fix merge problems

diff --git a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/abcd206/in/SpecimenImportUtility.java b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/abcd206/in/SpecimenImportUtility.java
index 4826b43ff2f63699fe25d6629d7b1e6adfda9a62..f97546db1fa5f604ce336c57aeb82608fe51f21d 100644 (file)
--- a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/abcd206/in/SpecimenImportUtility.java
+++ b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/abcd206/in/SpecimenImportUtility.java
@@ -1,45 +1,48 @@
-// $Id$
-/**
-* Copyright (C) 2015 EDIT
-* European Distributed Institute of Taxonomy
-* http://www.e-taxonomy.eu
-*
-* The contents of this file are subject to the Mozilla Public License Version 1.1
-* See LICENSE.TXT at the top of this package for the full license terms.
-*/
-package eu.etaxonomy.cdm.io.specimen.abcd206.in;
-
-import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
-
-/**
- * @author pplitzner
- * @date 16.06.2015
- *
- */
-public class AbcdImportUtility {
-
-    public static String getUnitID(DerivedUnit derivedUnit, Abcd206ImportConfigurator config){
-        if(config.isMapUnitIdToAccessionNumber()){
-            return derivedUnit.getAccessionNumber();
-        }
-        if(config.isMapUnitIdToBarcode()){
-            return derivedUnit.getBarcode();
-        }
-        return derivedUnit.getCatalogNumber();
-    }
-
-    public static void setUnitID(DerivedUnit derivedUnit, String unitId, Abcd206ImportConfigurator config){
-        if(config.isMapUnitIdToCatalogNumber()
-                || !(config.isMapUnitIdToAccessionNumber() || config.isMapUnitIdToBarcode() || config.isMapUnitIdToCatalogNumber())){
-            // set catalog number (default if nothing is set)
-            derivedUnit.setCatalogNumber(unitId);
-        }
-        if(config.isMapUnitIdToAccessionNumber()){
-            derivedUnit.setAccessionNumber(unitId);
-        }
-        if(config.isMapUnitIdToBarcode()){
-            derivedUnit.setBarcode(unitId);
-        }
-    }
-
-}
+// $Id$\r
+/**\r
+* Copyright (C) 2015 EDIT\r
+* European Distributed Institute of Taxonomy\r
+* http://www.e-taxonomy.eu\r
+*\r
+* The contents of this file are subject to the Mozilla Public License Version 1.1\r
+* See LICENSE.TXT at the top of this package for the full license terms.\r
+*/\r
+package eu.etaxonomy.cdm.io.specimen.abcd206.in;\r
+\r
+import eu.etaxonomy.cdm.io.specimen.SpecimenImportConfiguratorBase;\r
+import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;\r
+\r
+/**\r
+ * @author pplitzner\r
+ * @date 16.06.2015\r
+ *\r
+ */\r
+public class SpecimenImportUtility {\r
+\r
+    public static String getUnitID(DerivedUnit derivedUnit, SpecimenImportConfiguratorBase config){\r
+        if (config instanceof Abcd206ImportConfigurator){\r
+            if(((Abcd206ImportConfigurator)config).isMapUnitIdToAccessionNumber()){\r
+                return derivedUnit.getAccessionNumber();\r
+            }\r
+            if(((Abcd206ImportConfigurator)config).isMapUnitIdToBarcode()){\r
+                return derivedUnit.getBarcode();\r
+            }\r
+        }\r
+        return derivedUnit.getCatalogNumber();\r
+    }\r
+\r
+    public static void setUnitID(DerivedUnit derivedUnit, String unitId, Abcd206ImportConfigurator config){\r
+        if(config.isMapUnitIdToCatalogNumber()\r
+                || !(config.isMapUnitIdToAccessionNumber() || config.isMapUnitIdToBarcode() || config.isMapUnitIdToCatalogNumber())){\r
+            // set catalog number (default if nothing is set)\r
+            derivedUnit.setCatalogNumber(unitId);\r
+        }\r
+        if(config.isMapUnitIdToAccessionNumber()){\r
+            derivedUnit.setAccessionNumber(unitId);\r
+        }\r
+        if(config.isMapUnitIdToBarcode()){\r
+            derivedUnit.setBarcode(unitId);\r
+        }\r
+    }\r
+\r
+}\r

diff --git a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/abcd206/in/UnitAssociationParser.java b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/abcd206/in/UnitAssociationParser.java
index ba0ecc1b24bb0599f894aacddd2a2c97b820bd96..cdb94596e9e6fa993e8ba70068c07a33292d709c 100644 (file)
--- a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/abcd206/in/UnitAssociationParser.java
+++ b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/abcd206/in/UnitAssociationParser.java
@@ -1,119 +1,124 @@
-// $Id$
-/**
-* Copyright (C) 2015 EDIT
-* European Distributed Institute of Taxonomy
-* http://www.e-taxonomy.eu
-*
-* The contents of this file are subject to the Mozilla Public License Version 1.1
-* See LICENSE.TXT at the top of this package for the full license terms.
-*/
-package eu.etaxonomy.cdm.io.specimen.abcd206.in;
-
-import java.io.IOException;
-import java.io.InputStream;
-import java.net.URI;
-
-import org.apache.http.client.ClientProtocolException;
-import org.apache.log4j.Logger;
-import org.w3c.dom.Element;
-
-import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;
-import eu.etaxonomy.cdm.ext.occurrence.OccurenceQuery;
-import eu.etaxonomy.cdm.ext.occurrence.bioCase.BioCaseQueryServiceWrapper;
-
-/**
- * @author pplitzner
- * @date 16.06.2015
- *
- */
-public class UnitAssociationParser {
-
-    private static final Logger logger = Logger.getLogger(UnitAssociationParser.class);
-
-    private final String prefix;
-
-    private final Abcd206ImportReport report;
-
-    private final ICdmApplicationConfiguration cdmAppController;
-
-    public UnitAssociationParser(String prefix, Abcd206ImportReport report, ICdmApplicationConfiguration cdmAppController) {
-        this.prefix = prefix;
-        this.report = report;
-        this.cdmAppController = cdmAppController;
-    }
-
-    public UnitAssociationWrapper parse(Element unitAssociation){
-        if(prefix.equals("abcd:")){
-
-        }
-        else if(prefix.equals("abcd21:")){
-
-        }
-        //unit id
-        String unitId = AbcdParseUtility.parseFirstTextContent(unitAssociation.getElementsByTagName(prefix+"UnitID"));
-        if(unitId==null){
-            unitId = AbcdParseUtility.parseFirstTextContent(unitAssociation.getElementsByTagName(prefix+"AssociatedUnitID"));//abcd 2.0.6
-        }
-        //institution code
-        String institutionCode = AbcdParseUtility.parseFirstTextContent(unitAssociation.getElementsByTagName(prefix+"SourceInstitutionCode"));
-        if(institutionCode==null){
-            institutionCode = AbcdParseUtility.parseFirstTextContent(unitAssociation.getElementsByTagName(prefix+"AssociatedUnitSourceInstitutionCode"));//abcd 2.0.6
-        }
-        //institution name
-        String institutionName = AbcdParseUtility.parseFirstTextContent(unitAssociation.getElementsByTagName(prefix+"SourceName"));
-        if(institutionName==null){
-            institutionName = AbcdParseUtility.parseFirstTextContent(unitAssociation.getElementsByTagName(prefix+"AssociatedUnitSourceName"));//abcd 2.0.6
-        }
-        //data access point
-        URI datasetAccessPoint = AbcdParseUtility.parseFirstUri(unitAssociation.getElementsByTagName(prefix+"DatasetAccessPoint"), report);
-        if(datasetAccessPoint==null){
-            datasetAccessPoint = AbcdParseUtility.parseFirstUri(unitAssociation.getElementsByTagName(prefix+"Comment"), report);//abcd 2.0.6
-        }
-        //association type
-        String associationType = AbcdParseUtility.parseFirstTextContent(unitAssociation.getElementsByTagName(prefix+"AssociationType"));
-
-        String unableToLoadMessage = String.format("Unable to load unit %s from %s", unitId, datasetAccessPoint);
-        if(unitId!=null && datasetAccessPoint!=null){
-            BioCaseQueryServiceWrapper serviceWrapper = new BioCaseQueryServiceWrapper();
-            OccurenceQuery query = new OccurenceQuery(unitId);
-            try {
-                InputStream inputStream = serviceWrapper.query(query, datasetAccessPoint);
-                if(inputStream!=null){
-                    UnitAssociationWrapper unitAssociationWrapper = null;
-                    try {
-                        unitAssociationWrapper = AbcdParseUtility.parseUnitsNodeList(inputStream, report);
-                    } catch (Exception e) {
-                        String exceptionMessage = "An exception occurred during parsing of associated units!";
-                        logger.error(exceptionMessage, e);
-                        report.addException(exceptionMessage, e);
-                    }
-
-                    if(unitAssociationWrapper!=null){
-                        unitAssociationWrapper.setAssociationType(associationType);
-                        if(unitAssociationWrapper.getAssociatedUnits()!=null && unitAssociationWrapper.getAssociatedUnits().getLength()>1){
-                            String moreThanOneUnitFoundMessage = String.format("More than one unit was found for unit association to %s", unitId);
-                            logger.warn(moreThanOneUnitFoundMessage);
-                            report.addInfoMessage(moreThanOneUnitFoundMessage);
-                        }
-                    }
-                    return unitAssociationWrapper;
-                }
-                else{
-                    logger.error(unableToLoadMessage);
-                    report.addInfoMessage(unableToLoadMessage);
-                }
-            } catch (ClientProtocolException e) {
-                logger.error(unableToLoadMessage, e);
-                report.addInfoMessage(unableToLoadMessage);
-            } catch (IOException e) {
-                logger.error(unableToLoadMessage, e);
-                report.addInfoMessage(unableToLoadMessage);
-            }
-        }
-        else{
-            report.addInfoMessage(unableToLoadMessage);
-        }
-        return null;
-    }
-
-}
+// $Id$\r
+/**\r
+* Copyright (C) 2015 EDIT\r
+* European Distributed Institute of Taxonomy\r
+* http://www.e-taxonomy.eu\r
+*\r
+* The contents of this file are subject to the Mozilla Public License Version 1.1\r
+* See LICENSE.TXT at the top of this package for the full license terms.\r
+*/\r
+package eu.etaxonomy.cdm.io.specimen.abcd206.in;\r
+\r
+import java.io.IOException;\r
+import java.io.InputStream;\r
+import java.net.URI;\r
+import java.util.HashSet;\r
+import java.util.Set;\r
+\r
+import org.apache.http.client.ClientProtocolException;\r
+import org.apache.log4j.Logger;\r
+import org.w3c.dom.Element;\r
+\r
+import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;\r
+import eu.etaxonomy.cdm.ext.occurrence.OccurenceQuery;\r
+import eu.etaxonomy.cdm.ext.occurrence.bioCase.BioCaseQueryServiceWrapper;\r
+\r
+/**\r
+ * @author pplitzner\r
+ * @date 16.06.2015\r
+ *\r
+ */\r
+public class UnitAssociationParser {\r
+\r
+    private static final Logger logger = Logger.getLogger(UnitAssociationParser.class);\r
+\r
+    private final String prefix;\r
+\r
+    private final SpecimenImportReport report;\r
+\r
+    private final ICdmApplicationConfiguration cdmAppController;\r
+\r
+    public UnitAssociationParser(String prefix, SpecimenImportReport report, ICdmApplicationConfiguration cdmAppController) {\r
+        this.prefix = prefix;\r
+        this.report = report;\r
+        this.cdmAppController = cdmAppController;\r
+    }\r
+\r
+    public UnitAssociationWrapper parse(Element unitAssociation){\r
+        if(prefix.equals("abcd:")){\r
+\r
+        }\r
+        else if(prefix.equals("abcd21:")){\r
+\r
+        }\r
+        //unit id\r
+        String unitId = AbcdParseUtility.parseFirstTextContent(unitAssociation.getElementsByTagName(prefix+"UnitID"));\r
+        if(unitId==null){\r
+            unitId = AbcdParseUtility.parseFirstTextContent(unitAssociation.getElementsByTagName(prefix+"AssociatedUnitID"));//abcd 2.0.6\r
+        }\r
+        //institution code\r
+        String institutionCode = AbcdParseUtility.parseFirstTextContent(unitAssociation.getElementsByTagName(prefix+"SourceInstitutionCode"));\r
+        if(institutionCode==null){\r
+            institutionCode = AbcdParseUtility.parseFirstTextContent(unitAssociation.getElementsByTagName(prefix+"AssociatedUnitSourceInstitutionCode"));//abcd 2.0.6\r
+        }\r
+        //institution name\r
+        String institutionName = AbcdParseUtility.parseFirstTextContent(unitAssociation.getElementsByTagName(prefix+"SourceName"));\r
+        if(institutionName==null){\r
+            institutionName = AbcdParseUtility.parseFirstTextContent(unitAssociation.getElementsByTagName(prefix+"AssociatedUnitSourceName"));//abcd 2.0.6\r
+        }\r
+        //data access point\r
+        URI datasetAccessPoint = AbcdParseUtility.parseFirstUri(unitAssociation.getElementsByTagName(prefix+"DatasetAccessPoint"), report);\r
+        if(datasetAccessPoint==null){\r
+            datasetAccessPoint = AbcdParseUtility.parseFirstUri(unitAssociation.getElementsByTagName(prefix+"Comment"), report);//abcd 2.0.6\r
+        }\r
+        //association type\r
+        String associationType = AbcdParseUtility.parseFirstTextContent(unitAssociation.getElementsByTagName(prefix+"AssociationType"));\r
+\r
+        String unableToLoadMessage = String.format("Unable to load unit %s from %s", unitId, datasetAccessPoint);\r
+        if(unitId!=null && datasetAccessPoint!=null){\r
+            BioCaseQueryServiceWrapper serviceWrapper = new BioCaseQueryServiceWrapper();\r
+            Set<String[]> unitIds = new HashSet<String[]>();\r
+            String[] unitIdArray = {unitId};\r
+            unitIds.add(unitIdArray);\r
+            OccurenceQuery query = new OccurenceQuery(unitIds);\r
+            try {\r
+                InputStream inputStream = serviceWrapper.query(query, datasetAccessPoint);\r
+                if(inputStream!=null){\r
+                    UnitAssociationWrapper unitAssociationWrapper = null;\r
+                    try {\r
+                        unitAssociationWrapper = AbcdParseUtility.parseUnitsNodeList(inputStream, report);\r
+                    } catch (Exception e) {\r
+                        String exceptionMessage = "An exception occurred during parsing of associated units!";\r
+                        logger.error(exceptionMessage, e);\r
+                        report.addException(exceptionMessage, e);\r
+                    }\r
+\r
+                    if(unitAssociationWrapper!=null){\r
+                        unitAssociationWrapper.setAssociationType(associationType);\r
+                        if(unitAssociationWrapper.getAssociatedUnits()!=null && unitAssociationWrapper.getAssociatedUnits().getLength()>1){\r
+                            String moreThanOneUnitFoundMessage = String.format("More than one unit was found for unit association to %s", unitId);\r
+                            logger.warn(moreThanOneUnitFoundMessage);\r
+                            report.addInfoMessage(moreThanOneUnitFoundMessage);\r
+                        }\r
+                    }\r
+                    return unitAssociationWrapper;\r
+                }\r
+                else{\r
+                    logger.error(unableToLoadMessage);\r
+                    report.addInfoMessage(unableToLoadMessage);\r
+                }\r
+            } catch (ClientProtocolException e) {\r
+                logger.error(unableToLoadMessage, e);\r
+                report.addInfoMessage(unableToLoadMessage);\r
+            } catch (IOException e) {\r
+                logger.error(unableToLoadMessage, e);\r
+                report.addInfoMessage(unableToLoadMessage);\r
+            }\r
+        }\r
+        else{\r
+            report.addInfoMessage(unableToLoadMessage);\r
+        }\r
+        return null;\r
+    }\r
+\r
+}\r