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Revision 548a9ae0

Added by Andreas Müller almost 7 years ago

Cleanup

View differences:

app-import/src/main/java/eu/etaxonomy/cdm/app/abcdImport/SpecimenImport.java
32 32
    final static String xmlSource = "/home/pkelbert/Documents/Proibiosphere/Presentations/Demo/ABCD/calvum.xml";
33 33

  
34 34

  
35
    static final ICdmDataSource cdmDestination = CdmDestinations.mon_cdm();
35
    static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
36 36
//    static final ICdmDataSource cdmDestination = CdmDestinations.makeDestination(DatabaseTypeEnum.H2, "localhost", "abcd_import_test", 8082, "root", "root");
37 37
    static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
38 38

  
app-import/src/main/java/eu/etaxonomy/cdm/app/common/CdmDestinations.java
616 616
		return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null);
617 617
	}
618 618

  
619
	/**
620
     * patricia
621
     */
622
    public static ICdmDataSource mon_cdm() {
623
        DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;
624
        String cdmServer = "localhost";
625
        String cdmDB = "cdm_local";
626
        String cdmUserName = "root";
627
        return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null);
628
    }
629

  
630 619
   public static ICdmDataSource proibiosphere_chenopodium_local() {
631 620
        DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;
632 621
        String cdmServer = "localhost";
......
643 632
       return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null);
644 633
   }
645 634

  
646
   public static ICdmDataSource proibiosphere_fungi_local() {
647
       DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;
648
       String cdmServer = "localhost";
649
       String cdmDB = "cdm_production_proibiosphere_fungi_pilot";
650
       String cdmUserName = "root";
651
       return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null);
652
   }
653

  
654
   public static ICdmDataSource proibiosphere_campylopus_local() {
655
       DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;
656
       String cdmServer = "localhost";
657
       String cdmDB = "cdm_production_proibiosphere_campylopus_pilot";
658
       String cdmUserName = "root";
659
       return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null);
660
   }
661

  
662

  
663 635
   public static ICdmDataSource proibiosphere_eupolybothrus_local() {
664 636
       DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;
665 637
       String cdmServer = "localhost";
app-import/src/main/java/eu/etaxonomy/cdm/app/excelImport/taxa/NormalExplicitActivator.java
38 38
	private static DbSchemaValidation dbSchemaValidation = DbSchemaValidation.CREATE;
39 39

  
40 40
//	private static final ICdmDataSource destinationDb = CdmDestinations.cdm_test_jaxb();
41
	private static final ICdmDataSource destinationDb = CdmDestinations.mon_cdm();
41
	private static final ICdmDataSource destinationDb = CdmDestinations.localH2();
42 42

  
43 43
    public static void main(String[] args) {
44 44

  
app-import/src/main/java/eu/etaxonomy/cdm/app/proibiosphere/SynthesysCacheActivator.java
26 26
import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
27 27

  
28 28

  
29

  
30

  
31 29
/**
32 30
 * @author PK
33 31
 * @created 19.09.2008
34
 * @version 1.0
35 32
 */
36 33
public class SynthesysCacheActivator {
37 34
    @SuppressWarnings("unused")
......
43 40
    final static String xmlSource = "/home/pkelbert/Documents/Proibiosphere/ChenopodiumQuentin/dca UK records.xls";
44 41

  
45 42

  
46
    static final ICdmDataSource cdmDestination = CdmDestinations.mon_cdm();
47
    static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;
43
    static final ICdmDataSource cdmDestination = CdmDestinations.proibiosphere_spiders_local();
44
    static DbSchemaValidation hbm2dll = DbSchemaValidation.VALIDATE;
48 45
    //    static final ICdmDataSource cdmDestination = CdmDestinations.proibiosphere_local();
49 46
    //    static DbSchemaValidation hbm2dll = DbSchemaValidation.VALIDATE;
50 47
    static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/faunaEuropaea/FaunaEuropaeaAdditionalTaxonDataImport.java
22 22

  
23 23
import eu.etaxonomy.cdm.database.ICdmDataSource;
24 24
import eu.etaxonomy.cdm.model.common.CdmBase;
25
import eu.etaxonomy.cdm.model.name.INonViralName;
26
import eu.etaxonomy.cdm.model.name.ITaxonNameBase;
25 27
import eu.etaxonomy.cdm.model.name.NonViralName;
26 28
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
27 29
import eu.etaxonomy.cdm.model.taxon.Taxon;
......
31 33
/**
32 34
 * @author a.babadshanjan
33 35
 * @created 21.08.2010
34
 * @version 1.0
35 36
 */
36 37
@Component
37 38
public class FaunaEuropaeaAdditionalTaxonDataImport extends FaunaEuropaeaImportBase  {
39
    private static final long serialVersionUID = -6734273038256432559L;
38 40

  
39
	private static final Logger logger = Logger.getLogger(FaunaEuropaeaAdditionalTaxonDataImport.class);
41
    private static final Logger logger = Logger.getLogger(FaunaEuropaeaAdditionalTaxonDataImport.class);
40 42
//	private static final String parentPluralString = "Synonyms";
41 43
	private static final String pluralString = "InfraGenericEpithets";
42 44
	//private static final String acceptedTaxonUUID = "A9C24E42-69F5-4681-9399-041E652CF338"; // any accepted taxon uuid, taken from original fauna europaea database
43 45

  
44
	/* (non-Javadoc)
45
	 * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator)
46
	 */
47 46
	@Override
48 47
	protected boolean doCheck(FaunaEuropaeaImportState state) {
49 48
		boolean result = true;
50
		FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();
51 49
		logger.warn("Checking for Taxa not yet fully implemented");
52
//		result &= checkTaxonStatus(fauEuConfig);
53

  
54 50
		return result;
55 51
	}
56 52

  
......
77 73
	 * @return
78 74
	 */
79 75
	private void processAdditionalInfraGenericEpithets(FaunaEuropaeaImportState state) {
80
		int count = 0;
81 76
		int pageSize = 1000;
82 77
		Set<UUID> uuidSet = new HashSet<UUID>();
83 78
		FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();
......
108 103
		if (!uuidSet.isEmpty()){
109 104
			taxonNames = getNameService().find(uuidSet);
110 105

  
111
			for (TaxonNameBase taxonName : taxonNames) {
106
			for (TaxonNameBase<?,?> taxonName : taxonNames) {
112 107

  
113 108
				// Check whether its taxonName has an infraGenericEpithet
114 109
				if (taxonName != null && (taxonName.isInstanceOf(NonViralName.class))) {
115
					NonViralName targetNonViralName = CdmBase.deproxy(taxonName, NonViralName.class);
110
					INonViralName targetNonViralName = CdmBase.deproxy(taxonName, NonViralName.class);
116 111
					String infraGenericEpithet = targetNonViralName.getInfraGenericEpithet();
117 112
					if (infraGenericEpithet == null) {
118 113
						String genusOrUninomial = targetNonViralName.getGenusOrUninomial();
......
121 116
								"*", "*", null, pageSize, 1);
122 117
						if (foundTaxa.size() == 1) {
123 118
							// one matching Taxon found
124
							TaxonBase taxon = foundTaxa.iterator().next();
119
							TaxonBase<?> taxon = foundTaxa.iterator().next();
125 120
							if (taxon != null) {
126
								TaxonNameBase name = taxon.getName();
121
								ITaxonNameBase name = taxon.getName();
127 122
								if (name != null && name.isInstanceOf(NonViralName.class)) {
128
									NonViralName nonViralName = CdmBase.deproxy(name, NonViralName.class);
123
									INonViralName nonViralName = CdmBase.deproxy(name, NonViralName.class);
129 124
									infraGenericEpithet = nonViralName.getInfraGenericEpithet();
130 125

  
131 126
									// set infraGenericEpithet
132 127
	//									targetNonViralName.setInfraGenericEpithet(infraGenericEpithet);
133 128
									logger.debug("Added an InfraGenericEpithet to this TaxonName: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");
134
									count++;
135 129
								}
136 130
							}
137 131
						} else if (foundTaxa.size() > 1) {
138 132
							logger.warn("Multiple taxa match search criteria: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");
139
							for (TaxonBase foundTaxon : foundTaxa) {
133
							for (TaxonBase<?> foundTaxon : foundTaxa) {
140 134
								logger.warn(foundTaxon.getUuid() + ", " + foundTaxon.getTitleCache());
141 135
							}
142 136
						} else if (foundTaxa.size() == 0) {
......
157 151
		return;
158 152
	}
159 153

  
160

  
161
	/* (non-Javadoc)
162
	 * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IoStateBase)
163
	 */
164 154
	@Override
165 155
    protected boolean isIgnore(FaunaEuropaeaImportState state) {
166 156
		return ! state.getConfig().isDoTaxa();
167 157
	}
168

  
169 158
}
cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/faunaEuropaea/FaunaEuropaeaDistribution.java
1 1
/**
2 2
* Copyright (C) 2009 EDIT
3
* European Distributed Institute of Taxonomy 
3
* European Distributed Institute of Taxonomy
4 4
* http://www.e-taxonomy.eu
5
* 
5
*
6 6
* The contents of this file are subject to the Mozilla Public License Version 1.1
7 7
* See LICENSE.TXT at the top of this package for the full license terms.
8 8
*/
9 9

  
10 10
package eu.etaxonomy.cdm.io.pesi.faunaEuropaea;
11 11

  
12
import java.util.UUID;
13

  
14
import org.joda.time.DateTime;
15

  
16 12
/**
17 13
 * @author a.babadshanjan
18 14
 * @created 11.09.2009
19
 * @version 1.0
20 15
 */
21 16
public class FaunaEuropaeaDistribution {
22
	
23
	private UUID taxonUuid;
24
	private int taxonId;
17

  
25 18
	private int distributionId;
26 19
	private int occurrenceStatusId;
27 20
	private int areaId;
28 21
	private String areaName;
29 22
	private String areaCode;
30 23
	private int extraLimital;
31
	
32
	
33
	
34
	
35
//	/**
36
//	 * @return the taxonUuid
37
//	 */
38
//	public UUID getTaxonUuid() {
39
//		return taxonUuid;
40
//	}
41
//	/**
42
//	 * @param taxonUuid the taxonUuid to set
43
//	 */
44
//	public void setTaxonUuid(UUID taxonUuid) {
45
//		this.taxonUuid = taxonUuid;
46
//	}
47
//	/**
48
//	 * @return the taxonId
49
//	 */
50
//	public int getTaxonId() {
51
//		return taxonId;
52
//	}
53
//	/**
54
//	 * @param taxonId the taxonId to set
55
//	 */
56
//	public void setTaxonId(int taxonId) {
57
//		this.taxonId = taxonId;
58
//	}
24

  
59 25
	/**
60 26
	 * @return the distributionId
61 27
	 */
......
128 94
	public void setExtraLimital(int extraLimital) {
129 95
		this.extraLimital = extraLimital;
130 96
	}
131
	
97

  
132 98

  
133 99
}
cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/faunaEuropaea/FaunaEuropaeaDistributionImport.java
37 37
/**
38 38
 * @author a.babadshanjan
39 39
 * @created 12.05.2009
40
 * @version 1.0
41 40
 */
42 41
@Component
43 42
public class FaunaEuropaeaDistributionImport extends FaunaEuropaeaImportBase {
44
	private static final Logger logger = Logger.getLogger(FaunaEuropaeaDistributionImport.class);
43
    private static final long serialVersionUID = 746146902707885655L;
44
    private static final Logger logger = Logger.getLogger(FaunaEuropaeaDistributionImport.class);
45 45

  
46 46

  
47 47
	@Override
48 48
	protected boolean doCheck(FaunaEuropaeaImportState state) {
49 49
		boolean result = true;
50
		FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();
51
		logger.warn("Checking for Distributions not yet fully implemented");
52
		result &= checkReferenceStatus(fauEuConfig);
53

  
50
		logger.warn("Checking for Distributions not yet implemented");
54 51
		return result;
55 52
	}
56 53

  
57
	private boolean checkReferenceStatus(FaunaEuropaeaImportConfigurator fauEuConfig) {
58
		boolean result = true;
59
//		try {
60
//			Source source = fauEuConfig.getSource();
61
//			String sqlStr = "";
62
	//		ResultSet rs = source.getResultSet(sqlStr);
63
			return result;
64
//		} catch (SQLException e) {
65
//			e.printStackTrace();
66
//			return false;
67
//		}
68
	}
69

  
70 54
	@Override
71 55
	protected void doInvoke(FaunaEuropaeaImportState state) {
72 56
		/*
......
127 111
		String selectQuery =
128 112
			selectColumns + fromClause + orderBy;
129 113

  
130

  
131

  
132 114
		if(logger.isInfoEnabled()) { logger.info("Start making distributions..."); }
133 115

  
134 116
		try {
......
150 132
				if ((i++ % limit) == 0) {
151 133

  
152 134
					txStatus = startTransaction();
153
					taxonUuids = new HashSet<UUID>(limit);
154
					fauEuTaxonMap = new HashMap<UUID, FaunaEuropaeaDistributionTaxon>(limit);
135
					taxonUuids = new HashSet<>(limit);
136
					fauEuTaxonMap = new HashMap<>(limit);
155 137

  
156 138
					if(logger.isInfoEnabled()) {
157 139
						logger.info("i = " + i + " - Distribution import transaction started");
......
241 223
     *
242 224
     */
243 225
    private void createTermVocabulary(TransactionStatus txStatus, FaunaEuropaeaImportState state) {
244
        TermVocabulary<NamedArea> faunaEuAreaVocabulary = TermVocabulary.NewInstance(TermType.NamedArea, "Areas for Fauna Europaea distribution data", "FE areas", "FE", null);
245

  
246
       NamedArea area;
226
       TermVocabulary<NamedArea> faunaEuAreaVocabulary = TermVocabulary.NewInstance(TermType.NamedArea, "Areas for Fauna Europaea distribution data", "FE areas", "FE", null);
227
       faunaEuAreaVocabulary.setUuid(FaunaEuropaeaTransformer.uuidFauEuArea);
247 228

  
248
       area =NamedArea.NewInstance(null, "Andorra", "AD");
229
       NamedArea area =NamedArea.NewInstance(null, "Andorra", "AD");
249 230
       area.setUuid(UUID.randomUUID());
250 231
       area.setIdInVocabulary("AD");
251 232
       state.putNamedArea(area);
......
652 633
       logger.info("save voc");
653 634
       commitTransaction(txStatus);
654 635
       state.setAreaVoc(faunaEuAreaVocabulary);
655

  
656

  
657 636
    }
658 637

  
659 638
    private void commitTaxaAndDistribution(
......
661 640
			Set<UUID> taxonUuids,
662 641
			Map<UUID, FaunaEuropaeaDistributionTaxon> fauEuTaxonMap,
663 642
			TransactionStatus txStatus) throws Exception {
664
		 List<TaxonBase> taxonList = prepareTaxaAndDistribution(getTaxonService().find(taxonUuids), fauEuTaxonMap, state);
643

  
644
        List<TaxonBase> taxonList = prepareTaxaAndDistribution(getTaxonService().find(taxonUuids), fauEuTaxonMap, state);
665 645

  
666 646
		getTaxonService().save(taxonList);
667 647
		taxonList = null;
......
692 672
					continue;
693 673
				}
694 674

  
695

  
696 675
				Set<TaxonDescription> descriptionSet = taxon.getDescriptions();
697 676
				if (descriptionSet.size() > 0) {
698 677
					taxonDescription = descriptionSet.iterator().next();
cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/faunaEuropaea/FaunaEuropaeaTransformer.java
29 29
/**
30 30
 * @author a.babadshanjan
31 31
 * @created 12.05.2009
32
 * @version 1.0
33 32
 */
34 33

  
35 34
public final class FaunaEuropaeaTransformer {
36 35
	private static final Logger logger = Logger.getLogger(FaunaEuropaeaTransformer.class);
37 36

  
37
	public static final UUID uuidFauEuArea = UUID.fromString("16325043-e7da-4742-b012-9ce03362a124");
38

  
38 39
	// Query
39 40
	public static final int Q_NO_RESTRICTION = -1;
40 41

  
......
79 80
	public static final int R_SPECIES = 21;
80 81
	public static final int R_SUBSPECIES = 22;
81 82

  
82
	public static PresenceAbsenceTerm occStatus2PresenceAbsence(int occStatusId)  throws UnknownCdmTypeException{
83
	public static PresenceAbsenceTerm occStatus2PresenceAbsence(int occStatusId){
83 84

  
84 85
		if (Integer.valueOf(occStatusId) == null) {
85 86
			return PresenceAbsenceTerm.PRESENT();
86 87
		}
87 88
		switch (occStatusId){
88
		case 0: return PresenceAbsenceTerm.PRESENT();
89
		case 2: return PresenceAbsenceTerm.ABSENT();
90
		case 1: return PresenceAbsenceTerm.PRESENT_DOUBTFULLY();
91

  
92
		default: {
93

  
94
			return null;
95

  
96

  
89
    		case 0: return PresenceAbsenceTerm.PRESENT();
90
    		case 2: return PresenceAbsenceTerm.ABSENT();
91
    		case 1: return PresenceAbsenceTerm.PRESENT_DOUBTFULLY();
92
    		default: {
93
    		    return null;
94
    		}
97 95
		}
98

  
99
	}
100 96
	}
101 97

  
102 98

  
......
391 387
//	 	}
392 388

  
393 389

  
390
	 	public final static HashMap<Integer, Language> languageFK2Language  = new HashMap<>();
394 391

  
395
	 	public final static HashMap<Integer, Language> languageFK2Language  = new HashMap<Integer,Language>();
396
	 	static
392
        static
397 393
	 	{
398 394
	 		languageFK2Language.put(1, Language.ALBANIAN());
399 395
	 		languageFK2Language.put(4, Language.AZERBAIJANI());

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