String chromosomesPart = getChromosomesPart(value);\r
String references = value.replace(chromosomesPart, "").trim();\r
chromosomesPart = chromosomesPart.replace(":", "").trim();\r
- return addDescriptionElement(taxon, chromosomesPart, chromosomeFeature, references); \r
+ return addDescriptionElement(state, taxon, chromosomesPart, chromosomeFeature, references); \r
}\r
\r
\r
* @param attribute\r
* @return\r
*/\r
- private TextData handleDescriptiveElement(EfloraImportState state,\r
- Element element, Taxon taxon, String classValue) {\r
+ private TextData handleDescriptiveElement(EfloraImportState state, Element element, Taxon taxon, String classValue) {\r
TextData result = null;\r
Feature feature = getFeature(classValue, state);\r
if (feature == null){\r
String value = element.getValue();\r
value = replaceStart(value, "Notes");\r
value = replaceStart(value, "Note");\r
- result = addDescriptionElement(taxon, value, feature, null);\r
+ result = addDescriptionElement(state, taxon, value, feature, null);\r
}\r
return result;\r
}\r
String value = element.getTextNormalize();\r
value = replaceStart(value, "Uses");\r
Feature feature = Feature.USES();\r
- return addDescriptionElement(taxon, value, feature, null);\r
+ return addDescriptionElement(state, taxon, value, feature, null);\r
\r
}\r
\r
value = replaceStart(value, "Distribution");\r
Feature feature = Feature.DISTRIBUTION();\r
//distribution parsing almost impossible as there is lots of freetext in the distribution tag\r
- return addDescriptionElement(taxon, value, feature, null);\r
+ return addDescriptionElement(state, taxon, value, feature, null);\r
}\r
\r
\r
value = replaceStart(value, "Habitat");\r
feature = getFeature("Habitat", state);\r
}\r
- return addDescriptionElement(taxon, value, feature, null);\r
+ return addDescriptionElement(state, taxon, value, feature, null);\r
}\r
\r
\r
if (value.startsWith(replacementString) ){\r
value = value.substring(replacementString.length()).trim();\r
}\r
- while (value.startsWith("-") ){\r
+ while (value.startsWith("-") || value.startsWith("–") ){\r
value = value.substring("-".length()).trim();\r
}\r
return value;\r
}\r
\r
\r
+ /**\r
+ * @param value\r
+ * @param replacementString\r
+ */\r
+ protected String removeTrailing(String value, String replacementString) {\r
+ if (value == null){\r
+ return null;\r
+ }\r
+ if (value.endsWith(replacementString) ){\r
+ value = value.substring(0, value.length() - replacementString.length()).trim();\r
+ }\r
+ return value;\r
+ }\r
\r
/**\r
* @param state\r
\r
List<Element> elements = elNom.getChildren();\r
for (Element element : elements){\r
- if (element.getName().equals("name")){\r
+ if (element.getName().equals("name") || element.getName().equals("homonym") ){\r
if (taxonBaseClassType == false){\r
- logger.warn("Name tag not allowed in non taxon nom tag");\r
+ logger.warn("Name or homonym tag not allowed in non taxon nom tag");\r
}\r
}else{\r
unhandledNomChildren.add(element.getName());\r
*/\r
protected String removeStartingTypeRefMinus(String typeRef) {\r
typeRef = replaceStart(typeRef, "-");\r
- typeRef = replaceStart(typeRef, "\97");\r
+ typeRef = replaceStart(typeRef, "—");\r
typeRef = replaceStart(typeRef, "\u002d");\r
typeRef = replaceStart(typeRef, "\u2013");\r
typeRef = replaceStart(typeRef, "--");\r
//create name\r
BotanicalName nameType = (BotanicalName)parser.parseFullName(typeText, NomenclaturalCode.ICBN, Rank.SPECIES());\r
((NameTypeDesignation) typeDesignation).setTypeName(nameType);\r
- //TODO wie können NameTypes den Namen zugeordnet werden? - wird aber vom Portal via NameCache matching gemacht\r
+ //TODO wie können NameTypes den Namen zugeordnet werden? - wird aber vom Portal via NameCache matching gemacht\r
}\r
\r
\r
logger.warn("Unhandled name class: " + classValue);\r
}\r
}else if(element.getName().equals("homonym")){\r
- handleHomonym(element, name);\r
+ handleHomonym(state, element, name);\r
}else{\r
// child element is not "name"\r
unhandledNomChildren.add(element.getName());\r
}\r
\r
//test nom element has no text\r
- if (StringUtils.isNotBlank(elNom.getTextNormalize().replace("\97", "").replace("\u002d","").replace("\u2013", ""))){\r
+ if (StringUtils.isNotBlank(elNom.getTextNormalize().replace("—", "").replace("\u002d","").replace("\u2013", ""))){\r
String strElNom = elNom.getTextNormalize();\r
if ("?".equals(strElNom)){\r
handleQuestionMark(name, taxon);\r
\r
\r
//merge with handleNomTaxon \r
- private void handleHomonym(Element elHomonym, NonViralName upperName) {\r
+ private void handleHomonym(EfloraImportState state, Element elHomonym, NonViralName upperName) {\r
verifyNoAttribute(elHomonym);\r
\r
//hommonym name\r
homonymName.setSpecificEpithet(value);\r
}else if (classValue.equalsIgnoreCase("author")){\r
handleNameAuthors(elName, homonymName);\r
+ }else if (classValue.equalsIgnoreCase("paraut")){\r
+ handleBasionymAuthor(state, elName, homonymName, true);\r
}else if (classValue.equalsIgnoreCase("pub")){\r
handleNomenclaturalReference(homonymName, value);\r
}else if (classValue.equalsIgnoreCase("note")){\r
TimePeriod nameYear = upperName.getNomenclaturalReference().getDatePublished();\r
homonymIsLater = homonymYear.getStart().compareTo(nameYear.getStart()) > 0;\r
}else{\r
- logger.warn("Classification name has no nomenclatural reference");\r
+ if (upperName.getNomenclaturalReference() == null){\r
+ logger.warn("Homonym parent does not have a nomenclatural reference or year: " + upperName.getTitleCache());\r
+ }\r
+ if (homonymName.getNomenclaturalReference() == null){\r
+ logger.warn("Homonym does not have a nomenclatural reference or year: " + homonymName.getTitleCache());\r
+ }\r
}\r
if (homonymIsLater){\r
homonymName.addRelationshipToName(upperName, relType, null);\r
* @param element\r
* @param name\r
*/\r
- private void handleBasionymAuthor(EfloraImportState state, Element element, NonViralName name, boolean overwrite) {\r
- String strAuthor = element.getValue().trim();\r
+ private void handleBasionymAuthor(EfloraImportState state, Element elBasionymAuthor, NonViralName name, boolean overwrite) {\r
+ String strAuthor = elBasionymAuthor.getValue().trim();\r
Pattern reBasionymAuthor = Pattern.compile("^\\(.*\\)$");\r
if (reBasionymAuthor.matcher(strAuthor).matches()){\r
strAuthor = strAuthor.substring(1, strAuthor.length()-1);\r
if (strAuthor.endsWith(",")){\r
strAuthor = strAuthor.substring(0, strAuthor.length() -1);\r
}\r
+ if (strAuthor.indexOf("(") > -1 || strAuthor.indexOf(")") > -1){\r
+ logger.warn("Author has brackets. Basionym authors should be handled in separate tags: " + strAuthor);\r
+ }\r
TeamOrPersonBase[] team = getTeam(strAuthor);\r
name.setCombinationAuthorTeam(team[0]);\r
name.setExCombinationAuthorTeam(team[1]);\r
}\r
\r
\r
- private TeamOrPersonBase parseSingleTeam(String strBaseAuthor) {\r
+ protected TeamOrPersonBase parseSingleTeam(String strBaseAuthor) {\r
TeamOrPersonBase result;\r
String[] split = strBaseAuthor.split("&");\r
if (split.length > 1){\r
logger.warn("Unhandled feature: " + classValue);\r
}else{\r
String value = element.getValue();\r
- addDescriptionElement(taxon, value, feature, null);\r
+ addDescriptionElement(state, taxon, value, feature, null);\r
}\r
\r
}\r
* @param value\r
* @param taxonNameBase \r
*/\r
- private void handleGenus(String value, TaxonNameBase taxonName) {\r
+ protected void handleGenus(String value, TaxonNameBase taxonName) {\r
Matcher matcher = rexGenusAuthor.matcher(value);\r
if (matcher.find()){\r
String author = matcher.group();\r
\r
\r
/**\r
+ * @param state \r
* @param taxon\r
* @param value\r
* @param feature\r
* @return \r
*/\r
- private TextData addDescriptionElement(Taxon taxon, String value, Feature feature, String references) {\r
+ private TextData addDescriptionElement(EfloraImportState state, Taxon taxon, String value, Feature feature, String references) {\r
TextData textData = TextData.NewInstance(feature);\r
- textData.putText(value, Language.ENGLISH());\r
+ Language textLanguage = getDefaultLanguage(state);\r
+ textData.putText(value, textLanguage);\r
TaxonDescription description = getDescription(taxon);\r
description.addElement(textData);\r
if (references != null){\r
return textData;\r
}\r
\r
+ private Language getDefaultLanguage(EfloraImportState state) {\r
+ UUID defaultLanguageUuid = state.getConfig().getDefaultLanguageUuid();\r
+ if (defaultLanguageUuid != null){\r
+ Language result = state.getDefaultLanguage();\r
+ if (result == null || ! result.getUuid().equals(defaultLanguageUuid)){\r
+ result = (Language)getTermService().find(defaultLanguageUuid);\r
+ state.setDefaultLanguage(result);\r
+ if (result == null){\r
+ logger.warn("Default language for " + defaultLanguageUuid + " does not exist.");\r
+ }\r
+ }\r
+ return result;\r
+ }else{\r
+ return Language.DEFAULT();\r
+ }\r
+ }\r
+\r
+\r
/**\r
* @param elNomenclature\r
*/\r
BGBM BDI Projects / cdmlib.git / blobdiff