/**
* The contents of this file are subject to the OpenMRS Public License
* Version 1.0 (the "License"); you may not use this file except in
* compliance with the License. You may obtain a copy of the License at
* http://license.openmrs.org
*
* 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.
*
* Copyright (C) OpenMRS, LLC. All Rights Reserved.
*/
package org.openmrs.web.controller;
import java.util.Calendar;
import java.util.Collections;
import java.util.Date;
import java.util.HashMap;
import java.util.List;
import java.util.Locale;
import java.util.Map;
import java.util.Vector;
import javax.servlet.ServletException;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.jfree.chart.ChartFactory;
import org.jfree.chart.JFreeChart;
import org.jfree.chart.plot.PlotOrientation;
import org.jfree.data.general.DefaultPieDataset;
import org.jfree.data.statistics.HistogramDataset;
import org.jfree.data.time.Day;
import org.jfree.data.time.TimeSeries;
import org.jfree.data.time.TimeSeriesCollection;
import org.openmrs.Concept;
import org.openmrs.ConceptDatatype;
import org.openmrs.Obs;
import org.openmrs.api.ConceptService;
import org.openmrs.api.ObsService;
import org.openmrs.api.context.Context;
import org.openmrs.util.OpenmrsConstants;
import org.springframework.context.support.MessageSourceAccessor;
import org.springframework.validation.BindException;
import org.springframework.web.servlet.ModelAndView;
import org.springframework.web.servlet.mvc.SimpleFormController;
import org.springframework.web.servlet.view.RedirectView;
public class ConceptStatsFormController extends SimpleFormController {
/** Logger for this class and subclasses */
protected final Log log = LogFactory.getLog(getClass());
/**
* @see org.springframework.web.servlet.mvc.AbstractFormController#processFormSubmission(javax.servlet.http.HttpServletRequest,
* javax.servlet.http.HttpServletResponse, java.lang.Object,
* org.springframework.validation.BindException)
*/
protected ModelAndView processFormSubmission(HttpServletRequest request, HttpServletResponse response, Object object,
BindException errors) throws Exception {
Concept concept = (Concept) object;
ConceptService cs = Context.getConceptService();
// check to see if they clicked next/previous concept:
String jumpAction = request.getParameter("jumpAction");
if (jumpAction != null) {
Concept newConcept = null;
if ("previous".equals(jumpAction))
newConcept = cs.getPrevConcept(concept);
else if ("next".equals(jumpAction))
newConcept = cs.getNextConcept(concept);
if (newConcept != null)
return new ModelAndView(new RedirectView(getSuccessView() + "?conceptId=" + newConcept.getConceptId()));
}
return new ModelAndView(new RedirectView(getSuccessView()));
}
/**
* This is called prior to displaying a form for the first time. It tells Spring the
* form/command object to load into the request
*
* @see org.springframework.web.servlet.mvc.AbstractFormController#formBackingObject(javax.servlet.http.HttpServletRequest)
*/
protected Object formBackingObject(HttpServletRequest request) throws ServletException {
Concept concept = null;
ConceptService cs = Context.getConceptService();
String conceptId = request.getParameter("conceptId");
if (conceptId != null) {
concept = cs.getConcept(Integer.valueOf(conceptId));
}
if (concept == null)
concept = new Concept();
return concept;
}
/**
* Called prior to form display. Allows for data to be put in the request to be used in the view
*
* @see org.springframework.web.servlet.mvc.SimpleFormController#referenceData(javax.servlet.http.HttpServletRequest)
*/
protected Map<String, Object> referenceData(HttpServletRequest request) throws Exception {
Map<String, Object> map = new HashMap<String, Object>();
if (!Context.hasPrivilege("View Observations"))
return map;
MessageSourceAccessor msa = getMessageSourceAccessor();
Locale locale = Context.getLocale();
ConceptService cs = Context.getConceptService();
String conceptId = request.getParameter("conceptId");
//List<Obs> obs = new Vector<Obs>();
//List<Obs> obsAnswered = new Vector<Obs>();
if (conceptId != null) {
Concept concept = cs.getConcept(Integer.valueOf(conceptId));
ObsService obsService = Context.getObsService();
if (concept != null) {
// previous/next ids for links
map.put("previousConcept", cs.getPrevConcept(concept));
map.put("nextConcept", cs.getNextConcept(concept));
//obs = obsService.getObservations(concept, "valueNumeric, obsId");
//obsAnswered = obsService.getObservationsAnsweredByConcept(concept);
if (ConceptDatatype.NUMERIC.equals(concept.getDatatype().getHl7Abbreviation())) {
map.put("displayType", "numeric");
List<Obs> numericAnswers = obsService.getObservations(null, null, Collections.singletonList(concept),
null, Collections.singletonList(OpenmrsConstants.PERSON_TYPE.PERSON), null, Collections
.singletonList("valueNumeric"), null, null, null, null, false);
if (numericAnswers.size() > 0) {
Double min = numericAnswers.get(0).getValueNumeric();
Double max = (Double) numericAnswers.get(numericAnswers.size() - 1).getValueNumeric();
Double median = (Double) numericAnswers.get(numericAnswers.size() / 2).getValueNumeric();
Map<Double, Integer> counts = new HashMap<Double, Integer>(); // counts for the histogram
Double total = 0.0; // sum of values. used for mean
// dataset setup for lineChart
TimeSeries timeSeries = new TimeSeries(concept.getName().getName(), Day.class);
TimeSeriesCollection timeDataset = new TimeSeriesCollection();
Calendar calendar = Calendar.getInstance();
// array for histogram
double[] obsNumerics = new double[(numericAnswers.size())];
Integer i = 0;
for (Obs obs : numericAnswers) {
Date date = (Date) obs.getObsDatetime();
Double value = (Double) obs.getValueNumeric();
// for mean calculation
total += value;
// for histogram
obsNumerics[i++] = value;
Integer count = counts.get(value);
counts.put(value, count == null ? 1 : count + 1);
// for line chart
calendar.setTime(date);
Day day = new Day(calendar.get(Calendar.DAY_OF_MONTH), calendar.get(Calendar.MONTH) + 1, // January = 0
calendar.get(Calendar.YEAR) < 1900 ? 1900 : calendar.get(Calendar.YEAR) // jfree chart doesn't like the 19th century
);
timeSeries.addOrUpdate(day, value);
}
Double size = new Double(numericAnswers.size());
Double mean = total / size;
map.put("size", numericAnswers.size());
map.put("min", min);
map.put("max", max);
map.put("mean", mean);
map.put("median", median);
// create histogram chart
HistogramDataset histDataset = new HistogramDataset(); // dataset for histogram
histDataset.addSeries(concept.getName().getName(), obsNumerics, counts.size());
JFreeChart histogram = ChartFactory.createHistogram(concept.getName().getName(), msa
.getMessage("Concept.stats.histogramDomainAxisTitle"), msa
.getMessage("Concept.stats.histogramRangeAxisTitle"), histDataset, PlotOrientation.VERTICAL,
false, true, false);
map.put("histogram", histogram);
if (size > 25) {
// calculate 98th percentile of the data:
Double x = 0.98;
Integer xpercentile = (int) (x * size);
Double upperQuartile = numericAnswers.get(xpercentile).getValueNumeric();
Double lowerQuartile = numericAnswers.get((int) (size - xpercentile)).getValueNumeric();
Double innerQuartile = upperQuartile - lowerQuartile;
Double innerQuartileLimit = innerQuartile * 1.5; // outliers will be greater than this from the upper/lower quartile
Double upperQuartileLimit = upperQuartile + innerQuartileLimit;
Double lowerQuartileLimit = lowerQuartile - innerQuartileLimit;
List<Obs> outliers = new Vector<Obs>();
// move outliers to the outliers list
// removing lower quartile outliers
for (i = 0; i < size - xpercentile; i++) {
Obs possibleOutlier = numericAnswers.get(i);
if (possibleOutlier.getValueNumeric() >= lowerQuartileLimit)
break; // quit if this value is greater than the lower limit
outliers.add(possibleOutlier);
}
// removing upper quartile outliers
for (i = size.intValue() - 1; i >= xpercentile; i--) {
Obs possibleOutlier = numericAnswers.get(i);
if (possibleOutlier.getValueNumeric() <= upperQuartileLimit)
break; // quit if this value is less than the upper limit
outliers.add(possibleOutlier);
}
numericAnswers.removeAll(outliers);
double[] obsNumericsOutliers = new double[(numericAnswers.size())];
i = 0;
counts.clear();
for (Obs values : numericAnswers) {
Double value = values.getValueNumeric();
obsNumericsOutliers[i++] = value;
Integer count = counts.get(value);
counts.put(value, count == null ? 1 : count + 1);
}
// create outlier histogram chart
HistogramDataset outlierHistDataset = new HistogramDataset();
outlierHistDataset.addSeries(concept.getName().getName(), obsNumericsOutliers, counts.size());
JFreeChart histogramOutliers = ChartFactory.createHistogram(concept.getName().getName(), msa
.getMessage("Concept.stats.histogramDomainAxisTitle"), msa
.getMessage("Concept.stats.histogramRangeAxisTitle"), outlierHistDataset,
PlotOrientation.VERTICAL, false, true, false);
map.put("histogramOutliers", histogramOutliers);
map.put("outliers", outliers);
}
// create line graph chart
timeDataset.addSeries(timeSeries);
JFreeChart lineChart = ChartFactory.createTimeSeriesChart(concept.getName().getName(), msa
.getMessage("Concept.stats.lineChartDomainAxisLabel"), msa
.getMessage("Concept.stats.lineChartRangeAxisLabel"), timeDataset, false, true, false);
map.put("timeSeries", lineChart);
}
} else if (ConceptDatatype.BOOLEAN.equals(concept.getDatatype().getHl7Abbreviation())) {
// create bar chart for boolean answers
map.put("displayType", "boolean");
List<Obs> obs = obsService.getObservations(null, null, Collections.singletonList(concept), null,
Collections.singletonList(OpenmrsConstants.PERSON_TYPE.PERSON), null, null, null, null, null, null,
false);
DefaultPieDataset pieDataset = new DefaultPieDataset();
// count the number of unique answers
Map<String, Integer> counts = new HashMap<String, Integer>();
for (Obs o : obs) {
Boolean answer = o.getValueAsBoolean();
if (answer == null)
answer = false;
String name = answer.toString();
Integer count = counts.get(name);
counts.put(name, count == null ? 1 : count + 1);
}
// put the counts into the dataset
for (Map.Entry<String, Integer> entry : counts.entrySet())
pieDataset.setValue(entry.getKey(), entry.getValue());
JFreeChart pieChart = ChartFactory.createPieChart(concept.getName().getName(), pieDataset, true, true,
false);
map.put("pieChart", pieChart);
} else if (ConceptDatatype.CODED.equals(concept.getDatatype().getHl7Abbreviation())) {
// create pie graph for coded answers
map.put("displayType", "coded");
List<Obs> obs = obsService.getObservations(null, null, Collections.singletonList(concept), null,
Collections.singletonList(OpenmrsConstants.PERSON_TYPE.PERSON), null, null, null, null, null, null,
false);
DefaultPieDataset pieDataset = new DefaultPieDataset();
// count the number of unique answers
Map<String, Integer> counts = new HashMap<String, Integer>();
for (Obs o : obs) {
Concept value = o.getValueCoded();
String name;
if (value == null)
name = "[value_coded is null]";
else
name = value.getName().getName();
Integer count = counts.get(name);
counts.put(name, count == null ? 1 : count + 1);
}
// put the counts into the dataset
for (Map.Entry<String, Integer> entry : counts.entrySet())
pieDataset.setValue(entry.getKey(), entry.getValue());
JFreeChart pieChart = ChartFactory.createPieChart(concept.getName().getName(), pieDataset, true, true,
false);
map.put("pieChart", pieChart);
}
}
}
//map.put("obs", obs);
//map.put("obsAnswered", obsAnswered);
map.put("locale", locale.getLanguage().substring(0, 2));
return map;
}
}