From 96c10a8854e6362eb64722fde481934249f6646a Mon Sep 17 00:00:00 2001
From: =?utf8?q?Andreas=20M=C3=BCller?= <a.mueller@bgbm.org>
Date: Mon, 12 Sep 2016 16:25:07 +0200
Subject: [PATCH] fix #5957 fix IndexOutOfBound exception and some other
 improvements for groupByHigherTaxon

---
 .../persistence/dao/taxon/ITaxonNodeDao.java  | 20 ++++---
 .../service/ClassificationServiceImpl.java    |  2 +-
 .../cdm/api/service/TreeIndexComparator.java  | 11 +++-
 .../cdm/api/service/dto/GroupedTaxonDTO.java  | 11 ++++
 .../api/service/TreeIndexComparatorTest.java  | 52 +++++++++++++++++++
 5 files changed, 86 insertions(+), 10 deletions(-)
 create mode 100644 cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/TreeIndexComparatorTest.java

diff --git a/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/taxon/ITaxonNodeDao.java b/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/taxon/ITaxonNodeDao.java
index fd36c8eb27..4908eca48b 100644
--- a/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/taxon/ITaxonNodeDao.java
+++ b/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/taxon/ITaxonNodeDao.java
@@ -75,18 +75,24 @@ public interface ITaxonNodeDao extends IAnnotatableDao<TaxonNode> {
     long countTaxonNodeAgentRelations(UUID taxonUuid, UUID classificationUuid, UUID agentUuid, UUID rankUuid, UUID relTypeUuid);
 
     /**
-     * @param treeIndexClosure
-     * @param minRankOrderIndex
-     * @param maxRankOrderIndex
+     * Computes a map treeIndex->rank(sortIndex) for each given taxon node treeIndex. Required by #5957.
+     * If the taxon represented by the treeindex is not in the given rank range no record is returned for the given
+     * treeindex.
+     *
+     * @param treeIndex the list of treeIndexes
+     * @param minRankOrderIndex min rank
+     * @param maxRankOrderIndex max rank
      * @return
      */
-    Map<String, Integer> rankOrderIndexForTreeIndex(List<String> treeIndexClosure, Integer minRankOrderIndex,
+    Map<String, Integer> rankOrderIndexForTreeIndex(List<String> treeIndex, Integer minRankOrderIndex,
             Integer maxRankOrderIndex);
 
     /**
-     * @param keySet
-     * @return
+     * For a given set of taxon node tree indexes the uuid and title cache of the taxon represented
+     * by this treeindex is returned.
+     * @param treeIndexSet set of taxon node tree indexes
+     * @return map with treeindex and uuidAndTitleCache of the represented taxon
      */
-    Map<String, UuidAndTitleCache<?>> taxonUuidsForTreeIndexes(Set<String> keySet);
+    Map<String, UuidAndTitleCache<?>> taxonUuidsForTreeIndexes(Set<String> treeIndexSet);
 
 }
diff --git a/cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/ClassificationServiceImpl.java b/cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/ClassificationServiceImpl.java
index 0283481887..52b02a93e8 100755
--- a/cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/ClassificationServiceImpl.java
+++ b/cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/ClassificationServiceImpl.java
@@ -625,7 +625,7 @@ public class ClassificationServiceImpl extends IdentifiableServiceBase<Classific
         //get treeindex for each taxonUUID
         Map<UUID, String> taxonIdTreeIndexMap = dao.treeIndexForTaxonUuids(classificationUuid, originalTaxonUuids);
 
-        //build treeindex tree or list
+        //build treeindex list (or tree)
         List<String> treeIndexClosure = new ArrayList<>();
         for (String treeIndex : taxonIdTreeIndexMap.values()){
             String[] splits = treeIndex.substring(1).split(ITreeNode.separator);
diff --git a/cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/TreeIndexComparator.java b/cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/TreeIndexComparator.java
index 35c7be89a5..3fa24c6aa1 100644
--- a/cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/TreeIndexComparator.java
+++ b/cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/TreeIndexComparator.java
@@ -17,6 +17,9 @@ import eu.etaxonomy.cdm.model.common.ITreeNode;
  * @author a.mueller
  * @date 05.07.2016
  *
+ * Comparator for treeindexes.
+ * Compares the tree indexes node by node, sorted by node number.
+ * If one index is shorter than the other one but
  */
 public class TreeIndexComparator implements Comparator<String>{
 
@@ -29,12 +32,16 @@ public class TreeIndexComparator implements Comparator<String>{
         }else if (treeIndex2 == null){
             return 1;
         }
+        if (treeIndex1.equals(treeIndex2)){
+            return 0;
+        }
+
         String[] splits1 = treeIndex1.split(ITreeNode.separator);
         String[] splits2 = treeIndex2.split(ITreeNode.separator);
 
 
-        for (int i=0; i<splits1.length; i++){
-            if (splits2.length < i){
+        for (int i=0; i < splits1.length; i++){
+            if (splits2.length <= i){
                 return 1;
             }
             int c = splits1[i].compareTo(splits2[i]);
diff --git a/cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/dto/GroupedTaxonDTO.java b/cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/dto/GroupedTaxonDTO.java
index 83b9a4535a..43536f51af 100644
--- a/cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/dto/GroupedTaxonDTO.java
+++ b/cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/dto/GroupedTaxonDTO.java
@@ -65,4 +65,15 @@ public class GroupedTaxonDTO {
     public void setGroupTaxonName(String groupTaxonName) {
         this.groupTaxonName = groupTaxonName;
     }
+
+//*********************** toString() ***************************/
+    @Override
+    public String toString() {
+        String result = "taxon:" + (taxonUuid == null? "-":taxonUuid.toString())
+                + "; group:" + (groupTaxonUuid == null? "-":groupTaxonUuid.toString())
+                + "; group name:" + (groupTaxonName == null? "-":groupTaxonName.toString());
+        return result;
+    }
+
+
 }
diff --git a/cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/TreeIndexComparatorTest.java b/cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/TreeIndexComparatorTest.java
new file mode 100644
index 0000000000..ac057dbe76
--- /dev/null
+++ b/cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/TreeIndexComparatorTest.java
@@ -0,0 +1,52 @@
+// $Id$
+/**
+* Copyright (C) 2016 EDIT
+* European Distributed Institute of Taxonomy
+* http://www.e-taxonomy.eu
+*
+* The contents of this file are subject to the Mozilla Public License Version 1.1
+* See LICENSE.TXT at the top of this package for the full license terms.
+*/
+package eu.etaxonomy.cdm.api.service;
+
+import org.junit.Assert;
+import org.junit.Test;
+
+
+/**
+ * @author a.mueller
+ * @date 12.09.2016
+ *
+ */
+public class TreeIndexComparatorTest {
+
+    @Test
+    public void test() {
+        TreeIndexComparator comparator = new TreeIndexComparator();
+
+        //both null
+        Assert.assertTrue(0 == comparator.compare(null, null));
+        //one null
+        Assert.assertTrue(0 > comparator.compare(null, "#t10#10#"));
+        Assert.assertTrue(0 < comparator.compare("#t10#10#", null));
+        //equal
+        Assert.assertTrue(0 == comparator.compare("#t10#10#", "#t10#10#"));
+
+        //same start
+        Assert.assertTrue(0 > comparator.compare("#t10#10#", "#t10#10#20#"));
+        Assert.assertTrue(0 < comparator.compare("#t10#10#20#", "#t10#10#"));
+
+        //different ends
+        Assert.assertTrue(0 > comparator.compare("#t10#10#20#", "#t10#10#30#"));
+        Assert.assertTrue(0 < comparator.compare("#t10#10#30#", "#t10#10#20#"));
+
+        //different ends
+        Assert.assertTrue(0 > comparator.compare("#t10#10#20#", "#t10#10#30#"));
+        Assert.assertTrue(0 > comparator.compare("#t10#10#20#", "#t10#10#30#11"));
+
+        Assert.assertTrue(0 < comparator.compare("#t10#10#30#", "#t10#10#20#"));
+        Assert.assertTrue(0 < comparator.compare("#t10#10#30#11", "#t10#10#20#"));
+
+    }
+
+}
-- 
2.34.1