/** TODO */
private OrgDisambiguatedEntity findByDetails(RDFOrganization org) {
Iso3166Country country =
StringUtils.isBlank(org.country) ? null : Iso3166Country.valueOf(org.country);
// Find the org by name, city, country and state
OrgDisambiguatedEntity existingEntity =
orgDisambiguatedDao.findByNameCityRegionCountryAndSourceType(
org.name, org.stateCode, org.stateCode, country, FUNDREF_SOURCE_TYPE);
// If no match is found, try with the doi and source type
if (existingEntity == null) {
existingEntity =
orgDisambiguatedDao.findBySourceIdAndSourceType(org.doi, FUNDREF_SOURCE_TYPE);
}
return existingEntity;
}
/** Creates a disambiguated ORG in the org_disambiguated table */
private OrgDisambiguatedEntity createDisambiguatedOrg(RDFOrganization organization) {
LOGGER.info("Creating disambiguated org {}", organization.name);
String orgType =
organization.type
+ (StringUtils.isEmpty(organization.subtype) ? "" : "/" + organization.subtype);
Iso3166Country country =
StringUtils.isNotBlank(organization.country)
? Iso3166Country.fromValue(organization.country)
: null;
OrgDisambiguatedEntity orgDisambiguatedEntity = new OrgDisambiguatedEntity();
orgDisambiguatedEntity.setName(organization.name);
orgDisambiguatedEntity.setCountry(country);
orgDisambiguatedEntity.setCity(organization.city);
orgDisambiguatedEntity.setRegion(organization.stateCode);
orgDisambiguatedEntity.setOrgType(orgType);
orgDisambiguatedEntity.setSourceId(organization.doi);
orgDisambiguatedEntity.setSourceUrl(organization.doi);
orgDisambiguatedEntity.setSourceType(FUNDREF_SOURCE_TYPE);
orgDisambiguatedDao.persist(orgDisambiguatedEntity);
return orgDisambiguatedEntity;
}
/** Executes the import process */
private void execute() {
try {
long start = System.currentTimeMillis();
FileInputStream file = new FileInputStream(fileToLoad);
DocumentBuilderFactory builderFactory = DocumentBuilderFactory.newInstance();
DocumentBuilder builder = builderFactory.newDocumentBuilder();
Document xmlDocument = builder.parse(file);
// Parent node
NodeList nodeList =
(NodeList)
xPath.compile(conceptsExpression).evaluate(xmlDocument, XPathConstants.NODESET);
for (int i = 0; i < nodeList.getLength(); i++) {
RDFOrganization rdfOrganization =
getOrganization(xmlDocument, nodeList.item(i).getAttributes());
LOGGER.info(
"Processing organization from RDF, doi:{}, name:{}, country:{}, state:{}, stateCode:{}, type:{}, subtype:{}",
new String[] {
rdfOrganization.doi,
rdfOrganization.name,
rdfOrganization.country,
rdfOrganization.state,
rdfOrganization.stateCode,
rdfOrganization.type,
rdfOrganization.subtype
});
// #1: Look for an existing org
OrgDisambiguatedEntity existingEntity = findByDetails(rdfOrganization);
if (existingEntity != null) {
// #2: If the name, city or region changed, update those values
if (entityChanged(rdfOrganization, existingEntity)) {
existingEntity.setCity(rdfOrganization.city);
Iso3166Country country =
StringUtils.isNotBlank(rdfOrganization.country)
? Iso3166Country.fromValue(rdfOrganization.country)
: null;
existingEntity.setCountry(country);
existingEntity.setName(rdfOrganization.name);
String orgType =
rdfOrganization.type
+ (StringUtils.isNotBlank(rdfOrganization.subtype)
? ('/' + rdfOrganization.subtype)
: "");
existingEntity.setOrgType(orgType);
existingEntity.setRegion(rdfOrganization.stateCode);
existingEntity.setSourceId(rdfOrganization.doi);
existingEntity.setSourceType(FUNDREF_SOURCE_TYPE);
existingEntity.setSourceUrl(rdfOrganization.doi);
orgDisambiguatedDao.merge(existingEntity);
updatedOrgs += 1;
} else if (idChanged(rdfOrganization, existingEntity)) {
// #3: If the ID changed, create an external identifier
createExternalIdentifier(existingEntity, rdfOrganization.doi);
addedExternalIdentifiers += 1;
}
} else {
// #4: Else, create the new org
OrgDisambiguatedEntity newOrg = createDisambiguatedOrg(rdfOrganization);
addedDisambiguatedOrgs += 1;
}
}
long end = System.currentTimeMillis();
LOGGER.info("Time taken to process the files: {}", (end - start));
} catch (FileNotFoundException fne) {
LOGGER.error("Unable to read file {}", fileToLoad);
} catch (ParserConfigurationException pce) {
LOGGER.error("Unable to initialize the DocumentBuilder");
} catch (IOException ioe) {
LOGGER.error("Unable to parse document {}", fileToLoad);
} catch (SAXException se) {
LOGGER.error("Unable to parse document {}", fileToLoad);
} catch (XPathExpressionException xpe) {
LOGGER.error("XPathExpressionException {}", xpe.getMessage());
} finally {
LOGGER.info(
"Number new Disambiguated Orgs={}, Updated Orgs={}, new External Identifiers={}",
new Object[] {addedDisambiguatedOrgs, updatedOrgs, addedExternalIdentifiers, getTotal()});
}
}
