// 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.InputStream;
import java.text.DecimalFormat;
import java.text.DecimalFormatSymbols;
import java.text.NumberFormat;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import javax.servlet.http.HttpServletRequest;
import javax.ws.rs.FormParam;
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.MediaType;
import javax.ws.rs.core.Response;
import org.apache.log4j.Logger;
import org.apache.velocity.VelocityContext;
import org.bridgedb.DataSource;
import org.bridgedb.Xref;
import org.bridgedb.statistics.MappingSetInfo;
import org.bridgedb.statistics.OverallStatistics;
import org.bridgedb.statistics.SourceInfo;
import org.bridgedb.statistics.SourceTargetInfo;
import org.bridgedb.uri.api.Mapping;
import org.bridgedb.uri.api.MappingsBySet;
import org.bridgedb.uri.api.MappingsBySysCodeId;
import org.bridgedb.uri.api.SetMappings;
import org.bridgedb.uri.api.UriMapper;
import org.bridgedb.uri.lens.Lens;
import org.bridgedb.uri.lens.LensTools;
import org.bridgedb.uri.ws.WSUriInterface;
import org.bridgedb.uri.ws.WsUriConstants;
import org.bridgedb.uri.ws.bean.DataSourceUriPatternBean;
import org.bridgedb.uri.ws.bean.LensBean;
import org.bridgedb.uri.ws.bean.LensesBean;
import org.bridgedb.uri.ws.bean.MappingSetInfoBean;
import org.bridgedb.uri.ws.bean.MappingSetInfosBean;
import org.bridgedb.uri.ws.bean.MappingsBean;
import org.bridgedb.uri.ws.bean.MappingsBySetBean;
import org.bridgedb.uri.ws.bean.OverallStatisticsBean;
import org.bridgedb.uri.ws.bean.SourceInfosBean;
import org.bridgedb.uri.ws.bean.SourceTargetInfosBean;
import org.bridgedb.uri.ws.bean.UriExistsBean;
import org.bridgedb.uri.ws.bean.UriMappings;
import org.bridgedb.uri.ws.bean.UriSearchBean;
import org.bridgedb.utils.BridgeDBException;
import org.bridgedb.ws.WSCoreService;
import org.bridgedb.ws.WsConstants;
import org.bridgedb.ws.bean.XrefBean;
import org.bridgedb.ws.templates.WebTemplates;
@Path("/")
public class WSUriInterfaceService extends WSCoreService implements WSUriInterface {
protected UriMapper uriMapper;
// protected LinksetInterfaceMinimal linksetInterface;
// private String validationTypeString;
public final String MIME_TYPE = "mimeType";
public final String STORE_TYPE = "storeType";
public final String VALIDATION_TYPE = "validationType";
public final String INFO = "info";
public final String FILE = "file";
public final String NO_RESULT = null;
protected final NumberFormat formatter;
static final Logger logger = Logger.getLogger(WSUriInterfaceService.class);
public WSUriInterfaceService(UriMapper uriMapper) throws BridgeDBException {
super(uriMapper);
this.uriMapper = uriMapper;
formatter = configFormatter();
logger.info("WS Service running using supplied uriMapper");
}
private NumberFormat configFormatter() throws BridgeDBException {
NumberFormat numberFormat = NumberFormat.getInstance();
if (numberFormat instanceof DecimalFormat) {
DecimalFormatSymbols dfs = new DecimalFormatSymbols();
dfs.setGroupingSeparator(',');
((DecimalFormat) numberFormat).setDecimalFormatSymbols(dfs);
}
return numberFormat;
}
private MappingsBean mapFull(String id, String scrCode, String uri, String lensUri,
Boolean includeXrefResults, Boolean includeUriResults,
List<String> targetCodes, String graph, List<String> targetUriPatterns) throws BridgeDBException {
if (logger.isDebugEnabled()){
logger.debug("map called! ");
if (id != null){
logger.debug("id = " + id);
}
if (scrCode != null){
logger.debug(" scrCode = " + scrCode);
}
if (uri != null){
logger.debug(" uri = " + uri);
}
logger.debug(" lensUri = " + lensUri);
if (targetCodes!= null && !targetCodes.isEmpty()){
logger.debug(" targetCodes = " + targetCodes);
}
if (targetUriPatterns!= null && !targetUriPatterns.isEmpty()){
logger.debug(" targetUriPatterns = " + targetUriPatterns);
}
}
Collection<DataSource> targetDataSources = getDataSources(targetCodes);
if (id == null){
if (scrCode != null) {
throw new BridgeDBException (WsConstants.DATASOURCE_SYSTEM_CODE + " parameter " + scrCode
+ " should only be used together with " + WsConstants.ID + " parameter ");
}
if (uri == null){
throw new BridgeDBException ("Please provide either a " + WsConstants.ID + " or a "
+ WsUriConstants.URI + " parameter.");
}
return mapFull(uri, lensUri, includeXrefResults, targetDataSources, graph, targetUriPatterns);
} else {
if (uri != null){
throw new BridgeDBException ("Please provide either a " + WsConstants.ID + " or a "
+ WsConstants.DATASOURCE_SYSTEM_CODE + " parameter, but not both.");
}
if (scrCode == null) {
throw new BridgeDBException (WsConstants.ID + " parameter must come with a "
+ WsConstants.DATASOURCE_SYSTEM_CODE + " parameter.");
}
}
return mapFull(id, scrCode, lensUri, includeUriResults, targetDataSources, graph, targetUriPatterns);
}
@GET
@Produces({MediaType.APPLICATION_XML})
@Path("/" + WsUriConstants.MAP)
@Override
public Response map(
@QueryParam(WsConstants.ID) String id,
@QueryParam(WsConstants.DATASOURCE_SYSTEM_CODE) String scrCode,
@QueryParam(WsUriConstants.URI) String uri,
@QueryParam(WsUriConstants.LENS_URI) String lensUri,
@QueryParam(WsUriConstants.INCLUDE_XREF_RESULTS) Boolean includeXrefResults,
@QueryParam(WsUriConstants.INCLUDE_URI_RESULTS) Boolean includeUriResults,
@QueryParam(WsConstants.TARGET_DATASOURCE_SYSTEM_CODE) List<String> targetCodes,
@QueryParam(WsUriConstants.GRAPH) String graph,
@QueryParam(WsUriConstants.TARGET_URI_PATTERN) List<String> targetUriPatterns) throws BridgeDBException {
MappingsBean result = mapFull(id, scrCode, uri, lensUri,
includeXrefResults, includeUriResults,
targetCodes, graph, targetUriPatterns);
if (noContentOnEmpty & result.asMappings().isEmpty()){
return Response.status(Response.Status.NO_CONTENT).build();
}
return Response.ok(result, MediaType.APPLICATION_XML_TYPE).build();
}
@GET
@Produces({MediaType.APPLICATION_JSON})
@Path("/" + WsUriConstants.MAP)
public Response mapJson(
@QueryParam(WsConstants.ID) String id,
@QueryParam(WsConstants.DATASOURCE_SYSTEM_CODE) String scrCode,
@QueryParam(WsUriConstants.URI) String uri,
@QueryParam(WsUriConstants.LENS_URI) String lensUri,
@QueryParam(WsUriConstants.INCLUDE_XREF_RESULTS) Boolean includeXrefResults,
@QueryParam(WsUriConstants.INCLUDE_URI_RESULTS) Boolean includeUriResults,
@QueryParam(WsConstants.TARGET_DATASOURCE_SYSTEM_CODE) List<String> targetCodes,
@QueryParam(WsUriConstants.GRAPH) String graph,
@QueryParam(WsUriConstants.TARGET_URI_PATTERN) List<String> targetUriPatterns) throws BridgeDBException {
MappingsBean result = mapFull(id, scrCode, uri, lensUri,
includeXrefResults, includeUriResults,
targetCodes, graph, targetUriPatterns);
if (noContentOnEmpty & result.asMappings().isEmpty()){
return Response.noContent().build();
}
return Response.ok(result, MediaType.APPLICATION_JSON_TYPE).build();
}
@GET
@Produces({MediaType.TEXT_HTML})
@Path("/" + WsUriConstants.MAP)
public Response mapHtml(
@QueryParam(WsConstants.ID) String id,
@QueryParam(WsConstants.DATASOURCE_SYSTEM_CODE) String scrCode,
@QueryParam(WsUriConstants.URI) String uri,
@QueryParam(WsUriConstants.LENS_URI) String lensUri,
@QueryParam(WsUriConstants.INCLUDE_XREF_RESULTS) Boolean includeXrefResults,
@QueryParam(WsUriConstants.INCLUDE_URI_RESULTS) Boolean includeUriResults,
@QueryParam(WsConstants.TARGET_DATASOURCE_SYSTEM_CODE) List<String> targetCodes,
@QueryParam(WsUriConstants.GRAPH) String graph,
@QueryParam(WsUriConstants.TARGET_URI_PATTERN) List<String> targetUriPatterns,
@Context HttpServletRequest httpServletRequest) throws BridgeDBException {
MappingsBean result = mapFull (id, scrCode, uri, lensUri,
includeXrefResults, includeUriResults,
targetCodes, graph, targetUriPatterns);
if (noContentOnEmpty & result.asMappings().isEmpty()){
return noContentWrapper(httpServletRequest);
}
return Response.ok(result, MediaType.APPLICATION_XML_TYPE).build();
}
private UriMappings mapUriInner(List<String> uris, String lensUri, String graph, List<String> targetUriPatterns)
throws BridgeDBException {
if (logger.isDebugEnabled()){
logger.debug("map called! ");
logger.debug(" uri = " + uris);
logger.debug(" lensUri = " + lensUri);
if (targetUriPatterns!= null && !targetUriPatterns.isEmpty()){
logger.debug(" targetUriPatterns = " + targetUriPatterns);
}
}
Set<String> results = new HashSet<String>();
for(String single:uris){
results.addAll(uriMapper.mapUri(single, lensUri, graph, targetUriPatterns));
}
return UriMappings.asBean(results);
}
private MappingsBySysCodeId mapUriBySysCodeId(List<String> uris, String lensUri, String graph, List<String> targetUriPatterns)
throws BridgeDBException {
if (logger.isDebugEnabled()){
logger.debug("mapUriBySysCodeId called! ");
logger.debug(" uri = " + uris);
logger.debug(" lensUri = " + lensUri);
logger.debug(" graph = " + graph);
if (targetUriPatterns!= null && !targetUriPatterns.isEmpty()){
logger.debug(" targetUriPatterns = " + targetUriPatterns);
}
}
return uriMapper.mapUriBySysCodeId(lensUri, lensUri, graph, targetUriPatterns);
}
@GET
@Produces({MediaType.APPLICATION_XML})
@Path("/" + WsUriConstants.MAP_URI)
@Override
public Response mapUri(
@QueryParam(WsUriConstants.URI) List<String> uris,
@QueryParam(WsUriConstants.LENS_URI) String lensUri,
@QueryParam(WsUriConstants.GRAPH) String graph,
@QueryParam(WsUriConstants.TARGET_URI_PATTERN) List<String> targetUriPatterns) throws BridgeDBException {
UriMappings result = mapUriInner(uris, lensUri, graph, targetUriPatterns);
if (noContentOnEmpty & result.isEmpty()){
return Response.noContent().build();
}
return Response.ok(result, MediaType.APPLICATION_XML_TYPE).build();
}
@GET
@Produces({MediaType.APPLICATION_JSON})
@Path("/" + WsUriConstants.MAP_URI)
public Response mapUriJson(
@QueryParam(WsUriConstants.URI) List<String> uris,
@QueryParam(WsUriConstants.LENS_URI) String lensUri,
@QueryParam(WsUriConstants.GRAPH) String graph,
@QueryParam(WsUriConstants.TARGET_URI_PATTERN) List<String> targetUriPatterns) throws BridgeDBException {
UriMappings result = mapUriInner(uris, lensUri, graph, targetUriPatterns);
if (noContentOnEmpty & result.isEmpty()){
return Response.noContent().build();
}
return Response.ok(result, MediaType.APPLICATION_JSON_TYPE).build();
}
@GET
@Produces({MediaType.TEXT_HTML})
@Path("/" + WsUriConstants.MAP_URI)
public Response mapUriHtml(
@QueryParam(WsUriConstants.URI) List<String> uris,
@QueryParam(WsUriConstants.LENS_URI) String lensUri,
@QueryParam(WsUriConstants.GRAPH) String graph,
@QueryParam(WsUriConstants.TARGET_URI_PATTERN) List<String> targetUriPatterns,
@QueryParam(WsUriConstants.FORMAT) String format,
@Context HttpServletRequest httpServletRequest) {
Set<Mapping> mappings = new HashSet<Mapping>();
try {
if (uris == null || uris.isEmpty()){
throw new BridgeDBException(WsUriConstants.URI + " parameter missing!");
}
for (String uri:uris){
mappings.addAll(uriMapper.mapFull(uri, lensUri, true, graph, targetUriPatterns));
}
} catch (BridgeDBException exception) {
return mapUriHtmlResult(uris, lensUri, graph, targetUriPatterns, format, httpServletRequest, null, exception);
}
uris.remove("");
targetUriPatterns.remove("");
if (format == null || format.isEmpty()){
format = MediaType.TEXT_HTML;
}
if (format.equals("application/xml")){
if (noContentOnEmpty & mappings.isEmpty()){
return noContentWrapper(httpServletRequest);
}
return Response.ok(UriMappings.toBean(mappings), MediaType.APPLICATION_XML_TYPE).build();
}
else if (format.equals("application/json")){
if (noContentOnEmpty & mappings.isEmpty()){
return noContentWrapper(httpServletRequest);
}
return Response.ok(UriMappings.toBean(mappings), MediaType.APPLICATION_JSON_TYPE).build();
}
return mapUriHtmlResult(uris, lensUri, graph, targetUriPatterns, format, httpServletRequest, mappings, null);
}
private Response mapUriHtmlResult(List<String> uris, String lensUri, String graph, List<String> targetUriPatterns,
String format, HttpServletRequest httpServletRequest, Collection<Mapping> mappingSet, BridgeDBException exception) {
uris.remove("");
targetUriPatterns.remove("");
VelocityContext velocityContext = new VelocityContext();
velocityContext.put("contextPath", httpServletRequest.getContextPath());
velocityContext.put("sourceUris", uris);
velocityContext.put("URI", WsUriConstants.URI);
velocityContext.put("lensURI", lensUri);
velocityContext.put("lensURIName", WsUriConstants.LENS_URI);
velocityContext.put("defaultLensName", Lens.DEFAULT_LENS_NAME);
velocityContext.put("targetUriPatterns", targetUriPatterns);
velocityContext.put("targetUriPatternName", WsUriConstants.TARGET_URI_PATTERN);
velocityContext.put("graph", graph);
velocityContext.put("graphName", WsUriConstants.GRAPH);
if (mappingSet != null){
ArrayList<Mapping> mappingList = new ArrayList<Mapping>(mappingSet);
Collections.sort(mappingList);
velocityContext.put("mappings",mappingList);
} else {
velocityContext.put("mappings",new ArrayList<Mapping>());
velocityContext.put("exception", exception.getMessage());
}
String mainBody = WebTemplates.getForm(velocityContext, WebTemplates.MAP_URI_RESULTS);
String fullPage = this.createHtmlPage("Identity Mapping Service", mainBody, httpServletRequest);
return Response.ok(fullPage, MediaType.TEXT_HTML).build();
}
@POST
@Produces({MediaType.TEXT_HTML})
@Path("/" + WsUriConstants.MAP_URI)
public Response mapUriHtmlPost(
@FormParam(WsUriConstants.URI) List<String> uris,
@FormParam(WsUriConstants.LENS_URI) String lensUri,
@FormParam(WsUriConstants.GRAPH) String graph,
@FormParam(WsUriConstants.FORMAT) String format,
@FormParam(WsUriConstants.TARGET_URI_PATTERN) List<String> targetUriPatterns,
@Context HttpServletRequest httpServletRequest) throws BridgeDBException {
return mapUriHtml(uris, lensUri, graph, targetUriPatterns, format, httpServletRequest);
}
protected final MappingsBySet mapBySetInner(List<String> uris, String lensUri, String graph, List<String> targetUriPatterns) throws BridgeDBException {
HashSet<String> uriSet = new HashSet<String>(uris);
return uriMapper.mapBySet(uriSet, lensUri, graph, targetUriPatterns);
}
@GET
@Produces({MediaType.APPLICATION_XML})
@Path("/" + WsUriConstants.MAP_BY_SET)
public Response mapBySet(@QueryParam(WsUriConstants.URI) List<String> uris,
@QueryParam(WsUriConstants.LENS_URI) String lensUri,
@QueryParam(WsUriConstants.GRAPH) String graph,
@QueryParam(WsUriConstants.TARGET_URI_PATTERN) List<String> targetUriPatterns) throws BridgeDBException {
MappingsBySet mappingsBySet = mapBySetInner(uris, lensUri, graph, targetUriPatterns);
if (noContentOnEmpty & mappingsBySet.isEmpty()){
return Response.noContent().build();
}
MappingsBySetBean result = new MappingsBySetBean(mappingsBySet);
return Response.ok(result, MediaType.APPLICATION_XML_TYPE).build();
}
@GET
@Produces({MediaType.APPLICATION_JSON})
@Path("/" + WsUriConstants.MAP_BY_SET)
public Response mapBySetJson(@QueryParam(WsUriConstants.URI) List<String> uris,
@QueryParam(WsUriConstants.LENS_URI) String lensUri,
@QueryParam(WsUriConstants.GRAPH) String graph,
@QueryParam(WsUriConstants.TARGET_URI_PATTERN) List<String> targetUriPatterns) throws BridgeDBException {
MappingsBySet mappingsBySet = mapBySetInner(uris, lensUri, graph, targetUriPatterns);
if (noContentOnEmpty & mappingsBySet.isEmpty()){
return Response.noContent().build();
}
MappingsBySetBean result = new MappingsBySetBean(mappingsBySet);
return Response.ok(result, MediaType.APPLICATION_JSON_TYPE).build();
}
@GET
@Produces({MediaType.TEXT_HTML})
@Path("/" + WsUriConstants.MAP_BY_SET)
public Response mapBySetHtml(@QueryParam(WsUriConstants.URI) List<String> uris,
@QueryParam(WsUriConstants.LENS_URI) String lensUri,
@QueryParam(WsUriConstants.GRAPH) String graph,
@QueryParam(WsUriConstants.TARGET_URI_PATTERN) List<String> targetUriPatterns,
@Context HttpServletRequest httpServletRequest) throws BridgeDBException {
MappingsBySet mappingsBySet = mapBySetInner(uris, lensUri, graph, targetUriPatterns);
if (noContentOnEmpty & mappingsBySet.isEmpty()){
return noContentWrapper(httpServletRequest);
}
MappingsBySetBean result = new MappingsBySetBean(mappingsBySet);
return Response.ok(result, MediaType.APPLICATION_XML_TYPE).build();
}
@GET
@Produces({MediaType.APPLICATION_XML})
@Path("/" + WsUriConstants.URI_EXISTS)
@Override
public Response UriExists(@QueryParam(WsUriConstants.URI) String URI) throws BridgeDBException {
if (URI == null) throw new BridgeDBException(WsUriConstants.URI + " parameter missing.");
if (URI.isEmpty()) throw new BridgeDBException(WsUriConstants.URI + " parameter may not be null.");
boolean exists = uriMapper.uriExists(URI);
UriExistsBean bean = new UriExistsBean(URI, exists);
return Response.ok(bean, MediaType.APPLICATION_XML_TYPE).build();
}
@GET
@Produces({MediaType.APPLICATION_JSON})
@Path("/" + WsUriConstants.URI_EXISTS)
public Response UriExistsJson(@QueryParam(WsUriConstants.URI) String URI) throws BridgeDBException {
if (URI == null) throw new BridgeDBException(WsUriConstants.URI + " parameter missing.");
if (URI.isEmpty()) throw new BridgeDBException(WsUriConstants.URI + " parameter may not be null.");
boolean exists = uriMapper.uriExists(URI);
UriExistsBean bean = new UriExistsBean(URI, exists);
return Response.ok(bean, MediaType.APPLICATION_JSON_TYPE).build();
}
//No html as never no context
private UriSearchBean UriSearchInner(String text,String limitString) throws BridgeDBException {
if (text == null) throw new BridgeDBException(WsUriConstants.TEXT + " parameter missing.");
if (text.isEmpty()) throw new BridgeDBException(WsUriConstants.TEXT + " parameter may not be null.");
UriSearchBean bean;
if (limitString == null || limitString.isEmpty()){
Set<String> uris = uriMapper.uriSearch(text, Integer.MAX_VALUE);
return new UriSearchBean(text, uris);
} else {
int limit = Integer.parseInt(limitString);
Set<String> uris = uriMapper.uriSearch(text, limit);
return new UriSearchBean(text, uris);
}
}
@GET
@Produces({MediaType.APPLICATION_XML})
@Path("/" + WsUriConstants.URI_SEARCH)
@Override
public Response UriSearch(@QueryParam(WsUriConstants.TEXT) String text,
@QueryParam(WsUriConstants.LIMIT) String limitString) throws BridgeDBException {
UriSearchBean bean = UriSearchInner(text, limitString);
if (noContentOnEmpty & bean.isEmpty()){
return Response.noContent().build();
}
return Response.ok(bean, MediaType.APPLICATION_XML_TYPE).build();
}
@GET
@Produces({MediaType.APPLICATION_JSON})
@Path("/" + WsUriConstants.URI_SEARCH)
public Response UriSearchJson(@QueryParam(WsUriConstants.TEXT) String text,
@QueryParam(WsUriConstants.LIMIT) String limitString) throws BridgeDBException {
UriSearchBean bean = UriSearchInner(text, limitString);
if (noContentOnEmpty & bean.isEmpty()){
return Response.noContent().build();
}
return Response.ok(bean, MediaType.APPLICATION_JSON_TYPE).build();
}
@GET
@Produces({MediaType.TEXT_HTML})
@Path("/" + WsUriConstants.URI_SEARCH)
public Response UriSearchHtml(@QueryParam(WsUriConstants.TEXT) String text,
@QueryParam(WsUriConstants.LIMIT) String limitString,
@Context HttpServletRequest httpServletRequest) throws BridgeDBException {
UriSearchBean bean = UriSearchInner(text, limitString);
if (noContentOnEmpty & bean.isEmpty()){
return noContentWrapper(httpServletRequest);
}
return Response.ok(bean, MediaType.APPLICATION_XML_TYPE).build();
}
public XrefBean toXrefInner(String URI) throws BridgeDBException {
if (URI == null) throw new BridgeDBException(WsUriConstants.URI + " parameter missing.");
if (URI.isEmpty()) throw new BridgeDBException(WsUriConstants.URI + " parameter may not be null.");
Xref xref = uriMapper.toXref(URI);
return XrefBean.asBean(xref);
}
@GET
@Produces({MediaType.APPLICATION_XML})
@Path("/" + WsUriConstants.TO_XREF)
@Override
public Response toXref(@QueryParam(WsUriConstants.URI) String URI) throws BridgeDBException {
XrefBean bean = toXrefInner(URI);
if (noContentOnEmpty & bean.isEmpty()){
return Response.noContent().build();
}
return Response.ok(bean, MediaType.APPLICATION_XML_TYPE).build();
}
@GET
@Produces({MediaType.APPLICATION_XML})
@Path("/" + WsUriConstants.TO_URIS)
@Override
public Response toUris(@QueryParam(WsConstants.ID) String id,
@QueryParam(WsConstants.DATASOURCE_SYSTEM_CODE) String scrCode) throws BridgeDBException{
UriMappings result = toUrisInner(id, scrCode);
if (noContentOnEmpty & result.isEmpty()){
return Response.noContent().build();
}
return Response.ok(result, MediaType.APPLICATION_XML_TYPE).build();
}
@GET
@Produces({MediaType.APPLICATION_JSON})
@Path("/" + WsUriConstants.TO_URIS)
public Response toUrisJSon(@QueryParam(WsConstants.ID) String id,
@QueryParam(WsConstants.DATASOURCE_SYSTEM_CODE) String scrCode) throws BridgeDBException{
UriMappings result = toUrisInner(id, scrCode);
if (noContentOnEmpty & result.isEmpty()){
return Response.noContent().build();
}
return Response.ok(result, MediaType.APPLICATION_JSON_TYPE).build();
}
@GET
@Produces({MediaType.TEXT_HTML})
@Path("/" + WsUriConstants.TO_URIS)
public Response toUrisHtml(@QueryParam(WsConstants.ID) String id,
@QueryParam(WsConstants.DATASOURCE_SYSTEM_CODE) String scrCode,
@Context HttpServletRequest httpServletRequest) throws BridgeDBException{
UriMappings result = toUrisInner(id, scrCode);
Set<String> uris = result.getTargetUri();
VelocityContext velocityContext = new VelocityContext();
velocityContext.put("contextPath", httpServletRequest.getContextPath());
velocityContext.put("id", id);
velocityContext.put("sysCode", scrCode);
velocityContext.put("uris", uris);
String mainBody = WebTemplates.getForm(velocityContext, WebTemplates.TO_URIS_SCRIPT);
String fullPage = this.createHtmlPage("Identity Mapping Service", mainBody, httpServletRequest);
return Response.ok(fullPage, MediaType.TEXT_HTML).build();
}
public UriMappings toUrisInner(String id, String scrCode) throws BridgeDBException{
if (logger.isDebugEnabled()){
logger.debug("toUris called! ");
logger.debug("id = " + id);
logger.debug("srCode = " + scrCode);
}
if (id == null){
throw new BridgeDBException ("Please provide a " + WsConstants.ID + " parameter.");
}
if (scrCode == null) {
throw new BridgeDBException ("Please provide a " + WsConstants.DATASOURCE_SYSTEM_CODE + " parameter.");
}
DataSource dataSource = DataSource.getExistingBySystemCode(scrCode);
Xref sourceXref = new Xref(id, dataSource);
Set<String> results = uriMapper.toUris(sourceXref);
return UriMappings.asBean(results);
}
@GET
@Produces({MediaType.APPLICATION_JSON})
@Path("/" + WsUriConstants.TO_XREF)
public Response toXrefJson(@QueryParam(WsUriConstants.URI) String URI) throws BridgeDBException {
XrefBean bean = toXrefInner(URI);
if (noContentOnEmpty & bean.isEmpty()){
return Response.noContent().build();
}
return Response.ok(bean, MediaType.APPLICATION_JSON_TYPE).build();
}
@GET
@Produces({MediaType.TEXT_HTML})
@Path("/" + WsUriConstants.TO_XREF)
public Response toXrefHtml(@QueryParam(WsUriConstants.URI) String URI,
@Context HttpServletRequest httpServletRequest) throws BridgeDBException {
XrefBean bean = toXrefInner(URI);
if (noContentOnEmpty & bean.isEmpty()){
return noContentWrapper(httpServletRequest);
}
return Response.ok(bean, MediaType.APPLICATION_XML_TYPE).build();
}
@GET
@Produces({MediaType.APPLICATION_XML})
@Path("/" + WsUriConstants.GET_OVERALL_STATISTICS)
@Override
public Response getOverallStatistics(@QueryParam(WsUriConstants.LENS_URI) String lensUri)
throws BridgeDBException {
OverallStatistics overallStatistics = uriMapper.getOverallStatistics(lensUri);
OverallStatisticsBean bean = OverallStatisticsBean.asBean(overallStatistics);
return Response.ok(bean, MediaType.APPLICATION_XML_TYPE).build();
}
@GET
@Produces({MediaType.APPLICATION_JSON})
@Path("/" + WsUriConstants.GET_OVERALL_STATISTICS)
public Response getOverallStatisticsJson(@QueryParam(WsUriConstants.LENS_URI) String lensUri)
throws BridgeDBException {
OverallStatistics overallStatistics = uriMapper.getOverallStatistics(lensUri);
OverallStatisticsBean bean = OverallStatisticsBean.asBean(overallStatistics);
return Response.ok(bean, MediaType.APPLICATION_JSON_TYPE).build();
}
@Override
@GET
@Produces({MediaType.APPLICATION_XML})
@Path("/" + WsUriConstants.SOURCE_INFOS)
public Response getSourceInfos(@QueryParam(WsUriConstants.LENS_URI) String lensUri) throws BridgeDBException {
SourceInfosBean bean = getSourceInfosInner(lensUri);
if (noContentOnEmpty & bean.isEmpty()){
return Response.noContent().build();
}
return Response.ok(bean, MediaType.APPLICATION_XML_TYPE).build();
}
@GET
@Produces({MediaType.APPLICATION_JSON})
@Path("/" + WsUriConstants.SOURCE_INFOS)
public Response getSourceInfosJson(@QueryParam(WsUriConstants.LENS_URI) String lensUri) throws BridgeDBException {
SourceInfosBean bean = getSourceInfosInner(lensUri);
if (noContentOnEmpty & bean.isEmpty()){
return Response.noContent().build();
}
return Response.ok(bean, MediaType.APPLICATION_JSON_TYPE).build();
}
private SourceInfosBean getSourceInfosInner(String lensUri) throws BridgeDBException {
List<SourceInfo> infos = uriMapper.getSourceInfos(lensUri);
SourceInfosBean bean = new SourceInfosBean();
for (SourceInfo info:infos){
bean.addSourceInfo(info);
}
return bean;
}
@Override
@GET
@Produces({MediaType.APPLICATION_XML})
@Path("/" + WsUriConstants.SOURCE_TARGET_INFOS)
public Response getSourceTargetInfos(@QueryParam(WsUriConstants.SOURCE_DATASOURCE_SYSTEM_CODE) String scrCode,
@QueryParam(WsUriConstants.LENS_URI) String lensUri) throws BridgeDBException {
SourceTargetInfosBean bean = getSourceTargetInfosInner(scrCode, lensUri);
if (noContentOnEmpty & bean.isEmpty()){
return Response.noContent().build();
}
return Response.ok(bean, MediaType.APPLICATION_XML_TYPE).build();
}
@GET
@Produces({MediaType.APPLICATION_JSON})
@Path("/" + WsUriConstants.SOURCE_TARGET_INFOS)
public Response getSourceTargetInfosJson(@QueryParam(WsUriConstants.SOURCE_DATASOURCE_SYSTEM_CODE) String scrCode,
@QueryParam(WsUriConstants.LENS_URI) String lensUri) throws BridgeDBException {
SourceTargetInfosBean bean = getSourceTargetInfosInner(scrCode, lensUri);
if (noContentOnEmpty & bean.isEmpty()){
return Response.noContent().build();
}
return Response.ok(bean, MediaType.APPLICATION_JSON_TYPE).build();
}
private SourceTargetInfosBean getSourceTargetInfosInner(String scrCode, String lensUri) throws BridgeDBException {
List<SourceTargetInfo> infos = uriMapper.getSourceTargetInfos(scrCode, lensUri);
SourceTargetInfosBean bean = new SourceTargetInfosBean();
for (SourceTargetInfo info:infos){
bean.addSourceTargetInfo(info);
}
return bean;
}
@GET
@Produces({MediaType.APPLICATION_XML})
@Path("/" + WsUriConstants.MAPPING_SET + WsUriConstants.XML)
public Response getMappingSetInfosXML(@QueryParam(WsUriConstants.SOURCE_DATASOURCE_SYSTEM_CODE) String scrCode,
@QueryParam(WsUriConstants.TARGET_DATASOURCE_SYSTEM_CODE) String targetCode,
@QueryParam(WsUriConstants.LENS_URI) String lensUri) throws BridgeDBException {
return getMappingSetInfos(scrCode, targetCode, lensUri);
}
private MappingSetInfosBean getMappingSetInfosInner(String scrCode, String targetCode, String lensUri) throws BridgeDBException {
List<MappingSetInfo> infos = uriMapper.getMappingSetInfos(scrCode, targetCode, lensUri);
MappingSetInfosBean bean = new MappingSetInfosBean();
for (MappingSetInfo info:infos){
bean.addMappingSetInfo(info);
}
return bean;
}
@Override
@GET
@Produces({MediaType.APPLICATION_XML})
@Path("/" + WsUriConstants.MAPPING_SET)
public Response getMappingSetInfos(@QueryParam(WsUriConstants.SOURCE_DATASOURCE_SYSTEM_CODE) String scrCode,
@QueryParam(WsUriConstants.TARGET_DATASOURCE_SYSTEM_CODE) String targetCode,
@QueryParam(WsUriConstants.LENS_URI) String lensUri) throws BridgeDBException {
MappingSetInfosBean bean = getMappingSetInfosInner(scrCode, targetCode, lensUri);
if (noContentOnEmpty & bean.isEmpty()){
return Response.noContent().build();
}
return Response.ok(bean, MediaType.APPLICATION_XML_TYPE).build();
}
@GET
@Produces({MediaType.APPLICATION_JSON})
@Path("/" + WsUriConstants.MAPPING_SET)
public Response getMappingSetInfosJson(@QueryParam(WsUriConstants.SOURCE_DATASOURCE_SYSTEM_CODE) String scrCode,
@QueryParam(WsUriConstants.TARGET_DATASOURCE_SYSTEM_CODE) String targetCode,
@QueryParam(WsUriConstants.LENS_URI) String lensUri) throws BridgeDBException {
MappingSetInfosBean bean = getMappingSetInfosInner(scrCode, targetCode, lensUri);
if (noContentOnEmpty & bean.isEmpty()){
return Response.noContent().build();
}
return Response.ok(bean, MediaType.APPLICATION_JSON_TYPE).build();
}
private LensBean getLensInner(String id) throws BridgeDBException {
Lens lens = LensTools.byId(id);
return new LensBean(lens, null);
}
@GET
@Produces({MediaType.APPLICATION_XML})
@Path(Lens.URI_PREFIX + "{id}")
@Override
public Response getLens(@PathParam("id") String id) throws BridgeDBException {
LensBean bean = getLensInner(id);
if (noContentOnEmpty & bean.isEmpty()){
return Response.noContent().build();
}
return Response.ok(bean, MediaType.APPLICATION_XML_TYPE).build();
}
@GET
@Produces({MediaType.APPLICATION_JSON})
@Path(Lens.URI_PREFIX + "{id}")
public Response getLensJson(@PathParam("id") String id) throws BridgeDBException {
LensBean bean = getLensInner(id);
if (noContentOnEmpty & bean.isEmpty()){
return Response.noContent().build();
}
return Response.ok(bean, MediaType.APPLICATION_JSON_TYPE).build();
}
@GET
@Produces({MediaType.TEXT_HTML})
@Path(Lens.URI_PREFIX + "{id}")
public Response getLensHtml(@PathParam("id") String id,
@Context HttpServletRequest httpServletRequest) throws BridgeDBException {
LensBean bean = getLensInner(id);
if (noContentOnEmpty & bean.isEmpty()){
return noContentWrapper(httpServletRequest);
}
return Response.ok(bean, MediaType.APPLICATION_XML_TYPE).build();
}
@GET
@Produces({MediaType.APPLICATION_XML})
@Path("/" + Lens.METHOD_NAME + WsUriConstants.XML)
public Response getLensesXML(@QueryParam(WsUriConstants.LENS_URI) String lensUri,
@QueryParam(WsUriConstants.LENS_GROUP) String lensGroup) throws BridgeDBException {
return getLenses(lensUri, lensGroup);
}
protected List<Lens> getTheLens(String lensUri, String lensGroup) throws BridgeDBException{
if (lensUri == null || lensUri.isEmpty()){
return LensTools.getLens(lensGroup);
} else {
Lens lens = LensTools.byId(lensUri);
List<Lens> lenses = new ArrayList<Lens>();
lenses.add(lens);
return lenses;
}
}
@GET
@Produces({MediaType.APPLICATION_XML})
@Path("/" + Lens.METHOD_NAME)
@Override
public Response getLenses(@QueryParam(WsUriConstants.LENS_URI) String lensUri,
@QueryParam(WsUriConstants.LENS_GROUP) String lensGroup) throws BridgeDBException {
List<Lens> lenses = getTheLens(lensUri, lensGroup);
LensesBean bean = new LensesBean(lenses, null);
if (noContentOnEmpty & bean.isEmpty()){
return Response.noContent().build();
}
return Response.ok(bean, MediaType.APPLICATION_XML_TYPE).build();
}
@GET
@Produces({MediaType.APPLICATION_JSON})
@Path("/" + Lens.METHOD_NAME)
public Response getLensesJson(@QueryParam(WsUriConstants.LENS_URI) String lensUri,
@QueryParam(WsUriConstants.LENS_GROUP) String lensGroup) throws BridgeDBException {
List<Lens> lenses = getTheLens(lensUri, lensGroup);
LensesBean bean = new LensesBean(lenses, null);
if (noContentOnEmpty & bean.isEmpty()){
return Response.noContent().build();
}
return Response.ok(bean, MediaType.APPLICATION_JSON_TYPE).build();
}
@GET
@Produces({MediaType.APPLICATION_XML})
@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<Lens> lenses = getTheLens(lensUri, lensGroup);
LensesBean bean = new LensesBean(lenses, null);
if (noContentOnEmpty & bean.isEmpty()){
return noContentWrapper(httpServletRequest);
}
return Response.ok(bean, MediaType.APPLICATION_XML_TYPE).build();
}
private MappingSetInfoBean getMappingSetInfoInner(String idString) 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);
return new MappingSetInfoBean(info);
}
@GET
@Produces({MediaType.APPLICATION_XML})
@Path("/" + WsUriConstants.MAPPING_SET + "/{id}")
@Override
public Response getMappingSetInfo(@PathParam("id") String idString) throws BridgeDBException {
MappingSetInfoBean bean = getMappingSetInfoInner(idString);
if (noContentOnEmpty & bean.isEmpty()){
return Response.noContent().build();
}
return Response.ok(bean, MediaType.APPLICATION_XML_TYPE).build();
}
@GET
@Produces({MediaType.APPLICATION_JSON})
@Path("/" + WsUriConstants.MAPPING_SET + "/{id}")
public Response getMappingSetInfoJson(@PathParam("id") String idString) throws BridgeDBException {
MappingSetInfoBean bean = getMappingSetInfoInner(idString);
if (noContentOnEmpty & bean.isEmpty()){
return Response.noContent().build();
}
return Response.ok(bean, MediaType.APPLICATION_JSON_TYPE).build();
}
@GET
@Produces({MediaType.APPLICATION_XML, MediaType.APPLICATION_JSON, MediaType.TEXT_HTML})
@Path("/" + WsUriConstants.DATA_SOURCE)
public Response getDataSource() throws BridgeDBException {
throw new BridgeDBException("id path parameter missing.");
}
private DataSourceUriPatternBean getDataSourceInner(String id) throws BridgeDBException {
if (id == null) {
throw new BridgeDBException("Path parameter missing.");
}
if (id.isEmpty()) {
throw new BridgeDBException("Path parameter may not be null.");
}
DataSource ds = DataSource.getBySystemCode(id);
return new DataSourceUriPatternBean(ds, uriMapper.getUriPatterns(id));
}
@GET
@Produces({MediaType.APPLICATION_XML})
@Override
@Path("/" + WsUriConstants.DATA_SOURCE + "/{id}")
public Response getDataSource(@PathParam("id") String id) throws BridgeDBException {
DataSourceUriPatternBean bean = getDataSourceInner(id);
if (noContentOnEmpty & bean.isEmpty()){
return Response.noContent().build();
}
return Response.ok(bean, MediaType.APPLICATION_XML_TYPE).build();
}
@GET
@Produces({MediaType.APPLICATION_JSON})
@Path("/" + WsUriConstants.DATA_SOURCE + "/{id}")
public Response getDataSourceJson(@PathParam("id") String id) throws BridgeDBException {
DataSourceUriPatternBean bean = getDataSourceInner(id);
if (noContentOnEmpty & bean.isEmpty()){
return Response.noContent().build();
}
return Response.ok(bean, MediaType.APPLICATION_JSON_TYPE).build();
}
@GET
@Produces({MediaType.TEXT_PLAIN})
@Override
@Path("/" + WsUriConstants.SQL_COMPAT_VERSION)
public Response getSqlCompatVersion() throws BridgeDBException {
return Response.ok(uriMapper.getSqlCompatVersion(), MediaType.TEXT_PLAIN).build();
}
//****** Support functions *****
private MappingsBean mapFull(String uri, String lensUri, Boolean includeXrefResults,
Collection<DataSource> targetDataSources, String graph, Collection<String> targetPatterns)
throws BridgeDBException {
if (includeXrefResults == null){
includeXrefResults = false;
}
Set<Mapping> mappings;
if (targetDataSources.isEmpty()){
//if (targetPatterns == null){
// mappings = uriMapper.mapFull(uri, lensUri, includeXrefResults, graph);
//} else {
mappings = mapFull(uri, lensUri, includeXrefResults, graph, targetPatterns);
//}
} else {
mappings = mapFull (uri, lensUri, targetDataSources);
if (targetPatterns != null && !targetPatterns.isEmpty()){
//Include Xref results as targetDataSources set
mappings.addAll(mapFull(uri, lensUri, true, graph, targetPatterns));
}
}
return new MappingsBean(mappings);
}
/**
*
* @param id
* @param scrCode
* @param lensUri
* @param includeUriResults
* @param targetDataSources
* @param graph
* @param targetPatterns
* @return
* @throws BridgeDBException
* @throws IllegalStateException if targetCode is not known
*/
private MappingsBean mapFull(String id, String scrCode, String lensUri,
Boolean includeUriResults,
Collection<DataSource> targetDataSources, String graph, Collection<String> targetPatterns)
throws BridgeDBException {
DataSource dataSource = DataSource.getExistingBySystemCode(scrCode);
Xref sourceXref = new Xref(id, dataSource);
if (includeUriResults == null){
includeUriResults = false;
}
Set<Mapping> mappings;
if (targetPatterns == null ||targetPatterns.isEmpty()){
mappings = mapFull(sourceXref, lensUri, includeUriResults, targetDataSources);
} else {
mappings = mapFull(sourceXref, lensUri, graph, targetPatterns);
if (!targetDataSources.isEmpty()){
//Include UriResults as targetPatterns set
mappings.addAll(mapFull(sourceXref, lensUri, true, targetDataSources));
}
}
return new MappingsBean(mappings);
}
/**
*
* @param targetCodes
* @return
* @throws IllegalStateException if targetCode is not known
*/
private Set<DataSource> getDataSources(List<String> targetCodes){
HashSet<DataSource> targets = new HashSet<DataSource>();
if (targetCodes != null){
for (String targetCode:targetCodes){
if (targetCode != null && !targetCode.isEmpty()){
targets.add(DataSource.getExistingBySystemCode(targetCode));
} else {
targets.add(null);
}
}
}
return targets;
}
/**
* Returns both Xref and Uri results.
*
* @param sourceUri
* @param lensUri
* @param targetDataSources
* @return
* @throws BridgeDBException
*/
private Set<Mapping> mapFull(String sourceUri, String lensUri, Collection<DataSource> targetDataSources) throws BridgeDBException{
return uriMapper.mapFull(sourceUri, lensUri, targetDataSources);
}
/**
* Returns Xref results and Uri results only if requested.
*
* @param sourceXref
* @param lensUri
* @param includeUriResults
* @param targetDataSources
* @return
* @throws BridgeDBException
*/
private Set<Mapping> mapFull(Xref sourceXref, String lensUri,
boolean includeUriResults,
Collection<DataSource> targetDataSources) throws BridgeDBException{
return uriMapper.mapFull(sourceXref, lensUri, includeUriResults, targetDataSources);
}
/**
* Returns Uri results and Xref only if requested.
*
* @param sourceUri
* @param lensUri
* @param includeXrefResults
* @param graph
* @param targetUriPattern
* @return
* @throws BridgeDBException
*/
private Set<Mapping> mapFull(String sourceUri, String lensUri,
boolean includeXrefResults, String graph, Collection<String> targetUriPattern)
throws BridgeDBException{
return uriMapper.mapFull(sourceUri, lensUri, includeXrefResults, graph, targetUriPattern);
}
/**
* Returns both Xref and Uri results.
*
* @param sourceXref
* @param lensUri
* @param graph
* @param targetUriPattern
* @return
* @throws BridgeDBException
*/
private Set<Mapping> mapFull(Xref sourceXref, String lensUri, String graph, Collection<String> targetUriPattern) throws BridgeDBException{
return uriMapper.mapFull(sourceXref, lensUri, graph, targetUriPattern);
}
private String trim(String original){
String result = original.trim();
while (result.startsWith("\"")){
result = result.substring(1);
}
while (result.endsWith("\"")){
result = result.substring(0,result.length()-1);
}
return result.trim();
}
protected final void validateInfo(String info) throws BridgeDBException{
if (info == null){
throw new BridgeDBException (INFO + " parameter may not be null");
}
if (info.trim().isEmpty()){
throw new BridgeDBException (INFO + " parameter may not be empty");
}
}
void validateInputStream(InputStream inputStream) throws BridgeDBException {
if (inputStream == null){
throw new BridgeDBException (FILE + " parameter may not be null");
}
}
protected String serviceName(){
return "BridgeDb ";
}
protected String sideBar(HttpServletRequest httpServletRequest) {
StringBuilder sb = new StringBuilder("<div id=\"navBar\">");
addSideBarMiddle(sb, httpServletRequest);
addSideBarStatistics(sb, httpServletRequest);
sb.append("</div>\n");
return sb.toString();
}
protected void sideBar(StringBuilder sb, HttpServletRequest httpServletRequest) {
sb.append("<div id=\"navBar\">");
addSideBarMiddle(sb, httpServletRequest);
addSideBarStatistics(sb, httpServletRequest);
sb.append("</div>\n");
}
/**
* Allows Super classes to add to the side bar
*/
public void addSideBarMiddle(StringBuilder sb, HttpServletRequest httpServletRequest){
addSideBarBridgeDb(sb, httpServletRequest);
}
/**
* Allows Super classes to add to the side bar
*/
protected void addSideBarBridgeDb(StringBuilder sb, HttpServletRequest httpServletRequest) {
sb.append("<div class=\"menugroup\">BridgeDb Service</div>");
addSideBarItem(sb, WsUriConstants.BRIDGEDB_HOME, "Home", httpServletRequest);
String allMappingInfo = WsUriConstants.SOURCE_INFOS + "?" + WsUriConstants.LENS_URI + "=" + Lens.ALL_LENS_NAME;
addSideBarItem(sb, allMappingInfo,"All Mappings Summary", httpServletRequest);
addSideBarItem(sb, WsUriConstants.SOURCE_INFOS, "Default Mappings Summary", httpServletRequest);
//String allGraphwiz = WsUriConstants.GRAPHVIZ + "?" + WsUriConstants.LENS_URI + "=" + Lens.ALL_LENS_NAME;
//addSideBarItem(sb, allGraphwiz, "All Mappings Graphviz", httpServletRequest);
//addSideBarItem(sb, WsUriConstants.GRAPHVIZ, "Default Mappings Graphviz", httpServletRequest);
addSideBarItem(sb, Lens.METHOD_NAME, Lens.METHOD_NAME, httpServletRequest);
addSideBarItem(sb, WsUriConstants.URI_SPACES_PER_GRAPH, "UriSpace(s) per Graph", httpServletRequest);
addSideBarItem(sb, WsUriConstants.BRIDGEDB_API, "Api", httpServletRequest);
}
/**
* Allows Super classes to add to the side bar
*/
protected void addSideBarStatistics(StringBuilder sb, HttpServletRequest httpServletRequest) {
try {
OverallStatistics statistics = uriMapper.getOverallStatistics(Lens.DEFAULT_LENS_NAME);
//sb.append("\n<div class=\"menugroup\">Default Statistics</div>");
//addSideBarItem(sb, "getMappingInfo", formatter.format(statistics.getNumberOfMappings()) + " Mappings", httpServletRequest);
//addSideBarItem(sb, "getMappingInfo", formatter.format(statistics.getNumberOfMappingSets()) + " Mapping Sets", httpServletRequest);
//addSideBarItem(sb, "getSupportedSrcDataSources", formatter.format(statistics.getNumberOfSourceDataSources())
// + " Source Data Sources", httpServletRequest);
//addSideBarItem(sb, "getMappingInfo", formatter.format(statistics.getNumberOfPredicates()) + " Predicates", httpServletRequest);
//addSideBarItem(sb, "getSupportedTgtDataSources", formatter.format(statistics.getNumberOfTargetDataSources())
// + " Target Data Sources ", httpServletRequest);
statistics = uriMapper.getOverallStatistics(Lens.ALL_LENS_NAME);
//sb.append("\n<div class=\"menugroup\">All Statistics</div>");
sb.append("\n<div class=\"menugroup\">Statistics</div>");
addSideBarItem(sb, WsUriConstants.MAPPING_SET, formatter.format(statistics.getNumberOfMappings()) + " Mappings", httpServletRequest);
addSideBarItem(sb, WsUriConstants.MAPPING_SET, formatter.format(statistics.getNumberOfMappingSets()) + " Mapping Sets", httpServletRequest);
addSideBarItem(sb, WsUriConstants.GET_SUPPORTED_SOURCE_DATA_SOURCES, formatter.format(statistics.getNumberOfSourceDataSources())
+ " Source Data Sources", httpServletRequest);
addSideBarItem(sb, WsUriConstants.MAPPING_SET, formatter.format(statistics.getNumberOfPredicates()) + " Predicates", httpServletRequest);
addSideBarItem(sb, WsUriConstants.GET_SUPPORTED_TARGET_DATA_SOURCES, formatter.format(statistics.getNumberOfTargetDataSources())
+ " Target Data Sources ", httpServletRequest);
addSideBarItem(sb, Lens.METHOD_NAME, formatter.format(statistics.getNumberOfLenses())
+ " Lenses ", httpServletRequest);
} catch (BridgeDBException ex) {
sb.append("\nStatistics currenlty unavailable.");
logger.error("Error getting statistics.", ex);
}
}
/**
* Adds an item to the SideBar for this service
*/
public void addSideBarItem(StringBuilder sb, String page, String name, HttpServletRequest httpServletRequest) {
sb.append("\n<div id=\"menu");
sb.append(page);
sb.append("_text\" class=\"texthotlink\" ");
sb.append("onmouseout=\"DHTML_TextRestore('menu");
sb.append(page);
sb.append("_text'); return true; \" ");
sb.append("onmouseover=\"DHTML_TextHilight('menu");
sb.append(page);
sb.append("_text'); return true; \" ");
sb.append("onclick=\"document.location = "");
sb.append(httpServletRequest.getContextPath());
sb.append("/");
sb.append(page);
sb.append("";\">");
sb.append(name);
sb.append("</div>");
}
protected void footerAndEnd(StringBuilder sb) {
sb.append("</div>\n<div id=\"footer\">");
sb.append("\n<div></body></html>");
}
public void generateLensSelector(StringBuilder sb, HttpServletRequest httpServletRequest) throws BridgeDBException {
List<Lens> lenses = LensTools.getLens(LensTools.ALL_GROUP_NAME);
sb.append("<p>");
sb.append(WsUriConstants.LENS_URI);
sb.append("<select name=\"");
sb.append(WsUriConstants.LENS_URI);
sb.append("\">");
for (Lens lens : lenses) {
sb.append("<option value=\"");
sb.append(lens.toUri(httpServletRequest.getContextPath()));
sb.append("\">");
sb.append(lens.getName());
sb.append("</option>");
}
sb.append("</select>\n");
}
//html page stuff
protected final String createTablePage(String title, String table, HttpServletRequest httpServletRequest){
VelocityContext velocityContext = new VelocityContext();
velocityContext.put("title",title);
String tableStyle = WebTemplates.getForm(velocityContext, WebTemplates.TABLE_CSS);
String tableScript = WebTemplates.getForm(velocityContext, WebTemplates.TABLE_SORTER);
return this.createHtmlPage(tableStyle, tableScript, title, table, httpServletRequest);
}
public final String createHtmlPage(String title, String info, HttpServletRequest httpServletRequest){
return this.createHtmlPage("", "", title, info, httpServletRequest);
}
protected final String createHtmlPage(String style, String javaScript, String title, String info,
HttpServletRequest httpServletRequest){
VelocityContext velocityContext = new VelocityContext();
velocityContext.put("title",title);
style += WebTemplates.getForm(velocityContext, WebTemplates.MAIN_STYLE);
javaScript += WebTemplates.getForm(velocityContext, WebTemplates.MAIN_JAVASCRIPT);
String top = WebTemplates.getForm(velocityContext, WebTemplates.MAIN_TOP);
String menubar = sideBar(httpServletRequest);
String bottom = mainBottom();
return this.createHtmlPage(style, javaScript, title, top, menubar, info, bottom);
}
protected final String createHtmlPage(String style, String javaScript, String title, String top, String menuBar,
String info, String bottom){
VelocityContext velocityContext = new VelocityContext();
velocityContext.put("title",title);
velocityContext.put("style", style);
velocityContext.put("java_script", javaScript);
velocityContext.put("top", top);
velocityContext.put("menubar", menuBar);
velocityContext.put("info", info);
velocityContext.put("bottom", bottom);
return WebTemplates.getForm(velocityContext, WebTemplates.MAIN_FRAME);
}
protected final String mainBottom(){
return "";
}
}