X-Git-Url: https://dev.e-taxonomy.eu/gitweb/cdmlib.git/blobdiff_plain/3276f8e999deed06f894b7a1367b2da2cd109870..38d07becf34d8fb1d3c5790847bc6e5cb9ffc275:/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/jaxb/JaxbExport.java?ds=sidebyside

diff --git a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/jaxb/JaxbExport.java b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/jaxb/JaxbExport.java
index 13a0264f66..b6c87d605b 100644
--- a/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/jaxb/JaxbExport.java
+++ b/cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/jaxb/JaxbExport.java
@@ -12,24 +12,29 @@ package eu.etaxonomy.cdm.io.jaxb;
 import java.io.FileOutputStream;
 import java.io.OutputStreamWriter;
 import java.io.PrintWriter;
+import java.util.ArrayList;
 import java.util.List;
 
 import org.apache.log4j.Logger;
 import org.springframework.stereotype.Component;
 import org.springframework.transaction.TransactionStatus;
 
+import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
 import eu.etaxonomy.cdm.io.common.CdmExportBase;
-import eu.etaxonomy.cdm.io.common.CdmIoBase;
 import eu.etaxonomy.cdm.io.common.ICdmExport;
-import eu.etaxonomy.cdm.io.common.ICdmIO;
 import eu.etaxonomy.cdm.io.common.IExportConfigurator;
 import eu.etaxonomy.cdm.io.common.IImportConfigurator;
 import eu.etaxonomy.cdm.model.agent.AgentBase;
 import eu.etaxonomy.cdm.model.common.DefinedTermBase;
+import eu.etaxonomy.cdm.model.common.User;
+import eu.etaxonomy.cdm.model.description.FeatureNode;
+import eu.etaxonomy.cdm.model.description.FeatureTree;
 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
 import eu.etaxonomy.cdm.model.reference.ReferenceBase;
 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
+import eu.etaxonomy.cdm.model.taxon.TaxonNode;
+import eu.etaxonomy.cdm.model.taxon.TaxonomicTree;
 
 /**
  * @author a.babadshanjan
@@ -65,10 +70,10 @@ public class JaxbExport extends CdmExportBase<JaxbExportConfigurator, JaxbExport
 	protected boolean doInvoke(JaxbExportState state) {
 		
 		JaxbExportConfigurator jaxbExpConfig = (JaxbExportConfigurator)state.getConfig();
-		String dbname = jaxbExpConfig.getSource().getName();
+//		String dbname = jaxbExpConfig.getSource().getName();
     	String fileName = jaxbExpConfig.getDestination();
-		logger.info("Serializing DB " + dbname + " to file " + fileName);
-		logger.debug("DbSchemaValidation = " + jaxbExpConfig.getDbSchemaValidation());
+//		logger.info("Serializing DB " + dbname + " to file " + fileName);
+//		logger.debug("DbSchemaValidation = " + jaxbExpConfig.getDbSchemaValidation());
 
 		TransactionStatus txStatus = startTransaction(true);
 		DataSet dataSet = new DataSet();
@@ -90,8 +95,15 @@ public class JaxbExport extends CdmExportBase<JaxbExportConfigurator, JaxbExport
 		try {
 			cdmDocumentBuilder = new CdmDocumentBuilder();
 			PrintWriter writer = new PrintWriter(new OutputStreamWriter(new FileOutputStream(fileName), "UTF8"), true);
+			
+			/*SAXResult result = new SAXResult();
+			ContentHandler handler = new DefaultHandler();
+			
+			result.setHandler(handler);*/
+			
+			//cdmDocumentBuilder.marshal(dataSet, result);
 			cdmDocumentBuilder.marshal(dataSet, writer);
-
+			
 			// TODO: Split into one file per data set member to see whether performance improves?
 
 			logger.info("XML file written");
@@ -119,67 +131,89 @@ public class JaxbExport extends CdmExportBase<JaxbExportConfigurator, JaxbExport
 		int referenceBaseRows = numberOfRows;
 		int taxonNameBaseRows = numberOfRows;
 		int taxonBaseRows = numberOfRows;
+		int taxonNodeRows = numberOfRows;
 		int relationshipRows = numberOfRows;
 		int occurrencesRows = numberOfRows;
 		int mediaRows = numberOfRows;
 		int featureDataRows = numberOfRows;
+		int taxonomicTreeDataRows = numberOfRows;
 		int languageDataRows = numberOfRows;
 		int termVocabularyRows = numberOfRows;
 		int homotypicalGroupRows = numberOfRows;
+		int UserRows= numberOfRows;
 
+		if (jaxbExpConfig.isDoUsers() == true) {
+			
+			if (UserRows == 0) { UserRows = MAX_ROWS; }
+			logger.info("# User");
+			List<User> users = getUserService().list(null, UserRows, 0, null, null);
+		
+			
+			for (User user: users){
+				dataSet.addUser( (User)HibernateProxyHelper.deproxy(user));
+			}
+			
+		}
 		if (jaxbExpConfig.isDoTermVocabularies() == true) {
 			if (termVocabularyRows == 0) { termVocabularyRows = MAX_ROWS; }
 			logger.info("# TermVocabulary");
-			dataSet.setTermVocabularies(getTermService().getAllTermVocabularies(MAX_ROWS, 0));;
+			dataSet.setTermVocabularies((List)getVocabularyService().list(null,termVocabularyRows, 0, null, null));
 		}
+		
+		
 
 //		if (jaxbExpConfig.isDoLanguageData() == true) {
 //			if (languageDataRows == 0) { languageDataRows = MAX_ROWS; }
 //			logger.info("# Representation, Language String");
 //			dataSet.setLanguageData(getTermService().getAllRepresentations(MAX_ROWS, 0));
-//			dataSet.addLanguageData(getTermService().getAllLanguageStrings(MAX_ROWS, 0));
+		//TODO!!!	
+		dataSet.setLanguageStrings(getTermService().getAllLanguageStrings(MAX_ROWS, 0));
 //		}
 
 		if (jaxbExpConfig.isDoTerms() == true) {
 			if (definedTermBaseRows == 0) { definedTermBaseRows = getTermService().count(DefinedTermBase.class); }
 			logger.info("# DefinedTermBase: " + definedTermBaseRows);
-			dataSet.setTerms(getTermService().getAllDefinedTerms(definedTermBaseRows, 0));
+			dataSet.setTerms(getTermService().list(null,definedTermBaseRows, 0,null,null));
 		}
-
+		
 		if (jaxbExpConfig.isDoAuthors() == true) {
 			if (agentRows == 0) { agentRows = getAgentService().count(AgentBase.class); }
 			logger.info("# Agents: " + agentRows);
 			//logger.info("    # Team: " + appCtr.getAgentService().count(Team.class));
-			dataSet.setAgents(getAgentService().getAllAgents(agentRows, 0));
+			dataSet.setAgents(getAgentService().list(null,agentRows, 0,null,null));
 		}
+		
+		
 
 		if (jaxbExpConfig.getDoReferences() != IImportConfigurator.DO_REFERENCES.NONE) {
 			if (referenceBaseRows == 0) { referenceBaseRows = getReferenceService().count(ReferenceBase.class); }
 			logger.info("# ReferenceBase: " + referenceBaseRows);
-			dataSet.setReferences(getReferenceService().getAllReferences(referenceBaseRows, 0));
+			dataSet.setReferences(getReferenceService().list(null,referenceBaseRows, 0,null,null));
+		}
+		
+		if (jaxbExpConfig.isDoHomotypicalGroups() == true) {
+			if (homotypicalGroupRows == 0) { homotypicalGroupRows = MAX_ROWS; }
+			logger.info("# Homotypical Groups");
+			dataSet.setHomotypicalGroups(getNameService().getAllHomotypicalGroups(homotypicalGroupRows, 0));
 		}
 
 		if (jaxbExpConfig.isDoTaxonNames() == true) {
 			if (taxonNameBaseRows == 0) { taxonNameBaseRows = getNameService().count(TaxonNameBase.class); }
 			logger.info("# TaxonNameBase: " + taxonNameBaseRows);
 			//logger.info("    # Taxon: " + getNameService().count(BotanicalName.class));
-			dataSet.setTaxonomicNames(getNameService().getAllNames(taxonNameBaseRows, 0));
+			dataSet.setTaxonomicNames(getNameService().list(null,taxonNameBaseRows, 0,null,null));
 		}
 
-		if (jaxbExpConfig.isDoHomotypicalGroups() == true) {
-			if (homotypicalGroupRows == 0) { homotypicalGroupRows = MAX_ROWS; }
-			logger.info("# Homotypical Groups");
-			dataSet.setHomotypicalGroups(getNameService().getAllHomotypicalGroups(homotypicalGroupRows, 0));
-		}
+		
 
 		if (jaxbExpConfig.isDoTaxa() == true) {
 			if (taxonBaseRows == 0) { taxonBaseRows = getTaxonService().count(TaxonBase.class); }
 			logger.info("# TaxonBase: " + taxonBaseRows);
 //			dataSet.setTaxa(new ArrayList<Taxon>());
 //			dataSet.setSynonyms(new ArrayList<Synonym>());
-			List<TaxonBase> tb = getTaxonService().getAllTaxonBases(taxonBaseRows, 0);
+			List<TaxonBase> tb = getTaxonService().list(null,taxonBaseRows, 0,null,null);
 			for (TaxonBase taxonBase : tb) {
-				dataSet.addTaxonBase(taxonBase);
+				dataSet.addTaxonBase((TaxonBase)HibernateProxyHelper.deproxy(taxonBase));
 			}
 		}
 
@@ -198,22 +232,29 @@ public class JaxbExport extends CdmExportBase<JaxbExportConfigurator, JaxbExport
 //			Set<RelationshipBase> relationSet = new HashSet<RelationshipBase>(relationList);
 //			dataSet.setRelationships(relationSet);
 //		}
-
+		if (jaxbExpConfig.isDoOccurrence() == true) {
+			if (occurrencesRows == 0) { occurrencesRows = getOccurrenceService().count(SpecimenOrObservationBase.class); }
+			logger.info("# SpecimenOrObservationBase: " + occurrencesRows);
+			List<SpecimenOrObservationBase> occurrenceList = getOccurrenceService().list(null,occurrencesRows, 0,null,null);
+			/*List<SpecimenOrObservationBase> noProxyList = new ArrayList<SpecimenOrObservationBase>();
+			for (SpecimenOrObservationBase specimen : occurrenceList){
+				specimen = (SpecimenOrObservationBase)HibernateProxyHelper.deproxy(specimen);
+				noProxyList.add(specimen);
+			}*/
+			dataSet.setOccurrences(occurrenceList);
+		}
+		
 		if (jaxbExpConfig.isDoTypeDesignations() == true) {
 			logger.info("# TypeDesignations");
 			dataSet.addTypeDesignations(getNameService().getAllTypeDesignations(MAX_ROWS, 0));
 		}
 
-		if (jaxbExpConfig.isDoOccurrence() == true) {
-			if (occurrencesRows == 0) { occurrencesRows = getOccurrenceService().count(SpecimenOrObservationBase.class); }
-			logger.info("# SpecimenOrObservationBase: " + occurrencesRows);
-			dataSet.setOccurrences(getOccurrenceService().getAllSpecimenOrObservationBases(occurrencesRows, 0));
-		}
+		
 
 		if (jaxbExpConfig.isDoMedia() == true) {
 			if (mediaRows == 0) { mediaRows = MAX_ROWS; }
 			logger.info("# Media");
-			dataSet.setMedia(getMediaService().getAllMedia(mediaRows, 0));
+			dataSet.setMedia(getMediaService().list(null,mediaRows, 0,null,null));
 //			dataSet.addMedia(getMediaService().getAllMediaRepresentations(mediaRows, 0));
 //			dataSet.addMedia(getMediaService().getAllMediaRepresentationParts(mediaRows, 0));
 		}
@@ -221,8 +262,42 @@ public class JaxbExport extends CdmExportBase<JaxbExportConfigurator, JaxbExport
 		if (jaxbExpConfig.isDoFeatureData() == true) {
 			if (featureDataRows == 0) { featureDataRows = MAX_ROWS; }
 			logger.info("# Feature Tree, Feature Node");
-			dataSet.setFeatureTrees(getDescriptionService().getFeatureTreesAll(null));
+			List<FeatureTree> featureTrees = new ArrayList<FeatureTree>();
+			featureTrees= getFeatureTreeService().list(null,featureDataRows, 0, null, null);
+			List<FeatureTree> taxTreesdeproxy = new ArrayList<FeatureTree>();
+			for (FeatureTree featureTree : featureTrees){
+				HibernateProxyHelper.deproxy(featureTree);
+				taxTreesdeproxy.add(featureTree);
+			}
+			
+			dataSet.setFeatureTrees(getFeatureTreeService().list(null,null,null,null,null));
+		}
+		if (jaxbExpConfig.isDoTaxonomicTreeData() == true) {
+			if (taxonomicTreeDataRows == 0) { taxonomicTreeDataRows = MAX_ROWS; }
+			logger.info("# Taxonomic Tree");
+			
+			
+			List<TaxonomicTree> taxTrees = new ArrayList<TaxonomicTree>();
+			taxTrees= getTaxonTreeService().list(null,taxonomicTreeDataRows, 0, null, null);
+			
+			List<TaxonomicTree> taxTreesdeproxy = new ArrayList<TaxonomicTree>();
+			for (TaxonomicTree taxTree : taxTrees){
+				HibernateProxyHelper.deproxy(taxTree);
+				taxTreesdeproxy.add(taxTree);
+			}
+			List<TaxonNode> taxNodes = new ArrayList<TaxonNode>();
+			taxNodes= getTaxonTreeService().getAllNodes();
+			List<TaxonNode> taxNodesdeproxy = new ArrayList<TaxonNode>();
+			for (TaxonNode taxNode : taxNodes){
+				HibernateProxyHelper.deproxy(taxNode);
+				taxNodesdeproxy.add(taxNode);
+			}
+			
+			dataSet.setTaxonNodes(taxNodesdeproxy);
+			dataSet.setTaxonomicTrees(taxTreesdeproxy );
 		}
+		//TODO: FIXME!!!!!
+		dataSet.setLanguageStrings(null);
 	}