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) CIRG, University of Washington, Seattle WA. All Rights Reserved. * */ package us.mn.state.health.lims.analyzerimport.analyzerreaders; 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 us.mn.state.health.lims.common.util.StringUtil; import java.util.ArrayList; import java.util.Formatter; import java.util.List; public class FACSCantoReader extends AnalyzerLineInserter { private static final String CONTROL_ACCESSION_PREFIX = "IMM"; private static final String SAMPLE_ID_HEADER = "Sample ID"; private static final String DATE_ANALYZED_HEADER = "Date Analyzed"; private static final String CD3_CD8_CD45_CD4_CD3_PER_LYMPHS_HEADER = "CD3/CD8/CD45/CD4 CD3+ %Lymphs"; private static final String CD3_CD8_CD45_CD4_CD3_CD4_PER_LYMPHS_HEADER = "CD3/CD8/CD45/CD4 CD3+CD4+ %Lymphs"; private static final String DATE_PATTERN = "MM/dd/yyyy HH:mm"; private int Sample_ID; private int Date_Analyzed; private int CD3_CD8_CD45_CD4_CD3_perLymphs; private int CD3_CD8_CD45_CD4_CD3_CD4_perLymphs; private String[] testNameIndex; private String[] unitsIndex; private int maxViewedIndex = 0; public boolean insert(List<String> lines, String currentUserId) { boolean successful = true; List<AnalyzerResults> results = new ArrayList<AnalyzerResults>(); manageColumns(lines.get(0)); 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 manageColumns(String line) { String[] fields = StringUtil.separateCSVWithEmbededQuotes(line); if (fields.length < 10) { fields = line.split(","); } for (int i = 0; i < fields.length; i++) { String header = fields[i].replace("\"", ""); if (SAMPLE_ID_HEADER.equals(header)) { Sample_ID = i; maxViewedIndex = Math.max(maxViewedIndex, i); } else if (DATE_ANALYZED_HEADER.equals(header)) { Date_Analyzed = i; maxViewedIndex = Math.max(maxViewedIndex, i); } else if (CD3_CD8_CD45_CD4_CD3_CD4_PER_LYMPHS_HEADER.equals(header)) { CD3_CD8_CD45_CD4_CD3_CD4_perLymphs = i; maxViewedIndex = Math.max(maxViewedIndex, i); } else if (CD3_CD8_CD45_CD4_CD3_PER_LYMPHS_HEADER.equals(header)) { CD3_CD8_CD45_CD4_CD3_perLymphs = i; maxViewedIndex = Math.max(maxViewedIndex, i); } } testNameIndex = new String[fields.length]; unitsIndex = new String[fields.length]; testNameIndex[CD3_CD8_CD45_CD4_CD3_perLymphs] = "CD3_PER"; testNameIndex[CD3_CD8_CD45_CD4_CD3_CD4_perLymphs] = "CD4_PER"; unitsIndex[CD3_CD8_CD45_CD4_CD3_perLymphs] = "%"; unitsIndex[CD3_CD8_CD45_CD4_CD3_CD4_perLymphs] = "%"; } private void addAnalyzerResultFromLine(List<AnalyzerResults> results, String line) { String[] fields = StringUtil.separateCSVWithMixedEmbededQuotes(line); //This insures that the row has not been truncated if (fields.length < maxViewedIndex) { return; } AnalyzerReaderUtil readerUtil = new AnalyzerReaderUtil(); String analyzerAccessionNumber = fields[Sample_ID].replace("\"", ""); analyzerAccessionNumber = StringUtil.strip(analyzerAccessionNumber, " "); String date = fields[Date_Analyzed].replace("\"", ""); //this is sort of dumb, we have the indexes we are interested in for (int i = 0; i < testNameIndex.length; i++) { if (!GenericValidator.isBlankOrNull(testNameIndex[i])) { MappedTestName mappedName = AnalyzerTestNameCache.instance() .getMappedTest(AnalyzerTestNameCache.FACSCANTO, testNameIndex[i].replace("\"", "")); if (mappedName == null) { mappedName = AnalyzerTestNameCache.instance().getEmptyMappedTestName( AnalyzerTestNameCache.FACSCANTO, testNameIndex[i].replace("\"", "")); } AnalyzerResults analyzerResults = new AnalyzerResults(); analyzerResults.setAnalyzerId(mappedName.getAnalyzerId()); String result = fields[i].replace("\"", ""); result = roundTwoDigits(result); analyzerResults.setResult(result); analyzerResults.setUnits(unitsIndex[i]); analyzerResults.setCompleteDate( DateUtil.convertStringDateToTimestampWithPatternNoLocale(date, DATE_PATTERN)); //analyzerResults.setCompleteTime(DateUtil.convertStringDateToTimestamp(date)); analyzerResults.setTestId(mappedName.getTestId()); analyzerResults.setAccessionNumber(analyzerAccessionNumber); analyzerResults.setTestName(mappedName.getOpenElisTestName()); if (analyzerAccessionNumber != null) { analyzerResults.setIsControl(analyzerAccessionNumber.startsWith(CONTROL_ACCESSION_PREFIX)); } else { analyzerResults.setIsControl(false); } results.add(analyzerResults); AnalyzerResults resultFromDB = readerUtil.createAnalyzerResultFromDB(analyzerResults); if (resultFromDB != null) { results.add(resultFromDB); } } } } private String roundTwoDigits(String result) { try { Double doubleResult = Double.parseDouble(result); StringBuilder sb = new StringBuilder(); Formatter formatter = new Formatter(sb); formatter.format("%.2f", (Math.rint(doubleResult * 100.0) / 100.0)); return sb.toString(); } catch (NumberFormatException e) { return result; } } @Override public String getError() { return "FacsCANTO analyzer unable to write to database"; } }