class TestDBquery(unittest2.TestCase):
def setUp(self):
self.dbi = DBI()
self.dbi.connect()
# try:
# self.deleteData()
# except OperationalError as e:
# print(e.args[0])
# self.tearDown()
def deleteData(self):
# Reset all data so tests will work - so only use with a test db
self.dbi.deleteData('seriesprocess')
self.dbi.deleteData('dicomfiles')
self.dbi.deleteData('dicomdata')
def tearDown(self):
self.dbi.conn.close()
def test_getCaptions(self):
data = self.dbi.getCaptions()
expected = 0
print('Captions: ', data)
self.assertIsNotNone(data)
self.assertGreater(len(data), expected)
def test_getRefs(self):
data = self.dbi.getRefs()
expected = 0
print('Refs: ', data)
self.assertIsNotNone(data)
self.assertGreater(len(data), expected)
def test_getDescription(self):
caption = 'QSM'
data = self.dbi.getDescription(caption)
expected = 0
print('Description: ', data)
self.assertIsNotNone(data)
self.assertGreater(len(data), expected)
def test_getCaption(self):
caption = 'qsm'
data = self.dbi.getCaption(caption)
expected = 0
print('Caption: ', data)
self.assertIsNotNone(data)
self.assertGreater(len(data), expected)
def test_getProcessModule(self):
caption = 'qsm'
data = self.dbi.getProcessModule(caption)
expected = 0
print('Module: ', data)
self.assertIsNotNone(data)
self.assertGreater(len(data), expected)
def test_getProcessClass(self):
caption = 'qsm'
data = self.dbi.getProcessClass(caption)
expected = 0
print('Class: ', data)
self.assertIsNotNone(data)
self.assertGreater(len(data), expected)
def test_getFiles(self):
uuid = '5d74a20b44ec1dfd0af4fbc6bb680e0f557c14a08a143b843ef40977697e2bea'
data = self.dbi.getFiles(uuid)
expected = 0
print('Files: ', data)
self.assertIsNotNone(data)
self.assertGreater(len(data), expected)
def test_getNoFiles(self):
uuid = 't10001'
data = self.dbi.getFiles(uuid)
expected = 0
print('Files: ', data)
self.assertEqual(expected, len(data))
def test_addDicomdata(self):
dicomdata = {
'uuid': 't10000',
'patientid': 'p1',
'patientname': 'test patient',
'seriesnum': '1.001.111',
'sequence': 'ftest',
'protocol': 'aaa',
'imagetype': 'M'
}
try:
rtn = self.dbi.addDicomdata(dicomdata)
self.assertEqual(rtn, 1, 'Dicom data add failed')
except IntegrityError as e:
self.skipTest(e.args[0])
def test_hasUuid(self):
uuid = 't10000'
self.assertIs(self.dbi.hasUuid(uuid), True, 'Data already added')
def test_addDicomdataExisting(self):
dicomdata = {
'uuid': 't10000',
'patientid': 'p1',
'patientname': 'test patient',
'seriesnum': '1.001.111',
'sequence': 'ftest',
'protocol': 'aaa',
'imagetype': 'M'
}
try:
self.assertRaises(IntegrityError, self.dbi.addDicomdata, dicomdata)
except AssertionError as e:
self.skipTest(e.args[0])
def test_addDicomfileExisting(self):
uuid = 't10000'
dicomfile = "D:\\Projects\\XNAT\\data\\S1\\scans\\3\\1001DS.MR.RESEARCH_16022_OPTIMIZING_EXERCISE.0003.0001.2017.02.24.15.41.05.593750.93525560.IMA"
try:
self.assertRaises(IntegrityError, self.dbi.addDicomfile, uuid,
dicomfile)
#self.assertEqual(rtn, 1, 'Dicom file add failed')
except AssertionError as e:
self.skipTest(e.args[0])
def test_addDicomfile(self):
uuid = 't10000'
dicomfile = "D:\\Projects\\XNAT\\data\\S1\\scans\\3\\1001DS.MR.RESEARCH_16022_OPTIMIZING_EXERCISE.0003.0001.2017.02.24.15.41.05.593750.93525560.IMA"
try:
rtn = self.dbi.addDicomfile(uuid, dicomfile)
self.assertEqual(rtn, 1, 'Dicom file add failed')
except IntegrityError as e:
self.skipTest(e.args[0])
def test_getUuids(self):
data = self.dbi.getUuids()
expected = 0
print('UUIDS: ', data)
self.assertIsNotNone(data)
self.assertGreater(len(data), expected)
def test_getNumberFiles(self):
uuid = '5d74a20b44ec1dfd0af4fbc6bb680e0f557c14a08a143b843ef40977697e2bea'
data = self.dbi.getNumberFiles(uuid)
expected = 0
print('Num files: ', data)
self.assertIsNotNone(data)
self.assertGreater(data, expected)
def test_getDicomdataAll(self):
uuid = 't10000'
field = 'all'
data = self.dbi.getDicomdata(uuid, field)
expected = 0
print('Dicomdata for: ', field, '=', data)
self.assertIsNotNone(data)
self.assertGreater(data, expected)
def test_getDicomdata(self):
uuid = 't10000'
field = 'protocol'
data = self.dbi.getDicomdata(uuid, field)
expected = 0
print('Dicomdata for: ', field, '=', data)
self.assertIsNotNone(data)
self.assertGreater(data, expected)
def test_getRef(self):
pname = 'QSM'
expected = 'qsm'
data = self.dbi.getRef(pname)
self.assertEqual(expected, data)
# INSERTING DATA - USE TEST DB ONLY
# def test_setSeriesProcess(self):
# uuid = '5d74a20b44ec1dfd0af4fbc6bb680e0f557c14a08a143b843ef40977697e2bea'
# pid = 1
# server = 'AWS'
# status = 1
# starttime = datetime.datetime.now()
# try:
# rtn = self.dbi.setSeriesProcess(uuid, pid,server,status,starttime)
# self.assertEqual(rtn, 1, 'Series Process add failed')
# except IntegrityError as e:
# self.skipTest(e.args[0])
def test_getActiveProcesses(self):
data = self.dbi.getActiveProcesses()
print(data)
def test_deleteSeriesData(self):
uuid = '5d74a20b44ec1dfd0af4fbc6bb680e0f557c14a08a143b843ef40977697e2bea'
self.dbi.deleteSeriesData(uuid)
class ProcessThread(threading.Thread):
"""Multi Worker Thread Class."""
# wxGui, processname, self.cmodules[processref], targetdir, uuid, server, filenames, row, containername
# ----------------------------------------------------------------------
def __init__(self, wxObject, processname, inputdir, uuid, server, row):
"""Init Worker Thread Class."""
threading.Thread.__init__(self)
self.wxObject = wxObject
self.processname = processname
self.inputdir = inputdir
self.uuid = uuid
self.server = server
self.row = row
self.db = DBI()
self.db.connect()
if self.db.conn is not None:
# Dynamic process module
pref = self.db.getProcessField('ref', processname)
self.outputasfile = self.db.getProcessField(
'outputfile', processname) # file=1 or folder=0
self.module_name = self.db.getProcessModule(pref)
self.class_name = self.db.getProcessClass(pref)
# Instantiate module
module = importlib.import_module(self.module_name)
class_ = getattr(module, self.class_name)
# Docker Class
self.dcc = class_(self.processname)
# Record configs to log
if hasattr(self.dcc, 'CONTAINER_NAME'):
msg = "Running Container: %s [input=%s output=%s]" % (
self.dcc.CONTAINER_NAME, self.dcc.INPUT_TARGET,
join(self.dcc.OUTPUT_TARGET, self.dcc.OUTPUT))
print(msg)
logging.info(msg)
else:
raise Exception('Cannot access Database')
# ----------------------------------------------------------------------
def run(self):
print('Starting thread run')
msg = ''
ctr = 0
try:
event.set()
lock.acquire(True)
# Convert IMA files to MNC via Docker image
print('Running Docker image')
containerId = self.dcc.startDocker(join(self.inputdir, self.uuid))
if containerId is None:
raise Exception("ERROR: Unable to initialize Docker")
else:
print('Container ID:', containerId)
while (not self.dcc.checkIfDone(containerId)):
time.sleep(1)
wx.PostEvent(
self.wxObject,
ResultEvent((self.row, ctr, self.uuid, self.processname,
'Converting')))
ctr += 1
# restart for long running
if ctr == 100:
ctr = 1
# Check that everything ran ok (0 = success)
if self.dcc.getExitStatus(containerId):
raise Exception(
"ERROR: Docker unable to anonymize the dataset")
# Get the resulting mnc file back to the original directory
outputfile = self.dcc.finalizeJob(containerId, self.inputdir,
self.uuid, self.outputasfile)
print('Output:', outputfile)
if self.server.lower() != 'none':
msg = self.uploadCloud(outputfile)
else:
msg = 'Done: %s' % outputfile
ctr = 100
print(msg)
logger.info(msg)
except Exception as e:
msg = e.args[0]
print("ERROR:", msg)
ctr = -1
finally:
if lock.locked():
lock.release()
if event.is_set():
event.clear()
wx.PostEvent(
self.wxObject,
ResultEvent((self.row, ctr, self.uuid, self.processname, msg)))
def uploadCloud(self, mncfile):
"""
Send file to cloud for processing
:param mncfile:
:return:
"""
uploaderClass = get_class(self.server)
if uploaderClass is not None:
uploader = uploaderClass(self.uuid)
uploader.upload(mncfile, self.processname)
msg = 'Uploading to server[%s]: %s' % (self.server, mncfile)
else:
msg = 'No Uploader class available'
return msg