D-Net

package eu.dnetlib.resolver;

import java.io.IOException;

import java.util.HashMap;

import java.util.Map;

import eu.dnetlib.dli.DLIUtils;

import eu.dnetlib.resolver.model.CompletionStatus;

import eu.dnetlib.resolver.model.ObjectProvenance;

import eu.dnetlib.resolver.model.ObjectProvisionMode;

import eu.dnetlib.resolver.model.ResolvedObject;

import net.sf.ehcache.Cache;

import net.sf.ehcache.Element;

import org.apache.commons.lang3.StringUtils;

import org.apache.commons.logging.Log;

import org.apache.commons.logging.LogFactory;

import org.apache.http.HttpEntity;

import org.apache.http.client.ResponseHandler;

import org.apache.http.client.methods.HttpGet;

import org.apache.http.impl.client.CloseableHttpClient;

import org.apache.http.impl.client.HttpClients;

import org.apache.http.util.EntityUtils;

import org.springframework.beans.factory.annotation.Autowired;

import org.springframework.beans.factory.annotation.Required;

/**

 * Created by sandro on 9/8/16.

 */

public abstract class AbstractPIDResolver implements PIDResolver {

	public static final Map<String, String> resolvedTypes = new HashMap<String, String>() {

		{

			put("pdb", "http://www.rcsb.org/pdb/explore/explore.do?structureId=%s");

			put("ncbi-n", "http://www.ncbi.nlm.nih.gov/gquery/?term=%s");

			put("pmid", "http://www.ncbi.nlm.nih.gov/pubmed/%s");

			put("pmcid", "http://www.ncbi.nlm.nih.gov/pmc/articles/%s");

			put("pubmedid", "http://www.ncbi.nlm.nih.gov/pubmed/%s");

			put("doi", "http://dx.doi.org/%s");

			put("genbank", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");

			put("nuccore", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");

			put("swiss-prot", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");

			put("arrayexpress", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");

			put("biomodels", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");

			put("bmrb", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");

			put("ena", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");

			put("genbank", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");

			put("geo", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");

			put("ensembl", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");

			put("mgi", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");

			put("bind", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");

			put("pride", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");

			put("ddbj", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");

			put("bioproject", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");

			put("embl", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");

			put("sra", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");

		}

	};

	private static final Log log = LogFactory.getLog(AbstractPIDResolver.class);

	private Cache cache;

	private String name;

	@Autowired

	private ResolverStore storeManager;

	private ResponseHandler<String> responseHandler = response -> {

		int status = response.getStatusLine().getStatusCode();

		if (status >= 200 && status < 300) {

			HttpEntity entity = response.getEntity();

			return entity != null ? EntityUtils.toString(entity) : null;

		} else {

			log.debug("Unexpected response status: " + status);

			return null;

		}

	};

	public static void setDatasourceProvenace(final ObjectProvenance provenance, final String namespacePrefix) {

		try {

			provenance.setDatasourceId(DLIUtils.getIdFromDataSourcePrefix(namespacePrefix));

			provenance.setDatasource(DLIUtils.getNameFromDataSourcePrefix(namespacePrefix));

			provenance.setCompletionStatus(CompletionStatus.complete.toString());

			provenance.setProvisionMode(ObjectProvisionMode.resolved.toString());

		} catch (Throwable e) {

			log.error("Error on assignin datasource ");

		}

	}

	public ResolvedObject retrievePID(final String pid, final String pidType) {

		if (!canResolvePid(pidType)) return null;

		final Element item = cache.get(storeManager.generateDNetIdentifier(pid, pidType));

		if (item != null) return (ResolvedObject) item.getObjectValue();

		ResolvedObject resolvedObject = storeManager.getRecord(pid, pidType);

		if (resolvedObject != null) {

			cache.put(new Element(storeManager.generateDNetIdentifier(pid, pidType), resolvedObject));

			return resolvedObject;

		}

		resolvedObject = resolve(pid, pidType);

		if (resolvedObject != null) {

			storeManager.insertRecord(getName(), resolvedObject);

			cache.put(new Element(storeManager.generateDNetIdentifier(pid, pidType), resolvedObject));

			return resolvedObject;

		}

		return null;

	}

	public String retrieveDnetID(final String pid, final String pidType) {

		if (!canResolvePid(pidType)) return null;

		final String dnetIdentifier = storeManager.generateDNetIdentifier(pid, pidType);

		final Element item = cache.get(dnetIdentifier);

		if (item != null) return dnetIdentifier;

		String resolvedIdentifier = storeManager.getRecordIdentifier(pid, pidType);

		if (resolvedIdentifier != null && !StringUtils.isBlank(resolvedIdentifier))

			return resolvedIdentifier;

		ResolvedObject resolvedObject = resolve(pid, pidType);

		if (resolvedObject != null) {

			storeManager.insertRecord(getName(), resolvedObject);

			cache.put(new Element(dnetIdentifier, resolvedObject));

			return dnetIdentifier;

		}

		return null;

	}

	public String getName() {

		return this.getClass().getSimpleName();

	}

	public void setName(final String name) {

		this.name = name;

	}

	protected abstract boolean canResolvePid(final String pidType);

	protected abstract ResolvedObject resolve(final String pid, final String pidType);

	public Cache getCache() {

		return cache;

	}

	@Required

	public void setCache(final Cache cache) {

		this.cache = cache;

	}

	protected String requestURL(final String url) {

		final CloseableHttpClient httpclient = HttpClients.createDefault();

		try {

			HttpGet httpGet = new HttpGet(url);

			return httpclient.execute(httpGet, responseHandler);

		} catch (Throwable e) {

			log.debug("Error in getting url " + url, e);

			return null;

		} finally {

			try {

				httpclient.close();

			} catch (IOException e) {

				log.error("Error on closing httpclient", e);

			}

		}

	}

}