2 * Copyright (C) 2007 EDIT
3 * European Distributed Institute of Taxonomy
4 * http://www.e-taxonomy.eu
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.
10 package eu
.etaxonomy
.cdm
.app
.pesi
;
12 import java
.util
.UUID
;
14 import org
.apache
.log4j
.Logger
;
16 import eu
.etaxonomy
.cdm
.api
.application
.ICdmApplicationConfiguration
;
17 import eu
.etaxonomy
.cdm
.app
.common
.BerlinModelSources
;
18 import eu
.etaxonomy
.cdm
.app
.common
.CdmDestinations
;
19 import eu
.etaxonomy
.cdm
.app
.common
.TreeCreator
;
20 import eu
.etaxonomy
.cdm
.database
.DbSchemaValidation
;
21 import eu
.etaxonomy
.cdm
.database
.ICdmDataSource
;
22 import eu
.etaxonomy
.cdm
.io
.berlinModel
.in
.BerlinModelImportConfigurator
;
23 import eu
.etaxonomy
.cdm
.io
.common
.CdmDefaultImport
;
24 import eu
.etaxonomy
.cdm
.io
.common
.IImportConfigurator
.CHECK
;
25 import eu
.etaxonomy
.cdm
.io
.common
.IImportConfigurator
.DO_REFERENCES
;
26 import eu
.etaxonomy
.cdm
.io
.common
.IImportConfigurator
.EDITOR
;
27 import eu
.etaxonomy
.cdm
.io
.common
.Source
;
28 import eu
.etaxonomy
.cdm
.model
.description
.Feature
;
29 import eu
.etaxonomy
.cdm
.model
.description
.FeatureNode
;
30 import eu
.etaxonomy
.cdm
.model
.description
.FeatureTree
;
31 import eu
.etaxonomy
.cdm
.model
.name
.NomenclaturalCode
;
35 * TODO add the following to a wiki page:
36 * HINT: If you are about to import into a mysql data base running under windows and if you wish to dump and restore the resulting data bas under another operation systen
37 * you must set the mysql system variable lower_case_table_names = 0 in order to create data base with table compatible names.
43 public class EuroMedActivator
{
44 @SuppressWarnings("unused")
45 private static final Logger logger
= Logger
.getLogger(EuroMedActivator
.class);
47 //database validation status (create, update, validate ...)
48 static DbSchemaValidation hbm2dll
= DbSchemaValidation
.CREATE
;
49 static final Source berlinModelSource
= BerlinModelSources
.euroMed();
50 // static final Source berlinModelSource = BerlinModelSources.EDIT_Diptera();
52 // static final ICdmDataSource cdmDestination = CdmDestinations.cdm_euroMed_dev();
53 static final ICdmDataSource cdmDestination
= CdmDestinations
.cdm_test_local_mysql();
55 static final int sourceSecId
= 7000000; //500000
57 static final UUID classificationUuid
= UUID
.fromString("314a68f9-8449-495a-91c2-92fde8bcf344");
59 static final UUID featureTreeUuid
= UUID
.fromString("6a5e1c2b-ec0d-46c8-9c7d-a2059267ffb7");
60 static final Object
[] featureKeyList
= new Integer
[]{1, 31, 4, 98, 41};
62 // set to zero for unlimited nameFacts
63 static final int maximumNumberOfNameFacts
= 0;
65 static final int partitionSize
= 2000;
68 static final CHECK check
= CHECK
.IMPORT_WITHOUT_CHECK
;
71 static final EDITOR editor
= EDITOR
.EDITOR_AS_EDITOR
;
74 static final NomenclaturalCode nomenclaturalCode
= NomenclaturalCode
.ICBN
;
77 static final boolean ignoreNull
= true;
79 static boolean useClassification
= true;
81 static String taxonTable
= "v_cdm_exp_allTaxa";
83 static String classificationQuery
= " SELECT DISTINCT t.PTRefFk, r.RefCache FROM _EM_CDM_exp_accTaxa t INNER JOIN Reference r ON t.PTRefFk = r.RefId ";
85 static String relPTaxonIdQuery
= " SELECT r.RelPTaxonId " +
86 " FROM RelPTaxon AS r INNER JOIN v_cdm_exp_accTaxa AS a ON r.PTNameFk2 = a.PTNameFk AND r.PTRefFk2 = a.PTRefFk ";
88 static String nameIdTable
= "v_cdm_exp_allNames";
90 static String referenceFilter
= "SELECT refId FROM v_cdm_exp_allReferences";
97 // **************** ALL *********************
99 static final boolean doUser
= true;
101 static final boolean doAuthors
= true;
103 static final DO_REFERENCES doReferences
= DO_REFERENCES
.ALL
;
105 static final boolean doTaxonNames
= true;
106 static final boolean doRelNames
= true;
107 static final boolean doNameStatus
= true;
108 static final boolean doTypes
= true;
109 static final boolean doNameFacts
= true;
112 static final boolean doTaxa
= true;
113 static final boolean doRelTaxa
= true;
114 static final boolean doFacts
= true;
115 static final boolean doOccurences
= true;
116 static final boolean doCommonNames
= true;
119 static final boolean doMarker
= true;
122 // **************** SELECTED *********************
124 // static final boolean doUser = true;
126 // static final boolean doAuthors = false;
128 // static final DO_REFERENCES doReferences = DO_REFERENCES.NONE;
130 // static final boolean doTaxonNames = false;
131 // static final boolean doRelNames = false;
132 // static final boolean doNameStatus = false;
133 // static final boolean doTypes = false;
134 // static final boolean doNameFacts = false;
137 // static final boolean doTaxa = false;
138 // static final boolean doRelTaxa = false;
139 // static final boolean doFacts = false;
140 // static final boolean doOccurences = false;
141 // static final boolean doCommonNames = false;
144 // static final boolean doMarker = false;
150 public static void main(String
[] args
) {
151 System
.out
.println("Start import from BerlinModel("+ berlinModelSource
.getDatabase() + ") to " + cdmDestination
.getDatabase() + " ...");
153 //make BerlinModel Source
154 Source source
= berlinModelSource
;
155 ICdmDataSource destination
= CdmDestinations
.chooseDestination(args
) != null ? CdmDestinations
.chooseDestination(args
) : cdmDestination
;
157 BerlinModelImportConfigurator config
= BerlinModelImportConfigurator
.NewInstance(source
, destination
);
159 config
.setClassificationUuid(classificationUuid
);
160 config
.setSourceSecId(sourceSecId
);
162 config
.setNomenclaturalCode(nomenclaturalCode
);
164 config
.setIgnoreNull(ignoreNull
);
165 config
.setDoAuthors(doAuthors
);
166 config
.setDoReferences(doReferences
);
167 config
.setDoTaxonNames(doTaxonNames
);
168 config
.setDoRelNames(doRelNames
);
169 config
.setDoNameStatus(doNameStatus
);
170 config
.setDoTypes(doTypes
);
171 config
.setDoNameFacts(doNameFacts
);
172 config
.setUseClassification(useClassification
);
174 config
.setDoTaxa(doTaxa
);
175 config
.setDoRelTaxa(doRelTaxa
);
176 config
.setDoFacts(doFacts
);
177 config
.setDoOccurrence(doOccurences
);
178 config
.setDoCommonNames(doCommonNames
);
180 config
.setDoMarker(doMarker
);
181 config
.setDoUser(doUser
);
182 config
.setEditor(editor
);
183 config
.setDbSchemaValidation(hbm2dll
);
185 // maximum number of name facts to import
186 config
.setMaximumNumberOfNameFacts(maximumNumberOfNameFacts
);
189 config
.setTaxonTable(taxonTable
);
190 config
.setClassificationQuery(classificationQuery
);
191 config
.setRelTaxaIdQuery(relPTaxonIdQuery
);
194 config
.setCheck(check
);
195 config
.setEditor(editor
);
196 config
.setRecordsPerTransaction(partitionSize
);
199 CdmDefaultImport
<BerlinModelImportConfigurator
> bmImport
= new CdmDefaultImport
<BerlinModelImportConfigurator
>();
200 bmImport
.invoke(config
);
202 if (doFacts
&& config
.getCheck().equals(CHECK
.CHECK_AND_IMPORT
) || config
.getCheck().equals(CHECK
.IMPORT_WITHOUT_CHECK
) ){
203 ICdmApplicationConfiguration app
= bmImport
.getCdmAppController();
206 FeatureTree tree
= TreeCreator
.flatTree(featureTreeUuid
, config
.getFeatureMap(), featureKeyList
);
207 FeatureNode imageNode
= FeatureNode
.NewInstance(Feature
.IMAGE());
208 tree
.getRoot().addChild(imageNode
);
209 FeatureNode distributionNode
= FeatureNode
.NewInstance(Feature
.DISTRIBUTION());
210 tree
.getRoot().addChild(distributionNode
, 2);
211 app
.getFeatureTreeService().saveOrUpdate(tree
);
214 System
.out
.println("End import from BerlinModel ("+ source
.getDatabase() + ")...");