Java tutorial
/** * The contents of this file are subject to the Mozilla Public License * Version 1.1 (the "License"); you may not use this file except in * compliance with the License. You may obtain a copy of the License at * http://www.mozilla.org/MPL/ * * Software distributed under the License is distributed on an "AS IS" * basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the * License for the specific language governing rights and limitations under * the License. * * The Original Code is OpenELIS code. * * Copyright (C) The Minnesota Department of Health. All Rights Reserved. * * Contributor(s): CIRG, University of Washington, Seattle WA. */ package oe.plugin.analyzer; import org.apache.commons.validator.GenericValidator; import org.hibernate.Transaction; import us.mn.state.health.lims.analyzerimport.util.AnalyzerTestNameCache; import us.mn.state.health.lims.analyzerimport.util.MappedTestName; import us.mn.state.health.lims.analyzerresults.valueholder.AnalyzerResults; import us.mn.state.health.lims.common.exception.LIMSRuntimeException; import us.mn.state.health.lims.common.util.DateUtil; import us.mn.state.health.lims.common.util.HibernateProxy; import java.sql.Timestamp; import java.util.ArrayList; import java.util.List; import us.mn.state.health.lims.analyzerimport.analyzerreaders.AnalyzerLineInserter; import us.mn.state.health.lims.analyzerimport.analyzerreaders.AnalyzerReaderUtil; @SuppressWarnings("unused") public class SysmeXTImplementation extends AnalyzerLineInserter { private static final String CONTROL_ACCESSION_PREFIX = "QC-"; private static int index = 0; private static final int ID_INSTRUMENT = index++; private static final int DATE = index++; private static final int TIME = index++; private static final int RACK = index++; private static final int TUBE = index++; private static final int ACCESSION = index++; private static final int ACCESSION_INFO = index++; private static final int METHOD = index++; private static final int ID_PATIENT = index++; private static final int ANALYSIS_INFO = index++; private static final int POS_NEG = index++; private static final int POS_DIFF = index++; private static final int POS_MORF = index++; private static final int POS_COMP = index++; private static final int ERR_FUNC = index++; private static final int ERR_RESULT = index++; private static final int INFO_REQUEST = index++; private static final int GB_ABNORMAL = index++; private static final int GB_SUSPICIOUS = index++; private static final int GR_ABNORMAL = index++; private static final int GR_SUSPICIOUS = index++; private static final int PLQ_ABNORMAL = index++; private static final int PLQ_SUSPICIOUS = index++; private static final int INFO_UNITS = index++; private static final int INFO_PLQ = index++; private static final int VALID = index++; private static final int RET_MESSAGES = index++; private static final int DELTA_MESSAGES = index++; private static final int SAMPLE_COMMENT = index++; private static final int PATIENT_NAME = index++; private static final int PATIENT_BIRTH_DATE = index++; private static final int PATIENT_GENDER = index++; private static final int PATIENT_COMMENT = index++; private static final int SERVICE = index++; private static final int MEDS = index++; private static final int TRANSMISSION_PARMS = index++; private static final int SEQUENECE_COUNT = index++; private static final int GB_10_uL = index++; private static final int GB_M = index++; private static final int GR_100000_uL = index++; private static final int GR_M = index++; private static final int HBG_g_L = index++; private static final int HBG_M = index++; private static final int HCT_10_NEG_1_PER = index++; private static final int HCT_M = index++; private static final int VGM_10_NEG_1_fL = index++; private static final int VGM_M = index++; private static final int TCMH_10_NEG_1_pg = index++; private static final int TCMH_M = index++; private static final int CCMH_g_L = index++; private static final int CCMH_M = index++; private static final int PLQ_10_3_uL = index++; private static final int PLQ_M = index++; private static final int IDR_SD_10_NEG_1_fL = index++; private static final int IDR_SD_M = index++; private static final int IDR_CV_10_NEG_1_PER = index++; private static final int IDR_CV_M = index++; private static final int IDP = index++; private static final int IDP_M = index++; private static final int VPM_10_NEG_1_fL = index++; private static final int VPM_M = index++; private static final int P_RGC_10_NEG_1_PER = index++; private static final int P_RGC_M = index++; private static final int PCT_10_NEG_2_PER = index++; private static final int PCT_M = index++; private static final int NEUT_COUNT_10_uL = index++; private static final int NEUT_COUNT_M = index++; private static final int LYMPH_COUNT_10_uL = index++; private static final int LYMPH_COUNT_M = index++; private static final int MONO_COUNT_10_uL = index++; private static final int MONO_COUNT_M = index++; private static final int EO_COUNT_10_uL = index++; private static final int EO_COUNT_M = index++; private static final int BASO_COUNT_10_uL = index++; private static final int BASO_COUNT_M = index++; private static final int NEUT_PER_10_NEG_1_PER = index++; private static final int NEUT_PER_M = index++; private static final int LYMPH_PER_10_NEG_1_PER = index++; private static final int LYMPH_PER_M = index++; private static final int MONO_PER_10_NEG_1_PER = index++; private static final int MONO_PER_M = index++; private static final int EO_PER_10_NEG_1_PER = index++; private static final int EO_PER_M = index++; private static final int BASO_PER_10_NEG_1_PER = index++; private static final int BASO_PER_M = index++; private static final int RET_COUNT_10_2_uL = index++; private static final int RET_COUNT_M = index++; private static final int RET_PER_10_NEG_2_PER = index++; private static final int RET_PER_M = index++; private static final int LFR_10_NEG_1_PER = index++; private static final int LFR_M = index++; private static final int MFR_10_NEG_1_PER = index++; private static final int MFR_M = index++; private static final int HFR_10_NEG_1_PER = index++; private static final int HFR_M = index++; private static final int IRF_10_NEG_1_PER = index++; private static final int IRF_M = index++; private static final int IG_COUNT_10_uL = index++; private static final int IG_COUNT_M = index++; private static final int IG_PER_10_NEG_1_PER = index++; private static final int IG_PER_M = index++; private static final int NEUT_COUNT_AND_10_uL = index++; private static final int NEUT_COUNT_AND_M = index++; private static final int NEUT_PER_AND_10_NEG_1_PER = index++; private static final int NEUT_PER_AND_M = index++; private static final int NRBC_PLUS_W_10_uL = index++; private static final int NRBC_PLUS_W_M = index++; private static final int LYMPH_COUNT_AND_10_uL = index++; private static final int LYMPH_COUNT_AND_M = index++; private static final int LYMPH_PER_AND_10_NEG_1_PER = index++; private static final int LYMPH_PER_AND_M = index++; private static final int OTHER_COUNT_10_uL = index++; private static final int OTHER_COUNT_M = index++; private static final int OTHER_PER_10_NEG_1_PER = index++; private static final int OTHER_PER_M = index++; private static final int GR_O_10_4_uL = index++; private static final int GR_O_M = index++; private static final int PLQ_O_10_3_uL = index++; private static final int PLQ_O_M = index++; private static final int IP_Abn_GB_Scatterg_GB_Anorm = index++; private static final int IP_Abn_GB_NEUTROPENIA = index++; private static final int IP_Abn_GB_NEUTROPHILIE = index++; private static final int IP_Abn_GB_LYMPHOPENIA = index++; private static final int IP_Abn_GB_LYMPHCYTOSIS = index++; private static final int IP_Abn_GB_MONOCYTOSIS = index++; private static final int IP_Abn_GB_EOSINOPHILIE = index++; private static final int IP_Abn_GB_BASOPHILIE = index++; private static final int IP_Abn_GB_LEUCOPENIA = index++; private static final int IP_Abn_GB_LEUCOCYTOSIS = index++; private static final int IP_Abn_GR_Dist_GR_An = index++; private static final int IP_Abn_GR_D_pop_GR = index++; private static final int IP_Abn_GR_ANISOCYTOSIS = index++; private static final int IP_Abn_GR_MICROCYTOSIS = index++; private static final int IP_Abn_GR_MACROCYTOSIS = index++; private static final int IP_Abn_GR_HYPOCHROMIA = index++; private static final int IP_Abn_GR_ANEMIA = index++; private static final int IP_Abn_GR_ERYTHROCYTOSIS = index++; private static final int IP_Abn_GR_Scatterg_RET_Anorm = index++; private static final int IP_Abn_GR_RETICULOCYTOSIS = index++; private static final int IP_Abn_PLQ_Dist_PLQ_An = index++; private static final int IP_Abn_PLQ_THROMBOCYTOPENIA = index++; private static final int IP_Abn_PLQ_THROMBOCYTOSIS = index++; private static final int IP_Abn_PLQ_Scatterg_PLQ_Anorm = index++; private static final int IP_SUS_GB_Blasts = index++; private static final int IP_SUS_GB_Gra_Immat = index++; private static final int IP_SUS_GB_Dev_Gauche = index++; private static final int IP_SUS_GB_Lympho_Aty = index++; private static final int IP_SUS_GB_Anor_Ly_Blasts = index++; private static final int IP_SUS_GB_NRBC = index++; private static final int IP_SUS_GB_Rs_GR_Lyse=index++; private static final int IP_SUS_GR_Agglut_GR = index++; private static final int IP_SUS_GR_Turb_HGB_Interf = index++; private static final int IP_SUS_GR_IRON_DEFICIENCY = index++; private static final int IP_SUS_GR_Def_HGB = index++; private static final int IP_SUS_GR_Fragments = index++; private static final int IP_SUS_PLQ_Agg_PLQ = index++; private static final int IP_SUS_PLQ_Agg_PLQ_S = index++; private static final int DEFAULT_INFO = index++; private static final int Qflag_Blasts = index++; private static final int Qflag_Gra_Immat = index++; private static final int Qflag_Dev_Gauche = index++; private static final int Qflag_Lympho_Aty = index++; private static final int Qflag_NRBC = index++; private static final int Qflag_Abn_Ly_Bla = index++; private static final int Qflag_Rs_GR_Lysis=index++; private static final int Qflag_Agglut_GR = index++; private static final int Qflag_Turb_HGB = index++; private static final int Qflag_IRON_DEFICIENCY = index++; private static final int Qflag_Def_HGB = index++; private static final int Qflag_Fragments = index++; private static final int Qflag_Agg_PLQ = index++; private static final int Qflag_Agg_PLQ_S = index++; private static final int columns = index++; private static final String DELIMITER = ","; private static final String DATE_PATTERN = "yyyy/MM/dd HH:mm:ss"; private static String[] testNameIndex = new String[columns]; private static String[] unitsIndex = new String[columns]; private static Boolean[] readOnlyIndex = new Boolean[columns]; private static int[] scaleIndex = new int[columns]; private static int[] orderedTestIndexs = new int[18]; { testNameIndex[GB_10_uL] = "GB_10_uL"; testNameIndex[GR_100000_uL] = "GR_100000_uL"; testNameIndex[NEUT_PER_10_NEG_1_PER] = "NEUT_PER_10_NEG_1_PER"; testNameIndex[HBG_g_L] = "HBG_g_L"; testNameIndex[LYMPH_PER_10_NEG_1_PER] = "LYMPH_PER_10_NEG_1_PER"; testNameIndex[HCT_10_NEG_1_PER] = "HCT_10_NEG_1_PER"; testNameIndex[MONO_PER_10_NEG_1_PER] = "MONO_PER_10_NEG_1_PER"; testNameIndex[VGM_10_NEG_1_fL] = "VGM_10_NEG_1_fL"; testNameIndex[EO_PER_10_NEG_1_PER] = "EO_PER_10_NEG_1_PER"; testNameIndex[TCMH_10_NEG_1_pg] = "TCMH_10_NEG_1_pg"; testNameIndex[BASO_PER_10_NEG_1_PER] = "BASO_PER_10_NEG_1_PER"; testNameIndex[CCMH_g_L] = "CCMH_g_L"; testNameIndex[PLQ_10_3_uL] = "PLQ_10_3_uL"; testNameIndex[NEUT_COUNT_10_uL] = "NEUT_COUNT_10_uL"; testNameIndex[MONO_COUNT_10_uL] = "MONO_COUNT_10_uL"; testNameIndex[BASO_COUNT_10_uL] = "BASO_COUNT_10_uL"; testNameIndex[LYMPH_COUNT_10_uL] = "LYMPH_COUNT_10_uL"; testNameIndex[EO_COUNT_10_uL] = "EO_COUNT_10_uL"; unitsIndex[GB_10_uL] = "10^3/ul"; unitsIndex[GR_100000_uL] = "10^6/ul"; unitsIndex[NEUT_PER_10_NEG_1_PER] = "%"; unitsIndex[HBG_g_L] = "g/dl"; unitsIndex[LYMPH_PER_10_NEG_1_PER] = "%"; unitsIndex[HCT_10_NEG_1_PER] = "%"; unitsIndex[MONO_PER_10_NEG_1_PER] = "%"; unitsIndex[VGM_10_NEG_1_fL] = "fl"; unitsIndex[EO_PER_10_NEG_1_PER] = "%"; unitsIndex[TCMH_10_NEG_1_pg] = "pg"; unitsIndex[BASO_PER_10_NEG_1_PER] = "%"; unitsIndex[CCMH_g_L] = "g/dl"; unitsIndex[PLQ_10_3_uL] = "10^3/ul"; unitsIndex[NEUT_COUNT_10_uL] = "10^3/ul"; unitsIndex[MONO_COUNT_10_uL] = "10^3/ul"; unitsIndex[BASO_COUNT_10_uL] = "10^3/ul"; unitsIndex[LYMPH_COUNT_10_uL] = "10^3/ul"; unitsIndex[EO_COUNT_10_uL] = "10^3/ul"; for (int i = 0; i < readOnlyIndex.length; i++) { readOnlyIndex[i] = Boolean.FALSE; } /* readOnlyIndex[NEUT_COUNT_10_uL] = Boolean.TRUE; readOnlyIndex[MONO_COUNT_10_uL] = Boolean.TRUE; readOnlyIndex[BASO_COUNT_10_uL] = Boolean.TRUE; readOnlyIndex[LYMPH_COUNT_10_uL] = Boolean.TRUE; readOnlyIndex[EO_COUNT_10_uL] = Boolean.TRUE; */ scaleIndex[GB_10_uL] = 100; scaleIndex[GR_100000_uL] = 100; scaleIndex[NEUT_PER_10_NEG_1_PER] = 10; scaleIndex[HBG_g_L] = 10; scaleIndex[LYMPH_PER_10_NEG_1_PER] = 10; scaleIndex[HCT_10_NEG_1_PER] = 10; scaleIndex[MONO_PER_10_NEG_1_PER] = 10; scaleIndex[VGM_10_NEG_1_fL] = 10; scaleIndex[EO_PER_10_NEG_1_PER] = 10; scaleIndex[TCMH_10_NEG_1_pg] = 10; scaleIndex[BASO_PER_10_NEG_1_PER] = 10; scaleIndex[CCMH_g_L] = 10; scaleIndex[PLQ_10_3_uL] = 1; scaleIndex[NEUT_COUNT_10_uL] = 100; scaleIndex[MONO_COUNT_10_uL] = 100; scaleIndex[BASO_COUNT_10_uL] = 100; scaleIndex[LYMPH_COUNT_10_uL] = 100; scaleIndex[EO_COUNT_10_uL] = 100; orderedTestIndexs[0] = GB_10_uL; orderedTestIndexs[1] = GR_100000_uL; orderedTestIndexs[13] = NEUT_PER_10_NEG_1_PER; orderedTestIndexs[2] = HBG_g_L; orderedTestIndexs[14] = LYMPH_PER_10_NEG_1_PER; orderedTestIndexs[3] = HCT_10_NEG_1_PER; orderedTestIndexs[15] = MONO_PER_10_NEG_1_PER; orderedTestIndexs[4] = VGM_10_NEG_1_fL; orderedTestIndexs[16] = EO_PER_10_NEG_1_PER; orderedTestIndexs[5] = TCMH_10_NEG_1_pg; orderedTestIndexs[17] = BASO_PER_10_NEG_1_PER; orderedTestIndexs[6] = CCMH_g_L; orderedTestIndexs[7] = PLQ_10_3_uL; orderedTestIndexs[8] = NEUT_COUNT_10_uL; orderedTestIndexs[10] = MONO_COUNT_10_uL; orderedTestIndexs[12] = BASO_COUNT_10_uL; orderedTestIndexs[9] = LYMPH_COUNT_10_uL; orderedTestIndexs[11] = EO_COUNT_10_uL; } public boolean insert(List<String> lines, String currentUserId) { boolean successful = true; List<AnalyzerResults> results = new ArrayList<AnalyzerResults>(); for (int i = 1; i < lines.size(); i++) { addAnalyzerResultFromLine(results, lines.get(i)); } if (results.size() > 0) { Transaction tx = HibernateProxy.beginTransaction(); try { persistResults(results, currentUserId); tx.commit(); } catch (LIMSRuntimeException lre) { tx.rollback(); successful = false; } finally { HibernateProxy.closeSession(); } } return successful; } private void addAnalyzerResultFromLine(List<AnalyzerResults> results, String line) { String[] fields = line.split(DELIMITER); AnalyzerReaderUtil readerUtil = new AnalyzerReaderUtil(); String analyzerAccessionNumber = fields[ID_PATIENT]; //Timestamp timestamp = DateUtil.convertStringDateToTimestampWithPattern(fields[DATE] + " " + fields[TIME], DATE_PATTERN); Timestamp timestamp = DateUtil.convertStringDateToTimestampWithPattern(fields[DATE] + " " + fields[TIME], DATE_PATTERN); List<AnalyzerResults> readOnlyResults = new ArrayList<AnalyzerResults>(); //the reason for the indirection is to get the order of tests correct for (int i = 0; i < orderedTestIndexs.length; i++) { int testIndex = orderedTestIndexs[i]; if (!GenericValidator.isBlankOrNull(testNameIndex[testIndex])) { MappedTestName mappedName = AnalyzerTestNameCache.instance().getMappedTest("SysmeXT", testNameIndex[testIndex]); if (mappedName == null) { mappedName = AnalyzerTestNameCache.instance().getEmptyMappedTestName("SysmeXT", testNameIndex[testIndex]); } AnalyzerResults analyzerResults = new AnalyzerResults(); analyzerResults.setAnalyzerId(mappedName.getAnalyzerId()); double result = Double.NaN; try { result = Double.parseDouble(fields[testIndex]) / scaleIndex[testIndex]; } catch (NumberFormatException nfe) { //no-op -- defaults to NAN } analyzerResults.setResult(String.valueOf(result)); analyzerResults.setUnits(unitsIndex[testIndex]); analyzerResults.setCompleteDate(timestamp); analyzerResults.setTestId(mappedName.getTestId()); analyzerResults.setAccessionNumber(analyzerAccessionNumber); analyzerResults.setTestName(mappedName.getOpenElisTestName()); analyzerResults.setReadOnly(readOnlyIndex[testIndex]); if (analyzerAccessionNumber != null) { analyzerResults.setIsControl(analyzerAccessionNumber.startsWith(CONTROL_ACCESSION_PREFIX)); } else { analyzerResults.setIsControl(false); } if (analyzerResults.isReadOnly()) { readOnlyResults.add(analyzerResults); } else { results.add(analyzerResults); } AnalyzerResults resultFromDB = readerUtil.createAnalyzerResultFromDB(analyzerResults); if (resultFromDB != null) { results.add(resultFromDB); } } } results.addAll(readOnlyResults); } @Override public String getError() { return "Sysmex analyzer unable to write to database"; } }