Unifiy name and taxon creation

[cdmlib-apps.git] / app-import / src / main / java / eu / etaxonomy / cdm / io / algaterra / AlgaTerraDnaImport.java

diff --git a/app-import/src/main/java/eu/etaxonomy/cdm/io/algaterra/AlgaTerraDnaImport.java b/app-import/src/main/java/eu/etaxonomy/cdm/io/algaterra/AlgaTerraDnaImport.java
index 7d7fa0855276c3546209a9d9fa839fa4052801f5..57c73d04996bc7d07880341364ad92b1333b4302 100644 (file)
--- a/app-import/src/main/java/eu/etaxonomy/cdm/io/algaterra/AlgaTerraDnaImport.java
+++ b/app-import/src/main/java/eu/etaxonomy/cdm/io/algaterra/AlgaTerraDnaImport.java
@@ -85,6 +85,7 @@ public class AlgaTerraDnaImport  extends AlgaTerraSpecimenImportBase {
                                        " WHERE f.FactCategoryFk = 203 ";\r
                if (state.getAlgaTerraConfigurator().isRemoveRestricted()){\r
                                result = result + " AND df.ProtectedFlag = 0 ";\r
+                               logger.warn("DNA with protectedFlag = 0 is currently not imported");\r
                }\r
                result += " ORDER BY df.DNAFactID ";\r
                return result;\r
@@ -106,9 +107,7 @@ public class AlgaTerraDnaImport  extends AlgaTerraSpecimenImportBase {
                return strQuery;\r
        }\r
 \r
-       /* (non-Javadoc)\r
-        * @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#doPartition(eu.etaxonomy.cdm.io.berlinModel.in.ResultSetPartitioner, eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportState)\r
-        */\r
+       @Override\r
        public boolean doPartition(ResultSetPartitioner partitioner, BerlinModelImportState bmState) {\r
                boolean success = true;\r
                \r
@@ -237,10 +236,7 @@ public class AlgaTerraDnaImport  extends AlgaTerraSpecimenImportBase {
                                DerivationEvent.NewSimpleInstance(ecoFact, dnaSample, DerivationEventType.DNA_EXTRACTION());\r
                                samplesToSave.add(ecoFact);\r
                        }\r
-               }\r
-               \r
-               \r
-               \r
+               }       \r
        }\r
 \r
 \r
@@ -290,7 +286,9 @@ public class AlgaTerraDnaImport  extends AlgaTerraSpecimenImportBase {
                if (sequenceStr == null){\r
                        logger.warn("PlainSequence is null. Id: " + dnaFactId);\r
                }else{\r
-                       if (sequenceStr.length() != seqLen){\r
+                       if (seqLen == null){\r
+                               logger.warn("SeqLen is null for dnaFact: "  + dnaFactId);\r
+                       }else if (sequenceStr.length() != seqLen){\r
                                logger.warn("SeqLen (" + seqLen+ ") and OriginalLen ("+sequenceStr.length()+") differ for dnaFact: "  + dnaFactId);\r
                        }\r
                }\r
@@ -364,7 +362,7 @@ public class AlgaTerraDnaImport  extends AlgaTerraSpecimenImportBase {
        }\r
 \r
        @Override\r
-       public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {\r
+       public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, BerlinModelImportState state) {\r
                String nameSpace;\r
                Class<?> cdmClass;\r
                Set<String> idSet;\r
@@ -378,7 +376,6 @@ public class AlgaTerraDnaImport  extends AlgaTerraSpecimenImportBase {
                        while (rs.next()){\r
                                handleForeignKey(rs, taxonIdSet, "taxonId");\r
                                handleForeignKey(rs, ecoFactFkSet, "ecoFactId");\r
-\r
                        }\r
                        \r
                        //taxon map\r
@@ -408,10 +405,7 @@ public class AlgaTerraDnaImport  extends AlgaTerraSpecimenImportBase {
                return validator.validate(state);\r
        }\r
 \r
-\r
-       /* (non-Javadoc)\r
-        * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)\r
-        */\r
+       @Override\r
        protected boolean isIgnore(BerlinModelImportState state){\r
                return ! ((AlgaTerraImportState)state).getAlgaTerraConfigurator().isDoDna();\r
        }\r