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.proibiosphere;
|
11
|
import java.io.File;
|
12
|
import java.net.URI;
|
13
|
import java.net.URISyntaxException;
|
14
|
import java.util.UUID;
|
15
|
|
16
|
import org.apache.log4j.Logger;
|
17
|
|
18
|
import eu.etaxonomy.cdm.app.common.CdmDestinations;
|
19
|
import eu.etaxonomy.cdm.database.DbSchemaValidation;
|
20
|
import eu.etaxonomy.cdm.database.ICdmDataSource;
|
21
|
import eu.etaxonomy.cdm.io.common.CdmDefaultImport;
|
22
|
import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;
|
23
|
import eu.etaxonomy.cdm.io.specimen.excel.in.SpecimenSynthesysExcelImportConfigurator;
|
24
|
import eu.etaxonomy.cdm.model.reference.Reference;
|
25
|
import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
|
26
|
|
27
|
public class SpecimenImportActivator {
|
28
|
@SuppressWarnings("unused")
|
29
|
private static Logger logger = Logger.getLogger(SpecimenImportActivator.class);
|
30
|
|
31
|
//database validation status (create, update, validate ...)
|
32
|
static DbSchemaValidation hbm2dll = DbSchemaValidation.VALIDATE;
|
33
|
final static String excelSource = "/home/pkelbert/Documents/Proibiosphere/ChenopodiumQuentin/dca_UK_records.xls";
|
34
|
// final static String excelSource = "/home/pkelbert/Documents/Proibiosphere/ChenopodiumQuentin/dca_UK_specimens.xls";
|
35
|
|
36
|
// final static String xmlSource = "C:\\localCopy\\eclipse\\cdmlib\\app-import\\src\\main\\resources\\specimenABCD\\CDMtabular9c04a474e2_23_09_08.xls";
|
37
|
|
38
|
|
39
|
|
40
|
static final ICdmDataSource cdmDestination = CdmDestinations.proibiosphere_chenopodium_local();
|
41
|
//check - import
|
42
|
static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
|
43
|
|
44
|
/**
|
45
|
* @param args
|
46
|
*/
|
47
|
public static void main(String[] args) {
|
48
|
URI source;
|
49
|
try {
|
50
|
URI uri = new File(excelSource).toURI();
|
51
|
source = new URI(uri.toString());
|
52
|
System.out.println(source);
|
53
|
System.out.println("Start import from Synthesys Specimen data("+ source.toString() + ") ...");
|
54
|
|
55
|
ICdmDataSource destination = cdmDestination;
|
56
|
SpecimenSynthesysExcelImportConfigurator specimenImportConfigurator = SpecimenSynthesysExcelImportConfigurator.NewInstance(source, destination);
|
57
|
|
58
|
specimenImportConfigurator.setClassificationName("Goosefoots");
|
59
|
specimenImportConfigurator.setSourceSecId("dca UK records");
|
60
|
specimenImportConfigurator.setCheck(check);
|
61
|
specimenImportConfigurator.setDbSchemaValidation(hbm2dll);
|
62
|
specimenImportConfigurator.setDoAutomaticParsing(true);
|
63
|
specimenImportConfigurator.setReUseExistingMetadata(true);
|
64
|
specimenImportConfigurator.setDebugInstitutionOnly(true);
|
65
|
|
66
|
// specimenImportConfigurator.setDoMatchTaxa(true);
|
67
|
specimenImportConfigurator.setReUseTaxon(true);
|
68
|
|
69
|
// specimenImportConfigurator.setDoCreateIndividualsAssociations(true);
|
70
|
|
71
|
Reference<?> ref = ReferenceFactory.newBook();
|
72
|
ref.setUuid(UUID.fromString("98b0a618-a95b-464e-943a-25aaaef202f6"));//observations
|
73
|
ref.setTitle("Chenopodium vulvaria observations from the British Isles");
|
74
|
//
|
75
|
// ref.setUuid(UUID.fromString("5480eed1-1a23-4ce8-ac4d-c2893e178dea"));//specimens
|
76
|
// ref.setTitle("Chenopodium vulvaria specimens from the British Isles");
|
77
|
|
78
|
specimenImportConfigurator.setDataReference(ref);
|
79
|
specimenImportConfigurator.setSourceReference(null);
|
80
|
specimenImportConfigurator.setTaxonReference(null);
|
81
|
|
82
|
// invoke import
|
83
|
CdmDefaultImport<SpecimenSynthesysExcelImportConfigurator> specimenImport = new CdmDefaultImport<SpecimenSynthesysExcelImportConfigurator>();
|
84
|
//new Test().invoke(tcsImportConfigurator);
|
85
|
specimenImport.invoke(specimenImportConfigurator);
|
86
|
System.out.println("End import from SpecimenData ("+ source.toString() + ")...");
|
87
|
} catch (URISyntaxException e) {
|
88
|
e.printStackTrace();
|
89
|
}
|
90
|
|
91
|
}
|
92
|
|
93
|
}
|