app-import/src/main/java/eu/etaxonomy/cdm/app/iapt/IAPTActivator.java

   1 /**
   2 * Copyright (C) 2007 EDIT
   3 * European Distributed Institute of Taxonomy
   4 * http://www.e-taxonomy.eu
   5 *
   6 * The contents of this file are subject to the Mozilla Public License Version 1.1
   7 * See LICENSE.TXT at the top of this package for the full license terms.
   8 */
   9
  10 package eu.etaxonomy.cdm.app.iapt;
  11
  12 import java.io.File;
  13 import java.net.URI;
  14 import java.net.URISyntaxException;
  15 import java.util.UUID;
  16
  17 import eu.etaxonomy.cdm.common.monitor.DefaultProgressMonitor;
  18 import eu.etaxonomy.cdm.database.DatabaseTypeEnum;
  19 import eu.etaxonomy.cdm.model.common.TimePeriod;
  20 import org.apache.log4j.Logger;
  21
  22 import eu.etaxonomy.cdm.app.common.CdmDestinations;
  23 import eu.etaxonomy.cdm.database.DbSchemaValidation;
  24 import eu.etaxonomy.cdm.database.ICdmDataSource;
  25 import eu.etaxonomy.cdm.io.common.CdmDefaultImport;
  26 import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;
  27 import eu.etaxonomy.cdm.io.iapt.IAPTImportConfigurator;
  28 import eu.etaxonomy.cdm.model.reference.Reference;
  29 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  30
  31
  32 /**
  33  * @author a.kohlbecker
  34  * @date Jul 26, 2016
  35  *
  36  */
  37 public class IAPTActivator {
  38     private static final Logger logger = Logger.getLogger(IAPTActivator.class);
  39
  40     public static final String DATA_FILE_FULL = "Registration_DB_from_BGBM17.xls";
  41     public static final String DATA_FILE_0_100 = "iapt-100.xls";
  42     public static final String DATA_ENCODING_PROBLEMS = "encoding-problems.xls";
  43     public static final String DATA_IAPT_TYPES_100 = "iapt-types-100.xls";
  44     public static final String DATA_TYPE_LEG_100 = "iapt-type-leg-100.xls";
  45     public static final String DATA_NAME_TYPES = "iapt-name-types.xls";
  46     public static final String DATA_SINGLE = "single.xls";
  47     public static final String DATA_FILE = DATA_FILE_FULL;
  48
  49     public static final Boolean algaeOnly = false;
  50
  51     // ====================================================================================
  52
  53     //database validation status (create, update, validate ...)
  54     static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;
  55
  56     static ICdmDataSource cdmDestination = null;
  57     static {
  58         DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;
  59         String cdmServer = "127.0.0.1";
  60         String cdmDB = "cdm_algea_registry";
  61         String cdmUserName = "edit";
  62         cdmDestination =  CdmDestinations.makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null);
  63         // cdmDestination = CdmDestinations.localH2();
  64     }
  65
  66     static boolean invers = true;
  67
  68     static boolean include = !invers;
  69
  70     //classification
  71     static final UUID classificationUuid = UUID.fromString("8c51efb4-3d67-4bea-8f87-4bc1cba1310d");
  72     private static final String classificationName = "IAPT";
  73     static final String sourceReferenceTitle = "IAPT Import";
  74
  75     //check - import
  76     static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
  77
  78
  79     private void doImport(ICdmDataSource cdmDestination){
  80
  81         URI source = fileURI();
  82
  83         Reference secRef = ReferenceFactory.newDatabase();
  84         secRef.setTitle("IAPT");
  85
  86         Reference sourceRef = ReferenceFactory.newDatabase();
  87         sourceRef.setTitle("IAPT Registration of Plant Names Database");
  88         sourceRef.setDatePublished(TimePeriod.NewInstance(1998, 2016));
  89         sourceRef.setOrganization("International Association for Plant Taxonomy");
  90         try {
  91             sourceRef.setUri(new URI("http://archive.bgbm.org/scripts/ASP/registration/regSearch.asp"));
  92         } catch (URISyntaxException e) {
  93             e.printStackTrace();
  94         }
  95
  96
  97         //make Source
  98         IAPTImportConfigurator config= IAPTImportConfigurator.NewInstance(source, cdmDestination);
  99         config.setClassificationUuid(classificationUuid);
 100         config.setClassificationName(classificationName);
 101         config.setCheck(check);
 102         config.setDbSchemaValidation(hbm2dll);
 103         config.setSourceReference(sourceRef);
 104         config.setSecReference(secRef);
 105         config.setProgressMonitor(DefaultProgressMonitor.NewInstance());
 106         config.setDoAlgeaeOnly(algaeOnly);
 107         // config.setBatchSize(100); // causes Error during managed flush [Don't change the reference to a collection with delete-orphan enabled : eu.etaxonomy.cdm.model.taxon.TaxonNode.annotations]
 108
 109         CdmDefaultImport<IAPTImportConfigurator> myImport = new CdmDefaultImport<>();
 110
 111         doSingleSource(fileURI(), config, myImport);
 112
 113         System.exit(0);
 114
 115     }
 116
 117     /**
 118      * @param source
 119      * @param config
 120      * @param myImport
 121      */
 122     private void doSingleSource(URI source, IAPTImportConfigurator config, CdmDefaultImport<IAPTImportConfigurator> myImport) {
 123         config.setSource(source);
 124         String fileName = source.toString();
 125         fileName = fileName.substring(fileName.lastIndexOf("/") + 1 );
 126
 127         String message = "Start import from ("+ fileName + ") ...";
 128         System.out.println(message);
 129         logger.warn(message);
 130         config.setSourceReference(getSourceReference(fileName));
 131         myImport.invoke(config);
 132
 133         System.out.println("End import from ("+ source.toString() + ")...");
 134     }
 135
 136     private final Reference inRef = ReferenceFactory.newGeneric();
 137     private Reference getSourceReference(String string) {
 138         Reference result = ReferenceFactory.newGeneric();
 139         result.setTitleCache(string, true);
 140         result.setInReference(inRef);
 141         inRef.setTitleCache(sourceReferenceTitle, true);
 142         return result;
 143     }
 144
 145
 146
 147     public static URI fileURI() {
 148         File f = new File(System.getProperty("user.home") + "/data/Projekte/Algea Name Registry/registry/sources/IAPT/" + DATA_FILE);
 149         return f.toURI();
 150     }
 151
 152     /**
 153      * @param args
 154      */
 155     public static void main(String[] args) {
 156         IAPTActivator me = new IAPTActivator();
 157         me.doImport(cdmDestination);
 158     }
 159
 160 }