D-Net

package eu.dnetlib.parthenos.virtuoso;

import java.io.IOException;

import java.io.OutputStream;

import java.io.StringWriter;

import java.util.HashMap;

import java.util.Iterator;

import java.util.List;

import java.util.Map;

import com.google.common.collect.Iterators;

import com.google.common.collect.Lists;

import eu.dnetlib.parthenos.CRM;

import eu.dnetlib.parthenos.publisher.ParthenosPublisherException;

import freemarker.template.Configuration;

import freemarker.template.Template;

import freemarker.template.TemplateException;

import org.apache.commons.io.IOUtils;

import org.apache.commons.logging.Log;

import org.apache.commons.logging.LogFactory;

import org.apache.http.HttpEntity;

import org.apache.http.HttpHeaders;

import org.apache.http.NameValuePair;

import org.apache.http.client.entity.UrlEncodedFormEntity;

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

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

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

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

import org.apache.http.message.BasicNameValuePair;

import org.apache.http.util.EntityUtils;

import org.apache.jena.query.Query;

import org.apache.jena.query.QueryExecutionFactory;

import org.apache.jena.query.QueryFactory;

import org.apache.jena.query.ResultSet;

import org.apache.jena.sparql.engine.http.QueryEngineHTTP;

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

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

import org.springframework.web.bind.annotation.RequestMapping;

import org.springframework.web.bind.annotation.RequestMethod;

import org.springframework.web.bind.annotation.RequestParam;

import org.springframework.web.bind.annotation.RestController;

/**

 * Created by Alessia Bardi on 31/01/2018.

 * Read-only API for virtuoso.

 *

 * //TODO: error handling

 * //TODO: pagination

 * //TODO swagger documentation?

 *

 * @author Alessia Bardi

 */

@RestController

public class VirtuosoReadAPI {

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

	@Value("${virtuoso.sparqlurl}")

	private String sparqlUrl;

	@Value("${virtuoso.pwd}")

	private String username;

	@Value("${virtuoso.pwd}")

	private String password;

	@Value("${virtuoso.uri.base.default}")

	private String defaultBaseURI;

	@Value("${virtuoso.connectionstring")

	private String virtuosoConnectionString;

	@Autowired

	private Configuration freemarkerConfig;

	@RequestMapping(value = "/virtuoso/graphs", produces = { "application/json" }, method = RequestMethod.GET)

	public List<String> getGraphURLs(@RequestParam final String api) {

		String queryForGraphs =

				"SELECT DISTINCT ?g WHERE { ?g <dnetcollectedFrom> <"+defaultBaseURI+api+"> }";

		Query query = QueryFactory.create(queryForGraphs);

		final QueryEngineHTTP serviceRequest = QueryExecutionFactory.createServiceRequest(sparqlUrl, query);

		ResultSet graphs = serviceRequest.execSelect();

		Iterator<String> s = Iterators.transform(graphs, qs -> qs.getResource("g").getURI());

		List<String> res = Lists.newArrayList(s);

		serviceRequest.close();

		return res;

	}

	@RequestMapping(value = "/virtuoso/subjects", produces = { "application/json" }, method = RequestMethod.GET)

	public List<String> getSubjectsForGraph(@RequestParam final String graph) {

		// Based on FORTH observation, resources without a URL should not be interesting by themselves.

		// Here we filter out those + resources whose type is not in the parthenos namespace.

		//old query selecting any subjects in the given graph

		//String queryForSubjectsTemplate = "SELECT DISTINCT ?s WHERE {GRAPH <%s> {?s ?p ?o .}}";

		String queryForSubjectsTemplate = "SELECT DISTINCT ?s WHERE {GRAPH <%s> {?s ?p ?o . ?s a ?t. FILTER (isURI(?s) && ?t != <%s> && ?t != <%s>) }}";

		String q = String.format(queryForSubjectsTemplate, graph, CRM.E55_Type.getURI(), CRM.E41_Appellation.getURI());

		final QueryEngineHTTP serviceRequest =

				QueryExecutionFactory.createServiceRequest(sparqlUrl, QueryFactory.create(q));

		ResultSet subjects = serviceRequest.execSelect();

		Iterator<String> s = Iterators.transform(subjects, qs -> qs.getResource("s").getURI());

		List<String> res = Lists.newArrayList(s);

		serviceRequest.close();

		return res;

	}

	@RequestMapping(value = "/virtuoso/subjectsWithType", produces = { "application/json" }, method = RequestMethod.GET)

	public List<String> getSubjectsForGraphWithType(@RequestParam final String graph, @RequestParam final String typeNamespace, @RequestParam final String typeName) {

		String fullTypeName = typeNamespace + typeName;

		log.debug(String.format("Getting subjects of type %s for graph %s", fullTypeName, graph));

		String queryForSubjectsTemplate = "SELECT ?s WHERE {GRAPH <%s> {?s a <%s>. FILTER (isURI(?s)) }}";

		String q = String.format(queryForSubjectsTemplate, graph, fullTypeName);

		final QueryEngineHTTP serviceRequest =

				QueryExecutionFactory.createServiceRequest(sparqlUrl, QueryFactory.create(q));

		ResultSet subjects = serviceRequest.execSelect();

		Iterator<String> s = Iterators.transform(subjects, qs -> qs.getResource("s").getURI());

		List<String> res = Lists.newArrayList(s);

		serviceRequest.close();

		return res;

	}

	@RequestMapping(value = "/virtuoso/subject", produces = { "application/rdf+xml", "application/xml" }, method = RequestMethod.GET)

	public void getSubject(@RequestParam final String subjectURL, final OutputStream responseStream) throws IOException, ParthenosPublisherException {

		//String describeQuery = "DESCRIBE <" + subjectURL + ">";

		//log.debug(describeQuery);

		//Can't use DESCRIBE query: server decides what to return (i.e. not all triples) and cannot find out if and how Virtuoso can be configured

		String q = "DEFINE input:inference 'parthenos_rules' CONSTRUCT {<%s> ?p ?o . } WHERE { <%s> ?p ?o .}";

		String query = String.format(q, subjectURL, subjectURL);

		sendConstructResponse(query, responseStream);

	}

	@RequestMapping(value = "/virtuoso/subjectForJRR", produces = { "application/rdf+xml", "application/xml" }, method = RequestMethod.GET)

	public void getSubjectForJRR(@RequestParam final String subjectURL, @RequestParam final String typeName, final OutputStream responseStream)

			throws IOException, TemplateException, ParthenosPublisherException {

		String templateName = typeName+".sparql";

		Template temp = freemarkerConfig.getTemplate(templateName);

		Map<String, String> values = new HashMap<>();

		values.put("subjectURL", subjectURL);

		StringWriter sw = new StringWriter();

		temp.process(values, sw);

		String q = sw.toString();

		log.debug("Querying for "+subjectURL+" with query "+templateName);

		sendConstructResponse(q, responseStream);

	}

	protected void sendConstructResponse(final String query, final OutputStream responseStream) throws IOException, ParthenosPublisherException {

		String res = executeSparqlPost(query);

		IOUtils.write(res, responseStream);

	}

	protected String executeSparqlPost(final String query) throws IOException, ParthenosPublisherException {

		try (CloseableHttpClient httpclient = HttpClients.createDefault()) {

			HttpPost httpPost = new HttpPost(sparqlUrl);

			httpPost.setHeader(HttpHeaders.ACCEPT, "application/rdf+xml");

			List<NameValuePair> nvps = Lists.newArrayList();

			nvps.add(new BasicNameValuePair("query", query));

			httpPost.setEntity(new UrlEncodedFormEntity(nvps));

			try (CloseableHttpResponse response2 = httpclient.execute(httpPost)) {

				log.debug(response2.getStatusLine());

				HttpEntity entity2 = response2.getEntity();

				String res = IOUtils.toString(entity2.getContent());

				EntityUtils.consume(entity2);

				int statusCode = response2.getStatusLine().getStatusCode();

				switch(statusCode){

				case 200:

					return res;

				default:

					String errorMessage = String.format("ERROR HTTP STATUS CODE %d, REASON PHRASE: %s\n ERROR BODY: %s", statusCode, response2.getStatusLine(), res);

					log.error(errorMessage);

					throw new ParthenosPublisherException(errorMessage);

				}

			}

		}

	}

}