Examples with ArchiveFile org.gbif.dwc.ArchiveFile used on opensource projects

Example 1 with ArchiveFile

use of org.gbif.dwc.ArchiveFile in project eol-globi-data by jhpoelen.

the class DatasetImporterForDwCA method findResourceExtension.

static ArchiveFile findResourceExtension(Archive archive, String extensionType) {
    ArchiveFile resourceRelationExtension = null;
    Set<ArchiveFile> extensions = archive.getExtensions();
    for (ArchiveFile extension : extensions) {
        if (StringUtils.equals(extension.getRowType().qualifiedName(), extensionType)) {
            resourceRelationExtension = extension;
            break;
        }
    }
    return resourceRelationExtension;
}

Example 2 with ArchiveFile

use of org.gbif.dwc.ArchiveFile in project eol-globi-data by jhpoelen.

the class DatasetImporterForDwCA method importDescriptionExtension.

private static void importDescriptionExtension(Archive archive, InteractionListener interactionListener, ImportLogger logger) {
    ArchiveFile extension = findResourceExtension(archive, EXTENSION_DESCRIPTION);
    if (extension != null) {
        final BTreeMap<String, Map<String, String>> associationsMap = MapDBUtil.createBigMap();
        try {
            ArchiveFile core = archive.getCore();
            importDescriptionExtension(interactionListener, logger, extension, core, associationsMap);
        } finally {
            if (associationsMap != null) {
                associationsMap.close();
            }
        }
    }
}

Example 3 with ArchiveFile

use of org.gbif.dwc.ArchiveFile in project eol-globi-data by jhpoelen.

the class DatasetImporterForDwCA method createReferenceEnricher.

private static InteractionListenerClosable createReferenceEnricher(Archive archive, final InteractionListener interactionListener) {
    return new InteractionListenerClosable() {

        private BTreeMap<String, Map<String, String>> referenceMap = null;

        @Override
        public void close() {
            if (referenceMap != null) {
                referenceMap.close();
                referenceMap = null;
            }
        }

        private void initIfNeeded() {
            if (referenceMap == null) {
                referenceMap = MapDBUtil.createBigMap();
                ArchiveFile extension = findResourceExtension(archive, EXTENSION_REFERENCE);
                if (extension != null) {
                    for (Record record : extension) {
                        Map<String, String> props = new TreeMap<>();
                        termsToMap(record, props);
                        props.put(REFERENCE_CITATION, CitationUtil.citationFor(props));
                        appendResourceType(props, extension.getRowType());
                        referenceMap.put(record.id(), props);
                    }
                }
            }
        }

        @Override
        public void on(Map<String, String> interaction) throws StudyImporterException {
            initIfNeeded();
            String s = interaction.get(DWC_COREID);
            Map<String, String> enrichedLink = contains(referenceMap, s) ? new TreeMap<String, String>(interaction) {

                {
                    putAll(referenceMap.get(s));
                }
            } : interaction;
            interactionListener.on(enrichedLink);
        }
    };
}

Example 4 with ArchiveFile

use of org.gbif.dwc.ArchiveFile in project eol-globi-data by jhpoelen.

the class DatasetImporterForDwCA method importResourceRelationshipExtension.

static void importResourceRelationshipExtension(Archive archive, InteractionListener interactionListener) {
    ArchiveFile resourceExtension = findResourceRelationshipExtension(archive);
    if (resourceExtension != null) {
        final BTreeMap<String, Map<String, Map<String, String>>> termTypeIdPropertyMap = MapDBUtil.createBigMap();
        final DB sourceIdDb = MapDBUtil.tmpDB();
        final DB targetIdDb = MapDBUtil.tmpDB();
        try {
            importResourceRelationshipExtension(archive, interactionListener, resourceExtension, termTypeIdPropertyMap, sourceIdDb, targetIdDb);
        } finally {
            sourceIdDb.close();
            targetIdDb.close();
            if (termTypeIdPropertyMap != null) {
                termTypeIdPropertyMap.close();
            }
        }
    }
}

Example 5 with ArchiveFile

use of org.gbif.dwc.ArchiveFile in project eol-globi-data by jhpoelen.

the class DatasetImporterForDwCA method resolveLocalResourceIds.

private static void resolveLocalResourceIds(Archive archive, Map<String, Map<String, Map<String, String>>> termIdPropMap, Set<String> referencedSourceIds, Set<String> referencedTargetIds, List<DwcTerm> termTypes) {
    List<ArchiveFile> archiveFiles = new ArrayList<>();
    archiveFiles.add(archive.getCore());
    ArchiveFile taxon = findResourceExtension(archive, EXTENSION_TAXON);
    if (taxon != null) {
        archiveFiles.add(taxon);
    }
    for (ArchiveFile archiveFile : archiveFiles) {
        for (Record record : archiveFile) {
            for (DwcTerm termType : termTypes) {
                attemptLinkUsingTerm(termIdPropMap, referencedSourceIds, referencedTargetIds, record, termType);
            }
        }
    }
}