From 92131df02d4518142190d47952394dfd0696ff63 Mon Sep 17 00:00:00 2001
From: =?utf8?q?Andreas=20M=C3=BCller?= <a.mueller@bgbm.org>
Date: Thu, 17 Apr 2014 14:48:29 +0000
Subject: [PATCH] Latest updates to Specimen Excel import

---
 .../ExcelTaxonOrSpecimenImportBase.java       |  2 ++
 .../excel/in/ExtensionTypeExcelImport.java    |  5 ++---
 .../excel/in/NamedAreaLevelExcelImport.java   |  5 ++---
 .../excel/in/SpecimenCdmExcelImport.java      | 21 +++++++++++++++----
 .../excel/in/SpecimenCdmExcelTransformer.java | 13 +++++++++---
 .../cdm/io/specimen/excel/in/SpecimenRow.java | 11 ++++++++++
 6 files changed, 44 insertions(+), 13 deletions(-)

diff --git a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/excel/common/ExcelTaxonOrSpecimenImportBase.java b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/excel/common/ExcelTaxonOrSpecimenImportBase.java
index 1b1389260d..3fdf40fcdf 100644
--- a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/excel/common/ExcelTaxonOrSpecimenImportBase.java
+++ b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/excel/common/ExcelTaxonOrSpecimenImportBase.java
@@ -48,6 +48,8 @@ public abstract class ExcelTaxonOrSpecimenImportBase<STATE extends ExcelImportSt
 	protected static final String GENUS_COLUMN = "(?i)(Genus)";
 	protected static final String SPECIFIC_EPITHET_COLUMN = "(?i)(SpecificEpi(thet)?)";
 	protected static final String INFRASPECIFIC_EPITHET_COLUMN = "(?i)(InfraSpecificEpi(thet)?)";
+	
+	protected static final String LANGUAGE = "(?i)(Language)";
 
 	@Override
 	protected void analyzeRecord(HashMap<String, String> record, STATE state) {
diff --git a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/excel/in/ExtensionTypeExcelImport.java b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/excel/in/ExtensionTypeExcelImport.java
index 333725efdc..5f0bfa241c 100644
--- a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/excel/in/ExtensionTypeExcelImport.java
+++ b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/excel/in/ExtensionTypeExcelImport.java
@@ -23,9 +23,8 @@ import eu.etaxonomy.cdm.io.excel.common.ExcelImporterBase;
 import eu.etaxonomy.cdm.model.common.ExtensionType;
 
 /**
- * @author p.kelbert
- * @created 29.10.2008
- * @version 1.0
+ * @author a.mueller
+ * @created 18.05.2010
  */
 @Component
 public class ExtensionTypeExcelImport  extends ExcelImporterBase<SpecimenCdmExcelImportState>  implements ICdmIO<SpecimenCdmExcelImportState> {
diff --git a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/excel/in/NamedAreaLevelExcelImport.java b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/excel/in/NamedAreaLevelExcelImport.java
index f7f0f936ec..6f8e1a526a 100644
--- a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/excel/in/NamedAreaLevelExcelImport.java
+++ b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/excel/in/NamedAreaLevelExcelImport.java
@@ -23,9 +23,8 @@ import eu.etaxonomy.cdm.io.excel.common.ExcelImporterBase;
 import eu.etaxonomy.cdm.model.location.NamedAreaLevel;
 
 /**
- * @author p.kelbert
- * @created 29.10.2008
- * @version 1.0
+ * @author a.mueller
+ * @created 15.05.2010
  */
 @Component
 public class NamedAreaLevelExcelImport  extends ExcelImporterBase<SpecimenCdmExcelImportState>  implements ICdmIO<SpecimenCdmExcelImportState> {
diff --git a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/excel/in/SpecimenCdmExcelImport.java b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/excel/in/SpecimenCdmExcelImport.java
index 90c6fad216..e4e81cb7d0 100644
--- a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/excel/in/SpecimenCdmExcelImport.java
+++ b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/excel/in/SpecimenCdmExcelImport.java
@@ -185,7 +185,8 @@ public class SpecimenCdmExcelImport  extends ExcelTaxonOrSpecimenImportBase<Spec
 			}else{
 				logger.warn("Not yet implemented");
 			}
-		
+		} else if(keyValue.key.matches(LANGUAGE)) {
+			row.setLanguage(value);		
 			
 			
 		} else if(keyValue.key.matches(ACCESSION_NUMBER_COLUMN)) {
@@ -266,6 +267,18 @@ public class SpecimenCdmExcelImport  extends ExcelTaxonOrSpecimenImportBase<Spec
 		}
 		DerivedUnitFacade facade = DerivedUnitFacade.NewInstance(type);
 		
+		
+		Language lang = Language.DEFAULT();
+		if (StringUtils.isNotBlank(row.getLanguage())){
+			Language langIso = getTermService().getLanguageByIso(row.getLanguage());
+			if (langIso == null){
+				String message = "Language could not be recognized: %s. Use default language instead. Line %d.";
+				message = String.format(message, langIso, state.getCurrentLine());
+			}else{
+				lang = langIso;
+			}
+		}
+		
 		//country
 		handleCountry(facade, row, state);
 		handleAreas(facade,row, state);
@@ -274,15 +287,14 @@ public class SpecimenCdmExcelImport  extends ExcelTaxonOrSpecimenImportBase<Spec
 		facade.setLocality(row.getLocality());
 		facade.setFieldNotes(row.getFieldNotes());
 		facade.setFieldNumber(row.getCollectorsNumber());
-		facade.setEcology(row.getEcology());
-		facade.setPlantDescription(row.getPlantDescription());
+		facade.setEcology(row.getEcology(), lang);
+		facade.setPlantDescription(row.getPlantDescription(), lang);
 //		facade.setSex(row.get)
 		handleExactLocation(facade, row, state);
 		facade.setCollector(getOrMakeAgent(state, row.getCollectors()));
 		facade.setPrimaryCollector(getOrMakePrimaryCollector(facade, row.getPrimaryCollector(), state));
 		handleAbsoluteElevation(facade, row, state);
 		
-		
 		//derivedUnit
 		facade.setBarcode(row.getBarcode());
 		facade.setAccessionNumber(row.getAccessionNumber());
@@ -871,6 +883,7 @@ public class SpecimenCdmExcelImport  extends ExcelTaxonOrSpecimenImportBase<Spec
 			try {
 				refSys = state.getTransformer().getReferenceSystemByKey(strRefSys);
 				if (refSys == null){
+					//TODO we still need user defined Reference Systems here
 					refUuid = state.getTransformer().getReferenceSystemUuid(strRefSys);
 					if (refUuid == null){
 						String message = "Unknown reference system %s in line %d";
diff --git a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/excel/in/SpecimenCdmExcelTransformer.java b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/excel/in/SpecimenCdmExcelTransformer.java
index 24ff4f55ce..febf7818c5 100644
--- a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/excel/in/SpecimenCdmExcelTransformer.java
+++ b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/excel/in/SpecimenCdmExcelTransformer.java
@@ -33,13 +33,16 @@ public final class SpecimenCdmExcelTransformer extends InputTransformerBase {
 	public static final UUID uuidRefSysEstimated = UUID.fromString("3b625520-e5cf-4d9c-9599-0cb048e0e8d2");
 	public static final UUID uuidRefSysLabel = UUID.fromString("c72335ed-c9aa-4d1c-b6fc-9f307d207862");
 	public static final UUID uuidRefSysGps = UUID.fromString("b3c36751-b2ac-47f7-8ac1-3dc5c129e0b2");
+	public static final UUID uuidRefSysUtm = UUID.fromString("bc64f335-a80a-432a-82ff-5c08a308324f");
+	public static final UUID uuidRefSysDescription = UUID.fromString("a9c42b52-c8cf-4658-86ce-271dca569f2c");
+	public static final UUID uuidRefSysMapBR = UUID.fromString("64b8dc38-e532-45bf-bea7-86b9467973a1");
+	public static final UUID uuidRefSysUnsure = UUID.fromString("91781b31-29e9-4807-8172-e7e25433ea06");
+	
+	
 	
 	
 	//Languages
 	
-	/* (non-Javadoc)
-	 * @see eu.etaxonomy.cdm.io.common.mapping.InputTransformerBase#getMarkerTypeByKey(java.lang.String)
-	 */
 	@Override
 	public SpecimenTypeDesignationStatus getSpecimenTypeDesignationStatusByKey(String key) throws UndefinedTransformerMethodException {
 		return super.getSpecimenTypeDesignationStatusByKey(key);
@@ -67,6 +70,10 @@ public final class SpecimenCdmExcelTransformer extends InputTransformerBase {
 		}else if (key.matches("(?i)(estimated)")){return uuidRefSysEstimated;
 		}else if (key.matches("(?i)(label)")){return uuidRefSysLabel;
 		}else if (key.matches("(?i)(gps)")){return uuidRefSysLabel;
+		}else if (key.matches("(?i)(utm)")){return uuidRefSysUtm;
+		}else if (key.matches("(?i)(description)")){return uuidRefSysDescription;
+		}else if (key.matches("(?i)(mapBR)")){return uuidRefSysMapBR;
+		}else if (key.matches("(?i)(Unsure)")){return uuidRefSysUnsure;
 		}
 		return null;
 	}
diff --git a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/excel/in/SpecimenRow.java b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/excel/in/SpecimenRow.java
index bd412e57ca..0c5f65407b 100644
--- a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/excel/in/SpecimenRow.java
+++ b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/excel/in/SpecimenRow.java
@@ -49,6 +49,7 @@ public class SpecimenRow extends ExcelRowBase{
 	private String collectingDateEnd;
 	private String collectorsNumber;
 	private String primaryCollector;
+	private String language;
 
 	private String sex;
 
@@ -591,5 +592,15 @@ public class SpecimenRow extends ExcelRowBase{
 	public String getPrimaryCollector() {
 		return primaryCollector;
 	}
+
+
+	public String getLanguage() {
+		return language;
+	}
+
+
+	public void setLanguage(String language) {
+		this.language = language;
+	}
 	
 }
-- 
2.34.1