@Before
  public void setup() {
    // set small list of source column names representing a source file to be mapped
    columns = new ArrayList<String>();
    columns.add("identificationID");
    columns.add("identificationQualifier");
    columns.add("unknown");
    columns.add("occurrenceID");

    // create a new Extension, that represents the Darwin Core Occurrence Core
    Extension extension = new Extension();
    extension.setRowType(Constants.DWC_ROWTYPE_OCCURRENCE);
    List<ExtensionProperty> extensionProperties = new ArrayList<ExtensionProperty>();
    ExtensionProperty extensionProperty = new ExtensionProperty();
    extensionProperty.setQualname(DwcTerm.occurrenceID.qualifiedName());
    extensionProperties.add(extensionProperty);
    extension.setProperties(extensionProperties);

    // an ExtensionMapping to Extension Darwin Core Occurrence Core
    extensionMapping = new ExtensionMapping();
    extensionMapping.setExtension(extension);

    // 2 translated fields pointing at same source column
    Set<PropertyMapping> fields = Sets.newHashSet();

    PropertyMapping mappingCoreid = new PropertyMapping();
    mappingCoreid.setTerm(DwcTerm.occurrenceID);
    mappingCoreid.setIndex(0);
    fields.add(mappingCoreid);

    extensionMapping.setFields(fields);

    // Resource
    resource = new Resource();
    resource.setShortname("myResource");
    resource.addMapping(extensionMapping);

    validator = new ExtensionMappingValidator();
  }
Example #2
0
  /**
   * Reconstruct published version, using version's Eml file, version history, etc.
   *
   * @param version version to assign to reconstructed resource
   * @param shortname shortname to assign to reconstructed resource
   * @param doi DOI to assign to reconstructed resource
   * @param organisation organisation to assign to reconstructed resource
   * @param versionHistory VersionHistory corresponding to resource version being reconstructed
   * @param versionEmlFile eml file corresponding to version of resource being reconstructed
   * @param key GBIF UUID to assign to reconstructed resource
   * @return published version reconstructed
   */
  public static Resource reconstructVersion(
      @NotNull BigDecimal version,
      @NotNull String shortname,
      @NotNull DOI doi,
      @Nullable Organisation organisation,
      @Nullable VersionHistory versionHistory,
      @Nullable File versionEmlFile,
      @Nullable UUID key) {
    Preconditions.checkNotNull(version);
    Preconditions.checkNotNull(shortname);
    Preconditions.checkNotNull(doi);

    if (organisation == null || versionHistory == null || versionEmlFile == null) {
      throw new IllegalArgumentException(
          "Failed to reconstruct resource version because not all of organisation, version history, or version eml file were provided");
    }

    // initiate new version, and set properties
    Resource resource = new Resource();
    resource.setShortname(shortname);
    resource.setEmlVersion(version);
    resource.setDoi(doi);
    resource.setOrganisation(organisation);
    resource.setKey(key);
    resource.setStatus(versionHistory.getPublicationStatus());
    resource.setIdentifierStatus(versionHistory.getStatus());
    resource.setRecordsPublished(versionHistory.getRecordsPublished());
    resource.setLastPublished(versionHistory.getReleased());

    if (versionEmlFile.exists()) {
      Eml eml = EmlUtils.loadWithLocale(versionEmlFile, Locale.US);
      resource.setEml(eml);
    } else {
      throw new IllegalArgumentException(
          "Failed to reconstruct resource: " + versionEmlFile.getAbsolutePath() + " not found!");
    }
    return resource;
  }