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 Controller():
def __init__(self):
self.logger = self.__loadLogger()
self.db = DBI()
if self.db.c is None:
self.db.connect()
def __loadLogger(self, outputdir=None):
#### LoggingConfig
logger.setLevel(logging.DEBUG)
homedir = expanduser("~")
if outputdir is not None and access(outputdir, R_OK):
homedir = outputdir
if not access(join(homedir, ".d2c", "logs"), R_OK):
mkdir(join(homedir, ".d2c", "logs"))
self.logfile = join(homedir, ".d2c", "logs", 'd2c.log')
handler = RotatingFileHandler(filename=self.logfile,
maxBytes=10000000,
backupCount=10)
formatter = logging.Formatter(
'[ %(asctime)s %(levelname)-4s ] %(filename)s %(lineno)d : (%(threadName)-9s) %(message)s'
)
handler.setFormatter(formatter)
logger.addHandler(handler)
return logger
# ----------------------------------------------------------------------
def RunProcess(self, wxGui, inputdir, uuid, processname, server, row):
"""
Run processing in a thread
:param wxGui: Process Panel ref
:param inputdir: Directory with DICOM files
:param uuid: unique ID from series number
:param processname: Process eg QSM
:param server: Cloud server to use eg AWS
:param row: Row number in progress table in Process Panel
:return:
"""
filenames = self.db.getSessionFiles(uuid)
try:
if len(filenames) > 0:
msg = "Load Process Threads: %s [row: %d]" % (processname, row)
print(msg)
# Run thread
t = ProcessThread(wxGui, processname, inputdir, uuid, server,
row)
t.start()
msg = "Running Thread: %s" % processname
print(msg)
# Load to database for remote monitoring
self.db.setSessionProcess(uuid,
self.db.getProcessId(processname),
server, 1, datetime.datetime.now(),
inputdir)
else:
msg = "No files to process"
logger.error(msg)
raise ValueError(msg)
except ValueError as e:
raise e
except Exception as e:
raise e
def removeInputFiles(self, uuid, inputdir):
"""
Remove temporary files in outputdir (assumes tar file created and uploaded to Docker)
Remove file entries?
:return:
"""
files = iglob(join(inputdir, '*.IMA'))
for f in files:
os.remove(f)
# remove database entry - dicomdata and dicomfiles
self.db.deleteSessionData(uuid)
def checkRemote(self):
# Check if cloud processing is done and update database
seriesprocesses = self.db.getActiveProcesses()
for series in seriesprocesses:
print("CheckRemote:", series)
seriesid = series[0]
server = series[2].lower()
outputdir = series[6]
if outputdir is None or len(outputdir) <= 0:
files = self.db.getFiles(seriesid)
outputdir = dirname(files[0])
# Get uploader class and query
uploaderClass = get_class(server)
if uploaderClass is not None:
uploader = uploaderClass(seriesid)
if uploader.isDone():
downloadfile = join(outputdir, seriesid, 'download.tar')
uploader.download(downloadfile)
msg = 'Series: %s \n\tSTATUS: Complete (%s)\n' % (
seriesid, downloadfile)
print(msg)
self.db.setSessionProcessFinished(seriesid)
else:
# Still in progress
self.db.setSeriesProcessInprogress(seriesid)
else:
# assume done
msg = 'Series: %s \n\tSTATUS: Complete\n' % seriesid
print(msg)
self.db.setSessionProcessFinished(seriesid)
def parseDicom(self, wxObject, filelist):
'''
Read DICOM headers for filelist and load series info to db
:param filelist:
:return:
'''
t = DicomThread(wxObject, filelist)
t.start()