def test_connection_warning(self):
with pytest.warns(UserWarning):
Orthanc(WEAK_URL)
with pytest.warns(None) as skip:
Orthanc(WEAK_URL, warn_insecure=False)
with pytest.warns(None) as record:
Orthanc(URL)
assert len(record) == 0
assert len(skip) == 0
def test_export_stable_study():
"""Test exporting from Orthanc
This tests assumes an instace of Orthanc running on http://localhost:8042/
"""
study_id = "0e16a034-87328dd8-ab6277ec-5c5658bd-4734b513"
auth = HTTPBasicAuth("orthanc", "orthanc")
outdir = "deleteme"
orthanc = Orthanc("http://localhost:8042/", auth=auth)
if os.path.exists(outdir):
shutil.rmtree(outdir)
export_stable_study(orthanc, study_id, outdir)
files = glob.glob(outdir + "**/**/*.dcm", recursive=True)
assert len(files) == 183
"""
try:
db_conn.cursor().execute(table_update, (seriesId,))
return True
except Error as err:
print('\033[1;35mUPDATE ', seriesId, err, '. \033[0m')
return False
def mkdirs(path):
if not os.path.exists(path):
os.makedirs(path)
##########
mkdirs(output_path)
conn = sqlite3.connect(dbFile)
orthanc = Orthanc(orthancSrv, warn_insecure=False)
# SELECT State == 1
pseudoid_dict = {}
select_pseudoid_series(conn)
for (key, value) in pseudoid_dict.items():
# for each AccNumber
acc_path = output_path + '/' + value
mkdirs(acc_path)
# for each SerialNumber of current PseudoId
seriesnumber_dict = {}
select_id_series(conn, key)
for (skey, svalue) in seriesnumber_dict.items():
series_path = acc_path + '/' + svalue
mkdirs(series_path)
dcm_path = series_path + '/dcm'
# def get(self, study_id):
# conn = db_connect.connect()
# query = conn.execute("select trackid, name, composer, unitprice from tracks;")
# result = {'data': [dict(zip(tuple (query.keys()) ,i)) for i in query.cursor]}
# return jsonify(result)
app = Flask(__name__)
api = Api(app)
load_dotenv()
orthanc_url = os.environ['ORTHANC_URL']
user = os.environ['ORTHANC_USER']
psswd = os.environ['ORTHANC_PSSWD']
dicom_dir = os.environ['DICOM_DIR']
auth = HTTPBasicAuth(user, psswd)
orthanc = Orthanc(orthanc_url, auth=auth)
api.add_resource(DICOM_Export,
'/dicom',
resource_class_kwargs={
'orthanc_instance': orthanc,
'dicom_outdir': dicom_dir
})
def main(args):
"""Main entry point allowing external calls
Args:
args ([str]): command line parameter list
"""
from orthanc_rest_client import Orthanc
from requests.auth import HTTPBasicAuth
from unittest import mock
import warnings
import pytest
URL = "https://demo.orthanc-server.com"
WEAK_URL = "http://demo.orthanc-server.com"
auth = HTTPBasicAuth("orthanc", "orthanc")
auth_bad = HTTPBasicAuth("bad", "bad")
orthanc = Orthanc(URL, auth=auth)
class TestClass:
def test_server_target(self):
assert orthanc._target == URL
def test_server_auth(self):
assert orthanc._auth.password == orthanc._auth.username == "orthanc"
def test_domain_passing(self):
assert orthanc.instances.domain == URL
assert orthanc.series.domain == URL
assert orthanc.studies.domain == URL
assert orthanc.server.domain == URL
assert orthanc.patients.domain == URL
assert orthanc.queries.domain == URL
assert orthanc.modalities.domain == URL
def test_auth_wrapper(self):
orthanc.patients.patients = mock.MagicMock()
try:
db_conn.cursor().execute(table_update, (seriesId, ))
return True
except Error as err:
print('\033[1;35mUPDATE ', seriesId, err, '. \033[0m')
return False
def mkdirs(path):
if not os.path.exists(path):
os.makedirs(path)
##########
conn = sqlite3.connect(dbFile)
orthanc = Orthanc(orthancSrv, warn_insecure=False)
# SELECT State == 1
# select_series(conn)
# for (key, value) in series_dict.items():
# series_path = output_path + value
# mkdirs(series_path)
# print(series_path)
# dcm_path = series_path + '/dcm/'
# mkdirs(dcm_path)
# nii_path = series_path + '/nifti/'
# mkdirs(nii_path)
# print("Get series instances ", end='')
# os.system("find " + dcm_path + " -type l -delete")
# insts = orthanc.get_series_instances(key)
# for inst in insts:
VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?);
"""
try:
db_conn.cursor().execute(table_insert, (seriesId, \
PseudoID, PseudoName, PseudoAcc, \
SeriesNumber, SeriesBrief, SeriesDescription, \
AcquisitionMatrix, Rows, Columns, PixelSpacing, Height, Width, State))
return True
except Error as err:
print('\033[1;35mINSERT', seriesId, err, '. \033[0m')
return False
##########
conn = sqlite3.connect(dbFile)
orthanc = Orthanc(orthancSrv, warn_insecure=False)
# INSERT State = 0/1
all_series = orthanc.get_series()
seriesNew = 0
for series in all_series:
infoS = orthanc.get_series_shared_tags(series)
infoI = orthanc.get_series_instances_tags(series)
# PseudoID, PseudoName, PseudoAcc, \
PseudoID = infoS['0010,0020']['Value']
PseudoName = infoS['0010,0010']['Value']
PseudoAcc = infoS['0008,0050']['Value']
# SeriesNumber, SeriesBrief, SeriesDescription, State
SeriesNumber = infoS['0020,0011']['Value']
SeriesBrief = ''
SeriesDescription = ''
from orthanc_rest_client import Orthanc
orthanc = Orthanc('http://localhost:8042')