def prepare_mysql_metadata_stage5(
transaction: RedcapTransaction) -> RedcapTransaction:
"""
Prepare mysql metadata. (Stage 5)
*** Sometime some metadata are missing. Ex : Stage 4 is adding caseid, motherid etc and metadata is not updated.
This fonction will add the missing metadata to allow us to export all the data to mysql.
:param transaction: RedcapTransaction (Stage 4)
:return: Updated RedcapTransaction (stage 5)
"""
# Get entries to create. (Group by table name - get_mysql_tablename return the tablename to use)
entrieslist_redcap_queue = groupby(
transaction.redcap_queue,
lambda f: get_mysql_tablename(transaction.redcap_metadata, f[0]),
)
# For each table - (insert entries/lines).
for tablename_redcap_queue, entries_redcap_queue in entrieslist_redcap_queue:
# Get the list of metadata for a specific tablename - x[3] is the tablename.
table_redcap_metadata = [
x for x in transaction.redcap_metadata
if x[3] == tablename_redcap_queue
]
# For each entries / lines to add inside the database.
for fields in entries_redcap_queue:
# For each field we need to check if it's already inside the metadata.
for fieldname, fieldvalue in fields[0].items():
# Preparing vars.
found = False
# For each field inside the current metadata, check if the field already exist.
for field in table_redcap_metadata:
# If this is the current field that we are looking for. (Flag found to true and exit loop)
if field[0] == fieldname:
found = True
break
# If not found, then we need to add metadata.
if found == False:
data = [
fieldname,
convert_redcap_to_mysql_fieldtype("text"),
fieldname,
tablename_redcap_queue,
]
table_redcap_metadata.append(data)
transaction.redcap_metadata.append(data)
# We need to order the redcap_metadata using tablename - f[3]
# Otherwise group will not work.
transaction.redcap_metadata = sorted(transaction.redcap_metadata,
key=lambda f: f[3])
# Return the updated repcap transaction (stage 5)
return transaction
def load_metadata(transaction: RedcapTransaction) -> RedcapTransaction:
"""
Get all information about REDCap form names and fields.
:return: RedcapTransaction
"""
transaction.redcap_metadata = []
# For each REDCap project
for p in Project:
# Get all metadata rows.
payload = {
"token": get_project_token(p.name),
"format": "json",
"content": "metadata",
}
response = post(redcap_api_url, data=payload)
metadata = response.json()
# Add each metadata row to a local list.
for field in metadata:
transaction.redcap_metadata.append([
field["field_name"],
field["field_type"],
field["field_label"],
field["form_name"],
])
return transaction
def get_data_rows_for_patient_table(table_info,
transaction: RedcapTransaction) -> list:
"""
Gets all rows of data for a specific patient table.
:param table_info: Table Information
:param transaction: RedcapTransaction
:return: List of all the rows obtained from the query or None if table not found.
"""
if table_info is None:
return None
if table_info[DATABASE_TABLE_NAME] == "":
return None
primary_key_filter_name = str(
get_primary_key_name(table_info[PRIMARY_KEY_NAME]))
primary_key_filter_value = str(
transaction.get_primary_key_value(table_info[PRIMARY_KEY_VALUE]))
primary_key_data_type = get_primary_key_data_type(
table_info[PRIMARY_KEY_VALUE])
if (primary_key_filter_name == "" or primary_key_filter_value == ""
or primary_key_filter_value == "None"):
return None
if primary_key_data_type == DataType.String.value:
select_statement = ("SELECT * FROM [" +
table_info[DATABASE_TABLE_NAME] + "] WHERE [" +
primary_key_filter_name + "] = '" +
primary_key_filter_value + "'")
elif primary_key_data_type == DataType.Integer.value:
select_statement = ("SELECT * FROM [" +
table_info[DATABASE_TABLE_NAME] + "] WHERE [" +
primary_key_filter_name + "] = " +
primary_key_filter_value)
else:
select_statement = ""
if select_statement != "":
conn = pyodbc.connect(get_connection_string(table_info[DATABASE]))
odbc_cursor = conn.cursor()
odbc_cursor.execute(select_statement)
data = odbc_cursor.fetchall()
odbc_cursor.close()
conn.close
return data
else:
return None
def send_data(transaction: RedcapTransaction) -> (bool, str):
"""
Sends all records in the queue to REDCap.
:return: Successful or not and reason
"""
# If there is at least one record in the queue waiting to be sent to REDCap
if not len(transaction.redcap_queue) > 0:
return False, "REDCap queue is empty."
# Sort record queue by second column ascending (project).
transaction.redcap_queue = sorted(transaction.redcap_queue,
key=itemgetter(1))
# For each REDCap project
for p in Project:
batch_of_records = []
# For each record in the global queue
for index_record in range(len(transaction.redcap_queue)):
# If the current record belongs to the current project
if transaction.redcap_queue[index_record][1] == p.value:
# We add this record to the batch of records to send.
batch_of_records.append(
transaction.redcap_queue[index_record][0])
# If the maximum number of records per batch has been reached
if (len(batch_of_records)
) % environment.NUMBER_OF_RECORDS_PER_BATCH == 0:
# Send the batch of records to REDCap.
import_records(batch_of_records, get_project_token(p.name))
# Send the batch of records to REDCap.
import_records(batch_of_records, get_project_token(p.name))
return True, "All REDCap data in queue has been sent. "
def get_case_ids(transaction: RedcapTransaction) -> List[int]:
"""
Get Case Ids
:param transaction: RedcapTransaction
:return: List of all the case ids related to the current hospital record number or None if table not found.
"""
case_ids = []
primary_key_filter_name = Field.HospitalRecordNumber.name
primary_key_filter_value = str(
transaction.get_primary_key_value(Field.HospitalRecordNumber.value))
if (primary_key_filter_name == "" or primary_key_filter_value == ""
or primary_key_filter_value == "None"):
return None
select_statement = ("SELECT [CaseId] FROM [Admission] WHERE [" +
primary_key_filter_name + "] = '" +
primary_key_filter_value + "'")
conn = pyodbc.connect(get_connection_string(1))
odbc_cursor = conn.cursor()
odbc_cursor.execute(select_statement)
data = odbc_cursor.fetchall()
for index_case_id in range(len(data)):
# Add Case Id to list of Case Ids.
case_ids.append(data[index_case_id][0])
odbc_cursor.close()
conn.close
return case_ids
def prepare_patient_tables(transaction: RedcapTransaction) -> RedcapTransaction:
"""
Creates REDCap records for of all patient tables and adds them to the global queue (only for each hospital record
number loaded).
:param transaction: RedcapTransaction
:return: RedcapTransaction
"""
# For each hospital record number
for index_hospital_record_number in range(len(transaction.hospital_record_numbers)):
# Set hospital record number.
transaction.set_hospital_record_number(index_hospital_record_number)
# Set any additional id that has a 1 to 1 relationship with the hospital record number.
transaction.set_cnbp_id(get_CNBP(transaction.HospitalRecordNumber))
# Get all case ids related to this Hospital Record Number
cases = get_case_ids(transaction)
# If no data was retrieved from the database, skip.
if cases is None:
return
# Record caseIDs
set_CNNIDs(transaction.HospitalRecordNumber, cases)
# For each case related to this Hospital Record Number
for index_case in range(len(cases)):
# Set case id.
transaction.set_case_id(cases[index_case])
process_case(transaction)
return transaction
def update_redcap_data() -> None:
"""
This method is the main method of this script. It calls all methods necessary to transfer CNN and CNFUN data
to REDCap.
:return: None
"""
# Indicate that the script is started.
logger.info("Update REDCap Data Started: " + str(datetime.datetime.now()))
# Initialize the RedcapTransaction class object to be past and returned each step of the way.
transaction_stage0 = RedcapTransaction()
# Load data import configuration matrix.
logger.info("Loading Data Import Configuration...")
transaction_stage1_initialized = initialize_import_configuration(
transaction_stage0)
logger.info("Done.")
# Check if we have something to export.
if not mysql_export_enabled and not redcap_export_enabled:
logger.info(
"Nothing need to be exported! REDCAP_EXPORT_ENABLED & MYSQL_EXPORT_ENABLED is false. Please check your configuration file."
)
return
# Get all information about REDCap table names and fields.
logger.info("Loading REDCap Metadata...")
transaction_stage2_meta_added = load_metadata(
transaction_stage1_initialized)
logger.info("Done.")
# Get all hospital record numbers.
logger.info("Loading Hospital Record Numbers...")
# Change this flag in environment module or here to force local of DB loading.
transaction_stage2_meta_added.hospital_record_numbers = load_hospital_record_numbers(
environment.USE_LOCAL_HOSPITAL_RECORD_NUMBERS_LIST)
logger.info("Done.")
# Prepare Reference Data.
logger.info("Preparing Reference Data Transfer...")
transaction_stage3_references_added = prepare_reference_tables(
transaction_stage2_meta_added)
logger.info("Done.")
# Prepare Patient Data.
logger.info("Preparing Patient Data Transfer...")
transaction_stage4_patients_added = prepare_patient_tables(
transaction_stage3_references_added)
logger.info("Done.")
# If Redcap export is enabled, then we need to export the data.
if redcap_export_enabled:
# Indicate that the script is started.
logger.info("Update REDCap Data Started: " +
str(datetime.datetime.now()))
# Wipe all existing data from REDCap.
logger.info("Wiping ALL existing data from REDCap...")
wipe_all_redcap_data()
logger.info("Done.")
# Send data to REDCap.
logger.info("Sending ALL data to REDCap...")
send_data(transaction_stage4_patients_added)
logger.info("Done.")
# Indicate that the script is completed.
logger.info("Update REDCap Data Completed: " +
str(datetime.datetime.now()))
# If MySQL export is enabled, then we need to export the data to MySQL.
if mysql_export_enabled:
# Wiping old MySQL data.
logger.info("Wiping ALL existing data from MySQL...")
wipe_all_mysql_data()
logger.info("Done.")
# Preparing mysql metadata.
logger.info("Preparing mysql metadata...")
transaction_stage_5_metadata = prepare_mysql_metadata_stage5(
transaction_stage4_patients_added)
logger.info("Done.")
# Send data to MySQL.
logger.info("Sending ALL data to MySQL...")
send_mysql_data(transaction_stage_5_metadata)
logger.info("Done.")
return
def test_load_metadata() -> None:
from DICOMTransit.redcap.transaction import RedcapTransaction
from DICOMTransit.redcap.query import load_metadata
transact = RedcapTransaction()
load_metadata(transact)
def initialize_import_configuration(
transaction: RedcapTransaction) -> RedcapTransaction:
"""
Initialize the data import configuration matrix.
Columns:
0 IMPORT_SEQUENCE,
1 IS_IMPORT_ENABLED,
2 IS_REFERENCE_TABLE,
3 REDCAP_PROJECT,
4 DATABASE_TABLE_NAME,
5 DATABASE,
6 PRIMARY_KEY_NAME,
7 PRIMARY_KEY_VALUE,
8 AUTHORITY_ON_IDS,
9 IS_REPEATABLE_INSTRUMENT,
10 REDCAP_FORM_NAME
:return: RedcapTransaction
"""
transaction.data_import_configuration = [
[1, 1, 0, 1, "admission", 1, 2, 2, [3], 0, "admission"],
[2, 1, 0, 1, "admissionChart", 1, 2, 2, None, 1, "admissionChart"],
[3, 1, 0, 1, "admissionstate", 1, 2, 2, None, 1, "admissionstate"],
[4, 1, 0, 1, "Born", 1, 2, 2, None, 1, "Born"],
[5, 1, 0, 1, "Borndiagnosis", 1, 2, 2, None, 1, "Borndiagnosis"],
[6, 1, 0, 1, "Caffeine", 1, 2, 2, None, 1, "Caffeine"],
[
7, 1, 0, 1, "Congenitalanomalies", 1, 2, 2, None, 1,
"Congenitalanomalies"
],
[
8, 1, 0, 1, "Culturestransfusions", 1, 2, 2, None, 1,
"Culturestransfusions"
],
[
9, 1, 0, 1, "Diagnosisofinfection", 1, 2, 2, None, 1,
"Diagnosisofinfection"
],
[
10, 1, 0, 1, "Diagnosisprocedures", 1, 2, 2, None, 1,
"Diagnosisprocedures"
],
[11, 1, 0, 1, "Discharge", 1, 2, 2, None, 1, "Discharge"],
[12, 1, 0, 1, "Encephalopathy", 1, 2, 2, None, 1, "Encephalopathy"],
[13, 1, 0, 1, "Eol", 1, 2, 2, None, 1, "Eol"],
[
14, 1, 0, 1, "Epiqcentrallines", 1, 2, 2, None, 1,
"Epiqcentrallines"
],
[15, 1, 0, 1, "Formreviewed", 1, 2, 2, None, 1, "Formreviewed"],
[16, 1, 0, 1, "Ivh", 1, 2, 2, None, 1, "Ivh"],
[17, 1, 0, 1, "Nropexams", 1, 2, 2, None, 1, "Nropexams"],
[18, 1, 0, 1, "Nroptreatments", 1, 2, 2, None, 1, "Nroptreatments"],
[19, 1, 0, 1, "Ntiss1", 1, 2, 2, None, 1, "Ntiss1"],
[20, 1, 0, 1, "Ntiss3", 1, 2, 2, None, 1, "Ntiss3"],
[21, 1, 0, 1, "Otherdiagnosis", 1, 2, 2, None, 1, "Otherdiagnosis"],
[22, 1, 0, 1, "Pdatreatment", 1, 2, 2, None, 1, "Pdatreatment"],
[
23, 1, 0, 1, "Posbloodcsfcultures", 1, 2, 2, None, 1,
"Posbloodcsfcultures"
],
[
24, 1, 0, 1, "Postnatalsteroids", 1, 2, 2, None, 1,
"Postnatalsteroids"
],
[25, 1, 0, 1, "Posttransfer", 1, 2, 2, None, 1, "Posttransfer"],
[26, 1, 0, 1, "Rop", 1, 2, 2, None, 1, "Rop"],
[27, 1, 0, 1, "Screenlog", 1, 2, 2, None, 1, "Screenlog"],
[28, 1, 0, 1, "Snap", 1, 2, 2, None, 1, "Snap"],
[29, 1, 0, 1, "Surfactant", 1, 2, 2, None, 1, "Surfactant"],
[30, 1, 0, 1, "Transport", 1, 2, 2, None, 1, "Transport"],
[31, 1, 0, 1, "Trips", 1, 2, 2, None, 1, "Trips"],
[32, 1, 0, 1, "Validate", 1, 2, 2, None, 1, "Validate"],
[33, 1, 0, 2, "Baby", 1, 3, 3, [4, 5], 0, "Baby"],
[34, 1, 0, 2, "Bornbaby", 1, 3, 3, None, 1, "Bornbaby"],
[35, 1, 0, 2, "Epiq", 1, 3, 3, None, 1, "Epiq"],
[36, 1, 0, 2, "Resuscitation", 1, 3, 3, None, 1, "Resuscitation"],
[
37,
1,
0,
2,
"Antenatalinterventions",
1,
3,
3,
None,
1,
"Antenatalinterventions",
],
[38, 1, 0, 3, "Mother", 1, 4, 4, None, 0, "Mother"],
[
39,
1,
0,
3,
"Antenatalintervention",
1,
4,
4,
None,
1,
"Antenatalintervention",
],
[40, 1, 0, 3, "Bornmother", 1, 4, 4, None, 1, "Bornmother"],
[41, 1, 0, 4, "Patients", 2, 6, 5, [7], 0, "Patients"],
[
42,
1,
0,
4,
"18MonthAssessments",
2,
7,
7,
None,
1,
"EighteenMonthAssessments",
],
[
43,
1,
0,
4,
"36MonthAssessments",
2,
7,
7,
None,
1,
"ThirtySixMonthAssessments",
],
[
44, 1, 0, 4, "36MonthStatus", 2, 7, 7, None, 1,
"ThirtySixMonthStatus"
],
[
45,
1,
0,
4,
"3YearAuditoryAssessments",
2,
7,
7,
None,
1,
"ThreeYearAuditoryAssessments",
],
[
46, 1, 0, 4, "3YearFamilyInfo", 2, 7, 7, None, 1,
"ThreeYearFamilyInfo"
],
[
47,
1,
0,
4,
"3YearMedicalHistories",
2,
7,
7,
None,
1,
"ThreeYearMedicalHistories",
],
[
48,
1,
0,
4,
"3YearPrimaryCaregivers",
2,
7,
7,
None,
1,
"ThreeYearPrimaryCaregivers",
],
[
49,
1,
0,
4,
"3YearVisionAssessments",
2,
7,
7,
None,
1,
"ThreeYearVisionAssessments",
],
[
50, 1, 0, 4, "AuditoryAssessments", 2, 7, 7, None, 1,
"AuditoryAssessments"
],
[51, 1, 0, 4, "FamilyInfo", 2, 7, 7, None, 1, "FamilyInfo"],
[52, 1, 0, 4, "FollowupReasons", 2, 7, 7, None, 1, "FollowupReasons"],
[
53, 1, 0, 4, "MedicalHistories", 2, 7, 7, None, 1,
"MedicalHistories"
],
[
54, 1, 0, 4, "PrimaryCaregivers", 2, 7, 7, None, 1,
"PrimaryCaregivers"
],
[
55,
1,
0,
4,
"PsychologicalExaminations",
2,
7,
7,
None,
1,
"PsychologicalExaminations",
],
[
56, 1, 0, 4, "VisionAssessments", 2, 7, 7, None, 1,
"VisionAssessments"
],
[
57, 1, 1, 5, "mstadmissioncasetype", 1, 8, 8, None, 1,
"mstadmissioncasetype"
],
[
58,
1,
1,
5,
"mstadmissioninfantsex",
1,
8,
8,
None,
1,
"mstadmissioninfantsex",
],
[
59, 1, 1, 5, "mstadmissioninternal", 1, 8, 8, None, 1,
"mstadmissioninternal"
],
[
60, 1, 1, 5, "mstadmissionpayor", 1, 8, 8, None, 1,
"mstadmissionpayor"
],
[
61, 1, 1, 5, "mstadmissionstat", 1, 8, 8, None, 1,
"mstadmissionstat"
],
[
62,
1,
1,
5,
"mstborncordbloodteststatus",
1,
8,
8,
None,
1,
"mstborncordbloodteststatus",
],
[
63, 1, 1, 5, "mstborncountries", 1, 8, 8, None, 1,
"mstborncountries"
],
[
64,
1,
1,
5,
"mstborndrugscreenresult",
1,
8,
8,
None,
1,
"mstborndrugscreenresult",
],
[
65,
1,
1,
5,
"mstbornhealthcardtype",
1,
8,
8,
None,
1,
"mstbornhealthcardtype",
],
[
66,
1,
1,
5,
"mstbornnewbornfeeding",
1,
8,
8,
None,
1,
"mstbornnewbornfeeding",
],
[
67,
1,
1,
5,
"mstbornscreeningoffered",
1,
8,
8,
None,
1,
"mstbornscreeningoffered",
],
[68, 1, 1, 5, "mstbornynu", 1, 8, 8, None, 1, "mstbornynu"],
[69, 1, 1, 5, "mstbpdgrade", 1, 8, 8, None, 1, "mstbpdgrade"],
[70, 1, 1, 5, "mstcities", 1, 8, 8, None, 1, "mstcities"],
[71, 1, 1, 5, "mstcitygroups", 1, 8, 8, None, 1, "mstcitygroups"],
[
72, 1, 1, 5, "mstcnfunhospitallist", 1, 8, 8, None, 1,
"mstcnfunhospitallist"
],
[
73, 1, 1, 5, "mstculturesculture", 1, 8, 8, None, 1,
"mstculturesculture"
],
[
74, 1, 1, 5, "mstculturesdiagnosis", 1, 8, 8, None, 1,
"mstculturesdiagnosis"
],
[
75, 1, 1, 5, "mstculturesorganism", 1, 8, 8, None, 1,
"mstculturesorganism"
],
[
76,
1,
1,
5,
"mstdiagnosiscongenitaltype",
1,
8,
8,
None,
1,
"mstdiagnosiscongenitaltype",
],
[
77,
1,
1,
5,
"mstdiagnosisdiagnosistype",
1,
8,
8,
None,
1,
"mstdiagnosisdiagnosistype",
],
[78, 1, 1, 5, "mstdiagnosishie", 1, 8, 8, None, 1, "mstdiagnosishie"],
[
79,
1,
1,
5,
"mstdiagnosisintperforation",
1,
8,
8,
None,
1,
"mstdiagnosisintperforation",
],
[
80,
1,
1,
5,
"mstdiagnosisnecstages",
1,
8,
8,
None,
1,
"mstdiagnosisnecstages",
],
[
81, 1, 1, 5, "mstdiagnosispdayes", 1, 8, 8, None, 1,
"mstdiagnosispdayes"
],
[82, 1, 1, 5, "mstdiagnosisrds", 1, 8, 8, None, 1, "mstdiagnosisrds"],
[
83, 1, 1, 5, "mstdiagnosisseizures", 1, 8, 8, None, 1,
"mstdiagnosisseizures"
],
[
84,
1,
1,
5,
"mstdiagnosisthrombosislocationarterial",
1,
8,
8,
None,
1,
"mstdiagnosisthrombosislocationarterial",
],
[
85,
1,
1,
5,
"mstdiagnosisthrombosislocationvenous",
1,
8,
8,
None,
1,
"mstdiagnosisthrombosislocationvenous",
],
[
86,
1,
1,
5,
"mstdiagnosisthrombosismethod",
1,
8,
8,
None,
1,
"mstdiagnosisthrombosismethod",
],
[
87,
1,
1,
5,
"mstdiagnosisthrombosistreatment",
1,
8,
8,
None,
1,
"mstdiagnosisthrombosistreatment",
],
[
88,
1,
1,
5,
"mstdischargedestination",
1,
8,
8,
None,
1,
"mstdischargedestination",
],
[
89,
1,
1,
5,
"mstdischargeinpatientarea",
1,
8,
8,
None,
1,
"mstdischargeinpatientarea",
],
[
90, 1, 1, 5, "mstdischargeresult", 1, 8, 8, None, 1,
"mstdischargeresult"
],
[
91,
1,
1,
5,
"mstencephalopathyclinicalstatus",
1,
8,
8,
None,
1,
"mstencephalopathyclinicalstatus",
],
[
92,
1,
1,
5,
"mstencephalopathyclinicalstatusatcompletion",
1,
8,
8,
None,
1,
"mstencephalopathyclinicalstatusatcompletion",
],
[
93,
1,
1,
5,
"mstencephalopathymethod",
1,
8,
8,
None,
1,
"mstencephalopathymethod",
],
[
94,
1,
1,
5,
"mstencephalopathyreasonxprematurediscont",
1,
8,
8,
None,
1,
"mstencephalopathyreasonxprematurediscont",
],
[
95,
1,
1,
5,
"mstencephalopathytargettemp",
1,
8,
8,
None,
1,
"mstencephalopathytargettemp",
],
[96, 1, 1, 5, "msteol", 1, 8, 8, None, 1, "msteol"],
[
97, 1, 1, 5, "mstepiqchecklistused", 1, 8, 8, None, 1,
"mstepiqchecklistused"
],
[98, 1, 1, 5, "mstfacilitytype", 1, 8, 8, None, 1, "mstfacilitytype"],
[99, 1, 1, 5, "msthospitals", 1, 8, 8, None, 1, "msthospitals"],
[100, 1, 1, 5, "mstivhresponse", 1, 8, 8, None, 1, "mstivhresponse"],
[
101, 1, 1, 5, "mstivhventricular", 1, 8, 8, None, 1,
"mstivhventricular"
],
[
102, 1, 1, 5, "mstmotherantecort", 1, 8, 8, None, 1,
"mstmotherantecort"
],
[
103,
1,
1,
5,
"mstmotheranteintervention",
1,
8,
8,
None,
1,
"mstmotheranteintervention",
],
[
104,
1,
1,
5,
"mstmotherdeliverytype",
1,
8,
8,
None,
1,
"mstmotherdeliverytype",
],
[
105, 1, 1, 5, "mstmotherdiabetes", 1, 8, 8, None, 1,
"mstmotherdiabetes"
],
[
106, 1, 1, 5, "mstmotherethnicity", 1, 8, 8, None, 1,
"mstmotherethnicity"
],
[
107,
1,
1,
5,
"mstmotherhypertension",
1,
8,
8,
None,
1,
"mstmotherhypertension",
],
[
108, 1, 1, 5, "mstmotherlabourinit", 1, 8, 8, None, 1,
"mstmotherlabourinit"
],
[
109,
1,
1,
5,
"mstmotherpresentation",
1,
8,
8,
None,
1,
"mstmotherpresentation",
],
[110, 1, 1, 5, "mstmotherrom", 1, 8, 8, None, 1, "mstmotherrom"],
[
111,
1,
1,
5,
"mstmothertotalacgiven",
1,
8,
8,
None,
1,
"mstmothertotalacgiven",
],
[
112,
1,
1,
5,
"mstnropcomplications",
1,
8,
8,
None,
1,
"mstnropcomplications",
],
[
113, 1, 1, 5, "mstnropdurations", 1, 8, 8, None, 1,
"mstnropdurations"
],
[114, 1, 1, 5, "mstnropfollowup", 1, 8, 8, None, 1, "mstnropfollowup"],
[115, 1, 1, 5, "mstnropplus", 1, 8, 8, None, 1, "mstnropplus"],
[116, 1, 1, 5, "mstnropstage", 1, 8, 8, None, 1, "mstnropstage"],
[
117,
1,
1,
5,
"mstnroptreatmenteyes",
1,
8,
8,
None,
1,
"mstnroptreatmenteyes",
],
[
118,
1,
1,
5,
"mstnroptreatmentlocations",
1,
8,
8,
None,
1,
"mstnroptreatmentlocations",
],
[
119,
1,
1,
5,
"mstnroptreatmenttypes",
1,
8,
8,
None,
1,
"mstnroptreatmenttypes",
],
[120, 1, 1, 5, "mstnropzone", 1, 8, 8, None, 1, "mstnropzone"],
[
121, 1, 1, 5, "mstntissantibiotics", 1, 8, 8, None, 1,
"mstntissantibiotics"
],
[
122, 1, 1, 5, "mstntisschesttube", 1, 8, 8, None, 1,
"mstntisschesttube"
],
[
123, 1, 1, 5, "mstntisspacemaker", 1, 8, 8, None, 1,
"mstntisspacemaker"
],
[
124,
1,
1,
5,
"mstntisstracheostomy",
1,
8,
8,
None,
1,
"mstntisstracheostomy",
],
[125, 1, 1, 5, "mstpatientchart", 1, 8, 8, None, 1, "mstpatientchart"],
[126, 1, 1, 5, "mstpdatreatment", 1, 8, 8, None, 1, "mstpdatreatment"],
[
127,
1,
1,
5,
"mstpostnatalsteroidsindication",
1,
8,
8,
None,
1,
"mstpostnatalsteroidsindication",
],
[
128,
1,
1,
5,
"mstpostnatalsteroidsroute",
1,
8,
8,
None,
1,
"mstpostnatalsteroidsroute",
],
[
129,
1,
1,
5,
"mstpostnatalsteroidstype",
1,
8,
8,
None,
1,
"mstpostnatalsteroidstype",
],
[
130,
1,
1,
5,
"mstpostnatalsteroidstypeindication",
1,
8,
8,
None,
1,
"mstpostnatalsteroidstypeindication",
],
[
131, 1, 1, 5, "mstposttransferdest", 1, 8, 8, None, 1,
"mstposttransferdest"
],
[132, 1, 1, 5, "mstprovinces", 1, 8, 8, None, 1, "mstprovinces"],
[133, 1, 1, 5, "mstresponse", 1, 8, 8, None, 1, "mstresponse"],
[
134,
1,
1,
5,
"mstresponsetostimuli",
1,
8,
8,
None,
1,
"mstresponsetostimuli",
],
[135, 1, 1, 5, "mstrespstatus", 1, 8, 8, None, 1, "mstrespstatus"],
[
136,
1,
1,
5,
"mstresuscitationinitialgas",
1,
8,
8,
None,
1,
"mstresuscitationinitialgas",
],
[137, 1, 1, 5, "mstropplus", 1, 8, 8, None, 1, "mstropplus"],
[138, 1, 1, 5, "mstropstage", 1, 8, 8, None, 1, "mstropstage"],
[
139, 1, 1, 5, "mstroptreatmenteye", 1, 8, 8, None, 1,
"mstroptreatmenteye"
],
[
140, 1, 1, 5, "mstroptreatmenttype", 1, 8, 8, None, 1,
"mstroptreatmenttype"
],
[141, 1, 1, 5, "mstropzone", 1, 8, 8, None, 1, "mstropzone"],
[
142,
1,
1,
5,
"mstsearchgridcolumns",
1,
8,
8,
None,
1,
"mstsearchgridcolumns",
],
[
143,
1,
1,
5,
"mstsnapeffectivefio2",
1,
8,
8,
None,
1,
"mstsnapeffectivefio2",
],
[144, 1, 1, 5, "mstsnapfactor", 1, 8, 8, None, 1, "mstsnapfactor"],
[145, 1, 1, 5, "mstsnapseizures", 1, 8, 8, None, 1, "mstsnapseizures"],
[
146, 1, 1, 5, "mstsurfactanttype", 1, 8, 8, None, 1,
"mstsurfactanttype"
],
[147, 1, 1, 5, "mstsystolicbp", 1, 8, 8, None, 1, "mstsystolicbp"],
[148, 1, 1, 5, "msttemperature", 1, 8, 8, None, 1, "msttemperature"],
[149, 1, 1, 5, "mstvegfdrugs", 1, 8, 8, None, 1, "mstvegfdrugs"],
]
# Sort data import configuration matrix by first column ascending (import sequence).
transaction.data_import_configuration = sorted(
transaction.data_import_configuration, key=itemgetter(0))
return transaction
def test_send_mysql_data() -> None:
# Test empty / no redcap transaction.
assert send_mysql_data(RedcapTransaction())[0] is False