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package eu.dnetlib.data.mdstore.plugins;
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import java.io.StringReader;
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import java.net.URI;
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import java.net.URISyntaxException;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import java.util.stream.Collectors;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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import org.dom4j.Document;
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import org.dom4j.DocumentException;
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import org.dom4j.Element;
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import org.dom4j.Node;
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import org.dom4j.io.SAXReader;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.beans.factory.annotation.Value;
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import com.google.common.base.Splitter;
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import eu.dnetlib.data.mdstore.plugins.objects.MdRecord;
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import eu.dnetlib.data.mdstore.plugins.objects.MyURL;
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import eu.dnetlib.data.mdstore.plugins.objects.Project;
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import eu.dnetlib.data.utils.OpenAIREAuthenticationProvider;
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public class EnrichOpenairePlugin extends GenericDoiMdstorePlugin {
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private static final Log log = LogFactory.getLog(EnrichOpenairePlugin.class);
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@Value("${plugin.enrich.publications.openaire.url}")
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private String baseUrl;
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@Value("${plugin.enrich.openaire.datasources.blacklist}")
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private String datasourceBlackList;
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@Autowired
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private OpenAIREAuthenticationProvider openAIREAuthenticationProvider;
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private Map<String, Counter> counters = new HashMap<>();
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@Override
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protected URI prepareURI(final String doi) throws URISyntaxException {
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return new URI(String.format(baseUrl, doi));
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}
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@Override
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protected void reconfigure(final Map<String, String> params) {
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counters.clear();
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counters.put("subjects", new Counter());
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counters.put("citations", new Counter());
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counters.put("urls", new Counter());
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counters.put("projects", new Counter());
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counters.put("dois", new Counter());
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setAccessToken(openAIREAuthenticationProvider.obtainAccessToken());
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}
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@Override
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protected void resetConfiguration() {
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log.info("***** Openaire Enrichment - subjects : " + counters.get("subjects"));
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log.info("***** Openaire Enrichment - citations : " + counters.get("citations"));
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log.info("***** Openaire Enrichment - urls : " + counters.get("urls"));
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log.info("***** Openaire Enrichment - projects : " + counters.get("projects"));
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log.info("***** Openaire Enrichment - dois : " + counters.get("dois"));
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counters.clear();
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setAccessToken(null);
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}
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@Override
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protected boolean updateDocument(final MdRecord doc, final String response) {
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counters.get("subjects").incrementBefore(doc.getSubjects().size());
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counters.get("citations").incrementBefore(doc.getCitations().size());
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counters.get("urls").incrementBefore(doc.getUrls().size());
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counters.get("projects").incrementBefore(doc.getProjects().size());
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counters.get("dois").incrementBefore(doc.getDois().size());
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try {
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final Document docRes = (new SAXReader()).read(new StringReader(response));
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final List<?> results = docRes.selectNodes("/response/results/result");
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if (results.size() == 1) {
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final Node n = (Node) results.get(0);
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updateSubjects(doc, n);
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updateCitations(doc, n);
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updateUrls(doc, n);
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updateProjects(doc, n);
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updateDois(doc, n);
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updateBestRights(doc);
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return true;
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} else if (results.size() == 1) {
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log.warn("Too many responses");
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}
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} catch (final DocumentException e) {
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log.warn("Invalid response", e);
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} finally {
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counters.get("subjects").incrementAfter(doc.getSubjects().size());
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counters.get("citations").incrementAfter(doc.getCitations().size());
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counters.get("urls").incrementAfter(doc.getUrls().size());
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counters.get("projects").incrementAfter(doc.getProjects().size());
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counters.get("dois").incrementAfter(doc.getDois().size());
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}
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return false;
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}
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private void updateSubjects(final MdRecord doc, final Node n) {
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final Set<String> subjects = doc.getSubjects()
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.stream()
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.map(EnrichOpenairePlugin::cleanSubject)
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.flatMap(List::stream)
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.collect(Collectors.toSet());
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for (final Object o : n.selectNodes(".//subject[@classid='keyword']")) {
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subjects.addAll(cleanSubject(((Node) o).getText().trim()));
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}
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doc.setSubjects(subjects);
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}
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public static List<String> cleanSubject(final String s) {
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if (s.isEmpty()) {
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return new ArrayList<>();
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} else if (s.startsWith("info:eu-repo/classification/msc/")) {
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return new ArrayList<>();
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} else if (s.startsWith("info:eu-repo/classification/acm/")) {
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return Arrays.asList(s.replaceFirst("info:eu-repo/classification/acm/", ""));
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} else if (s.contains(";")) {
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return Splitter.on(";").trimResults().omitEmptyStrings().splitToList(s);
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} else if (s.contains(",")) {
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return Splitter.on(",").trimResults().omitEmptyStrings().splitToList(s);
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} else {
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return Arrays.asList(s);
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}
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}
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private void updateCitations(final MdRecord doc, final Node n) {
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doc.getCitations().clear();
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for (final Object o : n.selectNodes(".//citations/citation/rawText")) {
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doc.getCitations().add(((Node) o).getText());
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}
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}
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private void updateUrls(final MdRecord doc, final Node n) {
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doc.getUrls().addAll(doc.getUrls());
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final Set<String> blacklist =
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Arrays.stream(datasourceBlackList.split(",")).map(String::trim).filter(StringUtils::isNotBlank).collect(Collectors.toSet());
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for (final Object oin : n.selectNodes(".//instance")) {
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final String hostedByid = ((Element) oin).valueOf("./hostedby/@id").trim();
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if (!blacklist.contains(hostedByid)) {
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final String hostedByName = ((Element) oin).valueOf("./hostedby/@name").trim();
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final String rights = ((Element) oin).valueOf("./accessright/@classname").trim();
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for (final Object ourl : ((Element) oin).selectNodes("./webresource/url")) {
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final MyURL u = new MyURL(((Node) ourl).getText().trim(), hostedByName, rights);
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doc.getUrls().remove(u);
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doc.getUrls().add(u);
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}
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}
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}
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}
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private void updateProjects(final MdRecord doc, final Node n) {
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for (final Object op : n.selectNodes(".//rels/rel[./to/@type='project']")) {
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final Node p = (Node) op;
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final String name = p.valueOf("./title").trim();
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if (StringUtils.isNotBlank(name) && !name.equalsIgnoreCase("null") && !name.equalsIgnoreCase("unidentified") && !name.equalsIgnoreCase("unknown")) {
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final Project np = new Project();
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np.setOpenaireId(p.valueOf("./to"));
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np.setCode(p.valueOf("./code"));
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np.setName(name);
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np.setAcronym(p.valueOf("./acronym"));
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np.setFunder(p.valueOf(".//funder/@shortname"));
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np.setProgram(p.valueOf(".//funding_level_0/@name"));
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np.setJurisdiction(p.valueOf(".//funder/@jurisdiction"));
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np.setInfoId(String.format("info:eu-repo/grantAgreement/%s/%s/%s/%s/%s/%s", np.getFunder(), np.getProgram(), np.getCode(), np.getJurisdiction(),
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np.getName(), np.getAcronym()));
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doc.getProjects().add(np);
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}
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}
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}
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private void updateDois(final MdRecord doc, final Node n) {
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for (final Object od : n.selectNodes(".//*[local-name()='result']/pid[@classid='doi']")) {
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final String doi = ((Node) od).getText().trim();
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if (StringUtils.isNotBlank(doi)) {
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doc.getDois().add(doi);
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}
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}
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}
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private void updateBestRights(final MdRecord doc) {
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final Set<String> availables = doc.getUrls().stream().map(MyURL::getRights).map(String::toUpperCase).collect(Collectors.toSet());
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if (availables.contains("OPEN ACCESS")) {
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doc.setBestRights("Open Access");
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} else if (availables.contains("EMBARGO")) {
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doc.setBestRights("Embargo");
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} else if (availables.contains("RESTRICTED")) {
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doc.setBestRights("Restricted");
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} else if (availables.contains("CLOSED ACCESS")) {
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doc.setBestRights("Closed Access");
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} else {
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doc.setBestRights("Unknown");
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}
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}
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}
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