com.actelion.research.spiritapp.report.StatusReport.java Source code

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Here is the source code for com.actelion.research.spiritapp.report.StatusReport.java

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/*
 * Spirit, a study/biosample management tool for research.
 * Copyright (C) 2018 Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91,
 * CH-4123 Allschwil, Switzerland.
 *
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>
 *
 * @author Joel Freyss
 */

package com.actelion.research.spiritapp.report;

import org.apache.poi.ss.usermodel.Sheet;

import com.actelion.research.spiritapp.ui.SpiritFrame;
import com.actelion.research.spiritapp.ui.util.POIUtils;
import com.actelion.research.spiritcore.business.biosample.Biosample;
import com.actelion.research.spiritcore.business.biosample.Status;
import com.actelion.research.spiritcore.business.result.Result;
import com.actelion.research.spiritcore.business.result.Test;
import com.actelion.research.spiritcore.business.study.Group;
import com.actelion.research.spiritcore.business.study.Phase;
import com.actelion.research.spiritcore.services.dao.DAOResult;
import com.actelion.research.spiritcore.services.dao.DAOTest;
import com.actelion.research.spiritcore.util.MiscUtils;
import com.actelion.research.spiritcore.util.Pair;
import com.actelion.research.util.CompareUtils;

public class StatusReport extends AbstractReport {

    public StatusReport() {
        super(ReportCategory.PARTICIPANTS, "Living Status", "Living Status of each attached sample<br>" + MiscUtils
                .convert2Html("\tNo\tContainer\tGroup\tSt.\tStatus\tPhase\tObservation\n" + "ANL1\t\nANL2\t\n"));
    }

    @Override
    protected void populateWorkBook() throws Exception {

        //Create Header
        Sheet sheet = createSheet(wb, "Living Status");
        sheet.setFitToPage(true);
        createHeadersWithTitle(sheet, study, "Living Status");
        sheet.createRow(4).setHeightInPoints(23f);

        int col = 0;
        set(sheet, 5, col++, "Participant", Style.S_TH_CENTER);
        set(sheet, 5, col++, "No.", Style.S_TH_CENTER);
        set(sheet, 5, col++, "ContainerId", Style.S_TH_CENTER);
        set(sheet, 5, col++, "Group", Style.S_TH_CENTER);
        set(sheet, 5, col++, "St.", Style.S_TH_CENTER);
        set(sheet, 5, col++, "Status", Style.S_TH_CENTER);
        set(sheet, 5, col++, "Phase", Style.S_TH_CENTER);
        set(sheet, 5, col++, "Observation", Style.S_TH_CENTER);
        int maxCol = col - 1;

        //Group separator?
        int line = 5;
        String cageBefore = null;
        Group groupBefore = null;

        DAOResult.attachOrCreateStudyResultsToTops(study, study.getParticipants(), null, null);
        Test observationTest = DAOTest.getTest(DAOTest.OBSERVATION_TESTNAME);
        if (observationTest == null)
            throw new Exception("The test " + DAOTest.OBSERVATION_TESTNAME + " does not exist");
        for (Biosample a : study.getParticipantsSorted()) {
            if (CompareUtils.compare(groupBefore, a.getInheritedGroup()) != 0) {
                drawLineUnder(sheet, line, 0, maxCol, (short) 2);
            } else if (CompareUtils.compare(cageBefore, a.getContainerId()) != 0) {
                drawLineUnder(sheet, line, 0, maxCol, (short) 1);
            }

            Pair<Status, Phase> actionStatus = a.getLastActionStatus();
            Phase lastPhase = actionStatus.getSecond();
            Result lastObservation = lastPhase == null ? null : a.getAuxResult(observationTest, lastPhase);

            Group g = a.getInheritedGroup();
            line++;
            col = 0;
            set(sheet, line, col++, a.getSampleName(), Style.S_TD_CENTER);
            set(sheet, line, col++, a.getSampleId(), Style.S_TD_CENTER);
            set(sheet, line, col++, a.getContainerId(), Style.S_TD_CENTER);
            set(sheet, line, col++, g == null ? "" : g.getBlindedName(SpiritFrame.getUsername()), Style.S_TD_LEFT);
            set(sheet, line, col++, g == null || g.getNSubgroups() <= 1 ? "" : (a.getInheritedSubGroup() + 1),
                    Style.S_TD_CENTER);

            set(sheet, line, col++,
                    g == null ? "" : actionStatus.getFirst() == null ? "" : actionStatus.getFirst().getName(),
                    Style.S_TD_LEFT);
            set(sheet, line, col++, g == null ? "" : lastPhase == null ? "" : lastPhase.getAbsoluteDateAndName(),
                    Style.S_TD_LEFT);
            set(sheet, line, col++, g == null ? "" : lastObservation == null ? "" : lastObservation.getFirstValue(),
                    Style.S_TD_LEFT);

            cageBefore = a.getContainerId();
            groupBefore = a.getInheritedGroup();
        }
        drawLineUnder(sheet, line, 0, maxCol, (short) 1);
        POIUtils.autoSizeColumns(sheet);

        if (wb.getNumberOfSheets() == 0)
            throw new Exception("There was no randomization fone for " + study);
    }

}