public abstract class MarkupImportBase
extends java.lang.Object
Modifier and Type | Class and Description |
---|---|
protected class |
MarkupImportBase.LabeledReference |
protected class |
MarkupImportBase.StringReferences
container class more or less representing a list of labeled references
|
protected class |
MarkupImportBase.SubheadingResult |
Modifier and Type | Field and Description |
---|---|
protected static java.lang.String |
ACCEPTED |
protected static java.lang.String |
ACCEPTED_NAME |
protected static java.lang.String |
ADDENDA |
protected static java.lang.String |
ALTERNATEPUBTITLE |
protected static java.lang.String |
ALTITUDE |
protected static java.lang.String |
ANNOTATION |
protected static java.lang.String |
APPENDIX |
protected static java.lang.String |
AUTHOR |
protected static java.lang.String |
BIBLIOGRAPHY |
protected static java.lang.String |
BIOGRAPHIES |
protected static java.lang.String |
BOLD |
protected static java.lang.String |
BR |
protected static java.lang.String |
CHAR |
protected static java.lang.String |
CITATION |
protected static java.lang.String |
CLASS |
protected static java.lang.String |
COORDINATES |
protected static java.lang.String |
COUPLET |
protected static boolean |
CREATE_NEW |
protected static java.lang.String |
DATES |
protected static java.lang.String |
DEDICATION |
protected static java.lang.String |
DEFAULT_MEDIA_URL |
protected static java.lang.String |
DETAILS |
protected static java.lang.String |
DISTRIBUTION_LIST |
protected static java.lang.String |
DISTRIBUTION_LOCALITY |
protected MarkupDocumentImport |
docImport |
protected static java.lang.String |
DOUBTFUL |
protected static java.lang.String |
EDITION |
protected static java.lang.String |
EDITORS |
protected static java.lang.String |
EXISTS |
protected static java.lang.String |
FEATURE |
protected MarkupFeatureImport |
featureImport |
protected static java.lang.String |
FIGURE |
protected static java.lang.String |
FIGURE_LEGEND |
protected static java.lang.String |
FIGURE_PART |
protected static java.lang.String |
FIGURE_REF |
protected static java.lang.String |
FIGURE_TITLE |
protected static java.lang.String |
FOOTNOTE |
protected static java.lang.String |
FOOTNOTE_REF |
protected static java.lang.String |
FOOTNOTE_STRING |
protected static java.lang.String |
FREQUENCY |
protected static java.lang.String |
FULL_NAME |
protected static java.lang.String |
GATHERING |
protected static java.lang.String |
GATHERING_GROUP |
protected static java.lang.String |
GENUS_ABBREVIATION |
protected static java.lang.String |
HABITAT |
protected static java.lang.String |
HABITAT_LIST |
protected static java.lang.String |
HEADING |
protected static java.lang.String |
HOMONYM |
protected static java.lang.String |
HOMOTYPES |
protected static java.lang.String |
ID |
protected static boolean |
IMAGE_GALLERY |
protected static java.lang.String |
INFRANK |
protected static java.lang.String |
INFRAUT |
protected static java.lang.String |
INFRPARAUT |
protected static java.lang.String |
IS_FREETEXT |
protected static java.lang.String |
IS_SPOTCHARACTERS |
protected static java.lang.String |
ISSUE |
protected static java.lang.String |
ITALICS |
protected static java.lang.String |
KEY |
protected static java.lang.String |
KEY_TITLE |
protected static java.lang.String |
KEYNOTES |
protected static java.lang.String |
LIFE_CYCLE_PERIODS |
protected static java.lang.String |
LOCAL_LANGUAGE |
protected static java.lang.String |
LOCALITY |
protected static java.lang.String |
META_DATA |
protected static java.lang.String |
MODS |
protected static java.lang.String |
NAME |
protected static java.lang.String |
NAME_STATUS |
protected static java.lang.String |
NAME_TYPE |
protected static boolean |
NO_IMAGE_GALLERY |
protected static java.lang.String |
NOM |
protected static java.lang.String |
NOMENCLATURAL_NOTES |
protected static java.lang.String |
NOMENCLATURE |
protected static java.lang.String |
NOTES |
protected static java.lang.String |
NUM |
protected static java.lang.String |
ONLY_NUMBERED_TAXA_EXIST |
protected static java.lang.String |
PAGES |
protected static java.lang.String |
PARAUT |
protected static java.lang.String |
PUBFULLNAME |
protected static java.lang.String |
PUBLICATION |
protected static java.lang.String |
PUBLISHER |
protected static java.lang.String |
PUBLOCATION |
protected static java.lang.String |
PUBNAME |
protected static java.lang.String |
PUBTITLE |
protected static java.lang.String |
PUBTYPE |
protected static java.lang.String |
QUESTION |
protected static java.lang.String |
QUOTE |
protected static java.lang.String |
RANK |
protected static java.lang.String |
REF |
protected static java.lang.String |
REF_NUM |
protected static java.lang.String |
REF_PART |
protected static java.lang.String |
REFERENCE |
protected static java.lang.String |
REFERENCES |
protected static java.lang.String |
SERIALS_ABBREVIATIONS |
protected static java.lang.String |
SPECIMEN_TYPE |
protected static java.lang.String |
STATUS |
protected static java.lang.String |
STRING |
protected static java.lang.String |
SUB_CHAR |
protected static java.lang.String |
SUB_HEADING |
protected static java.lang.String |
SYNONYM |
protected static java.lang.String |
TAXON |
protected static java.lang.String |
TAXONTITLE |
protected static java.lang.String |
TAXONTYPE |
protected static java.lang.String |
TEXT |
protected static java.lang.String |
TEXT_SECTION |
protected static java.lang.String |
TO_COUPLET |
protected static java.lang.String |
TO_KEY |
protected static java.lang.String |
TO_TAXON |
protected static java.lang.String |
TRANSLATION |
protected static java.lang.String |
TREATMENT |
protected static java.lang.String |
TYPE |
protected static java.lang.String |
TYPE_STATUS |
protected static java.lang.String |
UNKNOWN |
protected static java.lang.String |
URL |
protected static java.lang.String |
USAGE |
protected static java.lang.String |
VERNACULAR_NAME |
protected static java.lang.String |
VERNACULAR_NAMES |
protected static java.lang.String |
VOLUME |
protected static java.lang.String |
WRITER |
protected static java.lang.String |
YEAR |
Constructor and Description |
---|
MarkupImportBase(MarkupDocumentImport docImport) |
Modifier and Type | Method and Description |
---|---|
protected void |
attachFigure(MarkupImportState state,
javax.xml.stream.events.XMLEvent next,
AnnotatableEntity entity,
Media figure) |
protected void |
attachFootnote(MarkupImportState state,
AnnotatableEntity entity,
FootnoteDataHolder footnote) |
protected boolean |
charIsSimpleType(java.lang.String text)
Text indicating that type information is following but no information about the type of the type
|
protected boolean |
checkAndRemoveAttributeValue(java.util.Map<java.lang.String,javax.xml.stream.events.Attribute> attributes,
java.lang.String attrName,
java.lang.String value)
Checks if the given attribute exists and has the given value.
|
protected void |
checkMandatoryElement(boolean exists,
javax.xml.stream.events.StartElement parentEvent,
java.lang.String attrName)
Fires an mandatory element is missing event if exists is
false . |
protected boolean |
checkMandatoryText(java.lang.String text,
javax.xml.stream.events.XMLEvent parentEvent)
Checks if a mandatory text is not empty or null.
|
protected void |
checkNoAttributes(java.util.Map<java.lang.String,javax.xml.stream.events.Attribute> attributes,
javax.xml.stream.events.XMLEvent event)
Throws an unexpected attributes event if the event has any attributes.
|
protected void |
checkNoAttributes(javax.xml.stream.events.XMLEvent event)
Throws an unexpected attributes event if the event has any attributes.
|
protected void |
checkNoAttributes(javax.xml.stream.events.XMLEvent event,
int stackDepth,
java.lang.String... exceptions)
Throws an unexpected attributes event if the event has any attributes except those mentioned in "exceptions".
|
protected TeamOrPersonBase<?> |
createAuthor(MarkupImportState state,
java.lang.String authorTitle) |
protected INonViralName |
createNameByCode(MarkupImportState state,
Rank rank)
Creates a
INonViralName object depending on the defined NomenclaturalCode
and the given parameters. |
protected void |
fillMissingEpithetsForTaxa(Taxon parentTaxon,
Taxon childTaxon) |
protected void |
fire(IIoEvent event) |
protected void |
fireNotYetImplementedAttribute(javax.xml.stream.Location location,
javax.xml.namespace.QName qName,
java.lang.String value,
int stackDepth) |
protected void |
fireNotYetImplementedCharacters(javax.xml.stream.Location location,
javax.xml.stream.events.Characters chars,
int stackDepth) |
protected void |
fireNotYetImplementedElement(javax.xml.stream.Location location,
javax.xml.namespace.QName qName,
int stackDepth) |
protected void |
fireSchemaConflictEventExpectedStartTag(java.lang.String elName,
javax.xml.stream.XMLEventReader reader) |
protected void |
fireUnexpectedAttributeValue(javax.xml.stream.events.XMLEvent parentEvent,
java.lang.String attrName,
java.lang.String attrValue) |
protected void |
fireUnexpectedEndElement(javax.xml.stream.Location location,
javax.xml.stream.events.EndElement endElement,
int stackDepth) |
protected void |
fireUnexpectedEvent(javax.xml.stream.events.XMLEvent xmlEvent,
int stackDepth) |
protected void |
fireUnexpectedStartElement(javax.xml.stream.Location location,
javax.xml.stream.events.StartElement startElement,
int stackDepth) |
protected void |
fireWarningEvent(java.lang.String message,
java.lang.String locationStr,
int severity) |
protected void |
fireWarningEvent(java.lang.String message,
java.lang.String locationStr,
java.lang.Integer severity,
java.lang.Integer depth) |
protected void |
fireWarningEvent(java.lang.String message,
javax.xml.stream.events.XMLEvent event,
java.lang.Integer severity) |
protected java.lang.String |
getAndRemoveAttributeValue(java.util.Map<java.lang.String,javax.xml.stream.events.Attribute> attributes,
java.lang.String attrName)
Returns the value of a given attribute name and removes the attribute from the attributes map.
|
protected java.lang.Boolean |
getAndRemoveBooleanAttributeValue(javax.xml.stream.events.XMLEvent event,
java.util.Map<java.lang.String,javax.xml.stream.events.Attribute> attributes,
java.lang.String attrName,
java.lang.Boolean defaultValue)
Returns the value of a boolean attribute with the given name and removes the attribute from the attributes map.
|
protected java.lang.String |
getAndRemoveMapKey(java.util.Map<java.lang.String,java.lang.String> map,
java.lang.String key) |
protected java.lang.String |
getAndRemoveRequiredAttributeValue(javax.xml.stream.events.XMLEvent xmlEvent,
java.util.Map<java.lang.String,javax.xml.stream.events.Attribute> attributes,
java.lang.String attrName)
Returns the value of a given attribute name and returns the attribute from the attributes map.
|
protected AnnotationType |
getAnnotationType(MarkupImportState state,
java.util.UUID uuid,
java.lang.String label,
java.lang.String text,
java.lang.String labelAbbrev,
TermVocabulary<AnnotationType> voc) |
protected java.util.Map<java.lang.String,javax.xml.stream.events.Attribute> |
getAttributes(javax.xml.stream.events.XMLEvent event)
Returns a map for all attributes of an start element
|
protected java.lang.String |
getCData(MarkupImportState state,
javax.xml.stream.XMLEventReader reader,
javax.xml.stream.events.XMLEvent next)
Reads character data.
|
protected java.lang.String |
getCData(MarkupImportState state,
javax.xml.stream.XMLEventReader reader,
javax.xml.stream.events.XMLEvent parent,
boolean checkAttributes)
Reads character data.
|
protected IClassificationService |
getClassificationService() |
protected java.lang.String |
getClassOnlyAttribute(javax.xml.stream.events.XMLEvent parentEvent)
Returns the REQUIRED "class" attribute for a given event and checks that it is the only attribute.
|
protected java.lang.String |
getClassOnlyAttribute(javax.xml.stream.events.XMLEvent parentEvent,
boolean required)
Returns the "class" attribute for a given event and checks that it is the only attribute.
|
protected Language |
getDefaultLanguage(MarkupImportState state)
Returns the default language defined in the state.
|
protected TaxonDescription |
getDefaultTaxonDescription(Taxon taxon,
boolean isImageGallery,
boolean createNewIfNotExists,
Reference source) |
protected ExtensionType |
getExtensionType(MarkupImportState state,
java.util.UUID uuid,
java.lang.String label,
java.lang.String text,
java.lang.String labelAbbrev) |
protected TaxonDescription |
getExtractedMarkupMarkedDescription(MarkupImportState state,
Taxon taxon,
Reference sourceReference) |
protected Feature |
getFeature(MarkupImportState state,
java.util.UUID uuid,
java.lang.String label,
java.lang.String text,
java.lang.String labelAbbrev,
TermVocabulary<Feature> voc) |
protected DefinedTerm |
getIdentifierType(MarkupImportState state,
java.util.UUID uuid,
java.lang.String label,
java.lang.String text,
java.lang.String labelAbbrev,
TermVocabulary<DefinedTerm> voc) |
protected Language |
getLanguage(MarkupImportState state,
java.util.UUID uuid,
java.lang.String label,
java.lang.String text,
java.lang.String labelAbbrev,
TermVocabulary<?> voc) |
protected TaxonDescription |
getMarkedTaxonDescription(Taxon taxon,
MarkerType markerType,
boolean isImageGallery,
boolean createNewIfNotExists,
Reference source,
java.lang.String title)
Returns the taxon description with marked as
true with the given marker type. |
protected MarkerType |
getMarkerType(MarkupImportState state,
java.util.UUID uuid,
java.lang.String label,
java.lang.String text,
java.lang.String labelAbbrev,
TermVocabulary<MarkerType> voc) |
protected NamedArea |
getNamedArea(MarkupImportState state,
java.util.UUID uuid,
java.lang.String label,
java.lang.String text,
java.lang.String labelAbbrev,
NamedAreaType areaType,
NamedAreaLevel level,
TermVocabulary voc,
CdmImportBase.TermMatchMode matchMode) |
protected NamedAreaLevel |
getNamedAreaLevel(MarkupImportState state,
java.util.UUID uuid,
java.lang.String label,
java.lang.String text,
java.lang.String labelAbbrev,
TermVocabulary<NamedAreaLevel> voc) |
protected java.lang.String |
getOnlyAttribute(javax.xml.stream.events.XMLEvent parentEvent,
java.lang.String attrName,
boolean required)
Returns the value for the only attribute for a given event and checks that it is the only attribute.
|
protected PresenceAbsenceTerm |
getPresenceAbsenceTerm(MarkupImportState state,
java.util.UUID uuid,
java.lang.String label,
java.lang.String text,
java.lang.String labelAbbrev,
boolean isAbsenceTerm,
TermVocabulary<PresenceAbsenceTerm> voc) |
protected TaxonDescription |
getTaxonDescription(Taxon taxon,
Reference ref,
boolean isImageGallery,
boolean createNewIfNotExists) |
protected ITermService |
getTermService() |
protected java.lang.String |
getXmlTag(javax.xml.stream.events.XMLEvent event) |
protected void |
handleAmbigousManually(MarkupImportState state,
javax.xml.stream.XMLEventReader reader,
javax.xml.stream.events.StartElement startElement) |
protected Media |
handleFigure(MarkupImportState state,
javax.xml.stream.XMLEventReader reader,
javax.xml.stream.events.XMLEvent parentEvent,
MarkupSpecimenImport specimenImport,
MarkupNomenclatureImport nomenclatureImport) |
protected FootnoteDataHolder |
handleFootnote(MarkupImportState state,
javax.xml.stream.XMLEventReader reader,
javax.xml.stream.events.XMLEvent parentEvent,
MarkupSpecimenImport specimenImport,
MarkupNomenclatureImport nomenclatureImport) |
protected void |
handleFullName(MarkupImportState state,
javax.xml.stream.XMLEventReader reader,
INonViralName name,
javax.xml.stream.events.XMLEvent event) |
protected void |
handleIgnoreElement(javax.xml.stream.events.XMLEvent event)
Fires an not yet implemented event and adds the element name to the unhandled elements stack.
|
protected Reference |
handleNonCitationSpecific(MarkupImportState state,
java.lang.String type,
java.lang.String authorStr,
java.lang.String titleStr,
java.lang.String titleCache,
java.lang.String volume,
java.lang.String issue,
java.lang.String edition,
java.lang.String editors,
java.lang.String pubName,
java.lang.String appendix,
java.lang.String pages,
javax.xml.stream.events.XMLEvent parentEvent)
Create reference for non nomenclatural references
|
protected void |
handleNotYetImplementedAttribute(java.util.Map<java.lang.String,javax.xml.stream.events.Attribute> attributes,
java.lang.String attrName,
javax.xml.stream.events.XMLEvent event)
Fires an not yet implemented event if the given attribute exists in attributes.
|
protected void |
handleNotYetImplementedAttributeValue(javax.xml.stream.events.XMLEvent xmlEvent,
java.lang.String attrName,
java.lang.String attrValue) |
protected void |
handleNotYetImplementedCharacters(javax.xml.stream.events.XMLEvent event)
Fires an not yet implemented event and adds the element name to the unhandled elements stack.
|
protected void |
handleNotYetImplementedElement(javax.xml.stream.events.XMLEvent event)
Fires an not yet implemented event and adds the element name to the unhandled elements stack.
|
protected java.lang.String |
handleRefPart(MarkupImportState state,
javax.xml.stream.XMLEventReader reader,
javax.xml.stream.events.XMLEvent parentEvent,
java.util.Map<java.lang.String,java.lang.String> refMap) |
protected java.lang.String |
handleSimpleAnnotation(MarkupImportState state,
javax.xml.stream.XMLEventReader reader,
javax.xml.stream.events.XMLEvent parentEvent)
For it returns a pure CData annotation string.
|
protected java.util.Map<java.lang.String,MarkupImportBase.SubheadingResult> |
handleString(MarkupImportState state,
javax.xml.stream.XMLEventReader reader,
javax.xml.stream.events.XMLEvent parentEvent,
Feature feature)
Handle < string > .
|
protected void |
handleUnexpectedAttributes(javax.xml.stream.Location location,
java.util.Map<java.lang.String,javax.xml.stream.events.Attribute> attributes,
java.lang.String... exceptions)
Fires an unhandled attributes event, if attributes exist in attributes map not covered by the exceptions.
|
protected void |
handleUnexpectedElement(javax.xml.stream.events.XMLEvent event)
Fires an unexpected element event if the unhandled element stack is empty.
|
protected void |
handleUnexpectedEndElement(javax.xml.stream.events.EndElement event) |
protected void |
handleUnexpectedEndElement(javax.xml.stream.events.EndElement event,
int stackDepth)
Fires an unexpected element event if the event is not the last on the stack.
|
protected void |
handleUnexpectedStartElement(javax.xml.stream.events.XMLEvent event)
Fires an unexpected element event if the unhandled elements stack is empty.
|
protected void |
handleUnexpectedStartElement(javax.xml.stream.events.XMLEvent event,
int stackDepth)
Fires an unexpected element event if the unhandled elements stack is empty.
|
protected WriterDataHolder |
handleWriter(MarkupImportState state,
javax.xml.stream.XMLEventReader reader,
javax.xml.stream.events.XMLEvent parentEvent) |
protected boolean |
isAbbreviation(java.lang.String str,
int allowedNumberOfCharacters,
boolean onlyFirstCapital)
Currently not used.
|
protected boolean |
isBlank(java.lang.String str) |
protected boolean |
isEndingElement(javax.xml.stream.events.XMLEvent event,
java.lang.String elName) |
protected boolean |
isFirstCapitalWord(java.lang.String word)
Checks if all words in the given string start with a capital letter but do not have any further capital letter.
|
protected boolean |
isGenusAbbrev(java.lang.String abbrev,
java.lang.String strGenusName)
Checks if
abbrev is the short form for the genus name (strGenusName). |
protected boolean |
isHtml(javax.xml.stream.events.XMLEvent event) |
protected boolean |
isMyEndingElement(javax.xml.stream.events.XMLEvent next,
javax.xml.stream.events.XMLEvent parentEvent)
Returns
true if the "next" event is the ending tag for the "parent" event. |
protected boolean |
isNotBlank(java.lang.String str) |
protected boolean |
isNotEmptyCollection(java.util.Collection<?> list) |
protected boolean |
isPunctuation(java.lang.String text)
True if text is single "." oder "," or ";" or ":"
|
protected boolean |
isStartingElement(javax.xml.stream.events.XMLEvent event,
java.lang.String elName) |
protected NamedArea |
makeArea(MarkupImportState state,
java.lang.String areaName,
NamedAreaLevel level) |
protected java.lang.String |
makeLocationStr(javax.xml.stream.Location location)
Creates a string from a location
|
protected NamedAreaLevel |
makeNamedAreaLevel(MarkupImportState state,
java.lang.String levelString,
javax.xml.stream.events.XMLEvent next) |
protected NomenclaturalCode |
makeNomenclaturalCode(MarkupImportState state)
Returns the
NomenclaturalCode for this import. |
protected Rank |
makeRank(MarkupImportState state,
java.lang.String value,
boolean byAbbrev) |
protected java.lang.String |
normalize(java.lang.String text)
Trims the text and removes turns all whitespaces into single empty space.
|
protected void |
popUnimplemented(javax.xml.stream.events.EndElement endElement) |
protected javax.xml.stream.events.XMLEvent |
readNoWhitespace(javax.xml.stream.XMLEventReader reader)
Read next event.
|
protected void |
registerFootnotes(MarkupImportState state,
AnnotatableEntity entity,
java.util.List<FootnoteDataHolder> footnotes) |
protected void |
registerGivenFootnote(MarkupImportState state,
FootnoteDataHolder footnote) |
protected void |
save(CdmBase cdmBase,
MarkupImportState state) |
protected <T extends CdmBase> |
save(java.util.Collection<T> collection,
MarkupImportState state) |
protected java.lang.String |
toFirstCapital(java.lang.String value)
Removes whitespaces at beginning and end and makes the first letter
a capital letter and all other letters small letters.
|
protected static final java.lang.String ALTITUDE
protected static final java.lang.String ANNOTATION
protected static final java.lang.String BOLD
protected static final java.lang.String BR
protected static final java.lang.String DOUBTFUL
protected static final java.lang.String CITATION
protected static final java.lang.String CLASS
protected static final java.lang.String COORDINATES
protected static final java.lang.String DATES
protected static final java.lang.String GATHERING
protected static final java.lang.String GATHERING_GROUP
protected static final java.lang.String GENUS_ABBREVIATION
protected static final java.lang.String FOOTNOTE
protected static final java.lang.String FOOTNOTE_REF
protected static final java.lang.String FULL_NAME
protected static final java.lang.String ITALICS
protected static final java.lang.String NUM
protected static final java.lang.String NOTES
protected static final java.lang.String PUBLICATION
protected static final java.lang.String SPECIMEN_TYPE
protected static final java.lang.String STATUS
protected static final java.lang.String SUB_HEADING
protected static final java.lang.String TYPE
protected static final java.lang.String TYPE_STATUS
protected static final java.lang.String UNKNOWN
protected static final boolean CREATE_NEW
protected static final boolean NO_IMAGE_GALLERY
protected static final boolean IMAGE_GALLERY
protected static final java.lang.String ADDENDA
protected static final java.lang.String BIBLIOGRAPHY
protected static final java.lang.String BIOGRAPHIES
protected static final java.lang.String CHAR
protected static final java.lang.String DEDICATION
protected static final java.lang.String DEFAULT_MEDIA_URL
protected static final java.lang.String DISTRIBUTION_LIST
protected static final java.lang.String DISTRIBUTION_LOCALITY
protected static final java.lang.String FEATURE
protected static final java.lang.String FIGURE
protected static final java.lang.String FIGURE_LEGEND
protected static final java.lang.String FIGURE_PART
protected static final java.lang.String FIGURE_REF
protected static final java.lang.String FIGURE_TITLE
protected static final java.lang.String FOOTNOTE_STRING
protected static final java.lang.String FREQUENCY
protected static final java.lang.String HEADING
protected static final java.lang.String HABITAT
protected static final java.lang.String HABITAT_LIST
protected static final java.lang.String IS_FREETEXT
protected static final java.lang.String ID
protected static final java.lang.String KEY
protected static final java.lang.String LIFE_CYCLE_PERIODS
protected static final java.lang.String META_DATA
protected static final java.lang.String MODS
protected static final java.lang.String NOMENCLATURE
protected static final java.lang.String QUOTE
protected static final java.lang.String RANK
protected static final java.lang.String REF
protected static final java.lang.String REF_NUM
protected static final java.lang.String REFERENCE
protected static final java.lang.String REFERENCES
protected static final java.lang.String SUB_CHAR
protected static final java.lang.String TAXON
protected static final java.lang.String TAXONTITLE
protected static final java.lang.String TAXONTYPE
protected static final java.lang.String TEXT_SECTION
protected static final java.lang.String TREATMENT
protected static final java.lang.String SERIALS_ABBREVIATIONS
protected static final java.lang.String STRING
protected static final java.lang.String URL
protected static final java.lang.String WRITER
protected static final java.lang.String LOCALITY
protected static final java.lang.String ACCEPTED
protected static final java.lang.String ACCEPTED_NAME
protected static final java.lang.String ALTERNATEPUBTITLE
protected static final java.lang.String APPENDIX
protected static final java.lang.String AUTHOR
protected static final java.lang.String DETAILS
protected static final java.lang.String EDITION
protected static final java.lang.String EDITORS
protected static final java.lang.String HOMONYM
protected static final java.lang.String HOMOTYPES
protected static final java.lang.String NOMENCLATURAL_NOTES
protected static final java.lang.String INFRANK
protected static final java.lang.String INFRAUT
protected static final java.lang.String INFRPARAUT
protected static final java.lang.String ISSUE
protected static final java.lang.String NAME_STATUS
protected static final java.lang.String NAME
protected static final java.lang.String NAME_TYPE
protected static final java.lang.String NOM
protected static final java.lang.String PAGES
protected static final java.lang.String PARAUT
protected static final java.lang.String PUBFULLNAME
protected static final java.lang.String PUBLOCATION
protected static final java.lang.String PUBLISHER
protected static final java.lang.String PUBNAME
protected static final java.lang.String PUBTITLE
protected static final java.lang.String PUBTYPE
protected static final java.lang.String REF_PART
protected static final java.lang.String SYNONYM
protected static final java.lang.String USAGE
protected static final java.lang.String VOLUME
protected static final java.lang.String YEAR
protected static final java.lang.String COUPLET
protected static final java.lang.String IS_SPOTCHARACTERS
protected static final java.lang.String ONLY_NUMBERED_TAXA_EXIST
protected static final java.lang.String EXISTS
protected static final java.lang.String KEYNOTES
protected static final java.lang.String KEY_TITLE
protected static final java.lang.String QUESTION
protected static final java.lang.String TEXT
protected static final java.lang.String TO_COUPLET
protected static final java.lang.String TO_KEY
protected static final java.lang.String TO_TAXON
protected static final java.lang.String VERNACULAR_NAMES
protected static final java.lang.String VERNACULAR_NAME
protected static final java.lang.String TRANSLATION
protected static final java.lang.String LOCAL_LANGUAGE
protected MarkupDocumentImport docImport
protected MarkupFeatureImport featureImport
public MarkupImportBase(MarkupDocumentImport docImport)
protected <T extends CdmBase> void save(java.util.Collection<T> collection, MarkupImportState state)
protected void save(CdmBase cdmBase, MarkupImportState state)
protected ITermService getTermService()
protected IClassificationService getClassificationService()
protected java.util.Map<java.lang.String,javax.xml.stream.events.Attribute> getAttributes(javax.xml.stream.events.XMLEvent event)
event
- protected void checkNoAttributes(java.util.Map<java.lang.String,javax.xml.stream.events.Attribute> attributes, javax.xml.stream.events.XMLEvent event)
event
- protected void checkNoAttributes(javax.xml.stream.events.XMLEvent event)
event
- protected void checkNoAttributes(javax.xml.stream.events.XMLEvent event, int stackDepth, java.lang.String... exceptions)
event
- exceptions
- protected boolean checkAndRemoveAttributeValue(java.util.Map<java.lang.String,javax.xml.stream.events.Attribute> attributes, java.lang.String attrName, java.lang.String value)
attributes
- attrName
- value
- true
if attribute has given value, false
otherwiseprotected java.lang.String getAndRemoveAttributeValue(java.util.Map<java.lang.String,javax.xml.stream.events.Attribute> attributes, java.lang.String attrName)
null
if attribute does not exist.attributes
- the list of all attributesattrName
- the requested attribute nameprotected java.lang.Boolean getAndRemoveBooleanAttributeValue(javax.xml.stream.events.XMLEvent event, java.util.Map<java.lang.String,javax.xml.stream.events.Attribute> attributes, java.lang.String attrName, java.lang.Boolean defaultValue)
defaultValue
if the attribute does not exist. ALso returns defaultValue
and throws a warning if the
attribute has no boolean value (true, false).attributes
- theattrName
- the name of the attributedefaultValue
- the default value to return if attribute does not exist or can not be definedprotected java.lang.String getAndRemoveRequiredAttributeValue(javax.xml.stream.events.XMLEvent xmlEvent, java.util.Map<java.lang.String,javax.xml.stream.events.Attribute> attributes, java.lang.String attrName)
xmlEvent
- attributes
- attrName
- protected void handleNotYetImplementedAttribute(java.util.Map<java.lang.String,javax.xml.stream.events.Attribute> attributes, java.lang.String attrName, javax.xml.stream.events.XMLEvent event)
attributes
- attrName
- event
- protected void handleUnexpectedAttributes(javax.xml.stream.Location location, java.util.Map<java.lang.String,javax.xml.stream.events.Attribute> attributes, java.lang.String... exceptions)
location
- attributes
- exceptions
- protected void fireUnexpectedAttributeValue(javax.xml.stream.events.XMLEvent parentEvent, java.lang.String attrName, java.lang.String attrValue)
protected void handleNotYetImplementedAttributeValue(javax.xml.stream.events.XMLEvent xmlEvent, java.lang.String attrName, java.lang.String attrValue)
protected void fireNotYetImplementedAttribute(javax.xml.stream.Location location, javax.xml.namespace.QName qName, java.lang.String value, int stackDepth)
protected void fireUnexpectedEvent(javax.xml.stream.events.XMLEvent xmlEvent, int stackDepth)
protected void fireUnexpectedStartElement(javax.xml.stream.Location location, javax.xml.stream.events.StartElement startElement, int stackDepth)
protected void fireUnexpectedEndElement(javax.xml.stream.Location location, javax.xml.stream.events.EndElement endElement, int stackDepth)
protected void fireNotYetImplementedElement(javax.xml.stream.Location location, javax.xml.namespace.QName qName, int stackDepth)
protected void fireNotYetImplementedCharacters(javax.xml.stream.Location location, javax.xml.stream.events.Characters chars, int stackDepth)
protected java.lang.String makeLocationStr(javax.xml.stream.Location location)
location
- protected void handleUnexpectedStartElement(javax.xml.stream.events.XMLEvent event)
event
- protected void handleUnexpectedStartElement(javax.xml.stream.events.XMLEvent event, int stackDepth)
event
- protected void handleUnexpectedEndElement(javax.xml.stream.events.EndElement event)
protected void handleUnexpectedEndElement(javax.xml.stream.events.EndElement event, int stackDepth)
event
- protected void popUnimplemented(javax.xml.stream.events.EndElement endElement)
endElement
- protected void handleUnexpectedElement(javax.xml.stream.events.XMLEvent event)
event
- protected void handleNotYetImplementedCharacters(javax.xml.stream.events.XMLEvent event)
event
- protected void handleNotYetImplementedElement(javax.xml.stream.events.XMLEvent event)
event
- protected void handleIgnoreElement(javax.xml.stream.events.XMLEvent event)
event
- protected void handleAmbigousManually(MarkupImportState state, javax.xml.stream.XMLEventReader reader, javax.xml.stream.events.StartElement startElement)
protected boolean checkMandatoryText(java.lang.String text, javax.xml.stream.events.XMLEvent parentEvent)
null
.text
- parentEvent
- protected void checkMandatoryElement(boolean exists, javax.xml.stream.events.StartElement parentEvent, java.lang.String attrName)
false
.hasMandatory
- parentEvent
- string
- protected boolean isMyEndingElement(javax.xml.stream.events.XMLEvent next, javax.xml.stream.events.XMLEvent parentEvent) throws javax.xml.stream.XMLStreamException
true
if the "next" event is the ending tag for the "parent" event.next
- end element to test, must not be nullparentEvent
- start element to testjavax.xml.stream.XMLStreamException
protected java.lang.String normalize(java.lang.String text)
text
- protected java.lang.String toFirstCapital(java.lang.String value)
value
- protected boolean isAbbreviation(java.lang.String str, int allowedNumberOfCharacters, boolean onlyFirstCapital)
str
- allowedNumberOfCharacters
- onlyFirstCapital
- protected boolean isGenusAbbrev(java.lang.String abbrev, java.lang.String strGenusName)
abbrev
is the short form for the genus name (strGenusName).
Usually this is the case if abbrev
is the first letter (optional with ".")
of strGenusName. But in older floras it may also be the first 2 or 3 letters (optional with dot).
However, we allow only a maximum of 2 letters to be anambigous. In cases with 3 letters better
change the original markup data.single
- strGenusName
- protected boolean isFirstCapitalWord(java.lang.String word)
word
- the string to be checekd. Usually should be a single word.protected javax.xml.stream.events.XMLEvent readNoWhitespace(javax.xml.stream.XMLEventReader reader) throws javax.xml.stream.XMLStreamException
reader
- javax.xml.stream.XMLStreamException
protected java.lang.String getClassOnlyAttribute(javax.xml.stream.events.XMLEvent parentEvent)
parentEvent
- protected java.lang.String getClassOnlyAttribute(javax.xml.stream.events.XMLEvent parentEvent, boolean required)
parentEvent
- protected java.lang.String getOnlyAttribute(javax.xml.stream.events.XMLEvent parentEvent, java.lang.String attrName, boolean required)
parentEvent
- protected void fireWarningEvent(java.lang.String message, java.lang.String locationStr, java.lang.Integer severity, java.lang.Integer depth)
protected void fireWarningEvent(java.lang.String message, javax.xml.stream.events.XMLEvent event, java.lang.Integer severity)
protected void fireSchemaConflictEventExpectedStartTag(java.lang.String elName, javax.xml.stream.XMLEventReader reader) throws javax.xml.stream.XMLStreamException
javax.xml.stream.XMLStreamException
protected void fireWarningEvent(java.lang.String message, java.lang.String locationStr, int severity)
protected void fire(IIoEvent event)
protected boolean isNotBlank(java.lang.String str)
protected boolean isBlank(java.lang.String str)
protected TaxonDescription getTaxonDescription(Taxon taxon, Reference ref, boolean isImageGallery, boolean createNewIfNotExists)
protected TaxonDescription getDefaultTaxonDescription(Taxon taxon, boolean isImageGallery, boolean createNewIfNotExists, Reference source)
protected TaxonDescription getMarkedTaxonDescription(Taxon taxon, MarkerType markerType, boolean isImageGallery, boolean createNewIfNotExists, Reference source, java.lang.String title)
true
with the given marker type.
If createNewIfNotExists a new description is created if it does not yet exist.
For the new description the source and the title are set if not null
.taxon
- markerType
- isImageGallery
- createNewIfNotExists
- source
- title
- protected Language getDefaultLanguage(MarkupImportState state)
state
- protected boolean isEndingElement(javax.xml.stream.events.XMLEvent event, java.lang.String elName) throws javax.xml.stream.XMLStreamException
javax.xml.stream.XMLStreamException
protected boolean isStartingElement(javax.xml.stream.events.XMLEvent event, java.lang.String elName) throws javax.xml.stream.XMLStreamException
javax.xml.stream.XMLStreamException
protected void fillMissingEpithetsForTaxa(Taxon parentTaxon, Taxon childTaxon)
protected Feature getFeature(MarkupImportState state, java.util.UUID uuid, java.lang.String label, java.lang.String text, java.lang.String labelAbbrev, TermVocabulary<Feature> voc)
protected PresenceAbsenceTerm getPresenceAbsenceTerm(MarkupImportState state, java.util.UUID uuid, java.lang.String label, java.lang.String text, java.lang.String labelAbbrev, boolean isAbsenceTerm, TermVocabulary<PresenceAbsenceTerm> voc)
protected ExtensionType getExtensionType(MarkupImportState state, java.util.UUID uuid, java.lang.String label, java.lang.String text, java.lang.String labelAbbrev)
protected DefinedTerm getIdentifierType(MarkupImportState state, java.util.UUID uuid, java.lang.String label, java.lang.String text, java.lang.String labelAbbrev, TermVocabulary<DefinedTerm> voc)
protected AnnotationType getAnnotationType(MarkupImportState state, java.util.UUID uuid, java.lang.String label, java.lang.String text, java.lang.String labelAbbrev, TermVocabulary<AnnotationType> voc)
protected MarkerType getMarkerType(MarkupImportState state, java.util.UUID uuid, java.lang.String label, java.lang.String text, java.lang.String labelAbbrev, TermVocabulary<MarkerType> voc)
protected NamedAreaLevel getNamedAreaLevel(MarkupImportState state, java.util.UUID uuid, java.lang.String label, java.lang.String text, java.lang.String labelAbbrev, TermVocabulary<NamedAreaLevel> voc)
protected NamedArea getNamedArea(MarkupImportState state, java.util.UUID uuid, java.lang.String label, java.lang.String text, java.lang.String labelAbbrev, NamedAreaType areaType, NamedAreaLevel level, TermVocabulary voc, CdmImportBase.TermMatchMode matchMode)
protected Language getLanguage(MarkupImportState state, java.util.UUID uuid, java.lang.String label, java.lang.String text, java.lang.String labelAbbrev, TermVocabulary<?> voc)
protected Rank makeRank(MarkupImportState state, java.lang.String value, boolean byAbbrev)
state
- classValue
- byAbbrev
- protected TeamOrPersonBase<?> createAuthor(MarkupImportState state, java.lang.String authorTitle)
protected java.lang.String getAndRemoveMapKey(java.util.Map<java.lang.String,java.lang.String> map, java.lang.String key)
protected INonViralName createNameByCode(MarkupImportState state, Rank rank)
INonViralName
object depending on the defined NomenclaturalCode
and the given parameters.state
- rank
- protected void handleFullName(MarkupImportState state, javax.xml.stream.XMLEventReader reader, INonViralName name, javax.xml.stream.events.XMLEvent event) throws javax.xml.stream.XMLStreamException
javax.xml.stream.XMLStreamException
protected NomenclaturalCode makeNomenclaturalCode(MarkupImportState state)
NomenclaturalCode
for this import. Default is NomenclaturalCode#ICBN
if
no code is defined.state
- protected NamedAreaLevel makeNamedAreaLevel(MarkupImportState state, java.lang.String levelString, javax.xml.stream.events.XMLEvent next)
state
- levelString
- next
- protected NamedArea makeArea(MarkupImportState state, java.lang.String areaName, NamedAreaLevel level)
state
- areaName
- level
- protected java.lang.String getCData(MarkupImportState state, javax.xml.stream.XMLEventReader reader, javax.xml.stream.events.XMLEvent next) throws javax.xml.stream.XMLStreamException
state
- reader
- next
- javax.xml.stream.XMLStreamException
getCData(MarkupImportState, XMLEventReader, XMLEvent, boolean)
protected java.lang.String getCData(MarkupImportState state, javax.xml.stream.XMLEventReader reader, javax.xml.stream.events.XMLEvent parent, boolean checkAttributes) throws javax.xml.stream.XMLStreamException
state
- reader
- next
- inlineMarkup
- map for inline markup, this is used for e.g. the locality markup within a subheading
The map will be filled by the markup element name as key. The value may be a String, a CdmBase or any other object.
If null any markup text will be neglected but a warning will be fired if they exist.removeInlineMarkupText
- if true the markedup text will be removed from the returned StringcheckAttributes
- javax.xml.stream.XMLStreamException
protected java.lang.String handleSimpleAnnotation(MarkupImportState state, javax.xml.stream.XMLEventReader reader, javax.xml.stream.events.XMLEvent parentEvent) throws javax.xml.stream.XMLStreamException
state
- reader
- parentEvent
- javax.xml.stream.XMLStreamException
protected boolean isPunctuation(java.lang.String text)
text
- protected boolean charIsSimpleType(java.lang.String text)
text
- protected java.lang.String getXmlTag(javax.xml.stream.events.XMLEvent event)
protected WriterDataHolder handleWriter(MarkupImportState state, javax.xml.stream.XMLEventReader reader, javax.xml.stream.events.XMLEvent parentEvent) throws javax.xml.stream.XMLStreamException
javax.xml.stream.XMLStreamException
protected void registerFootnotes(MarkupImportState state, AnnotatableEntity entity, java.util.List<FootnoteDataHolder> footnotes)
protected void attachFootnote(MarkupImportState state, AnnotatableEntity entity, FootnoteDataHolder footnote)
protected void attachFigure(MarkupImportState state, javax.xml.stream.events.XMLEvent next, AnnotatableEntity entity, Media figure)
protected void registerGivenFootnote(MarkupImportState state, FootnoteDataHolder footnote)
protected FootnoteDataHolder handleFootnote(MarkupImportState state, javax.xml.stream.XMLEventReader reader, javax.xml.stream.events.XMLEvent parentEvent, MarkupSpecimenImport specimenImport, MarkupNomenclatureImport nomenclatureImport) throws javax.xml.stream.XMLStreamException
javax.xml.stream.XMLStreamException
protected Media handleFigure(MarkupImportState state, javax.xml.stream.XMLEventReader reader, javax.xml.stream.events.XMLEvent parentEvent, MarkupSpecimenImport specimenImport, MarkupNomenclatureImport nomenclatureImport) throws javax.xml.stream.XMLStreamException
javax.xml.stream.XMLStreamException
protected boolean isHtml(javax.xml.stream.events.XMLEvent event)
protected java.util.Map<java.lang.String,MarkupImportBase.SubheadingResult> handleString(MarkupImportState state, javax.xml.stream.XMLEventReader reader, javax.xml.stream.events.XMLEvent parentEvent, Feature feature) throws javax.xml.stream.XMLStreamException
state
- reader
- parentEvent
- feature
- only needed for distributionLocalitiesjavax.xml.stream.XMLStreamException
protected Reference handleNonCitationSpecific(MarkupImportState state, java.lang.String type, java.lang.String authorStr, java.lang.String titleStr, java.lang.String titleCache, java.lang.String volume, java.lang.String issue, java.lang.String edition, java.lang.String editors, java.lang.String pubName, java.lang.String appendix, java.lang.String pages, javax.xml.stream.events.XMLEvent parentEvent)
protected java.lang.String handleRefPart(MarkupImportState state, javax.xml.stream.XMLEventReader reader, javax.xml.stream.events.XMLEvent parentEvent, java.util.Map<java.lang.String,java.lang.String> refMap) throws javax.xml.stream.XMLStreamException
javax.xml.stream.XMLStreamException
protected boolean isNotEmptyCollection(java.util.Collection<?> list)
references2
- protected TaxonDescription getExtractedMarkupMarkedDescription(MarkupImportState state, Taxon taxon, Reference sourceReference)
state
- taxon
- ref
- Copyright © 2007-2020 EDIT. All Rights Reserved.