import javax.xml.stream.events.XMLEvent;\r
\r
import org.apache.commons.lang.StringUtils;\r
+import org.apache.commons.lang.WordUtils;\r
import org.apache.log4j.Logger;\r
\r
import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;\r
private static final String COLLECTOR = "collector";\r
private static final String COLLECTION = "collection";\r
private static final String COORDINATES = "coordinates";\r
- private static final String COUPLET = "couplet";\r
private static final String DATES = "dates";\r
private static final String DEDICATION = "dedication";\r
private static final String DEFAULT_MEDIA_URL = "defaultMediaUrl";\r
private static final String INFRANK = "infrank";\r
private static final String INFRAUT = "infraut";\r
private static final String INFRPARAUT = "infrparaut";\r
- private static final String IS_SPOTCHARACTERS = "isSpotcharacters";\r
private static final String ISSUE = "issue";\r
private static final String ITALICS = "italics";\r
private static final String KEY = "key";\r
- private static final String KEY_TITLE = "keyTitle";\r
- private static final String KEYNOTES = "keynotes";\r
private static final String LIFE_CYCLE_PERIODS = "lifeCyclePeriods";\r
private static final String LOCALITY = "locality";\r
private static final String LOST = "lost";\r
private static final String NOT_FOUND = "notFound";\r
private static final String NOT_SEEN = "notSeen";\r
private static final String NOTES = "notes";\r
- private static final String NUM = "num";\r
private static final String ORIGINAL_DETERMINATION = "originalDetermination";\r
private static final String PAGES = "pages";\r
private static final String PARAUT = "paraut";\r
private static final String PUBNAME = "pubname";\r
private static final String PUBTITLE = "pubtitle";\r
private static final String PUBTYPE = "pubtype";\r
- private static final String QUESTION = "question";\r
private static final String QUOTE = "quote";\r
private static final String RANK = "rank";\r
private static final String REF = "ref";\r
private static final String TAXON = "taxon";\r
private static final String TAXONTITLE = "taxontitle";\r
private static final String TAXONTYPE = "taxontype";\r
- private static final String TEXT = "text";\r
private static final String TEXT_SECTION = "textSection";\r
- private static final String TO_COUPLET = "toCouplet";\r
- private static final String TO_KEY = "toKey";\r
- private static final String TO_TAXON = "toTaxon";\r
private static final String TYPE = "type";\r
private static final String TYPE_STATUS = "typeStatus";\r
private static final String TREATMENT = "treatment";\r
\r
private IEditGeoService editGeoService;\r
\r
+ private MarkupKeyImport keyImport;\r
+ \r
public MarkupDocumentImportNoComponent(MarkupDocumentImport docImport) {\r
super(docImport);\r
this.editGeoService = docImport.getEditGeoService();\r
+ keyImport = new MarkupKeyImport(docImport);\r
}\r
\r
public void doInvoke(MarkupImportState state) throws XMLStreamException { \r
XMLEventReader reader = state.getReader();\r
\r
- // publication\r
+ // publication (= root element)\r
String elName = PUBLICATION;\r
boolean hasPublication = false;\r
\r
\r
}\r
\r
- private void handlePublication(MarkupImportState state, XMLEventReader reader, XMLEvent currentEvent, \r
- String elName) throws XMLStreamException {\r
+ private void handlePublication(MarkupImportState state, XMLEventReader reader, XMLEvent currentEvent, String elName) throws XMLStreamException {\r
\r
// attributes\r
StartElement element = currentEvent.asStartElement();\r
fireWarningEvent(warning, next, 12);\r
}\r
\r
- makeKeyNodes(state, parentEvent, taxonTitle);\r
+ keyImport.makeKeyNodes(state, parentEvent, taxonTitle);\r
state.setCurrentTaxon(null);\r
state.setCurrentTaxonNum(null);\r
save(taxon, state);\r
} else if (isStartingElement(next, TEXT_SECTION)) {\r
handleNotYetImplementedElement(next);\r
} else if (isStartingElement(next, KEY)) {\r
- handleKey(state, reader, next);\r
+ keyImport.handleKey(state, reader, next);\r
} else if (isStartingElement(next, NOMENCLATURE)) {\r
handleNomenclature(state, reader, next);\r
hasNomenclature = true;\r
throw new IllegalStateException("<Taxon> has no closing tag");\r
}\r
\r
- private void makeKeyNodes(MarkupImportState state, XMLEvent event, String taxonTitle) {\r
- Taxon taxon = state.getCurrentTaxon();\r
- String num = state.getCurrentTaxonNum();\r
- \r
- String nameString = CdmBase.deproxy(taxon.getName(), NonViralName.class).getNameCache();\r
-// String nameString = taxonTitle;\r
- \r
- //try to find matching lead nodes \r
- UnmatchedLeadsKey leadsKey = UnmatchedLeadsKey.NewInstance(num, nameString);\r
- Set<PolytomousKeyNode> matchingNodes = handleMatchingNodes(state, taxon, leadsKey);\r
- \r
- if (num != null){//same without using the num\r
- UnmatchedLeadsKey noNumLeadsKey = UnmatchedLeadsKey.NewInstance("", nameString);\r
- Set<PolytomousKeyNode> noNumMatchingNodes = handleMatchingNodes(state, taxon, noNumLeadsKey);\r
- if(noNumMatchingNodes.size() > 0){\r
- String message ="Taxon matches additional key node when not considering <num> attribute in taxontitle. This may be correct but may also indicate an error.";\r
- fireWarningEvent(message, event, 1);\r
- }\r
- }\r
- //report missing match, if num exists\r
- if (matchingNodes.isEmpty() && num != null){\r
- String message = "Taxon has <num> attribute in taxontitle but no matching key nodes exist: %s, Key: %s";\r
- message = String.format(message, num, leadsKey.toString());\r
- fireWarningEvent(message, event, 1);\r
- }\r
- \r
- }\r
- \r
- private Set<PolytomousKeyNode> handleMatchingNodes(MarkupImportState state, Taxon taxon, UnmatchedLeadsKey leadsKey) {\r
- Set<PolytomousKeyNode> matchingNodes = state.getUnmatchedLeads().getNodes(leadsKey);\r
- for (PolytomousKeyNode matchingNode : matchingNodes){\r
- state.getUnmatchedLeads().removeNode(leadsKey, matchingNode);\r
- matchingNode.setTaxon(taxon);\r
- state.getPolytomousKeyNodesToSave().add(matchingNode);\r
- }\r
- return matchingNodes;\r
- }\r
-\r
- private void handleKey(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {\r
- // attributes\r
- Map<String, Attribute> attributes = getAttributes(parentEvent);\r
- String isSpotcharacters = getAndRemoveAttributeValue(attributes, IS_SPOTCHARACTERS);\r
- if (isNotBlank(isSpotcharacters) ) {\r
- //TODO isSpotcharacters\r
- String message = "Attribute isSpotcharacters not yet implemented for <key>";\r
- fireWarningEvent(message, parentEvent, 4);\r
- }\r
- \r
- PolytomousKey key = PolytomousKey.NewInstance();\r
- key.addTaxonomicScope(state.getCurrentTaxon());\r
- state.setCurrentKey(key);\r
- \r
- boolean isFirstCouplet = true;\r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (isMyEndingElement(next, parentEvent)) {\r
- save(key, state);\r
- state.setCurrentKey(null);\r
- return;\r
- } else if (isEndingElement(next, KEYNOTES)){\r
- popUnimplemented(next.asEndElement());\r
- } else if (isStartingElement(next, KEY_TITLE)) {\r
- handleKeyTitle(state, reader, next);\r
- } else if (isStartingElement(next, KEYNOTES)) {\r
- //TODO\r
- handleNotYetImplementedElement(next);\r
- } else if (isStartingElement(next, COUPLET)) {\r
- PolytomousKeyNode node = null;\r
- if (isFirstCouplet){\r
- node = key.getRoot();\r
- isFirstCouplet = false;\r
- }\r
- handleCouplet(state, reader, next, node);\r
- } else {\r
- handleUnexpectedElement(next);\r
- }\r
- }\r
- throw new IllegalStateException("<key> has no closing tag");\r
- }\r
-\r
- /**\r
- * @param state\r
- * @param reader\r
- * @param key\r
- * @param next\r
- * @throws XMLStreamException\r
- */\r
- private void handleKeyTitle(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {\r
- PolytomousKey key = state.getCurrentKey();\r
- String keyTitle = getCData(state, reader, parentEvent);\r
- String standardTitles = "(?i)(Key\\sto\\sthe\\s(genera|species|varieties|forms))";\r
- \r
- if (isNotBlank(keyTitle) ){\r
- if (!state.getConfig().isReplaceStandardKeyTitles() || ! keyTitle.matches(standardTitles)){\r
- key.setTitleCache(keyTitle, true);\r
- }\r
- }\r
- }\r
-\r
- private void handleCouplet(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent, PolytomousKeyNode parentNode) throws XMLStreamException {\r
- String num = getOnlyAttribute(parentEvent, NUM, true);\r
- List<PolytomousKeyNode> childList = new ArrayList<PolytomousKeyNode>(); \r
- \r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (isMyEndingElement(next, parentEvent)) {\r
- completeCouplet(state, parentEvent, parentNode, num, childList);\r
- return;\r
- } else if (isStartingElement(next, QUESTION)) {\r
- handleQuestion(state, reader, next, childList);\r
- } else if (isStartingElement(next, KEYNOTES)) {\r
- //TODO\r
- handleNotYetImplementedElement(next);\r
- } else if (isEndingElement(next, KEYNOTES)) {\r
- //TODO\r
- popUnimplemented(next.asEndElement());\r
- } else {\r
- handleUnexpectedElement(next);\r
- }\r
- }\r
- throw new IllegalStateException("<couplet> has no closing tag");\r
- }\r
-\r
- /**\r
- * @param state\r
- * @param parentEvent\r
- * @param parentNode\r
- * @param num\r
- * @param childList\r
- */\r
- private void completeCouplet(MarkupImportState state, XMLEvent parentEvent,\r
- PolytomousKeyNode parentNode, String num, List<PolytomousKeyNode> childList) {\r
- if (parentNode != null){\r
- for (PolytomousKeyNode childNode : childList){\r
- parentNode.addChild(childNode);\r
- }\r
- }else if (isNotBlank(num)){\r
- UnmatchedLeadsKey unmatchedKey = UnmatchedLeadsKey.NewInstance(state.getCurrentKey(), num);\r
- Set<PolytomousKeyNode> nodes = state.getUnmatchedLeads().getNodes(unmatchedKey);\r
- for(PolytomousKeyNode nodeToMatch: nodes){\r
- for (PolytomousKeyNode childNode : childList){\r
- nodeToMatch.addChild(childNode);\r
- }\r
- state.getUnmatchedLeads().removeNode(unmatchedKey, nodeToMatch);\r
- }\r
- }else{\r
- String message = "Parent num could not be matched. Please check if num (%s) is correct";\r
- message = String.format(message, num);\r
- fireWarningEvent(message, parentEvent, 6);\r
- }\r
- }\r
-\r
- private void handleQuestion(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent, List<PolytomousKeyNode> nodesList) throws XMLStreamException {\r
- // attributes\r
- Map<String, Attribute> attributes = getAttributes(parentEvent);\r
- //needed only for data lineage\r
- String questionNum = getAndRemoveRequiredAttributeValue(parentEvent, attributes, NUM);\r
- \r
- PolytomousKeyNode myNode = PolytomousKeyNode.NewInstance();\r
- myNode.setKey(state.getCurrentKey()); //to avoid NPE while computing num in PolytomousKeyNode in case this node is not matched correctly with a parent\r
- nodesList.add(myNode);\r
- \r
- while (reader.hasNext()) {\r
- XMLEvent next = readNoWhitespace(reader);\r
- if (isMyEndingElement(next, parentEvent)) {\r
- return;\r
- } else if (isStartingElement(next, TEXT)) {\r
- String text = getCData(state, reader, next);\r
- KeyStatement statement = KeyStatement.NewInstance(text);\r
- myNode.setStatement(statement);\r
- } else if (isStartingElement(next, COUPLET)) {\r
- //TODO test\r
- handleCouplet(state, reader, next, myNode);\r
- } else if (isStartingElement(next, TO_COUPLET)) {\r
- handleToCouplet(state, reader, next, myNode);\r
- } else if (isStartingElement(next, TO_TAXON)) {\r
- handleToTaxon(state, reader, next, myNode);\r
- } else if (isStartingElement(next, TO_KEY)) {\r
- //TODO\r
- handleNotYetImplementedElement(next);\r
- } else if (isEndingElement(next, TO_KEY)){\r
- //TODO\r
- popUnimplemented(next.asEndElement());\r
- } else if (isStartingElement(next, KEYNOTES)) {\r
- //TODO\r
- handleNotYetImplementedElement(next);\r
- } else if (isEndingElement(next, KEYNOTES)){\r
- //TODO\r
- popUnimplemented(next.asEndElement());\r
- } else {\r
- handleUnexpectedElement(next);\r
- }\r
- }\r
- throw new IllegalStateException("<question> has no closing tag");\r
- }\r
-\r
- private void handleToCouplet(MarkupImportState state, XMLEventReader reader, XMLEvent next, PolytomousKeyNode node) throws XMLStreamException {\r
- String num = getOnlyAttribute(next, NUM, true);\r
- String cData = getCData(state, reader, next, false);\r
- if (isNotBlank(cData) && ! cData.equals(num)){\r
- String message = "CData ('%s') not handled in <toCouplet>";\r
- message = String.format(message, cData);\r
- fireWarningEvent(message, next, 4);\r
- }\r
- UnmatchedLeadsKey unmatched = UnmatchedLeadsKey.NewInstance(state.getCurrentKey(), num);\r
- state.getUnmatchedLeads().addKey(unmatched, node);\r
- }\r
-\r
- private void handleToTaxon(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent, PolytomousKeyNode node) throws XMLStreamException {\r
- Map<String, Attribute> attributes = getAttributes(parentEvent);\r
- String num = getAndRemoveAttributeValue(attributes, NUM);\r
- String taxonStr = getCData(state, reader, parentEvent, false);\r
- //TODO ?\r
- taxonStr = makeTaxonKey(taxonStr, state.getCurrentTaxon());\r
- UnmatchedLeadsKey unmatched = UnmatchedLeadsKey.NewInstance(num, taxonStr);\r
- state.getUnmatchedLeads().addKey(unmatched, node);\r
- return;\r
- }\r
- \r
- private String makeTaxonKey(String strGoto, Taxon taxon) {\r
- String result = "";\r
- if (strGoto == null){\r
- return "";\r
- }\r
- \r
- NonViralName<?> name = CdmBase.deproxy(taxon.getName(), NonViralName.class);\r
- String strGenusName = name.getGenusOrUninomial();\r
- \r
- \r
- strGoto = strGoto.replaceAll("\\([^\\(\\)]*\\)", ""); //replace all brackets\r
- strGoto = strGoto.replaceAll("\\s+", " "); //replace multiple whitespaces by exactly one whitespace\r
- \r
- strGoto = strGoto.trim(); \r
- String[] split = strGoto.split("\\s");\r
- for (int i = 0; i<split.length; i++){\r
- String single = split[i];\r
- if (isGenusAbbrev(single, strGenusName)){\r
- split[i] = strGenusName;\r
- }\r
- if (isInfraSpecificMarker(single)){\r
- String strSpeciesEpi = name.getSpecificEpithet();\r
- if (isBlank(result)){\r
- result += strGenusName + " " + strSpeciesEpi;\r
- }\r
- }\r
- result = (result + " " + split[i]).trim();\r
- }\r
- return result;\r
- }\r
- \r
-\r
- private boolean isInfraSpecificMarker(String single) {\r
- try {\r
- if (Rank.getRankByAbbreviation(single).isInfraSpecific()){\r
- return true;\r
- }else{\r
- return false;\r
- }\r
- } catch (UnknownCdmTypeException e) {\r
- return false;\r
- }\r
- }\r
- \r
- private boolean isGenusAbbrev(String single, String strGenusName) {\r
- if (! single.matches("[A-Z]\\.?")) {\r
- return false;\r
- }else if (single.length() == 0 || strGenusName == null || strGenusName.length() == 0){\r
- return false; \r
- }else{\r
- return single.charAt(0) == strGenusName.charAt(0);\r
- }\r
- }\r
-\r
/**\r
* @param state\r
* @param reader\r
return createAuthor(collectorStr);\r
}\r
\r
- private String getCData(MarkupImportState state, XMLEventReader reader, XMLEvent next) throws XMLStreamException {\r
- return getCData(state, reader, next, true);\r
- }\r
- \r
- /**\r
- * Reads character data. Any element other than character data or the ending\r
- * tag will fire an unexpected element event.\r
- * \r
- * @param state\r
- * @param reader\r
- * @param next\r
- * @return\r
- * @throws XMLStreamException\r
- */\r
- private String getCData(MarkupImportState state, XMLEventReader reader, XMLEvent next,boolean checkAttributes) throws XMLStreamException {\r
- if (checkAttributes){\r
- checkNoAttributes(next);\r
- }\r
-\r
- String text = "";\r
- while (reader.hasNext()) {\r
- XMLEvent myNext = readNoWhitespace(reader);\r
- if (isMyEndingElement(myNext, next)) {\r
- return text;\r
- } else if (myNext.isCharacters()) {\r
- text += myNext.asCharacters().getData();\r
- } else {\r
- handleUnexpectedElement(myNext);\r
- }\r
- }\r
- throw new IllegalStateException("Event has no closing tag");\r
-\r
- }\r
-\r
/**\r
* Creates the name defined by a nom tag. Adds it to the given homotypical\r
* group (if not null).\r
} else if (rank.isInfraGeneric()) {\r
name.setInfraGenericEpithet(toFirstCapital(value));\r
} else if (rank.isSpecies()) {\r
- name.setSpecificEpithet(value.toLowerCase());\r
+ if (isFirstCapitalWord(value)){ //capital letters are allowed for species epithet in case of person names (e.g. Manilkara Welwitschii Engl.\r
+ name.setSpecificEpithet(value);\r
+ }else{\r
+ name.setSpecificEpithet(value.toLowerCase());\r
+ }\r
} else if (rank.isInfraSpecific()) {\r
name.setInfraSpecificEpithet(value.toLowerCase());\r
} else {\r
return name;\r
}\r
\r
- private void handleName(MarkupImportState state, XMLEventReader reader,\r
+ private void handleName(MarkupImportState state, XMLEventReader reader, \r
XMLEvent parentEvent, Map<String, String> nameMap)\r
throws XMLStreamException {\r
String classValue = getClassOnlyAttribute(parentEvent);\r
} else if (next.isCharacters()) {\r
text += next.asCharacters().getData();\r
} else {\r
- handleUnexpectedEndElement(next.asEndElement());\r
+ handleUnexpectedElement(next);\r
}\r
}\r
throw new IllegalStateException("<DistributionLocality> has no closing tag");\r
--- /dev/null
+/**\r
+ * Copyright (C) 2009 EDIT\r
+ * European Distributed Institute of Taxonomy\r
+ * http://www.e-taxonomy.eu\r
+ *\r
+ * The contents of this file are subject to the Mozilla Public License Version 1.1\r
+ * See LICENSE.TXT at the top of this package for the full license terms.\r
+ */\r
+\r
+package eu.etaxonomy.cdm.io.markup;\r
+\r
+import java.util.ArrayList;\r
+import java.util.List;\r
+import java.util.Map;\r
+import java.util.Set;\r
+\r
+import javax.xml.stream.XMLEventReader;\r
+import javax.xml.stream.XMLStreamException;\r
+import javax.xml.stream.events.Attribute;\r
+import javax.xml.stream.events.XMLEvent;\r
+\r
+import org.apache.log4j.Logger;\r
+\r
+import eu.etaxonomy.cdm.io.markup.UnmatchedLeads.UnmatchedLeadsKey;\r
+import eu.etaxonomy.cdm.model.common.CdmBase;\r
+import eu.etaxonomy.cdm.model.common.Language;\r
+import eu.etaxonomy.cdm.model.description.KeyStatement;\r
+import eu.etaxonomy.cdm.model.description.PolytomousKey;\r
+import eu.etaxonomy.cdm.model.description.PolytomousKeyNode;\r
+import eu.etaxonomy.cdm.model.name.NonViralName;\r
+import eu.etaxonomy.cdm.model.name.Rank;\r
+import eu.etaxonomy.cdm.model.taxon.Taxon;\r
+import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;\r
+\r
+/**\r
+ * @author a.mueller\r
+ * @created 26.04.2013\r
+ * \r
+ */\r
+public class MarkupKeyImport extends MarkupImportBase {\r
+ @SuppressWarnings("unused")\r
+ private static final Logger logger = Logger.getLogger(MarkupKeyImport.class);\r
+ \r
+ private static final String COUPLET = "couplet";\r
+ private static final String IS_SPOTCHARACTERS = "isSpotcharacters";\r
+ private static final String KEYNOTES = "keynotes";\r
+ private static final String KEY_TITLE = "keyTitle";\r
+ private static final String QUESTION = "question";\r
+ private static final String TEXT = "text";\r
+ private static final String TO_COUPLET = "toCouplet";\r
+ private static final String TO_KEY = "toKey";\r
+ private static final String TO_TAXON = "toTaxon";\r
+\r
+ \r
+ public MarkupKeyImport(MarkupDocumentImport docImport) {\r
+ super(docImport);\r
+ }\r
+ \r
+ public void handleKey(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {\r
+ // attributes\r
+ Map<String, Attribute> attributes = getAttributes(parentEvent);\r
+ String isSpotcharacters = getAndRemoveAttributeValue(attributes, IS_SPOTCHARACTERS);\r
+ if (isNotBlank(isSpotcharacters) ) {\r
+ //TODO isSpotcharacters\r
+ String message = "Attribute isSpotcharacters not yet implemented for <key>";\r
+ fireWarningEvent(message, parentEvent, 4);\r
+ }\r
+ \r
+ PolytomousKey key = PolytomousKey.NewInstance();\r
+ key.addTaxonomicScope(state.getCurrentTaxon());\r
+ state.setCurrentKey(key);\r
+ \r
+ boolean isFirstCouplet = true;\r
+ while (reader.hasNext()) {\r
+ XMLEvent next = readNoWhitespace(reader);\r
+ if (isMyEndingElement(next, parentEvent)) {\r
+ save(key, state);\r
+ state.setCurrentKey(null);\r
+ return;\r
+ } else if (isEndingElement(next, KEYNOTES)){\r
+ popUnimplemented(next.asEndElement());\r
+ } else if (isStartingElement(next, KEY_TITLE)) {\r
+ handleKeyTitle(state, reader, next);\r
+ } else if (isStartingElement(next, KEYNOTES)) {\r
+ //TODO\r
+ handleNotYetImplementedElement(next);\r
+ } else if (isStartingElement(next, COUPLET)) {\r
+ PolytomousKeyNode node = null;\r
+ if (isFirstCouplet){\r
+ node = key.getRoot();\r
+ isFirstCouplet = false;\r
+ }\r
+ handleCouplet(state, reader, next, node);\r
+ } else {\r
+ handleUnexpectedElement(next);\r
+ }\r
+ }\r
+ throw new IllegalStateException("<key> has no closing tag");\r
+ }\r
+\r
+\r
+ /**\r
+ * @param state\r
+ * @param reader\r
+ * @param key\r
+ * @param next\r
+ * @throws XMLStreamException\r
+ */\r
+ private void handleKeyTitle(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {\r
+ PolytomousKey key = state.getCurrentKey();\r
+ String keyTitle = getCData(state, reader, parentEvent);\r
+ String standardTitlesEngl = "(?i)(Key\\sto\\sthe\\s(genera|species|varieties|forms))";\r
+ String standardTitlesFrench = "(?i)(Cl\u00e9\\sdes\\s(genres|esp\u00e8ces))";\r
+ String standardTitles = standardTitlesEngl;\r
+ if (state.getDefaultLanguage() != null && state.getDefaultLanguage().equals(Language.FRENCH())){\r
+ standardTitles = standardTitlesFrench;\r
+ }\r
+ \r
+ if (isNotBlank(keyTitle) ){\r
+ if (!state.getConfig().isReplaceStandardKeyTitles() || ! keyTitle.matches(standardTitles)){\r
+ key.setTitleCache(keyTitle, true);\r
+ }\r
+ }\r
+ }\r
+ \r
+\r
+ private void handleCouplet(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent, PolytomousKeyNode parentNode) throws XMLStreamException {\r
+ String num = getOnlyAttribute(parentEvent, NUM, true);\r
+ List<PolytomousKeyNode> childList = new ArrayList<PolytomousKeyNode>(); \r
+ \r
+ while (reader.hasNext()) {\r
+ XMLEvent next = readNoWhitespace(reader);\r
+ if (isMyEndingElement(next, parentEvent)) {\r
+ completeCouplet(state, parentEvent, parentNode, num, childList);\r
+ return;\r
+ } else if (isStartingElement(next, QUESTION)) {\r
+ handleQuestion(state, reader, next, childList);\r
+ } else if (isStartingElement(next, KEYNOTES)) {\r
+ //TODO\r
+ handleNotYetImplementedElement(next);\r
+ } else if (isEndingElement(next, KEYNOTES)) {\r
+ //TODO\r
+ popUnimplemented(next.asEndElement());\r
+ } else {\r
+ handleUnexpectedElement(next);\r
+ }\r
+ }\r
+ throw new IllegalStateException("<couplet> has no closing tag");\r
+ }\r
+ \r
+\r
+ /**\r
+ * @param state\r
+ * @param parentEvent\r
+ * @param parentNode\r
+ * @param num\r
+ * @param childList\r
+ */\r
+ private void completeCouplet(MarkupImportState state, XMLEvent parentEvent,\r
+ PolytomousKeyNode parentNode, String num, List<PolytomousKeyNode> childList) {\r
+ if (parentNode != null){\r
+ for (PolytomousKeyNode childNode : childList){\r
+ parentNode.addChild(childNode);\r
+ }\r
+ }else if (isNotBlank(num)){\r
+ UnmatchedLeadsKey unmatchedKey = UnmatchedLeadsKey.NewInstance(state.getCurrentKey(), num);\r
+ Set<PolytomousKeyNode> nodes = state.getUnmatchedLeads().getNodes(unmatchedKey);\r
+ for(PolytomousKeyNode nodeToMatch: nodes){\r
+ for (PolytomousKeyNode childNode : childList){\r
+ nodeToMatch.addChild(childNode);\r
+ }\r
+ state.getUnmatchedLeads().removeNode(unmatchedKey, nodeToMatch);\r
+ }\r
+ }else{\r
+ String message = "Parent num could not be matched. Please check if num (%s) is correct";\r
+ message = String.format(message, num);\r
+ fireWarningEvent(message, parentEvent, 6);\r
+ }\r
+ }\r
+\r
+ private void handleQuestion(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent, List<PolytomousKeyNode> nodesList) throws XMLStreamException {\r
+ // attributes\r
+ Map<String, Attribute> attributes = getAttributes(parentEvent);\r
+ //needed only for data lineage\r
+ String questionNum = getAndRemoveRequiredAttributeValue(parentEvent, attributes, NUM);\r
+ \r
+ PolytomousKeyNode myNode = PolytomousKeyNode.NewInstance();\r
+ myNode.setKey(state.getCurrentKey()); //to avoid NPE while computing num in PolytomousKeyNode in case this node is not matched correctly with a parent\r
+ nodesList.add(myNode);\r
+ \r
+ while (reader.hasNext()) {\r
+ XMLEvent next = readNoWhitespace(reader);\r
+ if (isMyEndingElement(next, parentEvent)) {\r
+ return;\r
+ } else if (isStartingElement(next, TEXT)) {\r
+ String text = getCData(state, reader, next);\r
+ Language language = state.getDefaultLanguage();\r
+ if (language == null){\r
+ language = Language.DEFAULT();\r
+ }\r
+ KeyStatement statement = KeyStatement.NewInstance(language, text);\r
+ myNode.setStatement(statement);\r
+ } else if (isStartingElement(next, COUPLET)) {\r
+ //TODO test\r
+ handleCouplet(state, reader, next, myNode);\r
+ } else if (isStartingElement(next, TO_COUPLET)) {\r
+ handleToCouplet(state, reader, next, myNode);\r
+ } else if (isStartingElement(next, TO_TAXON)) {\r
+ handleToTaxon(state, reader, next, myNode);\r
+ } else if (isStartingElement(next, TO_KEY)) {\r
+ //TODO\r
+ handleNotYetImplementedElement(next);\r
+ } else if (isEndingElement(next, TO_KEY)){\r
+ //TODO\r
+ popUnimplemented(next.asEndElement());\r
+ } else if (isStartingElement(next, KEYNOTES)) {\r
+ //TODO\r
+ handleNotYetImplementedElement(next);\r
+ } else if (isEndingElement(next, KEYNOTES)){\r
+ //TODO\r
+ popUnimplemented(next.asEndElement());\r
+ } else {\r
+ handleUnexpectedElement(next);\r
+ }\r
+ }\r
+ throw new IllegalStateException("<question> has no closing tag");\r
+ }\r
+\r
+ private void handleToCouplet(MarkupImportState state, XMLEventReader reader, XMLEvent next, PolytomousKeyNode node) throws XMLStreamException {\r
+ String num = getOnlyAttribute(next, NUM, true);\r
+ String cData = getCData(state, reader, next, false);\r
+ if (isNotBlank(cData) && ! cData.equals(num)){\r
+ String message = "CData ('%s') not handled in <toCouplet>";\r
+ message = String.format(message, cData);\r
+ fireWarningEvent(message, next, 4);\r
+ }\r
+ UnmatchedLeadsKey unmatched = UnmatchedLeadsKey.NewInstance(state.getCurrentKey(), num);\r
+ state.getUnmatchedLeads().addKey(unmatched, node);\r
+ }\r
+\r
+ private void handleToTaxon(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent, PolytomousKeyNode node) throws XMLStreamException {\r
+ Map<String, Attribute> attributes = getAttributes(parentEvent);\r
+ String num = getAndRemoveAttributeValue(attributes, NUM);\r
+ String taxonStr = getCData(state, reader, parentEvent, false).trim();\r
+ if (taxonStr.endsWith(".")){\r
+ taxonStr = taxonStr.substring(0, taxonStr.length()-1).trim();\r
+ }\r
+ //TODO ?\r
+ taxonStr = makeTaxonKey(taxonStr, state.getCurrentTaxon());\r
+ UnmatchedLeadsKey unmatched = UnmatchedLeadsKey.NewInstance(num, taxonStr);\r
+ state.getUnmatchedLeads().addKey(unmatched, node);\r
+ return;\r
+ }\r
+ \r
+ \r
+ private String makeTaxonKey(String strGoto, Taxon taxon) {\r
+ String result = "";\r
+ if (strGoto == null){\r
+ return "";\r
+ }\r
+ \r
+ NonViralName<?> name = CdmBase.deproxy(taxon.getName(), NonViralName.class);\r
+ String strGenusName = name.getGenusOrUninomial();\r
+ \r
+ \r
+ strGoto = strGoto.replaceAll("\\([^\\(\\)]*\\)", ""); //replace all brackets\r
+ strGoto = strGoto.replaceAll("\\s+", " "); //replace multiple whitespaces by exactly one whitespace\r
+ \r
+ strGoto = strGoto.trim(); \r
+ String[] split = strGoto.split("\\s");\r
+ for (int i = 0; i<split.length; i++){\r
+ String single = split[i];\r
+ if (isGenusAbbrev(single, strGenusName)){\r
+ split[i] = strGenusName;\r
+ }\r
+ if (isInfraSpecificMarker(single)){\r
+ String strSpeciesEpi = name.getSpecificEpithet();\r
+ if (isBlank(result)){\r
+ result += strGenusName + " " + strSpeciesEpi;\r
+ }\r
+ }\r
+ result = (result + " " + split[i]).trim();\r
+ }\r
+ return result;\r
+ }\r
+ \r
+\r
+ private boolean isInfraSpecificMarker(String single) {\r
+ try {\r
+ if (Rank.getRankByAbbreviation(single).isInfraSpecific()){\r
+ return true;\r
+ }else{\r
+ return false;\r
+ }\r
+ } catch (UnknownCdmTypeException e) {\r
+ return false;\r
+ }\r
+ }\r
+ \r
+ private boolean isGenusAbbrev(String single, String strGenusName) {\r
+ if (! single.matches("[A-Z]\\.?")) {\r
+ return false;\r
+ }else if (single.length() == 0 || strGenusName == null || strGenusName.length() == 0){\r
+ return false; \r
+ }else{\r
+ return single.charAt(0) == strGenusName.charAt(0);\r
+ }\r
+ }\r
+ \r
+ \r
+//******************************** recognize nodes ***********/\r
+\r
+ public void makeKeyNodes(MarkupImportState state, XMLEvent event, String taxonTitle) {\r
+ Taxon taxon = state.getCurrentTaxon();\r
+ String num = state.getCurrentTaxonNum();\r
+ \r
+ String nameString = CdmBase.deproxy(taxon.getName(), NonViralName.class).getNameCache();\r
+// String nameString = taxonTitle;\r
+ \r
+ //try to find matching lead nodes \r
+ UnmatchedLeadsKey leadsKey = UnmatchedLeadsKey.NewInstance(num, nameString);\r
+ Set<PolytomousKeyNode> matchingNodes = handleMatchingNodes(state, taxon, leadsKey);\r
+ \r
+ if (num != null){//same without using the num\r
+ UnmatchedLeadsKey noNumLeadsKey = UnmatchedLeadsKey.NewInstance("", nameString);\r
+ Set<PolytomousKeyNode> noNumMatchingNodes = handleMatchingNodes(state, taxon, noNumLeadsKey);\r
+ if(noNumMatchingNodes.size() > 0){\r
+ String message ="Taxon matches additional key node when not considering <num> attribute in taxontitle. This may be correct but may also indicate an error.";\r
+ fireWarningEvent(message, event, 1);\r
+ }\r
+ }\r
+ //report missing match, if num exists\r
+ if (matchingNodes.isEmpty() && num != null){\r
+ String message = "Taxon has <num> attribute in taxontitle but no matching key nodes exist: %s, Key: %s";\r
+ message = String.format(message, num, leadsKey.toString());\r
+ fireWarningEvent(message, event, 1);\r
+ }\r
+ \r
+ }\r
+ \r
+ private Set<PolytomousKeyNode> handleMatchingNodes(MarkupImportState state, Taxon taxon, UnmatchedLeadsKey leadsKey) {\r
+ Set<PolytomousKeyNode> matchingNodes = state.getUnmatchedLeads().getNodes(leadsKey);\r
+ for (PolytomousKeyNode matchingNode : matchingNodes){\r
+ state.getUnmatchedLeads().removeNode(leadsKey, matchingNode);\r
+ matchingNode.setTaxon(taxon);\r
+ state.getPolytomousKeyNodesToSave().add(matchingNode);\r
+ }\r
+ return matchingNodes;\r
+ }\r
+\r
+}\r
BGBM BDI Projects / cdmlib.git / commitdiff