Chloroplast DNA Markers and some more Eukaryotes #3591

diff --git a/.gitattributes b/.gitattributes
index 8cfefa516b3652183c97af1edd60cf0feaac38a1..1b18dded893a5321c9ec1e0d7f8e1372be3449f4 100644 (file)
--- a/.gitattributes
+++ b/.gitattributes
@@ -1081,7 +1081,8 @@ cdmlib-model/src/main/resources/terms/AnnotationType.csv -text
 cdmlib-model/src/main/resources/terms/Continent.csv -text
 cdmlib-model/src/main/resources/terms/DerivationEventType.csv -text
 cdmlib-model/src/main/resources/terms/DeterminationModifier.csv -text
-cdmlib-model/src/main/resources/terms/DnaMarker.csv -text
+cdmlib-model/src/main/resources/terms/DnaMarkerChloroplast.csv -text
+cdmlib-model/src/main/resources/terms/DnaMarkerEukaryote.csv -text
 cdmlib-model/src/main/resources/terms/ExtensionType.csv -text
 cdmlib-model/src/main/resources/terms/Feature.csv -text
 cdmlib-model/src/main/resources/terms/HybridRelationshipType.csv -text

diff --git a/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/DefinedTermBase.java b/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/DefinedTermBase.java
index 81b9c831981a02af4202066fe1ac5a13fdf9ed13..3922aa3889a3cb619e8028007eca221eb86eebb0 100644 (file)
--- a/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/DefinedTermBase.java
+++ b/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/DefinedTermBase.java
@@ -375,9 +375,7 @@ public abstract class DefinedTermBase<T extends DefinedTermBase> extends TermBas
         return newInstance;
     }
 
-    /* (non-Javadoc)
-     * @see eu.etaxonomy.cdm.model.common.ILoadableTerm#writeCsvLine(au.com.bytecode.opencsv.CSVWriter)
-     */
+    @Override
     public void writeCsvLine(CSVWriter writer, T term) {
         String [] line = new String[4];
         line[0] = term.getUuid().toString();
@@ -387,9 +385,6 @@ public abstract class DefinedTermBase<T extends DefinedTermBase> extends TermBas
         writer.writeNext(line);
     }
 
-    /* (non-Javadoc)
-     * @see eu.etaxonomy.cdm.model.common.IDefinedTerm#getByUuid(java.util.UUID)
-     */
     @Transient
     public T getByUuid(UUID uuid){
         return this.vocabulary.findTermByUuid(uuid);

diff --git a/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/VocabularyEnum.java b/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/VocabularyEnum.java
index 9d92f81c2c1d20b58a61310ce2da7d3e48a2b1c9..44a60470f08d95c4209741fade1d6f91dd2a8e89 100644 (file)
--- a/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/VocabularyEnum.java
+++ b/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/VocabularyEnum.java
@@ -48,7 +48,6 @@ import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
 @Deprecated 
 public enum VocabularyEnum {
 
-       
        Language("45ac7043-7f5e-4f37-92f2-3874aaaef2de", Language.class),
        UndefinedLanguage("7fd1e6d0-2e76-4dfa-bad9-2673dd042c28", Language.class),
        Continent("e72cbcb6-58f8-4201-9774-15d0c6abc128", NamedArea.class),
@@ -87,7 +86,8 @@ public enum VocabularyEnum {
 //     NamedArea("57c25420-ae94-4848-9513-2aff9bdb502c", NamedArea.class),
        NaturalLanguageTerm("fdaba4b0-5c14-11df-a08a-0800200c9a66", NaturalLanguageTerm.class),
        Modifier("b9434774-4931-4f1e-99cb-40a3ecd61777", DefinedTerm.class),
-       DnaMarker("d219a463-1cc9-4800-b82f-3146d0afe31e", DefinedTerm.class),
+       DnaMarkerEukaryote("d219a463-1cc9-4800-b82f-3146d0afe31e", DefinedTerm.class),
+       DnaMarkerChloroplast("e572d370-a27b-40d3-974c-cb17562b59cf", DefinedTerm.class),
        PlantKindOfUnit("5167c47b-7726-4dba-b02f-dafb7629481b", DefinedTerm.class),
        SpecimenKindOfUnit("b0344ec4-12f7-40d3-82c1-0092e9780bbd", DefinedTerm.class)
        ;

diff --git a/cdmlib-model/src/main/resources/terms/DnaMarker.csv b/cdmlib-model/src/main/resources/terms/DnaMarker.csv
deleted file mode 100644 (file)
index 2a8ec23..0000000
--- a/cdmlib-model/src/main/resources/terms/DnaMarker.csv
+++ /dev/null
@@ -1,2 +0,0 @@
-"d219a463-1cc9-4800-b82f-3146d0afe31e",,"DNA Marker","DNA Marker","DMA","1"\r
-"3f2de4f6-d1a2-4c3a-be70-3c997ef92543",,"ITS1","ITS1","ITS1"
\ No newline at end of file

diff --git a/cdmlib-model/src/main/resources/terms/DnaMarkerChloroplast.csv b/cdmlib-model/src/main/resources/terms/DnaMarkerChloroplast.csv
new file mode 100644 (file)
index 0000000..56020dc
--- /dev/null
+++ b/cdmlib-model/src/main/resources/terms/DnaMarkerChloroplast.csv
@@ -0,0 +1,15 @@
+"e572d370-a27b-40d3-974c-cb17562b59cf",,"Chloroplast DNA Markers","Chloroplast Markers","DMA","1"\r
+"1c96fe56-1ffa-41e3-aa7c-91f0cd6a2c0f",,"matK gene","matK gene","matK gene"\r
+"2d1c6291-65f9-4777-b36b-949f786946cd",,"3' trnK intron","3' trnK intron","3' trnK intron"\r
+"c074fbd5-23ec-4fb1-a901-3cbcfd2a6c7d",,"5' trnK intron","5' trnK intron","5' trnK intron"\r
+"1cece771-fad7-4927-9edb-ffd2e5c39cf7",,"trnT(UGU)-trnL(UAA) spacer","trnT(UGU)-trnL(UAA) spacer","trnT(UGU)-trnL(UAA) spacer"\r
+"ab96d26b-f175-44b9-8c95-2f4e99472a45",,"5’trnL(UAA)-trnF(GAA) spacer","5’trnL(UAA)-trnF(GAA) spacer","5’trnL(UAA)-trnF(GAA) spacer"\r
+"c9f65fde-b8c0-4886-a8fd-2bc852f5a142",,"psbA-trnH spacer","psbA-trnH spacer","psbA-trnH spacer"\r
+"8b05202a-48d9-4a30-b1ff-0411449a6420",,"rpl32-trnL(UAG) spacer","rpl32-trnL(UAG) spacer","rpl32-trnL(UAG) spacer"\r
+"59595971-24ad-45b6-975a-38dfa2d71c11",,"trnQ(UUG)-5’rps16 spacer","trnQ(UUG)-5’rps16 spacer","trnQ(UUG)-5’rps16 spacer"\r
+"c2e9fecf-91e8-474f-a7a7-9c2b09ba0df1",,"atpB-rbcL spacer","atpB-rbcL spacer","atpB-rbcL spacer"\r
+"a98089de-44a5-42f3-9770-ae345deb0636",,"rps16 intron","rps16 intron","rps16 intron"\r
+"6c87a317-6670-422f-979d-21bbfdc63d03",,"rpl16 intron","rpl16 intron","rpl16 intron"\r
+"2c36df5d-757b-42e6-95e6-3fd5faeca2d9",,"trnS–trnG spacer","trnS–trnG spacer","trnS–trnG spacer"\r
+"33384b86-61f4-4dbf-a5e3-e7d65eb91641",,"petD intron","petD intron","petD intron"\r
+"70b31c70-71e3-4f22-a4f2-52ae7b161683",,"petB-petD spacer","petB-petD spacer","petB-petD spacer"
\ No newline at end of file

diff --git a/cdmlib-model/src/main/resources/terms/DnaMarkerEukaryote.csv b/cdmlib-model/src/main/resources/terms/DnaMarkerEukaryote.csv
new file mode 100644 (file)
index 0000000..7953305
--- /dev/null
+++ b/cdmlib-model/src/main/resources/terms/DnaMarkerEukaryote.csv
@@ -0,0 +1,5 @@
+"d219a463-1cc9-4800-b82f-3146d0afe31e",,"Eukaryote DNA Markers","Eukaryote Markers","DMA","1"\r
+"3f2de4f6-d1a2-4c3a-be70-3c997ef92543",,"ITS1","ITS1","ITS1"\r
+"386adca5-2b8a-4a5a-816f-0744fee753a6",,"5.8S rDNA","5.8S rDNA","5.8S rDNA"\r
+"6fe9c9c6-2841-404f-9483-56bc394506fc",,"ITS2","ITS2","ITS2"\r
+"bac298ae-6292-4eb2-b8af-c3e863205a5a",,"3'ETS","3'ETS","3'ETS"
\ No newline at end of file

diff --git a/cdmlib-persistence/src/test/resources/eu/etaxonomy/cdm/database/TermsDataSet-with_auditing_info.xml b/cdmlib-persistence/src/test/resources/eu/etaxonomy/cdm/database/TermsDataSet-with_auditing_info.xml
index b88d5bd5b87f296f55be50df9108224ccb091789..c053c5666fc3898bf0ceb4e8ccd5a3da2ffb31dc 100644 (file)
Binary files a/cdmlib-persistence/src/test/resources/eu/etaxonomy/cdm/database/TermsDataSet-with_auditing_info.xml and b/cdmlib-persistence/src/test/resources/eu/etaxonomy/cdm/database/TermsDataSet-with_auditing_info.xml differ