Examples with PolytomousKeyNode eu.etaxonomy.cdm.model.description.PolytomousKeyNode used on opensource projects

Example 1 with PolytomousKeyNode

use of eu.etaxonomy.cdm.model.description.PolytomousKeyNode in project cdmlib by cybertaxonomy.

the class MarkupKeyImport method handleKey.

public void handleKey(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent) throws XMLStreamException {
    // attributes
    Map<String, Attribute> attributes = getAttributes(parentEvent);
    String isSpotcharacters = getAndRemoveAttributeValue(attributes, IS_SPOTCHARACTERS);
    if (isNotBlank(isSpotcharacters)) {
        // TODO isSpotcharacters
        String message = "Attribute isSpotcharacters not yet implemented for <key>";
        fireWarningEvent(message, parentEvent, 4);
    }
    boolean onlyNumberedTaxaExist = checkAndRemoveAttributeValue(attributes, ONLY_NUMBERED_TAXA_EXIST, "true");
    state.setOnlyNumberedTaxaExist(onlyNumberedTaxaExist);
    PolytomousKey key = PolytomousKey.NewInstance();
    key.addPrimaryTaxonomicSource(state.getConfig().getSourceReference(), null);
    key.addTaxonomicScope(state.getCurrentTaxon());
    state.setCurrentKey(key);
    boolean isFirstCouplet = true;
    while (reader.hasNext()) {
        XMLEvent next = readNoWhitespace(reader);
        if (isMyEndingElement(next, parentEvent)) {
            save(key, state);
            // reset state
            state.setCurrentKey(null);
            state.setOnlyNumberedTaxaExist(false);
            return;
        } else if (isEndingElement(next, KEYNOTES)) {
            popUnimplemented(next.asEndElement());
        } else if (isStartingElement(next, KEY_TITLE)) {
            handleKeyTitle(state, reader, next);
        } else if (isStartingElement(next, KEYNOTES)) {
            // TODO
            handleNotYetImplementedElement(next);
        } else if (isStartingElement(next, COUPLET)) {
            PolytomousKeyNode node = null;
            if (isFirstCouplet) {
                node = key.getRoot();
                isFirstCouplet = false;
            }
            handleCouplet(state, reader, next, node);
        } else {
            handleUnexpectedElement(next);
        }
    }
    throw new IllegalStateException("<key> has no closing tag");
}

Example 2 with PolytomousKeyNode

use of eu.etaxonomy.cdm.model.description.PolytomousKeyNode in project cdmlib by cybertaxonomy.

the class MarkupKeyImport method handleQuestion.

private void handleQuestion(MarkupImportState state, XMLEventReader reader, XMLEvent parentEvent, List<PolytomousKeyNode> nodesList) throws XMLStreamException {
    // attributes
    Map<String, Attribute> attributes = getAttributes(parentEvent);
    // TODO needed only for data lineage
    String questionNum = getAndRemoveRequiredAttributeValue(parentEvent, attributes, NUM);
    PolytomousKeyNode myNode = PolytomousKeyNode.NewInstance();
    // to avoid NPE while computing num in PolytomousKeyNode in case this node is not matched correctly with a parent
    myNode.setKey(state.getCurrentKey());
    nodesList.add(myNode);
    int countToTaxon = 0;
    while (reader.hasNext()) {
        XMLEvent next = readNoWhitespace(reader);
        if (isMyEndingElement(next, parentEvent)) {
            return;
        } else if (isStartingElement(next, TEXT)) {
            String text = getCData(state, reader, next);
            KeyStatement statement = KeyStatement.NewInstance(getDefaultLanguage(state), text);
            myNode.setStatement(statement);
        } else if (isStartingElement(next, COUPLET)) {
            fireWarningEvent("Check if toCouplet in question is implemented correctly", next, 4);
            handleCouplet(state, reader, next, myNode);
        } else if (isStartingElement(next, TO_COUPLET)) {
            handleToCouplet(state, reader, next, myNode);
        } else if (isStartingElement(next, TO_TAXON)) {
            if (countToTaxon == 0) {
                handleToTaxon(state, reader, next, myNode);
            } else {
                if (countToTaxon == 1) {
                    // rearrange first taxon  //similar to PKNode.setOrAddTaxon(taxon) but the later can't be used here
                    // TODO this does not yet move the unmatched taxon keys to the new node
                    fireWarningEvent("Multiple toTaxon requires manual adjustment", next, 6);
                    Taxon firstTaxon = myNode.removeTaxon();
                    PolytomousKeyNode firstChildNode = PolytomousKeyNode.NewInstance();
                    firstChildNode.setTaxon(firstTaxon);
                    myNode.addChild(firstChildNode);
                }
                PolytomousKeyNode childNode = PolytomousKeyNode.NewInstance();
                myNode.addChild(childNode);
                handleToTaxon(state, reader, next, childNode);
            }
            countToTaxon++;
        } else if (isStartingElement(next, TO_KEY)) {
            // TODO
            handleNotYetImplementedElement(next);
        } else if (isStartingElement(next, KEYNOTES)) {
            handleAmbigousManually(state, reader, next.asStartElement());
        } else {
            handleUnexpectedElement(next);
        }
    }
    throw new IllegalStateException("<question> has no closing tag");
}

Example 3 with PolytomousKeyNode

use of eu.etaxonomy.cdm.model.description.PolytomousKeyNode in project cdmlib by cybertaxonomy.

the class MarkupKeyImport method handleMatchingNodes.

private Set<PolytomousKeyNode> handleMatchingNodes(MarkupImportState state, XMLEvent event, Taxon taxon, UnmatchedLeadsKey leadsKey) {
    Set<PolytomousKeyNode> matchingNodes = state.getUnmatchedLeads().getNodes(leadsKey);
    for (PolytomousKeyNode matchingNode : matchingNodes) {
        state.getUnmatchedLeads().removeNode(leadsKey, matchingNode);
        matchingNode.setTaxon(taxon);
        // just to be on the save side
        try {
            matchingNode.refreshNodeNumbering();
        } catch (Exception e) {
            String message = "An exception occurred when trying to referesh the node numbering: " + e.getMessage();
            fireWarningEvent(message, event, 6);
        }
        state.getPolytomousKeyNodesToSave().add(matchingNode);
    }
    return matchingNodes;
}

Example 4 with PolytomousKeyNode

use of eu.etaxonomy.cdm.model.description.PolytomousKeyNode in project cdmlib by cybertaxonomy.

the class FullCoverageDataGenerator method createDescriptions.

private void createDescriptions(List<CdmBase> cdmBases) {
    TermVocabulary<AnnotationType> voc = TermVocabulary.NewInstance(TermType.AnnotationType, AnnotationType.class, "my termVoc desc", "myTerm voc", "mtv", URI.create("http://www.abc.de"));
    handleIdentifiableEntity(voc);
    cdmBases.add(voc);
    Representation rep = voc.getRepresentations().iterator().next();
    handleAnnotatableEntity(rep);
    // Representation engRep = Language.ENGLISH().getRepresentations().iterator().next();
    // handleAnnotatableEntity(engRep);
    // cdmBases.add(engRep);  //needed?
    // Categorical data
    State state = State.NewInstance("Test state", "state", "st.");
    state.addMedia(Media.NewInstance());
    cdmBases.add(state);
    CategoricalData categoricalData = CategoricalData.NewInstance(state, Feature.CONSERVATION());
    StateData stateData = categoricalData.getStateData().get(0);
    stateData.addModifier(DefinedTerm.SEX_FEMALE());
    handleAnnotatableEntity(categoricalData);
    State nextState = State.NewInstance();
    cdmBases.add(nextState);
    StateData stateData2 = StateData.NewInstance(nextState);
    stateData2.setCount(3);
    stateData2.putModifyingText(Language.ENGLISH(), "State2 modifying text");
    categoricalData.addStateData(stateData2);
    categoricalData.setOrderRelevant(true);
    // Quantitative data
    Feature leaveLength = Feature.NewInstance("Leave length description", "leave length", "l.l.");
    cdmBases.add(leaveLength);
    leaveLength.setSupportsQuantitativeData(true);
    QuantitativeData quantitativeData = QuantitativeData.NewInstance(leaveLength);
    MeasurementUnit measurementUnit = MeasurementUnit.NewInstance("Measurement Unit", "munit", null);
    cdmBases.add(measurementUnit);
    quantitativeData.setUnit(measurementUnit);
    quantitativeData.setUuid(UUID.fromString("920fce5e-4913-4a3f-89bf-1611f5081869"));
    StatisticalMeasurementValue statisticalMeasurementValue = quantitativeData.setAverage(new BigDecimal("22.9215"), null);
    handleAnnotatableEntity(quantitativeData);
    handleIdentifiableEntity(measurementUnit);
    DefinedTerm valueModifier = DefinedTerm.NewModifierInstance("about", "about", null);
    statisticalMeasurementValue.addModifier(valueModifier);
    cdmBases.add(valueModifier);
    // Feature
    TermVocabulary<DefinedTerm> recommendedModifierEnumeration = TermVocabulary.NewInstance(TermType.Modifier, DefinedTerm.class);
    leaveLength.addRecommendedModifierEnumeration(recommendedModifierEnumeration);
    cdmBases.add(recommendedModifierEnumeration);
    TermVocabulary<State> supportedCategoricalEnumeration = TermVocabulary.NewInstance(TermType.State, State.class);
    leaveLength.addSupportedCategoricalEnumeration(supportedCategoricalEnumeration);
    cdmBases.add(supportedCategoricalEnumeration);
    leaveLength.addRecommendedMeasurementUnit(measurementUnit);
    leaveLength.addRecommendedStatisticalMeasure(StatisticalMeasure.AVERAGE());
    // CommonTaxonName
    CommonTaxonName commonTaxonName = CommonTaxonName.NewInstance("common name", Language.ENGLISH(), Country.UNITEDSTATESOFAMERICA());
    handleAnnotatableEntity(commonTaxonName);
    // TextData
    TextData textData = TextData.NewInstance(Feature.DIAGNOSIS());
    Language eng = Language.ENGLISH();
    textData.putText(eng, "My text data");
    LanguageString languageString = textData.getLanguageText(eng);
    Taxon referencedTaxon = getTaxon();
    cdmBases.add(referencedTaxon);
    languageString.addIntextReference(IntextReference.NewInstance(referencedTaxon, languageString, 2, 5));
    textData.putModifyingText(eng, "nice diagnosis");
    handleAnnotatableEntity(textData);
    handleAnnotatableEntity(languageString);
    TextFormat format = TextFormat.NewInstance("format", "format", null);
    textData.setFormat(format);
    cdmBases.add(format);
    handleAnnotatableEntity(format);
    // IndividualsAssociation
    DerivedUnit specimen = DerivedUnit.NewInstance(SpecimenOrObservationType.PreservedSpecimen);
    IndividualsAssociation indAssoc = IndividualsAssociation.NewInstance(specimen);
    indAssoc.putDescription(Language.ENGLISH(), "description for individuals association");
    handleAnnotatableEntity(indAssoc);
    // TaxonInteraction
    TaxonInteraction taxonInteraction = TaxonInteraction.NewInstance(Feature.HOSTPLANT());
    taxonInteraction.putDescription(Language.ENGLISH(), "interaction description");
    handleAnnotatableEntity(taxonInteraction);
    // Distribution
    NamedArea inCountryArea = NamedArea.NewInstance("My area in a country", "my area", "ma");
    inCountryArea.addCountry(Country.TURKEYREPUBLICOF());
    cdmBases.add(inCountryArea);
    Distribution distribution = Distribution.NewInstance(inCountryArea, PresenceAbsenceTerm.CULTIVATED());
    handleAnnotatableEntity(distribution);
    // TemporalData
    Feature floweringSeason = Feature.FLOWERING_PERIOD();
    TemporalData temporalData = TemporalData.NewInstance(ExtendedTimePeriod.NewExtendedMonthInstance(5, 8, 4, 9));
    temporalData.setFeature(floweringSeason);
    temporalData.getPeriod().setFreeText("My temporal text");
    handleAnnotatableEntity(temporalData);
    temporalData.setUuid(UUID.fromString("9a1c91c0-fc58-4310-94cb-8c26115985d3"));
    Taxon taxon = getTaxon();
    TaxonDescription taxonDescription = TaxonDescription.NewInstance(taxon);
    taxonDescription.addElements(categoricalData, quantitativeData, textData, commonTaxonName, taxonInteraction, indAssoc, distribution, temporalData);
    DerivedUnit describedSpecimenOrObservation = DerivedUnit.NewInstance(SpecimenOrObservationType.DerivedUnit);
    taxonDescription.setDescribedSpecimenOrObservation(describedSpecimenOrObservation);
    taxonDescription.addScope(DefinedTerm.SEX_FEMALE());
    taxonDescription.addGeoScope(Country.GERMANY());
    handleIdentifiableEntity(taxonDescription);
    taxon.addAggregationSource(taxonDescription);
    cdmBases.add(taxon);
    // DescriptionElmenetBase  + source
    textData.addMedia(Media.NewInstance());
    textData.addModifier(DefinedTerm.SEX_HERMAPHRODITE());
    textData.putModifyingText(Language.ENGLISH(), "no modification");
    textData.setTimeperiod(TimePeriodParser.parseString("1970-1980"));
    Reference ref = ReferenceFactory.newArticle();
    DescriptionElementSource source = textData.addSource(OriginalSourceType.Import, "22", "taxon description table", ref, "detail");
    source.setNameUsedInSource(TaxonNameFactory.NewBotanicalInstance(Rank.GENUS()));
    ExternalLink link = ExternalLink.NewInstance(ExternalLinkType.WebSite, URI.create("http://wwww.abd.de"), "Somehow useful link", 445);
    source.addLink(link);
    handleAnnotatableEntity(source);
    // as long as it still exists
    taxonDescription.addDescriptionSource(ref);
    // Specimen description
    SpecimenOrObservationBase<?> describedSpecimen = getSpecimen();
    SpecimenDescription specDesc = SpecimenDescription.NewInstance(specimen);
    cdmBases.add(describedSpecimen);
    handleAnnotatableEntity(specDesc);
    // Name description
    TaxonName name = TaxonNameFactory.NewBotanicalInstance(Rank.GENUS());
    TaxonNameDescription nameDesc = TaxonNameDescription.NewInstance(name);
    cdmBases.add(name);
    handleAnnotatableEntity(nameDesc);
    // Feature Tree
    TermTree<Feature> featureTree = TermTree.NewFeatureInstance();
    // featureTree
    TermNode<Feature> descriptionTermNode = featureTree.getRoot().addChild(Feature.DESCRIPTION());
    TermNode<Feature> leaveLengthNode = descriptionTermNode.addChild(leaveLength);
    handleIdentifiableEntity(featureTree);
    State inapplicableState = State.NewInstance("inapplicableState", "inapplicableState", null);
    State applicableState = State.NewInstance("only applicable state", "only applicable state", null);
    cdmBases.add(applicableState);
    cdmBases.add(inapplicableState);
    // this is semantically not correct, should be a parent feature
    leaveLengthNode.addInapplicableState(leaveLength, inapplicableState);
    leaveLengthNode.addApplicableState(leaveLength, applicableState);
    cdmBases.add(featureTree);
    cdmBases.add(leaveLengthNode);
    // DescriptiveDataSet
    DescriptiveDataSet descriptiveDataSet = DescriptiveDataSet.NewInstance();
    descriptiveDataSet.addDescription(taxonDescription);
    descriptiveDataSet.setLabel("My Descriptive Dataset");
    descriptiveDataSet.getDescriptiveSystem();
    handleAnnotatableEntity(descriptiveDataSet);
    descriptiveDataSet.addGeoFilterArea(Country.GERMANY());
    Classification classification = Classification.NewInstance("DescriptiveDataSet subtree classification");
    Taxon subTreeTaxon = getTaxon();
    TaxonNode subtree = classification.addChildTaxon(subTreeTaxon, null, null);
    descriptiveDataSet.addTaxonSubtree(subtree);
    cdmBases.add(classification);
    cdmBases.add(subtree);
    // polytomous keys
    Taxon coveredTaxon = Taxon.NewInstance(name, null);
    PolytomousKey key = PolytomousKey.NewTitledInstance("My Polykey");
    handleIdentificationKey(key, taxon, coveredTaxon);
    key.setStartNumber(10);
    PolytomousKeyNode firstChildNode = PolytomousKeyNode.NewInstance("Green", "What is the leave length?", coveredTaxon, leaveLength);
    key.getRoot().addChild(firstChildNode);
    PolytomousKeyNode secondChildNode = PolytomousKeyNode.NewInstance("234");
    firstChildNode.addChild(secondChildNode);
    PolytomousKey subkey = PolytomousKey.NewTitledInstance("Sub-key");
    firstChildNode.setSubkey(subkey);
    PolytomousKeyNode subKeyNode = PolytomousKeyNode.NewInstance("sub key couplet");
    subkey.getRoot().addChild(subKeyNode);
    secondChildNode.setOtherNode(subKeyNode);
    secondChildNode.putModifyingText(Language.GERMAN(), "manchmal");
    cdmBases.add(key);
    cdmBases.add(subkey);
    MediaKey mediaKey = MediaKey.NewInstance();
    mediaKey.addKeyRepresentation(Representation.NewInstance("Media Key Representation", "media key", null, Language.ENGLISH()));
    handleIdentificationKey(mediaKey, taxon, coveredTaxon);
    MultiAccessKey multiAccessKey = MultiAccessKey.NewInstance();
    handleIdentificationKey(multiAccessKey, taxon, coveredTaxon);
    cdmBases.add(mediaKey);
    cdmBases.add(multiAccessKey);
}

Example 5 with PolytomousKeyNode

use of eu.etaxonomy.cdm.model.description.PolytomousKeyNode in project cdmlib by cybertaxonomy.

the class PolytomousKeyNodeServiceTest method testDelete.

@Test
public final // @DataSet(value="CommonServiceImplTest.xml")
void testDelete() {
    PolytomousKey key = PolytomousKey.NewTitledInstance("TestPolytomousKey");
    UUID uuidKey = keyService.save(key).getUuid();
    PolytomousKeyNode node = PolytomousKeyNode.NewInstance("Test statement");
    key.setRoot(node);
    key.setStartNumber(0);
    PolytomousKeyNode child = PolytomousKeyNode.NewInstance("Test statement Nr 2");
    // child.setKey(key);
    node.addChild(child, 0);
    UUID uuidNode = service.save(node).getUuid();
    PolytomousKeyNode child1 = PolytomousKeyNode.NewInstance("Test statement Nr 3");
    // child.setKey(key);
    child.addChild(child1, 0);
    UUID uuidChild = service.save(child).getUuid();
    PolytomousKeyNode child2 = PolytomousKeyNode.NewInstance("Test statement Nr 4");
    // child.setKey(key);
    child1.addChild(child2, 0);
    UUID uuidChild1 = service.save(child1).getUuid();
    node = service.load(uuidChild1);
    UUID uuidChild2 = node.getChildAt(0).getUuid();
    assertNotNull(node);
    service.delete(uuidChild1, false);
    node = service.load(uuidChild1);
    assertNull(node);
    node = service.load(uuidChild2);
    assertNotNull(node);
    node = service.load(uuidChild);
    assertNotNull(node);
    service.delete(uuidChild, true);
    node = service.load(uuidChild);
    assertNull(node);
    node = service.load(uuidChild2);
    assertNull(node);
}