clearer getters for DerivedUnitFacade + PointBeanProcessor

[cdmlib.git] / cdmlib-io / src / main / java / eu / etaxonomy / cdm / io / specimen / abcd206 / in / Abcd206Import.java

diff --git a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/abcd206/in/Abcd206Import.java b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/abcd206/in/Abcd206Import.java
index 626e10e842071c2cc56e6cc3f08b14fc7652ed14..f8e4378c94c4c71a3f8cff61f8cf6b04fbd1834c 100644 (file)
--- a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/abcd206/in/Abcd206Import.java
+++ b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/abcd206/in/Abcd206Import.java
@@ -11,6 +11,7 @@ package eu.etaxonomy.cdm.io.specimen.abcd206.in;
 
 import java.io.IOException;
 import java.io.InputStream;
+import java.net.URI;
 import java.net.URL;
 import java.util.ArrayList;
 import java.util.HashMap;
@@ -34,9 +35,8 @@ import org.xml.sax.SAXException;
 
 import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;
 import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade.DerivedUnitType;
-import eu.etaxonomy.cdm.common.mediaMetaData.ImageMetaData;
 import eu.etaxonomy.cdm.io.common.ICdmIO;
-import eu.etaxonomy.cdm.io.specimen.SpecimenIoBase;
+import eu.etaxonomy.cdm.io.specimen.SpecimenImportBase;
 import eu.etaxonomy.cdm.io.specimen.UnitsGatheringArea;
 import eu.etaxonomy.cdm.io.specimen.UnitsGatheringEvent;
 import eu.etaxonomy.cdm.model.agent.Institution;
@@ -46,9 +46,7 @@ import eu.etaxonomy.cdm.model.description.Feature;
 import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
 import eu.etaxonomy.cdm.model.description.TaxonDescription;
 import eu.etaxonomy.cdm.model.location.NamedArea;
-import eu.etaxonomy.cdm.model.media.ImageFile;
 import eu.etaxonomy.cdm.model.media.Media;
-import eu.etaxonomy.cdm.model.media.MediaRepresentation;
 import eu.etaxonomy.cdm.model.name.BacterialName;
 import eu.etaxonomy.cdm.model.name.BotanicalName;
 import eu.etaxonomy.cdm.model.name.CultivarPlantName;
@@ -72,7 +70,7 @@ import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
  * @version 1.0
  */
 @Component
-public class Abcd206Import extends SpecimenIoBase<Abcd206ImportConfigurator, Abcd206ImportState> implements ICdmIO<Abcd206ImportState> {
+public class Abcd206Import extends SpecimenImportBase<Abcd206ImportConfigurator, Abcd206ImportState> implements ICdmIO<Abcd206ImportState> {
        private static final Logger logger = Logger.getLogger(Abcd206Import.class);
 
 
@@ -93,7 +91,7 @@ public class Abcd206Import extends SpecimenIoBase<Abcd206ImportConfigurator, Abc
                logger.info("INVOKE Specimen Import from ABCD2.06 XML File");
                boolean result = true;
                //AbcdIO test = new AbcdIO();
-               String sourceName = state.getConfig().getSource();
+               URI sourceName = state.getConfig().getSource();
                NodeList unitsList = getUnitsNodeList(sourceName);
                if (unitsList != null){
                        String message = "nb units to insert: "+unitsList.getLength();
@@ -184,32 +182,9 @@ public class Abcd206Import extends SpecimenIoBase<Abcd206ImportConfigurator, Abc
 
 //                     //add Multimedia URLs
                        if(dataHolder.multimediaObjects.size() > 0){
-                               MediaRepresentation representation;
-                               Media media;
-                               ImageMetaData imd ;
-                               URL url ;
-                               ImageFile imf;
                                for (String multimediaObject : dataHolder.multimediaObjects){
-                                       if( multimediaObject != null){
-                                               imd = ImageMetaData.newInstance();
-                                               url = new URL(multimediaObject);
-                                               try {
-                                                       imd.readMetaData(url.toURI(), 0);
-                                               } catch (Exception e) {
-                                                       String message = "An error occurred when trying to read image meta data: " +  e.getMessage();
-                                                       logger.warn(message);
-                                               }
-                                               //TODO do we really want to check the url?
-                                               if (imd != null){
-                                                       imf = ImageFile.NewInstance(multimediaObject, null, imd);
-                                                       representation = MediaRepresentation.NewInstance();
-                                                       representation.addRepresentationPart(imf);
-                                                       media = Media.NewInstance();
-                                                       media.addRepresentation(representation);
-                                                       
-                                                       derivedUnitFacade.addFieldObjectMedia(media);
-                                               }
-                                       }
+                                       Media media = getImageMedia(multimediaObject, true);
+                                       derivedUnitFacade.addDerivedUnitMedia(media);
                                }
                        }
                        
@@ -222,7 +197,7 @@ public class Abcd206Import extends SpecimenIoBase<Abcd206ImportConfigurator, Abc
                        }
                        getTermService().saveLanguageData(unitsGatheringEvent.getLocality());//TODO needs to be saved ?? save it sooner
                        
-                       getOccurrenceService().save(derivedUnitFacade.getDerivedUnit());
+                       getOccurrenceService().save(derivedUnitFacade.innerDerivedUnit());
                        logger.info("saved ABCD specimen ...");
 
 
@@ -236,7 +211,6 @@ public class Abcd206Import extends SpecimenIoBase<Abcd206ImportConfigurator, Abc
                return result;
        }
 
-
        private void setCollectionData(Abcd206ImportConfigurator config,
                        Abcd206DataHolder dataHolder, DerivedUnitFacade derivedUnitFacade) {
                //set catalogue number (unitID)
@@ -292,12 +266,12 @@ public class Abcd206Import extends SpecimenIoBase<Abcd206ImportConfigurator, Abc
         * @param fileName: the file's location
         * @return the list of root nodes ("Unit")
         */
-       private static NodeList getUnitsNodeList(String urlFileName){
+       private static NodeList getUnitsNodeList(URI urlFileName){
                NodeList unitList = null;
                try {
                        DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
                        DocumentBuilder builder = factory.newDocumentBuilder();
-                       URL url = new URL(urlFileName);
+                       URL url = urlFileName.toURL();
                        Object o = url.getContent();
                        InputStream is = (InputStream)o;
                        Document document = builder.parse(is);
@@ -1107,6 +1081,7 @@ public class Abcd206Import extends SpecimenIoBase<Abcd206ImportConfigurator, Abc
                        if (config.isDoMatchTaxa()){
                                taxon = getTaxonService().findBestMatchingTaxon(scientificName);
                        } 
+                       
                        if (taxon == null && config.isDoReUseTaxon()){
                                try{
                                        names = getTaxonService().searchTaxaByName(scientificName, sec);
@@ -1158,7 +1133,7 @@ public class Abcd206Import extends SpecimenIoBase<Abcd206ImportConfigurator, Abc
                                        }
                                }
                                IndividualsAssociation individualsAssociation = IndividualsAssociation.NewInstance();
-                               individualsAssociation.setAssociatedSpecimenOrObservation(facade.getDerivedUnit());
+                               individualsAssociation.setAssociatedSpecimenOrObservation(facade.innerDerivedUnit());
                                individualsAssociation.setFeature(Feature.INDIVIDUALS_ASSOCIATION());
                                for(ReferenceBase citation : determinationEvent.getReferences()){
                                        individualsAssociation.addSource(DescriptionElementSource.NewInstance(null, null, citation, null));
@@ -1363,12 +1338,12 @@ public class Abcd206Import extends SpecimenIoBase<Abcd206ImportConfigurator, Abc
                return value;
        }
 
-       private void compareABCDtoCDM(String urlFileName, ArrayList<String> knownElts, Abcd206DataHolder dataHolder){
+       private void compareABCDtoCDM(URI urlFileName, ArrayList<String> knownElts, Abcd206DataHolder dataHolder){
 
                try {
                        DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
                        DocumentBuilder constructeur = factory.newDocumentBuilder();
-                       URL url = new URL(urlFileName);
+                       URL url = urlFileName.toURL();
                        Object o = url.getContent();
                        InputStream is = (InputStream)o;
                        Document document = constructeur.parse(is);