department chart - progress of inclusions per site

core/src/main/java/org/phoenixctms/ctsms/adapt/ProbandListStatusEntryCollisionFinder.java

@@ -52,7 +52,7 @@ protected Collection<ProbandListStatusEntry> getCollidingItems(
 		} else {
 			probandId = root.getId();
 		}
-		return probandListStatusEntryDao.findByTrialProband(null, probandId, true, null);
+		return probandListStatusEntryDao.findByTrialProband(null, probandId, true, null, null);
 	}
 
 	@Override

core/src/main/java/org/phoenixctms/ctsms/domain/ProbandListStatusEntryDaoImpl.java

@@ -100,7 +100,7 @@ protected Collection<ProbandListStatusEntry> handleFindByListEntry(
 
 	@Override
 	protected Collection<ProbandListStatusEntry> handleFindByTrialProband(
-			Long trialId, Long probandId, boolean last, PSFVO psf)
+			Long trialId, Long probandId, boolean last, Boolean initial, PSFVO psf)
 			throws Exception {
 		org.hibernate.Criteria statusEntryCriteria = createStatusEntryCriteria("probandListStatusEntry");
 		SubCriteriaMap criteriaMap = new SubCriteriaMap(ProbandListStatusEntry.class, statusEntryCriteria);
@@ -110,6 +110,9 @@ protected Collection<ProbandListStatusEntry> handleFindByTrialProband(
 		if (probandId != null) {
 			criteriaMap.createCriteria("listEntry").add(Restrictions.eq("proband.id", probandId.longValue()));
 		}
+		if (initial != null) {
+			criteriaMap.createCriteria("status").add(Restrictions.eq("initial", initial.booleanValue()));
+		}
 		if (last) {
 			criteriaMap.createCriteria("listEntry.lastStatus").add(Restrictions.eqProperty("id", "probandListStatusEntry.id")); // didn't work without explicit id compare
 		}

core/src/main/java/org/phoenixctms/ctsms/service/trial/TrialServiceImpl.java

@@ -6695,7 +6695,7 @@ protected ProbandListEntryTagValuesOutVO handleGetProbandListEntryTagValues(
 
 	@Override
 	protected Collection<ProbandListStatusEntryOutVO> handleGetProbandListStatus(
-			AuthenticationVO auth, Long trialId, Long probandId, boolean last, PSFVO psf)
+			AuthenticationVO auth, Long trialId, Long probandId, boolean last, Boolean initial, PSFVO psf)
 			throws Exception {
 		if (trialId != null) {
 			CheckIDUtil.checkTrialId(trialId, this.getTrialDao());
@@ -6704,7 +6704,7 @@ protected Collection<ProbandListStatusEntryOutVO> handleGetProbandListStatus(
 			CheckIDUtil.checkProbandId(probandId, this.getProbandDao());
 		}
 		ProbandListStatusEntryDao probandListStatusEntryDao = this.getProbandListStatusEntryDao();
-		Collection statusEntries = probandListStatusEntryDao.findByTrialProband(trialId, probandId, last, psf);
+		Collection statusEntries = probandListStatusEntryDao.findByTrialProband(trialId, probandId, last, initial, psf);
 		probandListStatusEntryDao.toProbandListStatusEntryOutVOCollection(statusEntries);
 		return statusEntries;
 	}

web/src/main/java/org/phoenixctms/ctsms/web/model/shared/search/ProbandSearchBean.java

@@ -166,7 +166,7 @@ public Collection<IDVO> getProbandListStatus(ProbandOutVO proband) {
 			if (!probandListStatusCache.containsKey(proband.getId())) {
 				Collection probandListStatus = null;
 				try {
-					probandListStatus = WebUtil.getServiceLocator().getTrialService().getProbandListStatus(WebUtil.getAuthentication(), null, proband.getId(), true, null);
+					probandListStatus = WebUtil.getServiceLocator().getTrialService().getProbandListStatus(WebUtil.getAuthentication(), null, proband.getId(), true, null, null);
 				} catch (ServiceException | AuthorisationException | IllegalArgumentException e) {
 				} catch (AuthenticationException e) {
 					WebUtil.publishException(e);

web/src/main/java/org/phoenixctms/ctsms/web/model/trial/DepartmentChartBean.java

@@ -0,0 +1,300 @@
+package org.phoenixctms.ctsms.web.model.trial;
+
+import java.io.ByteArrayInputStream;
+import java.util.ArrayList;
+import java.util.Calendar;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.Date;
+import java.util.GregorianCalendar;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map.Entry;
+import java.util.TreeMap;
+import java.util.TreeSet;
+
+import org.phoenixctms.ctsms.compare.ProbandListStatusEntryOutVOComparator;
+import org.phoenixctms.ctsms.enumeration.Color;
+import org.phoenixctms.ctsms.enumeration.ProbandListStatusLogLevel;
+import org.phoenixctms.ctsms.enumeration.VariablePeriod;
+import org.phoenixctms.ctsms.exception.AuthenticationException;
+import org.phoenixctms.ctsms.exception.AuthorisationException;
+import org.phoenixctms.ctsms.exception.ServiceException;
+import org.phoenixctms.ctsms.util.CommonUtil;
+import org.phoenixctms.ctsms.vo.DepartmentVO;
+import org.phoenixctms.ctsms.vo.ProbandListExcelVO;
+import org.phoenixctms.ctsms.vo.ProbandListStatusEntryOutVO;
+import org.phoenixctms.ctsms.web.model.CartesianChartModel;
+import org.phoenixctms.ctsms.web.model.ManagedBeanBase;
+import org.phoenixctms.ctsms.web.util.DateUtil;
+import org.phoenixctms.ctsms.web.util.DefaultSettings;
+import org.phoenixctms.ctsms.web.util.MessageCodes;
+import org.phoenixctms.ctsms.web.util.Messages;
+import org.phoenixctms.ctsms.web.util.SettingCodes;
+import org.phoenixctms.ctsms.web.util.Settings;
+import org.phoenixctms.ctsms.web.util.Settings.Bundle;
+import org.phoenixctms.ctsms.web.util.WebUtil;
+import org.primefaces.model.DefaultStreamedContent;
+import org.primefaces.model.StreamedContent;
+import org.primefaces.model.chart.ChartSeries;
+
+public class DepartmentChartBean extends ManagedBeanBase {
+
+	private Long trialId;
+	//private TrialOutVO trial;
+	private CartesianChartModel chartModel;
+	private List<Color> departmentColors;
+	private ArrayList<Color> seriesColors;
+	private Date minX;
+	private Date maxX;
+	private Integer maxY;
+	private boolean stacked;
+
+	public DepartmentChartBean() {
+		super();
+		chartModel = new CartesianChartModel();
+		departmentColors = Settings.getColorList(SettingCodes.DEPARTMENT_CHART_DEPARTMENT_COLORS, Bundle.SETTINGS, DefaultSettings.DEPARTMENT_CHART_DEPARTMENT_COLORS);
+		seriesColors = new ArrayList<Color>();
+	}
+
+	@Override
+	protected String changeAction(Long id) {
+		this.trialId = id;
+		initIn();
+		initSets();
+		return CHANGE_OUTCOME;
+	}
+
+	private String dateToString(Date date) {
+		return WebUtil.quoteJSString(DateUtil.getJqPlotJsDateFormat().format(date), true);
+	}
+
+	public CartesianChartModel getChartModel() {
+		if (isChartEmpty()) {
+			CartesianChartModel emptyChartModel = new CartesianChartModel();
+			ChartSeries emptyChartSeries = new ChartSeries();
+			emptyChartSeries.setLabel(Messages.getString(MessageCodes.EMPTY_CHART_LABEL));
+			emptyChartSeries.set(dateToString(new Date()), 0);
+			emptyChartModel.addSeries(emptyChartSeries);
+			return emptyChartModel;
+		}
+		return chartModel;
+	}
+
+	public boolean getEnableExports() {
+		return Settings.getBoolean(SettingCodes.ENABLE_PROBAND_LIST_EXPORTS, Bundle.SETTINGS, DefaultSettings.ENABLE_PROBAND_LIST_EXPORTS);
+	}
+
+	public StreamedContent getEnrollmentLogExcelStreamedContent() throws Exception {
+		try {
+			ProbandListExcelVO excel = WebUtil.getServiceLocator().getTrialService().exportProbandList(WebUtil.getAuthentication(), trialId, ProbandListStatusLogLevel.ENROLLMENT);
+			return new DefaultStreamedContent(new ByteArrayInputStream(excel.getDocumentDatas()), excel.getContentType().getMimeType(), excel.getFileName());
+		} catch (AuthenticationException e) {
+			WebUtil.publishException(e);
+			throw e;
+		} catch (AuthorisationException | ServiceException | IllegalArgumentException e) {
+			throw e;
+		}
+	}
+
+	public long getMaxX() {
+		return (maxX != null ? maxX : WebUtil.subIntervals(new Date(), VariablePeriod.MONTH, null, 1)).getTime();
+	}
+
+	public Integer getMaxY() {
+		return maxY;
+	}
+
+	public long getMinX() {
+		return (minX != null ? minX : new Date()).getTime();
+	}
+
+	public StreamedContent getPreScreeningLogExcelStreamedContent() throws Exception {
+		try {
+			ProbandListExcelVO excel = WebUtil.getServiceLocator().getTrialService()
+					.exportProbandList(WebUtil.getAuthentication(), trialId, ProbandListStatusLogLevel.PRE_SCREENING);
+			return new DefaultStreamedContent(new ByteArrayInputStream(excel.getDocumentDatas()), excel.getContentType().getMimeType(), excel.getFileName());
+		} catch (AuthenticationException e) {
+			WebUtil.publishException(e);
+			throw e;
+		} catch (AuthorisationException | ServiceException | IllegalArgumentException e) {
+			throw e;
+		}
+	}
+
+	public StreamedContent getScreeningLogExcelStreamedContent() throws Exception {
+		try {
+			ProbandListExcelVO excel = WebUtil.getServiceLocator().getTrialService().exportProbandList(WebUtil.getAuthentication(), trialId, ProbandListStatusLogLevel.SCREENING);
+			return new DefaultStreamedContent(new ByteArrayInputStream(excel.getDocumentDatas()), excel.getContentType().getMimeType(), excel.getFileName());
+		} catch (AuthenticationException e) {
+			WebUtil.publishException(e);
+			throw e;
+		} catch (AuthorisationException | ServiceException | IllegalArgumentException e) {
+			throw e;
+		}
+	}
+
+	public String getSeriesColors() {
+		return WebUtil.getSeriesColors(seriesColors);
+	}
+
+	public StreamedContent getSiclExcelStreamedContent() throws Exception {
+		try {
+			ProbandListExcelVO excel = WebUtil.getServiceLocator().getTrialService().exportProbandList(WebUtil.getAuthentication(), trialId, ProbandListStatusLogLevel.SICL);
+			return new DefaultStreamedContent(new ByteArrayInputStream(excel.getDocumentDatas()), excel.getContentType().getMimeType(), excel.getFileName());
+		} catch (AuthenticationException e) {
+			WebUtil.publishException(e);
+			throw e;
+		} catch (AuthorisationException | ServiceException | IllegalArgumentException e) {
+			throw e;
+		}
+	}
+
+	private void initIn() {
+		stacked = true;
+	}
+
+	private void initSets() {
+		chartModel.clear();
+		seriesColors.clear();
+		minX = null;
+		maxX = null;
+		maxY = null;
+		//trial = WebUtil.getTrial(trialId);
+		Collection<DepartmentVO> departments = null;
+		try {
+			departments = WebUtil.getServiceLocator().getSelectionSetService().getAllDepartments(WebUtil.getAuthentication());
+		} catch (ServiceException | AuthorisationException | IllegalArgumentException e) {
+		} catch (AuthenticationException e) {
+			WebUtil.publishException(e);
+		}
+		HashMap<Long, DepartmentVO> departmentMap;
+		if (departments != null) {
+			departmentMap = new HashMap<Long, DepartmentVO>(departments.size());
+			Iterator<Color> departmentColorsIt = CommonUtil.getCircularIterator(departmentColors);
+			Iterator<DepartmentVO> departmentsIt = departments.iterator();
+			while (departmentsIt.hasNext()) {
+				DepartmentVO department = departmentsIt.next();
+				departmentMap.put(department.getId(), department);
+				seriesColors.add(departmentColorsIt.next());
+			}
+		} else {
+			departmentMap = new HashMap<Long, DepartmentVO>();
+		}
+		Collection<ProbandListStatusEntryOutVO> initialProbandListStatus = null;
+		if (trialId != null) {
+			try {
+				initialProbandListStatus = WebUtil.getServiceLocator().getTrialService().getProbandListStatus(WebUtil.getAuthentication(), trialId, null, false, true, null);
+			} catch (ServiceException | AuthorisationException | IllegalArgumentException e) {
+			} catch (AuthenticationException e) {
+				WebUtil.publishException(e);
+			}
+		}
+		if (initialProbandListStatus == null) {
+			initialProbandListStatus = new ArrayList<ProbandListStatusEntryOutVO>();
+		} else {
+			initialProbandListStatus = new ArrayList<ProbandListStatusEntryOutVO>(initialProbandListStatus);
+			Collections.sort((ArrayList<ProbandListStatusEntryOutVO>) initialProbandListStatus, new ProbandListStatusEntryOutVOComparator());
+		}
+		HashMap<Long, TreeMap<Date, Number>> seriesMap = new HashMap<Long, TreeMap<Date, Number>>();
+		LinkedHashMap<Long, ProbandListStatusEntryOutVO> probandMap = new LinkedHashMap<Long, ProbandListStatusEntryOutVO>();
+		Iterator<ProbandListStatusEntryOutVO> probandListStatusIt = initialProbandListStatus.iterator();
+		while (probandListStatusIt.hasNext()) {
+			ProbandListStatusEntryOutVO probandListStatusEntry = probandListStatusIt.next();
+			Long probandId = probandListStatusEntry.getListEntry().getProband().getId();
+			TreeMap<Long, ProbandListStatusEntryOutVO> enrollmentStatusMap;
+			if (!probandMap.containsKey(probandId)) {
+				probandMap.put(probandId, probandListStatusEntry);
+			}
+		}
+		maxY = probandMap.size();
+		TreeSet<Date> dates = new TreeSet<Date>();
+		probandListStatusIt = probandMap.values().iterator();
+		while (probandListStatusIt.hasNext()) {
+			ProbandListStatusEntryOutVO probandListStatusEntry = probandListStatusIt.next();
+			Long departmentId = probandListStatusEntry.getListEntry().getProband().getDepartment().getId();
+			//Long statusId = probandListStatusEntry.getStatus().getId();
+			GregorianCalendar cal = new GregorianCalendar();
+			cal.setTime(probandListStatusEntry.getRealTimestamp());
+			Date date = (new GregorianCalendar(cal.get(Calendar.YEAR), cal.get(Calendar.MONTH), cal.get(Calendar.DAY_OF_MONTH), 0, 0, 0)).getTime();
+			dates.add(date);
+			//TreeMap<Long, ProbandListStatusEntryOutVO> enrollmentStatusMap = probandMap.get(probandListStatusEntry.getListEntry().getProband().getId());
+			//Entry<Long, ProbandListStatusEntryOutVO> previousStatus = enrollmentStatusMap.lowerEntry(probandListStatusEntry.getId());
+			TreeMap<Date, Number> series;
+			if (seriesMap.containsKey(departmentId)) {
+				series = seriesMap.get(departmentId);
+			} else {
+				series = new TreeMap<Date, Number>();
+				seriesMap.put(departmentId, series);
+			}
+			if (series.containsKey(date)) {
+				series.put(date, series.get(date).intValue() + 1);
+			} else {
+				if (series.size() > 0) {
+					series.put(date, series.lastEntry().getValue().intValue() + 1);
+				} else {
+					series.put(date, 1);
+				}
+			}
+			//			if (previousStatus != null) {
+			//				series = seriesMap.get(previousStatus.getValue().getStatus().getId());
+			//				series.put(date, series.lastEntry().getValue().intValue() - 1);
+			//			}
+		}
+		if (dates.size() > 0) {
+			minX = dates.first();
+			maxX = dates.last();
+		}
+		Iterator<Long> seriesMapIt = seriesMap.keySet().iterator();
+		while (seriesMapIt.hasNext()) {
+			Long departmentId = seriesMapIt.next();
+			DepartmentVO department = departmentMap.get(departmentId);
+			TreeMap<Date, Number> series = seriesMap.get(departmentId);
+			if (department != null && series.size() > 0) {
+				ChartSeries chartLine = new ChartSeries();
+				chartLine.setLabel(department.getName());
+				Iterator<Date> datesIt = dates.iterator();
+				while (datesIt.hasNext()) {
+					Date date = datesIt.next();
+					if (series.containsKey(date)) {
+						chartLine.set(dateToString(date), series.get(date));
+					} else {
+						Entry<Date, Number> previousValue = series.lowerEntry(date);
+						chartLine.set(dateToString(date), previousValue == null ? 0 : previousValue.getValue());
+					}
+				}
+				chartModel.addSeries(chartLine);
+				//seriesColors.add(department.getColor());
+			}
+		}
+	}
+
+	public boolean isChartEmpty() {
+		return chartModel.getSeries().isEmpty();
+	}
+
+	@Override
+	public boolean isCreateable() {
+		return false;
+	}
+
+	@Override
+	public boolean isCreated() {
+		return false;
+	}
+
+	public boolean isStacked() {
+		return stacked;
+	}
+
+	public void setStacked(boolean stacked) {
+		this.stacked = stacked;
+	}
+
+	public void updateChart() {
+		initIn();
+		initSets();
+	}
+}

web/src/main/java/org/phoenixctms/ctsms/web/model/trial/EnrollmentChartBean.java

@@ -181,7 +181,7 @@ private void initSets() {
 		Collection<ProbandListStatusEntryOutVO> probandListStatus = null;
 		if (trialId != null) {
 			try {
-				probandListStatus = WebUtil.getServiceLocator().getTrialService().getProbandListStatus(WebUtil.getAuthentication(), trialId, null, false, null);
+				probandListStatus = WebUtil.getServiceLocator().getTrialService().getProbandListStatus(WebUtil.getAuthentication(), trialId, null, false, null, null);
 			} catch (ServiceException | AuthorisationException | IllegalArgumentException e) {
 			} catch (AuthenticationException e) {
 				WebUtil.publishException(e);

web/src/main/java/org/phoenixctms/ctsms/web/model/trial/ProbandListEntryBean.java

@@ -289,7 +289,8 @@ public Collection<IDVO> getProbandListStatus(ProbandOutVO proband) {
 				Collection<ProbandListStatusEntryOutVO> probandListStatus = null;
 				Collection probandListStatusFiltered = new ArrayList<ProbandListStatusEntryOutVO>();
 				try {
-					probandListStatus = WebUtil.getServiceLocator().getTrialService().getProbandListStatus(WebUtil.getAuthentication(), trialId, proband.getId(), false, null);
+					probandListStatus = WebUtil.getServiceLocator().getTrialService().getProbandListStatus(WebUtil.getAuthentication(), trialId, proband.getId(), false, null,
+							null);
 				} catch (ServiceException | AuthorisationException | IllegalArgumentException e) {
 				} catch (AuthenticationException e) {
 					WebUtil.publishException(e);