@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();
}
/**
* 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;
}