Java tutorial
/* * Copyright 2015 OpenCB * * 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.opencb.opencga.storage.server.rest; import com.fasterxml.jackson.annotation.JsonInclude; import com.fasterxml.jackson.core.JsonProcessingException; import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.ObjectWriter; import org.apache.commons.lang3.StringUtils; import org.opencb.biodata.models.alignment.Alignment; import org.opencb.biodata.models.feature.Genotype; import org.opencb.biodata.models.variant.StudyEntry; import org.opencb.biodata.models.variant.VariantSource; import org.opencb.biodata.models.variant.avro.VariantAnnotation; import org.opencb.biodata.models.variant.stats.VariantStats; import org.opencb.commons.datastore.core.*; import org.opencb.opencga.storage.core.StorageManagerFactory; import org.opencb.opencga.storage.core.alignment.json.AlignmentDifferenceJsonMixin; import org.opencb.opencga.storage.core.config.StorageConfiguration; import org.opencb.opencga.storage.core.variant.io.json.*; import org.opencb.opencga.storage.server.common.AuthManager; import org.opencb.opencga.storage.server.common.DefaultAuthManager; import org.opencb.opencga.storage.server.common.exceptions.NotAuthorizedHostException; import org.opencb.opencga.storage.server.common.exceptions.NotAuthorizedUserException; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import javax.servlet.ServletContext; import javax.servlet.http.HttpServletRequest; import javax.ws.rs.DefaultValue; import javax.ws.rs.PathParam; import javax.ws.rs.QueryParam; import javax.ws.rs.core.*; import java.io.IOException; import java.util.*; /** * Created by imedina on 23/10/14. */ public class GenericRestWebService { @DefaultValue("json") @QueryParam("of") protected String outputFormat; @DefaultValue("true") @QueryParam("metadata") protected Boolean metadata; @DefaultValue("v1") @QueryParam("version") protected String version; protected final String sessionIp; protected final UriInfo uriInfo; private final long startTime; protected QueryOptions queryOptions; protected MultivaluedMap<String, String> params; protected static StorageConfiguration storageConfiguration; protected static String defaultStorageEngine; protected static StorageManagerFactory storageManagerFactory; protected static AuthManager authManager; protected static Set<String> authorizedHosts; private static Logger privLogger; protected Logger logger; private static ObjectMapper jsonObjectMapper; private static ObjectWriter jsonObjectWriter; static { jsonObjectMapper = new ObjectMapper(); jsonObjectMapper.addMixIn(StudyEntry.class, VariantSourceEntryJsonMixin.class); jsonObjectMapper.addMixIn(VariantAnnotation.class, VariantAnnotationMixin.class); jsonObjectMapper.addMixIn(VariantSource.class, VariantSourceJsonMixin.class); jsonObjectMapper.addMixIn(VariantStats.class, VariantStatsJsonMixin.class); jsonObjectMapper.addMixIn(Genotype.class, GenotypeJsonMixin.class); jsonObjectMapper.addMixIn(Alignment.AlignmentDifference.class, AlignmentDifferenceJsonMixin.class); jsonObjectMapper.setSerializationInclusion(JsonInclude.Include.NON_NULL); jsonObjectWriter = jsonObjectMapper.writer(); privLogger = LoggerFactory.getLogger("org.opencb.opencga.storage.server.rest.GenericRestWebService"); } public GenericRestWebService(@PathParam("version") String version, @Context UriInfo uriInfo, @Context HttpServletRequest httpServletRequest, @Context ServletContext context) throws IOException { this.startTime = System.currentTimeMillis(); this.version = version; this.uriInfo = uriInfo; this.params = uriInfo.getQueryParameters(); this.queryOptions = new QueryOptions(params, true); this.sessionIp = httpServletRequest.getRemoteAddr(); logger = LoggerFactory.getLogger(this.getClass()); defaultStorageEngine = storageConfiguration.getDefaultStorageEngineId(); // Only one StorageManagerFactory is needed, this acts as a simple Singleton pattern which improves the performance significantly if (storageManagerFactory == null) { privLogger.debug("Creating the StorageManagerFactory object"); storageManagerFactory = StorageManagerFactory.get(storageConfiguration); } if (authorizedHosts == null) { privLogger.debug("Creating the authorizedHost HashSet"); authorizedHosts = new HashSet<>(storageConfiguration.getServer().getAuthorizedHosts()); } if (authManager == null) { try { if (StringUtils.isNotEmpty(context.getInitParameter("authManager"))) { privLogger.debug("Loading AuthManager in {} from {}", this.getClass(), context.getInitParameter("authManager")); authManager = (AuthManager) Class.forName(context.getInitParameter("authManager")) .newInstance(); } else { privLogger.debug("Loading DefaultAuthManager in {} from {}", this.getClass(), DefaultAuthManager.class); authManager = new DefaultAuthManager(); } } catch (InstantiationException | IllegalAccessException | ClassNotFoundException e) { e.printStackTrace(); } } } protected void checkAuthorizedHosts(Query query, String ip) throws NotAuthorizedHostException, NotAuthorizedUserException { if (authorizedHosts.contains("0.0.0.0") || authorizedHosts.contains("*") || authorizedHosts.contains(ip)) { authManager.checkPermission(query, ""); } else { throw new NotAuthorizedHostException("No queries are allowed from " + ip); } } protected Response createJsonResponse(Object object) { try { return buildResponse( Response.ok(jsonObjectWriter.writeValueAsString(object), MediaType.APPLICATION_JSON_TYPE)); } catch (JsonProcessingException e) { return createErrorResponse( "Error parsing QueryResponse object:\n" + Arrays.toString(e.getStackTrace())); } } protected Response createErrorResponse(Object o) { QueryResult<ObjectMap> result = new QueryResult<>(); result.setErrorMsg(o.toString()); System.out.println("ERROR" + o.toString()); return createOkResponse(result); } protected Response createOkResponse(Object obj) { QueryResponse queryResponse = new QueryResponse(); long endTime = System.currentTimeMillis() - startTime; queryResponse.setTime(new Long(endTime - startTime).intValue()); queryResponse.setApiVersion(version); queryResponse.setQueryOptions(queryOptions); // Guarantee that the QueryResponse object contains a coll of results List coll; if (obj instanceof List) { coll = (List) obj; } else { coll = new ArrayList(); coll.add(obj); } queryResponse.setResponse(coll); switch (outputFormat.toLowerCase()) { case "json": return createJsonResponse(queryResponse); case "xml": // return createXmlResponse(queryResponse); default: return buildResponse(Response.ok()); } } //Response methods protected Response createOkResponse(Object o1, MediaType o2) { return buildResponse(Response.ok(o1, o2)); } protected Response createOkResponse(Object o1, MediaType o2, String fileName) { return buildResponse( Response.ok(o1, o2).header("content-disposition", "attachment; filename =" + fileName)); } protected Response buildResponse(Response.ResponseBuilder responseBuilder) { return responseBuilder.header("Access-Control-Allow-Origin", "*") .header("Access-Control-Allow-Headers", "x-requested-with, content-type").build(); } public static void setStorageConfiguration(StorageConfiguration storageConfiguration) { GenericRestWebService.storageConfiguration = storageConfiguration; } }