prerna.rdf.main.LDCSDemoMaker Maven / Gradle / Ivy
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//package prerna.rdf.main;
//
//import java.io.FileInputStream;
//import java.io.IOException;
//import java.io.InputStream;
//import java.sql.Connection;
//import java.sql.DriverManager;
//import java.sql.PreparedStatement;
//import java.sql.Statement;
//import java.util.Properties;
//
//import org.apache.log4j.Logger;
//
//import prerna.algorithm.api.SemossDataType;
//import prerna.date.SemossDate;
//import prerna.poi.main.helper.CSVFileHelper;
//import prerna.test.TestUtilityMethods;
//import prerna.util.Constants;
//import prerna.util.DIHelper;
//import prerna.util.sql.AbstractSqlQueryUtil;
//import prerna.util.sql.RdbmsTypeEnum;
//import prerna.util.sql.SqlQueryUtilFactory;
//
//public class LDCSDemoMaker {
//
// private static Logger logger = Logger.getLogger(LDCSDemoMaker.class);
//
// private static final String DIR_SEPARATOR = java.nio.file.FileSystems.getDefault().getSeparator();
//
// private static final String CONFIGURATION_FILE = "config.properties";
// private static final String MYSQL_PASSWORD = "mysql_password";
// private static final String POSTGRES_PASSWORD = "postgres_password";
//
// private static final String VARCHAR_100 = "VARCHAR(100)";
// private static final String ENC_ID = "ENC_ID";
// private static final String ENCOUNTER = "ENCOUNTER";
// private static final String FLOAT = "FLOAT";
// static boolean useH2 = false;
//
// private static final String CLAIMS = "claims";
// static String[] claimsHeaders = new String[] {"BILLABLE_PERIOD", "DIAGNOSIS", ENC_ID, "ID", "ORGANIZATION", "SOCIAL_SECURITY_NUM", "TOTAL"};
// static String[] claimsTypes = new String[] {"DATE", VARCHAR_100, VARCHAR_100, VARCHAR_100, VARCHAR_100, VARCHAR_100, FLOAT};
//
// // ENCOUNTERS IS SLIGHTLY DIFFERENT
// // IT HAS THE THE PROC_DATE AS WELL
// private static final String ENCOUNTERS = "encounters";
// static String[] encountersHeaders = new String[] {"ENC_CD", "ENC_DESC", "ENC_DT", "ENC_REASON_CD", "ENC_REASON_DESC", ENC_ID, "SSN", "FACILITY" };
// static String[] encountersTypes = new String[] {VARCHAR_100, VARCHAR_100, VARCHAR_100, FLOAT, VARCHAR_100, VARCHAR_100, VARCHAR_100, VARCHAR_100};
//
// static String[] encountersFullHeaders = new String[] {"ENC_CD", "ENC_DESC", "ENC_DT", "ENC_REASON_CD", "ENC_REASON_DESC", ENC_ID, "SSN", "FACILITY", "PROC_DATE" };
// static String[] encountersFullTypes = new String[] {VARCHAR_100, VARCHAR_100, "DATE", FLOAT, VARCHAR_100, VARCHAR_100, VARCHAR_100, VARCHAR_100, "DATE"};
//
// /*
// * all the pampi files
// */
//
// static String[] allgergiesHeaders = new String[] {"ALL_CD", "ALL_DESC", "ALL_START", "ALL_STOP", "ENCNTR", "SSN"};
// static String[] allergiesTypes = new String[] {FLOAT, VARCHAR_100, "DATE", "DATE", VARCHAR_100, VARCHAR_100};
//
// static String[] careplansHeaders = new String[] {"CAR_CD", "CAR_DESC", "CAR_REASON_CD", "CAR_REASON_DESC", "CAR_START", "CAR_STOP", ENCOUNTER, "ID", "SOCIAL_SECURITY_NUMBER"};
// static String[] careplansTypes = new String[] {FLOAT, VARCHAR_100, FLOAT, VARCHAR_100, "DATE", "DATE", VARCHAR_100, VARCHAR_100, VARCHAR_100};
//
// static String[] conditionsHeaders = new String[] {"CON_CD", "CON_DESC", "CON_START", "CON_STOP", ENCOUNTER, "US_SOCIAL"};
// static String[] conditionsTypes = new String[] {FLOAT, VARCHAR_100, "DATE", "DATE", VARCHAR_100, VARCHAR_100};
//
// static String[] immunizationsHeaders = new String[] {ENCOUNTER, "IMM_CD", "IMM_DESC", "IMM_DT", "US_IDENTIFICATION_NUMBER"};
// static String[] immunizationsTypes = new String[] {VARCHAR_100, FLOAT, VARCHAR_100, "DATE", VARCHAR_100};
//
// static String[] medicationsHeaders = new String[] {"ENC", "MED_CD", "MED_DESC", "MED_REASON_DESC", "MED_START", "MED_STOP", "REASONDESCRIPTION", "SOCIAL_SECURITY"};
// static String[] medicationsTypes = new String[] {VARCHAR_100, FLOAT, VARCHAR_100, VARCHAR_100, "DATE", "DATE", VARCHAR_100, VARCHAR_100};
//
// static String[] observationsHeaders = new String[] {"ENC", "OBS_CD", "OBS_DESC", "OBS_DT", "SS_NUMBER", "UNITS", "VAL"};
// static String[] observationsTypes = new String[] {VARCHAR_100, VARCHAR_100, VARCHAR_100, "DATE", VARCHAR_100, VARCHAR_100, VARCHAR_100};
//
// private static final String PATIENTS = "patients";
// private static final String PATIENTS_CSV = "/patients.csv";
// static String[] patientsHeaders = new String[] {"ADDRESS", "BIRTHDATE", "BIRTHPLACE", "DEATHDATE", "DRIVERS", "ETHNICITY", "FIRST", "GENDER", "LAST", "MAIDEN", "MARITAL", "PASSPORT", "PREFIX", "RACE", "SOCIAL_SECURITY_NUMBER", "SUFFIX"};
// static String[] patientsTypes = new String[] {VARCHAR_100, VARCHAR_100, VARCHAR_100, VARCHAR_100, VARCHAR_100, VARCHAR_100, VARCHAR_100, VARCHAR_100, VARCHAR_100, VARCHAR_100, VARCHAR_100, VARCHAR_100, VARCHAR_100, VARCHAR_100, VARCHAR_100, VARCHAR_100};
//
// public static void main(String[] args) throws Exception {
// String basePath = "C:\\workspace\\Semoss_Dev";
// TestUtilityMethods.loadAll(basePath + "\\RDF_Map.prop");
//
// long start = System.currentTimeMillis();
//
// // load the database
// Connection cabacusMtf = null;
// Connection cabacusMaster = null;
// Connection pampi = null;
//
// AbstractSqlQueryUtil postgresHelper = SqlQueryUtilFactory.initialize(RdbmsTypeEnum.POSTGRES);
// AbstractSqlQueryUtil mySqlHelper = SqlQueryUtilFactory.initialize(RdbmsTypeEnum.MYSQL);
//
// if(useH2) {
// // NOTE ::: THESE USE THE basePath VARIABLE TO WRITE THE FILE!!!
// // THIS WILL MAKE A master.database, mtf.database, and pampi.database in that folder
// // and you can drag n drop the h2 file in the upload UI
// cabacusMtf = getH2CabacusMTF(basePath);
// cabacusMaster = getH2CabacusMaster(basePath);
// pampi = getH2Nemesis(basePath);
//
// // reassign to H2 anyway... dont worry about name
// postgresHelper = SqlQueryUtilFactory.initialize(RdbmsTypeEnum.H2_DB);
// mySqlHelper = SqlQueryUtilFactory.initialize(RdbmsTypeEnum.H2_DB);
// } else {
// cabacusMtf = getCabacusMTF();
// cabacusMaster = getCabacusMaster();
// pampi = getNemesis();
// }
//
// if (cabacusMtf != null) {
// cabacusMtf.setAutoCommit(false);
// }
//
// if (cabacusMaster != null) {
// cabacusMaster.setAutoCommit(false);
// }
//
// if (pampi !=null) {
// pampi.setAutoCommit(false);
// }
//
// String directory = "C:\\Users\\mahkhalil\\Desktop\\PAMPI";
//
// // first, CABACUS_MTF
// // need to load 2 different files
// {
// // claims
// {
// String file = directory + "/subset_claims.csv";
// CSVFileHelper helper = new CSVFileHelper();
// helper.parse(file);
// loadCsvFile(cabacusMtf, postgresHelper, helper, CLAIMS, claimsHeaders, claimsTypes);
// }
// // encounters
// {
// String file = directory + "/subset_encounters.csv";
// CSVFileHelper helper = new CSVFileHelper();
// helper.parse(file);
// loadCsvFile(cabacusMtf, postgresHelper, helper, ENCOUNTERS, encountersHeaders, encountersTypes);
// }
// // patients
// {
// String file = directory + PATIENTS_CSV;
// CSVFileHelper helper = new CSVFileHelper();
// helper.parse(file);
// loadCsvFile(cabacusMtf, postgresHelper, helper, PATIENTS, patientsHeaders, patientsTypes);
// }
// }
//
// // second, CABACUS_Master
// // need to load 2 different files
// {
// // claims
// {
// String file = directory + "/claims.csv";
// CSVFileHelper helper = new CSVFileHelper();
// helper.parse(file);
// loadCsvFile(cabacusMaster, mySqlHelper, helper, CLAIMS, claimsHeaders, claimsTypes);
// }
// // also load the other claims information as well
// {
// String file = directory + "/subset_claims.csv";
// CSVFileHelper helper = new CSVFileHelper();
// helper.parse(file);
// loadCsvFile(cabacusMaster, mySqlHelper, helper, CLAIMS, claimsHeaders, claimsTypes, false);
// }
// // encounters
// {
// String file = directory + "/encounters.csv";
// CSVFileHelper helper = new CSVFileHelper();
// helper.parse(file);
// loadCsvFile(cabacusMaster, mySqlHelper, helper, ENCOUNTERS, encountersFullHeaders, encountersFullTypes);
// }
// // patients
// {
// String file = directory + PATIENTS_CSV;
// CSVFileHelper helper = new CSVFileHelper();
// helper.parse(file);
// loadCsvFile(cabacusMaster, mySqlHelper, helper, PATIENTS, patientsHeaders, patientsTypes);
// }
// }
//
// // PAMPI
// {
// // allergies
// {
// String file = directory + "/allergies.csv";
// CSVFileHelper helper = new CSVFileHelper();
// helper.parse(file);
// loadCsvFile(pampi, mySqlHelper, helper, "allergies", allgergiesHeaders, allergiesTypes);
// }
// // careplans
// {
// String file = directory + "/careplans.csv";
// CSVFileHelper helper = new CSVFileHelper();
// helper.parse(file);
// loadCsvFile(pampi, mySqlHelper, helper, "careplans", careplansHeaders, careplansTypes);
// }
// // conditions
// {
// String file = directory + "/conditions.csv";
// CSVFileHelper helper = new CSVFileHelper();
// helper.parse(file);
// loadCsvFile(pampi, mySqlHelper, helper, "conditions", conditionsHeaders, conditionsTypes);
// }
// // immunizations
// {
// String file = directory + "/immunizations.csv";
// CSVFileHelper helper = new CSVFileHelper();
// helper.parse(file);
// loadCsvFile(pampi, mySqlHelper, helper, "immunizations", immunizationsHeaders, immunizationsTypes);
// }
// // medications
// {
// String file = directory + "/medications.csv";
// CSVFileHelper helper = new CSVFileHelper();
// helper.parse(file);
// loadCsvFile(pampi, mySqlHelper, helper, "medications", medicationsHeaders, medicationsTypes);
// }
// // observations
// {
// String file = directory + "/observations.csv";
// CSVFileHelper helper = new CSVFileHelper();
// helper.parse(file);
// loadCsvFile(pampi, mySqlHelper, helper, "observations", observationsHeaders, observationsTypes);
// }
// // patients
// {
// String file = directory + PATIENTS_CSV;
// CSVFileHelper helper = new CSVFileHelper();
// helper.parse(file);
// loadCsvFile(pampi, mySqlHelper, helper, PATIENTS, patientsHeaders, patientsTypes);
// }
// }
//
// if (cabacusMtf != null) {
// cabacusMtf.commit();
// }
//
// if (cabacusMaster != null) {
// cabacusMaster.commit();
// }
//
// if (pampi !=null) {
// pampi.commit();
// }
//
// long end = System.currentTimeMillis();
// logger.debug("Time to finish = " + (end - start) + "ms");
// }
//
// private static void loadCsvFile(Connection conn, AbstractSqlQueryUtil queryUtil, CSVFileHelper helper, String tableName, String[] columnNames, String[] types) throws Exception {
// loadCsvFile(conn, queryUtil, helper, tableName, columnNames, types, true);
// }
//
// private static void loadCsvFile(Connection conn, AbstractSqlQueryUtil queryUtil, CSVFileHelper helper, String tableName, String[] columnNames, String[] types, boolean remake) throws Exception {
// if(remake) {
// // drop table if exists
// {
// String createTable = queryUtil.dropTableIfExists(tableName);
// Statement stmt = conn.createStatement();
// stmt.execute(createTable);
// stmt.close();
// }
//
// // create table if not exists
// {
// String createTable = queryUtil.createTableIfNotExists(tableName, columnNames, types);
// Statement stmt = conn.createStatement();
// stmt.execute(createTable);
// stmt.close();
// }
// }
//
// String bulkInsert = queryUtil.createInsertPreparedStatementString(tableName, columnNames);
// PreparedStatement ps = conn.prepareStatement(bulkInsert);
//
// SemossDataType[] sTypes = new SemossDataType[types.length];
// for(int i = 0; i < types.length; i++) {
// sTypes[i] = SemossDataType.convertStringToDataType(types[i]);
// }
//
// int counter = 0;
// String[] row = null;
// while( (row = helper.getNextRow()) != null ) {
// for(int i = 0; i < row.length; i++) {
// String value = row[i];
//
// if(sTypes[i] == SemossDataType.STRING) {
// if(value.equals("NaN")) {
// ps.setNull(i+1, java.sql.Types.VARCHAR);
// } else {
// ps.setString(i+1, value);
// }
//
//
// } else if(sTypes[i] == SemossDataType.DOUBLE) {
// if(value.isEmpty() || value.equals("NaN")) {
// ps.setNull(i+1, java.sql.Types.DOUBLE);
// } else {
// Double d = Double.parseDouble(value);
// ps.setDouble(i+1, d);
// }
//
//
// } else if(sTypes[i] == SemossDataType.INT) {
// if(value.isEmpty() || value.equals("NaN")) {
// ps.setNull(i+1, java.sql.Types.INTEGER);
// } else {
// Integer d = Integer.parseInt(value);
// ps.setInt(i+1, d);
// }
//
//
// } else if(sTypes[i] == SemossDataType.DATE) {
// if(value.isEmpty() || value.equals("NaN")) {
// ps.setNull(i+1, java.sql.Types.DATE);
// } else {
// SemossDate date = SemossDate.genDateObj(value);
// ps.setDate(i+1, java.sql.Date.valueOf(date.getFormatted("yyyy-MM-dd")));
// }
//
// }
// }
//
// ps.addBatch();
// if(++counter % 1000 == 0) {
// logger.debug(tableName + " Executing batch row num = " + counter);
// ps.executeBatch();
// }
// }
//
// // execute whatever left over
// ps.executeBatch();
// logger.debug("Done with " + tableName + " total rows = " + counter);
// }
//
// /**
// * THIS WILL RETURN THE POSTGRES CABACUS_MTF SCHEMA
// * @return
// */
// private static Connection getCabacusMTF() throws Exception {
// Class.forName(RdbmsTypeEnum.POSTGRES.getDriver());
// String connectionUrl = RdbmsTypeEnum.POSTGRES.getUrlPrefix() + "://localhost:5432/postgres?currentSchema=mtf";
// Connection conn = null;
//
// try(InputStream input = new FileInputStream(DIHelper.getInstance().getProperty(Constants.BASE_FOLDER) + DIR_SEPARATOR + CONFIGURATION_FILE)) {
// Properties prop = new Properties();
// prop.load(input);
// conn = DriverManager.getConnection(connectionUrl, "postgres", prop.getProperty(POSTGRES_PASSWORD));
// } catch (IOException ex) {
// logger.error("Error with loading properties in config file for Postgres CABACUS_MTF Schema" + ex.getMessage());
// }
//
// return conn;
// }
//
// /**
// * THIS WILL RETURN THE MYSQL CABACUS_MASTER SCHEMA
// * @return
// */
// private static Connection getCabacusMaster() throws Exception {
// Class.forName(RdbmsTypeEnum.MYSQL.getDriver());
// String connectionUrl = RdbmsTypeEnum.MYSQL.getUrlPrefix() + "://localhost:3306/master";
// Connection conn = null;
//
// try(InputStream input = new FileInputStream(DIHelper.getInstance().getProperty(Constants.BASE_FOLDER) + DIR_SEPARATOR + CONFIGURATION_FILE)) {
// Properties prop = new Properties();
// prop.load(input);
// conn = DriverManager.getConnection(connectionUrl, "root", prop.getProperty(MYSQL_PASSWORD));
// } catch (IOException ex) {
// logger.error("Error with loading properties in config file for MySQL CABACUS_MASTER Schema" + ex.getMessage());
// }
//
// return conn;
// }
//
// /**
// * THIS WILL RETURN THE MYSQL PAMPI
// * @return
// */
// private static Connection getNemesis() throws Exception {
// Class.forName(RdbmsTypeEnum.MYSQL.getDriver());
// String connectionUrl = RdbmsTypeEnum.MYSQL.getUrlPrefix() + "://localhost:3306/pampi";
// Connection conn = null;
//
// try(InputStream input = new FileInputStream(DIHelper.getInstance().getProperty(Constants.BASE_FOLDER) + DIR_SEPARATOR + CONFIGURATION_FILE)) {
// Properties prop = new Properties();
// prop.load(input);
// conn = DriverManager.getConnection(connectionUrl, "root", prop.getProperty(MYSQL_PASSWORD));
// } catch (IOException ex) {
// logger.error("Error with loading properties in config file for MySQL PAMPI" + ex.getMessage());
// }
//
// return conn;
// }
//
// /**
// * THIS WILL RETURN THE H2 CABACUS_MTF SCHEMA
// * @return
// */
// private static Connection getH2CabacusMTF(String basePath) throws Exception {
// Class.forName(RdbmsTypeEnum.H2_DB.getDriver());
// String connectionUrl = RdbmsTypeEnum.H2_DB.getUrlPrefix() + ":nio:" + basePath + "/mtf";
// Connection conn = DriverManager.getConnection(connectionUrl, "", "");
// return conn;
// }
//
// /**
// * THIS WILL RETURN TEHE H2 CABACUS_MASTER SCHEMA
// * @return
// */
// private static Connection getH2CabacusMaster(String basePath) throws Exception {
// Class.forName(RdbmsTypeEnum.H2_DB.getDriver());
// String connectionUrl = RdbmsTypeEnum.H2_DB.getUrlPrefix() + ":nio:" + basePath + "/master";
// Connection conn = DriverManager.getConnection(connectionUrl, "", "");
// return conn;
// }
//
// /**
// * THIS WILL RETURN THE H2 PAMPI
// * @return
// */
// private static Connection getH2Nemesis(String basePath) throws Exception {
// Class.forName(RdbmsTypeEnum.H2_DB.getDriver());
// String connectionUrl = RdbmsTypeEnum.H2_DB.getUrlPrefix() + ":nio:" + basePath + "/pampi";
// Connection conn = DriverManager.getConnection(connectionUrl, "", "");
// return conn;
// }
//
//
//}
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