PDCIStatistics for FaoInstitute

src/main/java/org/genesys2/server/model/genesys/PDCI.java

@@ -24,6 +24,7 @@ import javax.persistence.FetchType;
 import javax.persistence.JoinColumn;
 import javax.persistence.OneToOne;
 import javax.persistence.PrePersist;
+import javax.persistence.PreUpdate;
 import javax.persistence.Table;
 import javax.persistence.Transient;
 
@@ -77,6 +78,7 @@ public class PDCI extends VersionedModel {
 	private int cropName = 0;
 
 	@PrePersist
+	@PreUpdate
 	protected void prePersist() {
 		this.score = calculateScore();
 		this.scoreHist = (float) (Math.ceil(this.score * 2) / 2);

src/main/java/org/genesys2/server/model/genesys/PDCIStatistics.java

+/**
+ * Copyright 2015 Global Crop Diversity Trust
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ **/
+
+package org.genesys2.server.model.genesys;
+
+import java.io.Serializable;
+import java.util.List;
+
+/**
+ * Institute PDCI statistics
+ */
+public class PDCIStatistics implements Serializable {
+
+	private Float min = null;
+	private Float max = null;
+	private Double avg = null;
+
+	private long[] histogram = new long[21];
+	private Long count;
+
+	public void setMin(Float value) {
+		this.min = value;
+	}
+
+	public Float getMin() {
+		return min;
+	}
+
+	public void setMax(Float value) {
+		this.max = value;
+	}
+
+	public Float getMax() {
+		return max;
+	}
+
+	public void setAvg(Double value) {
+		this.avg = value;
+	}
+
+	public Double getAvg() {
+		return avg;
+	}
+
+	public void setCount(Long value) {
+		this.count = value;
+	}
+
+	public Long getCount() {
+		return count;
+	}
+
+	public long[] getHistogram() {
+		return histogram;
+	}
+
+	/**
+	 * Converts {@link #histogram} to flot.categories compatible JSON
+	 * 
+	 * @return
+	 */
+	public String getHistogramJson() {
+		StringBuffer sb = new StringBuffer();
+		sb.append("[ ");
+		for (int i = 0; i < histogram.length; i++) {
+			if (i > 0)
+				sb.append(", ");
+			sb.append("['").append(i / 2.0).append("', ").append(histogram[i]).append("]");
+		}
+		sb.append(" ]");
+		return sb.toString();
+	}
+
+	/**
+	 * Fill {@link #histogram} with data
+	 * 
+	 * @param hist
+	 */
+	public void makeHistogram(List<Object[]> hist) {
+		for (Object[] h : hist) {
+
+			// Determining JPA data types
+			// System.err.println("Hist " + h[0].getClass() + " " +
+			// h[1].getClass());
+
+			int index = (int) (((Float) h[0]) * 2);
+			long count = (Long) h[1];
+
+			// System.err.println("Index for " + h[0] + " = " + index +
+			// " count=" + count);
+
+			histogram[index] = count;
+		}
+	}
+}

src/main/java/org/genesys2/server/persistence/domain/PDCIRepository.java

@@ -16,7 +16,10 @@
 
 package org.genesys2.server.persistence.domain;
 
+import java.util.List;
+
 import org.genesys2.server.model.genesys.PDCI;
+import org.genesys2.server.model.impl.FaoInstitute;
 import org.springframework.data.jpa.repository.JpaRepository;
 import org.springframework.data.jpa.repository.Query;
 
@@ -25,4 +28,25 @@ public interface PDCIRepository extends JpaRepository<PDCI, Long> {
 	@Query("select pdci from PDCI pdci where pdci.accession.id=?1")
 	PDCI findByAccessionId(Long accessionId);
 
+	/**
+	 * Gets [ min(pdci.score), max(pdci.score), avg(pdci.score), count(pdci) ]
+	 * for PDCI of {@link FaoInstitute}
+	 * 
+	 * @param faoInstitute
+	 * @return [ Float min(pdci.score), Float max(pdci.score), Double
+	 *         avg(pdci.score), Long count(pdci) ]
+	 */
+	@Query("select min(pdci.score), max(pdci.score), avg(pdci.score), count(pdci) from Accession a join a.accessionId.pdci pdci where a.institute = ?1")
+	Object statistics(FaoInstitute faoInstitute);
+
+	/**
+	 * Get PDCI histogram for {@link FaoInstitute} by
+	 * {@link PDCI#getScoreHist()}
+	 * 
+	 * @param faoInstitute
+	 * @return List of [ scoreHist, count ]
+	 */
+	@Query("select pdci.scoreHist, count(pdci) from Accession a join a.accessionId.pdci pdci where a.institute = ?1 group by pdci.scoreHist")
+	List<Object[]> histogram(FaoInstitute faoInstitute);
+
 }

src/main/java/org/genesys2/server/service/GenesysService.java

@@ -40,6 +40,7 @@ import org.genesys2.server.model.genesys.ExperimentTrait;
 import org.genesys2.server.model.genesys.Metadata;
 import org.genesys2.server.model.genesys.Method;
 import org.genesys2.server.model.genesys.PDCI;
+import org.genesys2.server.model.genesys.PDCIStatistics;
 import org.genesys2.server.model.genesys.SvalbardData;
 import org.genesys2.server.model.genesys.Taxonomy2;
 import org.genesys2.server.model.impl.AccessionIdentifier3;
@@ -232,4 +233,6 @@ public interface GenesysService {
 
 	PDCI loadPDCI(Long accessionId);
 
+	PDCIStatistics statisticsPDCI(FaoInstitute faoInstitute);
+
 }

src/main/java/org/genesys2/server/service/StatisticsService.java

@@ -16,6 +16,9 @@
 
 package org.genesys2.server.service;
 
+import org.genesys2.server.model.genesys.PDCIStatistics;
+import org.genesys2.server.model.impl.FaoInstitute;
+
 public interface StatisticsService {
 
 	long numberOfCountries();
@@ -24,4 +27,6 @@ public interface StatisticsService {
 
 	long numberOfAccessions();
 
+	PDCIStatistics statisticsPDCI(FaoInstitute faoInstitute);
+
 }

src/main/java/org/genesys2/server/service/impl/GenesysServiceImpl.java

@@ -61,6 +61,7 @@ import org.genesys2.server.model.genesys.ExperimentTrait;
 import org.genesys2.server.model.genesys.Metadata;
 import org.genesys2.server.model.genesys.Method;
 import org.genesys2.server.model.genesys.PDCI;
+import org.genesys2.server.model.genesys.PDCIStatistics;
 import org.genesys2.server.model.genesys.SelfCopy;
 import org.genesys2.server.model.genesys.SvalbardData;
 import org.genesys2.server.model.genesys.Taxonomy2;
@@ -1557,6 +1558,7 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 
 	@Override
 	@Transactional
+	@CacheEvict(value = "statistics", allEntries = true)
 	public PDCI updatePDCI(Long accessionId) {
 		if (pdciCalculator == null) {
 			return null;
@@ -1569,4 +1571,31 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 		}
 		return repoPdci.save(pdciCalculator.updatePdci(pdci, accessionId));
 	}
+
+	@Override
+	public PDCIStatistics statisticsPDCI(FaoInstitute faoInstitute) {
+		PDCIStatistics stats = new PDCIStatistics();
+
+		Object[] overall = (Object[]) repoPdci.statistics(faoInstitute);
+		if (overall == null) {
+			LOG.warn("No PDCI statistics for " + faoInstitute);
+			return null;
+		}
+
+		// Determining JPA data types
+		// System.err.println(overall[0].getClass());
+		// System.err.println(overall[1].getClass());
+		// System.err.println(overall[2].getClass());
+		// System.err.println(overall[3].getClass());
+
+		stats.setMin((Float) overall[0]);
+		stats.setMax((Float) overall[1]);
+		stats.setAvg((Double) overall[2]);
+		stats.setCount((Long) overall[3]);
+
+		List<Object[]> hist = repoPdci.histogram(faoInstitute);
+		stats.makeHistogram(hist);
+
+		return stats;
+	}
 }

src/main/java/org/genesys2/server/service/impl/StatisticsServiceImpl.java

@@ -16,6 +16,10 @@
 
 package org.genesys2.server.service.impl;
 
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+import org.genesys2.server.model.genesys.PDCIStatistics;
+import org.genesys2.server.model.impl.FaoInstitute;
 import org.genesys2.server.service.GenesysService;
 import org.genesys2.server.service.GeoService;
 import org.genesys2.server.service.InstituteService;
@@ -28,6 +32,8 @@ import org.springframework.transaction.annotation.Transactional;
 @Service
 @Transactional(readOnly = true)
 public class StatisticsServiceImpl implements StatisticsService {
+	public static final Log LOG = LogFactory.getLog(StatisticsServiceImpl.class);
+
 	@Autowired
 	private GeoService geoService;
 
@@ -54,4 +60,13 @@ public class StatisticsServiceImpl implements StatisticsService {
 	public long numberOfAccessions() {
 		return genesysService.countAll();
 	}
+
+	@Override
+	@Cacheable(unless = "#result == null", value = "statistics", key = "'stats.' + #root.methodName + '-' + #faoInstitute.id")
+	public PDCIStatistics statisticsPDCI(FaoInstitute faoInstitute) {
+		if (LOG.isInfoEnabled()) {
+			LOG.info("Regenerating PDCI statistics for " + faoInstitute);
+		}
+		return genesysService.statisticsPDCI(faoInstitute);
+	}
 }

src/main/java/org/genesys2/server/service/worker/ElasticUpdater.java

@@ -94,12 +94,6 @@ public class ElasticUpdater {
 	 * @param ids
 	 */
 	public void update(Class<?> clazz, Long id) {
-		// If Accession, update PDCI
-		if (Accession.class.equals(clazz) && id !=null) {
-			genesysService.updatePDCI(id);
-		}
-		
-		
 		ElasticNode node = new ElasticNode(clazz, id);
 
 		elasticRemoveQueue.remove(node);

src/main/java/org/genesys2/server/service/worker/ElasticUpdaterProcessor.java

@@ -8,7 +8,9 @@ import javax.annotation.Resource;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
+import org.genesys2.server.model.genesys.Accession;
 import org.genesys2.server.service.ElasticService;
+import org.genesys2.server.service.GenesysService;
 import org.genesys2.server.service.worker.ElasticUpdater.ElasticNode;
 import org.springframework.beans.factory.DisposableBean;
 import org.springframework.beans.factory.InitializingBean;
@@ -41,6 +43,9 @@ class ElasticUpdaterProcessor implements Runnable, InitializingBean, DisposableB
 	@Resource
 	private IQueue<ElasticNode> elasticUpdateQueue;
 
+	@Autowired
+	private GenesysService genesysService;
+
 	private long indexDelay = 5000;
 
 	private HashMap<String, Set<Long>> buckets = new HashMap<String, Set<Long>>();
@@ -130,6 +135,12 @@ class ElasticUpdaterProcessor implements Runnable, InitializingBean, DisposableB
 			return;
 
 		String className = toUpdate.getClassName();
+
+		// If Accession, update PDCI
+		if (Accession.class.getName().equals(className)) {
+			genesysService.updatePDCI(toUpdate.getId());
+		}
+
 		Set<Long> bucket = buckets.get(className);
 		if (bucket == null) {
 			buckets.put(className, bucket = new HashSet<Long>());

src/main/java/org/genesys2/server/servlet/controller/AccessionController.java

@@ -30,6 +30,7 @@ import org.genesys2.server.service.DSService;
 import org.genesys2.server.service.FilterConstants;
 import org.genesys2.server.service.GenesysService;
 import org.genesys2.server.service.InstituteService;
+import org.genesys2.server.service.StatisticsService;
 import org.genesys2.server.service.TaxonomyService;
 import org.genesys2.server.service.TraitService;
 import org.genesys2.server.service.impl.NonUniqueAccessionException;
@@ -69,6 +70,9 @@ public class AccessionController extends BaseController {
 	@Autowired(required = false)
 	private PDCICalculator pdciCalculator;
 
+	@Autowired
+	private StatisticsService statisticsService;
+
 	@RequestMapping("/id/{accessionId}")
 	public String view(ModelMap model, @PathVariable(value = "accessionId") long accessionId) {
 		_logger.debug("Viewing ACN " + accessionId);
@@ -118,6 +122,7 @@ public class AccessionController extends BaseController {
 				}
 
 				model.addAttribute("pdci", pdci);
+				model.addAttribute("institutePDCI", statisticsService.statisticsPDCI(accession.getInstitute()));
 				
 			} catch (Throwable e) {
 				_logger.warn(e.getMessage(), e);

src/main/java/org/genesys2/server/servlet/controller/WiewsController.java

@@ -37,6 +37,7 @@ import org.genesys2.server.service.GenesysService;
 import org.genesys2.server.service.GeoService;
 import org.genesys2.server.service.InstituteService;
 import org.genesys2.server.service.OrganizationService;
+import org.genesys2.server.service.StatisticsService;
 import org.genesys2.server.service.TaxonomyService;
 import org.genesys2.server.service.impl.FilterHandler;
 import org.genesys2.server.service.impl.FilterHandler.AppliedFilter;
@@ -83,6 +84,9 @@ public class WiewsController extends BaseController {
 	@Autowired
 	private DownloadService downloadService;
 
+	@Autowired
+	private StatisticsService statisticsService;
+
 	@RequestMapping("/")
 	public String view(ModelMap model, @RequestParam(value = "page", required = false, defaultValue = "1") int page) {
 		model.addAttribute("pagedData", instituteService.listPGRInstitutes(new PageRequest(page - 1, 50, new Sort("code"))));
@@ -128,6 +132,7 @@ public class WiewsController extends BaseController {
 
 		model.addAttribute("statisticsGenus", genesysService.statisticsGenusByInstitute(faoInstitute, new PageRequest(0, 30)));
 		model.addAttribute("statisticsTaxonomy", genesysService.statisticsSpeciesByInstitute(faoInstitute, new PageRequest(0, 30)));
+		model.addAttribute("statisticsPDCI", statisticsService.statisticsPDCI(faoInstitute));
 
 		return "/wiews/details";
 	}

src/main/resources/content/language.properties

@@ -622,7 +622,8 @@ admin.kpi.execution.page=KPI Execution
 admin.kpi.executionrun.page=Execution run details
 
 accession.pdci=Passport Data Completeness Index
-accession.pdci.jumbo=PDCI Score: {0} of 10.0
+accession.pdci.jumbo=PDCI Score: {0,number,0.00} of 10.0
+accession.pdci.institute-avg=Average PDCI score for this institute is {0,number,0.00}
 accession.pdci.about-link=Read about Passport Data Completeness Index
 accession.pdci.independent-items=Independent of the population type
 accession.pdci.dependent-items=Depending on the population type

src/main/sourceapp/js/crophub.js

@@ -11,7 +11,7 @@ var GenesysMaps = {
     this.lng = lng;
     this.noWrap = true;
   },
-  
+
   loaded : false,
   queue : [],
   loadedMaps : [],
@@ -89,6 +89,27 @@ GenesysMaps.BoundingBox.prototype.getBounds = function() {
 };
 
 var GenesysChart = {
+
+  histogram : function(placeholder, data) {
+    $.plot(placeholder, [ {
+      data : data,
+      color : '#88ba42'
+    } ], {
+      series : {
+        bars : {
+          show : true,
+          barWidth : 0.4,
+          fill : 1,
+          lineWidth : 0,
+          align : 'center'
+        }
+      },
+      xaxis : {
+        tickLength : 0
+      }
+    });
+  },
+
   chart : function(placeholder, url, options, labelCallback, clickCallback) {
 
     var defaultOptions = {
@@ -328,7 +349,7 @@ var GenesysFilterUtil = {
     fe.toggleClass('edit-filter');
     fe.find('.filter-values').parent().toggleClass('col-lg-9').toggleClass('col-lg-4');
   },
-  normKey: function(key) {
+  normKey : function(key) {
     return key.replace(/\./g, '-').replace(/:/g, '_');
   }
 };

src/main/webapp/WEB-INF/jsp/accession/details.jsp

@@ -645,7 +645,27 @@
 
   <security:authorize access="isAuthenticated()">
     <c:if test="${pdci ne null}">
-      <local:pdci value="${pdci}" />
+      <div class="crop-details">
+
+        <h4>
+          <spring:message code="accession.pdci" />
+        </h4>
+        <div class="jumbotron pdci-score">
+          <div>
+            <h3>
+              <spring:message code="accession.pdci.jumbo" arguments="${pdci.score}" />
+            </h3>
+            <small> <c:if test="${institutePDCI ne null}">
+                <spring:message code="accession.pdci.institute-avg" arguments="${institutePDCI.avg}" />
+              </c:if> <a href="<c:url value="/content/passport-data-completeness-index" />"><spring:message
+                  code="accession.pdci.about-link"
+                /></a></small>
+          </div>
+        </div>
+
+        <local:pdci value="${pdci}" />
+
+      </div>
     </c:if>
   </security:authorize>
 

src/main/webapp/WEB-INF/tags/pdci.tag

@@ -6,40 +6,23 @@
 <%
 	
 %>
-<div class="crop-details">
-
-<h4>
-  <spring:message code="accession.pdci" />
-</h4>
-<div class="jumbotron pdci-score">
-  <div>
-    <h3>
-      <spring:message code="accession.pdci.jumbo" arguments="${value.score}" />
-    </h3>
-    <small><a href="<c:url value="/content/passport-data-completeness-index" />"><spring:message
-          code="accession.pdci.about-link"
-        /></a></small>
-  </div>
-</div>
-
-  <%-- <h5>
+<%-- <h5>
     <spring:message code="accession.pdci.independent-items" />
   </h5> --%>
-  <div class="row">
-    <c:forEach items="${pdci.independentItems}" var="item">
-      <div class="col-sm-3 col-xs-5 ${pdci[item] == 0 ? 'pdci-improve' : ''}">${item.toUpperCase()}</div>
-      <div class="col-sm-1 col-xs-1">${pdci[item]}</div>
-    </c:forEach>
-  </div>
-  <h5>
-    <spring:message code="accession.pdci.dependent-items" />
-  </h5>
-  <div class="row">
-    <c:forEach items="${pdci.dependentItems}" var="item">
-      <div class="col-sm-3  col-xs-5 ${pdci[item] == 0 ? 'pdci-improve' : ''}">${item.toUpperCase()}</div>
-      <div class="col-sm-1 col-xs-1">${pdci[item]}</div>
-    </c:forEach>
-  </div>
+<div class="row">
+  <c:forEach items="${pdci.independentItems}" var="item">
+    <div class="col-sm-3 col-xs-5 ${pdci[item] == 0 ? 'pdci-improve' : ''}">${item.toUpperCase()}</div>
+    <div class="col-sm-1 col-xs-1">${pdci[item]}</div>
+  </c:forEach>
+</div>
+<h5>
+  <spring:message code="accession.pdci.dependent-items" />
+</h5>
+<div class="row">
+  <c:forEach items="${pdci.dependentItems}" var="item">
+    <div class="col-sm-3  col-xs-5 ${pdci[item] == 0 ? 'pdci-improve' : ''}">${item.toUpperCase()}</div>
+    <div class="col-sm-1 col-xs-1">${pdci[item]}</div>
+  </c:forEach>
 </div>
 <%-- <c:forEach items="${pdci.independentItems}" var="item">
 accession.pdci.${item}=<br />