AnalyzerLineReader.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 us.mn.state.health.lims.plugin.AnalyzerImporterPlugin;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.util.ArrayList;
import java.util.List;

public class AnalyzerLineReader extends AnalyzerReader {

	private static final String COBAS_INDICATOR = "COBAS INTEGRA400";
	private static final CharSequence SYSMEX_XT_INDICATOR = "XT-2000";
	private static final CharSequence FACSCALIBUR_INDICATOR = "MultiSET";
	private static final CharSequence EVOLIS_INTEGRAL_INDICATOR = "DBehring Enzygnost HIV integral II";
	private static final CharSequence EVOLIS_INTEGRAL_DBS_INDICATOR = "DBehring Enzygnost HIV integral IIDBS";
	private static final CharSequence EVOLIS_MUREX_INDICATOR = "Murex HIV 1_2";
	private static final CharSequence EVOLIS_MUREX_DBS_INDICATOR = "Murex HIV 1_2 DBS";
	private static final CharSequence COBAS_TAQMAN_INDICATOR = "HIV-HPS";
	private static final CharSequence COBAS_TAQMAN_INDICATOR_2 = "HIVHP2";
	private static final CharSequence COBAS_TAQMAN_INDICATOR_3 = "HI2CAP48";
	private static final CharSequence FACSCANTO_INDICATOR = "BD FACSCanto II";
	private static final CharSequence COBAS_TAQMAN_DBS_INDICATOR = "AMPLIPREP";
	private static final CharSequence COBAS_C311_INDICATOR = "R_Type1";
	
	private List<String> lines;
	private AnalyzerLineInserter inserter;
	private String error;
    private static ArrayList<AnalyzerImporterPlugin> analyzerPlugins = new ArrayList<AnalyzerImporterPlugin>();

    public static void registerAnalyzerPlugin( AnalyzerImporterPlugin plugin){
        analyzerPlugins.add(plugin);
    }
	@Override
	public boolean readStream(InputStreamReader reader) {
		error = null;
		inserter = null;
		lines = new ArrayList<String>();

		BufferedReader bufferedReader = new BufferedReader(reader);

		String line;
		try {
			line = bufferedReader.readLine();

			while (line != null) {
				lines.add(line);
				line = bufferedReader.readLine();
			}
		} catch (IOException e) {
			error = "Unable to read file";
			return false;
		}

		if( !lines.isEmpty()){
			setInserter();
			if( inserter == null){
				error = "Unable to understand which analyzer sent the file";
				return false;
			}
			return true;
		}else{
			error = "Empty file";
			return false;
		}

	}

	private void setInserter() {
        for( AnalyzerImporterPlugin plugin : analyzerPlugins){
            if( plugin.isTargetAnalyzer(lines)){
                inserter = plugin.getAnalyzerLineInserter();
                return;
            }
        }
		//This is going to be highly customized based on the characteristics of the file
		//being sent

		
		if( lines.get(0).contains(COBAS_INDICATOR)){ //Cobas is found on the first line
			inserter = new CobasReader();
		}else if( lines.get(0).contains(EVOLIS_INTEGRAL_INDICATOR) ||
				  lines.get(0).contains(EVOLIS_INTEGRAL_DBS_INDICATOR) || 
				  lines.get(0).contains(EVOLIS_MUREX_INDICATOR) || 
				  lines.get(0).contains(EVOLIS_MUREX_DBS_INDICATOR)){ //Evolis is found on the first line
			inserter = new EvolisReader();
		}else if( lines.get(1) != null && lines.get(1).contains(SYSMEX_XT_INDICATOR)){ //Sysmex model found on data line
			inserter = new SysmexReader();
		}else if( lines.get(1) != null && lines.get(1).contains(FACSCALIBUR_INDICATOR)){ //Fascalibur software found on data line
			inserter = new FacscaliburReader();
		}else if( lines.get(1) != null && (lines.get(1).contains(COBAS_TAQMAN_INDICATOR) || 
				                           lines.get(1).contains(COBAS_TAQMAN_INDICATOR_2) || 
				                           lines.get(1).contains(COBAS_TAQMAN_INDICATOR_3))){
			inserter = new CobasTaqmanReader();
		}else if( lines.get(1) != null && lines.get(1).contains(FACSCANTO_INDICATOR)){
			inserter = new FACSCantoReader();
		}else if( lines.get(1) != null && lines.get(1).toUpperCase().contains(COBAS_TAQMAN_DBS_INDICATOR)){
		    inserter = new CobasTaqmanDBSReader();
		}else{
			//we're into squishy territory.  It could be be TAQMAN with no test on first row
			for( String line : lines){
				if( line.contains(COBAS_TAQMAN_INDICATOR) || line.contains(COBAS_TAQMAN_INDICATOR_2)){
					inserter = new CobasTaqmanReader();
				}
			}
			if( inserter == null && lines.get(3).contains(COBAS_C311_INDICATOR)){
				inserter = new CobasC311Reader();
			}
		}
	}

	/*
	 * For testing purposes only
	 */
	public void insertTestLines( List<String> testLines){
		lines = testLines;
	}

	@Override
	public boolean insertAnalyzerData(String systemUserId) {
		if( inserter == null){
			error = "Unable to understand which analyzer sent the file";
			return false;
		}else{
			boolean success = inserter.insert(lines, systemUserId);
			if( !success){
				error = inserter.getError();
			}
			
			return success;
		}

	}

	@Override
	public String getError() {
		return error;
	}
}