D-Net

package eu.dnetlib.dli.resolver;

import com.google.common.collect.Lists;

import com.google.gson.JsonArray;

import com.google.gson.JsonElement;

import com.google.gson.JsonObject;

import com.google.gson.JsonParser;

import eu.dnetlib.dli.resolver.model.DLIObjectProvenance;

import eu.dnetlib.dli.resolver.model.DLIResolvedObject;

import eu.dnetlib.pid.resolver.model.ObjectType;

import eu.dnetlib.pid.resolver.AbstractPIDResolver;

import org.apache.commons.logging.Log;

import org.apache.commons.logging.LogFactory;

import java.util.List;

/**

 * @author sandro

 */

public class PubMedResolver extends AbstractPIDResolver {

	private static final Log log = LogFactory.getLog(PubMedResolver.class); // NOPMD by marko on 11/24/08 5:02 PM

	private static final String query = "http://www.ebi.ac.uk/europepmc/webservices/rest/search/query=%s&format=json";

	private static final String PUBMED_NS_PREFIX = "pubmed______";

	@Override

	protected boolean canResolvePid(final String pidType) {

		return pidType != null && (pidType.toLowerCase().trim().equals("pubmedid") || pidType.toLowerCase().trim().equals("pmcid"));

	}

	@Override

    protected DLIResolvedObject resolve(final String pid, final String pidType) {

        String requestUrl = null;

		String type = null;

		if (pidType.toLowerCase().trim().equals("pubmedid")) {

			requestUrl = String.format(query, "ext_id:" + pid);

			type = "pubmedid";

		} else if (pidType.toLowerCase().trim().equals("pmcid")) {

			requestUrl = String.format(query, "pmcid:" + pid);

			type = "pmcid";

		}

		if (requestUrl == null)

			return null;

		try {

			String result = requestURL(requestUrl);

			return parsingResponse(result, type);

		} catch (Throwable e) {

			log.error(String.format("Error on resolving pid %s type:%s requestUrl:%s", pid, pidType, requestUrl), e);

		}

		return null;

	}

    private DLIResolvedObject parsingResponse(final String response, final String type) {

        if (response == null) return null;

		JsonElement jElement = new JsonParser().parse(response);

		JsonObject jobject = jElement.getAsJsonObject();

		if (jobject.has("hitCount")) {

			long total = jobject.get("hitCount").getAsLong();

			if (total == 0) return null;

            DLIResolvedObject responseObj = new DLIResolvedObject();

			JsonElement hits = ((JsonObject) jobject.get("resultList")).get("result");

			JsonArray hitsObject = hits.getAsJsonArray();

			for (JsonElement elem : hitsObject) {

                String idType;

                if (type.equals("pmcid")) {

					idType = type;

				} else {

					idType = "pmid";

				}

                if (!((JsonObject) elem).has(idType)) {

                    continue;

                }

				String doi = ((JsonObject) elem).get(idType).getAsString();

				responseObj.setPid(doi);

				responseObj.setPidType(type);

				responseObj.setType(ObjectType.publication);

				List<String> authors = Lists.newArrayList();

				List<String> titles = Lists.newArrayList();

				// ADDING TITLES

				JsonElement titleElement = ((JsonObject) elem).get("title");

				if (titleElement != null) {

					String titleString = titleElement.getAsString();

					titles.add(titleString);

				}

				responseObj.setTitles(titles);

				// ADDING AUTHORS

				JsonElement contributorElement = ((JsonObject) elem).get("authorString");

				if (contributorElement != null) {

					String contributorString = contributorElement.getAsString();

					if (contributorString != null) {

						String[] splittedAuthors = contributorString.split(",");

						for (int i = 0; i < splittedAuthors.length; i++) {

							authors.add(splittedAuthors[i]);

						}

					}

				}

				responseObj.setAuthors(authors);

				JsonElement date = ((JsonObject) elem).get("pubYear");

				if (date.isJsonNull() == false) {

					responseObj.setDate(date.getAsString());

				}

                DLIObjectProvenance provenance = new DLIObjectProvenance(PUBMED_NS_PREFIX, "resolved", "complete", null, null, true);

                responseObj.fixContribution(provenance);

				responseObj.setDatasourceProvenance(Lists.newArrayList(provenance));

				return responseObj;

			}

			return null;

		}

		return null;

	}

}