Added percentiles

webapp/src/main/java/endafarrell/orla/OrlaJsonWriter.java

@@ -15,4 +15,8 @@ public interface OrlaJsonWriter {
     void writeGlucoseReadings(OutputStream outputStream, DateTime from, DateTime to) throws IOException;
 
     void writeGlucoseOverlays(OutputStream outputStream, DateTime from, DateTime to) throws IOException;
+
+    void writeHourlyBasalAsJson(OutputStream outputStream) throws IOException;
+
+    void writeHourlyPercentiles(OutputStream outputStream, DateTime from, DateTime to) throws IOException;
 }

webapp/src/main/java/endafarrell/orla/api/home/HourlyBasalServlet.java

@@ -0,0 +1,19 @@
+package endafarrell.orla.api.home;
+
+import endafarrell.orla.api.OrlaHttpServlet;
+
+import javax.servlet.ServletException;
+import javax.servlet.annotation.WebServlet;
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+import java.io.IOException;
+
+@WebServlet(urlPatterns = {"/api/home/hourlyBasal"})
+public class HourlyBasalServlet extends OrlaHttpServlet {
+
+    @Override
+    public void doGet(HttpServletRequest req, HttpServletResponse res) throws ServletException, IOException {
+        res.setContentType("application/json");
+        orla.writeHourlyBasalAsJson(res.getOutputStream());
+    }
+}

webapp/src/main/java/endafarrell/orla/api/home/HourlyPercentilesServlet.java

@@ -0,0 +1,22 @@
+package endafarrell.orla.api.home;
+
+import endafarrell.orla.api.OrlaHttpServlet;
+import org.apache.commons.lang3.tuple.Pair;
+import org.joda.time.DateTime;
+
+import javax.servlet.ServletException;
+import javax.servlet.annotation.WebServlet;
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+import java.io.IOException;
+
+@WebServlet(urlPatterns = {"/api/home/hourlyPercentiles"})
+public class HourlyPercentilesServlet extends OrlaHttpServlet {
+
+    @Override
+    public void doGet(HttpServletRequest req, HttpServletResponse res) throws ServletException, IOException {
+        res.setContentType("application/json");
+        Pair<DateTime, DateTime> fromTo = fromTo(req);
+        orla.writeHourlyPercentiles(res.getOutputStream(), fromTo.getLeft(), fromTo.getRight());
+    }
+}

webapp/src/main/java/endafarrell/orla/api/home/TwitterTriggerServlet.java

@@ -2,7 +2,6 @@
 
 import endafarrell.orla.api.OrlaHttpServlet;
 import endafarrell.orla.service.processor.ProcessResults;
-import org.apache.commons.lang.StringUtils;
 
 import javax.servlet.ServletException;
 import javax.servlet.annotation.WebServlet;

webapp/src/main/java/endafarrell/orla/service/Filter.java

@@ -83,6 +83,17 @@ public static List<Event> percentiles(Collection<Event> events, int lower, int h
         return percentiles;
     }
 
+    public static Map<Integer, Double> percentiles(List<Double> values, Set<Integer> percentiles) {
+        double[] vals = Convert.todoubleArray(values);
+        Map<Integer, Double> ps = new HashMap<Integer, Double>(percentiles.size());
+        Percentile percentile = new Percentile();
+        percentile.setData(vals);
+        for (Integer percentileLevel : percentiles) {
+            ps.put(percentileLevel, percentile.evaluate(percentileLevel));
+        }
+        return ps;
+    }
+
     public static List<Event> only(Collection<Event> events, Unit unit) {
         ArrayList<Event> eventList = new ArrayList<Event>(events.size());
         for (Event event : events) {

webapp/src/main/java/endafarrell/orla/service/OrlaImpl.java

@@ -6,6 +6,7 @@
 import endafarrell.orla.OrlaException;
 import endafarrell.orla.monitoring.OrlaMonitor;
 import endafarrell.orla.service.data.*;
+import endafarrell.orla.service.data.jackson.PairSerializer;
 import endafarrell.orla.service.data.persistence.Archiver;
 import endafarrell.orla.service.data.persistence.Database;
 import endafarrell.orla.service.data.persistence.FileSystemArchiver;
@@ -16,13 +17,23 @@
 import endafarrell.orla.service.processor.TwitterProcessor;
 import org.apache.commons.configuration.ConfigurationException;
 import org.apache.commons.configuration.PropertiesConfiguration;
+import org.apache.commons.lang3.tuple.ImmutablePair;
+import org.apache.commons.lang3.tuple.Pair;
 import org.codehaus.jackson.JsonFactory;
+import org.codehaus.jackson.JsonNode;
+import org.codehaus.jackson.Version;
+import org.codehaus.jackson.map.MapperConfig;
+import org.codehaus.jackson.map.Module;
 import org.codehaus.jackson.map.ObjectMapper;
+import org.codehaus.jackson.map.module.SimpleModule;
 import org.codehaus.jackson.node.ArrayNode;
 import org.codehaus.jackson.node.JsonNodeFactory;
 import org.codehaus.jackson.node.ObjectNode;
+import org.codehaus.jackson.type.TypeReference;
 import org.joda.time.DateTime;
 import org.xml.sax.SAXException;
+import twitter4j.internal.org.json.JSONException;
+import twitter4j.internal.org.json.JSONObject;
 
 import javax.servlet.http.Part;
 import javax.xml.parsers.ParserConfigurationException;
@@ -285,6 +296,65 @@ public void writeGlucoseOverlays(OutputStream outputStream, DateTime from, DateT
         outputStream.write(arrayNode.toString().getBytes());
     }
 
+    public void writeHourlyBasalAsJson(OutputStream outputStream) throws IOException {
+        ObjectMapper mapper = new ObjectMapper();
+        System.out.println("»OrlaImpl.writeHourlyBasalAsJson(outputStream)");
+        List<Event> eventList = getEvents();
+        List<PumpBasalProfileConfig> basalProfileConfigs = Filter.only(eventList, PumpBasalProfileConfig.class);
+        PumpBasalProfileConfig lastBasalProfile = basalProfileConfigs.get(basalProfileConfigs.size() - 1);
+        String hourlyString = lastBasalProfile.getText();
+        ArrayNode hours = JsonNodeFactory.instance.arrayNode();
+        JsonNode hourlyJson = mapper.readTree(hourlyString);
+        System.out.println(hourlyJson);
+        for (int hour = 0; hour < 24; hour++) {
+            double basalRate = 0;
+            basalRate = hourlyJson.get(Integer.toString(hour)).asDouble();
+            hours.add(basalRate);
+        }
+        ObjectNode objectNode = JsonNodeFactory.instance.objectNode();
+        objectNode.put("daily_total", lastBasalProfile.getValue().doubleValue());
+        objectNode.put("hours", hours);
+        mapper.writeValue(outputStream, objectNode);
+    }
+
+    public void writeHourlyPercentiles(OutputStream outputStream, DateTime from, DateTime to) throws IOException {
+        List<Event> eventList = getEventsList(from,  to, false);
+        List<BloodGlucoseEvent> bgList = Filter.only(eventList, BloodGlucoseEvent.class);
+        Map<Integer, List<Double>> hoursBgList = new HashMap<Integer, List<Double>>(24);
+        for (int hour=0; hour < 24; hour++){
+            hoursBgList.put(hour, new ArrayList<Double>(150));
+        }
+        for(BloodGlucoseEvent bg: bgList) {
+            hoursBgList.get(bg.getStartTime().getHourOfDay()).add(bg.value.doubleValue());
+        }
+
+        Set<Integer> percentileLevels = Sets.newHashSet(15,25,50,75,85);
+
+        SortedMap<Integer, List<Pair<Integer, Double>>> data = new TreeMap<Integer, List<Pair<Integer, Double>>>();
+        for (Integer pl: percentileLevels) {
+            ArrayList<Pair<Integer, Double>> hourlyPercentiles = new ArrayList<Pair<Integer, Double>>(24);
+            for (int i=0; i<24; i++) {
+                hourlyPercentiles.add(null);
+            }
+            data.put(pl, hourlyPercentiles);
+        }
+
+        for (Integer hour: hoursBgList.keySet()) {
+            List<Double> hourBgList = hoursBgList.get(hour);
+            Map<Integer, Double> percentiles = Filter.percentiles(hourBgList, percentileLevels);
+
+            for(Integer pl: percentileLevels){
+                data.get(pl).set(hour, new ImmutablePair(hour, percentiles.get(pl)));
+            }
+        }
+        ObjectMapper mapper = new ObjectMapper();
+        SimpleModule module = new SimpleModule("Pair<Integer,Double> as [L,R]", new Version(0,0,1,null));
+        module.addSerializer(new PairSerializer(Pair.class));
+        mapper.registerModule(module);
+        mapper.writeValue(outputStream, data);
+
+    }
+
     public String getHealthGraphAuthorisation() throws OrlaException {
         System.out.println("»OrlaImpl.getHealthGraphAuthorisation()");
         try {

webapp/src/main/java/endafarrell/orla/service/data/DailyStats.java

@@ -1,6 +1,5 @@
 package endafarrell.orla.service.data;
 
-import endafarrell.orla.service.Convert;
 import endafarrell.orla.service.OrlaDateTimeFormat;
 import endafarrell.orla.service.OrlaObject;
 import org.codehaus.jackson.JsonNode;

webapp/src/main/java/endafarrell/orla/service/data/jackson/PairSerializer.java

@@ -0,0 +1,23 @@
+package endafarrell.orla.service.data.jackson;
+
+import org.apache.commons.lang3.tuple.Pair;
+import org.codehaus.jackson.JsonGenerationException;
+import org.codehaus.jackson.JsonGenerator;
+import org.codehaus.jackson.map.SerializerProvider;
+import org.codehaus.jackson.map.ser.std.SerializerBase;
+
+import java.io.IOException;
+
+public class PairSerializer<Integer,Double> extends SerializerBase<Pair<Integer,Double>> {
+    public PairSerializer(Class<Pair<Integer, Double>> t) {
+        super(t);
+    }
+
+    @Override
+    public void serialize(Pair<Integer, Double> value, JsonGenerator jgen, SerializerProvider provider) throws IOException, JsonGenerationException {
+        jgen.writeStartArray();
+        jgen.writeNumber((java.lang.Integer) value.getLeft());
+        jgen.writeNumber((java.lang.Double) value.getRight());
+        jgen.writeEndArray();
+    }
+}

webapp/src/main/webapp/graph.jsp

@@ -5,6 +5,7 @@
     <script type="text/javascript" src="<%=application.getContextPath()%>/js/jquery-1.7.2.min.js"></script>
     <script type="text/javascript" src="<%=application.getContextPath()%>/js/jquery.tmpl.min.js"></script>
     <script type="text/javascript" src="<%=application.getContextPath()%>/js/jquery.flot.js"></script>
+    <script type="text/javascript" src="<%=application.getContextPath()%>/js/jquery.flot.fillbetween.js"></script>
     <script type="text/javascript" src="<%=application.getContextPath()%>/js/orla.js"></script>
     <link  rel="stylesheet" type="text/css" media="all" href="<%=application.getContextPath()%>/css/orla.css">
     <script type="text/javascript">
@@ -18,7 +19,7 @@
     <div class="graph">
         <h3>Glucose readings</h3>
         <p>These are the bG readings in this time-frame.</p>
-        <div id="ph0" style="width: 90%; height: 300px"></div>
+        <div id="ph0" style="width: 85%; height: 300px"></div>
     </div>
     <div class="graph">
         <h3>Mean bG</h3>
@@ -32,6 +33,19 @@
         readings here suggest stability.</p>
         <div id="pha" style="width: 85%; height: 300px"></div>
     </div>
+
+    <div class="graph">
+        <h3>Hourly basal rates</h3>
+        <p>Here are the most recent hourly basal rates: totalling <span id="basalTotal"></span> IU/day.</p>
+        <div id="hourlyBasal"></div>
+        <div id="phh" style="width: 85%; height: 300px"></div>
+    </div>
+    <div class="graph">
+        <h3>Hourly percentile values</h3>
+        <p>Here are percentiled values for each hour</p>
+        <div id="php" style="width: 85%; height: 300px"></div>
+    </div>
+
     <div class="graph">
         <h3>Daily overlay</h3>
         <p>Here are the daily readings overlaid for this time-frame.</p>
@@ -88,11 +102,58 @@
             plots.push($.plot($("#pho"), overlays,
                     $.extend(true,{},
                              flotOptions, {
+                                grid:{markings: nightAreas },
                                 yaxes:[{tickFormatter: bGFormatter, tickDecimals:1}],
                                 legend:{show: false}
                             })));
         });
 
+        $.getJSON("<%=application.getContextPath()%>/api/home/hourlyBasal" + window.location.search, function (model) {
+            var basal = [];
+            var html = '<table width="85%">';
+            for (var index=0; index<6; index+=1){
+                html += '<tr>';
+                for (var subindex=0; subindex<24; subindex+=6){
+                    var hour = index+subindex;
+                    html+='<td width="25%" style="text-align: right">'+(hour)+":00 - "+(hour+1)+":00 " + (model.hours[hour]).toFixed(1) + " IU/hr</td>";
+                }
+                html += '</tr>'
+            }
+            html+='</table>';
+            $('#hourlyBasal').html(html);
+            $('#basalTotal').html(model["daily_total"]);
+            for (var index = 0; index < model.hours.length; index++) {
+                var dt =  new Date();
+                dt.setMinutes(0);
+                dt.setHours(index - (dt.getTimezoneOffset()/60));
+                basal.push([dt, model.hours[index]]);
+            }
+
+            plots.push($.plot($("#phh"), [{ data: basal, label: "Hourly basal rates", lines: { show: true, steps: true }}],
+                    $.extend(true,{},
+                            flotOptions, {
+                                yaxes:[{tickFormatter: bolusRateFormatter, tickDecimals:1}]}
+                    )));
+        });
+
+        $.getJSON("<%=application.getContextPath()%>/api/home/hourlyPercentiles" + window.location.search, function (model) {
+            var dataset = [
+                  { label: 'Glucose percentiles', data: model['50'], lines: { show: true }, color: "rgb(255,50,50)" },
+                  { id: 'bg15%', data: model['15'], lines: { show: true, lineWidth: 0, fill: false }, color: "rgb(255,50,50)" },
+                  { id: 'bg25%', data: model['25'], lines: { show: true, lineWidth: 0, fill: 0.2 }, color: "rgb(255,50,50)", fillBetween: 'bg15%' },
+                  { id: 'bg50%', data: model['50'], lines: { show: true, lineWidth: 0.5, fill: 0.4, shadowSize: 0 }, color: "rgb(255,50,50)", fillBetween: 'bg25%' },
+                  { id: 'bg75%', data: model['75'], lines: { show: true, lineWidth: 0, fill: 0.4 }, color: "rgb(255,50,50)", fillBetween: 'bg50%' },
+                  { id: 'bg85%', data: model['85'], lines: { show: true, lineWidth: 0, fill: 0.2 }, color: "rgb(255,50,50)", fillBetween: 'bg75%' }
+            ];
+            plots.push($.plot($("#php"), dataset, $.extend(true, {},
+                    flotOptions, {
+                        xaxis: { mode: null, min: 0, max: 23, ticks:[2,4,6,8,10,12,14,16,18,20,22] },
+                        yaxes: [{tickFormatter: bGFormatter, tickDecimals:1}],
+                        legend: { position: 'se' }
+                    })));
+        });
+
+
         setTimeout(function(){
             for (var index = 0; index < plots.length; index++){
                 plots[index].getPlaceholder().bind("plothover", function (event, pos, item) {

webapp/src/main/webapp/index.jsp

@@ -1,4 +1,4 @@
-<%@ page import="org.joda.time.DateTime,endafarrell.orla.service.OrlaDateTimeFormat"%><%
+<%
     String to = OrlaDateTimeFormat.PRETTY_yyyyMMdd.print(DateTime.now());
     String from = OrlaDateTimeFormat.PRETTY_yyyyMMdd.print(DateTime.now().minusWeeks(12));
 %><!DOCTYPE HTML>
@@ -33,7 +33,7 @@
                             <span class="unit">g carbs</span>
                         {{else clazz=="BloodGlucoseEvent"}}
                             <span class="time">${hhmm}</span>
-                            <span class="bG">${value}</span>
+                            <span class="bG">${value.toFixed(1)}</span>
                             <span class="unit">mmol/L</span>
                         {{else clazz=="TwitterEvent"}}
                             <span class="time">${hhmm}</span>