Examples with GatheringEvent eu.etaxonomy.cdm.model.occurrence.GatheringEvent used on opensource projects

Example 1 with GatheringEvent

use of eu.etaxonomy.cdm.model.occurrence.GatheringEvent in project cdmlib by cybertaxonomy.

the class DerivedUnitFacade method distanceToGroundToString.

// distance to ground
/**
 * Returns the correctly formatted <code>distance to ground</code> information.
 * If distanceToGroundText is not blank, it will be returned,
 * otherwise distanceToGround will be returned, followed by distanceToGroundMax
 * if existing, separated by " - "
 * @return
 */
@Transient
public String distanceToGroundToString() {
    if (!hasGatheringEvent()) {
        return null;
    } else {
        GatheringEvent ev = getGatheringEvent(true);
        String text = ev.getDistanceToGroundText();
        Double min = getDistanceToGround();
        Double max = getDistanceToGroundMax();
        return DistanceStringFormatter.distanceString(min, max, text, METER);
    }
}

Example 2 with GatheringEvent

use of eu.etaxonomy.cdm.model.occurrence.GatheringEvent in project cdmlib by cybertaxonomy.

the class CdmLightClassificationExport method handleSpecimen.

private void handleSpecimen(CdmLightExportState state, SpecimenOrObservationBase<?> specimen) {
    try {
        state.addSpecimenToStore(specimen);
        CdmLightExportTable table = CdmLightExportTable.SPECIMEN;
        String specimenId = getId(state, specimen);
        String[] csvLine = new String[table.getSize()];
        /*
             * SpecimenCitation = “El Salvador, Municipio La Libertad, San
             * Diego, El Amatal, 14.4.1993, González 159” [Auch ohne Punkt] ->
             * FieldUnit TitleCache HerbariumAbbrev = “B” [wie gehabt]
             * HerbariumCode
             *
             */
        csvLine[table.getIndex(CdmLightExportTable.SPECIMEN_ID)] = specimenId;
        csvLine[table.getIndex(CdmLightExportTable.SPECIMEN_CITATION)] = specimen.getTitleCache();
        Collection<FieldUnit> fieldUnits = this.getOccurrenceService().findFieldUnits(specimen.getUuid(), null);
        if (fieldUnits.size() == 1) {
            Iterator<FieldUnit> iterator = fieldUnits.iterator();
            if (iterator.hasNext()) {
                FieldUnit fieldUnit = iterator.next();
                csvLine[table.getIndex(CdmLightExportTable.FIELDUNIT_CITATION)] = fieldUnit.getTitleCache();
            }
        }
        if (specimen.isInstanceOf(DerivedUnit.class)) {
            DerivedUnit derivedUnit = (DerivedUnit) specimen;
            if (!StringUtils.isBlank(derivedUnit.getBarcode())) {
                csvLine[table.getIndex(CdmLightExportTable.BARCODE)] = derivedUnit.getBarcode();
            }
            if (!StringUtils.isBlank(derivedUnit.getAccessionNumber())) {
                csvLine[table.getIndex(CdmLightExportTable.ACCESSION_NUMBER)] = derivedUnit.getAccessionNumber();
            }
            if (!StringUtils.isBlank(derivedUnit.getCatalogNumber())) {
                csvLine[table.getIndex(CdmLightExportTable.CATALOGUE_NUMBER)] = derivedUnit.getCatalogNumber();
            }
        }
        csvLine[table.getIndex(CdmLightExportTable.PREFERREDSTABLE_ID)] = specimen.getPreferredStableUri() != null ? specimen.getPreferredStableUri().toString() : null;
        csvLine[table.getIndex(CdmLightExportTable.SPECIMEN_IMAGE_URIS)] = extractMediaURIs(state, specimen.getDescriptions(), Feature.IMAGE());
        if (specimen instanceof DerivedUnit) {
            DerivedUnit derivedUnit = HibernateProxyHelper.deproxy(specimen, DerivedUnit.class);
            if (derivedUnit.getCollection() != null) {
                csvLine[table.getIndex(CdmLightExportTable.HERBARIUM_ABBREV)] = derivedUnit.getCollection().getCode();
            }
            if (specimen instanceof MediaSpecimen) {
                MediaSpecimen mediaSpecimen = (MediaSpecimen) specimen;
                Iterator<MediaRepresentation> it = mediaSpecimen.getMediaSpecimen().getRepresentations().iterator();
                String mediaUris = extractMediaUris(it);
                csvLine[table.getIndex(CdmLightExportTable.MEDIA_SPECIMEN_URL)] = mediaUris;
            }
            if (derivedUnit.getDerivedFrom() != null) {
                for (SpecimenOrObservationBase<?> original : derivedUnit.getDerivedFrom().getOriginals()) {
                    // FieldUnit??
                    if (original instanceof FieldUnit) {
                        FieldUnit fieldUnit = (FieldUnit) original;
                        csvLine[table.getIndex(CdmLightExportTable.COLLECTOR_NUMBER)] = fieldUnit.getFieldNumber();
                        GatheringEvent gathering = fieldUnit.getGatheringEvent();
                        if (gathering != null) {
                            if (gathering.getLocality() != null) {
                                csvLine[table.getIndex(CdmLightExportTable.LOCALITY)] = gathering.getLocality().getText();
                            }
                            if (gathering.getCountry() != null) {
                                csvLine[table.getIndex(CdmLightExportTable.COUNTRY)] = gathering.getCountry().getLabel();
                            }
                            csvLine[table.getIndex(CdmLightExportTable.COLLECTOR_STRING)] = createCollectorString(state, gathering, fieldUnit);
                            if (gathering.getGatheringDate() != null) {
                                csvLine[table.getIndex(CdmLightExportTable.COLLECTION_DATE)] = gathering.getGatheringDate().toString();
                            }
                            if (!gathering.getCollectingAreas().isEmpty()) {
                                int index = 0;
                                csvLine[table.getIndex(CdmLightExportTable.FURTHER_AREAS)] = "0";
                                for (NamedArea area : gathering.getCollectingAreas()) {
                                    if (index == 0) {
                                        csvLine[table.getIndex(CdmLightExportTable.AREA_CATEGORY1)] = area.getLevel() != null ? area.getLevel().getLabel() : "";
                                        csvLine[table.getIndex(CdmLightExportTable.AREA_NAME1)] = area.getLabel();
                                    }
                                    if (index == 1) {
                                        csvLine[table.getIndex(CdmLightExportTable.AREA_CATEGORY2)] = area.getLevel() != null ? area.getLevel().getLabel() : "";
                                        csvLine[table.getIndex(CdmLightExportTable.AREA_NAME2)] = area.getLabel();
                                    }
                                    if (index == 2) {
                                        csvLine[table.getIndex(CdmLightExportTable.AREA_CATEGORY3)] = area.getLevel() != null ? area.getLevel().getLabel() : "";
                                        csvLine[table.getIndex(CdmLightExportTable.AREA_NAME3)] = area.getLabel();
                                    }
                                    if (index == 3) {
                                        csvLine[table.getIndex(CdmLightExportTable.FURTHER_AREAS)] = "1";
                                        break;
                                    }
                                    index++;
                                }
                            }
                        }
                    }
                }
            } else {
                state.getResult().addWarning("The specimen with uuid " + specimen.getUuid() + " is not an DerivedUnit.");
            }
        }
        state.getProcessor().put(table, specimen, csvLine);
    } catch (Exception e) {
        state.getResult().addException(e, "An unexpected error occurred when handling specimen " + cdmBaseStr(specimen) + ": " + e.getMessage());
    }
}

Example 3 with GatheringEvent

use of eu.etaxonomy.cdm.model.occurrence.GatheringEvent in project cdmlib by cybertaxonomy.

the class SpecimenSythesysExcelImport method start.

/*
     * Store the unit with it's Gathering informations in the CDM
     */
public boolean start(SpecimenSynthesysExcelImportConfigurator config) {
    boolean result = true;
    // refreshTransaction();
    try {
        /**
         * SPECIMEN OR OBSERVATION OR LIVING
         */
        DerivedUnitFacade derivedUnitFacade = getFacade();
        derivedUnitBase = derivedUnitFacade.innerDerivedUnit();
        // set catalogue number (unitID)
        derivedUnitFacade.setCatalogNumber(unitID);
        derivedUnitFacade.setAccessionNumber(accessionNumber);
        if (!originalsource.isEmpty()) {
            Reference reference = ReferenceFactory.newGeneric();
            reference.setTitleCache(originalsource, true);
            derivedUnitBase.addSource(OriginalSourceType.Import, originalsource, "", reference, "");
        } else {
            derivedUnitBase.addSource(OriginalSourceType.Import, unitID, "", ref, ref.getCitation());
        }
        // manage institution
        if (!institutionCode.isEmpty()) {
            Institution institution = getInstitution(config);
            // manage collection
            if (!collectionCode.isEmpty()) {
                Collection collection = getCollection(institution, config);
                // link specimen & collection
                derivedUnitFacade.setCollection(collection);
            }
        }
        /**
         * GATHERING EVENT
         */
        // gathering event
        UnitsGatheringEvent unitsGatheringEvent = new UnitsGatheringEvent(getTermService(), locality, languageIso, longitude, latitude, gatheringAgent, gatheringTeam, config);
        // country
        UnitsGatheringArea unitsGatheringArea = new UnitsGatheringArea();
        unitsGatheringArea.useTDWGareas(this.useTDWGarea);
        // unitsGatheringArea.setConfig(config, getOccurrenceService(),getTermService());
        unitsGatheringArea.setParams(isocountry, country, config, getTermService(), getVocabularyService());
        DefinedTermBase areaCountry = unitsGatheringArea.getCountry();
        // copy gathering event to facade
        GatheringEvent gatheringEvent = unitsGatheringEvent.getGatheringEvent();
        // join gatheringEvent to fieldObservation
        derivedUnitFacade.setGatheringEvent(gatheringEvent);
        derivedUnitFacade.setLocality(gatheringEvent.getLocality());
        derivedUnitFacade.setExactLocation(gatheringEvent.getExactLocation());
        // derivedUnitFacade.setCollector(gatheringEvent.getCollector());
        derivedUnitFacade.setCountry((NamedArea) areaCountry);
        for (DefinedTermBase<?> area : unitsGatheringArea.getAreas()) {
            derivedUnitFacade.addCollectingArea((NamedArea) area);
        }
        if (gatheringNotes != null && !gatheringNotes.isEmpty()) {
            derivedUnitFacade.setFieldNotes(gatheringNotes);
        }
        /*
             * merge AND STORE DATA
             */
        // getTermService().saveOrUpdate(areaCountry);// TODO save area sooner
        getTermService().saveLanguageData(unitsGatheringEvent.getLocality());
        // add gathering date
        if (keepAtomisedDate && (!gatheringYear.isEmpty() || !gatheringMonth.isEmpty() || !gatheringDay.isEmpty())) {
            Calendar calendar = Calendar.getInstance();
            if (!gatheringYear.isEmpty()) {
                TimePeriod tp = TimePeriod.NewInstance(Integer.parseInt(gatheringYear));
                if (!gatheringMonth.isEmpty()) {
                    tp.setStartMonth(Integer.parseInt(gatheringMonth));
                    if (!gatheringDay.isEmpty()) {
                        tp.setStartDay(Integer.parseInt(gatheringDay));
                    }
                }
                unitsGatheringEvent.setGatheringDate(tp);
            }
        } else {
            if (!gatheringDate.isEmpty()) {
                TimePeriod tp = TimePeriodParser.parseString(gatheringDate);
                unitsGatheringEvent.setGatheringDate(tp);
            }
        }
        // add fieldNumber
        derivedUnitFacade.setFieldNumber(fieldNumber);
        // add Multimedia URLs
        if (multimediaObjects.size() > 0) {
            for (String multimediaObject : multimediaObjects) {
                Media media;
                try {
                    media = getImageMedia(multimediaObject, READ_MEDIA_DATA);
                    derivedUnitFacade.addDerivedUnitMedia(media);
                } catch (MalformedURLException e) {
                    // TODO Auto-generated catch block
                    e.printStackTrace();
                }
            }
        }
        getOccurrenceService().saveOrUpdate(derivedUnitBase);
        setTaxonName(config);
        // refreshTransaction();
        if (DEBUG) {
            logger.info("saved new specimen ...");
        }
    } catch (Exception e) {
        logger.warn("Error when reading record!!");
        e.printStackTrace();
        result = false;
    }
    if (DEBUG) {
        logger.info("commit done");
    }
    // app.close();
    return result;
}

Example 4 with GatheringEvent

use of eu.etaxonomy.cdm.model.occurrence.GatheringEvent in project cdmlib by cybertaxonomy.

the class TestSpecimen method testSpecimen.

public void testSpecimen() {
    logger.info("Create test taxon ...");
    Reference sec = ReferenceFactory.newDatabase();
    String fullNameString = "Acanthostyles saucechicoensis (Hieron.) R.M. King & H. Rob.";
    INonViralName name = NonViralNameParserImpl.NewInstance().parseFullName(fullNameString);
    TaxonName botanicalName = TaxonName.castAndDeproxy(name);
    Taxon taxon = Taxon.NewInstance(botanicalName, sec);
    Collection collection = Collection.NewInstance();
    String collectionCode = "ABCDE";
    collection.setCode(collectionCode);
    Institution institution = Institution.NewInstance();
    String institutionCode = "Inst444";
    institution.setCode(institutionCode);
    collection.setInstitute(institution);
    logger.info("Create determination event");
    DeterminationEvent determinationEvent = DeterminationEvent.NewInstance();
    determinationEvent.setTaxon(taxon);
    Person actor = Person.NewTitledInstance("J. M�ller (JE)");
    determinationEvent.setActor(actor);
    logger.info("Create gathering event");
    GatheringEvent gatheringEvent = GatheringEvent.NewInstance();
    AgentBase<?> gatherer = Person.NewTitledInstance("Lorentz,P.G. s.n.");
    gatheringEvent.setActor(gatherer);
    Calendar gatheringDate = Calendar.getInstance();
    int year = 1922;
    int month = 10;
    int date = 05;
    gatheringDate.set(year, month, date);
    gatheringEvent.setGatheringDate(gatheringDate);
    logger.info("Create locality");
    NamedArea namedArea = NamedArea.NewInstance();
    Country country = Country.ARGENTINAARGENTINEREPUBLIC();
    namedArea.addCountry(country);
    namedArea.setType(NamedAreaType.ADMINISTRATION_AREA());
    // XX
    gatheringEvent.addCollectingArea(namedArea);
    String localityString = "Sierras Pampeanas, Sauce Chico";
    LanguageString locality = LanguageString.NewInstance(localityString, Language.DEFAULT());
    gatheringEvent.setLocality(locality);
    logger.info("Create new specimen ...");
    DerivedUnit specimen = DerivedUnit.NewPreservedSpecimenInstance();
    specimen.setCatalogNumber("JE 00004506");
    // ??
    specimen.setStoredUnder(botanicalName);
    specimen.setCollection(collection);
    String annotation = "originally designated as type specimen 2000, but corrected 2005-11";
    specimen.addAnnotation(Annotation.NewDefaultLanguageInstance(annotation));
    Media media = Media.NewInstance();
    URI uri = null;
    try {
        uri = new URI("http://131.130.131.9/database/img/imgBrowser.php?ID=50599");
    } catch (URISyntaxException e) {
        throw new RuntimeException(e);
    }
    String mimeType = null;
    Integer size = null;
    MediaRepresentation mediaRepresentation = MediaRepresentation.NewInstance(mimeType, "jpg");
    media.addRepresentation(mediaRepresentation);
    MediaRepresentationPart mediaRepresentationPart = MediaRepresentationPart.NewInstance(uri, size);
    mediaRepresentation.addRepresentationPart(mediaRepresentationPart);
    // specimen.addMedia(media);    #3597
    // Original ID
    String id = "22";
    IdentifiableSource source = IdentifiableSource.NewDataImportInstance(id);
    specimen.addSource(source);
    FieldUnit fieldUnit = FieldUnit.NewInstance();
    DerivationEvent derivationEvent = DerivationEvent.NewInstance(DerivationEventType.GATHERING_IN_SITU());
    derivationEvent.addDerivative(specimen);
    fieldUnit.addDerivationEvent(derivationEvent);
    fieldUnit.setGatheringEvent(gatheringEvent);
    // type information
    // typified by
    logger.warn("Specimen: " + specimen);
    DerivationEvent dEvent = specimen.getDerivedFrom();
    logger.warn("DerivationEvent: " + dEvent);
    Set<SpecimenOrObservationBase> originals = dEvent.getOriginals();
    logger.warn("Originals: " + originals);
    for (SpecimenOrObservationBase<?> original : originals) {
        if (original instanceof FieldUnit) {
            FieldUnit fieldUnit2 = (FieldUnit) original;
            logger.warn("FieldUnit: " + fieldUnit2);
            GatheringEvent gatheringEvent2 = fieldUnit2.getGatheringEvent();
            logger.warn("GatheringEvent: " + gatheringEvent2);
            AgentBase<?> gatherer2 = gatheringEvent2.getCollector();
            logger.warn("Gatherer: " + gatherer2);
        }
    }
}

Example 5 with GatheringEvent

use of eu.etaxonomy.cdm.model.occurrence.GatheringEvent in project cdmlib by cybertaxonomy.

the class SpecimenTest method testUnmarshalSpecimen.

@Test
public void testUnmarshalSpecimen() throws Exception {
    CdmDocumentBuilder cdmDocumentBuilder = new CdmDocumentBuilder();
    URI uri = new URI(URIEncoder.encode(this.getClass().getResource(resource).toString()));
    DataSet dataSet = cdmDocumentBuilder.unmarshal(DataSet.class, new InputStreamReader(this.getClass().getResourceAsStream(resource)), uri.toString());
    // List<SpecimenOrObservationBase> occurrences = dataSet.getOccurrences();
    DerivedUnit specimen = (DerivedUnit) dataSet.getOccurrences().get(0);
    assertNotNull("Specimen must not be null", specimen);
    Institution institution = (Institution) dataSet.getAgents().get(0);
    assertNotNull("Institution must not be null", institution);
    Person person = (Person) dataSet.getAgents().get(1);
    assertNotNull("Person must not be null", person);
    Taxon taxon = (Taxon) dataSet.getTaxonBases().get(0);
    assertNotNull("Taxon must not be null", taxon);
    TaxonName name = dataSet.getTaxonomicNames().get(0);
    assertNotNull("TaxonName must not be null", name);
    DefinedTerm sex = (DefinedTerm) dataSet.getTerms().get(1);
    Collection collection = dataSet.getCollections().get(0);
    assertNotNull("Collection must not be null", collection);
    FieldUnit fieldUnit = (FieldUnit) dataSet.getOccurrences().get(1);
    assertNotNull("FieldUnit must not be null", fieldUnit);
    assertEquals("Specimen.collection must equal Collection", collection, specimen.getCollection());
    assertEquals("Collection.institute must equal Institution", institution, collection.getInstitute());
    assertEquals("TaxonName must equal Specimen.storedUnder", name, specimen.getStoredUnder());
    assertEquals("Sex must equal Specimen.sex", sex, specimen.getSex());
    assertNotNull("Specimen.determinations must not be null", specimen.getDeterminations());
    assertFalse("Specimen.determinations must not be empty", specimen.getDeterminations().isEmpty());
    DeterminationEvent determination = specimen.getDeterminations().iterator().next();
    assertEquals("Person must equal Determination.actor", person, determination.getActor());
    GatheringEvent gatheringEvent = (GatheringEvent) dataSet.getEventBases().get(0);
    assertNotNull("GatheringEvent must not be null", gatheringEvent);
    DerivationEvent derivationEvent = (DerivationEvent) dataSet.getEventBases().get(1);
    assertNotNull("DerivationEvent must not be null", derivationEvent);
    assertEquals("GatheringEvent must be equal to FieldUnit.getGatheringEvent()", gatheringEvent, fieldUnit.getGatheringEvent());
    assertTrue("DerivationEvent.derivatives must contain Specimen", derivationEvent.getDerivatives().contains(specimen));
    assertEquals("DerivationEvent must equal Specimen.derivedFrom", derivationEvent, specimen.getDerivedFrom());
}