(
self.db_conn.db_session.query(self.db_conn.Provenance).count(), 1)
# Visit DICOM files
acquisition_step_id = files_recording.visit(
'./data/dcm/',
provenance_id,
'ACQUISITION',
config=['sid_by_patient', 'pid_in_vid'],
db_url=DB_URL)
assert_equal(
self.db_conn.db_session.query(self.db_conn.DataFile).count(), 4)
# Create a provenance with some fake Matlab and SPM version numbers
provenance_id = files_recording.create_provenance('TEST_DATA',
software_versions={
'matlab_version':
'2016R',
'spm_version':
'v12'
},
db_url=DB_URL)
assert_equal(
self.db_conn.db_session.query(self.db_conn.Provenance).count(), 2)
# Visit NIFTI files
files_recording.visit('./data/nii/',
provenance_id,
'DICOM2NIFTI',
acquisition_step_id,
config=['sid_by_patient', 'pid_in_vid'],
db_url=DB_URL)
assert_equal(
self.db_conn.db_session.query(self.db_conn.DataFile).count(), 7)
# A few more things to check
assert_equal(
self.db_conn.db_session.query(
self.db_conn.DataFile).filter_by(type='DICOM').count(), 3)
assert_equal(
self.db_conn.db_session.query(
self.db_conn.DataFile).filter_by(type='NIFTI').count(), 3)
def test_02_visit_again(self):
"""
Here, run again the test_01_visit so we can check that there are no duplicates in the DB.
"""
# Create a simple provenance
provenance_id = files_recording.create_provenance('TEST_DATA',
db_url=DB_URL)
assert_equal(
self.db_conn.db_session.query(self.db_conn.Provenance).count(), 2)
# Visit DICOM files
acquisition_step_id = files_recording.visit(
'./data/dcm/',
provenance_id,
'ACQUISITION',
config=['sid_by_patient', 'pid_in_vid'],
db_url=DB_URL)
assert_equal(
self.db_conn.db_session.query(self.db_conn.DataFile).count(), 7)
# Create a provenance with some fake Matlab and SPM version numbers
provenance_id = files_recording.create_provenance('TEST_DATA',
software_versions={
'matlab_version':
'2016R',
'spm_version':
'v12'
},
db_url=DB_URL)
assert_equal(
self.db_conn.db_session.query(self.db_conn.Provenance).count(), 2)
# Visit NIFTI files
files_recording.visit('./data/nii/',
provenance_id,
'DICOM2NIFTI',
acquisition_step_id,
config=['sid_by_patient', 'pid_in_vid'],
db_url=DB_URL)
assert_equal(
self.db_conn.db_session.query(self.db_conn.DataFile).count(), 7)
# A few more things to check
assert_equal(
self.db_conn.db_session.query(
self.db_conn.DataFile).filter_by(type='DICOM').count(), 3)
assert_equal(
self.db_conn.db_session.query(
self.db_conn.DataFile).filter_by(type='NIFTI').count(), 3)
def test_01_visit(self):
"""
This is a basic use case.
First, we want to visit a DICOM data-set after the 'ACQUISITION' process. Then, we want to visit a NIFTI
data-set generated from the previous DICOM files after the 'DICOM2NIFTI' process.
"""
# Create a simple provenance
provenance_id = files_recording.create_provenance('TEST_DATA', db_url=DB_URL)
assert_equal(self.db_conn.db_session.query(self.db_conn.Provenance).filter_by(
dataset='TEST_DATA', matlab_version=None).count(), 1)
# Visit DICOM files
acquisition_step_id = files_recording.visit('./data/dcm/', provenance_id, 'ACQUISITION',
config=['sid_by_patient', 'pid_in_vid'], db_url=DB_URL)
assert_equal(self.db_conn.db_session.query(self.db_conn.DataFile).filter_by(
processing_step_id=acquisition_step_id).count(), 4)
# Create a provenance with some fake Matlab and SPM version numbers
provenance_id2 = files_recording.create_provenance('TEST_DATA',
software_versions={
'matlab_version': '2016R', 'spm_version': 'v12'},
db_url=DB_URL)
assert_equal(self.db_conn.db_session.query(self.db_conn.Provenance).filter_by(
dataset='TEST_DATA', matlab_version='2016R').count(), 1)
assert_equal(self.db_conn.db_session.query(self.db_conn.DataFile).filter_by(
type='DICOM', processing_step_id=acquisition_step_id).count(), 3)
assert_equal(self.db_conn.db_session.query(self.db_conn.DataFile).filter_by(
type='NIFTI', processing_step_id=acquisition_step_id).count(), 0)
assert_equal(self.db_conn.db_session.query(self.db_conn.DataFile).filter_by(
type='other', processing_step_id=acquisition_step_id).count(), 1)
# Visit NIFTI files
acquisition_step_id2 = files_recording.visit('./data/nii/', provenance_id2, 'DICOM2NIFTI', acquisition_step_id,
config=['sid_by_patient', 'pid_in_vid'], db_url=DB_URL)
assert_equal(self.db_conn.db_session.query(self.db_conn.DataFile).filter_by(
processing_step_id=acquisition_step_id2).count(), 3)
assert_equal(self.db_conn.db_session.query(self.db_conn.DataFile).filter_by(
type='DICOM', processing_step_id=acquisition_step_id2).count(), 0)
assert_equal(self.db_conn.db_session.query(self.db_conn.DataFile).filter_by(
type='NIFTI', processing_step_id=acquisition_step_id2).count(), 3)
assert_equal(self.db_conn.db_session.query(self.db_conn.DataFile).filter_by(
type='other', processing_step_id=acquisition_step_id2).count(), 0)
def test_02_visit_again(self):
"""
Here, run again the test_01_visit so we can check that there are no duplicates in the DB.
"""
# Create a simple provenance
provenance_id = files_recording.create_provenance('TEST_DATA', db_url=DB_URL)
assert_equal(self.db_conn.db_session.query(self.db_conn.Provenance).filter_by(
dataset='TEST_DATA', matlab_version=None).count(), 1)
# Visit DICOM files
acquisition_step_id = files_recording.visit('./data/dcm/', provenance_id, 'ACQUISITION',
config=['sid_by_patient', 'pid_in_vid'], db_url=DB_URL)
assert_equal(self.db_conn.db_session.query(self.db_conn.DataFile).filter_by(
processing_step_id=acquisition_step_id).count(), 4)
# Create a provenance with some fake Matlab and SPM version numbers
provenance_id2 = files_recording.create_provenance('TEST_DATA',
software_versions={
'matlab_version': '2016R', 'spm_version': 'v12'},
db_url=DB_URL)
assert_equal(self.db_conn.db_session.query(self.db_conn.Provenance).filter_by(
dataset='TEST_DATA', matlab_version='2016R').count(), 1)
assert_equal(self.db_conn.db_session.query(self.db_conn.DataFile).filter_by(
type='DICOM', processing_step_id=acquisition_step_id).count(), 3)
assert_equal(self.db_conn.db_session.query(self.db_conn.DataFile).filter_by(
type='NIFTI', processing_step_id=acquisition_step_id).count(), 0)
assert_equal(self.db_conn.db_session.query(self.db_conn.DataFile).filter_by(
type='other', processing_step_id=acquisition_step_id).count(), 1)
# Visit NIFTI files
acquisition_step_id2 = files_recording.visit('./data/nii/', provenance_id2, 'DICOM2NIFTI', acquisition_step_id,
config=['sid_by_patient', 'pid_in_vid'], db_url=DB_URL)
assert_equal(self.db_conn.db_session.query(self.db_conn.DataFile).filter_by(
processing_step_id=acquisition_step_id2).count(), 3)
assert_equal(self.db_conn.db_session.query(self.db_conn.DataFile).filter_by(
type='DICOM', processing_step_id=acquisition_step_id2).count(), 0)
assert_equal(self.db_conn.db_session.query(self.db_conn.DataFile).filter_by(
type='NIFTI', processing_step_id=acquisition_step_id2).count(), 3)
assert_equal(self.db_conn.db_session.query(self.db_conn.DataFile).filter_by(
type='other', processing_step_id=acquisition_step_id2).count(), 0)
def test_03_visit_special(self):
"""
This test tries to visit special files.
These can be copies from already loaded files, DICOM with missing fields, etc.
"""
# Create a simple provenance
provenance_id = files_recording.create_provenance('TEST_DATA2', db_url=DB_URL)
assert_equal(self.db_conn.db_session.query(self.db_conn.Provenance).filter_by(dataset='TEST_DATA2').count(), 1)
# Visit various files
acquisition_step_id = files_recording.visit('./data/any/', provenance_id, 'SPECIAL', 1, db_url=DB_URL)
assert_equal(self.db_conn.db_session.query(self.db_conn.DataFile).filter_by(
processing_step_id=acquisition_step_id).count(), 1)
# A few more things to check
assert_equal(self.db_conn.db_session.query(self.db_conn.DataFile).filter_by(
type='DICOM', processing_step_id=acquisition_step_id).count(), 1)
assert_equal(self.db_conn.db_session.query(self.db_conn.DataFile).filter_by(
type='NIFTI', processing_step_id=acquisition_step_id).count(), 0)
assert_equal(self.db_conn.db_session.query(self.db_conn.DataFile).filter_by(
is_copy=True, processing_step_id=acquisition_step_id).count(), 1)