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SparqlServlet.java
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SparqlServlet.java
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package uk.ac.ebi.fgpt.lode.servlet;
import com.hp.hpl.jena.query.QueryParseException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.HttpHeaders;
import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
import org.springframework.stereotype.Controller;
import org.springframework.web.bind.MissingServletRequestParameterException;
import org.springframework.web.bind.annotation.*;
import org.springframework.web.method.annotation.MethodArgumentConversionNotSupportedException;
import org.springframework.web.method.annotation.MethodArgumentTypeMismatchException;
import uk.ac.ebi.fgpt.lode.exception.LodeException;
import uk.ac.ebi.fgpt.lode.service.SparqlService;
import uk.ac.ebi.fgpt.lode.utils.GraphQueryFormats;
import uk.ac.ebi.fgpt.lode.utils.QueryType;
import uk.ac.ebi.fgpt.lode.utils.TupleQueryFormats;
import javax.servlet.ServletOutputStream;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import java.io.IOException;
/**
* @author Simon Jupp
* @date 21/02/2013
* Functional Genomics Group EMBL-EBI
*/
@Controller
@RequestMapping("/query")
public class SparqlServlet {
private Logger log = LoggerFactory.getLogger(getClass());
public SparqlService getSparqlService() {
return sparqlService;
}
@Autowired
public void setSparqlService(SparqlService sparqlService) {
this.sparqlService = sparqlService;
}
private SparqlService sparqlService;
protected Logger getLog() {
return log;
}
@RequestMapping (produces="application/sparql-results+xml")
public @ResponseBody
void getSparqlXml(
@RequestParam(value = "query", required = false) String query,
@RequestParam(value = "offset", required = false) Integer offset,
@RequestParam(value = "limit", required = false) Integer limit,
@RequestParam(value = "inference", required = false) boolean inference,
HttpServletRequest request,
HttpServletResponse response) throws QueryParseException, LodeException, IOException {
log.trace("querying for sparql xml");
query(query, "XML", offset, limit, inference, request, response);
}
@RequestMapping (produces="application/sparql-results+json")
public @ResponseBody
void getSparqlJson(
@RequestParam(value = "query", required = false) String query,
@RequestParam(value = "offset", required = false) Integer offset,
@RequestParam(value = "limit", required = false) Integer limit,
@RequestParam(value = "inference", required = false) boolean inference,
HttpServletRequest request,
HttpServletResponse response) throws QueryParseException, LodeException, IOException {
log.trace("querying for sparql json");
query(query, "JSON", offset, limit, inference, request, response);
}
@RequestMapping (produces="text/csv")
public @ResponseBody
void getSparqlCsv(
@RequestParam(value = "query", required = false) String query,
@RequestParam(value = "offset", required = false) Integer offset,
@RequestParam(value = "limit", required = false) Integer limit,
@RequestParam(value = "inference", required = false) boolean inference,
HttpServletRequest request,
HttpServletResponse response) throws QueryParseException, LodeException, IOException {
log.trace("querying for sparql csv");
query(query, "CSV", offset, limit, inference, request, response);
}
@RequestMapping (produces="text/tab-separated-values")
public @ResponseBody
void getSparqlTsv(
@RequestParam(value = "query", required = false) String query,
@RequestParam(value = "offset", required = false) Integer offset,
@RequestParam(value = "limit", required = false) Integer limit,
@RequestParam(value = "inference", required = false) boolean inference,
HttpServletRequest request,
HttpServletResponse response) throws QueryParseException, LodeException, IOException {
log.trace("querying for sparql tsv");
query(query, "TSV", offset, limit, inference, request, response);
}
@RequestMapping (produces="application/rdf+xml")
public @ResponseBody
void getGraphXML(
@RequestParam(value = "query", required = false) String query,
HttpServletResponse response) throws QueryParseException, LodeException, IOException {
log.trace("querying for graph rdf+xml");
ServletOutputStream out = response.getOutputStream();
if (query == null) {
response.setContentType("application/rdf+xml; charset=utf-8");
sparqlService.getServiceDescription(out, "RDF/XML");
}
else {
getSparqlService().query(
query,
"RDF/XML",
false,
out
);
out.close();
}
}
@RequestMapping (produces="application/rdf+n3")
public @ResponseBody
void getGraphN3(
@RequestParam(value = "query", required = false) String query,
HttpServletResponse response) throws QueryParseException, LodeException, IOException {
log.trace("querying for graph rdf+n3");
ServletOutputStream out = response.getOutputStream();
if (query == null) {
response.setContentType("application/rdf+n3; charset=utf-8");
sparqlService.getServiceDescription(out, "N3");
}
else {
getSparqlService().query(
query,
"N3",
false,
out
);
out.close();
}
}
@RequestMapping (produces="application/rdf+json")
public @ResponseBody
void getGraphJson(
@RequestParam(value = "query", required = false) String query,
HttpServletResponse response) throws QueryParseException, LodeException, IOException {
log.trace("querying for graph rdf+json");
ServletOutputStream out = response.getOutputStream();
if (query == null) {
response.setContentType("application/rdf+json; charset=utf-8");
sparqlService.getServiceDescription(out, "JSON-LD");
}
else {
getSparqlService().query(
query,
"JSON-LD",
false,
out
);
out.close();
}
}
@RequestMapping (produces="text/plain")
public @ResponseBody
void getGraphNTriples(
@RequestParam(value = "query", required = false) String query,
HttpServletResponse response) throws QueryParseException, LodeException, IOException {
log.trace("querying for graph text/plain (rdf+ntriples)");
response.setContentType("text/plain; charset=utf-8");
ServletOutputStream out = response.getOutputStream();
if (query == null) {
getSparqlService().getServiceDescription(out, "N-TRIPLES");
}
else {
getSparqlService().query(
query,
"N-TRIPLES",
false,
out
);
out.close();
}
}
@RequestMapping (produces="text/turtle")
public @ResponseBody
void getGraphTurtle(
@RequestParam(value = "query", required = false) String query,
HttpServletResponse response) throws QueryParseException, LodeException, IOException {
log.trace("querying for graph turtle");
ServletOutputStream out = response.getOutputStream();
if (query == null) {
response.setContentType("text/turtle; charset=utf-8");
sparqlService.getServiceDescription(out, "TURTLE");
}
else {
getSparqlService().query(
query,
"TURTLE",
false,
out
);
out.close();
}
}
/*The Post methods had the HttpServletRequest request initally, I added it to all the other functions*/
@RequestMapping ( method = RequestMethod.POST, produces="application/sparql-results+xml", consumes = "application/x-www-form-urlencoded")
public void postRequest (
@RequestParam(value = "query", required = false) String query,
@RequestParam(value = "offset", required = false) Integer offset,
@RequestParam(value = "limit", required = false) Integer limit,
@RequestParam(value = "inference", required = false) boolean inference,
HttpServletRequest request,
HttpServletResponse response) throws QueryParseException, IOException, LodeException {
getSparqlXml (query, offset, limit, inference, request,response);
}
/*The Post methods had the HttpServletRequest request initally, I added it to all the other functions*/
@RequestMapping ( method = RequestMethod.POST, produces="application/sparql-results+xml", consumes = "application/sparql-query")
public void directPostRequest (
@RequestBody String query,
HttpServletRequest request,
HttpServletResponse response) throws QueryParseException, IOException, LodeException {
query (query, "XML", 0, null, false, request, response);
}
@RequestMapping
public @ResponseBody
void query(
@RequestParam(value = "query", required = false) String query,
@RequestParam(value = "format", required = false) String format,
@RequestParam(value = "offset", required = false) Integer offset,
@RequestParam(value = "limit", required = false) Integer limit,
@RequestParam(value = "inference", required = false) boolean inference,
HttpServletRequest request,
HttpServletResponse response) throws QueryParseException, LodeException, IOException {
log.info("What user information can we retrieve here");
log.info(request.getRemoteAddr());
log.info(request.getRequestedSessionId());
log.info((Long.toString(request.getSession().getCreationTime())));
log.info(request.getSession().getId());
ServletOutputStream out = response.getOutputStream();
if (query == null) {
// Default to format N3 unless an acceptable format is given
if (format == null || !(format.equals("TURTLE")
|| format.equals("N-TRIPLES")
|| format.equals("JSON-LD")
|| format.equals("N3")
|| format.equals("RDF/XML"))) {
response.setContentType("text/plain; charset=utf-8");
sparqlService.getServiceDescription(out, "N3");
} else {
response.setContentType( getMimeType(format));
sparqlService.getServiceDescription(out, format);
}
out.close();
return;
}
log.info("Processing raw query:\n" + query + "\nEnd of query.");
//HERE WE COULD DO ADVANCED LOGGING TO FILE
// Adding HttpServletRequest request as parameter to this query method might enable us to ask for IP
// via request.getRemoteAddr() and similar methods, getting more information about the USER associated with a request
// if no format, try and work out the query type
String outputFormat = format;
if (outputFormat == null) {
QueryType qType = getSparqlService().getQueryType(query);
if (qType.equals(QueryType.BOOLEANQUERY) || qType.equals(QueryType.TUPLEQUERY)) {
log.debug("no format, tuple query: setting format to XML");
outputFormat = TupleQueryFormats.XML.toString();
}
else if (qType.equals(QueryType.CONSTRUCTQUERY) || qType.equals(QueryType.DESCRIBEQUERY)) {
outputFormat = GraphQueryFormats.RDFXML.toString();
}
else {
response.setStatus(406);
response.setContentType("text/plain; charset=utf-8");
out.println("406 Not Acceptable: Can't handle this query type");
out.println("Supported queries are BOOLEAN, SELECT, CONSTRUCT, DESCRIBE, ASK and SERVICE");
out.close();
return;
}
}
if (validFormat(outputFormat)) {
response.setContentType( getMimeType(outputFormat) );
getSparqlService().query(
query,
outputFormat.toUpperCase(),
offset,
limit,
inference,
out
);
out.close();
}
else {
response.setStatus(406);
response.setContentType("text/plain");
out.println("406 Not Acceptable: The requested data format is not supported.");
out.println("Must be one of XML, JSON, RDF/XML, TURTLE or N3");
out.close();
return;
}
}
private boolean validFormat(String format) {
for (GraphQueryFormats gf : GraphQueryFormats.values()) {
if (format.toUpperCase().equals(gf.toString())) {
return true;
}
}
for (TupleQueryFormats tf : TupleQueryFormats.values()) {
if (format.toUpperCase().equals(tf.toString())) {
return true;
}
}
return false ;
}
private String getMimeType(String format) {
for (GraphQueryFormats gf : GraphQueryFormats.values()) {
if (format.toUpperCase().equals(gf.toString())) {
return gf.toMimeType()+"; charset=utf-8";
}
}
for (TupleQueryFormats tf : TupleQueryFormats.values()) {
if (format.toUpperCase().equals(tf.toString())) {
return tf.toMimeType()+"; charset=utf-8";
}
}
return "text/plain; charset=utf-8" ;
}
@ExceptionHandler(QueryParseException.class)
public ResponseEntity<String> handleQueryException(QueryParseException e) {
getLog().error(e.getMessage(), e);
return buildErrorResponse(e.getMessage(), HttpStatus.BAD_REQUEST);
}
@ExceptionHandler(MethodArgumentTypeMismatchException.class)
public ResponseEntity<String> handleParameterException(MethodArgumentTypeMismatchException e) {
getLog().error(e.getMessage(), e);
String typeName = (e.getRequiredType()==Integer.class ? "integer" : e.getRequiredType().toString());
String message = String.format("Parameter [%s] should be a [%s]", e.getName(), typeName);
return buildErrorResponse(message, HttpStatus.BAD_REQUEST);
}
@ExceptionHandler(MethodArgumentConversionNotSupportedException.class)
public ResponseEntity<String> handleParameterException(MethodArgumentConversionNotSupportedException e) {
getLog().error(e.getMessage(), e);
String typeName = (e.getRequiredType()==Integer.class ? "integer" : e.getRequiredType().toString());
String message = String.format("Parameter [%s] should be a [%s]", e.getName(), typeName);
return buildErrorResponse(message, HttpStatus.BAD_REQUEST);
}
@ExceptionHandler(MissingServletRequestParameterException.class)
public ResponseEntity<String> handleMissingParameterException(MissingServletRequestParameterException e) {
getLog().error(e.getMessage(), e);
String message = String.format("Parameter [%s] is required", e.getParameterName());
return buildErrorResponse(message, HttpStatus.BAD_REQUEST);
}
@ExceptionHandler(LodeException.class)
public ResponseEntity<String> handleLodException(LodeException e) {
getLog().error(e.getMessage(), e);
return buildErrorResponse(e.getMessage(), HttpStatus.INTERNAL_SERVER_ERROR);
}
@ExceptionHandler(IOException.class)
public ResponseEntity<String> handleIOException(IOException e) {
getLog().error(e.getMessage(), e);
return buildErrorResponse(e.getMessage(), HttpStatus.INTERNAL_SERVER_ERROR);
}
@ExceptionHandler(Exception.class)
public ResponseEntity<String> handleException(Exception e) {
getLog().error(e.getMessage(), e);
return buildErrorResponse(e.getMessage(), HttpStatus.INTERNAL_SERVER_ERROR);
}
/**
* All exception handlers call this method to assure that the Sparql endpoint returns text/plain.
* This assures that the browser will not attempt to execute any malicious scripts in the URL,
* and thus prevent XSS attacks.
*
* @param message A string message, formatted by the caller
* @param status An HttpStatus code
* @return Spring ResponseEntity<String> wrapping the string, content type, and status code.
*/
private ResponseEntity<String> buildErrorResponse(String message, HttpStatus status) {
HttpHeaders headers = new HttpHeaders();
headers.set(HttpHeaders.CONTENT_TYPE, "text/plain; charset=utf-8");
return new ResponseEntity<String>(message, headers, status);
}
}