Revision 4ae09d10
Added by Patrick Plitzner almost 8 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/gefaesspflanzen/RedListGefaesspflanzenImportClassification.java | ||
|---|---|---|
| 94 | 94 |
ResultSet rs = partitioner.getResultSet(); |
| 95 | 95 |
Classification gesamtListeClassification = getClassificationService().load(state.getConfig().getClassificationUuid()); |
| 96 | 96 |
Classification checklistClassification = getClassificationService().load(RedListUtil.checkListClassificationUuid); |
| 97 |
Classification classificationE = getClassificationService().load(RedListUtil.uuidClassificationE); |
|
| 98 |
Classification classificationW = getClassificationService().load(RedListUtil.uuidClassificationW); |
|
| 99 |
Classification classificationK = getClassificationService().load(RedListUtil.uuidClassificationK); |
|
| 100 |
Classification classificationAW = getClassificationService().load(RedListUtil.uuidClassificationAW); |
|
| 101 |
Classification classificationAO = getClassificationService().load(RedListUtil.uuidClassificationAO); |
|
| 102 |
Classification classificationR = getClassificationService().load(RedListUtil.uuidClassificationR); |
|
| 103 |
Classification classificationO = getClassificationService().load(RedListUtil.uuidClassificationO); |
|
| 104 |
Classification classificationS = getClassificationService().load(RedListUtil.uuidClassificationS); |
|
| 97 | 105 |
try {
|
| 98 | 106 |
while (rs.next()){
|
| 99 |
makeSingleTaxonNode(state, rs, gesamtListeClassification, checklistClassification); |
|
| 107 |
makeSingleTaxonNode(state, rs, gesamtListeClassification, checklistClassification, |
|
| 108 |
classificationE, classificationW, classificationK, classificationAW |
|
| 109 |
, classificationAO, classificationR, classificationO, classificationS); |
|
| 100 | 110 |
|
| 101 | 111 |
} |
| 102 | 112 |
} catch (SQLException e) {
|
| ... | ... | |
| 109 | 119 |
return true; |
| 110 | 120 |
} |
| 111 | 121 |
|
| 112 |
private void makeSingleTaxonNode(RedListGefaesspflanzenImportState state, ResultSet rs, Classification gesamtListeClassification, Classification checklistClassification) |
|
| 122 |
private void makeSingleTaxonNode(RedListGefaesspflanzenImportState state, ResultSet rs, |
|
| 123 |
Classification gesamtListeClassification, Classification checklistClassification, |
|
| 124 |
Classification classificationE, Classification classificationW, Classification classificationK, |
|
| 125 |
Classification classificationAW, Classification classificationAO, Classification classificationR, |
|
| 126 |
Classification classificationO, Classification classificationS) |
|
| 113 | 127 |
throws SQLException {
|
| 114 | 128 |
long id = rs.getLong(RedListUtil.NAMNR); |
| 115 | 129 |
String parentId = String.valueOf(rs.getLong(RedListUtil.LOWER)); |
| ... | ... | |
| 137 | 151 |
} |
| 138 | 152 |
|
| 139 | 153 |
//add taxa for concept relationships to E, W, K, AW, AO, R, O, S |
| 140 |
addTaxonToClassification(RedListUtil.uuidClassificationE, RedListUtil.CLASSIFICATION_NAMESPACE_E, id, state);
|
|
| 141 |
addTaxonToClassification(RedListUtil.uuidClassificationW, RedListUtil.CLASSIFICATION_NAMESPACE_W, id, state);
|
|
| 142 |
addTaxonToClassification(RedListUtil.uuidClassificationK, RedListUtil.CLASSIFICATION_NAMESPACE_K, id, state);
|
|
| 143 |
addTaxonToClassification(RedListUtil.uuidClassificationAW, RedListUtil.CLASSIFICATION_NAMESPACE_AW, id, state);
|
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| 144 |
addTaxonToClassification(RedListUtil.uuidClassificationAO, RedListUtil.CLASSIFICATION_NAMESPACE_AO, id, state);
|
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| 145 |
addTaxonToClassification(RedListUtil.uuidClassificationR, RedListUtil.CLASSIFICATION_NAMESPACE_R, id, state);
|
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| 146 |
addTaxonToClassification(RedListUtil.uuidClassificationO, RedListUtil.CLASSIFICATION_NAMESPACE_O, id, state);
|
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| 147 |
addTaxonToClassification(RedListUtil.uuidClassificationS, RedListUtil.CLASSIFICATION_NAMESPACE_S, id, state);
|
|
| 154 |
addTaxonToClassification(classificationE, RedListUtil.CLASSIFICATION_NAMESPACE_E, id, state);
|
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| 155 |
addTaxonToClassification(classificationW, RedListUtil.CLASSIFICATION_NAMESPACE_W, id, state);
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| 156 |
addTaxonToClassification(classificationK, RedListUtil.CLASSIFICATION_NAMESPACE_K, id, state);
|
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| 157 |
addTaxonToClassification(classificationAW, RedListUtil.CLASSIFICATION_NAMESPACE_AW, id, state);
|
|
| 158 |
addTaxonToClassification(classificationAO, RedListUtil.CLASSIFICATION_NAMESPACE_AO, id, state);
|
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| 159 |
addTaxonToClassification(classificationR, RedListUtil.CLASSIFICATION_NAMESPACE_R, id, state);
|
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| 160 |
addTaxonToClassification(classificationO, RedListUtil.CLASSIFICATION_NAMESPACE_O, id, state);
|
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| 161 |
addTaxonToClassification(classificationS, RedListUtil.CLASSIFICATION_NAMESPACE_S, id, state);
|
|
| 148 | 162 |
} |
| 149 | 163 |
|
| 150 |
private void addTaxonToClassification(UUID classificationUuid, String classificationNamespace, long id, RedListGefaesspflanzenImportState state){
|
|
| 164 |
private void addTaxonToClassification(Classification classification, String classificationNamespace, long id, RedListGefaesspflanzenImportState state){
|
|
| 151 | 165 |
Taxon taxon = HibernateProxyHelper.deproxy(state.getRelatedObject(classificationNamespace, String.valueOf(id), TaxonBase.class), Taxon.class); |
| 152 |
Classification classification = getClassificationService().load(classificationUuid); |
|
| 153 | 166 |
classification.addChildTaxon(taxon, null, null); |
| 154 | 167 |
} |
| 155 | 168 |
|
| app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/gefaesspflanzen/RedListGefaesspflanzenImportNames.java | ||
|---|---|---|
| 152 | 152 |
*/ |
| 153 | 153 |
//checklist |
| 154 | 154 |
if(CdmUtils.isNotBlank(clTaxonString) && !clTaxonString.trim().equals("-")){
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| 155 |
cloneTaxon(taxonBase, name, TaxonRelationshipType.CONGRUENT_TO(), taxaToSave, id, RedListUtil.TAXON_CHECKLISTE_NAMESPACE, state); |
|
| 155 |
cloneTaxon(taxonBase, name, TaxonRelationshipType.CONGRUENT_TO(), taxaToSave, id, RedListUtil.TAXON_CHECKLISTE_NAMESPACE, false, true, state);
|
|
| 156 | 156 |
} |
| 157 | 157 |
//E, W, K, AW, AO, R, O, S |
| 158 | 158 |
addConceptRelation(relationE, RedListUtil.CLASSIFICATION_NAMESPACE_E, taxonBase, name, taxaToSave, id, state); |
| ... | ... | |
| 171 | 171 |
|
| 172 | 172 |
private void addConceptRelation(String relationString, String classificationNamespace, TaxonBase taxonBase, TaxonNameBase name, Set<TaxonBase> taxaToSave, long id, RedListGefaesspflanzenImportState state){
|
| 173 | 173 |
if(CdmUtils.isNotBlank(relationString) && !relationString.equals(".")){
|
| 174 |
TaxonRelationshipType taxonRelationshipTypeByKey = new RedListGefaesspflanzenTransformer().getTaxonRelationshipTypeByKey(relationString); |
|
| 174 |
String substring = relationString.substring(relationString.length()-1, relationString.length()); |
|
| 175 |
TaxonRelationshipType taxonRelationshipTypeByKey = new RedListGefaesspflanzenTransformer().getTaxonRelationshipTypeByKey(substring); |
|
| 175 | 176 |
if(taxonRelationshipTypeByKey==null){
|
| 176 |
RedListUtil.logMessage(id, "Could not interpret relationship "+relationString+" for taxon "+taxonBase, logger); |
|
| 177 |
RedListUtil.logMessage(id, "Could not interpret relationship "+relationString+" for taxon "+taxonBase.generateTitle(), logger); |
|
| 178 |
} |
|
| 179 |
//there is no type "included in" so we have to reverse the direction |
|
| 180 |
if(substring.equals("<")){
|
|
| 181 |
cloneTaxon(taxonBase, name, taxonRelationshipTypeByKey, taxaToSave, id, classificationNamespace, true, false, state); |
|
| 182 |
} |
|
| 183 |
else{
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| 184 |
cloneTaxon(taxonBase, name, taxonRelationshipTypeByKey, taxaToSave, id, classificationNamespace, false, false, state); |
|
| 177 | 185 |
} |
| 178 |
cloneTaxon(taxonBase, name, taxonRelationshipTypeByKey, taxaToSave, id, classificationNamespace, state); |
|
| 179 | 186 |
} |
| 180 | 187 |
} |
| 181 | 188 |
|
| 182 | 189 |
/** |
| 183 | 190 |
* <b>NOTE:</b> the {@link TaxonRelationshipType} passed as parameter is
|
| 184 |
* directed <b>from the clone</b> to the taxon |
|
| 191 |
* directed <b>from the clone</b> to the taxon.<br> |
|
| 192 |
* This can be changed with parameter <i>reverseRelation</i> |
|
| 185 | 193 |
*/ |
| 186 |
private void cloneTaxon(TaxonBase taxonBase, TaxonNameBase name, TaxonRelationshipType relationFromCloneToTaxon, Set<TaxonBase> taxaToSave, long id, String sourceNameSpace, RedListGefaesspflanzenImportState state){
|
|
| 187 |
TaxonBase clone = (TaxonBase) taxonBase.clone(); |
|
| 188 |
clone.setName(name); |
|
| 189 |
if(taxonBase.isInstanceOf(Taxon.class)){
|
|
| 190 |
TaxonRelationship taxonRelation = ((Taxon) clone).addTaxonRelation((Taxon) taxonBase, relationFromCloneToTaxon, null, null); |
|
| 191 |
taxonRelation.setDoubtful(true);//TODO Ist das mit " mit Fragezeichen" gemeint? |
|
| 194 |
private void cloneTaxon(TaxonBase taxonBase, TaxonNameBase name, TaxonRelationshipType relationFromCloneToTaxon, Set<TaxonBase> taxaToSave, long id, String sourceNameSpace, boolean reverseRelation, boolean doubtful, RedListGefaesspflanzenImportState state){
|
|
| 195 |
TaxonBase clone = (TaxonBase) taxonBase.clone(); |
|
| 196 |
clone.setName(name); |
|
| 197 |
if(taxonBase.isInstanceOf(Taxon.class)){
|
|
| 198 |
TaxonRelationship taxonRelation; |
|
| 199 |
if(reverseRelation){
|
|
| 200 |
taxonRelation = ((Taxon) taxonBase).addTaxonRelation((Taxon) clone, relationFromCloneToTaxon, null, null); |
|
| 192 | 201 |
} |
| 193 |
ImportHelper.setOriginalSource(clone, state.getTransactionalSourceReference(), id, sourceNameSpace); |
|
| 194 |
taxaToSave.add(clone); |
|
| 202 |
else {
|
|
| 203 |
taxonRelation = ((Taxon) clone).addTaxonRelation((Taxon) taxonBase, relationFromCloneToTaxon, null, null); |
|
| 204 |
} |
|
| 205 |
taxonRelation.setDoubtful(doubtful); |
|
| 206 |
} |
|
| 207 |
ImportHelper.setOriginalSource(clone, state.getTransactionalSourceReference(), id, sourceNameSpace); |
|
| 208 |
taxaToSave.add(clone); |
|
| 195 | 209 |
} |
| 196 | 210 |
|
| 197 | 211 |
private TaxonBase importTaxon(long id, String taxNameString, String gueltString, String authorBasiString, |
| app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/gefaesspflanzen/RedListGefaesspflanzenTransformer.java | ||
|---|---|---|
| 72 | 72 |
public TaxonRelationshipType getTaxonRelationshipTypeByKey(String key) {
|
| 73 | 73 |
if (key == null){return null;}
|
| 74 | 74 |
else {
|
| 75 |
String substring = key.substring(key.length()-1, key.length()); |
|
| 76 | 75 |
// if (key.equals("<")){return TaxonRelationshipType.();}//TODO: what to do here?
|
| 77 |
if (substring.equals("=")){return TaxonRelationshipType.CONGRUENT_TO();}
|
|
| 78 |
else if (substring.equals(">")){return TaxonRelationshipType.INCLUDES();}
|
|
| 79 |
else if (substring.equals("!")){return TaxonRelationshipType.OVERLAPS();}
|
|
| 80 |
else if (substring.equals("?")){return TaxonRelationshipType.ALL_RELATIONSHIPS();}
|
|
| 76 |
if (key.equals("=")){return TaxonRelationshipType.CONGRUENT_TO();}
|
|
| 77 |
else if (key.equals(">")){return TaxonRelationshipType.INCLUDES();}
|
|
| 78 |
else if (key.equals("<")){return TaxonRelationshipType.INCLUDES();}
|
|
| 79 |
else if (key.equals("!")){return TaxonRelationshipType.OVERLAPS();}
|
|
| 80 |
// else if (key.equals("?")){return TaxonRelationshipType.;}//TODO: what to do here?
|
|
| 81 | 81 |
// else if (key.equals("x")){return TaxonRelationshipType.();}//TODO: what to do here?
|
| 82 | 82 |
} |
| 83 | 83 |
return null; |
Also available in: Unified diff
Add taxa to classifications #5448