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
.wp6
.diptera
;
12 import java
.lang
.reflect
.Method
;
13 import java
.util
.UUID
;
15 import org
.apache
.log4j
.Logger
;
17 import eu
.etaxonomy
.cdm
.api
.application
.ICdmRepository
;
18 import eu
.etaxonomy
.cdm
.app
.berlinModelImport
.BerlinModelSources
;
19 import eu
.etaxonomy
.cdm
.app
.berlinModelImport
.TreeCreator
;
20 import eu
.etaxonomy
.cdm
.app
.common
.CdmDestinations
;
21 import eu
.etaxonomy
.cdm
.common
.CdmUtils
;
22 import eu
.etaxonomy
.cdm
.database
.DbSchemaValidation
;
23 import eu
.etaxonomy
.cdm
.database
.ICdmDataSource
;
24 import eu
.etaxonomy
.cdm
.io
.berlinModel
.in
.BerlinModelImportConfigurator
;
25 import eu
.etaxonomy
.cdm
.io
.berlinModel
.in
.BerlinModelTaxonImport
.PublishMarkerChooser
;
26 import eu
.etaxonomy
.cdm
.io
.common
.CdmDefaultImport
;
27 import eu
.etaxonomy
.cdm
.io
.common
.IImportConfigurator
.CHECK
;
28 import eu
.etaxonomy
.cdm
.io
.common
.IImportConfigurator
.DO_REFERENCES
;
29 import eu
.etaxonomy
.cdm
.io
.common
.IImportConfigurator
.EDITOR
;
30 import eu
.etaxonomy
.cdm
.io
.common
.ImportResult
;
31 import eu
.etaxonomy
.cdm
.io
.common
.Source
;
32 import eu
.etaxonomy
.cdm
.model
.description
.Feature
;
33 import eu
.etaxonomy
.cdm
.model
.description
.FeatureNode
;
34 import eu
.etaxonomy
.cdm
.model
.description
.FeatureTree
;
35 import eu
.etaxonomy
.cdm
.model
.name
.NameTypeDesignationStatus
;
36 import eu
.etaxonomy
.cdm
.model
.name
.NomenclaturalCode
;
40 * TODO add the following to a wiki page:
41 * 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
42 * you must set the mysql system variable lower_case_table_names = 0 in order to create data base with table compatible names.
48 public class DipteraActivator
{
49 private static final Logger logger
= Logger
.getLogger(DipteraActivator
.class);
51 //database validation status (create, update, validate ...)
52 static DbSchemaValidation hbm2dll
= DbSchemaValidation
.CREATE
;
53 static final Source berlinModelSource
= BerlinModelSources
.EDIT_Diptera();
54 static final ICdmDataSource cdmDestination
= CdmDestinations
.localH2();
56 static final UUID secUuid
= UUID
.fromString("06fd671f-1226-4e3b-beca-1959b3b32e20");
57 static final UUID treeUuid
= UUID
.fromString("1e3093f6-c761-4e96-8065-2c1334ddd0c1");
58 static final int sourceSecId
= 1000000;
59 static final UUID featureTreeUuid
= UUID
.fromString("ae9615b8-bc60-4ed0-ad96-897f9226d568");
60 static final Object
[] featureKeyList
= new Integer
[]{1, 4, 5, 10, 11, 12, 99};
62 static boolean useClassification
= true;
64 static final EDITOR editor
= EDITOR
.EDITOR_AS_EDITOR
;
66 static final CHECK check
= CHECK
.CHECK_AND_IMPORT
;
67 //taxon publish marker
68 static final PublishMarkerChooser taxonPublish
= PublishMarkerChooser
.NO_MARKER
;
70 static final boolean doDistributionParser
= true; //also run DipteraDistributionParser
73 static final NomenclaturalCode nomenclaturalCode
= NomenclaturalCode
.ICZN
;
76 static final boolean ignoreNull
= true;
81 static final boolean updateCitations
= true;
83 //include collections and add to specimen
84 static final boolean updateCollections
= true;
87 static final boolean doAuthors
= true;
89 static final DO_REFERENCES doReferences
= DO_REFERENCES
.ALL
;
91 static final boolean doTaxonNames
= true;
92 static final boolean doRelNames
= true;
93 static final boolean doNameStatus
= true;
94 static final boolean doTypes
= true;
95 static final boolean doNameFacts
= true;
98 static final boolean doTaxa
= true;
99 static final boolean doRelTaxa
= true;
100 static final boolean doFacts
= true;
101 static final boolean doOccurences
= false; //There are no occurrence data in diptera
102 static final boolean doCommonNames
= false; //no common names in diptera
105 static final boolean doMarker
= true;
106 static final boolean doUser
= true;
108 // **************** SELECTED *********************
111 // static final boolean doAuthors = false;
113 // static final DO_REFERENCES doReferences = DO_REFERENCES.NONE;
115 // static final boolean doTaxonNames = true;
116 // static final boolean doRelNames = false;
117 // static final boolean doNameStatus = false;
118 // static final boolean doTypes = true;
119 // static final boolean doNameFacts = false;
122 // static final boolean doTaxa = false;
123 // static final boolean doRelTaxa = false;
124 // static final boolean doFacts = false;
125 // static final boolean doOccurences = false;
128 // static final boolean doMarker = false;
129 // static final boolean doUser = true;
136 public ImportResult
doImport(ICdmDataSource destination
) {
137 ImportResult success
;
138 System
.out
.println("Start import from BerlinModel("+ berlinModelSource
.getDatabase() + ") ...");
140 //make BerlinModel Source
141 Source source
= berlinModelSource
;
144 BerlinModelImportConfigurator bmImportConfigurator
= BerlinModelImportConfigurator
.NewInstance(source
, destination
);
146 bmImportConfigurator
.setClassificationUuid(treeUuid
);
147 bmImportConfigurator
.setSourceSecId(sourceSecId
);
148 bmImportConfigurator
.setNomenclaturalCode(nomenclaturalCode
);
150 bmImportConfigurator
.setIgnoreNull(ignoreNull
);
151 bmImportConfigurator
.setDoAuthors(doAuthors
);
152 bmImportConfigurator
.setDoReferences(doReferences
);
153 bmImportConfigurator
.setDoTaxonNames(doTaxonNames
);
154 bmImportConfigurator
.setDoRelNames(doRelNames
);
155 bmImportConfigurator
.setDoNameStatus(doNameStatus
);
156 bmImportConfigurator
.setDoTypes(doTypes
);
157 bmImportConfigurator
.setDoNameFacts(doNameFacts
);
158 bmImportConfigurator
.setUseClassification(useClassification
);
160 bmImportConfigurator
.setDoTaxa(doTaxa
);
161 bmImportConfigurator
.setDoRelTaxa(doRelTaxa
);
162 bmImportConfigurator
.setDoFacts(doFacts
);
163 bmImportConfigurator
.setDoOccurrence(doOccurences
);
164 bmImportConfigurator
.setDoCommonNames(doCommonNames
);
166 bmImportConfigurator
.setDoMarker(doMarker
);
167 bmImportConfigurator
.setDoUser(doUser
);
168 bmImportConfigurator
.setEditor(editor
);
169 bmImportConfigurator
.setTaxonPublishMarker(taxonPublish
);
171 Method nameTypeDesignationStatusMethod
= DipteraActivator
.class.getDeclaredMethod("nameTypeDesignationStatueMethod", String
.class);
172 bmImportConfigurator
.setNameTypeDesignationStatusMethod(nameTypeDesignationStatusMethod
);
173 } catch (Exception e
) {
175 success
= new ImportResult();
176 success
.addException(e
);
180 bmImportConfigurator
.setDbSchemaValidation(hbm2dll
);
182 bmImportConfigurator
.setCheck(check
);
185 CdmDefaultImport
<BerlinModelImportConfigurator
> bmImport
= new CdmDefaultImport
<BerlinModelImportConfigurator
>();
186 success
= bmImport
.invoke(bmImportConfigurator
);
188 if (bmImportConfigurator
.getCheck().equals(CHECK
.CHECK_AND_IMPORT
) || bmImportConfigurator
.getCheck().equals(CHECK
.IMPORT_WITHOUT_CHECK
) ){
189 ICdmRepository app
= bmImport
.getCdmAppController();
191 //parse distributions
192 if (doDistributionParser
){
193 DipteraDistributionParser dipDist
= new DipteraDistributionParser();
194 dipDist
.doDistribution(app
);
197 app
= bmImport
.getCdmAppController();
198 FeatureTree tree
= TreeCreator
.flatTree(featureTreeUuid
, bmImportConfigurator
.getFeatureMap(), featureKeyList
);
200 FeatureNode imageNode
= FeatureNode
.NewInstance(Feature
.IMAGE());
201 tree
.getRoot().addChild(imageNode
);
203 FeatureNode distributionNode
= FeatureNode
.NewInstance(Feature
.DISTRIBUTION());
204 tree
.getRoot().addChild(distributionNode
);
205 app
.getFeatureTreeService().saveOrUpdate(tree
);
207 System
.out
.println("End import from BerlinModel ("+ source
.getDatabase() + ")...");
211 public static void main(String
[] args
) {
212 ImportResult success
;
213 logger
.debug("start");
214 ICdmDataSource destination
= CdmDestinations
.chooseDestination(args
) != null ? CdmDestinations
.chooseDestination(args
) : cdmDestination
;
215 DipteraActivator me
= new DipteraActivator();
216 success
= me
.doImport(destination
);
218 DipteraPostImportUpdater updater
= new DipteraPostImportUpdater();
219 if (updateCitations
){
220 success
= updater
.updateCitations(destination
);
223 if (updateCollections
){
224 success
= updater
.updateCollections(destination
);
234 private static NameTypeDesignationStatus
nameTypeDesignationStatueMethod(String note
){
235 if (CdmUtils
.isEmpty(note
)){
239 if (note
.equalsIgnoreCase("aut.") || note
.equalsIgnoreCase("automatic")){
240 return NameTypeDesignationStatus
.AUTOMATIC();
241 }else if (note
.equalsIgnoreCase("subs. mon.") ){
242 return NameTypeDesignationStatus
.SUBSEQUENT_MONOTYPY();
243 }else if (note
.startsWith("mon.") ){
244 return NameTypeDesignationStatus
.MONOTYPY();
245 }else if (note
.startsWith("orig. des") ){
246 return NameTypeDesignationStatus
.ORIGINAL_DESIGNATION();
247 }else if (note
.startsWith("des") ){
248 return NameTypeDesignationStatus
.SUBSEQUENT_DESIGNATION();
250 logger
.warn("NameTypeDesignationStatus could not be defined for: " + note
);