cleanup

diff --git a/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/statistics/StatisticsDaoHibernateImpl.java b/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/statistics/StatisticsDaoHibernateImpl.java
index 88b6aec567cc0833b40d4ed9accd9696bfb43305..3bb0f5482538e1eabd41680d49bb459f86fe5e72 100644 (file)
--- a/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/statistics/StatisticsDaoHibernateImpl.java
+++ b/cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/statistics/StatisticsDaoHibernateImpl.java
@@ -477,8 +477,8 @@ public class StatisticsDaoHibernateImpl
                        + "FROM TaxonNode tn "
                                + "  JOIN tn.taxon.relationsFromThisTaxon as tr "
                                + "WHERE tn.classification=:classification "
-                               + "  AND tn.taxon is not null "
-                               + "  AND tr.source.citation is not null ");
+                               + "  AND tn.taxon IS NOT NULL "
+                               + "  AND tr.source.citation IS NOT NULL ");
 
 
                // get hybrid relation citations
@@ -487,8 +487,8 @@ public class StatisticsDaoHibernateImpl
                        + "FROM TaxonNode tn "
                                + "  JOIN tn.taxon.name.hybridParentRelations as hr "
                                + "WHERE tn.classification=:classification "
-                               + "  AND tn.taxon is not null "
-                               + "  AND tn.taxon.name is not null ");
+                               + "  AND tn.taxon IS NOT NULL "
+                               + "  AND tn.taxon.name IS NOT NULL ");
 
                // synonyms:
                queryStrings.add("SELECT distinct hr.source.citation.uuid "
@@ -496,9 +496,9 @@ public class StatisticsDaoHibernateImpl
                                + "  JOIN tn.taxon.synonyms as sy "
                                + "  JOIN sy.name.hybridParentRelations as hr "
                                + "WHERE tn.classification=:classification "
-                               + "  AND sy is not null "
+                               + "  AND sy IS NOT NULL "
                                // TODO: is this case actually possible???
-                               + "  AND sy.name is not null ");
+                               + "  AND sy.name IS NOT NULL ");
 
                // get name relations references:
                // -------------------------------------------------------
@@ -506,8 +506,8 @@ public class StatisticsDaoHibernateImpl
                queryStrings.add("SELECT distinct nr.source.citation.uuid from TaxonNode tn "
                                + "JOIN tn.taxon.name.relationsFromThisName as nr "
                                + "WHERE tn.classification=:classification "
-                               + "  AND tn.taxon is not null "
-                               + "  AND tn.taxon.name is not null ");
+                               + "  AND tn.taxon IS NOT NULL "
+                               + "  AND tn.taxon.name IS NOT NULL ");
 
                // synonyms:
                queryStrings.add("SELECT distinct nr.source.citation.uuid "
@@ -515,8 +515,8 @@ public class StatisticsDaoHibernateImpl
                                + "  JOIN tn.taxon.synonyms as sy "
                                + "  JOIN sy.name.relationsFromThisName as nr "
                                + "WHERE tn.classification=:classification "
-                               + "  AND sy is not null " // TODO: is this case actually possible???
-                               + "  AND sy.name is not null ");
+                               + "  AND sy IS NOT NULL " // TODO: is this case actually possible???
+                               + "  AND sy.name IS NOT NULL ");
 
                // get Nomenclatural status citation
 
@@ -525,8 +525,8 @@ public class StatisticsDaoHibernateImpl
                        + "FROM TaxonNode tn "
                                + "  JOIN tn.taxon.name.status as s "
                                + "WHERE tn.classification=:classification "
-                               + "  AND tn.taxon is not null "
-                               + "  AND tn.taxon.name is not null ");
+                               + "  AND tn.taxon IS NOT NULL "
+                               + "  AND tn.taxon.name IS NOT NULL ");
 
                // get sequences which contain citations and publishedIn ------
                // and contain "Media" which could be of the subtype
@@ -541,7 +541,7 @@ public class StatisticsDaoHibernateImpl
                                + "  JOIN seq.citations as cit "
                                + "WHERE so.class=:dnaSample "
                                + "  AND tn.classification=:classification "
-                               + "  AND cit is not null ");
+                               + "  AND cit IS NOT NULL ");
 
                // traverse to specimenOrObservation via individualsAssociation
 
@@ -555,7 +555,7 @@ public class StatisticsDaoHibernateImpl
                                + "WHERE so.class=:dnaSample "
                                + "  AND ia.class=:individualsAssociation "
                                + "  AND tn.classification=:classification "
-                               + "  AND cit is not null ");
+                               + "  AND cit IS NOT NULL ");
 
                // we do assume, that a name description would not have a
                // SpecimenOrObservation element
@@ -849,7 +849,7 @@ public class StatisticsDaoHibernateImpl
                        + "FROM TaxonNode tn "
                                + "  JOIN tn.taxon.relationsFromThisTaxon as tr "
                                + "WHERE tn.classification=:classification "
-                               + "  AND tn.taxon is not null "
+                               + "  AND tn.taxon IS NOT NULL "
                                + "  AND tr.source.citation is not null ");
 
                // get hybrid relation citations
@@ -861,7 +861,6 @@ public class StatisticsDaoHibernateImpl
                                + "  AND tn.taxon is not null "
                                + "  AND tn.taxon.name is not null ");
 
-
                // synonyms:
                queryStrings.add("SELECT COUNT(DISTINCT hr.source.citation.id) from TaxonNode tn "
                                + "join tn.taxon.synonyms as sy "

diff --git a/cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/TaxonNodeServiceImplTest.java b/cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/TaxonNodeServiceImplTest.java
index 6598cc0c0f48d77d8bed240470684cc140030f5e..5378a6e6ce1b1c8cd60035ae5b0f7db2f89c99fd 100644 (file)
--- a/cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/TaxonNodeServiceImplTest.java
+++ b/cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/TaxonNodeServiceImplTest.java
@@ -758,8 +758,6 @@ public class TaxonNodeServiceImplTest extends CdmTransactionalIntegrationTest{
     @DataSet("TaxonNodeServiceImplTest.testSetSecundumForSubtree.xml")
     public void testSetSecundumForSubtreeNoOverwrite(){
         UUID subTreeUuid = UUID.fromString("484a1a77-689c-44be-8e65-347d835f47e8");
-//        UUID taxon1uuid = UUID.fromString("55c3e41a-c629-40e6-aa6a-ff274ac6ddb1");
-//        UUID taxon5uuid = UUID.fromString("d0b99fee-a783-4dda-b8a2-8960703cfcc2");
         Reference newSec = referenceService.find(UUID.fromString("1d3fb074-d7ba-47e4-be94-b4cb1a99afa7"));
 
         //assert current state

diff --git a/cdmlib-services/src/test/resources/eu/etaxonomy/cdm/api/service/TaxonServiceImplTest.xml b/cdmlib-services/src/test/resources/eu/etaxonomy/cdm/api/service/TaxonServiceImplTest.xml
index bcf82c4a590f454d4ebc61667ad180c626a8b609..ae0f8a059de455f8c44a55abb2924d0677d6d4e3 100644 (file)
--- a/cdmlib-services/src/test/resources/eu/etaxonomy/cdm/api/service/TaxonServiceImplTest.xml
+++ b/cdmlib-services/src/test/resources/eu/etaxonomy/cdm/api/service/TaxonServiceImplTest.xml
@@ -1,13 +1,13 @@
 <?xml version='1.0' encoding='UTF-8'?>\r
 <dataset xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="../../database/schema/dataset.xsd">\r
-  <TAXONBASE DTYPE="Taxon" ID="4" CREATED="2009-02-03 17:52:26.0" UUID="aafce7fe-0c5f-42ed-814b-4c7c2c715660" TITLECACHE="Abies sec. ???"                      PROTECTEDTITLECACHE="false" DOUBTFUL="false" PUBLISH="true" USENAMECACHE="false" TAXONSTATUSUNKNOWN="false" NAME_ID="4"/>\r
-  <TAXONBASE DTYPE="Taxon" ID="5" CREATED="2009-02-03 17:52:26.0" UUID="5c1a3d10-3a32-45d1-a5ae-1e982533b79f" TITLECACHE="Abies alba sec. ???"                 PROTECTEDTITLECACHE="false" DOUBTFUL="false" PUBLISH="true" USENAMECACHE="false" TAXONSTATUSUNKNOWN="false" NAME_ID="5"/>\r
-  <TAXONBASE DTYPE="Synonym" ID="6" CREATED="2009-02-03 17:52:26.0" UUID="4de9d002-d68c-49af-84f1-7f9eddaa1226" TITLECACHE="Abies alba sec. ???"       PROTECTEDTITLECACHE="false" DOUBTFUL="false" PUBLISH="true" USENAMECACHE="false" NAME_ID="6"/>\r
-  <TAXONBASE DTYPE="Synonym" ID="7" CREATED="2009-02-03 17:52:26.0" UUID="294cd25b-f557-4734-9fd0-a6aceeacdebe" TITLECACHE="Abies alba sec. ???"       PROTECTEDTITLECACHE="false" DOUBTFUL="false" PUBLISH="true" USENAMECACHE="false" NAME_ID="6"/>\r
-  <TAXONNAME NAMETYPE="ICNAFP" ID="1" CREATED="2009-02-03 17:52:26.0" UUID="88fab5b3-0d9a-42c3-9915-71fc17266116" TITLECACHE="" PROTECTEDTITLECACHE="false" PARSINGPROBLEM="0" FULLTITLECACHE="" PROBLEMENDS="-1" PROBLEMSTARTS="-1" PROTECTEDFULLTITLECACHE="false" AUTHORSHIPCACHE="" NAMECACHE="" PROTECTEDAUTHORSHIPCACHE="false" PROTECTEDNAMECACHE="false" ANAMORPHIC="false" BINOMHYBRID="false" HYBRIDFORMULA="false" MONOMHYBRID="false" TRINOMHYBRID="false" HOMOTYPICALGROUP_ID="1"/>\r
-  <TAXONNAME NAMETYPE="ICNAFP" ID="2" CREATED="2009-02-03 17:52:26.0" UUID="984e4304-57b0-4ce8-8f94-7c39be7396d9" TITLECACHE="Abies" PROTECTEDTITLECACHE="false" PARSINGPROBLEM="0" FULLTITLECACHE="Abies" PROBLEMENDS="-1" PROBLEMSTARTS="-1" PROTECTEDFULLTITLECACHE="false" AUTHORSHIPCACHE="" GENUSORUNINOMIAL="Abies" NAMECACHE="Abies" PROTECTEDAUTHORSHIPCACHE="false" PROTECTEDNAMECACHE="false" ANAMORPHIC="false" BINOMHYBRID="false" HYBRIDFORMULA="false" MONOMHYBRID="false" TRINOMHYBRID="false" HOMOTYPICALGROUP_ID="2" RANK_ID="774"/>\r
-  <TAXONNAME NAMETYPE="ICNAFP" ID="3" CREATED="2009-02-03 17:52:26.0" UUID="a7e666e7-0d96-4284-9cc4-8e5ccc3b9a36" TITLECACHE="Abies alba" PROTECTEDTITLECACHE="false" PARSINGPROBLEM="0" FULLTITLECACHE="Abies alba" PROBLEMENDS="-1" PROBLEMSTARTS="-1" PROTECTEDFULLTITLECACHE="false" AUTHORSHIPCACHE="" GENUSORUNINOMIAL="Abies" NAMECACHE="Abies alba" PROTECTEDAUTHORSHIPCACHE="false" PROTECTEDNAMECACHE="false" SPECIFICEPITHET="alba" ANAMORPHIC="false" BINOMHYBRID="false" HYBRIDFORMULA="false" MONOMHYBRID="false" TRINOMHYBRID="false" HOMOTYPICALGROUP_ID="3" RANK_ID="765"/>\r
-  <TAXONNAME NAMETYPE="ICNAFP" ID="4" CREATED="2009-02-03 17:52:26.0" UUID="ebd459a6-52ec-4f7c-a520-32c82aa31011" TITLECACHE="Abies" PROTECTEDTITLECACHE="false" PARSINGPROBLEM="0" FULLTITLECACHE="Abies" PROBLEMENDS="-1" PROBLEMSTARTS="-1" PROTECTEDFULLTITLECACHE="false" AUTHORSHIPCACHE="" GENUSORUNINOMIAL="Abies" NAMECACHE="Abies" PROTECTEDAUTHORSHIPCACHE="false" PROTECTEDNAMECACHE="false" ANAMORPHIC="false" BINOMHYBRID="false" HYBRIDFORMULA="false" MONOMHYBRID="false" TRINOMHYBRID="false" HOMOTYPICALGROUP_ID="4" RANK_ID="774" COMBINATIONAUTHORSHIP_ID="1"/>\r
-  <TAXONNAME NAMETYPE="ICNAFP" ID="5" CREATED="2009-02-03 17:52:26.0" UUID="5d74500b-9fd5-4d18-b9cd-cc1c8a372fec" TITLECACHE="Abies alba" PROTECTEDTITLECACHE="false" PARSINGPROBLEM="0" FULLTITLECACHE="Abies alba" PROBLEMENDS="-1" PROBLEMSTARTS="-1" PROTECTEDFULLTITLECACHE="false" AUTHORSHIPCACHE="" GENUSORUNINOMIAL="Abies" NAMECACHE="Abies alba" PROTECTEDAUTHORSHIPCACHE="false" PROTECTEDNAMECACHE="false" SPECIFICEPITHET="alba" ANAMORPHIC="false" BINOMHYBRID="false" HYBRIDFORMULA="false" MONOMHYBRID="false" TRINOMHYBRID="false" HOMOTYPICALGROUP_ID="5" RANK_ID="765" COMBINATIONAUTHORSHIP_ID="1"/>\r
-  <TAXONNAME NAMETYPE="ICNAFP" ID="6" CREATED="2009-02-03 17:52:26.0" UUID="55e6ee55-371e-418e-8775-d885d28453c4" TITLECACHE="Abies alba" PROTECTEDTITLECACHE="false" PARSINGPROBLEM="0" FULLTITLECACHE="Abies alba" PROBLEMENDS="-1" PROBLEMSTARTS="-1" PROTECTEDFULLTITLECACHE="false" AUTHORSHIPCACHE="" GENUSORUNINOMIAL="Abies" NAMECACHE="Abies alba" PROTECTEDAUTHORSHIPCACHE="false" PROTECTEDNAMECACHE="false" SPECIFICEPITHET="alba" ANAMORPHIC="false" BINOMHYBRID="false" HYBRIDFORMULA="false" MONOMHYBRID="false" TRINOMHYBRID="false" HOMOTYPICALGROUP_ID="6" RANK_ID="765" COMBINATIONAUTHORSHIP_ID="2"/>\r
+  <TAXONBASE DTYPE="Taxon"   ID="4" UUID="aafce7fe-0c5f-42ed-814b-4c7c2c715660" TITLECACHE="Abies sec. ???"            PROTECTEDTITLECACHE="false" DOUBTFUL="false" PUBLISH="true" USENAMECACHE="false" TAXONSTATUSUNKNOWN="false" NAME_ID="4"/>\r
+  <TAXONBASE DTYPE="Taxon"   ID="5" UUID="5c1a3d10-3a32-45d1-a5ae-1e982533b79f" TITLECACHE="Abies alba sec. ???"       PROTECTEDTITLECACHE="false" DOUBTFUL="false" PUBLISH="true" USENAMECACHE="false" TAXONSTATUSUNKNOWN="false" NAME_ID="5"/>\r
+  <TAXONBASE DTYPE="Synonym" ID="6" UUID="4de9d002-d68c-49af-84f1-7f9eddaa1226" TITLECACHE="Abies alba sec. ???"       PROTECTEDTITLECACHE="false" DOUBTFUL="false" PUBLISH="true" USENAMECACHE="false" NAME_ID="6"/>\r
+  <TAXONBASE DTYPE="Synonym" ID="7" UUID="294cd25b-f557-4734-9fd0-a6aceeacdebe" TITLECACHE="Abies alba sec. ???"       PROTECTEDTITLECACHE="false" DOUBTFUL="false" PUBLISH="true" USENAMECACHE="false" NAME_ID="6"/>\r
+  <TAXONNAME NAMETYPE="ICNAFP" ID="1" UUID="88fab5b3-0d9a-42c3-9915-71fc17266116" TITLECACHE=""           PROTECTEDTITLECACHE="false" PARSINGPROBLEM="0" FULLTITLECACHE=""           PROBLEMENDS="-1" PROBLEMSTARTS="-1" PROTECTEDFULLTITLECACHE="false" AUTHORSHIPCACHE=""                          NAMECACHE=""           PROTECTEDAUTHORSHIPCACHE="false" PROTECTEDNAMECACHE="false"                        ANAMORPHIC="false" BINOMHYBRID="false" HYBRIDFORMULA="false" MONOMHYBRID="false" TRINOMHYBRID="false" HOMOTYPICALGROUP_ID="1"/>\r
+  <TAXONNAME NAMETYPE="ICNAFP" ID="2" UUID="984e4304-57b0-4ce8-8f94-7c39be7396d9" TITLECACHE="Abies"      PROTECTEDTITLECACHE="false" PARSINGPROBLEM="0" FULLTITLECACHE="Abies"      PROBLEMENDS="-1" PROBLEMSTARTS="-1" PROTECTEDFULLTITLECACHE="false" AUTHORSHIPCACHE="" GENUSORUNINOMIAL="Abies" NAMECACHE="Abies"      PROTECTEDAUTHORSHIPCACHE="false" PROTECTEDNAMECACHE="false"                        ANAMORPHIC="false" BINOMHYBRID="false" HYBRIDFORMULA="false" MONOMHYBRID="false" TRINOMHYBRID="false" HOMOTYPICALGROUP_ID="2" RANK_ID="774"/>\r
+  <TAXONNAME NAMETYPE="ICNAFP" ID="3" UUID="a7e666e7-0d96-4284-9cc4-8e5ccc3b9a36" TITLECACHE="Abies alba" PROTECTEDTITLECACHE="false" PARSINGPROBLEM="0" FULLTITLECACHE="Abies alba" PROBLEMENDS="-1" PROBLEMSTARTS="-1" PROTECTEDFULLTITLECACHE="false" AUTHORSHIPCACHE="" GENUSORUNINOMIAL="Abies" NAMECACHE="Abies alba" PROTECTEDAUTHORSHIPCACHE="false" PROTECTEDNAMECACHE="false" SPECIFICEPITHET="alba" ANAMORPHIC="false" BINOMHYBRID="false" HYBRIDFORMULA="false" MONOMHYBRID="false" TRINOMHYBRID="false" HOMOTYPICALGROUP_ID="3" RANK_ID="765"/>\r
+  <TAXONNAME NAMETYPE="ICNAFP" ID="4" UUID="ebd459a6-52ec-4f7c-a520-32c82aa31011" TITLECACHE="Abies"      PROTECTEDTITLECACHE="false" PARSINGPROBLEM="0" FULLTITLECACHE="Abies"      PROBLEMENDS="-1" PROBLEMSTARTS="-1" PROTECTEDFULLTITLECACHE="false" AUTHORSHIPCACHE="" GENUSORUNINOMIAL="Abies" NAMECACHE="Abies"      PROTECTEDAUTHORSHIPCACHE="false" PROTECTEDNAMECACHE="false"                        ANAMORPHIC="false" BINOMHYBRID="false" HYBRIDFORMULA="false" MONOMHYBRID="false" TRINOMHYBRID="false" HOMOTYPICALGROUP_ID="4" RANK_ID="774" COMBINATIONAUTHORSHIP_ID="1"/>\r
+  <TAXONNAME NAMETYPE="ICNAFP" ID="5" UUID="5d74500b-9fd5-4d18-b9cd-cc1c8a372fec" TITLECACHE="Abies alba" PROTECTEDTITLECACHE="false" PARSINGPROBLEM="0" FULLTITLECACHE="Abies alba" PROBLEMENDS="-1" PROBLEMSTARTS="-1" PROTECTEDFULLTITLECACHE="false" AUTHORSHIPCACHE="" GENUSORUNINOMIAL="Abies" NAMECACHE="Abies alba" PROTECTEDAUTHORSHIPCACHE="false" PROTECTEDNAMECACHE="false" SPECIFICEPITHET="alba" ANAMORPHIC="false" BINOMHYBRID="false" HYBRIDFORMULA="false" MONOMHYBRID="false" TRINOMHYBRID="false" HOMOTYPICALGROUP_ID="5" RANK_ID="765" COMBINATIONAUTHORSHIP_ID="1"/>\r
+  <TAXONNAME NAMETYPE="ICNAFP" ID="6" UUID="55e6ee55-371e-418e-8775-d885d28453c4" TITLECACHE="Abies alba" PROTECTEDTITLECACHE="false" PARSINGPROBLEM="0" FULLTITLECACHE="Abies alba" PROBLEMENDS="-1" PROBLEMSTARTS="-1" PROTECTEDFULLTITLECACHE="false" AUTHORSHIPCACHE="" GENUSORUNINOMIAL="Abies" NAMECACHE="Abies alba" PROTECTEDAUTHORSHIPCACHE="false" PROTECTEDNAMECACHE="false" SPECIFICEPITHET="alba" ANAMORPHIC="false" BINOMHYBRID="false" HYBRIDFORMULA="false" MONOMHYBRID="false" TRINOMHYBRID="false" HOMOTYPICALGROUP_ID="6" RANK_ID="765" COMBINATIONAUTHORSHIP_ID="2"/>\r
 </dataset>
\ No newline at end of file