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

Example 1 with Vocabulary

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

the class ExtensionManagerImpl method migrateResourceToNewExtensionVersion.

/**
 * Migrate a resource's extension mappings to an extension to a newer version of that extension.
 *
 * @param r       resource whose mappings must be migrated
 * @param current extension
 * @param newer   newer version of extension to migrate mappings to
 */
protected void migrateResourceToNewExtensionVersion(Resource r, Extension current, Extension newer) {
    // sanity check that the current and newer extensions share same rowType
    if (!current.getRowType().equalsIgnoreCase(newer.getRowType()) || r.getMappings(current.getRowType()).isEmpty()) {
        throw new IllegalStateException();
    }
    LOG.info("Migrating " + r.getShortname() + " mappings to extension " + current.getRowType() + " to latest extension version");
    // populate various set to keep track of how many terms were deprecated, how terms' vocabulary was updated, etc
    Set<ExtensionProperty> deprecated = new HashSet<>();
    Set<ExtensionProperty> vocabulariesRemoved = new HashSet<>();
    Set<ExtensionProperty> vocabulariesUnchanged = new HashSet<>();
    Set<ExtensionProperty> vocabulariesUpdated = new HashSet<>();
    for (ExtensionProperty property : current.getProperties()) {
        // newer extension still contain this property?
        if (!newer.hasProperty(property.qualifiedName())) {
            deprecated.add(property);
        } else // if so, check if this property uses a vocabulary, and whether the newer extension uses a newer version of it
        {
            if (property.getVocabulary() != null) {
                Vocabulary v1 = property.getVocabulary();
                Vocabulary v2 = newer.getProperty(property.qualifiedName()).getVocabulary();
                // case 1: vocabulary removed in newer version
                if (v2 == null) {
                    vocabulariesRemoved.add(property);
                } else // case 2: vocabulary versions are unchanged between versions
                if (v1.getUriString().equalsIgnoreCase(v2.getUriString())) {
                    vocabulariesUnchanged.add(property);
                } else // case 3: vocabulary has been updated in newer version
                if (!v1.getUriString().equalsIgnoreCase(v2.getUriString())) {
                    vocabulariesUpdated.add(property);
                }
            }
        }
    }
    LOG.debug(deprecated.size() + " properties have been deprecated in the newer version");
    LOG.debug(vocabulariesRemoved.size() + " properties in the newer version of extension no longer use a vocabulary");
    LOG.debug(vocabulariesUnchanged.size() + " properties in the newer version of extension use the same vocabulary");
    LOG.debug(vocabulariesUpdated.size() + " properties in the newer version of extension use a newer vocabulary");
    // set of new terms (terms to add)
    Set<ExtensionProperty> added = new HashSet<>();
    for (ExtensionProperty property : newer.getProperties()) {
        // older extension contain this property?
        if (!current.hasProperty(property.qualifiedName())) {
            added.add(property);
        }
    }
    LOG.debug("Newer version of extension has " + added.size() + " new properties");
    for (ExtensionMapping extensionMapping : r.getMappings(current.getRowType())) {
        migrateExtensionMapping(extensionMapping, newer, deprecated);
    }
}

Example 2 with Vocabulary

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

the class VocabulariesManagerImpl method getLatestDefaults.

/**
 * Return the latest versions of default vocabularies (that the IPT is configured to use) from the registry.
 *
 * @return list containing latest versions of default vocabularies
 */
private List<Vocabulary> getLatestDefaults(List<Vocabulary> registered) {
    List<Vocabulary> defaults = new ArrayList<>();
    for (Vocabulary v : registered) {
        if (v.getUriString() != null && DEFAULT_VOCABS.contains(v.getUriString()) && v.isLatest()) {
            defaults.add(v);
        }
    }
    // throw exception if not all default vocabularies could not be loaded
    if (DEFAULT_VOCABS.size() != defaults.size()) {
        String msg = "Not all default vocabularies were loaded!";
        LOG.error(msg);
        throw new InvalidConfigException(InvalidConfigException.TYPE.INVALID_DATA_DIR, msg);
    }
    return defaults;
}

Example 3 with Vocabulary

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

the class VocabulariesManagerImpl method loadFromFile.

/**
 * Load the Vocabulary object from the XML definition file.
 *
 * @param localFile vocabulary XML definition file
 *
 * @return vocabulary loaded from file
 *
 * @throws InvalidConfigException if vocabulary could not be loaded successfully
 */
private Vocabulary loadFromFile(File localFile) throws InvalidConfigException {
    Objects.requireNonNull(localFile);
    if (!localFile.exists()) {
        throw new IllegalStateException();
    }
    try (InputStream fileIn = new FileInputStream(localFile)) {
        Vocabulary v = vocabFactory.build(fileIn);
        // filesystem date
        v.setModified(new Date(localFile.lastModified()));
        LOG.info("Successfully loaded vocabulary: " + v.getUriString());
        return v;
    } catch (IOException e) {
        LOG.error("Can't access local vocabulary file (" + localFile.getAbsolutePath() + ")", e);
        throw new InvalidConfigException(InvalidConfigException.TYPE.INVALID_VOCABULARY, "Can't access local vocabulary file");
    } catch (SAXException e) {
        LOG.error("Can't parse local extension file (" + localFile.getAbsolutePath() + ")", e);
        throw new InvalidConfigException(InvalidConfigException.TYPE.INVALID_VOCABULARY, "Can't parse local vocabulary file");
    } catch (ParserConfigurationException e) {
        LOG.error("Can't create sax parser", e);
        throw new InvalidConfigException(InvalidConfigException.TYPE.INVALID_VOCABULARY, "Can't create sax parser");
    }
}

Example 4 with Vocabulary

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

the class VocabulariesManagerImpl method uninstall.

/**
 * Uninstall vocabulary by its unique identifier.
 *
 * @param identifier identifier of vocabulary to uninstall
 */
private void uninstall(String identifier) {
    if (vocabulariesById.containsKey(identifier)) {
        // 1. delete persisted vocab file
        Vocabulary toUninstall = vocabulariesById.get(identifier);
        File f = getVocabFile(toUninstall.getUriResolvable());
        if (f.exists()) {
            f.delete();
            LOG.debug("Successfully deleted (uninstalled) vocabulary file: " + f.getAbsolutePath());
        } else {
            LOG.warn("Vocabulary file doesn't exist locally - can't delete: " + f.getAbsolutePath());
        }
        // 2. delete from local lookup
        vocabulariesById.remove(identifier);
    } else {
        LOG.warn("Vocabulary not installed locally, can't uninstall: " + identifier);
    }
}

Example 5 with Vocabulary

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

the class ThesaurusHandlingRule method begin.

@Override
public void begin(String namespace, String name, Attributes attributes) throws Exception {
    for (int i = 0; i < attributes.getLength(); i++) {
        if (ThesaurusHandlingRule.ATTRIBUTE_THESAURUS.equals(attributes.getQName(i))) {
            Vocabulary tv = null;
            try {
                URL url = new URL(attributes.getValue(i));
                tv = vocabManager.get(url);
                // install vocabulary if it's new
                if (tv == null) {
                    LOG.warn("Installing new vocabulary with URL (" + attributes.getValue(i) + ")...");
                    tv = vocabManager.install(url);
                }
            } catch (MalformedURLException e) {
                LOG.error("Thesaurus URL (" + attributes.getValue(i) + ") is malformed: " + e.getMessage(), e);
            }
            if (tv == null) {
                LOG.error("No Vocabulary object exists for the URL (" + attributes.getValue(i) + ") so cannot be set");
            } else {
                Object extensionPropertyAsObject = getDigester().peek();
                if (extensionPropertyAsObject instanceof ExtensionProperty) {
                    ExtensionProperty eProperty = (ExtensionProperty) extensionPropertyAsObject;
                    eProperty.setVocabulary(tv);
                    LOG.debug("Vocabulary with URI[" + tv.getUriString() + "] added to extension property");
                }
            }
            // since we found the attribute
            break;
        }
    }
}