Examples with NomenclaturalSource eu.etaxonomy.cdm.model.name.NomenclaturalSource used on opensource projects

Example 1 with NomenclaturalSource

use of eu.etaxonomy.cdm.model.name.NomenclaturalSource in project cdmlib by cybertaxonomy.

the class CommonServiceImpl method getReferencingObjectTarget.

private UuidAndTitleCache<CdmBase> getReferencingObjectTarget(CdmBase entity) {
    CdmBase targetEntity;
    entity = CdmBase.deproxy(entity);
    if (entity instanceof SecundumSource) {
        targetEntity = ((SecundumSource) entity).getSourcedTaxon();
    } else if (entity instanceof NomenclaturalSource) {
        targetEntity = ((NomenclaturalSource) entity).getSourcedName();
    } else if (entity instanceof DescriptionElementSource) {
        DescriptionElementBase element = ((DescriptionElementSource) entity).getSourcedElement();
        targetEntity = getTarget(element);
    } else if (entity instanceof DescriptionElementBase) {
        targetEntity = getTarget((DescriptionElementBase) entity);
    } else if (entity instanceof IdentifiableSource) {
        IdentifiableSource source = (IdentifiableSource) entity;
        targetEntity = originalSourceDao.findIdentifiableBySourceId(IdentifiableEntity.class, source.getId());
    } else if (entity instanceof NamedSource) {
        NamedSource source = (NamedSource) entity;
        SingleSourcedEntityBase singleSourced = originalSourceDao.findSingleSourceBySourceId(SingleSourcedEntityBase.class, source.getId());
        if (singleSourced != null) {
            targetEntity = singleSourced;
        } else {
            // TODO
            targetEntity = entity;
        }
    } else if (entity instanceof DescriptionBase) {
        targetEntity = getTarget((DescriptionBase<?>) entity);
    } else {
        targetEntity = entity;
    }
    targetEntity = CdmBase.deproxy(targetEntity);
    if (targetEntity == null) {
        targetEntity = entity;
    }
    String targetLabel = targetEntity instanceof IdentifiableEntity ? ((IdentifiableEntity<?>) targetEntity).getTitleCache() : null;
    UuidAndTitleCache<CdmBase> result = new UuidAndTitleCache<>(targetEntity.getClass(), targetEntity.getUuid(), targetEntity.getId(), targetLabel);
    return result;
}

Example 2 with NomenclaturalSource

use of eu.etaxonomy.cdm.model.name.NomenclaturalSource in project cdmlib by cybertaxonomy.

the class CdmLightClassificationExport method handleName.

private void handleName(CdmLightExportState state, TaxonName name, Taxon acceptedTaxon, boolean acceptedName) {
    if (name == null || state.getNameStore().containsKey(name.getId())) {
        return;
    }
    try {
        Rank rank = name.getRank();
        CdmLightExportTable table = CdmLightExportTable.SCIENTIFIC_NAME;
        name = HibernateProxyHelper.deproxy(name);
        state.getNameStore().put(name.getId(), name.getUuid());
        String[] csvLine = new String[table.getSize()];
        csvLine[table.getIndex(CdmLightExportTable.NAME_ID)] = getId(state, name);
        if (name.getLsid() != null) {
            csvLine[table.getIndex(CdmLightExportTable.LSID)] = name.getLsid().getLsid();
        } else {
            csvLine[table.getIndex(CdmLightExportTable.LSID)] = "";
        }
        handleIdentifier(state, name);
        handleDescriptions(state, name);
        csvLine[table.getIndex(CdmLightExportTable.RANK)] = getTitleCache(rank);
        if (rank != null) {
            csvLine[table.getIndex(CdmLightExportTable.RANK_SEQUENCE)] = String.valueOf(rank.getOrderIndex());
            if (rank.isInfraGeneric()) {
                try {
                    csvLine[table.getIndex(CdmLightExportTable.INFRAGENERIC_RANK)] = name.getRank().getInfraGenericMarker();
                } catch (UnknownCdmTypeException e) {
                    state.getResult().addError("Infrageneric marker expected but not available for rank " + name.getRank().getTitleCache());
                }
            }
            if (rank.isInfraSpecific()) {
                csvLine[table.getIndex(CdmLightExportTable.INFRASPECIFIC_RANK)] = name.getRank().getAbbreviation();
            }
        } else {
            csvLine[table.getIndex(CdmLightExportTable.RANK_SEQUENCE)] = "";
        }
        if (name.isProtectedTitleCache()) {
            csvLine[table.getIndex(CdmLightExportTable.FULL_NAME_WITH_AUTHORS)] = name.getTitleCache();
        } else {
            // TODO: adapt the tropicos titlecache creation
            csvLine[table.getIndex(CdmLightExportTable.FULL_NAME_WITH_AUTHORS)] = name.getTitleCache();
        }
        if (!state.getConfig().isAddHTML()) {
            csvLine[table.getIndex(CdmLightExportTable.FULL_NAME_WITH_REF)] = name.getFullTitleCache();
        } else {
            List<TaggedText> taggedFullTitleCache = name.getTaggedFullTitle();
            List<TaggedText> taggedName = name.getTaggedName();
            String fullTitleWithHtml = createNameWithItalics(taggedFullTitleCache);
            // TODO: adapt the tropicos titlecache creation
            csvLine[table.getIndex(CdmLightExportTable.FULL_NAME_WITH_REF)] = fullTitleWithHtml.trim();
        }
        csvLine[table.getIndex(CdmLightExportTable.FULL_NAME_NO_AUTHORS)] = name.getNameCache();
        csvLine[table.getIndex(CdmLightExportTable.GENUS_UNINOMIAL)] = name.getGenusOrUninomial();
        csvLine[table.getIndex(CdmLightExportTable.INFRAGENERIC_EPITHET)] = name.getInfraGenericEpithet();
        csvLine[table.getIndex(CdmLightExportTable.SPECIFIC_EPITHET)] = name.getSpecificEpithet();
        csvLine[table.getIndex(CdmLightExportTable.INFRASPECIFIC_EPITHET)] = name.getInfraSpecificEpithet();
        csvLine[table.getIndex(CdmLightExportTable.APPENDED_PHRASE)] = name.getAppendedPhrase();
        csvLine[table.getIndex(CdmLightExportTable.BAS_AUTHORTEAM_FK)] = getId(state, name.getBasionymAuthorship());
        if (name.getBasionymAuthorship() != null) {
            if (state.getAuthorFromStore(name.getBasionymAuthorship().getId()) == null) {
                handleAuthor(state, name.getBasionymAuthorship());
            }
        }
        csvLine[table.getIndex(CdmLightExportTable.BAS_EX_AUTHORTEAM_FK)] = getId(state, name.getExBasionymAuthorship());
        if (name.getExBasionymAuthorship() != null) {
            if (state.getAuthorFromStore(name.getExBasionymAuthorship().getId()) == null) {
                handleAuthor(state, name.getExBasionymAuthorship());
            }
        }
        csvLine[table.getIndex(CdmLightExportTable.COMB_AUTHORTEAM_FK)] = getId(state, name.getCombinationAuthorship());
        if (name.getCombinationAuthorship() != null) {
            if (state.getAuthorFromStore(name.getCombinationAuthorship().getId()) == null) {
                handleAuthor(state, name.getCombinationAuthorship());
            }
        }
        csvLine[table.getIndex(CdmLightExportTable.COMB_EX_AUTHORTEAM_FK)] = getId(state, name.getExCombinationAuthorship());
        if (name.getExCombinationAuthorship() != null) {
            if (state.getAuthorFromStore(name.getExCombinationAuthorship().getId()) == null) {
                handleAuthor(state, name.getExCombinationAuthorship());
            }
        }
        csvLine[table.getIndex(CdmLightExportTable.AUTHOR_TEAM_STRING)] = name.getAuthorshipCache();
        Reference nomRef = name.getNomenclaturalReference();
        NomenclaturalSource nomenclaturalSource = name.getNomenclaturalSource();
        if (nomenclaturalSource != null && nomenclaturalSource.getNameUsedInSource() != null) {
            handleName(state, nomenclaturalSource.getNameUsedInSource(), null);
            csvLine[table.getIndex(CdmLightExportTable.NAME_USED_IN_SOURCE)] = getId(state, nomenclaturalSource.getNameUsedInSource());
        }
        if (nomRef != null) {
            if (!state.getReferenceStore().contains(nomRef.getUuid())) {
                handleReference(state, nomRef);
            }
            csvLine[table.getIndex(CdmLightExportTable.REFERENCE_FK)] = getId(state, nomRef);
            csvLine[table.getIndex(CdmLightExportTable.PUBLICATION_TYPE)] = nomRef.getType().name();
            if (nomRef.getVolume() != null) {
                csvLine[table.getIndex(CdmLightExportTable.VOLUME_ISSUE)] = nomRef.getVolume();
                csvLine[table.getIndex(CdmLightExportTable.COLLATION)] = createCollatation(name);
            }
            if (nomRef.getDatePublished() != null) {
                csvLine[table.getIndex(CdmLightExportTable.DATE_PUBLISHED)] = nomRef.getTimePeriodPublishedString();
                csvLine[table.getIndex(CdmLightExportTable.YEAR_PUBLISHED)] = nomRef.getDatePublished().getYear();
                csvLine[table.getIndex(CdmLightExportTable.VERBATIM_DATE)] = nomRef.getDatePublished().getVerbatimDate();
            }
            if (name.getNomenclaturalMicroReference() != null) {
                csvLine[table.getIndex(CdmLightExportTable.DETAIL)] = name.getNomenclaturalMicroReference();
            }
            nomRef = HibernateProxyHelper.deproxy(nomRef);
            if (nomRef.getInReference() != null) {
                Reference inReference = nomRef.getInReference();
                if (inReference.getDatePublished() != null && nomRef.getDatePublished() == null) {
                    csvLine[table.getIndex(CdmLightExportTable.DATE_PUBLISHED)] = inReference.getDatePublishedString();
                    csvLine[table.getIndex(CdmLightExportTable.YEAR_PUBLISHED)] = inReference.getDatePublished().getYear();
                }
                if (nomRef.getVolume() == null && inReference.getVolume() != null) {
                    csvLine[table.getIndex(CdmLightExportTable.VOLUME_ISSUE)] = inReference.getVolume();
                    csvLine[table.getIndex(CdmLightExportTable.COLLATION)] = createCollatation(name);
                }
                if (inReference.getInReference() != null) {
                    inReference = inReference.getInReference();
                }
                if (inReference.getAbbrevTitle() == null) {
                    csvLine[table.getIndex(CdmLightExportTable.ABBREV_TITLE)] = CdmUtils.Nz(inReference.getTitle());
                } else {
                    csvLine[table.getIndex(CdmLightExportTable.ABBREV_TITLE)] = CdmUtils.Nz(inReference.getAbbrevTitle());
                }
                if (inReference.getTitle() == null) {
                    csvLine[table.getIndex(CdmLightExportTable.FULL_TITLE)] = CdmUtils.Nz(inReference.getAbbrevTitle() != null ? inReference.getAbbrevTitle() : inReference.getTitleCache());
                } else {
                    csvLine[table.getIndex(CdmLightExportTable.FULL_TITLE)] = CdmUtils.Nz(inReference.getTitle());
                }
                TeamOrPersonBase<?> author = inReference.getAuthorship();
                if (author != null && (nomRef.isOfType(ReferenceType.BookSection) || nomRef.isOfType(ReferenceType.Section))) {
                    csvLine[table.getIndex(CdmLightExportTable.ABBREV_REF_AUTHOR)] = author.isProtectedTitleCache() ? author.getTitleCache() : CdmUtils.Nz(author.getNomenclaturalTitleCache());
                    csvLine[table.getIndex(CdmLightExportTable.FULL_REF_AUTHOR)] = CdmUtils.Nz(author.getTitleCache());
                } else {
                    csvLine[table.getIndex(CdmLightExportTable.ABBREV_REF_AUTHOR)] = "";
                    csvLine[table.getIndex(CdmLightExportTable.FULL_REF_AUTHOR)] = "";
                }
            } else {
                if (nomRef.getAbbrevTitle() == null) {
                    csvLine[table.getIndex(CdmLightExportTable.ABBREV_TITLE)] = CdmUtils.Nz(nomRef.getTitle() != null ? nomRef.getTitle() : nomRef.getAbbrevTitleCache());
                } else {
                    csvLine[table.getIndex(CdmLightExportTable.ABBREV_TITLE)] = CdmUtils.Nz(nomRef.getAbbrevTitle());
                }
                if (nomRef.getTitle() == null) {
                    csvLine[table.getIndex(CdmLightExportTable.FULL_TITLE)] = CdmUtils.Nz(nomRef.getAbbrevTitle() != null ? nomRef.getAbbrevTitle() : nomRef.getTitleCache());
                } else {
                    csvLine[table.getIndex(CdmLightExportTable.FULL_TITLE)] = CdmUtils.Nz(nomRef.getTitle());
                }
                TeamOrPersonBase<?> author = nomRef.getAuthorship();
                if (author != null) {
                    csvLine[table.getIndex(CdmLightExportTable.ABBREV_REF_AUTHOR)] = author.isProtectedTitleCache() ? author.getTitleCache() : CdmUtils.Nz(author.getNomenclaturalTitleCache());
                    csvLine[table.getIndex(CdmLightExportTable.FULL_REF_AUTHOR)] = CdmUtils.Nz(author.getTitleCache());
                } else {
                    csvLine[table.getIndex(CdmLightExportTable.ABBREV_REF_AUTHOR)] = "";
                    csvLine[table.getIndex(CdmLightExportTable.FULL_REF_AUTHOR)] = "";
                }
            }
        } else {
            csvLine[table.getIndex(CdmLightExportTable.PUBLICATION_TYPE)] = "";
        }
        /*
             * Collation
             *
             * Detail
             *
             * TitlePageYear
             */
        String protologueUriString = extractProtologueURIs(state, name);
        csvLine[table.getIndex(CdmLightExportTable.PROTOLOGUE_URI)] = protologueUriString;
        Collection<TypeDesignationBase> specimenTypeDesignations = new ArrayList<>();
        List<TextualTypeDesignation> textualTypeDesignations = new ArrayList<>();
        for (TypeDesignationBase<?> typeDesignation : name.getTypeDesignations()) {
            if (typeDesignation.isInstanceOf(TextualTypeDesignation.class)) {
                if (((TextualTypeDesignation) typeDesignation).isVerbatim()) {
                    Set<IdentifiableSource> sources = typeDesignation.getSources();
                    boolean isProtologue = false;
                    if (sources != null && !sources.isEmpty()) {
                        IdentifiableSource source = sources.iterator().next();
                        if (name.getNomenclaturalReference() != null) {
                            isProtologue = source.getCitation() != null ? source.getCitation().getUuid().equals(name.getNomenclaturalReference().getUuid()) : false;
                        }
                    }
                    if (isProtologue) {
                        csvLine[table.getIndex(CdmLightExportTable.PROTOLOGUE_TYPE_STATEMENT)] = ((TextualTypeDesignation) typeDesignation).getPreferredText(Language.DEFAULT());
                    } else {
                        textualTypeDesignations.add((TextualTypeDesignation) typeDesignation);
                    }
                } else {
                    textualTypeDesignations.add((TextualTypeDesignation) typeDesignation);
                }
            } else if (typeDesignation.isInstanceOf(SpecimenTypeDesignation.class)) {
                SpecimenTypeDesignation specimenType = HibernateProxyHelper.deproxy(typeDesignation, SpecimenTypeDesignation.class);
                specimenTypeDesignations.add(specimenType);
                handleSpecimenType(state, specimenType);
            } else if (typeDesignation instanceof NameTypeDesignation) {
                specimenTypeDesignations.add(HibernateProxyHelper.deproxy(typeDesignation, NameTypeDesignation.class));
            }
        }
        TypeDesignationSetManager manager = new TypeDesignationSetManager(specimenTypeDesignations, name);
        HTMLTagRules rules = new HTMLTagRules();
        rules.addRule(TagEnum.name, "i");
        String test = manager.print(false, false, false, rules);
        ;
        csvLine[table.getIndex(CdmLightExportTable.TYPE_SPECIMEN)] = manager.print(false, false, false, rules);
        StringBuilder stringbuilder = new StringBuilder();
        int i = 1;
        for (TextualTypeDesignation typeDesignation : textualTypeDesignations) {
            stringbuilder.append(typeDesignation.getPreferredText(Language.DEFAULT()));
            if (typeDesignation.getSources() != null && !typeDesignation.getSources().isEmpty()) {
                stringbuilder.append(" [");
                int index = 1;
                for (IdentifiableSource source : typeDesignation.getSources()) {
                    if (source.getCitation() != null) {
                        stringbuilder.append(OriginalSourceFormatter.INSTANCE.format(source));
                    }
                    if (index < typeDesignation.getSources().size()) {
                        stringbuilder.append(", ");
                    }
                    index++;
                }
                stringbuilder.append("]");
            }
            if (i < textualTypeDesignations.size()) {
                stringbuilder.append("; ");
            } else {
                stringbuilder.append(".");
            }
            i++;
        }
        csvLine[table.getIndex(CdmLightExportTable.TYPE_STATEMENT)] = stringbuilder.toString();
        if (name.getStatus() == null || name.getStatus().isEmpty()) {
            csvLine[table.getIndex(CdmLightExportTable.NOM_STATUS)] = "";
            csvLine[table.getIndex(CdmLightExportTable.NOM_STATUS_ABBREV)] = "";
        } else {
            String statusStringAbbrev = extractStatusString(state, name, true);
            String statusString = extractStatusString(state, name, false);
            csvLine[table.getIndex(CdmLightExportTable.NOM_STATUS)] = statusString.trim();
            csvLine[table.getIndex(CdmLightExportTable.NOM_STATUS_ABBREV)] = statusStringAbbrev.trim();
        }
        HomotypicalGroup group = HibernateProxyHelper.deproxy(name.getHomotypicalGroup(), HomotypicalGroup.class);
        csvLine[table.getIndex(CdmLightExportTable.HOMOTYPIC_GROUP_FK)] = getId(state, group);
        List<TaxonName> typifiedNames = new ArrayList<>();
        if (acceptedTaxon != null) {
            HomotypicGroupTaxonComparator comparator = new HomotypicGroupTaxonComparator(acceptedTaxon);
            List<Synonym> synonymsInGroup = null;
            if (group.equals(acceptedTaxon.getHomotypicGroup())) {
                synonymsInGroup = acceptedTaxon.getHomotypicSynonymsByHomotypicGroup(comparator);
                typifiedNames.add(name);
            } else {
                synonymsInGroup = acceptedTaxon.getSynonymsInGroup(group, comparator);
            }
            synonymsInGroup.stream().forEach(synonym -> typifiedNames.add(HibernateProxyHelper.deproxy(synonym.getName(), TaxonName.class)));
        } else {
            typifiedNames.addAll(group.getTypifiedNames());
        }
        Integer seqNumber = typifiedNames.indexOf(name);
        csvLine[table.getIndex(CdmLightExportTable.HOMOTYPIC_GROUP_SEQ)] = String.valueOf(seqNumber);
        state.getProcessor().put(table, name, csvLine);
        handleNameRelationships(state, name);
    } catch (Exception e) {
        state.getResult().addException(e, "An unexpected error occurred when handling the name " + cdmBaseStr(name) + ": " + name.getTitleCache() + ": " + e.getMessage());
        e.printStackTrace();
    }
}

Example 3 with NomenclaturalSource

use of eu.etaxonomy.cdm.model.name.NomenclaturalSource in project cdmlib by cybertaxonomy.

the class TaxonGraphBeforeTransactionCompleteProcess method doBeforeTransactionCompletion.

@Override
public void doBeforeTransactionCompletion(SessionImplementor session) {
    if (logger.isDebugEnabled()) {
        String message = eventType.name() + " for ";
        message += taxonName != null ? taxonName.toString() : "";
        message += nomenclaturalSource != null ? nomenclaturalSource.toString() : "";
        if (eventType.equals(EventType.UPDATE)) {
            message += " with dirty properties: " + Arrays.stream(dirtyProperties).mapToObj(i -> propertyNames[i]).collect(Collectors.joining(", "));
        }
        logger.debug(message);
    }
    try {
        if (eventType.equals(EventType.INSERT)) {
            // ---- INSERT ----
            if (taxonName != null) {
                // 1. do the sanity checks first
                if (taxonName.getNomenclaturalSource() == null || taxonName.getNomenclaturalSource().getCitation() == null) {
                    if (failOnMissingNomRef) {
                        throw new TaxonGraphException("TaxonName.nomenclaturalSource or TaxonName.nomenclaturalSource.citation must never be null.");
                    } else {
                        logger.warn("TaxonName.nomenclaturalSource or TaxonName.nomenclaturalSource.citation must never be null. (" + taxonName.toString() + ")");
                    }
                }
                createTempSession(session);
                onNewTaxonName(taxonName);
                getSession().flush();
            } else if (nomenclaturalSource != null) {
                TaxonName taxonName = (TaxonName) findValueByName(state, NOMENCLATURALSOURCE_SOURCEDNAME);
                Reference reference = (Reference) findValueByName(state, NOMENCLATURALSOURCE_CITATION);
                if (taxonName != null && reference != null) {
                    createTempSession(session);
                    // load name and reference also into this session
                    taxonName = getSession().load(TaxonName.class, taxonName.getId());
                    reference = getSession().load(Reference.class, reference.getId());
                    onNewNomenClaturalSource(taxonName, reference);
                    getSession().flush();
                }
            }
        } else if (eventType.equals(EventType.DELETE)) {
            if (taxonName != null) {
                // handling this case explicitly should not be needed as this is expected to be done by orphan removal in
                // hibernate
                Reference reference = (Reference) oldState[Arrays.binarySearch(propertyNames, TAXONNAME_NOMENCLATURALSOURCE)];
                if (reference != null) {
                    createTempSession(session);
                    onTaxonNameDeleted(taxonName, reference);
                    getSession().flush();
                }
            } else if (nomenclaturalSource != null) {
                TaxonName taxonName = (TaxonName) findValueByName(oldState, NOMENCLATURALSOURCE_SOURCEDNAME);
                Reference reference = (Reference) findValueByName(oldState, NOMENCLATURALSOURCE_CITATION);
                if (taxonName != null && reference != null) {
                    createTempSession(session);
                    onNomReferenceRemoved(taxonName, reference);
                    getSession().flush();
                }
            }
        } else {
            // either taxonName or nomenclaturalSource not null, never both!
            if (taxonName != null) {
                // 1. do the sanity checks first
                Map<String, PropertyStateChange> changedNomenclaturalSourceProp = checkStateChange(TAXONNAME_NOMENCLATURALSOURCE);
                if (!changedNomenclaturalSourceProp.isEmpty()) {
                    if (changedNomenclaturalSourceProp.get(TAXONNAME_NOMENCLATURALSOURCE[0]).newState == null) {
                        throw new TaxonGraphException("TaxonName.nomenclaturalSource must never be reverted to null.");
                    }
                    if (((NomenclaturalSource) changedNomenclaturalSourceProp.get(TAXONNAME_NOMENCLATURALSOURCE[0]).newState).getCitation() == null) {
                        throw new TaxonGraphException("TaxonName.nomenclaturalSource.citation must never be reverted to null.");
                    }
                    createTempSession(session);
                    NomenclaturalSource oldNomenclaturalSource = (NomenclaturalSource) changedNomenclaturalSourceProp.get(TAXONNAME_NOMENCLATURALSOURCE[0]).oldState;
                    onNomReferenceChange(taxonName, oldNomenclaturalSource.getCitation());
                    getSession().flush();
                }
                // 2. update the graph
                Map<String, PropertyStateChange> changedProps = checkStateChange(TAXONNAME_NAMEPARTS_OR_RANK_PROPS);
                if (!changedProps.isEmpty()) {
                    createTempSession(session);
                    onNameOrRankChange(taxonName);
                    getSession().flush();
                }
            } else if (nomenclaturalSource != null) {
                Map<String, PropertyStateChange> changedProps = checkStateChange(CITATION_OR_SOURCEDNAME);
                if (!changedProps.isEmpty()) {
                    TaxonName newTaxonNameState = null;
                    Reference newCitationState = null;
                    TaxonName oldTaxonNameState = null;
                    Reference oldCitationState = null;
                    if (changedProps.containsKey(NOMENCLATURALSOURCE_SOURCEDNAME)) {
                        newTaxonNameState = (TaxonName) changedProps.get(NOMENCLATURALSOURCE_SOURCEDNAME).newState;
                        oldTaxonNameState = (TaxonName) changedProps.get(NOMENCLATURALSOURCE_SOURCEDNAME).oldState;
                    }
                    if (changedProps.containsKey(NOMENCLATURALSOURCE_CITATION)) {
                        newCitationState = (Reference) changedProps.get(NOMENCLATURALSOURCE_CITATION).newState;
                        oldCitationState = (Reference) changedProps.get(NOMENCLATURALSOURCE_CITATION).oldState;
                    }
                    // 1. do the sanity checks first
                    if (oldTaxonNameState != null && oldTaxonNameState.getNomenclaturalSource() == null) {
                        createTempSession(session);
                        onNomReferenceChange(oldTaxonNameState, null);
                        getSession().flush();
                    }
                    // 2. update the graph
                    if (newTaxonNameState != null && newCitationState == null) {
                        createTempSession(session);
                        onNomReferenceChange(newTaxonNameState, nomenclaturalSource.getCitation());
                        getSession().flush();
                    }
                    if (newTaxonNameState == null && newCitationState != null) {
                        createTempSession(session);
                        onNomReferenceChange(nomenclaturalSource.getSourcedName(), oldCitationState);
                        getSession().flush();
                    }
                }
            }
        }
    } catch (TaxonGraphException e) {
        throw new HibernateException(e);
    } finally {
        if (getSession() != null) {
            // temporarySession.close(); // no need to close the session since the session is configured for auto close, see createTempSession()
            if (origLoggerLevel != null) {
                Logger.getLogger("org.hibernate.SQL").setLevel(origLoggerLevel);
            }
        }
    }
}

Example 4 with NomenclaturalSource

use of eu.etaxonomy.cdm.model.name.NomenclaturalSource in project cdmlib by cybertaxonomy.

the class TaxonGraphHibernateListener method onPostUpdate.

@Override
public void onPostUpdate(PostUpdateEvent event) {
    if (event.getEntity() instanceof TaxonName || event.getEntity() instanceof NomenclaturalSource) {
        for (Class<? extends BeforeTransactionCompletionProcess> type : beforeTransactionCompletionProcessTypes.keySet()) {
            try {
                ProcessConstructorData<? extends BeforeTransactionCompletionProcess> pcd = beforeTransactionCompletionProcessTypes.get(type);
                BeforeTransactionCompletionProcess processorInstance = pcd.postUpdateEventConstructor.newInstance(pcd.buildConstructorArgs(event));
                event.getSession().getActionQueue().registerProcess(processorInstance);
            } catch (InstantiationException | IllegalAccessException | IllegalArgumentException | InvocationTargetException | SecurityException e) {
                Logger.getLogger(TaxonGraphHibernateListener.class).error("Error creating new instance of " + type.toString(), e);
            }
        }
    }
}

Example 5 with NomenclaturalSource

use of eu.etaxonomy.cdm.model.name.NomenclaturalSource in project cdmlib by cybertaxonomy.

the class TaxonGraphHibernateListener method onPostInsert.

@Override
public void onPostInsert(PostInsertEvent event) {
    if (event.getEntity() instanceof TaxonName || event.getEntity() instanceof NomenclaturalSource) {
        for (Class<? extends BeforeTransactionCompletionProcess> type : beforeTransactionCompletionProcessTypes.keySet()) {
            try {
                ProcessConstructorData<? extends BeforeTransactionCompletionProcess> pcd = beforeTransactionCompletionProcessTypes.get(type);
                BeforeTransactionCompletionProcess processorInstance = pcd.postInsertEventConstructor.newInstance(pcd.buildConstructorArgs(event));
                event.getSession().getActionQueue().registerProcess(processorInstance);
            } catch (InstantiationException | IllegalAccessException | IllegalArgumentException | InvocationTargetException | SecurityException e) {
                Logger.getLogger(TaxonGraphHibernateListener.class).error("Error creating new instance of " + type.toString(), e);
            }
        }
    }
}