def test_ini(self, client):
ini = client.get(
url_for("init", init_code='invalid_ini_code_sdfsad6324234df'))
# No existing record, so setup the system.
assert ini.json == ["", "", 0]
assert ini.status == '200 OK'
ini_service = InitialService()
conn = ini_service.get_connection()
user_service = UserService(conn)
user_service.insert("*****@*****.**", "qi chang",
"ASDF#$#!!@$!123", "sdfsad6324234df", 0)
user_service.insert("*****@*****.**", "hua fu", "ASDF#$#!!@$!123",
"12345678", 0)
ini = client.get(
url_for("init", init_code='invalid_ini_code_sdfsad6324234df'))
assert ini.json == []
assert ini.status == '200 OK'
ini = client.get(url_for("init", init_code='sdfsad6324234df'))
assert ini.json[0] == "qi chang"
assert ini.json[1] == "*****@*****.**"
assert ini.status == '200 OK'
def test_delete(self):
ini_service = InitialService()
conn = ini_service.get_connection()
instance_service = InstanceService(conn)
# In case the record doesn't exist.
try:
instance_service.insert("Stroke Annotation-del1", "CT", "Stroke annotation descriptions.",
"./data/stroke_instance-del1", 0, 50, 10, 0)
except Error:
pass
last_rowid = instance_service.query({"name": "Stroke Annotation-del1"})[0]["instance_id"]
labelcandidates_service = LabelCandidatesService(conn)
labelcandidates_service.insert(last_rowid, 0, None, "Ischemic Stroke")
candidate_id = labelcandidates_service.query({"text": "Ischemic Stroke", "instance_id": last_rowid})[0][
"candidate_id"]
status = labelcandidates_service.delete({"candidate_id": candidate_id})
assert status is True
labelcandidates_service.insert(last_rowid, 0, None, "Ischemic Stroke")
candidate_id = labelcandidates_service.query({"text": "Ischemic Stroke", "instance_id": last_rowid})
status = labelcandidates_service.delete({"text": "Ischemic Stroke", "instance_id": last_rowid})
assert status is True
status = labelcandidates_service.delete({"text": "Ischemic Stroke", "instance_id": last_rowid})
assert status is False
def test_update(self):
ini_service = InitialService()
conn = ini_service.get_connection()
instance_service = InstanceService(conn)
try:
instance_service.insert("Stroke Annotation-update1", "CT", "Stroke annotation descriptions.",
"./data/stroke_instance-update1", 0, 50, 10, 0)
except Error:
pass
last_rowid = instance_service.query({"name": "Stroke Annotation-update1"})[0]["instance_id"]
labelcandidates_service = LabelCandidatesService(conn)
labelcandidates_service.insert(last_rowid, 0, None, "Ischemic Stroke-update1")
status = labelcandidates_service.update({"instance_id": last_rowid},
{"text": "Ischemic Stroke-update2", "label_type": 1})
update_item = labelcandidates_service.query({"instance_id": last_rowid})
assert status is True
assert update_item[0]["text"] == "Ischemic Stroke-update2"
status = labelcandidates_service.update({"instance_id": 1000},
{"text": "Ischemic Stroke-update2", "label_type": 1})
assert status is False
def test_query_and_create(self):
ini_service = InitialService()
conn = ini_service.get_connection()
label_service = LabelService(conn)
label_result = label_service.query({"series_id": 1, "user_id": 1, "file_id": "2_DCM.dcm"})
assert len(label_result) == 0
insert_status = label_service.insert(1, 1, "2_DCM.dcm", "content_data_232rwer2r232erwer2r")
assert insert_status is True
label_result = label_service.query({"series_id": 1, "user_id": 1, "file_id": "2_DCM.dcm"})
assert len(label_result) == 1
insert_status = label_service.insert(1, 1, "2_DCM.dcm", "content_data2222222_232rwer2r232erwer2r")
assert insert_status is True
label_result = label_service.query({"series_id": 1, "user_id": 1, "file_id": "2_DCM.dcm"})
assert len(label_result) == 1
assert label_result[0]["content"] == "content_data2222222_232rwer2r232erwer2r"
insert_status = label_service.insert(1, 1, "3_DCM.dcm", "content_data3333_232rwer2r232erwer2r")
assert insert_status is True
label_result = label_service.query({"series_id": 1, "user_id": 1, "file_id": "3_DCM.dcm"})
assert len(label_result) == 1
assert label_result[0]["series_id"] == 1
assert label_result[0]["user_id"] == 1
assert label_result[0]["file_id"] == "3_DCM.dcm"
assert label_result[0]["content"] == "content_data3333_232rwer2r232erwer2r"
def test_initial_database_file(self):
ini_service = InitialService()
conn = ini_service.get_connection()
cur = conn.cursor()
cur.execute('select * from users')
records = cur.fetchall()
assert (len(records) == 2)
has_record = ini_service.has_records()
assert (has_record is True)
def setup_class(self):
print("Setup Testing Environment....")
setup_sql()
qry = open(os.path.join(DbPool.DATABASE_PATH, "mock_data.sql"), 'r').read()
ini_service = InitialService()
conn = ini_service.get_connection()
cur = conn.cursor()
cur.executescript(qry)
def test_update(self):
ini_service = InitialService()
conn = ini_service.get_connection()
label_service = LabelService(conn)
status = label_service.update({"series_id": 1, "user_id": 1, "file_id": "not_exist_DCM.dcm"},
{"content": "asf"})
assert status is False
status = label_service.update({"series_id": 1, "user_id": 1, "file_id": "2_DCM.dcm"},
{"content": "asf"})
assert status is True
def test_initial_database_nofile(self):
ini_service = InitialService()
conn = ini_service.get_connection()
records = conn.cursor().fetchall()
assert (len(records) == 0)
has_record = ini_service.has_records()
assert (has_record is False)
rowid = mock_data_1(conn)
assert (rowid != 0)
has_record = ini_service.has_records()
assert (has_record is True)
def test_create(self):
ini_service = InitialService()
conn = ini_service.get_connection()
labelcandidates_service = LabelCandidatesService(conn)
insert_status = labelcandidates_service.insert(1, 0, None, "Ischemic Stroke")
assert insert_status is False
instance_service = InstanceService(conn)
instance_service.insert("Stroke annotation", "CT", "description...", "./data/stroke_data", 0, 100, 10, 0)
last_rowid = instance_service.query({"name": "Stroke annotation"})[0]["instance_id"]
insert_rowid = labelcandidates_service.insert(last_rowid, 0, None, "Ischemic Stroke")
assert insert_rowid == 1
def test_deleteUser(self):
ini_service = InitialService()
conn = ini_service.get_connection()
user_service = UserService(conn)
# In case the record doesn't exist.
try:
user_service.insert("*****@*****.**", "qi chang",
"**(SDFDSF", None, 0)
except Error:
pass
result = user_service.delete("*****@*****.**")
assert result is True
result = user_service.delete("*****@*****.**")
assert result is False
def init(init_code=None):
ini_service = InitialService()
has_record = ini_service.has_records()
if not has_record:
return jsonify(["", "", 0]), 200
elif init_code is not None:
user_service = UserService(get_conn())
user = user_service.query({"init_code": init_code})
if len(user) > 0:
user = user[0]
return jsonify(
[user["name"], user["email"], user["user_type"]]), 200
return jsonify([]), 200
def test_delete(self):
ini_service = InitialService()
conn = ini_service.get_connection()
label_service = LabelService(conn)
status = label_service.delete({"series_id": 1, "user_id": 1, "file_id": "not_exist_DCM.dcm"})
assert status is False
label_service.insert(1, 1, "2_DCM.dcm", "content_data_232rwer2r232erwer2r")
label_result = label_service.query({"series_id": 1, "user_id": 1, "file_id": "2_DCM.dcm"})
assert len(label_result) == 1
status = label_service.delete({"series_id": 1, "user_id": 1, "file_id": "2_DCM.dcm"})
assert status is True
label_result = label_service.query({"series_id": 1, "user_id": 1, "file_id": "2_DCM.dcm"})
assert len(label_result) == 0
def test_query_one_record(self):
ini_service = InitialService()
conn = ini_service.get_connection()
instance_service = InstanceService(conn)
labelcandidates_service = LabelCandidatesService(conn)
# In case the record doesn't exist.
try:
instance_service.insert("Stroke annotation", "CT", "Stroke annotation descriptions.",
"./data/stroke_data", 0, 50, 10, 0)
except Error:
print(Error)
pass
last_rowid = instance_service.query({"name": "Stroke annotation"})[0]["instance_id"]
labelcandidates_service.insert(last_rowid, 0, None, "Ischemic Stroke")
result = labelcandidates_service.query({"instance_id": last_rowid})
assert result[0]["text"] == "Ischemic Stroke"
def test_instance_detail(self, client):
ini_service = InitialService()
conn = ini_service.get_connection()
label_candidate = LabelCandidatesService(conn)
label_candidate.insert(1, 0, 0,
"['10,10;12,12;14,16;','10,10;12,12;14,16;']")
label_candidate.insert(1, 1, 1, "['selectoption1','selectoption2']")
res = client.get(url_for('instance_detail', instance_id=1))
# Verify instance record items.
assert res.json["name"] == "Stroke Annotation Task"
assert res.json["modality"] == "CT"
assert len(res.json["label_candidates"]) == 2
res = client.get(url_for('instance_detail', instance_id=1000))
assert res.json == {}
def test_instance_detail_delete(self, client):
ini_service = InitialService()
conn = ini_service.get_connection()
instance_service = InstanceService(conn)
instance_id = instance_service.insert(
"Stroke Annotation Task2", "CT",
"The stroke CT scans for annotation tasks.",
"tests/services/sample_data", 0, 200, 1, 0)
res = client.delete(url_for('instance_detail',
instance_id=instance_id))
assert res.json == {}
assert res.status == "200 OK"
res = client.delete(url_for('instance_detail',
instance_id=instance_id))
assert res.json == {}
assert res.status == "404 NOT FOUND"
def test_list_all_studies(self, client):
res = client.get(url_for('list_all_studies', instance_id=1))
assert res.json == {}
assert res.status == '200 OK'
# Setup studies sample data
ini_service = InitialService()
conn = ini_service.get_connection()
instance_service = InstanceService(conn)
instance_service.insert("Stroke Annotation Task", "CT",
"The stroke CT scans for annotation tasks.",
"tests/services/sample_data", 0, 200, 1, 0)
result = instance_service.query({})
assert result[0]["instance_id"] == 1
assert result[0]["name"] == "Stroke Annotation Task"
studies_service = StudiesService(conn)
studies_service.insert(1, "Dicom_691_2", 25, 0, "folder", 100, 1)
studies_service.insert(1, "Raw_1003/3CH_tagging", 30, 1, "folder", 100,
1)
series_service = SeriesService(conn)
series_service.insert(1, "series1", "series1/path", ["1"], 1, "200",
"200", "0.5", "0.5", "0.5", 512, 512, 512, 1,
100101, "", "", "")
series_service.insert(1, "series2", "series2/path", ["1"], 1, "200",
"200", "0.5", "0.5", "0.5", 512, 512, 512, 1,
100101, "", "", "")
series_service.insert(2, "series3", "series3/path", ["1"], 1, "200",
"200", "0.5", "0.5", "0.5", 512, 512, 512, 1,
100101, "", "", "")
series_service.insert(2, "series4", "series4/path", ["1"], 1, "200",
"200", "0.5", "0.5", "0.5", 512, 512, 512, 1,
100101, "", "", "")
res = client.get(url_for('list_all_studies', instance_id=1))
assert len(res.json[0]) == 2
assert res.json[0][0]["instance_id"] == 1
assert res.json[0][0]["patient_uid"] == "Dicom_691_2"
assert res.json[1][0]["instance_id"] == 1
assert res.json[1][0]["patient_uid"] == "Raw_1003/3CH_tagging"
assert res.status == '200 OK'
def test_list_series_in_one_study(self, client):
ini_service = InitialService()
conn = ini_service.get_connection()
series_service = SeriesService(conn)
series_service.delete({"study_id": 1})
series_service.delete({"study_id": 2})
series_service.insert(
2, "series_description1", "series_path",
"['export0001.dcm','export0002.dcm','export0003.dcm','export0004.dcm']",
4, None, None, None, None, None, None, None, None, None, None,
None, None, None)
res = client.get(url_for('list_all_series', study_id=1))
assert res.json == {}
res = client.get(url_for('list_all_series', study_id=2))
assert len(res.json) == 1
assert res.json[0]["study_id"] == 2
assert res.json[0]["series_description"] == "series_description1"
assert len(eval(res.json[0]["series_files_list"])) == 4
def test_createUser(self):
ini_service = InitialService()
conn = ini_service.get_connection()
cursor = conn.cursor()
user_service = UserService(conn)
user_service.insert("*****@*****.**", "qi chang", "**(SDFDSF",
None, 0)
cursor.execute("SELECT * from users")
records = cursor.fetchall()
assert len(records) == 1
# email is a unique key, should just update record.
result = user_service.insert("*****@*****.**", "qi chang",
"**(SDFDSF", None, 0)
assert result is False
cursor.execute("SELECT * from users")
records = cursor.fetchall()
assert len(records) == 1
def test_queryUser(self):
ini_service = InitialService()
conn = ini_service.get_connection()
user_service = UserService(conn)
# In case the record doesn't exist.
try:
user_service.insert("*****@*****.**", "qi chang",
"**(SDFDSF", None, 0)
except Error:
pass
result = user_service.query({"email": "*****@*****.**"})
assert result[0]["email"] == "*****@*****.**"
assert result[0]["name"] == "qi chang"
assert "pwd" not in result[0]
# assert result[0]["pwd"] == '**(SDFDSF'
assert result[0]["init_code"] is None
assert result[0]["user_type"] == 0
result = user_service.query({"email": "*****@*****.**"})
assert len(result) == 0
def get_conn():
ini_service = InitialService()
return ini_service.get_connection()
content_3D = labeldb[f"study:{study_uid}-series:{series_uid}/label"][()]
print(f"Import label for: study:{study_uid}-series:{series_uid}/")
for i in range(len(slice_file_name)):
content_2D = content_3D[:, :, i]
x_dim = content_2D.shape[0]
y_dim = content_2D.shape[1]
content_1D = np.reshape(content_2D, x_dim * y_dim)
unique_id = np.unique(content_1D).tolist()
compressed_content_1D = LabelService.compress_content(content_1D)
content = {
"labelmap2D": {"pixelData": compressed_content_1D, "segmentsOnLabelmap": unique_id,
"dataLength": content_1D.shape[0]}}
labelService.insert(series[0]['series_id'], 1, slice_file_name[i],
str.encode(json.dumps(content)))
seriesService.update({"series_instance_uid": series_uid}, {SERIES_STATUS.mask_is_ready.value})
elif load_type == 'mhd':
raise NotImplementedError()
if __name__ == "__main__":
ini_service = InitialService()
importService = ImportService(ini_service.get_connection())
# importService.import_annotations("h5", "/Users/qichang/PycharmProjects/pytorch-template/data/ACDC/processed/Export-1-Cardial_MRI_DB-0-predict-final-x4.h5")
importService.import_annotations("h5",
"/ajax/users/qc58/work/projects/pytorch-template/saved/test_results/ACDC_segmentation_exp1/test_result-ACDC_segmentation_exp1_512x512_smooth.h5")
# http://127.0.0.1:5000/load_data/2/NYU_CMR_Raw
# http://127.0.0.1:5000/export_label/studies/2
def test_updateUser(self):
ini_service = InitialService()
conn = ini_service.get_connection()
user_service = UserService(conn)
try:
user_service.insert("*****@*****.**", "qi chang",
"**(SDFDSF", None, 0)
user_result = user_service.query(
{'email': '*****@*****.**'})
assert user_result[0]['name'] == 'qi chang'
assert 'pwd' not in user_result
assert user_result[0]['init_code'] is None
assert user_result[0]['user_type'] == 0
user_result = user_service.query({
'email': '*****@*****.**',
'pwd': '**(SDFDSF'
})
assert user_result[0]['name'] == 'qi chang'
assert 'pwd' not in user_result
assert user_result[0]['init_code'] is None
assert user_result[0]['user_type'] == 0
user_result = user_service.query({
'email': '*****@*****.**',
'pwd': 'WrongPwd'
})
assert len(user_result) == 0
except Error:
pass
result = user_service.update("*****@*****.**", {
"name": "MK",
"pwd": "pwdpwd",
"init_code": "*&**I",
"user_type": 1
})
assert result is True
user_result = user_service.query({'email': '*****@*****.**'})
assert user_result[0]['name'] == 'MK'
assert 'pwd' not in user_result
assert user_result[0]['init_code'] == '*&**I'
assert user_result[0]['user_type'] == 1
user_result = user_service.query({
'email': '*****@*****.**',
'pwd': 'pwdpwd'
})
assert user_result[0]['name'] == 'MK'
assert 'pwd' not in user_result
assert user_result[0]['init_code'] == '*&**I'
assert user_result[0]['user_type'] == 1
user_result = user_service.query({
'email': '*****@*****.**',
'pwd': '**(SDFDSF'
})
assert len(user_result) == 0
# not existing email will return False
result = user_service.update("*****@*****.**", {
"name": "MK",
"pwd": "***",
"init_code": "*&**I",
"user_type": 1
})
assert result is False
# unqualified key will ignored.
result = user_service.update(
"*****@*****.**", {
"email": "*****@*****.**",
"name": "MK",
"pwd": "***",
"init_code": "*&**I",
"user_type": 1
})
assert result is True
result = user_service.query({"email": "*****@*****.**"})
assert len(result) == 1