def test_bad_instance_none(self):
"""Test that instances with bad data aren't added."""
keywords = [
('PatientID', 16),
('PatientName', 64),
('StudyInstanceUID', 64),
('StudyDate', 8),
('StudyTime', 14),
('AccessionNumber', 16),
('StudyID', 16),
('SeriesInstanceUID', 64),
('Modality', 16),
#('SeriesNumber', None),
('SOPInstanceUID', 64),
#('InstanceNumber', None),
]
ds = Dataset()
ds.PatientID = None
ds.StudyInstanceUID = None
ds.SeriesInstanceUID = None
ds.SOPInstanceUID = None
with pytest.raises(IntegrityError):
db.add_instance(ds, self.session)
self.session.rollback()
assert not self.session.query(db.Instance).all()
def setup(self):
"""Run prior to each test"""
engine = db.create('sqlite:///:memory:')
pydicom.config.use_none_as_empty_text_VR_value = True
self.session = sessionmaker(bind=engine)()
for fname in DATASETS:
fpath = os.path.join(DATA_DIR, fname)
ds = dcmread(fpath)
db.add_instance(ds, self.session)
def test_add_instance(self):
"""Test adding to the instance database."""
fpath = os.path.join(DATA_DIR, 'CTImageStorage.dcm')
ds = dcmread(fpath)
db.add_instance(ds, self.session)
obj = self.session.query(db.Instance).all()
assert 1 == len(obj)
for kk, vv in DATASETS['CTImageStorage.dcm'].items():
assert vv == getattr(obj[0], kk)
def test_instance_exists(self):
"""Test that adding already existing instance updates it."""
db.add_instance(self.minimal, self.session)
result = self.session.query(db.Instance).all()
assert 1 == len(result)
assert None == result[0].modality
self.minimal.Modality = 'CT'
db.add_instance(self.minimal, self.session)
result = self.session.query(db.Instance).all()
assert 1 == len(result)
assert 'CT' == result[0].modality
def setup(self):
"""Run prior to each test"""
engine = db.create('sqlite:///:memory:')
pydicom.config.use_none_as_empty_text_VR_value = True
self.session = sessionmaker(bind=engine)()
ds = Dataset()
ds.PatientID = '1234'
ds.StudyInstanceUID = '1.2'
ds.SeriesInstanceUID = '1.2.3'
ds.SOPInstanceUID = '1.2.3.4'
db.add_instance(ds, self.session)
self.minimal = ds
def test_add_multiple_instances(self):
"""Test adding multiple data to the instance database."""
for fname in DATASETS:
fpath = os.path.join(DATA_DIR, fname)
ds = dcmread(fpath)
db.add_instance(ds, self.session)
obj = self.session.query(db.Instance).all()
assert 5 == len(obj)
obj = self.session.query(db.Instance, db.Instance.patient_name).all()
names = [val[1] for val in obj]
assert 'CompressedSamples^CT1' in names
assert 'CompressedSamples^MR1' in names
assert 'ANON^A^B^C^D' in names
assert '^^^^' in names
def test_add_minimal(self):
"""Test adding a minimal dataset."""
db.add_instance(self.minimal, self.session)
obj = self.session.query(db.Instance).all()
assert 1 == len(obj)
assert '1234' == obj[0].patient_id
assert '1.2' == obj[0].study_instance_uid
assert '1.2.3' == obj[0].series_instance_uid
assert '1.2.3.4' == obj[0].sop_instance_uid
rest = [
'patient_name', 'study_date', 'study_time', 'accession_number',
'study_id', 'modality', 'series_number', 'instance_number',
]
for attr in rest:
assert getattr(obj[0], attr) is None
def test_bad_instance(self):
"""Test that instances with bad data aren't added."""
keywords = [
('PatientID', 16),
('PatientName', 64),
('StudyInstanceUID', 64),
('StudyDate', 8),
('StudyTime', 14),
('AccessionNumber', 16),
('StudyID', 16),
('SeriesInstanceUID', 64),
('Modality', 16),
#('SeriesNumber', None),
('SOPInstanceUID', 64),
#('InstanceNumber', None),
]
ds = self.minimal[:]
for kw, max_len in keywords:
setattr(ds, kw, 'a' * (max_len + 1))
with pytest.raises(AssertionError):
db.add_instance(ds, self.session)
assert not self.session.query(db.Instance).all()
def test_add_minimal(self):
"""Test adding a minimal dataset."""
db.add_instance(self.minimal, self.session)
obj = self.session.query(db.Instance).all()
assert 1 == len(obj)
assert "1234" == obj[0].patient_id
assert "1.2" == obj[0].study_instance_uid
assert "1.2.3" == obj[0].series_instance_uid
assert "1.2.3.4" == obj[0].sop_instance_uid
rest = [
"patient_name",
"study_date",
"study_time",
"accession_number",
"study_id",
"modality",
"series_number",
"instance_number",
]
for attr in rest:
assert getattr(obj[0], attr) is None
def handle_store(event, storage_dir, db_path, cli_config, logger):
"""Handler for evt.EVT_C_STORE.
Parameters
----------
event : pynetdicom.events.Event
The C-STORE request :class:`~pynetdicom.events.Event`.
storage_dir : str
The path to the directory where instances will be stored.
db_path : str
The database path to use with create_engine().
cli_config : dict
A :class:`dict` containing configuration settings passed via CLI.
logger : logging.Logger
The application's logger.
Returns
-------
int or pydicom.dataset.Dataset
The C-STORE response's *Status*. If the storage operation is successful
but the dataset couldn't be added to the database then the *Status*
will still be ``0x0000`` (Success).
"""
requestor = event.assoc.requestor
timestamp = event.timestamp.strftime("%Y-%m-%d %H:%M:%S")
addr, port = requestor.address, requestor.port
logger.info(f"Received C-STORE request from {addr}:{port} at {timestamp}")
try:
ds = event.dataset
# Remove any Group 0x0002 elements that may have been included
ds = ds[0x00030000:]
sop_instance = ds.SOPInstanceUID
except Exception as exc:
logger.error("Unable to decode the dataset")
logger.exception(exc)
# Unable to decode dataset
return 0xC210
# Add the file meta information elements - must be before adding to DB
ds.file_meta = event.file_meta
logger.info(f"SOP Instance UID '{sop_instance}'")
# Try and add the instance to the database
# If we fail then don't even try to store
fpath = os.path.join(storage_dir, sop_instance)
db_dir = os.path.dirname(db_path)
if os.path.exists(fpath):
logger.warning(
'Instance already exists in storage directory, overwriting')
try:
ds.save_as(fpath, write_like_original=False)
except Exception as exc:
logger.error('Failed writing instance to storage directory')
logger.exception(exc)
# Failed - Out of Resources
return 0xA700
logger.info("Instance written to storage directory")
# Dataset successfully written, try to add to/update database
engine = create_engine(db_path)
with engine.connect() as conn:
Session = sessionmaker(bind=engine)
session = Session()
try:
# Path is relative to the database file
matches = session.query(Instance).filter(
Instance.sop_instance_uid == ds.SOPInstanceUID).all()
add_instance(ds, session, os.path.abspath(fpath))
if not matches:
logger.info("Instance added to database")
else:
logger.info("Database entry for instance updated")
except Exception as exc:
session.rollback()
logger.error('Unable to add instance to the database')
logger.exception(exc)
finally:
session.close()
return 0x0000
