172 lines
7.4 KiB
Java
172 lines
7.4 KiB
Java
package eu.dnetlib.ariadneplus.virtuoso;
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import java.io.IOException;
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import java.io.OutputStream;
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import java.io.StringWriter;
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import java.util.HashMap;
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import java.util.Iterator;
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import java.util.List;
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import java.util.Map;
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import com.google.common.collect.Iterators;
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import com.google.common.collect.Lists;
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import eu.dnetlib.ariadneplus.CRM;
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import eu.dnetlib.ariadneplus.publisher.AriadnePlusPublisherException;
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import freemarker.template.Configuration;
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import freemarker.template.Template;
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import freemarker.template.TemplateException;
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import org.apache.commons.io.IOUtils;
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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.apache.http.HttpEntity;
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import org.apache.http.HttpHeaders;
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import org.apache.http.NameValuePair;
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import org.apache.http.client.entity.UrlEncodedFormEntity;
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import org.apache.http.client.methods.CloseableHttpResponse;
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import org.apache.http.client.methods.HttpPost;
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import org.apache.http.impl.client.CloseableHttpClient;
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import org.apache.http.impl.client.HttpClients;
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import org.apache.http.message.BasicNameValuePair;
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import org.apache.http.util.EntityUtils;
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import org.apache.jena.query.ResultSet;
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import org.apache.jena.sparql.engine.http.QueryEngineHTTP;
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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 org.springframework.http.HttpStatus;
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import org.springframework.web.bind.annotation.*;
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/**
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* Created by Alessia Bardi on 31/01/2018.
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* Read-only API for virtuoso.
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*
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* //TODO: error handling (http://www.springboottutorial.com/spring-boot-exception-handling-for-rest-services)
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* //TODO: pagination
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* //TODO swagger documentation?
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*
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* @author Alessia Bardi
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*/
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@RestController
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public class VirtuosoReadAPI {
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private static final Log log = LogFactory.getLog(VirtuosoReadAPI.class);
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@Value("${virtuoso.sparqlurl}")
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private String sparqlUrl;
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@Value("${virtuoso.pwd}")
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private String username;
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@Value("${virtuoso.pwd}")
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private String password;
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@Value("${virtuoso.uri.base.default}")
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private String defaultBaseURI;
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@Value("${virtuoso.connectionstring")
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private String virtuosoConnectionString;
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@Autowired
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private Configuration freemarkerConfig;
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@RequestMapping(value = "/virtuoso/apiSubjectsWithType", produces = { "application/json" }, method = RequestMethod.GET)
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public List<String> getSubjectsForApiWithType(@RequestParam final String api, @RequestParam final String typeNamespace, @RequestParam final String typeName, @RequestParam final int limit, @RequestParam final int offset){
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String fullTypeName = typeNamespace + typeName;
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log.debug(String.format("Getting subjects of type %s for API %s limit %d offset %d", fullTypeName, api, limit, offset));
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//if I add the ORDER BY the query is too slow: let's hope we are not getting the same subjects over and over again
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String queryForSubjectsTemplate = "DEFINE input:inference 'ariadneplus_rules' SELECT DISTINCT ?s WHERE { GRAPH ?g {?s a <%s> .} . GRAPH dnet:graph {?g dnet:collectedFrom <%s> .}} LIMIT %d OFFSET %d";
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String q = String.format(queryForSubjectsTemplate, fullTypeName, defaultBaseURI+api, limit, offset);
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log.debug("SPARQL query: "+q);
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final QueryEngineHTTP serviceRequest = new QueryEngineHTTP(sparqlUrl, q);
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ResultSet subjects = serviceRequest.execSelect();
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Iterator<String> s = Iterators.transform(subjects, qs -> qs.getResource("s").getURI());
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List<String> res = Lists.newArrayList(s);
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serviceRequest.close();
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return res;
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}
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/**
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* Returns the paginated list of resource URI used as subjects in the context of a given api. All subject URIs are returned, except from CRM.E55_Type and CRM.E41_Appellation.
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* TODO: probably we can remove this, as it is used only for testing.
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* @param api
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* @param limit
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* @param offset
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* @return a page of URIs that are subjects in the context of a given api
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*
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*/
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@Deprecated
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@RequestMapping(value = "/virtuoso/apiSubjects", produces = { "application/json" }, method = RequestMethod.GET)
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public List<String> getSubjectsForApi(@RequestParam final String api, @RequestParam final int limit, @RequestParam final int offset){
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log.debug(String.format("Getting subjects for API %s, limit %d offset %d", api, limit, offset));
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//if I add the ORDER BY the query is too slow: let's hope we are not getting the same subjects over and over again
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String queryForSubjectsTemplate = "DEFINE input:inference 'ariadneplus_rules' SELECT DISTINCT ?s WHERE { GRAPH ?g {?s a ?t . FILTER (?t != <%s> && ?t != <%s>)} . GRAPH dnet:graph {?g dnet:collectedFrom <%s> .}} LIMIT %d OFFSET %d ";
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String q = String.format(queryForSubjectsTemplate, CRM.E55_Type.getURI(), CRM.E41_Appellation.getURI(), defaultBaseURI+api, limit, offset);
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log.debug("SPARQL query: "+q);
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final QueryEngineHTTP serviceRequest = new QueryEngineHTTP(sparqlUrl, q);
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ResultSet subjects = serviceRequest.execSelect();
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Iterator<String> s = Iterators.transform(subjects, qs -> qs.getResource("s").getURI());
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List<String> res = Lists.newArrayList(s);
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serviceRequest.close();
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return res;
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}
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@RequestMapping(value = "/virtuoso/subject", produces = { "application/rdf+xml", "application/xml" }, method = RequestMethod.GET)
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@ResponseStatus(value = HttpStatus.OK)
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public void getSubject(@RequestParam final String subjectURL, @RequestParam final String typeName, @RequestParam(name="timeout") final String timeoutMs, final OutputStream responseStream)
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throws IOException, TemplateException, AriadnePlusPublisherException {
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String templateName = typeName+".sparql";
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Template temp = freemarkerConfig.getTemplate(templateName);
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Map<String, String> values = new HashMap<>();
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values.put("subjectURL", subjectURL);
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StringWriter sw = new StringWriter();
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temp.process(values, sw);
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String q = sw.toString();
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log.debug("Querying for "+subjectURL+" with query "+templateName);
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sendConstructResponse(q, timeoutMs, responseStream);
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}
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protected void sendConstructResponse(final String query, final String timeoutMs, final OutputStream responseStream) throws IOException, AriadnePlusPublisherException {
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String res = executeSparqlPost(query, timeoutMs);
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IOUtils.write(res, responseStream);
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}
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protected String executeSparqlPost(final String query, final String timeoutMs) throws IOException, AriadnePlusPublisherException {
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try (CloseableHttpClient httpclient = HttpClients.createDefault()) {
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HttpPost httpPost = new HttpPost(sparqlUrl);
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httpPost.setHeader(HttpHeaders.ACCEPT, "application/rdf+xml");
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List<NameValuePair> nvps = Lists.newArrayList();
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nvps.add(new BasicNameValuePair("query", query));
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if (StringUtils.isNotBlank(timeoutMs)) {
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nvps.add(new BasicNameValuePair("timeout", timeoutMs));
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}
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httpPost.setEntity(new UrlEncodedFormEntity(nvps));
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try (CloseableHttpResponse response2 = httpclient.execute(httpPost)) {
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HttpEntity entity2 = response2.getEntity();
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String res = IOUtils.toString(entity2.getContent());
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EntityUtils.consume(entity2);
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int statusCode = response2.getStatusLine().getStatusCode();
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switch(statusCode){
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case 200:
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return res;
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case 504:
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String msg = String.format("ERROR 504 on query %s", query);
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throw new AriadnePlusPublisherException(msg);
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default:
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String errorMessage = String.format("ERROR HTTP STATUS CODE %d, REASON PHRASE: %s\n ERROR BODY: %s", statusCode, response2.getStatusLine(), res);
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log.error(errorMessage);
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return "";
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//throw new AriadnePlusPublisherException(errorMessage);
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}
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}
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}
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}
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}
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