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app-import/src/main/java/eu/etaxonomy/cdm/app/caryophyllales/CaryoActivator.java
29	29	/**
30	30	* @author a.mueller
31	31	* @created 16.10.2012
32		* @version 1.0
33	32	*/
34	33	public class CaryoActivator extends SourceBase{
35	34	private static final Logger logger = Logger.getLogger(CaryoActivator.class);

     	//static final Source faunaEuropaeaSource = FaunaEuropaeaSources.faunEu();
     //	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();
     //	static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
     	static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
     //	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_central_africa_production();
     //	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_edit_cichorieae_preview();
     	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_cyprus_production();
     //	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_cyprus_production();
     	static final int limitSave = 2000;

         //database validation status (create, update, validate ...)
         static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;
     //    static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
         static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
     //  static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_test();
         static final ICdmDataSource cdmDestination = CdmDestinations.cdm_greece_checklist_production();
     //    static final ICdmDataSource cdmDestination = CdmDestinations.cdm_greece_checklist_production();
         //feature tree uuid
         public static final UUID featureTreeUuid = UUID.fromString("9e1e0e81-7475-4b28-8619-b7f42cd760b6");

     /**
     * Copyright (C) 2007 EDIT
     * European Distributed Institute of Taxonomy
     * 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.
     */
-...
     import eu.etaxonomy.cdm.api.application.CdmApplicationController;
     import eu.etaxonomy.cdm.api.service.IAgentService;
     import eu.etaxonomy.cdm.api.service.IClassificationService;
     import eu.etaxonomy.cdm.api.service.ICommonService;
     import eu.etaxonomy.cdm.api.service.IDescriptionService;
     import eu.etaxonomy.cdm.api.service.IReferenceService;
     import eu.etaxonomy.cdm.api.service.ITaxonService;
     import eu.etaxonomy.cdm.api.service.IClassificationService;
     import eu.etaxonomy.cdm.io.common.CdmIoBase;
     import eu.etaxonomy.cdm.io.common.ICdmIO;
     import eu.etaxonomy.cdm.io.common.CdmImportBase;
     /**
+     *
      * @author n.hoffmann
      * @created 11.11.2008
      * @version 1.0
      */
     public abstract class AbstractImageImporter extends CdmIoBase<ImageImportState> implements ICdmIO<ImageImportState> {
     	private static final Logger logger = Logger.getLogger(AbstractImageImporter.class);
     public abstract class AbstractImageImporter
             extends CdmImportBase<ImageImportConfigurator, ImageImportState> {
         private static final long serialVersionUID = 6178173988325980060L;
         private static final Logger logger = Logger.getLogger(AbstractImageImporter.class);
     	protected CdmApplicationController appCtr;
     	protected CdmApplicationController cdmApp;
     	protected ITaxonService taxonService;
     	protected IClassificationService classificationService;
-...
     	protected IDescriptionService descriptionService;
     	protected IReferenceService referenceService;
     	protected ICommonService commonService;
     	/* (non-Javadoc)
     	 * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doInvoke(eu.etaxonomy.cdm.io.common.IImportConfigurator, java.util.Map)
     	 */
-...
     	public void doInvoke(ImageImportState state) {
     		//cdmApp = config.getCdmAppController();
     		//if (config instanceof ImageImportConfigurator){
     		TransactionStatus status = startTransaction();
     		taxonService = getTaxonService();
     		agentService = getAgentService();
     		referenceService = getReferenceService();
-...
     		classificationService = getClassificationService();
     		invokeImageImport(state);
     		commitTransaction(status);
     		return;
+    	}
     	/**
     	 * This method defines the image import.
     	 * This method defines the image import.
     	 * It should take care of where to get the images from and what object they get attached to.
+    	 *
+    	 *
     	 * @param config
     	 */
     	protected abstract void invokeImageImport(ImageImportState state);
-...
+    	}
+    }

app-import/src/main/java/eu/etaxonomy/cdm/app/wp6/palmae/PalmaeActivator.java
38	38	/**
39	39	* @author a.mueller
40	40	* @created 20.06.2008
41		* @version 1.0
42	41	*/
43	42	public class PalmaeActivator {
44	43	private static final Logger logger = Logger.getLogger(PalmaeActivator.class);

     /**
     * Copyright (C) 2007 EDIT
     * European Distributed Institute of Taxonomy
     * 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.
     */
-...
     import org.springframework.stereotype.Component;
     import eu.etaxonomy.cdm.app.images.AbstractImageImporter;
     import eu.etaxonomy.cdm.app.images.ImageImportConfigurator;
     import eu.etaxonomy.cdm.app.images.ImageImportState;
     import eu.etaxonomy.cdm.common.ExcelUtils;
     import eu.etaxonomy.cdm.model.description.Feature;
-...
     /**
      * @author n.hoffmann
      * @created 19.11.2008
      * @version 1.0
      */
     @Component
     public class PalmaeProtologueImport extends AbstractImageImporter {
     	private static final Logger logger = Logger.getLogger(PalmaeProtologueImport.class);
         private static final long serialVersionUID = -7178567387220714414L;
         private static final Logger logger = Logger.getLogger(PalmaeProtologueImport.class);
     	public static final String SPECIES = "Species";
     	public static final String TAXONID = "Taxon ID";
     	public static final String LINK_PROTO = "Link proto";
     	/* (non-Javadoc)
     	 * @see eu.etaxonomy.cdm.app.images.AbstractImageImporter#invokeImageImport(eu.etaxonomy.cdm.io.common.IImportConfigurator)
     	 */
     	@Override
     	protected void invokeImageImport(ImageImportState state) {
     		ArrayList<HashMap<String, String>> contents;
     		try {
     			contents = ExcelUtils.parseXLS(state.getConfig().getSource());
-...
     			state.setUnsuccessfull();
     			return;
+    		}
     		Set<TaxonNameBase> taxonNameStore = new HashSet<TaxonNameBase>();
     		int count = 0;
     		for (HashMap<String, String> row : contents){
     			count++;
     			TaxonNameBase taxonNameBase = null;
     			String species = null;
     			String taxonId = null;
-...
     			}catch (Exception e){
     				logger.error("The row has errors: rowNumber: " +count + ", content: "  + row, e);
+    			}
     			if(taxonNameBase == null){
     				logger.warn("no taxon with this name found: " + species + ", idInSource: " + taxonId);
     			}else{
     				URI uri;
     				try {
     					uri = new URI(linkProto);
     					MediaRepresentationPart representationPart = MediaRepresentationPart.NewInstance(uri, 0);
     					MediaRepresentation representation = MediaRepresentation.NewInstance("text/html", null);
     					representation.addRepresentationPart(representationPart);
     					Media media = Media.NewInstance();
     					media.addRepresentation(representation);
     					TaxonNameDescription description = TaxonNameDescription.NewInstance();
     					TextData protolog = TextData.NewInstance(Feature.PROTOLOGUE());
     					protolog.addMedia(media);
-...
     					logger.error(message);
     					e.printStackTrace();
+    				}
     				taxonNameStore.add(taxonNameBase);
     				if(count % 50 == 0){
     					logger.info(count + " protologues processed.");
+    				}
+    			}
+    		}
     		getNameService().save(taxonNameStore);
     		logger.info(count + " protologues imported to CDM store.");
     		return;
+    	}
+    }

     /**
     * Copyright (C) 2007 EDIT
     * European Distributed Institute of Taxonomy
     * 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.
     */
-...
     import eu.etaxonomy.cdm.api.service.ICommonService;
     import eu.etaxonomy.cdm.app.wp6.palmae.config.PalmaeProtologueImportConfigurator;
     import eu.etaxonomy.cdm.common.CdmUtils;
     import eu.etaxonomy.cdm.io.common.CdmIoBase;
     import eu.etaxonomy.cdm.io.common.CdmImportBase;
     import eu.etaxonomy.cdm.io.common.DefaultImportState;
     import eu.etaxonomy.cdm.model.description.Feature;
     import eu.etaxonomy.cdm.model.description.TaxonNameDescription;
-...
     /**
      * @author a.mueller
      * @created 29.07.2008
      * @version 1.0
      */
     @Component
     public class ProtologueImport extends CdmIoBase<DefaultImportState<PalmaeProtologueImportConfigurator>>  {
     	private static final Logger logger = Logger.getLogger(ProtologueImport.class);
     public class ProtologueImport
             extends CdmImportBase<PalmaeProtologueImportConfigurator, DefaultImportState<PalmaeProtologueImportConfigurator>>{
         private static final long serialVersionUID = 4580327331805229644L;
         private static final Logger logger = Logger.getLogger(ProtologueImport.class);
     	private String pluralString = "protologues";
     	private static int modCount = 200;
-...
     		super();
+    	}
     	public void doInvoke(DefaultImportState<PalmaeProtologueImportConfigurator> state){
     	@Override
         public void doInvoke(DefaultImportState<PalmaeProtologueImportConfigurator> state){
     		logger.info("start make Protologues from files ...");
     		Set<TaxonNameBase> nameStore = new HashSet<TaxonNameBase>();
     		PalmaeProtologueImportConfigurator config = state.getConfig();
     		File source = config.getSource();
     		TaxonNameBase name;
-...
     		logger.info("end make Protologues from files ...");
     		return;
+    	}
     	private void storeName(Set<TaxonNameBase> nameStore, TaxonNameBase name, DefaultImportState<PalmaeProtologueImportConfigurator> state){
     		if (name != null){
     			nameStore.add(name);
-...
     			return;
+    		}
+    	}
     	private TaxonNameBase importFile(File file, DefaultImportState<PalmaeProtologueImportConfigurator> state){
     		String originalSourceId = file.getName();
     		originalSourceId =originalSourceId.replace("_P.pdf", "");
     		originalSourceId =originalSourceId.replace("_tc_", "_tn_");
     		String namespace = state.getConfig().getOriginalSourceTaxonNamespace();
     		//for testing only
     		TaxonNameBase taxonName = getTaxonName(originalSourceId, namespace);
     		if (taxonName == null){
     			logger.warn("Name not found for " + originalSourceId);
     			return null;
+    		}
     //		TaxonNameDescription nameDescription = null;
     //		if (taxonName.getDescriptions().size() > 0){
     //			nameDescription = (TaxonNameDescription)taxonName.getDescriptions().iterator().next();
-...
     				description.addElement(protolog);
     				return taxonName;
+    			}
     		}catch(NullPointerException e){
     			logger.warn("MediaUrl and/or MediaPath not set. Could not get protologue.");
     			return null;
+    		}
     		return null;
+    	}
     	private TaxonNameDescription getNameDescription(TaxonNameBase taxonName) {
-...
     			result = TaxonNameDescription.NewInstance();
     			taxonName.addDescription(result);
+    		}
     		return result;
+    	}
     	private Media getMedia(DefaultImportState<PalmaeProtologueImportConfigurator> state, File file){
     		try {
     			//File file = (File)state.getConfig().getSource();
     			String url = file.toURI().toURL().toString();
     			String mimeTypePdf = "application/pdf";
     			String suffixPdf = "pdf";
     			String urlStringPdf = state.getConfig().getUrlString() + file.getName();
     			String mimeTypePdf = "application/pdf";
     			String suffixPdf = "pdf";
     			String urlStringPdf = state.getConfig().getUrlString() + file.getName();
     			URI uri = CdmUtils.string2Uri(urlStringPdf);
     			Integer size = null;
     			if (file.exists()){
     			if (file.exists()){
     				Media media = Media.NewInstance();
     				MediaRepresentation representationPdf = MediaRepresentation.NewInstance(mimeTypePdf, suffixPdf);
     			    representationPdf.addRepresentationPart(MediaRepresentationPart.NewInstance(uri, size));
     			    media.addRepresentation(representationPdf);
     				MediaRepresentation representationPdf = MediaRepresentation.NewInstance(mimeTypePdf, suffixPdf);
     			    representationPdf.addRepresentationPart(MediaRepresentationPart.NewInstance(uri, size));
     			    media.addRepresentation(representationPdf);
     			    return media;
     			}else{
     				return null;
-...
     			logger.error(e.getMessage());
     			return null;
+    		}
+     	}
     	private TaxonNameBase getTaxonName(String originalSourceId, String namespace){
     		TaxonNameBase result;
     		ICommonService commonService = getCommonService();
     		result = (TaxonNameBase)commonService.getSourcedObjectByIdInSource(TaxonNameBase.class, originalSourceId , namespace);
     		if (result == null){
     			logger.warn("Taxon (id: " + originalSourceId + ", namespace: " + namespace + ") could not be found");
+    		}
     		return result;
+    	}
     	public boolean doCheck(DefaultImportState state){
     	@Override
         public boolean doCheck(DefaultImportState state){
     		boolean result = true;
     		return result;
+    	}
     	/* (non-Javadoc)
     	 * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
     	 */
     	protected boolean isIgnore(DefaultImportState state){
     	@Override
         protected boolean isIgnore(DefaultImportState state){
     		return false; // ! state.getConfig();
+    	}
     	protected void doCount(int count, int modCount, String pluralString){
     		if ((count % modCount ) == 0 && count!= 0 ){ logger.info(pluralString + " handled: " + (count));}
+    	}

+    	}
     	/* (non-Javadoc)
     	 * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getIdQuery()
     	 */
     	@Override
     	protected String getIdQuery(BerlinModelImportState bmState) {
     		AlgaTerraImportState state = (AlgaTerraImportState)bmState;
-...
     		String nameSpace;
     		Class<?> cdmClass;
     		Set<String> idSet;
     		Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
     		Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();
     		try{
     			Set<String> taxonIdSet = new HashSet<String>();
     			Set<String> taxonIdSet = new HashSet<>();
     			Set<String> ecoFactFkSet = new HashSet<String>();
     			Set<String> ecoFactFkSet = new HashSet<>();
     			while (rs.next()){
     				handleForeignKey(rs, taxonIdSet, "taxonId");

     import eu.etaxonomy.cdm.model.taxon.Taxon;
     /**
      * Import for the Flora Hellenica taxon comments.
+     *
      * @author a.mueller
      * @date 14.12.2016
+     *
      */
     @Component
-...
             return ;
+        }
+    }

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Revision b9fdd7f4

Added by unknown about 7 years ago