def append_SeriesUID(MRN: int, SeriesUID: List[str]):
"""
Append record with SeriesUID list. which has particular MRN
:param MRN:
:return:
"""
database_path = config_get("LocalDatabasePath")
existing_series_UID = get_SeriesUIDs(MRN)
if existing_series_UID is None:
total_series_UID = SeriesUID
else:
total_series_UID = existing_series_UID + SeriesUID
# JSON dumps.
json_seriesUID = json.dumps(total_series_UID)
# Update the MRN record with SeriesUID
LocalDB_query.update_entry(
database_path,
CNBP_blueprint.table_name,
CNBP_blueprint.keyfield,
MRN,
"SeriesUID",
json_seriesUID,
)
def findTimePointUpdateDatabase(token, DCCID, database_path, table_name):
"""
Find the timepoint of the subject, IF they exist, then update the given database by finding its relevant MRN.
:param token:
:param DCCID:
:param database_path:
:param table_name:
:return:
"""
MRN = -1
# @todo: permission must be checked to ensure we are not geting 401 error! which is an access issue.
# @todo: 2018-07-24 continue debug this code about entry creation.
time_point = LORIS_timepoint.findLatestTimePoint(token, DCCID)
# Timepoint Check
if time_point is None:
return False, "No timepoint found"
else:
logger.info(f"Timepoint retrieved okay: {time_point}")
# Validate table and schema congruency
success, reason = LocalDB_query.validateLocalTableAndSchema(
database_path, table_name, "DCCID")
if not success:
return False, reason
# Check local database for the rows with matching DCCID.
success, subject_rows = LocalDB_query.check_value(database_path,
table_name, "DCCID",
DCCID)
if not success:
return False, "No entries with this DCCID!"
# Recall each row WILL conform to schema.
for row in subject_rows:
# Get MRN:
DCCID_table_index = LocalDB_query.check_header_index(
database_path, table_name, "DCCID")
assert str(DCCID) == str(row[DCCID_table_index])
# Need to update these rows with the new value.
MRN = row[0] # the identifier of the record.
try:
LocalDB_query.update_entry(
database_path,
table_name,
CNBP_blueprint.keyfield,
MRN,
"Timepoint",
time_point,
)
except IOError:
return False, "Check the database is not read only. "
return True, "Timepoint successfully updated in the local SQLite database."
def append_StudyUID(MRN: int, StudyUID: str):
"""
Update record with proper completion status which STUDY has particular MRN
:param MRN:
:return:
"""
# convert new study UID to list.
list_StudyUID_single_new = [StudyUID]
database_path = config_get("LocalDatabasePath")
# obtain
list_StudyUID_existing_ones = get_StudyUIDs(MRN)
if list_StudyUID_existing_ones is None:
list_StudyUID_total = list_StudyUID_single_new
else:
list_StudyUID_total = list_StudyUID_existing_ones + list_StudyUID_single_new
# JSON dumps.
json_seriesUID = json.dumps(list_StudyUID_total)
# Update the MRN record with StudyUID
LocalDB_query.update_entry(
database_path,
CNBP_blueprint.table_name,
CNBP_blueprint.keyfield,
MRN,
"StudyUID",
json_seriesUID,
)
def set_timepoint(MRN: int, Timepoint: str):
"""
Update record with proper Timepoint which has particular MRN
:param MRN:
:return:
"""
database_path = config_get("LocalDatabasePath")
# Update the MRN record with Timepoint
LocalDB_query.update_entry(
database_path,
CNBP_blueprint.table_name,
CNBP_blueprint.keyfield,
MRN,
"Timepoint",
Timepoint,
)
def set_DCCID(MRN: int, DCCID: int):
"""
Update record with proper DCCID which has particular MRN
:param MRN:
:return:
"""
database_path = config_get("LocalDatabasePath")
# Update the MRN record with DCCID
LocalDB_query.update_entry(
database_path,
CNBP_blueprint.table_name,
CNBP_blueprint.keyfield,
MRN,
"DCCID",
DCCID,
)
def set_CNNIDs(MRN: int, CaseIDs: List[int]):
"""
Update record with proper CNN which has particular MRN
:param MRN:
:return:
"""
database_path = config_get("LocalDatabasePath")
# JSON dumps.
json_CaseIDs = json.dumps(CaseIDs)
# Update the MRN record with DCCID
LocalDB_query.update_entry(
database_path,
CNBP_blueprint.table_name,
CNBP_blueprint.keyfield,
MRN,
"CNNID",
json_CaseIDs,
)
def set_StudyUID(MRN: int, StudyUID: List[str]):
"""
Update record with SeriesUID list. which has particular MRN
:param MRN:
:return:
"""
database_path = config_get("LocalDatabasePath")
# JSON dumps.
json_seriesUID = json.dumps(StudyUID)
# Update the MRN record with SeriesUID
LocalDB_query.update_entry(
database_path,
CNBP_blueprint.table_name,
CNBP_blueprint.keyfield,
MRN,
"StudyUID",
json_seriesUID,
)
def set_CNBP(
MRN: int, CNBPID: str
): # fixme: all the SET RECORDS NEED TO CONSIDER THE MULTIROW possiblities.
"""
Update record with proper CNBPID which has particular MRN
:param MRN:
:return:
"""
database_path = config_get("LocalDatabasePath")
# Update the MRN record with CNBPID
LocalDB_query.create_entry(database_path, CNBP_blueprint.table_name,
CNBP_blueprint.keyfield, MRN)
LocalDB_query.update_entry(
database_path,
CNBP_blueprint.table_name,
CNBP_blueprint.keyfield,
MRN,
"CNBPID",
CNBPID,
)
def test_updateLocalTimepoint():
import os
database_path = "Test.sqlite"
DCCID = 768766
table_name = CNBP_blueprint.table_name
# Remove database if previously existed.
if os.path.exists(database_path):
os.remove(database_path)
# Create Database
LocalDB_createCNBP.database(database_path)
# Get login token:
success, token = LORIS_query.login()
# Create the entry with the right PSCID with proper DCCID on dev.cnbp.ca
LocalDB_query.create_entry(database_path, table_name,
CNBP_blueprint.keyfield, "8987888")
# Update above entry with the right mock PSCID.
LocalDB_query.update_entry(
database_path,
table_name,
CNBP_blueprint.keyfield,
"8987888",
"DCCID",
DCCID,
)
# Now, the big guy.
success, reason = findTimePointUpdateDatabase(token, DCCID,
database_path,
table_name)
# Clean up database.
os.remove(database_path)
assert success
def test_SubjectUpdate(self):
PathString = "TestCNBPQuery.sqlite"
# if SQL already exist, quit script.
SQLPath = Path(PathString)
# check if path is a file and exist.
if SQLPath.is_file():
logger.info(
"Test SQLite database file already exist. Gonna mess with it!")
"""'Delete current database! During testing only"""
os.remove(PathString)
# Create the database
assert LocalDB_createCNBP.database(PathString)
logger.info(
"Test SQLite database successfully created. Gonna mess with it!")
tableName = "id_table" # All CNBP database should have this table name.
MRNColumn = "MRN"
CNBPIDColumn = "CNBPID"
LocalDB_query.create_entry(PathString, tableName, MRNColumn, 2918210)
LocalDB_query.create_entry(PathString, tableName, MRNColumn, 23452346)
LocalDB_query.create_entry(PathString, tableName, MRNColumn, 2345234)
LocalDB_query.create_entry(PathString, tableName, MRNColumn, 273411)
LocalDB_query.create_entry(PathString, tableName, MRNColumn, 364573)
LocalDB_query.create_entry(PathString, tableName, MRNColumn, 7424141)
Prefix = config_get("institutionID")
LocalDB_query.update_entry(PathString, tableName, MRNColumn, 7424141,
CNBPIDColumn, f"{Prefix}0010001")
LocalDB_query.update_entry(PathString, tableName, MRNColumn, 2345234,
CNBPIDColumn, f"{Prefix}0010002")
LocalDB_query.update_entry(PathString, tableName, MRNColumn, 2918210,
CNBPIDColumn, f"{Prefix}0010003")
LocalDB_query.update_entry(PathString, tableName, MRNColumn, 273411,
CNBPIDColumn, f"{Prefix}0010004")
success, _ = LocalDB_query.check_value(PathString, tableName,
CNBPIDColumn, "CNBPID0010006")
assert not success
success, _ = LocalDB_query.check_value(PathString, tableName,
CNBPIDColumn,
f"{Prefix}0010001")
assert success
success, _ = LocalDB_query.check_value(PathString, tableName,
CNBPIDColumn, 55555)
assert not success
success, _ = LocalDB_query.check_value(PathString, tableName,
CNBPIDColumn, 742)
assert not success
success, _ = LocalDB_query.check_value(PathString, tableName,
CNBPIDColumn,
f"{Prefix}0010003")
assert success
logger.info("Tested SQLIte database entry. ")
# Remove test data base created
os.remove(PathString)
return True