def db_dict(table, module):
db_tables = {
"Patient_Information_History": names.names_info(module),
"Biopsy_Report_Data": names.names_biopsy_new(module),
"Radiology": names.names_radio(module),
"Neo_Adjuvant_Therapy": names.names_nact(module),
"Surgery_Report": names.names_surgery_information(module),
"Surgery_Block_Report_Data": names.names_surgery(module),
"Adjuvant_ChemoTherapy": names.names_chemotherapy(module),
"Radiotherapy": names.names_radiation(),
"HormoneTherapy_Survival": names.names_longterm(module),
"Follow_up_Data": names.name_follow_up()
}
cols = db_tables.get(table)
return cols
def db_dict(table, module):
db_tables = {
"patient_information_history": names.names_info(module),
"radiology": names.names_radio(module),
'pet_reports': names.names_pet(module),
'biopsy_path_report_data': names.names_biopsy(module),
"neo_adjuvant_therapy": names.names_nact(module),
"surgery_report": names.names_surgery_information(module),
'surgery_path_report_data': names.names_surgery(module),
"adjuvant_chemotherapy": names.names_chemotherapy(module),
"radiotherapy": names.names_radiation(),
"hormonetherapy_survival": names.names_longterm(module),
"follow_up_data": names.name_follow_up(),
'block_list': names.block_list(module)
}
cols = db_tables.get(table)
return cols
if table_check(cursor, table) == 0:
cursor.execute('CREATE TABLE {tn}({nf})'.format(tn=table, nf='pk'))
module_names = [
'pet_report_identifier', 'pet_report_findings', 'pet_breast_cancer'
]
for index in module_names:
col_name = pccm_names.names_pet(index)
add_columns(cursor, table, col_name)
print(table + ' created')
table = "surgery_report"
if table_check(cursor, table) == 0:
module_names = ["surgery_information", "node_excision", "post_surgery"]
cursor.execute('CREATE TABLE {tn}({nf})'.format(tn=table, nf=file_number))
for index in module_names:
col_name = pccm_names.names_surgery_information(index)
add_columns(cursor, table, col_name)
print(table + ' created')
table = "general_medical_history"
if table_check(cursor, table) == 0:
columns2 = "file_number, Condition, Diagnosis_date, Treatment"
cursor.execute('CREATE TABLE {tn}({nf})'.format(tn=table, nf=columns2))
print(table + ' created')
table = "family_cancer_history"
if table_check(cursor, table) == 0:
columns3 = 'file_number, type_cancer, relation_to_patient, type_relation, age_at_detection_yrs'
cursor.execute('CREATE TABLE {tn}({nf})'.format(tn=table, nf=columns3))
print(table + ' created')
df.to_excel(writer, sheet_name=table, index=False)
writer.save()
table = "Radiology"
sql = "SELECT File_number FROM '" + table + "'"
df = pd.read_sql(sql, conn)
df_list = list(df['File_number'])
module_names = [
"mammography", "tomosynthesis", "abvs", "sonomammo", "mri_breast"
]
col_list = ["File_number"]
for index in module_names:
col_list = col_list + names.names_radio(index)
sql = ('SELECT ' + ", ".join(col_list) + " FROM '" + table + "'")
df = pd.read_sql(sql, conn)
df.to_excel(writer, sheet_name=table, index=False)
writer.save()
table = "Surgery_Report"
sql = "SELECT File_number FROM '" + table + "'"
df = pd.read_sql(sql, conn)
df_list = list(df['File_number'])
module_names = ["surgery_information", "node_excision", "post_surgery"]
col_list = ["File_number"]
for index in module_names:
col_list = col_list + names.names_surgery_information(index)
sql = ('SELECT ' + ", ".join(col_list) + " FROM '" + table + "'")
df = pd.read_sql(sql, conn)
df.to_excel(writer, sheet_name=table, index=False)
writer.save()