com.imsweb.algorithms.icd.IcdUtils Maven / Gradle / Ivy
/*
* Copyright (C) 2017 Information Management Services, Inc.
*/
package com.imsweb.algorithms.icd;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.apache.commons.lang3.math.NumberUtils;
import com.opencsv.CSVReader;
import com.opencsv.CSVReaderBuilder;
import com.opencsv.exceptions.CsvException;
import com.imsweb.algorithms.icd.IcdO2Entry.ConversionResultType;
public class IcdUtils {
public static final String SEX_MALE = "1";
public static final String SEX_FEMALE = "2";
public static final String REPORTABILITY_YES = "Y";
public static final String REPORTABILITY_OPTIONAL = "O";
private static final Map _ICD_9_CM_TO_O3_CONVERSION = new HashMap<>();
private static final Map _ICD_10_CM_TO_O3_CONVERSION = new HashMap<>();
private static final Map _ICD_10_TO_O3_CONVERSION = new HashMap<>();
private static final Map _ICD_O3_SITE_LOOKUP = new HashMap<>();
private static final List _ICDO3_TO_ICDO2_LOOKUP_SPECIAL = new ArrayList<>();
private static final List _ICDO3_TO_ICDO2_LOOKUP = new ArrayList<>();
private static final int _ICDO3_TO_ICDO2_LOOKUP_FLAG_HAND_POS = 4;
private static final int _ICDO3_TO_ICDO2_LOOKUP_FLAG_BEH_POS = 5;
private static final int _ICDO3_TO_ICDO2_LOOKUP_FLAG_SITE_POS = 6;
private static final int _ICDO3_TO_ICDO2_LOOKUP_SPECIAL_FLAG_HIST3_POS = 0;
private static final int _ICDO3_TO_ICDO2_LOOKUP_SPECIAL_FLAG_BEH3_POS = 4;
private static final int _ICDO3_TO_ICDO2_LOOKUP_SPECIAL_FLAG_HIST2_POS = 5;
private static final int _ICDO3_TO_ICDO2_LOOKUP_SPECIAL_FLAG_BEH2_POS = 9;
static {
_ICD_O3_SITE_LOOKUP.put("C000", "External upper lip");
_ICD_O3_SITE_LOOKUP.put("C001", "External lower lip");
_ICD_O3_SITE_LOOKUP.put("C002", "External lip, NOS");
_ICD_O3_SITE_LOOKUP.put("C003", "Mucosa of upper lip");
_ICD_O3_SITE_LOOKUP.put("C004", "Mucosa of lower lip");
_ICD_O3_SITE_LOOKUP.put("C005", "Mucosa of lip, NOS");
_ICD_O3_SITE_LOOKUP.put("C006", "Commissure of lip");
_ICD_O3_SITE_LOOKUP.put("C008", "Overlapping lesion of lip");
_ICD_O3_SITE_LOOKUP.put("C009", "Lip, NOS");
_ICD_O3_SITE_LOOKUP.put("C019", "Base of tongue, NOS");
_ICD_O3_SITE_LOOKUP.put("C020", "Dorsal surface of tongue, NOS");
_ICD_O3_SITE_LOOKUP.put("C021", "Border of tongue");
_ICD_O3_SITE_LOOKUP.put("C022", "Ventral surface of tongue, NOS");
_ICD_O3_SITE_LOOKUP.put("C023", "Anterior 2/3 of tongue, NOS");
_ICD_O3_SITE_LOOKUP.put("C024", "Lingual tonsil");
_ICD_O3_SITE_LOOKUP.put("C028", "Overlapping lesion of tongue");
_ICD_O3_SITE_LOOKUP.put("C029", "Tongue, NOS");
_ICD_O3_SITE_LOOKUP.put("C030", "Upper gum");
_ICD_O3_SITE_LOOKUP.put("C031", "Lower gum");
_ICD_O3_SITE_LOOKUP.put("C039", "Gum, NOS");
_ICD_O3_SITE_LOOKUP.put("C040", "Anterior floor of mouth");
_ICD_O3_SITE_LOOKUP.put("C041", "Lateral floor of mouth");
_ICD_O3_SITE_LOOKUP.put("C048", "Overlapping lesion of floor of mouth");
_ICD_O3_SITE_LOOKUP.put("C049", "Floor of mouth, NOS");
_ICD_O3_SITE_LOOKUP.put("C050", "Hard palate");
_ICD_O3_SITE_LOOKUP.put("C051", "Soft palate, NOS");
_ICD_O3_SITE_LOOKUP.put("C052", "Uvula");
_ICD_O3_SITE_LOOKUP.put("C058", "Overlapping lesion of palate");
_ICD_O3_SITE_LOOKUP.put("C059", "Palate, NOS");
_ICD_O3_SITE_LOOKUP.put("C060", "Cheek mucosa");
_ICD_O3_SITE_LOOKUP.put("C061", "Vestibule of mouth");
_ICD_O3_SITE_LOOKUP.put("C062", "Retromolar area");
_ICD_O3_SITE_LOOKUP.put("C068", "Overlapping lesion of other and unspecified parts of mouth");
_ICD_O3_SITE_LOOKUP.put("C069", "Mouth, NOS");
_ICD_O3_SITE_LOOKUP.put("C079", "Parotid gland");
_ICD_O3_SITE_LOOKUP.put("C080", "Submandibular gland");
_ICD_O3_SITE_LOOKUP.put("C081", "Sublingual gland");
_ICD_O3_SITE_LOOKUP.put("C088", "Overlapping lesion of major salivary glands");
_ICD_O3_SITE_LOOKUP.put("C089", "Major salivary gland, NOS");
_ICD_O3_SITE_LOOKUP.put("C090", "Tonsillar fossa");
_ICD_O3_SITE_LOOKUP.put("C091", "Tonsillar pillar");
_ICD_O3_SITE_LOOKUP.put("C098", "Overlapping lesion of tonsil");
_ICD_O3_SITE_LOOKUP.put("C099", "Tonsil, NOS");
_ICD_O3_SITE_LOOKUP.put("C100", "Vallecula");
_ICD_O3_SITE_LOOKUP.put("C101", "Anterior surface of epiglottis");
_ICD_O3_SITE_LOOKUP.put("C102", "Lateral wall of oropharynx");
_ICD_O3_SITE_LOOKUP.put("C103", "Posterior wall of oropharynx");
_ICD_O3_SITE_LOOKUP.put("C104", "Branchial cleft");
_ICD_O3_SITE_LOOKUP.put("C108", "Overlapping lesion of oropharynx");
_ICD_O3_SITE_LOOKUP.put("C109", "Oropharynx, NOS");
_ICD_O3_SITE_LOOKUP.put("C110", "Superior wall of nasopharynx");
_ICD_O3_SITE_LOOKUP.put("C111", "Posterior wall of nasopharynx");
_ICD_O3_SITE_LOOKUP.put("C112", "Lateral wall of nasopharynx");
_ICD_O3_SITE_LOOKUP.put("C113", "Anterior wall of nasopharynx");
_ICD_O3_SITE_LOOKUP.put("C118", "Overlapping lesion of nasopharynx");
_ICD_O3_SITE_LOOKUP.put("C119", "Nasopharynx, NOS");
_ICD_O3_SITE_LOOKUP.put("C129", "Pyriform sinus");
_ICD_O3_SITE_LOOKUP.put("C130", "Postcricoid region");
_ICD_O3_SITE_LOOKUP.put("C131", "Hypopharyngeal aspect of aryepiglottic fold");
_ICD_O3_SITE_LOOKUP.put("C132", "Posterior wall of hypopharynx");
_ICD_O3_SITE_LOOKUP.put("C138", "Overlapping lesion of hypopharynx");
_ICD_O3_SITE_LOOKUP.put("C139", "Hypopharynx, NOS");
_ICD_O3_SITE_LOOKUP.put("C140", "Pharynx, NOS");
_ICD_O3_SITE_LOOKUP.put("C142", "Waldeyer ring");
_ICD_O3_SITE_LOOKUP.put("C148", "Overlapping lesion of lip, oral cavity and pharynx");
_ICD_O3_SITE_LOOKUP.put("C150", "Cervical esophagus");
_ICD_O3_SITE_LOOKUP.put("C151", "Thoracic esophagus");
_ICD_O3_SITE_LOOKUP.put("C152", "Abdominal esophagus");
_ICD_O3_SITE_LOOKUP.put("C153", "Upper third of esophagus");
_ICD_O3_SITE_LOOKUP.put("C154", "Middle third of esophagus");
_ICD_O3_SITE_LOOKUP.put("C155", "Lower third of esophagus");
_ICD_O3_SITE_LOOKUP.put("C158", "Overlapping lesion of esophagus");
_ICD_O3_SITE_LOOKUP.put("C159", "Esophagus, NOS");
_ICD_O3_SITE_LOOKUP.put("C160", "Cardia, NOS");
_ICD_O3_SITE_LOOKUP.put("C161", "Fundus of stomach");
_ICD_O3_SITE_LOOKUP.put("C162", "Body of stomach");
_ICD_O3_SITE_LOOKUP.put("C163", "Gastric antrum");
_ICD_O3_SITE_LOOKUP.put("C164", "Pylorus");
_ICD_O3_SITE_LOOKUP.put("C165", "Lesser curvature of stomach, NOS");
_ICD_O3_SITE_LOOKUP.put("C166", "Greater curvature of stomach, NOS");
_ICD_O3_SITE_LOOKUP.put("C168", "Overlapping lesion of stomach");
_ICD_O3_SITE_LOOKUP.put("C169", "Stomach, NOS");
_ICD_O3_SITE_LOOKUP.put("C170", "Duodenum");
_ICD_O3_SITE_LOOKUP.put("C171", "Jejunum");
_ICD_O3_SITE_LOOKUP.put("C172", "Ileum");
_ICD_O3_SITE_LOOKUP.put("C173", "Meckel diverticulum");
_ICD_O3_SITE_LOOKUP.put("C178", "Overlapping lesion of smallintestine");
_ICD_O3_SITE_LOOKUP.put("C179", "Small intestine, NOS");
_ICD_O3_SITE_LOOKUP.put("C180", "Cecum");
_ICD_O3_SITE_LOOKUP.put("C181", "Appendix");
_ICD_O3_SITE_LOOKUP.put("C182", "Ascending colon");
_ICD_O3_SITE_LOOKUP.put("C183", "Hepatic flexure of colon");
_ICD_O3_SITE_LOOKUP.put("C184", "Transverse colon");
_ICD_O3_SITE_LOOKUP.put("C185", "Splenic flexure of colon");
_ICD_O3_SITE_LOOKUP.put("C186", "Descending colon");
_ICD_O3_SITE_LOOKUP.put("C187", "Sigmoid colon");
_ICD_O3_SITE_LOOKUP.put("C188", "Overlapping lesion of colon");
_ICD_O3_SITE_LOOKUP.put("C189", "Colon, NOS");
_ICD_O3_SITE_LOOKUP.put("C199", "Rectosigmoid junction");
_ICD_O3_SITE_LOOKUP.put("C209", "Rectum, NOS");
_ICD_O3_SITE_LOOKUP.put("C210", "Anus, NOS");
_ICD_O3_SITE_LOOKUP.put("C211", "Anal canal");
_ICD_O3_SITE_LOOKUP.put("C212", "Cloacogenic zone");
_ICD_O3_SITE_LOOKUP.put("C218", "Overlapping lesion of rectum, anus and anal canal");
_ICD_O3_SITE_LOOKUP.put("C220", "Liver");
_ICD_O3_SITE_LOOKUP.put("C221", "Intrahepatic bile duct");
_ICD_O3_SITE_LOOKUP.put("C239", "Gallbladder");
_ICD_O3_SITE_LOOKUP.put("C240", "Extrahepatic bile duct");
_ICD_O3_SITE_LOOKUP.put("C241", "Ampulla of Vater");
_ICD_O3_SITE_LOOKUP.put("C248", "Overlapping lesion of biliary tract Note:");
_ICD_O3_SITE_LOOKUP.put("C249", "Biliary tract, NOS");
_ICD_O3_SITE_LOOKUP.put("C250", "Head of pancreas");
_ICD_O3_SITE_LOOKUP.put("C251", "Body of pancreas");
_ICD_O3_SITE_LOOKUP.put("C252", "Tail of pancreas");
_ICD_O3_SITE_LOOKUP.put("C253", "Pancreatic duct");
_ICD_O3_SITE_LOOKUP.put("C254", "Islets of Langerhans");
_ICD_O3_SITE_LOOKUP.put("C257", "Other specified parts of pancreas");
_ICD_O3_SITE_LOOKUP.put("C258", "Overlapping lesion of pancreas");
_ICD_O3_SITE_LOOKUP.put("C259", "Pancreas, NOS");
_ICD_O3_SITE_LOOKUP.put("C260", "Intestinal tract, NOS");
_ICD_O3_SITE_LOOKUP.put("C268", "Overlapping lesion of digestive system");
_ICD_O3_SITE_LOOKUP.put("C269", "Gastrointestinal tract, NOS");
_ICD_O3_SITE_LOOKUP.put("C300", "Nasal cavity");
_ICD_O3_SITE_LOOKUP.put("C301", "Middle ear");
_ICD_O3_SITE_LOOKUP.put("C310", "Maxillary sinus");
_ICD_O3_SITE_LOOKUP.put("C311", "Ethmoid sinus");
_ICD_O3_SITE_LOOKUP.put("C312", "Frontal sinus");
_ICD_O3_SITE_LOOKUP.put("C313", "Sphenoid sinus");
_ICD_O3_SITE_LOOKUP.put("C318", "Overlapping lesion of accessory sinuses");
_ICD_O3_SITE_LOOKUP.put("C319", "Accessory sinus, NOS");
_ICD_O3_SITE_LOOKUP.put("C320", "Glottis");
_ICD_O3_SITE_LOOKUP.put("C321", "Supraglottis");
_ICD_O3_SITE_LOOKUP.put("C322", "Subglottis");
_ICD_O3_SITE_LOOKUP.put("C323", "Laryngeal cartilage");
_ICD_O3_SITE_LOOKUP.put("C328", "Overlapping lesion of larynx");
_ICD_O3_SITE_LOOKUP.put("C329", "Larynx, NOS");
_ICD_O3_SITE_LOOKUP.put("C339", "Trachea");
_ICD_O3_SITE_LOOKUP.put("C340", "Main bronchus");
_ICD_O3_SITE_LOOKUP.put("C341", "Upper lobe, lung");
_ICD_O3_SITE_LOOKUP.put("C342", "Middle lobe, lung");
_ICD_O3_SITE_LOOKUP.put("C343", "Lower lobe, lung");
_ICD_O3_SITE_LOOKUP.put("C348", "Overlapping lesion of lung");
_ICD_O3_SITE_LOOKUP.put("C349", "Lung, NOS");
_ICD_O3_SITE_LOOKUP.put("C379", "Thymus");
_ICD_O3_SITE_LOOKUP.put("C380", "Heart");
_ICD_O3_SITE_LOOKUP.put("C381", "Anterior mediastinum");
_ICD_O3_SITE_LOOKUP.put("C382", "Posterior mediastinum");
_ICD_O3_SITE_LOOKUP.put("C383", "Mediastinum, NOS");
_ICD_O3_SITE_LOOKUP.put("C384", "Pleura, NOS");
_ICD_O3_SITE_LOOKUP.put("C388", "Overlapping lesion of heart, mediastinum and pleura");
_ICD_O3_SITE_LOOKUP.put("C390", "Upper respiratory tract, NOS");
_ICD_O3_SITE_LOOKUP.put("C398", "Overlapping lesion of respiratory system and intrathoracic organs");
_ICD_O3_SITE_LOOKUP.put("C399", "Ill-defined sites within respiratory system");
_ICD_O3_SITE_LOOKUP.put("C400", "Long bones of upper limb, scapula and associated joints");
_ICD_O3_SITE_LOOKUP.put("C401", "Short bones of upper limb and associated joints");
_ICD_O3_SITE_LOOKUP.put("C402", "Long bones of lower limb and associated joints");
_ICD_O3_SITE_LOOKUP.put("C403", "Short bones of lower limb and associated joints");
_ICD_O3_SITE_LOOKUP.put("C408", "Overlapping lesion of bones, joints and articular cartilage of limbs");
_ICD_O3_SITE_LOOKUP.put("C409", "Bone of limb, NOS");
_ICD_O3_SITE_LOOKUP.put("C410", "Bones of skull and face and associated joints");
_ICD_O3_SITE_LOOKUP.put("C411", "Mandible");
_ICD_O3_SITE_LOOKUP.put("C412", "Vertebral column");
_ICD_O3_SITE_LOOKUP.put("C413", "Rib, sternum, clavicle and associated joints");
_ICD_O3_SITE_LOOKUP.put("C414", "Pelvic bones, sacrum, coccyx and associated joints");
_ICD_O3_SITE_LOOKUP.put("C418", "Overlapping lesion of bones, joints and articular cartilage");
_ICD_O3_SITE_LOOKUP.put("C419", "Bone, NOS");
_ICD_O3_SITE_LOOKUP.put("C420", "Blood");
_ICD_O3_SITE_LOOKUP.put("C421", "Bone marrow");
_ICD_O3_SITE_LOOKUP.put("C422", "Spleen");
_ICD_O3_SITE_LOOKUP.put("C423", "Reticuloendothelial system,NOS");
_ICD_O3_SITE_LOOKUP.put("C424", "Hematopoietic system, NOS");
_ICD_O3_SITE_LOOKUP.put("C440", "Skin of lip, NOS");
_ICD_O3_SITE_LOOKUP.put("C441", "Eyelid");
_ICD_O3_SITE_LOOKUP.put("C442", "External ear");
_ICD_O3_SITE_LOOKUP.put("C443", "Skin of other and unspecified parts of face");
_ICD_O3_SITE_LOOKUP.put("C444", "Skin of scalp and neck");
_ICD_O3_SITE_LOOKUP.put("C445", "Skin of trunk");
_ICD_O3_SITE_LOOKUP.put("C446", "Skin of upper limb and shoulder");
_ICD_O3_SITE_LOOKUP.put("C447", "Skin of lower limb and hip");
_ICD_O3_SITE_LOOKUP.put("C448", "Overlapping lesion of skin");
_ICD_O3_SITE_LOOKUP.put("C449", "Skin, NOS");
_ICD_O3_SITE_LOOKUP.put("C470", "Peripheral nerves and autonomic nervous system of head, face, and neck");
_ICD_O3_SITE_LOOKUP.put("C471", "Peripheral nerves and autonomic nervous system of upper limb and shoulder");
_ICD_O3_SITE_LOOKUP.put("C472", "Peripheral nerves and autonomic nervous system of lower limband hip");
_ICD_O3_SITE_LOOKUP.put("C473", "Peripheral nerves and autonomic nervous system of thorax");
_ICD_O3_SITE_LOOKUP.put("C474", "Peripheral nerves and autonomic nervous system of abdomen");
_ICD_O3_SITE_LOOKUP.put("C475", "Peripheral nerves and autonomic nervous system of pelvis");
_ICD_O3_SITE_LOOKUP.put("C476", "Peripheral nerves and autonomic nervous system of trunk, NOS");
_ICD_O3_SITE_LOOKUP.put("C478", "Overlapping lesion of peripheral nerves and autonomic nervous system");
_ICD_O3_SITE_LOOKUP.put("C479", "Autonomic nervous system, NOS");
_ICD_O3_SITE_LOOKUP.put("C480", "Retroperitoneum");
_ICD_O3_SITE_LOOKUP.put("C481", "Specified parts of peritoneum");
_ICD_O3_SITE_LOOKUP.put("C482", "Peritoneum, NOS");
_ICD_O3_SITE_LOOKUP.put("C488", "Overlapping lesion of retroperitoneum and peritoneum");
_ICD_O3_SITE_LOOKUP.put("C490", "Connective, subcutaneous and other soft tissues of head, face, and neck");
_ICD_O3_SITE_LOOKUP.put("C491", "Connective, subcutaneous and other soft tissues of upper limb and shoulder");
_ICD_O3_SITE_LOOKUP.put("C492", "Connective, subcutaneous and other soft tissues of lower limb and hip");
_ICD_O3_SITE_LOOKUP.put("C493", "Connective, subcutaneous and other soft tissues of thorax");
_ICD_O3_SITE_LOOKUP.put("C494", "Connective, subcutaneous and other soft tissues of abdomen");
_ICD_O3_SITE_LOOKUP.put("C495", "Connective, subcutaneous and other soft tissues of pelvis");
_ICD_O3_SITE_LOOKUP.put("C496", "Connective, subcutaneous and other soft tissues of trunk NOS");
_ICD_O3_SITE_LOOKUP.put("C498", "Overlapping lesion of connective, subcutaneous and other soft tissues");
_ICD_O3_SITE_LOOKUP.put("C499", "Connective, subcutaneous and other soft tissues, NOS");
_ICD_O3_SITE_LOOKUP.put("C500", "Nipple");
_ICD_O3_SITE_LOOKUP.put("C501", "Central portion of breast");
_ICD_O3_SITE_LOOKUP.put("C502", "Upper-inner quadrant of breast");
_ICD_O3_SITE_LOOKUP.put("C503", "Lower-inner quadrant of breast");
_ICD_O3_SITE_LOOKUP.put("C504", "Upper-outer quadrant of breast");
_ICD_O3_SITE_LOOKUP.put("C505", "Lower-outer quadrant of breast");
_ICD_O3_SITE_LOOKUP.put("C506", "Axillary tail of breast");
_ICD_O3_SITE_LOOKUP.put("C508", "Overlapping lesion of breast");
_ICD_O3_SITE_LOOKUP.put("C509", "Breast, NOS");
_ICD_O3_SITE_LOOKUP.put("C510", "Labium majus");
_ICD_O3_SITE_LOOKUP.put("C511", "Labium minus");
_ICD_O3_SITE_LOOKUP.put("C512", "Clitoris");
_ICD_O3_SITE_LOOKUP.put("C518", "Overlapping lesion of vulva");
_ICD_O3_SITE_LOOKUP.put("C519", "Vulva, NOS");
_ICD_O3_SITE_LOOKUP.put("C529", "Vagina, NOS");
_ICD_O3_SITE_LOOKUP.put("C530", "Endocervix");
_ICD_O3_SITE_LOOKUP.put("C531", "Exocervix");
_ICD_O3_SITE_LOOKUP.put("C538", "Overlapping lesion of cervix uteri");
_ICD_O3_SITE_LOOKUP.put("C539", "Cervix uteri");
_ICD_O3_SITE_LOOKUP.put("C540", "Isthmus uteri");
_ICD_O3_SITE_LOOKUP.put("C541", "Endometrium");
_ICD_O3_SITE_LOOKUP.put("C542", "Myometrium");
_ICD_O3_SITE_LOOKUP.put("C543", "Fundus uteri");
_ICD_O3_SITE_LOOKUP.put("C548", "Overlapping lesion of corpus uteri");
_ICD_O3_SITE_LOOKUP.put("C549", "Corpus uteri");
_ICD_O3_SITE_LOOKUP.put("C559", "Uterus, NOS");
_ICD_O3_SITE_LOOKUP.put("C569", "Ovary");
_ICD_O3_SITE_LOOKUP.put("C570", "Fallopian tube");
_ICD_O3_SITE_LOOKUP.put("C571", "Broad ligament");
_ICD_O3_SITE_LOOKUP.put("C572", "Round ligament");
_ICD_O3_SITE_LOOKUP.put("C573", "Parametrium");
_ICD_O3_SITE_LOOKUP.put("C574", "Uterine adnexa");
_ICD_O3_SITE_LOOKUP.put("C577", "Other specified parts of female genital organs");
_ICD_O3_SITE_LOOKUP.put("C578", "Overlapping lesion of female genital organs");
_ICD_O3_SITE_LOOKUP.put("C579", "Female genital tract, NOS");
_ICD_O3_SITE_LOOKUP.put("C589", "Placenta");
_ICD_O3_SITE_LOOKUP.put("C600", "Prepuce");
_ICD_O3_SITE_LOOKUP.put("C601", "Glans penis");
_ICD_O3_SITE_LOOKUP.put("C602", "Body of penis");
_ICD_O3_SITE_LOOKUP.put("C608", "Overlapping lesion of penis");
_ICD_O3_SITE_LOOKUP.put("C609", "Penis, NOS");
_ICD_O3_SITE_LOOKUP.put("C619", "Prostate gland");
_ICD_O3_SITE_LOOKUP.put("C620", "Undescended testis");
_ICD_O3_SITE_LOOKUP.put("C621", "Descended testis");
_ICD_O3_SITE_LOOKUP.put("C629", "Testis, NOS");
_ICD_O3_SITE_LOOKUP.put("C630", "Epididymis");
_ICD_O3_SITE_LOOKUP.put("C631", "Spermatic cord");
_ICD_O3_SITE_LOOKUP.put("C632", "Scrotum, NOS");
_ICD_O3_SITE_LOOKUP.put("C637", "Other specified parts of male genital organs");
_ICD_O3_SITE_LOOKUP.put("C638", "Overlapping lesion of male genital organs Note:");
_ICD_O3_SITE_LOOKUP.put("C639", "Male genital organs, NOS");
_ICD_O3_SITE_LOOKUP.put("C649", "Kidney, NOS");
_ICD_O3_SITE_LOOKUP.put("C659", "Renal pelvis");
_ICD_O3_SITE_LOOKUP.put("C669", "Ureter");
_ICD_O3_SITE_LOOKUP.put("C670", "Trigone of bladder");
_ICD_O3_SITE_LOOKUP.put("C671", "Dome of bladder");
_ICD_O3_SITE_LOOKUP.put("C672", "Lateral wall of bladder");
_ICD_O3_SITE_LOOKUP.put("C673", "Anterior wall of bladder");
_ICD_O3_SITE_LOOKUP.put("C674", "Posterior wall of bladder");
_ICD_O3_SITE_LOOKUP.put("C675", "Bladder neck");
_ICD_O3_SITE_LOOKUP.put("C676", "Ureteric orifice");
_ICD_O3_SITE_LOOKUP.put("C677", "Urachus");
_ICD_O3_SITE_LOOKUP.put("C678", "Overlapping lesion of bladder");
_ICD_O3_SITE_LOOKUP.put("C679", "Bladder, NOS");
_ICD_O3_SITE_LOOKUP.put("C680", "Urethra");
_ICD_O3_SITE_LOOKUP.put("C681", "Paraurethral gland");
_ICD_O3_SITE_LOOKUP.put("C688", "Overlapping lesion of urinary organs");
_ICD_O3_SITE_LOOKUP.put("C689", "Urinary system, NOS");
_ICD_O3_SITE_LOOKUP.put("C690", "Conjunctiva");
_ICD_O3_SITE_LOOKUP.put("C691", "Cornea, NOS");
_ICD_O3_SITE_LOOKUP.put("C692", "Retina");
_ICD_O3_SITE_LOOKUP.put("C693", "Choroid");
_ICD_O3_SITE_LOOKUP.put("C694", "Ciliary body");
_ICD_O3_SITE_LOOKUP.put("C695", "Lacrimal gland");
_ICD_O3_SITE_LOOKUP.put("C696", "Orbit, NOS");
_ICD_O3_SITE_LOOKUP.put("C698", "Overlapping lesion of eye and adnexa");
_ICD_O3_SITE_LOOKUP.put("C699", "Eye, NOS");
_ICD_O3_SITE_LOOKUP.put("C700", "Cerebral meninges");
_ICD_O3_SITE_LOOKUP.put("C701", "Spinal meninges");
_ICD_O3_SITE_LOOKUP.put("C709", "Meninges, NOS");
_ICD_O3_SITE_LOOKUP.put("C710", "Cerebrum");
_ICD_O3_SITE_LOOKUP.put("C711", "Frontal lobe");
_ICD_O3_SITE_LOOKUP.put("C712", "Temporal lobe");
_ICD_O3_SITE_LOOKUP.put("C713", "Parietal lobe");
_ICD_O3_SITE_LOOKUP.put("C714", "Occipital lobe");
_ICD_O3_SITE_LOOKUP.put("C715", "Ventricle, NOS");
_ICD_O3_SITE_LOOKUP.put("C716", "Cerebellum, NOS");
_ICD_O3_SITE_LOOKUP.put("C717", "Brain stem");
_ICD_O3_SITE_LOOKUP.put("C718", "Overlapping lesion of brain");
_ICD_O3_SITE_LOOKUP.put("C719", "Brain, NOS");
_ICD_O3_SITE_LOOKUP.put("C720", "Spinal cord");
_ICD_O3_SITE_LOOKUP.put("C721", "Cauda equina");
_ICD_O3_SITE_LOOKUP.put("C722", "Olfactory nerve");
_ICD_O3_SITE_LOOKUP.put("C723", "Optic nerve");
_ICD_O3_SITE_LOOKUP.put("C724", "Acoustic nerve");
_ICD_O3_SITE_LOOKUP.put("C725", "Cranial nerve, NOS");
_ICD_O3_SITE_LOOKUP.put("C728", "Overlapping lesion of brain and central nervous system");
_ICD_O3_SITE_LOOKUP.put("C729", "Nervous system, NOS");
_ICD_O3_SITE_LOOKUP.put("C739", "Thyroid gland");
_ICD_O3_SITE_LOOKUP.put("C740", "Cortex of adrenal gland");
_ICD_O3_SITE_LOOKUP.put("C741", "Medulla of adrenal gland");
_ICD_O3_SITE_LOOKUP.put("C749", "Adrenal gland, NOS");
_ICD_O3_SITE_LOOKUP.put("C750", "Parathyroid gland");
_ICD_O3_SITE_LOOKUP.put("C751", "Pituitary gland");
_ICD_O3_SITE_LOOKUP.put("C752", "Craniopharyngeal duct");
_ICD_O3_SITE_LOOKUP.put("C753", "Pineal gland");
_ICD_O3_SITE_LOOKUP.put("C754", "Carotid body");
_ICD_O3_SITE_LOOKUP.put("C755", "Aortic body and other paraganglia");
_ICD_O3_SITE_LOOKUP.put("C758", "Overlapping lesion of endocrine glands and related structures");
_ICD_O3_SITE_LOOKUP.put("C759", "Endocrine gland, NOS");
_ICD_O3_SITE_LOOKUP.put("C760", "Head, face or neck, NOS");
_ICD_O3_SITE_LOOKUP.put("C761", "Thorax, NOS");
_ICD_O3_SITE_LOOKUP.put("C762", "Abdomen, NOS");
_ICD_O3_SITE_LOOKUP.put("C763", "Pelvis, NOS");
_ICD_O3_SITE_LOOKUP.put("C764", "Upper limb, NOS");
_ICD_O3_SITE_LOOKUP.put("C765", "Lower limb, NOS");
_ICD_O3_SITE_LOOKUP.put("C767", "Other ill-defined sites");
_ICD_O3_SITE_LOOKUP.put("C768", "Overlapping lesion of ill-defined sites");
_ICD_O3_SITE_LOOKUP.put("C770", "Lymph nodes of head, face and neck");
_ICD_O3_SITE_LOOKUP.put("C771", "Intrathoracic lymph nodes");
_ICD_O3_SITE_LOOKUP.put("C772", "Intra-abdominal lymph nodes");
_ICD_O3_SITE_LOOKUP.put("C773", "Lymph nodes of axilla or arm");
_ICD_O3_SITE_LOOKUP.put("C774", "Lymph nodes of inguinal region or leg");
_ICD_O3_SITE_LOOKUP.put("C775", "Pelvic lymph nodes");
_ICD_O3_SITE_LOOKUP.put("C778", "Lymph nodes of multiple regions");
_ICD_O3_SITE_LOOKUP.put("C779", "Lymph node, NOS");
_ICD_O3_SITE_LOOKUP.put("C809", "Unknown primary site");
}
/**
* Initializes the ICD data (this method is called lazily if needed).
*/
public static synchronized void initalize() {
if (!_ICD_9_CM_TO_O3_CONVERSION.isEmpty())
return;
loadDataFile("icd-9-cm-to-icd-o-3.csv", _ICD_9_CM_TO_O3_CONVERSION);
loadDataFile("icd-10-cm-to-icd-o-3.csv", _ICD_10_CM_TO_O3_CONVERSION);
loadDataFile("icd-10-to-icd-o-3.csv", _ICD_10_TO_O3_CONVERSION);
loadIcdO3toIcdO2DataFile("icdo3.to.icdo2.morphology.special.txt", _ICDO3_TO_ICDO2_LOOKUP_SPECIAL);
loadIcdO3toIcdO2DataFile("icdo3.to.icdo2.morphology.txt", _ICDO3_TO_ICDO2_LOOKUP);
}
/**
* Returns the internal conversions from ICD-9CM to ICD-O-3.
* @return internal conversions as a map
*/
public static Map getIcd9CmToO3Conversions() {
initalize();
return Collections.unmodifiableMap(_ICD_9_CM_TO_O3_CONVERSION);
}
/**
* Returns the internal conversions from ICD-10CM to ICD-O-3.
* @return internal conversions as a map
*/
public static Map getIcd10CmToO3Conversions() {
initalize();
return Collections.unmodifiableMap(_ICD_10_CM_TO_O3_CONVERSION);
}
/**
* Returns the internal conversions from ICD-10 to ICD-O-3.
* @return internal conversions as a map
*/
public static Map getIcd10ToO3Conversions() {
initalize();
return Collections.unmodifiableMap(_ICD_10_TO_O3_CONVERSION);
}
/**
* Return the ICD-O-3 site lookup (codes and labels).
*/
public static Map getIcdO3SiteLookup() {
return Collections.unmodifiableMap(_ICD_O3_SITE_LOOKUP);
}
/**
* Returns the ICD-O-3 conversion entry for the provided ICD9-CM code.
* @param icd9CmCode ICD9-CM code (required)
* @param sex sex value, optional. If provided, needs to be "1" (MALE) or "2" (FEMALE), otherwise it will be ignored.
* @return corresponding ICD-O-3 conversion entry, maybe null
*/
public static IcdO3Entry getIcdO3FromIcd9Cm(String icd9CmCode, String sex) {
initalize();
IcdO3Entry result = null;
// if we have a value for the sex, try to use it
if (SEX_MALE.equals(sex) || SEX_FEMALE.equals(sex))
result = _ICD_9_CM_TO_O3_CONVERSION.get(icd9CmCode + sex);
// if we didn't find any result, try without the sex
if (result == null)
result = _ICD_9_CM_TO_O3_CONVERSION.get(icd9CmCode);
// if we still didn't get a value and no sex was provided, assume MALE
if (result == null && sex == null)
result = _ICD_9_CM_TO_O3_CONVERSION.get(icd9CmCode + SEX_MALE);
return result;
}
/**
* Returns the ICD-O-3 conversion entry for the provided ICD10-CM code.
* @param icd10CmCode ICD10-CM code (required)
* @return corresponding ICD-O-3 conversion entry, maybe null
*/
public static IcdO3Entry getIcdO3FromIcd10Cm(String icd10CmCode) {
initalize();
return _ICD_10_CM_TO_O3_CONVERSION.get(icd10CmCode);
}
/**
* Returns the ICD-O-3 conversion entry for the provided ICD10 code.
* @param icd10Code ICD10 code (required)
* @return corresponding ICD-O-3 conversion entry, maybe null
*/
public static IcdO3Entry getIcdO3FromIcd10(String icd10Code) {
return getIcdO3FromIcd10(icd10Code, true);
}
/**
* Returns the ICD-O-3 conversion entry for the provided ICD10 code.
* @param icd10Code ICD10 code (required)
* @param allowNullResult if set to false, then a fake result will be returned if the internal data doesn't contain the requested code.
* @return corresponding ICD-O-3 conversion entry, maybe null (depending on allowNullResult)
*/
public static IcdO3Entry getIcdO3FromIcd10(String icd10Code, boolean allowNullResult) {
initalize();
String code = icd10Code == null ? null : icd10Code.toUpperCase();
if (code != null && code.length() == 3)
code = code + "9";
IcdO3Entry result = _ICD_10_TO_O3_CONVERSION.get(code);
// if the data doesn't contain the code, build a fake one if we have to
if (result == null && !allowNullResult) {
result = new IcdO3Entry();
result.setSourceCode(code);
result.setSite(_ICD_O3_SITE_LOOKUP.containsKey(code) ? code : "C809");
result.setHistology("8000");
result.setBehavior(icd10Code != null && icd10Code.startsWith("C") ? "3" : icd10Code != null && icd10Code.startsWith("D") ? "2" : null);
result.setGrade("9");
result.setLaterality(null);
result.setReportable(null);
result.setSex(null);
}
return result;
}
/**
* Returns the ICD-O-2 conversion entry for the provided ICD-O-3 code.
* @param icdO3Site ICD-O-3 site(required)
* @param icdO3Histology ICD-O-3 histology (required)
* @param icdO3Behavior ICD-O-3 behavior (required)
* @param allowNullResult if set to false, then a fake result will be returned if the internal data doesn't contain the requested code.
* @return corresponding ICD-O-2 conversion entry, maybe null (depending on allowNullResult)
*/
public static IcdO2Entry getIcdO2FromIcdO3(String icdO3Site, String icdO3Histology, String icdO3Behavior, boolean allowNullResult) {
initalize();
IcdO2Entry result = new IcdO2Entry();
result.setSite(icdO3Site);
result.setHistology("9999");
result.setBehavior("9");
result.setConversionResult(ConversionResultType.CONVERSION_SUCCESSFUL);
checkForInvalidIcdO3Codes(icdO3Site, icdO3Histology, icdO3Behavior, result);
if (result.getConversionResult() == ConversionResultType.CONVERSION_SUCCESSFUL) {
/////////////////////////////////////////////////////////////////////////
// Conversion function calls:
// ConvertMorph: Search by Hist. Provides base ICD-O-2 Histology.
// Assumes behavior is unchanged. If hand review flag
// is not 'X', set Hand Review='1'. If Beh flag is not
// 'X', calls ConvertMorphSpec. If site flag is not
// 'X', calls ConvertSite.
// ConvertMorphSpec: Search by Hist/Beh. Called if Beh flag is not 'X'.
// ConvertSite: Site specific conversions. Hard coded. Called if
// Site flag is not 'X'.
//
/////////////////////////////////////////////////////////////////////////
result.setSite(icdO3Site);
int histologyValue = Integer.parseInt(icdO3Histology);
convertIcdO3Morphology(icdO3Site, histologyValue, icdO3Behavior, result);
}
ConversionResultType res = result.getConversionResult();
boolean invalid = res == ConversionResultType.CONVERSION_FAILED_INVALID_SITE || res == ConversionResultType.CONVERSION_FAILED_INVALID_HISTOLOGY || res ==
ConversionResultType.CONVERSION_FAILED_INVALID_BEHAVIOR;
if (invalid && allowNullResult)
result = null;
return result;
}
/**
* Checks the incoming ICD-O-3 codes for values which are out of range. Sets appropriate flags and returns 1 if any of the flags have been turned on.
* @param icdO3Site ICD-O-3 site
* @param icdO3Histology ICD-O-3 histology
* @param icdO3Behavior ICD-O-3 behavior
* @param result gets set with possible invalid flag.
*/
static void checkForInvalidIcdO3Codes(String icdO3Site, String icdO3Histology, String icdO3Behavior, IcdO2Entry result) {
result.setConversionResult(ConversionResultType.CONVERSION_SUCCESSFUL);
// Check for invalid data being entered (Out of range, not specific codes)
// Site out of range
if (icdO3Site == null)
result.setConversionResult(ConversionResultType.CONVERSION_FAILED_INVALID_SITE);
else if (icdO3Site.length() != 4)
result.setConversionResult(ConversionResultType.CONVERSION_FAILED_INVALID_SITE);
else if ((!icdO3Site.startsWith("C") && !icdO3Site.startsWith("c")) || (!NumberUtils.isDigits(icdO3Site.substring(1, 4).trim())))
result.setConversionResult(ConversionResultType.CONVERSION_FAILED_INVALID_SITE);
else {
int siteValue = Integer.parseInt(icdO3Site.substring(1, 4).trim());
if (siteValue < 0 || siteValue > 809)
result.setConversionResult(ConversionResultType.CONVERSION_FAILED_INVALID_SITE);
}
// Histology out of range
if (icdO3Histology == null)
result.setConversionResult(ConversionResultType.CONVERSION_FAILED_INVALID_HISTOLOGY);
else if (!NumberUtils.isDigits(icdO3Histology.trim()))
result.setConversionResult(ConversionResultType.CONVERSION_FAILED_INVALID_HISTOLOGY);
else {
int histologyValue = Integer.parseInt(icdO3Histology.trim());
if (histologyValue < 8000 || histologyValue > 9999)
result.setConversionResult(ConversionResultType.CONVERSION_FAILED_INVALID_HISTOLOGY);
}
// Behavior invalid
if (icdO3Behavior == null)
result.setConversionResult(ConversionResultType.CONVERSION_FAILED_INVALID_BEHAVIOR);
else if ((!icdO3Behavior.equals("0")) && (!icdO3Behavior.equals("1")) && (!icdO3Behavior.equals("2")) &&
(!icdO3Behavior.equals("3")) && (!icdO3Behavior.equals("6")) && (!icdO3Behavior.equals("9")))
result.setConversionResult(ConversionResultType.CONVERSION_FAILED_INVALID_BEHAVIOR);
}
/**
* Takes ICD-O-3 Hist code and retrieves the most common ICD-O-2 Hist code. Assumes that Beh remains the same. Also retrieves the hand review flag,
* the behavior specific conversion flag (which may cause ConvertMorphSpec to be called) and the site specific conversion flag (which may cause ConvertSite to be called).
* FLAG values:
* 0-3, 6, 9 -> this behavior is sent to next function
* A -> all behaviors have flag set
* X -> Invalid morph, not in ICD-O-3
* @param icdO3Site ICD-O-3 site
* @param icdO3HistologyValue ICD-O-3 histology number
* @param icdO3Behavior ICD-O-3 behavior
* @param result corresponding ICD-O-2 conversion entry.
*/
static void convertIcdO3Morphology(String icdO3Site, int icdO3HistologyValue, String icdO3Behavior, IcdO2Entry result) {
result.setConversionResult(ConversionResultType.CONVERSION_SUCCESSFUL);
String lookupEntry = _ICDO3_TO_ICDO2_LOOKUP.get(icdO3HistologyValue - 8000);
//is this an invalid Histology?
if (lookupEntry.equals("9999XXX"))
result.setConversionResult(ConversionResultType.CONVERSION_FAILED_INVALID_HISTOLOGY);
else {
//Get standard ICD-O-2 hist and beh
result.setHistology(lookupEntry.substring(0, 4));
result.setBehavior(icdO3Behavior);
//Set hand review flag if needed
String handFlag = lookupEntry.substring(_ICDO3_TO_ICDO2_LOOKUP_FLAG_HAND_POS, _ICDO3_TO_ICDO2_LOOKUP_FLAG_HAND_POS + 1);
if (handFlag.equals("A") || handFlag.equals(icdO3Behavior))
result.setConversionResult(ConversionResultType.CONVERSION_SUCCESSFUL_NEEDS_HAND_REVIEW);
else if (icdO3HistologyValue == 8402 && icdO3Behavior.equals("3"))
result.setConversionResult(ConversionResultType.CONVERSION_SUCCESSFUL_NEEDS_HAND_REVIEW);
//Is there a special behavior based conversion?
String behaviorFlag = lookupEntry.substring(_ICDO3_TO_ICDO2_LOOKUP_FLAG_BEH_POS, _ICDO3_TO_ICDO2_LOOKUP_FLAG_BEH_POS + 1);
if (behaviorFlag.equals(icdO3Behavior) || behaviorFlag.equals("A"))
convertIcdO3MorphologySpecial(icdO3HistologyValue, icdO3Behavior, result);
//Is there a special site based conversion?
String siteFlag = lookupEntry.substring(_ICDO3_TO_ICDO2_LOOKUP_FLAG_SITE_POS, _ICDO3_TO_ICDO2_LOOKUP_FLAG_SITE_POS + 1);
if (siteFlag.equals(icdO3Behavior))
convertIcdO3Site(icdO3Site, icdO3HistologyValue, icdO3Behavior, result);
}
}
/**
* Takes an ICD-O-3 Hist & Behavior and retrieves the ICD-O-2 Hist and Behavior.
* @param icdO3HistologyValue ICD-O-3 histology number
* @param icdO3Behavior ICD-O-3 behavior
* @param result corresponding ICD-O-2 conversion entry.
*/
static void convertIcdO3MorphologySpecial(int icdO3HistologyValue, String icdO3Behavior, IcdO2Entry result) {
boolean isFound = false;
String icdO3histology = Integer.toString(icdO3HistologyValue);
for (int i = 0; i < _ICDO3_TO_ICDO2_LOOKUP_SPECIAL.size() && !isFound; i++) {
String lookupSpecialEntry = _ICDO3_TO_ICDO2_LOOKUP_SPECIAL.get(i);
String histology3Flag = lookupSpecialEntry.substring(_ICDO3_TO_ICDO2_LOOKUP_SPECIAL_FLAG_HIST3_POS, _ICDO3_TO_ICDO2_LOOKUP_SPECIAL_FLAG_HIST3_POS + 4);
String behavior3Flag = lookupSpecialEntry.substring(_ICDO3_TO_ICDO2_LOOKUP_SPECIAL_FLAG_BEH3_POS, _ICDO3_TO_ICDO2_LOOKUP_SPECIAL_FLAG_BEH3_POS + 1);
if ((histology3Flag.equals(icdO3histology)) && (behavior3Flag.equals(icdO3Behavior))) {
isFound = true;
result.setHistology(lookupSpecialEntry.substring(_ICDO3_TO_ICDO2_LOOKUP_SPECIAL_FLAG_HIST2_POS, _ICDO3_TO_ICDO2_LOOKUP_SPECIAL_FLAG_HIST2_POS + 4));
result.setBehavior(lookupSpecialEntry.substring(_ICDO3_TO_ICDO2_LOOKUP_SPECIAL_FLAG_BEH2_POS, _ICDO3_TO_ICDO2_LOOKUP_SPECIAL_FLAG_BEH2_POS + 1));
}
}
}
/**
* For ICD-O-3 histology & behavior with Site flag turned on, checks site and returns the ICD-O-2 histology and behavior.
* @param icdO3Site ICD-O-3 site number
* @param icdO3HistologyValue ICD-O-3 histology number
* @param icdO3Behavior ICD-O-3 behavior
* @param result corresponding ICD-O-2 conversion entry.
*/
static void convertIcdO3Site(String icdO3Site, int icdO3HistologyValue, String icdO3Behavior, IcdO2Entry result) {
int siteValue = Integer.parseInt(icdO3Site.substring(1, 4).trim());
//Since there are so few cases, these are hard coded.
String behaviorFirstDigit = icdO3Behavior.substring(0, 1);
if (icdO3HistologyValue == 8240 && behaviorFirstDigit.equals("1")) {
if (siteValue != 181)
result.setHistology("8241");
else
result.setConversionResult(ConversionResultType.CONVERSION_SUCCESSFUL_NEEDS_HAND_REVIEW);
}
if (icdO3HistologyValue == 8245 && behaviorFirstDigit.equals("1")) {
result.setHistology("8240");
result.setConversionResult(ConversionResultType.CONVERSION_SUCCESSFUL_NEEDS_HAND_REVIEW);
if (siteValue == 181)
result.setBehavior("1");
else
result.setBehavior("3");
}
if (icdO3HistologyValue == 8249 && behaviorFirstDigit.equals("3") && siteValue == 181)
result.setBehavior("1");
if (icdO3HistologyValue == 9133 && behaviorFirstDigit.equals("3") && (siteValue >= 340 && siteValue <= 349)) {
result.setHistology("9134");
result.setBehavior("1");
result.setConversionResult(ConversionResultType.CONVERSION_SUCCESSFUL_NEEDS_HAND_REVIEW);
}
if (icdO3HistologyValue == 9160 && behaviorFirstDigit.equals("0")) {
result.setConversionResult(ConversionResultType.CONVERSION_SUCCESSFUL_NEEDS_HAND_REVIEW);
if (siteValue >= 440 && siteValue <= 449)
result.setHistology("8724");
}
if (icdO3HistologyValue == 9590 && behaviorFirstDigit.equals("3") && (siteValue >= 710 && siteValue <= 719)) {
result.setHistology("9594");
result.setConversionResult(ConversionResultType.CONVERSION_SUCCESSFUL_NEEDS_HAND_REVIEW);
}
}
/**
* Loads a lookup data file for use in getIcdO2FromIcdO3().
* @param file The name of the test file to load.
* @param result The list of strings which will contain the strings from the file.
*/
private static void loadIcdO3toIcdO2DataFile(String file, List result) {
result.clear();
try (BufferedReader reader = new BufferedReader(new InputStreamReader(Thread.currentThread().getContextClassLoader().getResourceAsStream("icd/" + file), StandardCharsets.US_ASCII))) {
String line;
while ((line = reader.readLine()) != null) {
// process the line.
line = line.trim();
if (line.length() > 0)
result.add(line);
}
}
catch (IOException e) {
throw new RuntimeException(e);
}
}
private static void loadDataFile(String file, Map result) {
try (InputStream is = Thread.currentThread().getContextClassLoader().getResourceAsStream("icd/" + file);
CSVReader reader = new CSVReaderBuilder(new InputStreamReader(is, StandardCharsets.US_ASCII)).withSkipLines(1).build()) {
for (String[] row : reader.readAll()) {
if (row.length != 8)
throw new RuntimeException("Was expecting 8 values, got " + row.length + " - " + Arrays.toString(row));
IcdO3Entry entry = new IcdO3Entry();
entry.setSourceCode(row[0]);
entry.setSite(row[1]);
entry.setHistology(row[2].isEmpty() ? null : row[2]);
entry.setBehavior(row[3].isEmpty() ? null : row[3]);
entry.setGrade(row[4].isEmpty() ? null : row[4]);
entry.setLaterality(row[5].isEmpty() ? null : row[5]);
entry.setReportable(row[6].isEmpty() ? null : row[6]);
entry.setSex(row[7].isEmpty() ? null : row[7]);
// the key will contain the sex if it's not blank in the data files (blank means the value applies for any sex value)
if (entry.getSex() != null)
result.put(entry.getSourceCode() + entry.getSex(), entry);
else
result.put(entry.getSourceCode(), entry);
}
}
catch (CsvException | IOException e) {
throw new RuntimeException(e);
}
}
}
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