org.bridgedb.ws.uri.WSUriServer Maven / Gradle / Ivy
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// BridgeDb,
// An abstraction layer for identifier mapping services, both local and online.
//
// Copyright 2006-2009 BridgeDb developers
// Copyright 2012-2013 Christian Y. A. Brenninkmeijer
// Copyright 2012-2013 OpenPhacts
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.
//
package org.bridgedb.ws.uri;
import java.io.File;
import java.io.InputStream;
import java.io.UnsupportedEncodingException;
import java.net.MalformedURLException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import javax.servlet.ServletContext;
import javax.servlet.ServletContextEvent;
import javax.servlet.ServletContextListener;
import javax.servlet.http.HttpServletRequest;
import javax.ws.rs.Consumes;
import javax.ws.rs.GET;
import javax.ws.rs.POST;
import javax.ws.rs.Path;
import javax.ws.rs.PathParam;
import javax.ws.rs.Produces;
import javax.ws.rs.QueryParam;
import javax.ws.rs.core.Context;
import javax.ws.rs.core.HttpHeaders;
import javax.ws.rs.core.MediaType;
import javax.ws.rs.core.Request;
import javax.ws.rs.core.Response;
import javax.ws.rs.core.Response.ResponseBuilder;
import javax.ws.rs.core.Variant;
import javax.ws.rs.core.Variant.VariantListBuilder;
import org.apache.log4j.Logger;
import org.apache.velocity.VelocityContext;
import org.bridgedb.DataSource;
import org.bridgedb.rdf.BridgeDbRdfTools;
import org.bridgedb.rdf.UriPattern;
import org.bridgedb.sql.SQLUriMapper;
import org.bridgedb.statistics.MappingSetInfo;
import org.bridgedb.uri.api.Mapping;
import org.bridgedb.uri.api.MappingsBySet;
import org.bridgedb.uri.api.UriMapper;
import org.bridgedb.uri.lens.Lens;
import org.bridgedb.uri.lens.LensTools;
import org.bridgedb.uri.tools.DirectStatementMaker;
import org.bridgedb.uri.tools.GraphResolver;
import org.bridgedb.uri.tools.RegexUriPattern;
import org.bridgedb.uri.tools.StatementMaker;
import org.bridgedb.uri.ws.WsUriConstants;
import org.bridgedb.uri.ws.bean.URISpacesInGraphBean;
import org.bridgedb.utils.BridgeDBException;
import org.bridgedb.ws.WsConstants;
import org.bridgedb.ws.templates.WebTemplates;
import org.eclipse.rdf4j.model.Statement;
import org.eclipse.rdf4j.rio.RDFFormat;
import com.sun.jersey.core.header.MediaTypes;
/**
*
* @author Christian
*/
public class WSUriServer extends WSAPI {
private static boolean EXCLUDE_GRAPH = false;
private static boolean INCLUDE_GRAPH = true;
private final String GET_BASE_URI_FROM_CONTEXT = null;
private final String DO_NOT_CONVERT_TO_RDF = null;
private final boolean XREF_DATA_NOT_REQUIRED = false;
private static final HashMap setMappings = new HashMap();
private final StatementMaker statementMaker;
static final Logger logger = Logger.getLogger(WSUriServer.class);
static List rdfFormats = new ArrayList<>();
{{
rdfFormats.add(RDFFormat.N3);
rdfFormats.add(RDFFormat.NQUADS);
rdfFormats.add(RDFFormat.NTRIPLES);
rdfFormats.add(RDFFormat.JSONLD);
rdfFormats.add(RDFFormat.RDFA);
rdfFormats.add(RDFFormat.RDFJSON);
rdfFormats.add(RDFFormat.RDFXML);
rdfFormats.add(RDFFormat.TRIG);
rdfFormats.add(RDFFormat.TRIX);
rdfFormats.add(RDFFormat.TURTLE);
}}
public WSUriServer() throws BridgeDBException {
this(SQLUriMapper.getExisting(), new DirectStatementMaker());
}
public WSUriServer(UriMapper uriMapper, StatementMaker statementMaker) throws BridgeDBException {
super(uriMapper);
logger.info("WsUriServer setup");
this.statementMaker = statementMaker;
}
/**
* Welcome page for the Serivce.
*
* Expected to be overridden by the QueryExpander
*
* @param httpServletRequest
* @return
* @throws BridgeDBException
* @throws UnsupportedEncodingException
*/
@GET
@Produces(MediaType.TEXT_HTML)
public Response welcomeMessage(@Context HttpServletRequest httpServletRequest) throws BridgeDBException, UnsupportedEncodingException {
if (logger.isDebugEnabled()){
logger.debug("welcomeMessage called!");
}
return bridgeDbHome(httpServletRequest);
}
/**
* Welcome page for the Service.
*
* Expected to be overridden by the QueryExpander
*
* @param httpServletRequest
* @return
* @throws BridgeDBException
* @throws UnsupportedEncodingException
*/
@GET
@Produces(MediaType.TEXT_HTML)
@Path("/" + WsUriConstants.BRIDGEDB_HOME)
public Response bridgeDbHome(@Context HttpServletRequest httpServletRequest) throws BridgeDBException, UnsupportedEncodingException {
if (logger.isDebugEnabled()){
logger.debug("bridgeDbHome called");
}
VelocityContext velocityContext = new VelocityContext();
velocityContext.put("targetUriPatterns", UriPattern.getUriPatterns());
velocityContext.put("lenses", LensTools.getLens(LensTools.ALL_GROUP_NAME));
String mapUriScripts = WebTemplates.getForm(velocityContext, WebTemplates.SELECTORS_SCRIPTS);
String mapUriForm = mapUriForm(EXCLUDE_GRAPH, httpServletRequest);
velocityContext.put("api", WsUriConstants.BRIDGEDB_API);
velocityContext.put("contextPath", httpServletRequest.getContextPath());
velocityContext.put("getMappingInfo", WsUriConstants.MAPPING_SET);
velocityContext.put("map",WsUriConstants.MAP);
velocityContext.put("mapURI", WsUriConstants.MAP_URI);
velocityContext.put("mapUriForm", mapUriForm);
String mainBody = WebTemplates.getForm(velocityContext, WebTemplates.BRIDGEDB_HOME);
String fullPage = this.createHtmlPage("Home page for BridgeDb WebServer", mainBody, httpServletRequest);
return Response.ok(fullPage, MediaType.TEXT_HTML).build();
}
@GET
@Produces(MediaType.TEXT_HTML)
@Path("/mapURI")
public Response mapURI(@Context HttpServletRequest httpServletRequest) throws BridgeDBException {
if (logger.isDebugEnabled()){
logger.debug("mapURI called");
}
VelocityContext velocityContext = new VelocityContext();
velocityContext.put("targetUriPatterns", UriPattern.getUriPatterns());
velocityContext.put("lenses", LensTools.getLens(LensTools.ALL_GROUP_NAME));
String mainBody = WebTemplates.getForm(velocityContext, WebTemplates.SELECTORS_SCRIPTS);
String fullPage = this.createHtmlPage("mapURI Service", mainBody, httpServletRequest);
return Response.ok(fullPage, MediaType.TEXT_HTML).build();
}
@GET
@Produces({MediaType.TEXT_HTML})
@Path("/" + WsUriConstants.DATA_SOURCE + "/{id}")
public Response getDataSourceHtml(@PathParam("id") String id,
@Context HttpServletRequest httpServletRequest) throws BridgeDBException {
DataSource ds = DataSource.getExistingBySystemCode(id);
if (noContentOnEmpty & ds == null){
return noContentWrapper(httpServletRequest);
}
Set uriPatterns = uriMapper.getUriPatterns(id);
VelocityContext velocityContext = new VelocityContext();
velocityContext.put("dataSource", ds);
velocityContext.put("id", "$id");
velocityContext.put("Patterns", uriPatterns);
String mainBody = WebTemplates.getForm(velocityContext, WebTemplates.DATA_SOURCE_SCRIPT);
String fullPage = this.createHtmlPage("Data Source " + id + " Summary", mainBody, httpServletRequest);
return Response.ok(fullPage, MediaType.TEXT_HTML).build();
}
@GET
@Produces(MediaType.TEXT_HTML)
@Path("/" + WsUriConstants.SOURCE_INFOS)
public Response getSourceInfosHtml(@QueryParam(WsUriConstants.LENS_URI) String lensUri,
@Context HttpServletRequest httpServletRequest) throws BridgeDBException {
if (logger.isDebugEnabled()){
logger.debug("getSourceInfosHtml called");
}
return getSourceInfosHtml(lensUri, httpServletRequest, null);
}
private Response getSourceInfosHtml(String lensUri, HttpServletRequest httpServletRequest, String message) throws BridgeDBException {
VelocityContext velocityContext = new VelocityContext();
velocityContext.put("SourceInfos", uriMapper.getSourceInfos(lensUri));
velocityContext.put("lens", lensUri);
velocityContext.put("contextPath", httpServletRequest.getContextPath() );
velocityContext.put("message", message);
String mainBody = WebTemplates.getForm(velocityContext, WebTemplates.SOURCE_INFO_SCRIPT);
String fullPage = this.createHtmlPage("Data Source Summary", mainBody, httpServletRequest);
return Response.ok(fullPage, MediaType.TEXT_HTML).build();
}
@GET
@Produces(MediaType.TEXT_HTML)
@Path("/" + WsUriConstants.SOURCE_TARGET_INFOS)
public Response getSourceTargetInfosHtml(@QueryParam(WsUriConstants.SOURCE_DATASOURCE_SYSTEM_CODE) String scrCode,
@QueryParam(WsUriConstants.LENS_URI) String lensUri,
@Context HttpServletRequest httpServletRequest) throws BridgeDBException {
if (logger.isDebugEnabled()){
logger.debug("getSourceTargetInfosHtml called with " + scrCode);
}
if (scrCode == null || scrCode.isEmpty()){
return getSourceInfosHtml(lensUri, httpServletRequest,
"Due to the size of your request only a summary by source is being shown");
}
return getSourceTargetInfosHtml(scrCode, lensUri, httpServletRequest, null);
}
private Response getSourceTargetInfosHtml(String scrCode, String lensUri,
HttpServletRequest httpServletRequest, String message) throws BridgeDBException {
VelocityContext velocityContext = new VelocityContext();
velocityContext.put("SourceTargetInfos", uriMapper.getSourceTargetInfos(scrCode, lensUri));
velocityContext.put("scrCode", scrCode);
velocityContext.put("contextPath", httpServletRequest.getContextPath() );
velocityContext.put("lens", lensUri);
velocityContext.put("message", message);
String mainBody = WebTemplates.getForm(velocityContext, WebTemplates.SOURCE_TARGET_INFO_SCRIPT);
String fullPage = this.createHtmlPage("Data Source Summary for " + scrCode, mainBody, httpServletRequest);
return Response.ok(fullPage, MediaType.TEXT_HTML).build();
}
@GET
@Produces({MediaType.TEXT_HTML})
@Path("/" + WsUriConstants.MAPPING_SET)
public Response getMappingSetInfosHtml(@QueryParam(WsUriConstants.SOURCE_DATASOURCE_SYSTEM_CODE) String scrCode,
@QueryParam(WsUriConstants.TARGET_DATASOURCE_SYSTEM_CODE) String targetCode,
@QueryParam(WsUriConstants.LENS_URI) String lensUri,
@Context HttpServletRequest httpServletRequest) throws BridgeDBException {
if (logger.isDebugEnabled()){
logger.debug("getMappingSetInfosHtml called with " + scrCode + " and " + targetCode);
}
if (scrCode == null || scrCode.isEmpty()){
return getSourceInfosHtml(lensUri, httpServletRequest, "Due to the size of your request only a summary by source is being shown");
}
if (targetCode == null || targetCode.isEmpty()){
return getSourceTargetInfosHtml(scrCode, lensUri, httpServletRequest,
"Due to the size of your request only a summary by target is being shown");
}
VelocityContext velocityContext = new VelocityContext();
velocityContext.put("MappingSetInfos", uriMapper.getMappingSetInfos(scrCode, targetCode, lensUri));
velocityContext.put("scrCode", scrCode);
velocityContext.put("targetCode", targetCode);
velocityContext.put("contextPath", httpServletRequest.getContextPath() );
velocityContext.put("lens", lensUri);
String mainBody = WebTemplates.getForm(velocityContext, WebTemplates.MAPPING_SET_INFO_SCRIPT);
String title = "Mapping Summary for " + scrCode + " -> " + targetCode;
String fullPage = this.createHtmlPage(title, mainBody, httpServletRequest);
return Response.ok(fullPage, MediaType.TEXT_HTML).build();
}
@GET
@Produces({MediaType.TEXT_HTML})
@Path("/" + WsUriConstants.MAPPING_SET + "/{id}")
public Response getMappingSetInfo(@PathParam("id") String idString,
@Context HttpServletRequest httpServletRequest) throws BridgeDBException {
if (idString == null) {
throw new BridgeDBException("Path parameter missing.");
}
if (idString.isEmpty()) {
throw new BridgeDBException("Path parameter may not be null.");
}
int id = Integer.parseInt(idString);
MappingSetInfo info = uriMapper.getMappingSetInfo(id);
VelocityContext velocityContext = new VelocityContext();
velocityContext.put("mappingSetInfo", info);
String mainBody = WebTemplates.getForm(velocityContext, WebTemplates.MAPPING_SET_SCRIPT);
String fullPage = this.createHtmlPage("Mapping Set " + id, mainBody, httpServletRequest);
return Response.ok(fullPage, MediaType.TEXT_HTML).build();
}
@GET
@Path("/" + WsUriConstants.MAPPING_SET + WsUriConstants.RDF + "/{id}")
@Produces(MediaType.TEXT_HTML)
public Response getMappingSetRdfHtml(@PathParam("id") String idString, @Context HttpServletRequest httpServletRequest)
throws BridgeDBException{
return getMappingSetRdfHtml(idString, GET_BASE_URI_FROM_CONTEXT, DO_NOT_CONVERT_TO_RDF, httpServletRequest);
}
@GET
@Path("/" + WsUriConstants.MAPPING_SET + WsUriConstants.RDF + "/{id}")
@Produces(MediaType.TEXT_PLAIN)
public Response getMappingSetRdfText(@PathParam("id") String idString,
@Context Request request,
@Context HttpServletRequest httpServletRequest)
throws BridgeDBException{
return getMappingSetRdfText(idString, GET_BASE_URI_FROM_CONTEXT, DO_NOT_CONVERT_TO_RDF, request, httpServletRequest);
}
@GET
@Path("/" + WsUriConstants.MAPPING_SET + WsUriConstants.RDF)
@Produces({MediaType.TEXT_PLAIN,
"text/turtle",
"application/rdf+xml",
"application/n-triples",
"application/ld+json",
"application/trig"
})
public Response getMappingSetRdfText(@QueryParam(WsConstants.ID) String idString,
@QueryParam(WsUriConstants.BASE_URI) String baseUri,
@QueryParam(WsUriConstants.RDF_FORMAT) String formatName,
@Context Request request,
@Context HttpServletRequest httpServletRequest)
throws BridgeDBException{
baseUri = checkBaseUri(baseUri, httpServletRequest);
String context = checkContext(baseUri, httpServletRequest);
Set statements = getMappingSetStatements(idString, baseUri, context);
if (noContentOnEmpty & statements.isEmpty()){
return Response.noContent().build();
}
List types = new ArrayList();
for (RDFFormat f: rdfFormats){
types.add(MediaType.valueOf(f.getDefaultMIMEType()));
types.addAll(MediaTypes.createMediaTypes(f.getMIMETypes().toArray(new String[]{})));
}
List variants = VariantListBuilder.newInstance().mediaTypes(types.toArray(new MediaType[]{})).build();
Variant variant = request.selectVariant(variants);
RDFFormat format = RDFFormat.matchMIMEType(variant.getMediaType().toString(), rdfFormats).get();
String rdfInfo = BridgeDbRdfTools.writeRDF(statements, format);
return Response.ok(rdfInfo, MediaType.TEXT_PLAIN_TYPE).build();
}
@GET
@Path("/" + WsUriConstants.MAPPING_SET + WsUriConstants.RDF)
@Produces(MediaType.TEXT_HTML)
public Response getMappingSetRdfHtml(@QueryParam(WsConstants.ID) String idString,
@QueryParam(WsUriConstants.BASE_URI) String baseUri,
@QueryParam(WsUriConstants.RDF_FORMAT) String formatName,
@Context HttpServletRequest httpServletRequest)
throws BridgeDBException{
StringBuilder sb = new StringBuilder();
baseUri = checkBaseUri(baseUri, httpServletRequest);
String context = checkContext(baseUri, httpServletRequest);
Set statements = getMappingSetStatements(idString, baseUri, context);
sb.append("Use MediaType.TEXT_PLAIN to return remove HTML stuff
");
sb.append("Warning MediaType.TEXT_PLAIN version returns status 204 if no mappings found.
");
RDFFormat format = RDFFormat.matchMIMEType(formatName, rdfFormats).get();
if (formatName != null || formatName != null){
generateTextarea(sb, "RDF", BridgeDbRdfTools.writeRDF(statements, format));
} else {
sb.append("Warning MediaType.TEXT_PLAIN version returns RDF using the default format even if no format specified.
");
VelocityContext velocityContext = new VelocityContext();
velocityContext.put("statements", statements);
velocityContext.put("subject", WsUriConstants.MAPPING_SET);
sb.append(WebTemplates.getForm(velocityContext, WebTemplates.RDF_QUAD_SCRIPT));
}
String fullPage = this.createHtmlPage("MappingSet " + idString, sb.toString(), httpServletRequest);
return Response.ok(fullPage, MediaType.TEXT_HTML).build();
}
private int[] splitId(String idString) throws BridgeDBException{
String[] stringIds = idString.split("_");
int[] ids = new int[stringIds.length];
for (int i = 0; i< ids.length; i++){
try{
ids[i] = Integer.parseInt(stringIds[i]);
} catch (NumberFormatException ex){
throw new BridgeDBException("Illegal id String: " + idString
+ " Expected 1 or more numbers seperated by underscore. ", ex);
}
}
return ids;
}
/**
* Gets known Statements about the mappingSet.
*
* This method is expected to be overwritten by services like the Open PHACTS IMS
* that have better rdf data about the mappingSet
*
* @param idString
* @param baseUri
* @return
* @throws BridgeDBException
*/
protected Set getMappingSetStatements(String idString, String baseUri, String context)
throws BridgeDBException{
if (idString == null || idString.isEmpty()){
throw new BridgeDBException (WsConstants.ID + " parameter is missing");
}
int[] ids = splitId(idString);
if (ids.length == 1){
return statementMaker.asRDF(uriMapper.getMappingSetInfo(ids[0]), baseUri, context);
} else {
Set statements = new HashSet();
for (int id:ids){
statements.addAll(statementMaker.asRDF(uriMapper.getMappingSetInfo(id), baseUri, context));
}
return statements;
}
}
private Set getMappingSetStatements(Set mappings, String baseUri, String context) throws BridgeDBException {
Set results = new HashSet();
for (Mapping mapping:mappings){
if (mapping.getPredicate() != null){
results.addAll(getMappingSetStatements(mapping.getMappingSetId(), baseUri, context));
}
}
return results;
}
private String checkBaseUri(String baseUri, HttpServletRequest httpServletRequest)
throws BridgeDBException{
if (baseUri == null || baseUri.isEmpty()){
StringBuffer url = httpServletRequest.getRequestURL();
return url.substring(0, url.length()- httpServletRequest.getPathInfo().length() + 1);
}
return baseUri;
}
private String checkContext(String baseUri, HttpServletRequest httpServletRequest) {
if (httpServletRequest.getQueryString() == null){
return baseUri + httpServletRequest.getPathInfo();
} else {
return baseUri + httpServletRequest.getPathInfo() + "?" + httpServletRequest.getQueryString();
}
}
@GET
@Path("/" + WsUriConstants.MAP_URI + WsUriConstants.RDF)
@Produces(MediaType.TEXT_HTML)
public Response mapUriRdfHtml(
@QueryParam(WsUriConstants.URI) List uris,
@QueryParam(WsUriConstants.LENS_URI) String lensUri,
@QueryParam(WsUriConstants.GRAPH) String graph,
@QueryParam(WsUriConstants.TARGET_URI_PATTERN) List targetUriPatterns,
@QueryParam(WsUriConstants.BASE_URI) String baseUri,
@QueryParam(WsUriConstants.RDF_FORMAT) String formatName,
@QueryParam(WsUriConstants.LINKSET_INFO) Boolean linksetInfo,
@QueryParam(WsUriConstants.OVERRIDE_PREDICATE_URI) String overridePredicateURI,
@Context HttpServletRequest httpServletRequest)
throws BridgeDBException{
Set statements = this.mapUriRdfInner(uris, lensUri, graph, targetUriPatterns, baseUri, formatName,
linksetInfo, overridePredicateURI, httpServletRequest);
String fullPage;
if (formatName != null || formatName != null){
StringBuilder sb = new StringBuilder();
RDFFormat format = RDFFormat.matchMIMEType(formatName, rdfFormats).get();
generateTextarea(sb, "RDF", BridgeDbRdfTools.writeRDF(statements, format));
fullPage = this.createHtmlPage(WsUriConstants.MAP_URI + " as RDF", sb.toString(), httpServletRequest);
} else {
String contextPath = httpServletRequest.getContextPath();
VelocityContext velocityContext = new VelocityContext();
velocityContext.put("statements", statements);
velocityContext.put("subject", WsUriConstants.MAP_URI);
velocityContext.put("contextPath", contextPath);
String table = WebTemplates.getForm(velocityContext, WebTemplates.RDF_QUAD_SCRIPT);
fullPage = this.createTablePage(WsUriConstants.MAP_URI + " as RDF", table, httpServletRequest);
}
return Response.ok(fullPage, MediaType.TEXT_HTML).build();
}
//Did not work when tried
private void addTableCss(StringBuilder sb){
VelocityContext velocityContext = new VelocityContext();
sb.append(WebTemplates.getForm(velocityContext, WebTemplates.TABLE_CSS));
}
//Did not work when tried
private void addJQuery(StringBuilder sb){
VelocityContext velocityContext = new VelocityContext();
sb.append(WebTemplates.getForm(velocityContext, WebTemplates.JQUERY_SCRIPT));
}
private void addDataTable(StringBuilder sb){
VelocityContext velocityContext = new VelocityContext();
sb.append(WebTemplates.getForm(velocityContext, WebTemplates.DATATABLE_SCRIPT));
}
@GET
@Path("/" + WsUriConstants.MAP_URI + WsUriConstants.RDF)
@Produces(MediaType.TEXT_PLAIN)
public Response mapUriRdfText(
@QueryParam(WsUriConstants.URI) List uris,
@QueryParam(WsUriConstants.LENS_URI) String lensUri,
@QueryParam(WsUriConstants.GRAPH) String graph,
@QueryParam(WsUriConstants.TARGET_URI_PATTERN) List targetUriPatterns,
@QueryParam(WsUriConstants.BASE_URI) String baseUri,
@QueryParam(WsUriConstants.RDF_FORMAT) String formatName,
@QueryParam(WsUriConstants.LINKSET_INFO) Boolean linksetInfo,
@QueryParam(WsUriConstants.OVERRIDE_PREDICATE_URI) String overridePredicateURI,
@Context HttpServletRequest httpServletRequest)
throws BridgeDBException{
Set statements = this.mapUriRdfInner(uris, lensUri, graph, targetUriPatterns, baseUri, formatName,
linksetInfo, overridePredicateURI, httpServletRequest);
if (noContentOnEmpty & statements.isEmpty()){
return Response.noContent().build();
}
RDFFormat format = RDFFormat.matchMIMEType(formatName, rdfFormats).get();
String rdfInfo = BridgeDbRdfTools.writeRDF(statements, format);
return Response.ok(rdfInfo, MediaType.TEXT_PLAIN_TYPE).build();
}
private Set mapUriRdfInner(List uris, String lensUri, String graph, List targetUriPatterns,
String baseUri, String formatName,
Boolean linksetInfo, String overridePredicateURI, HttpServletRequest httpServletRequest) throws BridgeDBException{
boolean addLinks;
if (linksetInfo == null){
addLinks = false;
} else {
addLinks = linksetInfo;
}
if (overridePredicateURI != null && overridePredicateURI.isEmpty()) {
overridePredicateURI = null;
}
Set mappings;
if (uris.size() == 1){
mappings = uriMapper.mapFull(uris.iterator().next(), lensUri, XREF_DATA_NOT_REQUIRED, graph, targetUriPatterns);
} else {
mappings = new HashSet();
for(String single:uris){
mappings.addAll(uriMapper.mapFull(single, lensUri, XREF_DATA_NOT_REQUIRED, graph, targetUriPatterns));
}
}
baseUri = checkBaseUri(baseUri, httpServletRequest);
String context = checkContext(baseUri, httpServletRequest);
Set statements = statementMaker.asRDF(mappings, baseUri, addLinks, overridePredicateURI);
if (formatName != null || formatName != null){
RDFFormat format = RDFFormat.matchMIMEType(formatName, rdfFormats).get();
if (linksetInfo != null && linksetInfo){
if (format.supportsContexts()){
statements.addAll(getMappingSetStatements(mappings, baseUri, context));
}
}
} else {
if (linksetInfo != null && linksetInfo){
statements.addAll(getMappingSetStatements(mappings, baseUri, context));
}
}
return statements;
}
private String mapUriForm(boolean includeGraph, HttpServletRequest httpServletRequest) throws BridgeDBException{
VelocityContext velocityContext = new VelocityContext();
velocityContext.put("targetUriPatterns", UriPattern.getUriPatterns());
velocityContext.put("lenses", LensTools.getLens(LensTools.ALL_GROUP_NAME));
velocityContext.put("contextPath", httpServletRequest.getContextPath());
velocityContext.put("defaultLens", LensTools.byId(Lens.DEFAULT_LENS_NAME));
velocityContext.put("formatName", WsUriConstants.FORMAT);
if (includeGraph){
velocityContext.put("graphName", WsUriConstants.GRAPH);
velocityContext.put("graphs", GraphResolver.knownGraphs());
}
velocityContext.put("lenses", LensTools.getLens(LensTools.ALL_GROUP_NAME));
velocityContext.put("lensURIName", WsUriConstants.LENS_URI);
velocityContext.put("mapURI", WsUriConstants.MAP_URI);
velocityContext.put("targetUriPatternName", WsUriConstants.TARGET_URI_PATTERN);
velocityContext.put("URI", WsUriConstants.URI);
return WebTemplates.getForm(velocityContext, WebTemplates.MAP_URI_FORM);
}
/**
* Forwarding page for "/api".
*
* This is expected to be overwirriten by the QueryExpander
* @param httpServletRequest
* @return
* @throws BridgeDBException
* @throws UnsupportedEncodingException
*/
@GET
@Produces(MediaType.TEXT_HTML)
@Path("/api")
public Response apiPage(@Context HttpServletRequest httpServletRequest) throws BridgeDBException, UnsupportedEncodingException {
return imsApiPage(httpServletRequest);
}
@GET
@Produces(MediaType.TEXT_HTML)
@Path("/" + Lens.METHOD_NAME)
public Response getLensesHtml(@QueryParam(WsUriConstants.LENS_URI) String lensUri,
@QueryParam(WsUriConstants.LENS_GROUP) String lensGroup,
@Context HttpServletRequest httpServletRequest) throws BridgeDBException {
List lenses = getTheLens(lensUri, lensGroup);
StringBuilder sb = new StringBuilder();
if (lensUri != null && !lensUri.isEmpty()){
sb.append("For ").append(WsUriConstants.LENS_URI).append("=").append(lensUri).append("
");
}else if (lensGroup != null && !lensGroup.isEmpty()){
sb.append("For ").append(WsUriConstants.LENS_GROUP).append("=").append(lensGroup).append("
");
} else {
sb.append("For the public lens
");
}
VelocityContext velocityContext = new VelocityContext();
velocityContext.put("lenses", lenses);
velocityContext.put("contextPath", httpServletRequest.getContextPath());
velocityContext.put("dataSourceMethod", WsUriConstants.DATA_SOURCE + "/");
sb.append(WebTemplates.getForm(velocityContext, WebTemplates.LENS));
sb.append("");
sb.append("XML Format");
sb.append("
\n");
addLensGroups(sb, httpServletRequest);
String fullPage = createHtmlPage("Lens Summary", sb.toString(), httpServletRequest);
return Response.ok(fullPage, MediaType.TEXT_HTML).build();
}
@GET
@Produces(MediaType.TEXT_HTML)
@Path("/" + WsUriConstants.LENS_GROUP)
public Response getLensGroup(@Context HttpServletRequest httpServletRequest) throws BridgeDBException {
StringBuilder sb = new StringBuilder();
addLensGroups(sb, httpServletRequest);
String fullPage = createHtmlPage("Lens Groups", sb.toString(), httpServletRequest);
return Response.ok(fullPage, MediaType.TEXT_HTML).build();
}
private void addLensGroups(StringBuilder sb, HttpServletRequest httpServletRequest){
Set lensGroups = LensTools.getLensGroups();
VelocityContext velocityContext = new VelocityContext();
velocityContext.put("lensGroups", lensGroups);
velocityContext.put("lensCall", httpServletRequest.getContextPath() + "/"
+ Lens.METHOD_NAME + "?" + WsUriConstants.LENS_GROUP + "=");
sb.append(WebTemplates.getForm(velocityContext, WebTemplates.LENS_GROUP));
}
/**
* Not longer works as it did not scale
* @deprecated Will now always throw an Exception
*/
@GET
@Produces(MediaType.TEXT_HTML)
@Path("/" + WsUriConstants.GRAPHVIZ)
public Response graphvizDot(@QueryParam(WsUriConstants.LENS_URI) String lensUri)
throws BridgeDBException, UnsupportedEncodingException {
StringBuilder sb = new StringBuilder();
List rawProvenaceinfos = uriMapper.getMappingSetInfos(null, null, lensUri);
SourceTargetCounter sourceTargetCounter = new SourceTargetCounter(rawProvenaceinfos);
sb.append("digraph G {");
for (MappingSetInfo info:sourceTargetCounter.getSummaryInfos()){
if (info.getSource().compareTo(info.getTarget()) < 0 ){
sb.append("\"");
sb.append(info.getSource().getFullName());
sb.append("\" -> \"");
sb.append(info.getTarget().getFullName());
sb.append("\" [dir = both, label=\"");
sb.append(formatter.format(info.getNumberOfLinks()) + "(" + info.getStringId() + ")");
sb.append("\"");
if (info.isTransitive()){
sb.append(", style=dashed");
}
sb.append("];\n");
}
}
sb.append("}");
return Response.ok(sb.toString(), MediaType.TEXT_HTML).build();
}
@GET
@Produces({MediaType.TEXT_PLAIN})
@Path("/" + WsUriConstants.MAP_BY_SET + WsUriConstants.RDF)
@Deprecated
public Response mapBySetRdfText(@QueryParam(WsUriConstants.URI) List uris,
@QueryParam(WsUriConstants.LENS_URI) String lensUri,
@QueryParam(WsUriConstants.GRAPH) String graph,
@QueryParam(WsUriConstants.TARGET_URI_PATTERN) List targetUriPatterns,
@QueryParam(WsUriConstants.RDF_FORMAT) String formatName,
@Context HttpServletRequest httpServletRequest) throws BridgeDBException {
MappingsBySet mappingsBySet = mapBySetInner(uris, lensUri, graph, targetUriPatterns);
if (mappingsBySet.isEmpty()){
return Response.noContent().build();
} else {
Set statements = statementMaker.asRDF(mappingsBySet, getBaseUri(httpServletRequest),
WsUriConstants.MAPPING_SET + WsUriConstants.RDF);
RDFFormat format = RDFFormat.matchMIMEType(formatName, rdfFormats).get();
String rdf =BridgeDbRdfTools.writeRDF(statements, format);
return Response.ok(rdf, MediaType.TEXT_PLAIN_TYPE).build();
}
}
protected final void generateTextarea(StringBuilder sb, String fieldName, String text) {
sb.append("").append(fieldName);
sb.append("
\n");
}
@GET
@Produces({MediaType.TEXT_HTML})
@Path("/" + WsUriConstants.MAP_BY_SET + WsUriConstants.RDF)
@Deprecated
public Response mapBySetRdfHtml(@QueryParam(WsUriConstants.URI) List uris,
@QueryParam(WsUriConstants.LENS_URI) String lensUri,
@QueryParam(WsUriConstants.GRAPH) String graph,
@QueryParam(WsUriConstants.TARGET_URI_PATTERN) List targetUriPatterns,
@QueryParam(WsUriConstants.RDF_FORMAT) String formatName,
@Context HttpServletRequest httpServletRequest
) throws BridgeDBException {
MappingsBySet mappingsBySet = mapBySetInner(uris, lensUri, graph, targetUriPatterns);
StringBuilder sb = new StringBuilder();
sb.append("Warning unlike ");
sb.append(WsUriConstants.MAP_BY_SET);
sb.append(" this method does not include any protential mapping to self.
");
sb.append("Use MediaType.TEXT_PLAIN to remove HTML stuff
");
sb.append("Warning MediaType.TEXT_PLAIN version returns status 204 if no mappings found.
");
String fullBaseUri = getBaseUri(httpServletRequest);
int pureLenght = fullBaseUri.length() - WsUriConstants.MAP_BY_SET.length() - WsUriConstants.RDF.length();
String pureBaseUri = fullBaseUri.substring(0, pureLenght);
Set statements = statementMaker.asRDF(mappingsBySet, pureBaseUri,
WsUriConstants.MAPPING_SET + WsUriConstants.RDF);
RDFFormat format = RDFFormat.matchMIMEType(formatName, rdfFormats).get();
String rdf =BridgeDbRdfTools.writeRDF(statements, format);
generateTextarea(sb, "RDF", rdf);
String title = "HTML friendly " + WsUriConstants.MAP_BY_SET + WsUriConstants.RDF + " Output";
String fullPage = this.createHtmlPage(title, sb.toString(), httpServletRequest);
return Response.ok(fullPage, MediaType.TEXT_HTML).build();
}
@GET
@Produces({MediaType.TEXT_PLAIN})
@Path("/" + Lens.METHOD_NAME + WsUriConstants.RDF)
public Response lensRdfText(@QueryParam(WsUriConstants.RDF_FORMAT) String formatName,
@Context HttpServletRequest httpServletRequest) throws BridgeDBException {
Set statements = LensTools.getLensAsRdf(getBaseUri(httpServletRequest), LensTools.ALL_GROUP_NAME);
if (statements.isEmpty()){
return Response.noContent().build();
} else {
RDFFormat format = RDFFormat.matchMIMEType(formatName, rdfFormats).get();
String rdf = BridgeDbRdfTools.writeRDF(statements, format);
return Response.ok(rdf, MediaType.TEXT_PLAIN_TYPE).build();
}
}
@GET
@Produces({MediaType.TEXT_HTML})
@Path("/" + Lens.METHOD_NAME + WsUriConstants.RDF)
public Response lensRdfHtml(@QueryParam(WsUriConstants.RDF_FORMAT) String formatName,
@Context HttpServletRequest httpServletRequest
) throws BridgeDBException {
Set statements = LensTools.getLensAsRdf(getBaseUri(httpServletRequest), LensTools.ALL_GROUP_NAME);
StringBuilder sb = new StringBuilder();
sb.append("Warning unlike ");
sb.append(WsUriConstants.MAP_BY_SET);
sb.append(" this method does not include any protential mapping to self.
");
sb.append("Use MediaType.TEXT_PLAIN to remove HTML stuff
");
sb.append("Warning MediaType.TEXT_PLAIN version returns status 204 if no mappings found.
");
RDFFormat format = RDFFormat.matchMIMEType(formatName, rdfFormats).get();
String rdf = BridgeDbRdfTools.writeRDF(statements, format);
generateTextarea(sb, "RDF", rdf);
String title = "HTML friendly " + WsUriConstants.MAP_BY_SET + WsUriConstants.RDF + " Output";
String fullPage = this.createHtmlPage(title, sb.toString(), httpServletRequest);
return Response.ok(fullPage, MediaType.TEXT_HTML).build();
}
@GET
@Produces({MediaType.TEXT_HTML})
@Path("/" + WsUriConstants.MAP_BY_SET)
public Response mapBySetHtml(@QueryParam(WsUriConstants.URI) List uris,
@QueryParam(WsUriConstants.LENS_URI) String lensUri,
@QueryParam(WsUriConstants.GRAPH) String graph,
@QueryParam(WsUriConstants.TARGET_URI_PATTERN) List targetUriPatterns,
@Context HttpServletRequest httpServletRequest) throws BridgeDBException {
Response result = mapBySet(uris, lensUri, graph, targetUriPatterns);
if (noContentOnEmpty & result.getStatus() == Response.Status.NO_CONTENT.getStatusCode()){
return noContentWrapper(httpServletRequest);
}
return result;
}
@Override
protected Response noContentWrapper(HttpServletRequest httpServletRequest) {
StringBuilder sb = new StringBuilder();
sb.append("Reply is an Empty Set or Empty Object
\n");
sb.append("Note: The XML and Json versions of this request simply return status 204 (No Context)
");
String fullPage = this.createHtmlPage("Empty Reply", sb.toString(), httpServletRequest);
return Response.ok(fullPage, MediaType.TEXT_HTML).build();
}
private String getBaseUri(HttpServletRequest httpServletRequest) {
return httpServletRequest.getScheme() + "://" + httpServletRequest.getServerName() + ":" + httpServletRequest.getServerPort() + httpServletRequest.getRequestURI();
}
@POST
@Produces({MediaType.APPLICATION_XML, MediaType.APPLICATION_JSON})
@Path("/" + WsUriConstants.URI_SPACES_PER_GRAPH)
public List URISpacesPerGraphAsXML() throws BridgeDBException {
Map> mappings =
GraphResolver.getInstance().getAllowedUriPatterns();
ArrayList results = new ArrayList();
for (String graph:mappings.keySet()){
Set patternStrings = new HashSet();
for (RegexUriPattern pattern:mappings.get(graph)){
patternStrings.add(pattern.getUriPattern());
}
results.add(new URISpacesInGraphBean(graph, patternStrings));
}
return results;
}
@GET
@Produces({MediaType.APPLICATION_XML, MediaType.APPLICATION_JSON})
@Path("/" + WsUriConstants.URI_SPACES_PER_GRAPH)
public List URISpacesPerGraphAsXMLGet() throws BridgeDBException {
return URISpacesPerGraphAsXML();
}
@POST
@Produces(MediaType.TEXT_HTML)
@Path("/" + WsUriConstants.URI_SPACES_PER_GRAPH)
public Response URISpacesPerGraphAsHtml(@Context HttpServletRequest httpServletRequest)
throws BridgeDBException {
VelocityContext velocityContext = new VelocityContext();
velocityContext.put("mappings", GraphResolver.getInstance().getAllowedUriPatterns());
String mainBody = WebTemplates.getForm(velocityContext, WebTemplates.GRAPH_INFO_SCRIPT);
String fullPage = this.createHtmlPage("URI Spaces per Graph", mainBody, httpServletRequest);
return Response.ok(fullPage, MediaType.TEXT_HTML).build();
}
@GET
@Produces(MediaType.TEXT_HTML)
@Path("/" + WsUriConstants.URI_SPACES_PER_GRAPH)
public Response URISpacesPerGraphAsHtmlGet(@Context HttpServletRequest httpServletRequest)
throws BridgeDBException {
return URISpacesPerGraphAsHtml(httpServletRequest);
}
@GET
@Path("/file/{id}")
@Produces(MediaType.TEXT_PLAIN)
public Response getFile(@PathParam("id") String idString) throws MalformedURLException {
ClassLoader classLoader = this.getClass().getClassLoader();
InputStream input = classLoader.getResourceAsStream(idString);
ResponseBuilder response;
if (input != null){
response = Response.ok();
response.header("Content-Disposition", "attachment; filename=" + idString);
response.entity(input);
} else {
String message = "File : " + idString + " not found";
response = Response.status(Response.Status.NOT_FOUND).entity(message);
}
return response.build();
}
@GET
@Path("/image/{id}")
@Produces("image/png")
public Response getImage(@PathParam("id") String idString) throws MalformedURLException {
return getFile(idString);
}
}
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