Revision 18d660e0
fix specimen fact export
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/outputmodel/OutputModelClassificationExport.java | ||
|---|---|---|
| 13 | 13 |
import java.util.HashSet; |
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import java.util.Iterator; |
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import java.util.List; |
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import java.util.Map; |
|
| 16 | 17 |
import java.util.Set; |
| 17 | 18 |
import java.util.UUID; |
| 18 | 19 |
|
| ... | ... | |
| 28 | 29 |
import eu.etaxonomy.cdm.model.agent.Person; |
| 29 | 30 |
import eu.etaxonomy.cdm.model.agent.Team; |
| 30 | 31 |
import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase; |
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import eu.etaxonomy.cdm.model.common.Annotation; |
|
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import eu.etaxonomy.cdm.model.common.AnnotationType; |
|
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import eu.etaxonomy.cdm.model.common.CdmBase; |
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import eu.etaxonomy.cdm.model.common.DefinedTerm; |
| 33 | 36 |
import eu.etaxonomy.cdm.model.common.ICdmBase; |
| ... | ... | |
| 293 | 296 |
String[] csvLine = new String[table.getSize()]; |
| 294 | 297 |
|
| 295 | 298 |
for (DescriptionElementBase element: specimenFacts){
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csvLine = new String[table.getSize()]; |
|
| 296 | 300 |
if (element instanceof IndividualsAssociation){
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csvLine = new String[table.getSize()]; |
|
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|
|
| 298 | 302 |
IndividualsAssociation indAssociation = (IndividualsAssociation)element; |
| 299 | 303 |
csvLine[table.getIndex(OutputModelTable.FACT_ID)] = getId(state, element); |
| 300 | 304 |
handleSource(state, element, table); |
| ... | ... | |
| 306 | 310 |
handleSpecimen(state, derivedUnit); |
| 307 | 311 |
csvLine[table.getIndex(OutputModelTable.TAXON_FK)] = getId(state, taxon); |
| 308 | 312 |
csvLine[table.getIndex(OutputModelTable.SPECIMEN_FK)] = getId(state, indAssociation.getAssociatedSpecimenOrObservation()); |
| 309 |
state.getProcessor().put(table, indAssociation, csvLine, state); |
|
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|
|
| 310 | 314 |
}else{
|
| 311 | 315 |
state.getResult().addError("The associated Specimen of taxon " + taxon.getUuid() + " is not an DerivedUnit. Could not be exported.");
|
| 312 | 316 |
} |
| 313 | 317 |
|
| 314 | 318 |
} |
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csvLine[table.getIndex(OutputModelTable.SPECIMEN_NOTES)] = createAnnotationsString(indAssociation.getAnnotations()); |
|
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state.getProcessor().put(table, indAssociation, csvLine, state); |
|
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|
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} else if (element instanceof TextData){
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TextData textData = HibernateProxyHelper.deproxy(element, TextData.class); |
|
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csvLine[table.getIndex(OutputModelTable.FACT_ID)] = getId(state, textData); |
|
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handleSource(state, textData, table); |
|
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csvLine[table.getIndex(OutputModelTable.SPECIMEN_NOTES)] = createAnnotationsString(textData.getAnnotations()); |
|
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|
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csvLine[table.getIndex(OutputModelTable.SPECIMEN_DESCRIPTION)] = createMultilanguageString(textData.getMultilanguageText()); |
|
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state.getProcessor().put(table, element, csvLine, state); |
|
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// state.getResult().addError("The specimen description for the taxon " + taxon.getUuid() + " is not of type individual association. Could not be exported. UUID of the description element: " + element.getUuid());
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} |
|
| 315 | 332 |
|
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} else{
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state.getResult().addError("The specimen description for the taxon " + taxon.getUuid() + " is not of type individual association. Could not be exported. UUID of the description element: " + element.getUuid());
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|
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} |
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} |
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|
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/** |
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* @param multilanguageText |
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* @return |
|
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*/ |
|
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private String createMultilanguageString(Map<Language, LanguageString> multilanguageText) {
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String text = ""; |
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int index = multilanguageText.size(); |
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for(LanguageString langString: multilanguageText.values()){
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text += langString.getText(); |
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if (index > 1){
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text += "; "; |
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} |
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index --; |
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} |
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return text; |
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} |
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|
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/** |
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* @param annotations |
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* @return |
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*/ |
|
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private String createAnnotationsString(Set<Annotation> annotations) {
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StringBuffer strBuff = new StringBuffer(); |
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for (Annotation ann:annotations){
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if (ann.getAnnotationType() == null ||!ann.getAnnotationType().equals(AnnotationType.TECHNICAL())){
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strBuff.append(ann.getText()); |
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strBuff.append("; ");
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|
| 318 | 365 |
} |
| 319 | 366 |
} |
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return strBuff.toString(); |
|
| 320 | 368 |
} |
| 321 | 369 |
|
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/** |
| ... | ... | |
| 1078 | 1126 |
private String createShortCitation(Reference reference) {
|
| 1079 | 1127 |
TeamOrPersonBase authorship = reference.getAuthorship(); |
| 1080 | 1128 |
String shortCitation = ""; |
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if (authorship == null) {
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return null; |
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} |
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authorship = HibernateProxyHelper.deproxy(authorship); |
|
| 1081 | 1133 |
if (authorship instanceof Person){ shortCitation = ((Person)authorship).getLastname();}
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else{
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else if (authorship instanceof Team){
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|
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Team authorTeam = HibernateProxyHelper.deproxy(authorship, Team.class); |
| 1084 | 1137 |
int index = 0; |
| 1138 |
|
|
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for (Person teamMember : authorTeam.getTeamMembers()){
|
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index++; |
| 1087 | 1141 |
String concat = concatString(authorTeam, authorTeam.getTeamMembers(), index); |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/outputmodel/OutputModelTable.java | ||
|---|---|---|
| 49 | 49 |
protected static final String REFERENCE_ID = "Reference_ID"; |
| 50 | 50 |
protected static final String BIBLIO_SHORT_CITATION = "BibliographicShortCitation"; |
| 51 | 51 |
protected static final String REF_TITLE = "Title"; |
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protected static final String ABBREV_REF_TITLE = "Abbrev. Title"; |
|
| 52 | 53 |
protected static final String DATE_PUBLISHED = "DatePublished"; |
| 53 | 54 |
protected static final String EDITION = "Edition"; |
| 54 | 55 |
protected static final String EDITOR= "Editor"; |
| ... | ... | |
| 178 | 179 |
protected static final String FACT_CATEGORY = "FactCategory"; |
| 179 | 180 |
|
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// Specimen Facts |
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protected static final String SPECIMEN_NOTES = "Specimen Notes"; |
|
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protected static final String SPECIMEN_DESCRIPTION = "Specimen Description"; |
|
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|
|
| 181 | 185 |
|
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//Geographic Area Facts |
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protected static final String AREA_LABEL = "AreaLabel"; |
| ... | ... | |
| 202 | 206 |
} |
| 203 | 207 |
|
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final static String[] specimenFactsColumns() {
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return new String[]{FACT_ID, TAXON_FK, SPECIMEN_FK};
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return new String[]{FACT_ID, TAXON_FK, SPECIMEN_FK, SPECIMEN_DESCRIPTION, SPECIMEN_NOTES};
|
|
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} |
| 207 | 211 |
|
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final static String[] commonNameFactsColumns() {
|
| ... | ... | |
| 251 | 255 |
return new String[]{SYNONYM_ID, TAXON_FK, NAME_FK, SEC_REFERENCE_FK, SEC_REFERENCE};
|
| 252 | 256 |
} |
| 253 | 257 |
final static String[] referenceColumns(){
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return new String[]{REFERENCE_ID, BIBLIO_SHORT_CITATION, REF_TITLE, DATE_PUBLISHED, EDITION, EDITOR, ISBN,ISSN, ORGANISATION, PAGES, PLACE_PUBLISHED, PUBLISHER,
|
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return new String[]{REFERENCE_ID, BIBLIO_SHORT_CITATION, REF_TITLE,ABBREV_REF_TITLE, DATE_PUBLISHED, EDITION, EDITOR, ISBN,ISSN, ORGANISATION, PAGES, PLACE_PUBLISHED, PUBLISHER,
|
|
| 255 | 259 |
REF_ABSTRACT, SERIES_PART, VOLUME, YEAR, AUTHORSHIP_TITLE, AUTHOR_FK, IN_REFERENCE, INSTITUTION, LSID, SCHOOL, REF_TYPE, URI}; |
| 256 | 260 |
} |
| 257 | 261 |
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