Exemple #1
0
 def report(self):
     data_list = ask.default_data_list(self.col_list_all)
     check = False
     while not check:
         reason_report = ask.ask_option(
             "What is the purpose of this report"
             "?", MultiTest.test_reason_imaging)
         report_date = ask.check_date("Date of examination of ABVS: ")
         abvs_acc = input("Accession number of ABVS: ")
         abvs_lesion = ask.ask_option("Location of lesion",
                                      MultiTest.breast_cancer)
         if abvs_lesion in {MultiTest.breast_cancer}:
             abvs_lesion_data = radio_tables.lesion_location(abvs_lesion)
         else:
             abvs_lesion_data = "NA"
         abvs_size = ask.ask_option("Size of lesion",
                                    ["<2 cm", "2-5 cm", ">5 cm", "Other"])
         abvs_dist = ask.ask_option("Distance from Skin (cm)",
                                    ["<0.5 cm", ">0.5 cm", "Other"])
         abvs_pect = input("Distance from Pectoralis Major (cm): ")
         abvs_diagnosis = ask.ask_option("ABVS Diagnosis", Radio.diagnosis)
         data_list = [
             self.file_number, reason_report, report_date, abvs_acc,
             abvs_lesion, abvs_lesion_data, abvs_size, abvs_dist, abvs_pect,
             abvs_diagnosis
         ]
         check = sql.review_input(self.file_number, self.col_list_all[:-2],
                                  data_list)
     data_list = data_list + [self.user_name, sql.last_update()]
     return data_list
Exemple #2
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 def mammo_mass(self, mass_id):
     print(self.table, mass_id)
     check = False
     data_list = ask.default_data_list(self.col_list)
     while not check:
         mass_location = self.mammo_breast
         if self.mammo_breast == "bilateral":
             mass_location = ask.ask_option("Location of mass "
                                            + str(mass_id),
                                            RadioTables.breast)
         mass_quadrant = ask.ask_list('Quadrant location of lesion',
                                      Radio.lesion_quadrant)
         mammo_mass_shape = ask.ask_option("Shape of mass",
                                           RadioTables.mass_shape)
         mammo_mass_margin = ask.ask_option("Margins of mass",
                                            RadioTables.mass_margin)
         mass_nipple = input("Distance from nipple (cm): ")
         mass_dimension,
         mass_size_unit,
         mass_longest_dimension = self.lesion_size()
         modality = self.table
         data_list = [self.file_number, mass_location, mass_name,
                      mass_quadrant, mammo_mass_shape, mammo_mass_margin,
                      mass_nipple, mass_dimension, mass_longest_dimension,
                      mass_size_unit, modality]
         check = sql.review_input(self.file_number, columns=self.col_list,
                                  data=data_list)
         data_list = data_list + [self.user_name, sql.last_update()]
     return data_list
def node_excision (file_number):
    check = False
    while not check:
        surgery_guide, frozen, gross_tumour, skin, nodes, number_lymph, level_lymph, sentinel_method, sentinel_blue, \
        sentinel_hot, sentinel_blue_hot, sentinel_non_blue_hot, sentinel_palpable = (" ",)*13
        guide_add = True
        guide = []
        while guide_add:
            surgery_guide = ask_option("Excision guided by",
                                       ["Palpation", "USG guided", "Wire placement guided", 'Gamma camera guided',
                                        'Clipped node'])
            guide.append(surgery_guide)
            guide_add = ask_y_n("Add another method to guide?")
        surgery_guide = "; ".join(guide)
        frozen_samples = ask_option_y_n("Any samples sent for histopathology (frozen)?")
        if frozen_samples == 'Yes':
            frozen_samples = []
            sn_frozen = ask_y_n("Sentinel Node sent for histopathology (frozen)?", yes_ans="Sentinel Node")
            if sn_frozen == 'Sentinel Node':
                frozen_samples.append(sn_frozen)
            specimen_frozen = ask_y_n_na("Specimen sent for histopathology (frozen)?")
            if specimen_frozen == 'Yes':
                nipple_frozen = ask_y_n_na("Under Nipple Surface sent for histopathology (frozen)?",
                                           yes_ans='Under Nipple Surface')
                if nipple_frozen == 'Under Nipple Surface':
                    frozen_samples.append(nipple_frozen)
                other_frozen = ask_y_n_na("Any other specimen sent for histopathology (frozen)?")
                if other_frozen == 'Yes':
                    other_frozen = input("Type of tissue sent for histopathology (frozen): ")
                    frozen_samples.append(other_frozen)
            frozen = "; ".join(frozen_samples)
        else:
            frozen = "NA"
        gross_tumour = input ("Size of tumour on cross section (cm): ")
        skin = ask_option_y_n("Skin involved", yes_ans="Skin involved", no_ans="Skin not involved")
        nodes = ask_option("Nodes excised", ["Sentinel Node", "Sentinel and Axillary Nodes", "Axillary Nodes only",
                                             "Other"])
        number_lymph = input("Number of lymph nodes excised (if available): ")
        level_lymph = ask_option("Level of lymph node excised", ["I", "II", "III", "Data not available", "Other"])
        if nodes == 'Axillary Nodes only':
            sentinel_method, sentinel_blue, sentinel_hot, sentinel_blue_hot, sentinel_non_blue_hot, sentinel_palpable = \
                ('No Sentinel Node excised', )*6
        else:
            sentinel_method = ask_option("Method of labelling Sentinel Node", ["Isotope", "Blue Dye", "Isotope + Blue Dye",
                                                                               "Not done", "Other"])
            sentinel_blue = ask_option_y_n("Blue Node", yes_ans="Blue Node", no_ans="No Blue Node")
            sentinel_hot = ask_option_y_n("Hot Node", yes_ans="Hot Node", no_ans="No Hot Node")
            sentinel_blue_hot = ask_option_y_n("Blue Hot Node", yes_ans="Blue Hot Node", no_ans="No Blue Hot Node")
            sentinel_non_blue_hot = ask_option_y_n("Non Blue, Hot Node", yes_ans= "Non Blue, Hot Node",
                                               no_ans="No Non Blue, Hot Node")
            sentinel_palpable = ask_option_y_n("Palpable Node", yes_ans="Palpable Node", no_ans="No Palpable Node")
        data_list = [surgery_guide, frozen, gross_tumour, skin, nodes, number_lymph, level_lymph, sentinel_method,
                     sentinel_blue, sentinel_hot, sentinel_blue_hot, sentinel_non_blue_hot, sentinel_palpable]
        col_list = names("node_excision")
        check = add_update_sql.review_input(file_number, col_list, data_list)
    return data_list
Exemple #4
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 def bio_info(self):
     module_name = "bio_info"
     new_data = ['NA'] * 16
     check = False
     while not check:
         mr_number = input('MR number :')
         name = input('Name :')
         aadhaar_card = input("Aadhaar card number (if available): ")
         date_first = check_date("Date of first visit: ")
         permanent_address = input('Permanent Address :')
         current_address_check = ask_option(
             'Current Address', ["Same as Permanent", "Different"])
         if current_address_check == "Different":
             current_address = input("Current Address: ")
         else:
             current_address = permanent_address
         phone = input('Phone :')
         email_id = input('Email_ID :')
         gender = ask_option('Gender', ["Female", "Male", "Other"])
         age_yrs = input('Age at first visit (yrs) :')
         age_diag = input('Age at diagnosis (yrs): ')
         date_of_birth = check_date('Date of Birth (dd/mm/yyyy):')
         place_birth = input('Place of Birth :')
         height = ask_option("Height unit",
                             ["cm", "feet/inches", "Height not available"])
         height_cm, height_feet, height_inch, weight, bmi = ['NA'] * 5
         if height == "Height not available":
             height_cm = "NA"
             weight_kg = input('Weight (kg) (if available else enter NA) :')
             bmi = "NA"
         else:
             if height == "cm":
                 height_cm = input('Height (cm) :')
             else:
                 height_feet = float(input("Height (feet)"))
                 height_inch = float(input("Height (inches)"))
                 height_inch = height_inch + 12 * height_feet
                 height_cm = height_inch * 2.54
             weight_kg = input('Weight (kg) (if available else enter NA) :')
             try:
                 weight = float(weight_kg)
                 height = float(height_cm) / 100
                 bmi = str(round(weight / (height * height)))
             except ValueError:
                 bmi = 'NA'
         columns_list = pccm_names.names_info(module_name)
         new_data = [
             mr_number, name, aadhaar_card, date_first, permanent_address,
             current_address, phone, email_id, gender, age_yrs, age_diag,
             date_of_birth, place_birth, height_cm, weight_kg, bmi
         ]
         check = review_input(self.file_number, columns_list, new_data)
     return new_data
def tox_table(file_number, drug_cyc, tox_all):
    tox_index = 0
    check_tox = False
    while not check_tox:
        tox = ask.ask_y_n(
            "Were there any toxic effects in  administration of " + drug_cyc)
        if tox:
            add_tox = True
            while add_tox:
                check = False
                while not check:
                    tox_present = ask.ask_option("Toxic effects of type",
                                                 chemo.toxicity())
                    tox_grade = ask.ask_option(
                        ("the grade of " + tox_present + "? "),
                        ["Mild", "Moderate", "Severe", "Other"])
                    treatment = input("Treatment given for " + tox_grade +
                                      " " + tox_present +
                                      " (include all details): ")
                    resp_treatment = ask.ask_option(
                        ("Response to treatment given for " + tox_grade + " " +
                         tox_present),
                        ["Partial", "Complete", "No Effect", "Other"])
                    cyc_tox = input("Cycle at which toxicity occurred: ")
                    change_tox = ask.ask_option("Changes to treatment", [
                        "No change", "Therapy changed due to toxicity",
                        "Therapy "
                        "stopped  due to toxicity", "Therapy changed due "
                        "to other reasons",
                        "Therapy stopped due to other reasons"
                    ])
                    if change_tox == "Therapy changed due to toxicity" or change_tox == "Therapy changed due to other reasons":
                        change = input("Please describe changes to Therapy: ")
                        change_tox = change_tox + ": " + change
                data = [
                    file_number, drug_cyc, tox_present, tox_grade, treatment,
                    resp_treatment, cyc_tox, change_tox
                ]
                tox_all.loc[tox_index] = data
            check = review_df_row(tox_all)
            tox_index = tox_index + 1
            add_tox = ask.ask_y_n('Add another toxicity type?')
        else:
            tox_present, tox_grade, treatment, resp_treatment, cyc_tox,
            change_tox = ("No Toxicity", ) * 6
            data = [
                file_number, drug_cyc, tox_present, tox_grade, treatment,
                resp_treatment, cyc_tox, change_tox
            ]
            tox_all.loc[tox_index] = data
    check_tox = review_df(tox_all)
    return tox_all
Exemple #6
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def patient_status():
    status = ask.ask_option("Status at last follow up", [
        "Survivor", "Deceased", "Lost to follow-up",
        'Case of Non Malignant Breast Disease', "Other"
    ])
    if status == "Survivor":
        type_survivor = ask.ask_list("the Survivor is ",
                                     FollowUpStatus.survivor_status)
        status = status + ": " + type_survivor
    if status == "Deceased":
        type_death = ask.ask_option("Cause of death",
                                    FollowUpStatus.deceased_status)
        status = status + ": " + type_death
    return status
def review_data_key(conn, cursor, table, key_name, key_value, columns, col_name, col_value):
    if 'file_number' in columns:
        # remove 1st position from column names (assumes it is file_number)
        col_list = columns[1:]
    else:
        col_list = columns
    sql_statement = 'SELECT ' + ", ".join(col_list) + ' FROM ' + table + " WHERE " + key_name + "= '" + key_value + "'"
    data = cursor.execute(sql_statement)
    data_list = data.fetchall()
    if not data_list:
        print("This " + col_name + ' ' + col_value + ' has not been entered in ' + table)
        enter = ask.ask_y_n("Do you want to enter now")
        if enter:
            add_pk_fk_to_table(conn, cursor, table, col_name=key_name, pk=key_value)
            print('added new row for this ' + key_name)
            return enter
    else:
        data_list = list(data_list[0])
    col_number = len(col_list)
    if data_list == [None]*len(data_list):
        print("This section of the database has not been entered")
        enter = ask.ask_y_n("Do you want to enter now")
        return enter
    elif None in set(data_list):
        print("Some entries are missing from the database: ")
        for index in range(0, col_number):
            print(col_list[index] + " : " + str(data_list[index]))
        enter = ask.ask_option("Do you want to proceed?", ["Edit all", "Add new data only"])
        if enter == "Edit all":
            return True
        else:
            enter = edit_few(conn, cursor, table, col_list, key_value, data_list)
            return enter
    else:
        print("Entries present in database are as follows : ")
        for index in range(0, col_number):
            print(col_list[index] + " : " + str(data_list[index]))
        enter = ask.ask_option("Do you want to", ["Edit all", "Edit some entries", "Edit None"])
        if enter == "Edit some entries":
            for index in range(0, col_number):
                print(col_list[index] + " : " + str(data_list[index]))
                edit = ask.ask_y_n("Edit")
                if edit:
                    data = input("Data for " + col_list[index] + ": ")
                    update_single_pk(conn, cursor, table, col_list[index], pk_value=key_name, pk=key_value, var=data)
            return False
        elif enter == "Edit all":
            return True
        else:
            return False
Exemple #8
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def edit_table(df, pk_col, df_col):
    import helper_function.ask_y_n_statement as ask
    rows = (df.shape)[0]
    for row in range(0,rows):
        print(df.iloc[row].to_string()+'\n')
    to_correct = ask.ask_y_n("Are entries correct?")
    if not to_correct:
        to_correct = ask.ask_y_n("Re-enter entire table?")
        if to_correct:
            return to_correct, df
        else:
            change_row = True
            while change_row:
                pk_list = list(df[pk_col])
                print(pk_list)
                pk = input("Enter " + pk_col + " to change: ")
                index = pk_list.index(id)
                to_do = True
                while to_do:
                    print(df.loc[index, :])
                    col_change = ask.ask_option("Name of column to change", df_col)
                    old_val = df.loc[index, col_change]
                    print(old_val + '\n')
                    new_val = input("Enter correct value for " + col_change + ' for ' + pk + ": ")
                    df.loc[index, col_change] = new_val
                    print(df.iloc[index].to_string() + '\n')
                    to_do = ask.ask_y_n("Make more changes to " + pk_col + ' ' + pk + '?')
                print_df(df)
                change_row = ask.ask_y_n("Change another row?")
            to_correct = False
    return to_correct, df
def family_cancer_table(conn, cursor, file_number):
    add_family = True
    type_cancer_list, relation_degree_list, type_relation_list, age_detect_list = [], [], [], []
    all_data = []
    while add_family:
        type_of_cancer = input("Type of Cancer: ")
        type_cancer_list.append(type_of_cancer)
        relation_to_patient = ask_option("Relation to patient",
                                         PatientInfo.family)
        relation_degree_list.append(relation_to_patient)
        type_relation = input("Specific Relationship:")
        type_relation_list.append(type_relation)
        age_at_detection_yrs = input('Age at detection (yrs) :')
        age_detect_list.append(age_at_detection_yrs)
        family_history = file_number, type_of_cancer, relation_to_patient, type_relation, age_at_detection_yrs
        family_history_list = "; ".join([
            type_of_cancer, relation_to_patient, type_relation,
            age_at_detection_yrs
        ])
        all_data.append(family_history_list)
        columns = 'file_number, type_cancer, relation_to_patient, type_relation, age_at_detection_yrs'
        table = "family_cancer_history"
        sql.insert(conn, cursor, table, columns, family_history)
        add_family = ask_y_n("Add more family cancer history? ")
    all_data_flat = "|".join(all_data)
    return (all_data_flat)
Exemple #10
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def check_path_report_entry(conn, cursor, file_number, table_to_check, pk,
                            block_id, number_of_blocks, user_name):
    from reports.biopsy_report import BiopsyData
    from reports.surgery_block import SurgeryBlockData
    table_data = BiopsyData(conn, cursor, file_number, pk, block_id,
                            number_of_blocks, user_name)
    col_name = 'pk'
    if 'surgery' in table_to_check:
        table_data = SurgeryBlockData(conn, cursor, file_number, pk, block_id,
                                      number_of_blocks, user_name)
        col_filter = 'fk'
    pk_fk_present = sql.check_pk_fk_exist(cursor, col_name, pk, table_to_check)
    if not pk_fk_present:
        sql.add_pk_fk_to_table(conn, cursor, table_to_check, col_name, pk)
        print("This block_id -'" + block_id + "' for " + file_number +
              " does not exist in table " + table_to_check +
              ". Enter new record")
        table_data.add_data()
    else:
        todo = ask.ask_option(
            file_number + " already exists in table " + table_to_check + ".",
            ["Edit record", "Edit None"])
        if todo == "Edit record":
            table_data.edit_data()
    return
Exemple #11
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 def mri_mass(self, mass_id):
     check = False
     data_list = ask.default_data_list(self.col_list)
     while not check:
         if self.mammo_breast == "bilateral":
             mass_location = ask.ask_option("Location of mass " + str(
                                            mass_id), RadioTables.breast)
         else:
             mass_location = self.mammo_breast
         check_t1_t2 = ask.ask_y_n('Are both T1 and T2 image analysis'
                                   'available for this mass?')
         type_of_imaging = ['T1', 'T2']
         if not check_t1_t2:
             type_of_imaging = ask.ask_list('Observation of this mass is a'
                                            'result of which type of'
                                            'imaging? ',
                                            RadioTables.mri_image_type)
         data_list = self.mri_mass_detail(type_of_imaging, mass_id)
         if type_of_imaging in {'T1', 'T2'}:
             data_list = [('{0}_{1}'.format(type_of_imaging, data)) for
                          data in data_list]
         mass_name = "Lesion " + str(mass_id)
         data_list = [self.file_number, mass_location, mass_name]+data_list
         check = sql.review_input(self.file_number, columns=self.col_list,
                                  data=data_list)
         data_list = [data_list] + [self.user_name, sql.last_update()]
         data_list = data_list + [self.user_name, sql.last_update()]
     return data_list
Exemple #12
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def metastasis(file_number, user_name):
    check = False
    while not check:
        met_has = ask.ask_y_n(
            "Has the patient been examined for metastatic disease?")
        if not met_has:
            met_has = "Not examined for metastatic disease"
        else:
            met_has = "Examined for metastatic disease"
        date_last = ask.check_date("Date of last follow-up: ")
        recur = ask.ask_y_n("Has the patient experienced a recurrence?")
        if recur:
            time_recur = input("Time to disease recurrence: ")
            nature_recur = ask.ask_option("Nature of recurrence",
                                          ["Distant", "Local", "Other"])
            if nature_recur == "Distant":
                distant_site = input("Site of distant recurrence: ")
            else:
                distant_site = "NA"
        else:
            time_recur, nature_recur, distant_site = ("NA", ) * 3
        status = patient_status()
        data_list = [
            met_has, date_last, time_recur, nature_recur, distant_site, status,
            user_name,
            last_update()
        ]
        col_list = names.names_longterm("metastasis")
        check = review_input(file_number, col_list, data_list)
    return data_list
Exemple #13
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def lesion_location(lesion, option=MultiTest.breast_cancer):
    lesion_data = {}
    category = ["Location on right_breast", "Location on left_breast",
                'Other Location']
    if lesion in {"right_breast", "bilateral"}:
        lesion_rb = ask.ask_option(category[0], )
        lesion_rb_data = "RB-" + lesion_rb
        lesion_data.append(lesion_rb_data)
    if lesion in {"right_breast", "bilateral"}:
        lesion_lb = ask.ask_option(category[1], option)
        lesion_lb_data = "LB-" + lesion_lb
        lesion_data.append(lesion_lb_data)
    if lesion not in {MultiTest.breast_cancer}:
        lesion_other = str.lower(str.replace(lesion, ' ', '_'))
        lesion_data.append(lesion_other)
    lesion_data = "|".join(lesion_data)
    return lesion_data
Exemple #14
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def view_multiple(conn, table, col_list, file_number):
    import pandas as pd
    from helper_function.ask_y_n_statement import ask_option
    sql_statement = ('SELECT '+ ", ".join(col_list) +' FROM '+ table + " WHERE file_number = '" +file_number+"'")
    df = pd.read_sql(sql_statement, conn)
    print_df(df)
    enter = ask_option("Do you want to add or edit data", ["Add data", 'Edit data', 'Do not add or edit'])
    return enter
Exemple #15
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 def usg_mass(self, mass_id):
     print(self.table, mass_id)
     check = False
     data_list = ask.default_data_list(self.col_list)
     while not check:
         mass_location = self.mammo_breast
         if self.mammo_breast == "bilateral":
             mass_location = ask.ask_option("Location of mass "
                                            + str(mass_id),
                                            RadioTables.breast)
         location_clock = ask.check_number_input("What is the clock"
                                                 "position of mass "
                                                 + str(mass_id) + "?",
                                                 'Please enter only numbers'
                                                 ' additional paramters '
                                                 'can be entered '
                                                 'next')
         location_add = input('Additional parameters for clock position')
         location_clock = location_clock + location_add + " o'clock"
         mass_quadrant = 'data_not_available'
         quad = ask.ask_y_n('Is the quadrant location given?')
         if quad:
             mass_quadrant = ask.ask_list('what is the quadrant location',
                                          Radio.lesion_quadrant)
         mass_shape = ask.ask_list("Shape of mass " + str(mass_id),
                                   RadioTables.mass_shape)
         mass_name = "lesion_" + str(mass_id)
         mass_dimension,
         mass_size_unit,
         mass_longest_dimension = self.lesion_size()
         mass_margin = ask.ask_option("Margin of mass " + str(mass_id),
                                      RadioTables.mass_margin_usg)
         mass_echo = ask.ask_option("Echo pattern of mass " + str(mass_id),
                                    RadioTables.mass_echo)
         mass_id = "Mass " + str(mass_id)
         modality = self.table
         data_list = [self.file_number, mass_name, mass_location,
                      location_clock, mass_quadrant, mass_shape,
                      mass_margin, mass_echo, mass_dimension,
                      mass_longest_dimension, mass_size_unit, modality]
         check = sql.review_input(self.file_number, columns=self.col_list,
                                  data=data_list)
         data_list = data_list + [self.user_name, sql.last_update()]
     return data_list
Exemple #16
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def nipple_cytology(file_number):
    module_name = "nipple_cytology"
    check = False
    while not check:
        cyto = ask.ask_option("Nipple Cytology", ["Done", "Not Done"])
        if cyto == "Not Done":
            cyto_date, cyto_number, cyto_report = ("NA", ) * 3
        else:
            cyto_date = input("Date of nipple cytology: ")
            cyto_number = input("Nipple Cytology number: ")
            cyto_report = ask.ask_option(
                "Nipple Cytology report and interpretation",
                ["Normal", "Suspicious", "Diagnostic for "
                 "Cancer", "Other"])
        data_list = [cyto, cyto_date, cyto_number, cyto_report]
        columns_list = pccm_names.name_clinical(module_name)
        check = add_update_sql.review_input(file_number, columns_list,
                                            data_list)
    return (tuple(data_list))
Exemple #17
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def ffpe_csv():
    folder_name, file_name, database_folder_name, database_name = (
        'D:/repos/pccm_db/main/DB', "FFPE_new_blocks.csv",
        'D:/repos/pccm_db/main/DB',
        'PCCM_BreastCancerDB_FFPE_dk_2018-11-20.db')
    check_folder = None
    while check_folder != 'All are correct':
        print('\nFolder location of FFPE new blocks data is set as: \n' +
              folder_name + '\n')
        print('File name of FFPE new blocks data is set as: \n' + file_name +
              '\n')
        print('Database file folder is set as \n' + database_folder_name +
              '\n')
        print('Database file name is set as \n' + database_name + '\n')
        check_folder = ask_option("Do you want to change any options?", [
            'FFPE File Folder', 'FFPE File Name', 'Database Folder',
            'Database Name', 'All are correct'
        ])
        if check_folder == 'FFPE File Folder':
            print('Folder location of FFPE new blocks data is set as \n' +
                  folder_name + '\n')
            folder_name = input(
                "Please enter folder location of FFPE new blocks data: ")
        elif check_folder == 'FFPE File Name':
            print('File name of FFPE new blocks data is set as: \n' +
                  file_name + '\n')
            file_name = input(
                "Please input correct File name of FFPE new blocks data (with .csv extension): "
            )
        elif check_folder == 'Database Folder':
            print('Database file folder is set as: \n' + database_folder_name +
                  '\n')
            database_folder_name = input(
                "Please input correct database file destination: ")
        elif check_folder == 'Database Name':
            print('Database file name is set as: \n' + database_name + '\n')
            database_name = input(
                "Please input correct database file name (with .db extension): "
            )
    conn_path = os.path.join(database_folder_name, database_name)
    conn = sqlite3.connect(conn_path)
    cursor = conn.cursor()
    ffpe_data = FFPECSVData(conn, cursor, folder_name, file_name)
    ffpe_df = ffpe_data.read_file()
    n_rows = ffpe_df.shape[1]
    print(str(n_rows) + ' block entries read from file uploaded')
    ffpe_str = ffpe_df.astype(dtype='str')
    ffpe_data.write_file(ffpe_str)
    print(
        str(n_rows) + ' block entries added to ' + database_name + ' database')
    output_file_name = 'Uploaded_Database_' + file_name + str(
        date.today()) + '.xlsx'
    file_information = database_folder_name, database_name, folder_name, output_file_name
    print_file = OutputData(file_information)
    print_file.output_data()
Exemple #18
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def birads():
    check = False
    while not check:
        birad_list = [i for i in Radio.birads]
        mammo_birads = ask.ask_option("BI-RADS Category", birad_list)
        mammo_birads_det = Radio.birads.get(mammo_birads)
        birad = mammo_birads + ": " + mammo_birads_det
        print(birad)
        check = ask.ask_y_n("Is this correct?")
        data_list = birad
    return data_list
 def surgery_block_information_0(self):
     module_name = self.module_list[0]
     check = False
     data_list = ['NA']*17
     surgery_block_data_type = 'primary'
     while not check:
         data_type = ask.ask_y_n("Is surgery type: '" + surgery_block_data_type + "'")
         if not data_type:
             surgery_block_data_type = ask.ask_option("Type of surgery", ['revision', 'recurrence'])
         block_list_table = BlockInformation(self.conn, self.cursor, self.file_number)
         block_data = ['block_sr_number', 'block_location', 'current_block_location', 'block_series']
         block_sr_number, block_location, current_block_location, surgery_block_series = \
             block_list_table.get_block_information(self.surgery_block_id, block_data)
         surgery_block_source = ask.ask_option("Pathology Lab (source of block)", PathReports.path_labs)
         breast_cancer_yes_no = ask.ask_y_n('Is this a case of breast cancer (Unilateral OR Bilateral)',
                                            yes_ans="breast_cancer_yes", no_ans="breast_cancer_no")
         pathology_report_available_yes_no = ask.ask_y_n('Is the pathology report available', yes_ans="yes",
                                                         no_ans="no")
         nat = ask.ask_y_n('Has Neo-Adjuvant therapy been administered to the patient (NACT or NAHT)?')
         if nat:
             nact = ask.ask_list('What type of therapy has been givent to the patient?',
                                 ['NACT', 'NAHT', 'NACT_and_NAHT'])
             neoadjuvant_therapy = nact.lower() + '_yes'
             surgery_block_primary_tissue = 'treated_tissue'
         else:
             neoadjuvant_therapy = 'nact_no'
             surgery_block_primary_tissue = 'primary_tissue'
         date_of_surgery = ask.check_date("Date of Surgery: ")
         surgeon_s = ask.ask_option("Name of the Surgeon/s", PathReports.surgeon)
         surgery_hospital_id = input("Hospital ID: ")
         surgery_lesion_site = ask.ask_list("Lesion on", ["right_breast", "left_breast", "bilateral"])
         surgery_type = self.bilateral_treatment(surgery_lesion_site, 'Type of surgery', PathReports.surgery_type)
         data_list = [self.file_number, surgery_block_data_type, block_sr_number, block_location,
                      current_block_location, self.surgery_block_id, self.surgery_number_of_blocks,
                      surgery_block_series, breast_cancer_yes_no, pathology_report_available_yes_no,
                      neoadjuvant_therapy, str(surgery_block_primary_tissue).lower(), surgery_block_source,
                      date_of_surgery, surgeon_s, surgery_hospital_id, surgery_lesion_site, surgery_type]
         columns_list = names(module_name)
         check = sql.review_input(self.file_number, columns_list, data_list)
     return data_list
Exemple #20
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 def pet_report_identifier(self):
     module_name = self.module_list[0]
     check = False
     report_identifier = ['NA'] * 12
     while not check:
         pet_scan_date = ask.check_date('Please enter PET report date: ')
         pet_scan_number = input(
             'Please enter PET scan number as given on the report: ')
         pet_scan_source = input(
             'Please enter the facility at which PET scan was done: ')
         pet_scan_reg_number = input(
             "Please enter PET report registration number: ")
         pet_scan_history = input(
             'Please input patient history as given on report: ')
         pet_carcinoma_status = ask.ask_option(
             'Please enter breast cancer status',
             MultiTest.carcinoma_status)
         pet_cancer_location = ask.ask_list(
             'What is the location of the cancer', MultiTest.breast_cancer)
         pet_recurrence = ask.ask_y_n(
             'Does the patient have a previously detected recurrence/mets?')
         if pet_recurrence:
             pet_recurrence_known = input(
                 'Please describe the recurrence/metastasis: ')
         else:
             pet_recurrence_known = 'no_known_recurrence_or_metastasis'
         pet_procedure_body_region = ask.ask_list(
             "Region of body monitored by PET scan", PetReport.body_region)
         pet_procedure_fdg_dose_mci = ask.check_number_input(
             "Please enter dose of 18F-FDG used in mCi. ",
             "(Please enter only dose. If given in other units "
             "enter under additional notes.): ")
         pet_procedure_bsl = input(
             "Please enter basal sugar level with units as given: ")
         pet_scanner_name = ask.ask_list('Please enter name of scanner',
                                         PetReport.machine_name)
         pet_procedure_additional_notes = input(
             'Please enter additional notes, if any for PET scan and patient '
             'conditions: ')
         report_identifier = [
             self.file_number, pet_scan_date, pet_scan_number,
             pet_scan_source, pet_scan_reg_number, pet_scan_history,
             pet_carcinoma_status, pet_cancer_location,
             pet_recurrence_known, pet_procedure_body_region,
             pet_procedure_fdg_dose_mci, pet_procedure_bsl,
             pet_scanner_name, pet_procedure_additional_notes
         ]
         columns_list = names(module_name)
         check = sql.review_input(self.file_number, columns_list,
                                  report_identifier)
     return report_identifier
Exemple #21
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def abvs(file_number):
    module_name = "abvs"
    check = False
    while not check:
        abvs = ask.ask_y_n("Automated Breast Volume Scanner (ABVS) done?")
        if abvs:
            abvs = "Automated Breast Volume Scanner done"
            abvs_date = input("Date of examination of ABVS: ")
            abvs_acc = input("Accession number of ABVS: ")
            abvs_lesion = ask.ask_option(
                "Location of lesion",
                ["Right Breast", "Left Breast", "Both", "Not present"])
            if abvs_lesion in {"Right Breast", "Left Breast", "Both"}:
                abvs_lesion_data = radio_tables_old.lesion_location(
                    abvs_lesion)
            else:
                abvs_lesion_data = "NA"
            abvs_size = ask.ask_option("Size of lesion",
                                       ["<2 cm", "2-5 cm", ">5 cm", "Other"])
            abvs_dist = ask.ask_option("Distance from Skin (cm)",
                                       ["<0.5 cm", ">0.5 cm", "Other"])
            abvs_pect = input("Distance from Pectoralis Major (cm): ")
            abvs_diagnosis = ask.ask_option(
                "ABVS Diagnosis",
                ["Normal", "Benign", "Suspicious", "Diagnostic for Cancer"])
        else:
            abvs = "Automated Breast Volume Scanner done"
            abvs_date, abvs_acc, abvs_lesion, abvs_lesion_data, abvs_size, abvs_dist, abvs_pect, \
            abvs_diagnosis = ("NA",) * 8

        data_list = [
            abvs, abvs_date, abvs_acc, abvs_lesion, abvs_lesion_data,
            abvs_size, abvs_dist, abvs_pect, abvs_diagnosis
        ]
        columns_list = names(module_name)
        check = add_update_sql.review_input(file_number, columns_list,
                                            data_list)
    return (tuple(data_list))
Exemple #22
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 def mri_mass_detail(self, image_type, mass_id):
     print(self.table, mass_id)
     data_list = ask.default_data_list(self.col_list)
     check = False
     while not check:
         non_mass = ask.ask_y_n('Is the enhancement non-mass?')
         enhancement_type = 'mass'
         if non_mass:
             enhancement_type = 'non_mass'
         location_clock = input("What is the clock position of mass "
                                + str(mass_id) + "? (Enter NA if clock"
                                "position not available)")
         if location_clock != 'NA':
             location_clock = location_clock + " o'clock"
         mass_quadrant = ask.ask_option('Quadrant location of mass',
                                        Radio.lesion_quadrant)
         mass_shape = ask.ask_option("Shape of mass " + str(mass_id),
                                     RadioTables.mass_shape)
         mass_margin = ask.ask_option("Margin of mass " + str(mass_id),
                                      RadioTables.mass_margin_mri)
         mass_dimension,
         mass_size_unit,
         mass_longest_dimension = self.lesion_size()
         mass_echo = ask.ask_option("Internal enhancement characteristics"
                                    " " + str(mass_id),
                                    RadioTables.mass_iec)
         mass_id = "Mass " + str(mass_id)
         modality = self.table
         data_list = [mass_id, image_type, enhancement_type, location_clock,
                      mass_quadrant, mass_shape,  mass_margin,
                      mass_echo, mass_dimension,
                      str(mass_longest_dimension), mass_size_unit, modality]
         col_list = self.col_list[3:]
         check = sql.review_input(self.file_number, columns=col_list,
                                  data=data_list)
         data_list = data_list + [self.user_name, sql.last_update()]
     return data_list
Exemple #23
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 def review_data(self):
     sql = ('SELECT ' + ", ".join(self.columns) + ' FROM ' + self.table + " WHERE file_number = '" +
            self.file_number + "'")
     data = self.cursor.execute(sql)
     data_list = data.fetchall()
     data_list = list(data_list[0])
     col_number = len(self.columns)
     if data_list == [None]*len(data_list):
         print("This section of the database has not been entered")
         enter = ask.ask_y_n("Do you want to enter now")
         return enter
     if None in set(data_list):
         print("Some entries are missing from the database: ")
         for index in range(0, col_number):
             print(self.columns[index] + " : " + str(self.data[index]))
         enter = ask.ask_option("Do you want to proceed?", ["Edit all", "Add new data only"])
         if enter == "Edit all":
             return True
         else:
             edit_few(self.conn, self.cursor, self.table, self.columns, self.file_number, self.data)
     else:
         print("Entries present in database are as follows : ")
         for index in range(0, col_number):
             print(self.columns[index] + " : " + str(self.data[index]))
         enter = ask.ask_option("Do you want to", ["Edit all", "Edit some entries", "Edit None"])
         if enter == "Edit some entries":
             for index in range(0, col_number):
                 print(self.columns[index] + " : " + str(self.data[index]))
                 edit = ask.ask_y_n("Edit")
                 if edit:
                     data = input("Data for " + self.columns[index] + ": ")
                     update_single(self.conn, self.cursor, self.table, self.columns, self.file_number, data)
             return False
         elif enter == "Edit all":
             return True
         else:
             return False
 def bilateral_treatment(surgery_lesion_site, data_type_statement, data_type_options):
     if data_type_options != 'input':
         if surgery_lesion_site.lower == "bilateral":
             print("Right Breast")
             data_type = ask.ask_option(data_type_statement, data_type_options)
             data_type_rb = "rb_" + data_type
             print("Left Breast")
             data_type = ask.ask_option(data_type_statement, data_type_options)
             data_type_lb = "lb_" + data_type
             data = data_type_rb + "; " + data_type_lb
         else:
             data = ask.ask_option(data_type_statement, data_type_options)
     else:
         if surgery_lesion_site.lower == "bilateral":
             print("Right Breast")
             data_type = input(data_type_statement)
             data_type_rb = "rb_" + data_type
             print("Left Breast")
             data_type = input(data_type_statement)
             data_type_lb = "lb_" + data_type
             data = data_type_rb + "; " + data_type_lb
         else:
             data = input(data_type_statement)
     return data
Exemple #25
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def det_by(file_number):
    module_name = "det_by"
    check = False
    while not check:
        category = "Current Breast Cancer Detected by"
        options = ["Self", "Physician", "Screening Camp", "Other"]
        determined_by = ask_option(category, options)
        if determined_by == "Screening Camp":
            sc_id = input("Screening Camp ID: ")
            determined_by = "Screening Camp ID " + sc_id
        det_date = input("Date of current breast cancer detection: ")
        columns_list = pccm_names.names_info(module_name)
        data_list = [determined_by, det_date]
        check = review_input(file_number, columns_list, data_list)
    return (tuple(data_list))
def drug_table_enter(file_number, drug_table):
    drug_add = True
    drug_index = 0
    while drug_add:
        check_drug = False
        while not check_drug:
            drugs_administered = ask.ask_option("Drug used for therapy",
                                                chemo.drug_list())
            dose_check = ask.ask_y_n('Is the drug dose available?')
            if dose_check:
                dose = ask.check_number_input(
                    "Dose of " + drugs_administered + ':',
                    'Please input dose amount'
                    'without unit')
                if dose == 'NA':
                    dose_unit = 'NA'
                else:
                    dose_unit = input("Dose unit: ")
            else:
                dose, dose_unit = [
                    'NA',
                ] * 2
            cycle_check = ask.ask_y_n('Is the drug cycle available?')
            if cycle_check:
                cycle_frequency_per_week = ask.check_number_input(
                    "Cycle Frequency: ", 'Please enter frequency per '
                    'week, so three weekly is 3 and '
                    'weekly is 1')
                number_cycle = ask.check_number_input(
                    "Number of cycles actually given: ",
                    'Please enter numbers only')
            else:
                cycle_frequency_per_week, number_cycle = [
                    'NA',
                ] * 2
            drug_dose = 'NA'
            if number_cycle != 'NA' and dose != 'NA':
                drug_dose = float(dose) * int(number_cycle)
            data_drug = [
                file_number, drugs_administered, number_cycle,
                cycle_frequency_per_week,
                str(drug_dose), dose_unit
            ]
            drug_table.loc[drug_index] = data_drug
            check_drug, drug_table = review_df_row(drug_table)
            drug_index = drug_index + 1
        drug_add = ask.ask_y_n("Add another drug")
    return drug_table
def hormone_therapy_chemo():
    hormone_therapy = ask.ask_y_n_na("Was hormone therapy given?")
    if hormone_therapy == 'Yes':
        hormone_therapy = "Hormone therapy given"
        therapy_type = ask.ask_option("Hormone therapy type",
                                      ["Sequential", "Concurrent"])
        therapy_duration = input("What was the duration of therapy? ")
        therapy_side = ask.ask_y_n_na("Were any side effects observed ?")
        if therapy_side == 'Yes':
            therapy_side = input(
                "Please give details of side effects observed: ")
    elif hormone_therapy == 'No':
        hormone_therapy = "No hormone therapy given"
        therapy_type, therapy_duration, therapy_side = (hormone_therapy, ) * 3
    else:
        therapy_type, therapy_duration, therapy_side = (hormone_therapy, ) * 3
    return hormone_therapy, therapy_type, therapy_duration, therapy_side
 def output_data(self):
     cursor = self.conn.cursor()
     tables_to_print = []
     summary_df = pd.DataFrame(columns=["table_name", "number_entries"])
     output_name = self.output_name
     if self.research:
         output_name = 'Research_' + self.output_name
     output_path = os.path.join(self.output_folder, output_name)
     for table in print_db_tables():
         check = table_check(cursor, table)
         if check:
             tables_to_print.append(table)
     if not tables_to_print:
         print(
             "Selected Database has no tables. Please re-start and edit database file"
         )
         return
     else:
         writer = pd.ExcelWriter(output_path, engine='xlsxwriter')
         print('This database contains the following tables:')
         i = 1
         for table in tables_to_print:
             print(str(i) + ". " + table)
             i = i + 1
         to_print = ask_option(
             "Do you want to print all tables or only select tables?",
             ["All tables", "Select tables"])
         if to_print == "All tables":
             index = 0
             for table in tables_to_print:
                 self.print_table(writer, table)
                 number = self.print_table(writer, table)
                 summary_df.loc[index] = [table, number]
                 index = index + 1
         elif to_print == "Select tables":
             for table in tables_to_print:
                 to_print = ask_y_n("Do you want to print " + table)
                 if to_print:
                     self.print_table(writer, table)
                     number = self.print_table(writer, table)
                     summary_df.loc[table] = [table, number]
         self.print_summary(summary_df)
         print("Data file " + output_name + " has been created at " +
               self.output_folder + '\n')
     writer.save()
Exemple #29
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def check_file(conn, cursor, table, file_number, user_name, folders):
    sql_statement = "SELECT rowid FROM " + table + " WHERE file_number = ?"
    cursor.execute(sql_statement, (file_number, ))
    data = cursor.fetchall()
    if len(data) == 0:
        if table != "Follow_up_Data":
            cursor.execute("INSERT INTO " + table + "(file_number) VALUES ('" + file_number + "')")
        print(file_number + " does not exist in table " + table + ". Enter new record")
        add_new.add_new(conn, cursor, file_number, table, user_name,folders)
    else:
        todo = ask.ask_option(file_number + " already exists in table " + table + ".",
                                            ["Edit record", "Add new record for same file number", "Edit None"])
        if todo == "Edit record":
            edit_record.edit_record(conn, cursor, file_number, table, user_name, folders)
        elif todo == "Add new record for same file number":
            print("Add additional record module TBD")
    ask_table = ask.ask_y_n("Add another table?")
    return ask_table
def feed_duration(conn, cursor, file_number, children_number):
    table = "breast_feeding"
    child_list, feeding_duration_list, feeding_details_list = [], [], []
    child_number = int(children_number)
    for index in range(0, child_number):
        kid = str(index + 1)
        kid_add = "Child " + kid
        child_list.append(kid_add)
        feeding_duration = input("Breast feeding duration for " + kid_add +
                                 " (months) ?")
        feeding_duration_list.append(feeding_duration)
        feeding_details = ask_option("Breast feeding for child " + kid,
                                     PatientInfo.breast_feeding)
        feeding_details_list.append(feeding_details)
        columns = 'file_number, child_number, feeding_duration, breast_usage_feeding'
        data = file_number, kid, feeding_duration, feeding_details
        sql.insert(conn, cursor, table, columns, data)
    data_list = [child_list, feeding_duration_list, feeding_details_list]
    data_return = join_lists(data_list, "; ")
    return (data_return)