cleanup

diff --git a/cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/ErmsReferenceImport.java b/cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/ErmsReferenceImport.java
index edf91a1a92180a6a87d0914b0ee97d86dc1780ed..7a3497902610d3fbd1d09b1b10fdaf75c44b23e4 100644 (file)
--- a/cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/ErmsReferenceImport.java
+++ b/cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/ErmsReferenceImport.java
@@ -42,9 +42,11 @@ import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  * @since 20.02.2010\r
  */\r
 @Component\r
-public class ErmsReferenceImport  extends ErmsImportBase<Reference> implements IMappingImport<Reference, ErmsImportState>{\r
-    private static final long serialVersionUID = -2345972558542643378L;\r
+public class ErmsReferenceImport\r
+            extends ErmsImportBase<Reference>\r
+            implements IMappingImport<Reference, ErmsImportState>{\r
 \r
+    private static final long serialVersionUID = -2345972558542643378L;\r
     private static final Logger logger = Logger.getLogger(ErmsReferenceImport.class);\r
 \r
        private DbImportMapping<ErmsImportState, ErmsImportConfigurator> mapping;\r
@@ -140,5 +142,4 @@ public class ErmsReferenceImport  extends ErmsImportBase<Reference> implements I
     protected boolean isIgnore(ErmsImportState state){\r
                return state.getConfig().getDoReferences() != IImportConfigurator.DO_REFERENCES.ALL;\r
        }\r
-\r
 }\r

diff --git a/cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/ErmsSourceUsesImport.java b/cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/ErmsSourceUsesImport.java
index e823c21206fe76dc2f5a37f70183f41a790e73ab..d1ebb7cf7dedeae430f4e77da6f29e6898459be4 100644 (file)
--- a/cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/ErmsSourceUsesImport.java
+++ b/cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/ErmsSourceUsesImport.java
@@ -116,32 +116,32 @@ public class ErmsSourceUsesImport  extends ErmsImportBase<CommonTaxonName> {
                                Reference ref = (Reference)state.getRelatedObject(ErmsImportBase.REFERENCE_NAMESPACE, strSourceId);\r
 \r
                                try {\r
-                               IdentifiableEntity<?> objectToSave = null;\r
-                               //invoke methods for each sourceUse type\r
-                               if (sourceUseId == SOURCE_USE_ORIGINAL_DESCRIPTION){\r
-                                       objectToSave = makeOriginalDescription(partitioner, state, ref, strTaxonId, strPageNr);\r
-                               }else if (sourceUseId == SOURCE_USE_BASIS_OF_RECORD){\r
-                                       objectToSave = makeBasisOfRecord(partitioner, state, ref, strTaxonId, strPageNr);\r
-                               }else if (sourceUseId == SOURCE_USE_ADDITIONAL_SOURCE){\r
-                                       objectToSave = makeAdditionalSource(partitioner, state, ref, strTaxonId, strPageNr);\r
-                               }else if (sourceUseId == SOURCE_USE_SOURCE_OF_SYNONYMY){\r
-                                       objectToSave = makeSourceOfSynonymy(partitioner, state, ref, strTaxonId, strPageNr);\r
-                               }else if (sourceUseId == SOURCE_USE_REDESCRIPTION){\r
-                                       objectToSave = makeRedescription(partitioner, state, ref, strTaxonId, strPageNr);\r
-                               }else if (sourceUseId == SOURCE_USE_NEW_COMBINATION_REFERENCE){\r
-                                       objectToSave = makeCombinationReference(partitioner, state, ref, strTaxonId, strPageNr);\r
-                               }else if (sourceUseId == SOURCE_USE_STATUS_SOURCE){\r
-                                       objectToSave = makeStatusSource(partitioner, state, ref, strTaxonId, strPageNr);\r
-                               }else if (sourceUseId == SOURCE_USE_EMENDATION){\r
-                                       objectToSave = makeEmendation(partitioner, state, ref, strTaxonId, strPageNr);\r
-                               }\r
-                               if(objectToSave != null){\r
-                                       objectsToSave.add(objectToSave);\r
-                               }\r
+                               IdentifiableEntity<?> objectToSave = null;\r
+                               //invoke methods for each sourceUse type\r
+                               if (sourceUseId == SOURCE_USE_ORIGINAL_DESCRIPTION){\r
+                                       objectToSave = makeOriginalDescription(partitioner, state, ref, strTaxonId, strPageNr);\r
+                               }else if (sourceUseId == SOURCE_USE_BASIS_OF_RECORD){\r
+                                       objectToSave = makeBasisOfRecord(partitioner, state, ref, strTaxonId, strPageNr);\r
+                               }else if (sourceUseId == SOURCE_USE_ADDITIONAL_SOURCE){\r
+                                       objectToSave = makeAdditionalSource(partitioner, state, ref, strTaxonId, strPageNr);\r
+                               }else if (sourceUseId == SOURCE_USE_SOURCE_OF_SYNONYMY){\r
+                                       objectToSave = makeSourceOfSynonymy(partitioner, state, ref, strTaxonId, strPageNr);\r
+                               }else if (sourceUseId == SOURCE_USE_REDESCRIPTION){\r
+                                       objectToSave = makeRedescription(partitioner, state, ref, strTaxonId, strPageNr);\r
+                               }else if (sourceUseId == SOURCE_USE_NEW_COMBINATION_REFERENCE){\r
+                                       objectToSave = makeCombinationReference(partitioner, state, ref, strTaxonId, strPageNr);\r
+                               }else if (sourceUseId == SOURCE_USE_STATUS_SOURCE){\r
+                                       objectToSave = makeStatusSource(partitioner, state, ref, strTaxonId, strPageNr);\r
+                               }else if (sourceUseId == SOURCE_USE_EMENDATION){\r
+                                       objectToSave = makeEmendation(partitioner, state, ref, strTaxonId, strPageNr);\r
+                               }\r
+                               if(objectToSave != null){\r
+                                       objectsToSave.add(objectToSave);\r
+                               }\r
                                } catch (Exception e) {\r
                                        e.printStackTrace();\r
                                        success = false;\r
-                       }\r
+                               }\r
                        }\r
                } catch (SQLException e) {\r
                        logger.error("SQLException:" +  e);\r

diff --git a/cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/ErmsVernacularSourcesImport.java b/cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/ErmsVernacularSourcesImport.java
index efe538713480f6b2be65a8380d320cf0e1c338e1..4605d3caf3020c790ee6edf66b7518b0f6925262 100644 (file)
--- a/cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/ErmsVernacularSourcesImport.java
+++ b/cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/ErmsVernacularSourcesImport.java
@@ -37,7 +37,6 @@ public class ErmsVernacularSourcesImport
         extends ErmsImportBase<CommonTaxonName> {\r
 \r
     private static final long serialVersionUID = 8334548532717058431L;\r
-\r
     @SuppressWarnings("unused")\r
     private static final Logger logger = Logger.getLogger(ErmsVernacularSourcesImport.class);\r
 \r

diff --git a/cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiDescriptionExport.java b/cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiDescriptionExport.java
index 3a20ed8ecda305ec6ee29c72a5f4c7faa101249f..b70fc30d00935b718cad3e9c657681e75b8a26c8 100644 (file)
--- a/cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiDescriptionExport.java
+++ b/cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiDescriptionExport.java
@@ -573,13 +573,6 @@ public class PesiDescriptionExport extends PesiExportBase {
                return success;\r
        }\r
 \r
-       /**\r
-        * @param taxComment\r
-        * @param noteCategoryFk\r
-        * @param noteCategoryCache\r
-        * @param object\r
-        * @param object2\r
-        */\r
        private void invokeNotes(String note, Integer noteCategoryFk,\r
                        String noteCategoryCache, Integer languageFk, String languageCache,\r
                        Integer taxonFk, Connection connection) {\r
@@ -628,8 +621,6 @@ public class PesiDescriptionExport extends PesiExportBase {
                        logger.error("Note could not be created: " + note);\r
                        e.printStackTrace();\r
                }\r
-\r
-\r
        }\r
 \r
        /**\r
@@ -655,15 +646,11 @@ public class PesiDescriptionExport extends PesiExportBase {
                return true;\r
        }\r
 \r
-       /* (non-Javadoc)\r
-        * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IoStateBase)\r
-        */\r
        @Override\r
        protected boolean isIgnore(PesiExportState state) {\r
                return ! state.getConfig().isDoDescription();\r
        }\r
 \r
-\r
        /**\r
         * Returns the <code>Note_2</code> attribute.\r
         * @param descriptionElement The {@link DescriptionElementBase DescriptionElement}.\r
@@ -709,9 +696,6 @@ public class PesiDescriptionExport extends PesiExportBase {
                return state.getTransformer().getCacheByFeature(descriptionElement.getFeature());\r
        }\r
 \r
-\r
-\r
-\r
        /**\r
         * Returns the <code>LanguageFk</code> attribute.\r
         * @param descriptionElement The {@link DescriptionElementBase DescriptionElement}.\r

diff --git a/cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiTaxonExport.java b/cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiTaxonExport.java
index a9bf068ac578298a2c394fa0c60565c3cc205b9a..4ad6629e24c596280611715bb56394c39fd9d1ea 100644 (file)
--- a/cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiTaxonExport.java
+++ b/cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiTaxonExport.java
@@ -247,7 +247,7 @@ public class PesiTaxonExport extends PesiExportBase {
                rankTypeExpertsUpdateStmt = connection.prepareStatement(sql);
        }
 
-       private boolean doPhase01(PesiExportState state, PesiExportMapping mapping, PesiExportMapping additionalSourceMapping) throws SQLException {
+       private boolean doPhase01(PesiExportState state, PesiExportMapping mapping, PesiExportMapping additionalSourceMapping){
                int count = 0;
                int pastCount = 0;
                List<TaxonBase> list;
@@ -1452,8 +1452,6 @@ public class PesiTaxonExport extends PesiExportBase {
        /**
         * Returns the rank cache for the taxon name based on the names nomenclatural code.
         * You may not use this method for kingdoms other then Animalia, Plantae and Bacteria.
-        * @param taxonName
-        * @return
         */
        @SuppressWarnings("unused")  //used by mapper
        private static String getRankCache(TaxonName taxonName, PesiExportState state) {
@@ -2081,22 +2079,22 @@ public class PesiTaxonExport extends PesiExportBase {
         * @param taxonName The {@link TaxonNameBase TaxonName}.
         * @return The Sources.
         */
-       private static Set<IdentifiableSource> getPesiSources(IdentifiableEntity identEntity) {
-               Set<IdentifiableSource> sources = new java.util.HashSet<IdentifiableSource>();
+       private static Set<IdentifiableSource> getPesiSources(IdentifiableEntity<?> identifiableEntity) {
+               Set<IdentifiableSource> sources = new HashSet<>();
 
                //Taxon Names
-               if (identEntity.isInstanceOf(TaxonName.class)){
+               if (identifiableEntity.isInstanceOf(TaxonName.class)){
                        // Sources from TaxonName
-                   TaxonName taxonName = CdmBase.deproxy(identEntity, TaxonName.class);
-                       Set<IdentifiableSource> testSources = identEntity.getSources();
-                       sources = filterPesiSources(identEntity.getSources());
+                   TaxonName taxonName = CdmBase.deproxy(identifiableEntity, TaxonName.class);
+                       Set<IdentifiableSource> testSources = identifiableEntity.getSources();
+                       sources = filterPesiSources(identifiableEntity.getSources());
 
                        if (sources.size() == 0 && testSources.size()>0){
                                IdentifiableSource source = testSources.iterator().next();
                                logger.warn("There are sources, but they are no pesi sources!!!" + source.getIdInSource() + " - " + source.getIdNamespace() + " - " + source.getCitation().getTitleCache());
                        }
                        if (sources.size() > 1) {
-                               logger.warn("This TaxonName has more than one Source: " + identEntity.getUuid() + " (" + identEntity.getTitleCache() + ")");
+                               logger.warn("This TaxonName has more than one Source: " + identifiableEntity.getUuid() + " (" + identifiableEntity.getTitleCache() + ")");
                        }
 
                        // name has no PESI source, take sources from TaxonBase
@@ -2108,8 +2106,8 @@ public class PesiTaxonExport extends PesiExportBase {
                        }
 
                //for TaxonBases
-               }else if (identEntity.isInstanceOf(TaxonBase.class)){
-                       sources = filterPesiSources(identEntity.getSources());
+               }else if (identifiableEntity.isInstanceOf(TaxonBase.class)){
+                       sources = filterPesiSources(identifiableEntity.getSources());
                }
 
                /*TODO: deleted only for testing the inferred synonyms
@@ -2124,7 +2122,7 @@ public class PesiTaxonExport extends PesiExportBase {
 
        // return all sources with a PESI reference
        private static Set<IdentifiableSource> filterPesiSources(Set<? extends IdentifiableSource> sources) {
-               Set<IdentifiableSource> result = new HashSet<IdentifiableSource>();
+               Set<IdentifiableSource> result = new HashSet<>();
                for (IdentifiableSource source : sources){
                        Reference ref = source.getCitation();
                        UUID refUuid = ref.getUuid();
@@ -2456,7 +2454,7 @@ public class PesiTaxonExport extends PesiExportBase {
 
                mapping.addMapper(MethodMapper.NewInstance("DerivedFromGuid", this));
                mapping.addMapper(MethodMapper.NewInstance("CacheCitation", this));
-               mapping.addMapper(MethodMapper.NewInstance("AuthorString", this));  //For Taxon because Misallied Names are handled differently
+               mapping.addMapper(MethodMapper.NewInstance("AuthorString", this));  //For Taxon because Misapllied Names are handled differently
                mapping.addMapper(MethodMapper.NewInstance("WebShowName", this));
 
                // DisplayName

diff --git a/cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiTransformer.java b/cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiTransformer.java
index a44e65a80947b67f0f5a35e86deb9e2649200ea3..995d4f3addd56874a865f7bad35ad64e27ccbcbb 100644 (file)
--- a/cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiTransformer.java
+++ b/cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiTransformer.java
@@ -1350,8 +1350,6 @@ public final class PesiTransformer extends ExportTransformerBase{
 \r
        /**\r
         * Returns the identifier of the given Language.\r
-        * @param language\r
-        * @return\r
         */\r
        public static Integer language2LanguageId(Language language) {\r
                if (language == null ) {\r
@@ -1487,8 +1485,6 @@ public final class PesiTransformer extends ExportTransformerBase{
 \r
        /**\r
         * Returns the NodeCategoryCache for a given TextData.\r
-        * @param feature\r
-        * @return\r
         */\r
        @Override\r
     public String getCacheByFeature(Feature feature) {\r
@@ -1501,8 +1497,6 @@ public final class PesiTransformer extends ExportTransformerBase{
 \r
        /**\r
         * Returns the NodeCategoryFk for a given TextData.\r
-        * @param feature\r
-        * @return\r
         */\r
        public static Integer feature2NoteCategoryFk(Feature feature) {\r
                if (feature == null) {\r

diff --git a/cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/old/PesiNoteExport.java b/cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/old/PesiNoteExport.java
index 6e132d81e058dc380334e5862ec18b8626ca14d7..e2aa00a48420ee2622ffe1773d9a6afbf26b6712 100644 (file)
--- a/cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/old/PesiNoteExport.java
+++ b/cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/old/PesiNoteExport.java
@@ -61,8 +61,11 @@ import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  */\r
 @Component\r
 public class PesiNoteExport extends PesiExportBase {\r
-       private static final Logger logger = Logger.getLogger(PesiNoteExport.class);\r
-       private static final Class<? extends CdmBase> standardMethodParameter = DescriptionElementBase.class;\r
+\r
+    private static final long serialVersionUID = 2113856079824112001L;\r
+    private static final Logger logger = Logger.getLogger(PesiNoteExport.class);\r
+\r
+    private static final Class<? extends CdmBase> standardMethodParameter = DescriptionElementBase.class;\r
 \r
        private static int modCount = 1000;\r
        private static final String dbTableName = "Note";\r
@@ -73,26 +76,17 @@ public class PesiNoteExport extends PesiExportBase {
                super();\r
        }\r
 \r
-       /* (non-Javadoc)\r
-        * @see eu.etaxonomy.cdm.io.common.DbExportBase#getStandardMethodParameter()\r
-        */\r
        @Override\r
        public Class<? extends CdmBase> getStandardMethodParameter() {\r
                return standardMethodParameter;\r
        }\r
 \r
-       /* (non-Javadoc)\r
-        * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IoStateBase)\r
-        */\r
        @Override\r
        protected boolean doCheck(PesiExportState state) {\r
                boolean result = true;\r
                return result;\r
        }\r
 \r
-       /* (non-Javadoc)\r
-        * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doInvoke(eu.etaxonomy.cdm.io.common.IoStateBase)\r
-        */\r
        @Override\r
        protected void doInvoke(PesiExportState state) {\r
                try {\r
@@ -110,11 +104,9 @@ public class PesiNoteExport extends PesiExportBase {
                        // Start transaction\r
                        success &= doPhase01(state);\r
 \r
-\r
                        logger.info("PHASE 2...");\r
                        doPhase02(state, limit);\r
 \r
-\r
                        logger.info("*** Finished Making " + pluralString + " ..." + getSuccessString(success));\r
 \r
                        if (!success){\r
@@ -328,9 +320,6 @@ public class PesiNoteExport extends PesiExportBase {
                return true;\r
        }\r
 \r
-       /* (non-Javadoc)\r
-        * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IoStateBase)\r
-        */\r
        @Override\r
        protected boolean isIgnore(PesiExportState state) {\r
                return ! state.getConfig().isDoNotes();\r