Examples with VocabularyConcept org.gbif.ipt.model.VocabularyConcept used on opensource projects

Example 1 with VocabularyConcept

use of org.gbif.ipt.model.VocabularyConcept in project ipt by gbif.

the class Eml2Rtf method addNaturalCollections.

/**
 * Add natural collections section.
 *
 * @param doc Document
 * @param eml EML
 * @throws DocumentException if problem occurs during add
 */
private void addNaturalCollections(Document doc, Eml eml) throws DocumentException {
    if (!eml.getCollections().isEmpty() || !eml.getTemporalCoverages().isEmpty() || !eml.getSpecimenPreservationMethods().isEmpty() || !eml.getJgtiCuratorialUnits().isEmpty()) {
        Paragraph p = new Paragraph();
        p.setAlignment(Element.ALIGN_JUSTIFIED);
        p.setFont(font);
        for (org.gbif.metadata.eml.Collection collection : eml.getCollections()) {
            if (exists(collection.getParentCollectionId()) || exists(collection.getCollectionName()) || exists(collection.getCollectionId())) {
                p.add(new Phrase(getText("rtf.collections.description"), fontTitle));
                p.add(Chunk.NEWLINE);
                p.add(Chunk.NEWLINE);
                if (exists(collection.getParentCollectionId())) {
                    p.add(new Phrase(getText("rtf.collections.parent") + ": ", fontTitle));
                    p.add(collection.getParentCollectionId());
                    p.add(Chunk.NEWLINE);
                }
                if (exists(collection.getCollectionName())) {
                    p.add(new Phrase(getText("rtf.collections.name") + ": ", fontTitle));
                    p.add(collection.getCollectionName());
                    p.add(Chunk.NEWLINE);
                }
                if (exists(collection.getCollectionId())) {
                    p.add(new Phrase(getText("rtf.collections.identifier") + ": ", fontTitle));
                    p.add(collection.getCollectionId());
                    p.add(Chunk.NEWLINE);
                }
            }
        }
        for (TemporalCoverage coverage : eml.getTemporalCoverages()) {
            if (coverage.getType() == TemporalCoverageType.FORMATION_PERIOD) {
                p.add(new Phrase(getText("rtf.collections.formatPeriod") + ": ", fontTitle));
                p.add(coverage.getFormationPeriod());
                p.add(Chunk.NEWLINE);
            }
        }
        for (TemporalCoverage coverage : eml.getTemporalCoverages()) {
            if (coverage.getType() == TemporalCoverageType.LIVING_TIME_PERIOD) {
                p.add(new Phrase(getText("rtf.collections.livingPeriod") + ": ", fontTitle));
                p.add(coverage.getLivingTimePeriod());
                p.add(Chunk.NEWLINE);
            }
        }
        for (String preservationMethod : eml.getSpecimenPreservationMethods()) {
            if (exists(preservationMethod)) {
                p.add(new Phrase(getText("rtf.collections.specimen") + ": ", fontTitle));
                VocabularyConcept vocabConcept = vocabManager.get(Constants.VOCAB_URI_PRESERVATION_METHOD).findConcept(preservationMethod);
                // write preservation method in default language as matched from vocabulary or original value
                if (exists(vocabConcept)) {
                    p.add(vocabConcept.getPreferredTerm(DEFAULT_LANGUAGE).getTitle());
                } else {
                    p.add(preservationMethod.replace("\r\n", "\n"));
                }
                p.add(Chunk.NEWLINE);
            }
        }
        for (JGTICuratorialUnit unit : eml.getJgtiCuratorialUnits()) {
            p.add(new Phrase(getText("rtf.collections.curatorial") + ": ", fontTitle));
            if (unit.getType() == JGTICuratorialUnitType.COUNT_RANGE) {
                p.add("Between " + unit.getRangeStart() + " and " + unit.getRangeEnd());
            }
            if (unit.getType() == JGTICuratorialUnitType.COUNT_WITH_UNCERTAINTY) {
                p.add(unit.getRangeMean() + " " + getText("rtf.collections.curatorial.text") + " " + unit.getUncertaintyMeasure());
            }
            p.add(" (" + unit.getUnitType() + ")");
            p.add(Chunk.NEWLINE);
        }
        if (!p.isEmpty()) {
            doc.add(p);
        }
        p.clear();
    }
}

Example 2 with VocabularyConcept

use of org.gbif.ipt.model.VocabularyConcept in project ipt by gbif.

the class VocabularyFactoryTest method testBuild.

@Test
public void testBuild() {
    try {
        Vocabulary tv = getFactory().build(VocabularyFactoryTest.class.getResourceAsStream("/thesauri/type-vocabulary.xml"));
        assertEquals("Dublin Core Type Vocabulary", tv.getTitle());
        assertEquals("http://dublincore.org/documents/dcmi-type-vocabulary/", tv.getUriString());
        assertEquals("The DCMI Type Vocabulary provides a general, cross-domain list of approved terms that may be used as values for the Resource Type element to identify the genre of a resource. The terms documented here are also included in the more comprehensive document \"DCMI Metadata Terms\" at http://dublincore.org/documents/dcmi-terms/.", tv.getDescription());
        assertEquals("http://dublincore.org/documents/dcmi-type-vocabulary/", tv.getLink().toString());
        assertNotNull(tv.getConcepts());
        assertEquals(12, tv.getConcepts().size());
        VocabularyConcept tc = tv.getConcepts().get(0);
        assertEquals("Collection", tc.getIdentifier());
        assertNull(tc.getLink());
        assertEquals("http://purl.org/dc/dcmitype/Collection", tc.getUri());
        assertEquals(tv, tc.getVocabulary());
        assertEquals("Collection", tc.getPreferredTerm("en").getTitle());
        assertEquals("Sammlung", tc.getPreferredTerm("de").getTitle());
        assertNotNull(tc.getTerms());
        assertNotNull(tc.getPreferredTerms());
        assertEquals(2, tc.getPreferredTerms().size());
        assertEquals(0, tc.getAlternativeTerms().size());
        assertEquals(2, tc.getTerms().size());
        // previously there was an assertion that caused IPT to fail when built with Java 5
        // Java 5 - term that comes off iterator 1st is de
        // Java 6 - term that comes off iterator 1st is en
        VocabularyTerm tt = tc.getTerms().iterator().next();
        if (tt.getLang().equals("en")) {
            assertEquals("Collection", tt.getTitle());
        } else {
            assertEquals("de", tt.getLang());
            assertEquals("Sammlung", tt.getTitle());
        }
    } catch (Exception e) {
        e.printStackTrace();
        fail(e.getMessage());
    }
}

Example 3 with VocabularyConcept

use of org.gbif.ipt.model.VocabularyConcept in project ipt by gbif.

the class TranslationAction method automap.

/**
 * Automatically map source values to the terms in a vocabulary. A match occurs when the source value matches
 * against one of the vocabulary's term's name, preferred name, or alternate name.
 *
 * @return SUCCESS result, staying on translation page
 */
public String automap() {
    if (property == null || property.getVocabulary() == null) {
        addActionError(getText("manage.translation.cantfind.vocabulary"));
    } else {
        Vocabulary vocab = property.getVocabulary();
        int count = 0;
        for (Entry<String, String> sourceValueEntry : getSourceValuesMap().entrySet()) {
            // only if not yet mapped
            if (!getTmap().containsValue(sourceValueEntry.getValue())) {
                VocabularyConcept vc = vocab.findConcept(sourceValueEntry.getValue());
                if (vc != null) {
                    getTmap().put(sourceValueEntry.getKey(), vc.getIdentifier());
                    count++;
                }
            }
        }
        addActionMessage(getText("manage.translation.mapped.terms", new String[] { String.valueOf(count) }));
    }
    return SUCCESS;
}

Example 4 with VocabularyConcept

use of org.gbif.ipt.model.VocabularyConcept in project ipt by gbif.

the class VocabularyFactoryTest method testBuildVersionedVocabulary.

/**
 * Test building Quantity Type vocabulary that has issued date (used to version the vocabulary).
 */
@Test
public void testBuildVersionedVocabulary() {
    try {
        Vocabulary v = getFactory().build(VocabularyFactoryTest.class.getResourceAsStream("/thesauri/quantity_type-2015-05-04.xml"));
        assertEquals("Quantity Type Vocabulary", v.getTitle());
        assertEquals("http://rs.gbif.org/vocabulary/gbif/quantityType", v.getUriString());
        assertNull(v.getLink());
        assertEquals("The quantityType Vocabulary is a recommended set of values to use for the Darwin Core quantityType property.", v.getDescription());
        // issued date parsed correctly?
        DateFormat df = new SimpleDateFormat("yyyy-MM-dd");
        String issued = "2015-05-04";
        Date result = df.parse(issued);
        assertEquals(result.toString(), v.getIssued().toString());
        assertNotNull(v.getConcepts());
        assertEquals(12, v.getConcepts().size());
        VocabularyConcept tc = v.getConcepts().get(0);
        assertEquals("percentageOfSpecies", tc.getIdentifier());
        assertNull(tc.getLink());
        assertEquals("http://rs.gbif.org/vocabulary/gbif/quantityType/percentageOfSpecies", tc.getUri());
        assertEquals(v, tc.getVocabulary());
        assertEquals("percentage of species", tc.getPreferredTerm("en").getTitle());
        assertNotNull(tc.getTerms());
        assertEquals(1, tc.getTerms().size());
        assertNotNull(tc.getPreferredTerms());
        assertEquals(1, tc.getPreferredTerms().size());
        assertEquals(0, tc.getAlternativeTerms().size());
    } catch (Exception e) {
        e.printStackTrace();
        fail(e.getMessage());
    }
}

Example 5 with VocabularyConcept

use of org.gbif.ipt.model.VocabularyConcept in project ipt by gbif.

the class TranslationActionTest method setup.

@BeforeEach
public void setup() throws Exception {
    // mock needed managers
    SimpleTextProvider mockTextProvider = mock(SimpleTextProvider.class);
    LocaleProviderFactory localeProviderFactory = new DefaultLocaleProviderFactory();
    AppConfig mockCfg = mock(AppConfig.class);
    ResourceManager mockResourceManager = mock(ResourceManager.class);
    SourceManager mockSourceManager = mock(SourceManager.class);
    VocabulariesManager mockVocabManager = mock(VocabulariesManager.class);
    TranslationAction.Translation translation = new TranslationAction.Translation();
    RegistrationManager mockRegistrationManager = mock(RegistrationManager.class);
    Container container = mock(Container.class);
    // mock getting list of values back for BasisOfRecord field/column in source
    Set<String> values = new LinkedHashSet<>();
    values.add("spe");
    values.add("obs");
    values.add("fos");
    when(mockSourceManager.inspectColumn(any(SourceBase.class), anyInt(), anyInt(), anyInt())).thenReturn(values);
    // mock getI18nVocab - only called in prepare()
    Map<String, String> mockVocab = new HashMap<>();
    mockVocab.put("NomenclaturalChecklist", "Nomenclatural Checklist");
    mockVocab.put("MachineObservation", "Machine Observation");
    when(mockVocabManager.getI18nVocab(anyString(), anyString(), anyBoolean())).thenReturn(mockVocab);
    // initialize new Resource
    Resource resource = new Resource();
    String resourceShortName = "TestResource";
    resource.setShortname(resourceShortName);
    // initialize new ExtensionMapping
    ExtensionMapping mapping = new ExtensionMapping();
    // add source to mapping
    mapping.setSource(new TextFileSource());
    ExtensionFactory factory = ExtensionFactoryTest.getFactory();
    Extension e = factory.build(ExtensionFactoryTest.class.getResourceAsStream("/extensions/dwc_occurrence.xml"));
    // ensure rowType for Extension is set
    if (e.getRowType() == null) {
        e.setRowType(Constants.DWC_ROWTYPE_TAXON);
    }
    // add extension to ExtensionMapping
    mapping.setExtension(e);
    // create map of source value
    TreeMap<String, String> sourceValues = new TreeMap<>();
    sourceValues.put("k1", "spe");
    sourceValues.put("k2", "obs");
    // create map of translation values
    TreeMap<String, String> translatedValues = new TreeMap<>();
    translatedValues.put("k1", "Preserved Specimen");
    translatedValues.put("k2", "observation");
    // create map of translations that get persisted
    Map<String, String> persistedTranslations = new HashMap<>();
    persistedTranslations.put("spe", "Preserved Specimen");
    persistedTranslations.put("obs", "observation");
    // initialize PropertyMapping for BasisOfRecord term
    PropertyMapping field = new PropertyMapping();
    // set ConceptTerm
    field.setTerm(DwcTerm.basisOfRecord);
    // set index
    field.setIndex(1);
    // add translations to field
    field.setTranslation(persistedTranslations);
    // add set of PropertyMapping, including field, to ExtensionMapping
    Set<PropertyMapping> fields = new TreeSet<>();
    fields.add(field);
    mapping.setFields(fields);
    // add ExtensionMapping to resource, with mapping ID 0
    List<ExtensionMapping> mappings = new LinkedList<>();
    mappings.add(mapping);
    resource.setMappings(mappings);
    // mock resourceManager.get - called only in ManagerBaseAction.prepare()
    when(mockResourceManager.get(anyString())).thenReturn(resource);
    // mock a locale provider
    when(container.getInstance(LocaleProviderFactory.class)).thenReturn(localeProviderFactory);
    // create mock Action
    action = new TranslationAction(mockTextProvider, mockCfg, mockRegistrationManager, mockResourceManager, mockSourceManager, mockVocabManager, translation);
    action.setContainer(container);
    // initialize ExtensionProperty representing BasisOfRecord field on Occurrence core Extension
    ExtensionProperty property = mapping.getExtension().getProperty(field.getTerm());
    // set a vocabulary for the BasisOfRecord field
    // mock creation of BasisOfRecord vocabulary
    VocabularyConcept concept = new VocabularyConcept();
    concept.setIdentifier("PreservedSpecimen");
    concept.setUri("http://rs.tdwg.org/dwc/dwctype/PreservedSpecimen");
    // preferred titles
    Set<VocabularyTerm> preferredTerms = new HashSet<>();
    VocabularyTerm term = new VocabularyTerm();
    term.setLang("en");
    term.setTitle("Preserved Specimen");
    preferredTerms.add(term);
    concept.setPreferredTerms(preferredTerms);
    // alternative titles
    Set<VocabularyTerm> alternateTerms = new HashSet<>();
    term = new VocabularyTerm();
    term.setLang("en");
    term.setTitle("Conserved Specimen");
    alternateTerms.add(term);
    concept.setAlternativeTerms(alternateTerms);
    Vocabulary vocab = new Vocabulary();
    List<VocabularyConcept> concepts = new ArrayList<>();
    concepts.add(concept);
    vocab.setConcepts(concepts);
    vocab.setUriString("http://rs.gbif.org/vocabulary/dwc/basis_of_record");
    property.setVocabulary(vocab);
    // create sessionScoped Translation
    // populate sessionScoped Translation with translations
    action.getTrans().setTmap(mapping.getExtension().getRowType(), property, sourceValues, translatedValues);
    // set various properties on Action
    action.setField(field);
    action.setExtensionMapping(mapping);
    action.setProperty(property);
    // mock servlet request
    HttpServletRequest mockRequest = mock(HttpServletRequest.class);
    // the mapping id is 0 - relates to resource's List<ExtensionMapping> mappings
    when(mockRequest.getParameter(TranslationAction.REQ_PARAM_MAPPINGID)).thenReturn("0");
    when(mockRequest.getParameter(TranslationAction.REQ_PARAM_ROWTYPE)).thenReturn(Constants.DWC_ROWTYPE_OCCURRENCE);
    when(mockRequest.getParameter(TranslationAction.REQ_PARAM_TERM)).thenReturn(DwcTerm.basisOfRecord.qualifiedName());
    when(mockRequest.getParameter(Constants.REQ_PARAM_RESOURCE)).thenReturn(resourceShortName);
    action.setServletRequest(mockRequest);
    // ensure the resource is set
    action.setResource(resource);
}