cleanup

diff --git a/app-import/src/main/java/eu/etaxonomy/cdm/app/berlinModelImport/CaucasusEuroMedActivator.java b/app-import/src/main/java/eu/etaxonomy/cdm/app/berlinModelImport/CaucasusEuroMedActivator.java
index 650bef8d5685e4c97c9b58ba761d721da32a0a7a..1a97f3fc9b953508c64cc0b0148b132f267a032c 100644 (file)
--- a/app-import/src/main/java/eu/etaxonomy/cdm/app/berlinModelImport/CaucasusEuroMedActivator.java
+++ b/app-import/src/main/java/eu/etaxonomy/cdm/app/berlinModelImport/CaucasusEuroMedActivator.java
@@ -415,52 +415,6 @@ public class CaucasusEuroMedActivator {
            }
     }
 
-
-//    //5.Mark areas to be hidden #3979 .5
-//    private void markAreasAsHidden(BerlinModelImportConfigurator config,
-//            CdmDefaultImport<BerlinModelImportConfigurator> bmImport) {
-//
-//        if (config.isDoOccurrence() && (config.getCheck().isImport())){
-//             try {
-//                ICdmRepository app = bmImport.getCdmAppController();
-//                TransactionStatus tx = app.startTransaction();
-//
-//                MarkerType hiddenAreaMarkerType = MarkerType.NewInstance("Used to hide distributions for the named areas in publications", "Hidden Area", null);
-//                hiddenAreaMarkerType.setUuid(BerlinModelTransformer.uuidHiddenArea);
-//                @SuppressWarnings("unchecked")
-//                TermVocabulary<MarkerType> vocUserDefinedMarkerTypes = app.getVocabularyService().find(CdmImportBase.uuidUserDefinedMarkerTypeVocabulary);
-//                if (vocUserDefinedMarkerTypes == null){
-//                    String message = "Marker type vocabulary could not be found. Hidden areas not added.";
-//                    logger.error(message);
-//                    System.out.println(message);
-//                }else{
-//                    vocUserDefinedMarkerTypes.addTerm(hiddenAreaMarkerType);
-//                    app.getVocabularyService().saveOrUpdate(vocUserDefinedMarkerTypes);
-//
-//                    //Add hidden area marker to Rs(C) and Rs(N)
-//                    hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs);
-//                    hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_B);
-//                    hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_C);
-//                    hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_E);
-//                    hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_N);
-//                    hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_K);
-//                    hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_W);
-//                 }
-//                app.commitTransaction(tx);
-//            } catch (Exception e) {
-//                e.printStackTrace();
-//                logger.error("Exception in markAreasAsHidden: " + e.getMessage());
-//            }
-//         }
-//    }
-//
-//    private void hideArea(ICdmRepository app, MarkerType hiddenAreaMarkerType, UUID areaUuid) {
-//        NamedArea area = (NamedArea)app.getTermService().find(areaUuid);
-//        area.addMarker(Marker.NewInstance(hiddenAreaMarkerType, true));
-//        app.getTermService().saveOrUpdate(area);
-//    }
-
-
     //4. Create users and assign roles  #3979
     private void createUsersAndRoles(BerlinModelImportConfigurator config,
             CdmDefaultImport<BerlinModelImportConfigurator> bmImport) {

diff --git a/app-import/src/main/java/eu/etaxonomy/cdm/app/berlinModelImport/EuroMedActivator.java b/app-import/src/main/java/eu/etaxonomy/cdm/app/berlinModelImport/EuroMedActivator.java
index 7adb248179ab83ce7eb7c3587c9c9719d60bdb3c..084ce1d45b3fcf78dc5b927a363b77a784b59c02 100644 (file)
--- a/app-import/src/main/java/eu/etaxonomy/cdm/app/berlinModelImport/EuroMedActivator.java
+++ b/app-import/src/main/java/eu/etaxonomy/cdm/app/berlinModelImport/EuroMedActivator.java
@@ -298,8 +298,6 @@ public class EuroMedActivator {
 
 //      createPreferences(config, bmImport); => manual
 
-//        markAreasAsHidden(config, bmImport);  //has been moved to BM occurrence import
-
                System.out.println("End import from BerlinModel ("+ source.getDatabase() + ")...");
        }
 
@@ -487,50 +485,6 @@ public class EuroMedActivator {
         }
     }
 
-//    //5.Mark areas to be hidden #3979 .5
-//    private void markAreasAsHidden(BerlinModelImportConfigurator config,
-//            CdmDefaultImport<BerlinModelImportConfigurator> bmImport) {
-//
-//        if (config.isDoOccurrence() && (config.getCheck().isImport())){
-//             try {
-//                ICdmRepository app = bmImport.getCdmAppController();
-//                TransactionStatus tx = app.startTransaction();
-//
-//                MarkerType hiddenAreaMarkerType = MarkerType.NewInstance("Used to hide distributions for the named areas in publications", "Hidden Area", null);
-//                hiddenAreaMarkerType.setUuid(BerlinModelTransformer.uuidHiddenArea);
-//                @SuppressWarnings("unchecked")
-//                TermVocabulary<MarkerType> vocUserDefinedMarkerTypes = app.getVocabularyService().find(CdmImportBase.uuidUserDefinedMarkerTypeVocabulary);
-//                if (vocUserDefinedMarkerTypes == null){
-//                    String message = "Marker type vocabulary could not be found. Hidden areas not added.";
-//                    logger.error(message);
-//                    System.out.println(message);
-//                }else{
-//                    vocUserDefinedMarkerTypes.addTerm(hiddenAreaMarkerType);
-//                    app.getVocabularyService().saveOrUpdate(vocUserDefinedMarkerTypes);
-//
-//                    //Add hidden area marker to Rs(C) and Rs(N)
-//                    hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs);
-//                    hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_B);
-//                    hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_C);
-//                    hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_E);
-//                    hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_N);
-//                    hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_K);
-//                    hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_W);
-//                 }
-//                app.commitTransaction(tx);
-//            } catch (Exception e) {
-//                e.printStackTrace();
-//                logger.error("Exception in markAreasAsHidden: " + e.getMessage());
-//            }
-//         }
-//    }
-//
-//    private void hideArea(ICdmRepository app, MarkerType hiddenAreaMarkerType, UUID areaUuid) {
-//        NamedArea area = (NamedArea)app.getTermService().find(areaUuid);
-//        area.addMarker(Marker.NewInstance(hiddenAreaMarkerType, true));
-//        app.getTermService().saveOrUpdate(area);
-//    }
-
     //2. import shapefile attributes #3979 .2
     private void importShapefile(BerlinModelImportConfigurator config,
             CdmDefaultImport<BerlinModelImportConfigurator> bmImport) {

diff --git a/app-import/src/main/java/eu/etaxonomy/cdm/app/caryophyllales/KewCaryophyllaceaeActivator.java b/app-import/src/main/java/eu/etaxonomy/cdm/app/caryophyllales/KewCaryophyllaceaeActivator.java
index 022d85dfbaf50e9f69426cbc4239879f692ff62c..7a49a2877fc8fe9cf4d01ceccc09a444a78b397f 100644 (file)
--- a/app-import/src/main/java/eu/etaxonomy/cdm/app/caryophyllales/KewCaryophyllaceaeActivator.java
+++ b/app-import/src/main/java/eu/etaxonomy/cdm/app/caryophyllales/KewCaryophyllaceaeActivator.java
@@ -37,7 +37,7 @@ public class KewCaryophyllaceaeActivator extends SourceBase{
        private static final DbSchemaValidation hbm2dll = DbSchemaValidation.VALIDATE;
        private static final URI source = caryophyllaceae();
 
-       private static final ICdmDataSource cdmDestination = CdmDestinations.cdm_local_caryo_spp();
+       private static final ICdmDataSource cdmDestination = CdmDestinations.cdm_local_caryo();
 //    private static final ICdmDataSource cdmDestination = CdmDestinations.cdm_production_caryophyllales_spp();
 
 

diff --git a/app-import/src/main/java/eu/etaxonomy/cdm/app/caryophyllales/KewNyctaginaceaeActivator.java b/app-import/src/main/java/eu/etaxonomy/cdm/app/caryophyllales/KewNyctaginaceaeActivator.java
index a76cda494077dd8b2b4245fb13ac19e1c08c9958..548df975e3589ca334f75e16cfd450f7848b1300 100644 (file)
--- a/app-import/src/main/java/eu/etaxonomy/cdm/app/caryophyllales/KewNyctaginaceaeActivator.java
+++ b/app-import/src/main/java/eu/etaxonomy/cdm/app/caryophyllales/KewNyctaginaceaeActivator.java
@@ -40,7 +40,7 @@ public class KewNyctaginaceaeActivator extends SourceBase{
        private static final DbSchemaValidation hbm2dll = DbSchemaValidation.VALIDATE;
        private static final URI source = nyctaginaceae();
 
-       private static final ICdmDataSource cdmDestination = CdmDestinations.cdm_local_caryo_spp();
+       private static final ICdmDataSource cdmDestination = CdmDestinations.cdm_local_caryo();
 //    private static final ICdmDataSource cdmDestination = CdmDestinations.cdm_production_caryophyllales_spp();
 
 

diff --git a/app-import/src/main/java/eu/etaxonomy/cdm/app/caryophyllales/SileneaeImportActivator.java b/app-import/src/main/java/eu/etaxonomy/cdm/app/caryophyllales/SileneaeImportActivator.java
index 0d981ff0e6ec7b3795b791454c730431355bea06..f915ad1e9a1766280d618386761e04433f2f0c1a 100644 (file)
--- a/app-import/src/main/java/eu/etaxonomy/cdm/app/caryophyllales/SileneaeImportActivator.java
+++ b/app-import/src/main/java/eu/etaxonomy/cdm/app/caryophyllales/SileneaeImportActivator.java
@@ -37,8 +37,7 @@ public class SileneaeImportActivator {
     private static final DbSchemaValidation hbm2dll = DbSchemaValidation.VALIDATE;
     private static final URI source = sileneae();
 
-    private static final ICdmDataSource cdmDestination = CdmDestinations.cdm_local_caryo_spp();
-//    private static final ICdmDataSource cdmDestination = CdmDestinations.cdm_local_caryo_spp1();
+    private static final ICdmDataSource cdmDestination = CdmDestinations.cdm_local_caryo();
 //    private static final ICdmDataSource cdmDestination = CdmDestinations.cdm_production_caryophyllales_spp();
 
     private static final UUID acceptedUuid = UUID.fromString("8ac4a182-1281-4473-b6a1-c4f681f7dea3");

diff --git a/app-import/src/main/java/eu/etaxonomy/cdm/app/caryophyllales/TaxonExcelCaryophyllalesActivator.java b/app-import/src/main/java/eu/etaxonomy/cdm/app/caryophyllales/TaxonExcelCaryophyllalesActivator.java
index 94d5854b226bfb650cf0fd3307c53f12b8955877..57d9b81e638c05d2f60a14e466e79d01c235bb1d 100644 (file)
--- a/app-import/src/main/java/eu/etaxonomy/cdm/app/caryophyllales/TaxonExcelCaryophyllalesActivator.java
+++ b/app-import/src/main/java/eu/etaxonomy/cdm/app/caryophyllales/TaxonExcelCaryophyllalesActivator.java
@@ -28,7 +28,8 @@ public class TaxonExcelCaryophyllalesActivator {
     @SuppressWarnings("unused")\r
     private static final Logger logger = LogManager.getLogger();\r
 \r
-       private static final ICdmDataSource destinationDb = CdmDestinations.cdm_production_caryophyllales_genus();\r
+//     private static final ICdmDataSource destinationDb = CdmDestinations.cdm_production_caryophyllales_genus();\r
+    private static final ICdmDataSource destinationDb = CdmDestinations.cdm_local_caryo();\r
 \r
     public static void main(String[] args) {\r
 \r

diff --git a/app-import/src/main/java/eu/etaxonomy/cdm/app/common/CdmDestinations.java b/app-import/src/main/java/eu/etaxonomy/cdm/app/common/CdmDestinations.java
index 279e38c5a7c7032ad0305534e4206b1b2ffbf534..28405cde407f7b37694a7490d793e33954535c26 100644 (file)
--- a/app-import/src/main/java/eu/etaxonomy/cdm/app/common/CdmDestinations.java
+++ b/app-import/src/main/java/eu/etaxonomy/cdm/app/common/CdmDestinations.java
@@ -616,14 +616,6 @@ public class CdmDestinations {
                return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null);
        }
 
-       public static ICdmDataSource cdm_test_globis(){
-               DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;
-               String cdmServer = "160.45.63.175";
-               String cdmDB = "cdm_edit_globis";
-               String cdmUserName = "edit";
-               return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null);
-       }
-
     public static ICdmDataSource cdm_local_edaphobase(){
         DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;
         String cdmServer = "127.0.0.1";
@@ -650,31 +642,6 @@ public class CdmDestinations {
         return makeDestination(dbType, cdmServer, cdmDB, port, cdmUserName, null);
     }
 
-    public static ICdmDataSource cdm_test_postgres__ssh_edaphobase(){
-        DatabaseTypeEnum dbType = DatabaseTypeEnum.PostgreSQL;
-        String cdmServer = "localhost";
-        String cdmDB = "cdm_edaphobase";
-        String cdmUserName = "edaphobase";
-        int port = 13306;
-        return makeDestination(dbType, cdmServer, cdmDB, port, cdmUserName, null);
-    }
-
-    public static ICdmDataSource cdm_local_caryo_spp(){
-        DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;
-        String cdmServer = "127.0.0.1";
-        String cdmDB = "cdm_local_caryophyllales_spp";
-        String cdmUserName = "edit";
-        return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null);
-    }
-
-    public static ICdmDataSource cdm_local_caryo_spp1(){
-        DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;
-        String cdmServer = "127.0.0.1";
-        String cdmDB = "cdm_local_caryophyllales_spp1";
-        String cdmUserName = "edit";
-        return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null);
-    }
-
        public static ICdmDataSource cdm_local_globis(){
                DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;
                String cdmServer = "127.0.0.1";
@@ -853,14 +820,6 @@ public class CdmDestinations {
                return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null);
        }
 
-       public static ICdmDataSource cdm_production_caryophyllales_genus(){
-               DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;
-               String cdmServer = "160.45.63.171";
-               String cdmDB = "cdm_production_caryophyllales_genera";
-               String cdmUserName = "edit";
-               return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null);
-       }
-
        public static ICdmDataSource cdm_production_caryophyllales(){
         DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;
         String cdmServer = "160.45.63.171";

diff --git a/app-import/src/main/java/eu/etaxonomy/cdm/app/globis/GlobisActivator.java b/app-import/src/main/java/eu/etaxonomy/cdm/app/globis/GlobisActivator.java
index 2983df04efb59bab17ee0ee9679d4093bad91dc8..b8bb1a2561d70bc7ccbce5cb626041aa926f31f7 100644 (file)
--- a/app-import/src/main/java/eu/etaxonomy/cdm/app/globis/GlobisActivator.java
+++ b/app-import/src/main/java/eu/etaxonomy/cdm/app/globis/GlobisActivator.java
@@ -41,8 +41,7 @@ public class GlobisActivator {
        static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;\r
        static final Source globisSource = CdmImportSources.GLOBIS_MDB_20140113_PESIIMPORT_SQLSERVER();\r
 //     static final ICdmDataSource cdmDestination = CdmDestinations.localH2();\r
-//     static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();\r
-       static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_globis();\r
+       static final ICdmDataSource cdmDestination = CdmDestinations.cdm_local_test_mysql();\r
 //     static final ICdmDataSource cdmDestination = CdmDestinations.cdm_production_globis();\r
 \r
 \r

diff --git a/app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelAreaImport.java b/app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelAreaImport.java
index 663cc5f2074d46e294f634b7a2a9237d8b1a5d4b..e90af042aaea73a0b5f51706a22c5fd54c85e845 100644 (file)
--- a/app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelAreaImport.java
+++ b/app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelAreaImport.java
@@ -313,17 +313,17 @@ public class BerlinModelAreaImport  extends BerlinModelImportBase {
 
         try {
 
-            MarkerType hiddenAreaMarkerType = getMarkerType(state, BerlinModelTransformer.uuidHiddenArea,
+            MarkerType fallbackAreaMarkerType = getMarkerType(state, BerlinModelTransformer.uuidHiddenArea,
                     "Hidden Area","Used to hide distributions for the named areas in publications", null, getEuroMedMarkerTypeVoc(state));
 
             //Add hidden area marker to Rs(C) and Rs(N)
-            hideArea(euroMedAreasVoc, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs);
-            hideArea(euroMedAreasVoc, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_B);
-            hideArea(euroMedAreasVoc, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_C);
-            hideArea(euroMedAreasVoc, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_E);
-            hideArea(euroMedAreasVoc, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_N);
-            hideArea(euroMedAreasVoc, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_K);
-            hideArea(euroMedAreasVoc, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_W);
+            hideArea(euroMedAreasVoc, fallbackAreaMarkerType, BerlinModelTransformer.uuidRs);
+            hideArea(euroMedAreasVoc, fallbackAreaMarkerType, BerlinModelTransformer.uuidRs_B);
+            hideArea(euroMedAreasVoc, fallbackAreaMarkerType, BerlinModelTransformer.uuidRs_C);
+            hideArea(euroMedAreasVoc, fallbackAreaMarkerType, BerlinModelTransformer.uuidRs_E);
+            hideArea(euroMedAreasVoc, fallbackAreaMarkerType, BerlinModelTransformer.uuidRs_N);
+            hideArea(euroMedAreasVoc, fallbackAreaMarkerType, BerlinModelTransformer.uuidRs_K);
+            hideArea(euroMedAreasVoc, fallbackAreaMarkerType, BerlinModelTransformer.uuidRs_W);
         } catch (Exception e) {
             e.printStackTrace();
             logger.error("Exception in markAreasAsHidden: " + e.getMessage());
@@ -331,10 +331,10 @@ public class BerlinModelAreaImport  extends BerlinModelImportBase {
 
     }
 
-    private void hideArea(TermVocabulary<NamedArea> euroMedAreasVoc, MarkerType hiddenAreaMarkerType, UUID areaUuid) {
+    private void hideArea(TermVocabulary<NamedArea> euroMedAreasVoc, MarkerType fallbackAreaMarkerType, UUID areaUuid) {
         for (NamedArea namedArea : euroMedAreasVoc.getTerms()){
             if (namedArea.getUuid().equals(areaUuid)){
-                namedArea.addMarker(Marker.NewInstance(hiddenAreaMarkerType, true));
+                namedArea.addMarker(Marker.NewInstance(fallbackAreaMarkerType, true));
                 return;
             }
         }