FacscaliburReader.java

/**
* 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 java.sql.Timestamp;
import java.util.ArrayList;
import java.util.List;

@SuppressWarnings("unused")
public class FacscaliburReader extends AnalyzerLineInserter {

	private static final String CONTROL_ACCESSION_PREFIX = "IMM";

	private static int index = 0;
	private static final int Institution = index++;
	private static final int Director = index++;
	private static final int Operator = index++;
	private static final int Cytometer = index++;
	private static final int Cytometer_Serial_Number = index++;
	private static final int Software_Version = index++;
	private static final int Sample_Name = index++;
	private static final int Sample_ID = index++;
	private static final int Case_Number = index++;
	private static final int Column_1 = index++;
	private static final int Column_2 = index++;
	private static final int Column_3 = index++;
	private static final int Panel_Name = index++;
	private static final int Collection_Date = index++;
	private static final int Date_Analyzed = index++;
	private static final int Lab_Report_File_Name = index++;
	private static final int Physicians_Report_File_Name = index++;
	private static final int WBC_Count_x1000 = index++;
	private static final int Lymphs_per = index++;
	private static final int Lymphs_x1000 = index++;
	private static final int Abs_Cnt_Bead_Name = index++;
	private static final int Abs_Cnt_Bead_Lot_ID = index++;
	private static final int Abs_Cnt_Beads_Pellet = index++;
	private static final int Control_Bead_Name = index++;
	private static final int Control_Bead_Lot_ID = index++;
	private static final int Control_Low_Beads_µL = index++;
	private static final int Control_Medium_Beads_µL = index++;
	private static final int Control_High_Beads_µL = index++;
	private static final int Control_Low_SD = index++;
	private static final int Control_Medium_SD = index++;
	private static final int Control_High_SD = index++;
	private static final int Ref_Range = index++;
	private static final int Comments = index++;
	private static final int Lymphosum = index++;
	private static final int CD3_per_Lymph_Difference = index++;
	private static final int T_Helper_Suppressor_Ratio = index++;
	private static final int Min_CD3_Abs_Cnt_Range = index++;
	private static final int Max_CD3_Abs_Cnt_Range = index++;
	private static final int Avg_CD3_CD4_per_T_Lymph = index++;
	private static final int Avg_CD3_CD8__per_T_Lymph = index++;
	private static final int Avg_CD3_CD4_CD8__per_T_Lymph = index++;
	private static final int Avg_CD3__per_Lymph = index++;
	private static final int Avg_CD3__Abs_Cnt = index++;
	private static final int Avg_CD3_CD4__per_Lymph = index++;
	private static final int Avg_CD3_CD4__Abs_Cnt = index++;
	private static final int Avg_CD3_CD8__per_Lymph = index++;
	private static final int Avg_CD3_CD8__Abs_Cnt = index++;
	private static final int Avg_CD3_CD4_CD8__per_Lymph = index++;
	private static final int Avg_CD3_CD4_CD8__Abs_Cnt = index++;
	private static final int Avg_CD19__per_Lymph = index++;
	private static final int Avg_CD19__Abs_Cnt = index++;
	private static final int Avg_CD16_56__per_Lymph = index++;
	private static final int Avg_CD16_56__Abs_Cnt = index++;
	private static final int CD45__Abs_Cnt = index++;
	private static final int CD3_CD4_CD45_FCS_File_Name = index++;
	private static final int CD3_CD4_CD45_Lot_ID = index++;
	private static final int CD3_CD4_CD45_Collection_Time = index++;
	private static final int CD3_CD4_CD45_Total_Events = index++;
	private static final int CD3_CD4_CD45_Tube_Name = index++;
	private static final int CD3_CD4_CD45_Attr_Def_File_Name = index++;
	private static final int CD3_CD4_CD45_Error_Codes = index++;
	private static final int CD3_CD4_CD45_Lymph_Events = index++;
	private static final int CD3_CD4_CD45_CD3__per_Lymph = index++;
	private static final int CD3_CD4_CD45_CD3__Abs_Cnt = index++;
	private static final int CD3_CD4_CD45_CD3_CD4__per_Lymph = index++;
	private static final int columns = index++;

	private static final String DELIMITER = "\t";

	private static final String DATE_PATTERN = "dd-MMMM-yy kk:mm:ss";
	private static final String ALT_DATE_PATTERN = "dd MMM yyyy KK:mm";
	private static String[] testNameIndex = new String[columns];
	private static String[] unitsIndex = new String[columns];

	{
		testNameIndex[Avg_CD3__per_Lymph] = "CD3_PER";
		testNameIndex[Avg_CD3_CD4__per_Lymph] = "CD4_PER";

		unitsIndex[Avg_CD3__per_Lymph] = "%";
		unitsIndex[Avg_CD3_CD4__per_Lymph] = "%";

	}

	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[Sample_ID];

		String date = fields[Collection_Date];

		for (int i = 0; i < testNameIndex.length; i++) {
			if (!GenericValidator.isBlankOrNull(testNameIndex[i])) {
				MappedTestName mappedName = AnalyzerTestNameCache.instance().getMappedTest(AnalyzerTestNameCache.FACSCALIBUR, testNameIndex[i]);

				if( mappedName == null){
					mappedName = AnalyzerTestNameCache.instance().getEmptyMappedTestName(AnalyzerTestNameCache.FACSCALIBUR, testNameIndex[i]);
				}

				AnalyzerResults analyzerResults = new AnalyzerResults();

				analyzerResults.setAnalyzerId(mappedName.getAnalyzerId());

				String result = fields[i];

				analyzerResults.setResult(result);
				analyzerResults.setUnits(unitsIndex[i]);
				String dateTime = date;
				Timestamp timestamp = getTimestampFromDate(dateTime);
				analyzerResults.setCompleteDate(timestamp);
				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 Timestamp getTimestampFromDate(String dateTime) {
		//Mixed date formats are sneaking in ie 24-Jul-12 15:07:09 or Mer 25 juil 2012 9:46
		if( dateTime.contains("-")){
			return DateUtil.convertStringDateToTimestampWithPatternNoLocale(dateTime , DATE_PATTERN);	
		}
		
		String[] dateSegs = dateTime.split(" ");
		String month = getCorrectedMonth( dateSegs[2] );
		
		String date = dateSegs[1] + " " + month + " " + dateSegs[3] + " " + dateSegs[4];
		
		return DateUtil.convertStringDateToTimestampWithPattern(date , ALT_DATE_PATTERN);	
	}

	//The analyzer is sending abbreviated months without the '.'
	private String getCorrectedMonth(String month) {
		if( month.endsWith(".") || month.equals("mars") || month.equals("mai") || month.equals("juin") || month.equals("août") ){
			return month;
		}
		
		return month + ".";
	}

	@Override
	public String getError() {
		return "Facscalibur analyzer unable to write to database";
	}
}