diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ReactomeConnector.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ReactomeConnector.java
index dcc5cdb14ec81803fbffab2d59318a2717d3aae1..f41b6ae6261905346b8845af1fe16a21fa5c64fc 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ReactomeConnector.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ReactomeConnector.java
@@ -1,778 +1,779 @@
-package lcsb.mapviewer.reactome.utils;
-
-import java.io.DataOutputStream;
-import java.io.IOException;
-import java.lang.reflect.InvocationTargetException;
-import java.lang.reflect.Method;
-import java.lang.reflect.Modifier;
-import java.net.HttpURLConnection;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import org.apache.commons.io.IOUtils;
-import org.apache.log4j.Logger;
-import org.springframework.stereotype.Service;
-import org.springframework.transaction.annotation.Transactional;
-import org.w3c.dom.Document;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-
-import lcsb.mapviewer.annotation.cache.CachableInterface;
-import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
-import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
-import lcsb.mapviewer.annotation.services.ExternalServiceStatus;
-import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
-import lcsb.mapviewer.common.HttpConnectionMethodType;
-import lcsb.mapviewer.common.MimeType;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.reactome.model.ReactomeCandidateSet;
-import lcsb.mapviewer.reactome.model.ReactomeCatalystActivity;
-import lcsb.mapviewer.reactome.model.ReactomeComplex;
-import lcsb.mapviewer.reactome.model.ReactomeDatabaseObject;
-import lcsb.mapviewer.reactome.model.ReactomeEntitySet;
-import lcsb.mapviewer.reactome.model.ReactomeEntityWithAccessionedSequence;
-import lcsb.mapviewer.reactome.model.ReactomePhysicalEntity;
-import lcsb.mapviewer.reactome.model.ReactomeReactionlikeEvent;
-import lcsb.mapviewer.reactome.model.ReactomeReferenceMolecule;
-import lcsb.mapviewer.reactome.model.ReactomeReferenceSequence;
-import lcsb.mapviewer.reactome.model.ReactomeSimpleEntity;
-import lcsb.mapviewer.reactome.model.ReactomeStableIdentifier;
-import lcsb.mapviewer.reactome.model.ReactomeStatus;
-import lcsb.mapviewer.reactome.xml.ReactomeNodeParser;
-import lcsb.mapviewer.reactome.xml.ReactomeParserFactory;
-
-/**
- * Data access object for reactome data.
- *
- * @author Piotr Gawron
- *
- */
-@Transactional
-@Service
-public class ReactomeConnector extends CachableInterface implements DataSourceUpdater {
-
- /**
- * Identifier of the object in reactome database used for testing connection.
- */
- private static final int CHECK_SERVICE_STATUS_EXAMPLE = 109581;
-
- /**
- * Default timeout of http connection (in miliseconds).
- */
- private static final int CONNECTION_TIMEOUT = 10000;
-
- /**
- * Prefix used in cache entries for objects queried by the identifier.
- */
- private static final String IDENTIFIER_QUERY_PREFIX = "ID: ";
-
- @Override
- public Object refreshCacheQuery(Object query) throws SourceNotAvailable {
- ReactomeConnector connector = new ReactomeConnector();
-
- String name;
- Object result = null;
- if (query instanceof String) {
- name = (String) query;
- if (name.startsWith(IDENTIFIER_QUERY_PREFIX)) {
- String strId = name.substring(IDENTIFIER_QUERY_PREFIX.length());
- Integer id = Integer.valueOf(strId);
- try {
- return connector.getFullNodeForDbId(id);
- } catch (InvalidXmlSchemaException e) {
- throw new SourceNotAvailable(e);
- }
- } else if (name.contains("\n")) {
- String[] tmp = name.split("\n");
- if (tmp.length != 2) {
- throw new InvalidArgumentException("Don't know what to do with string \"" + query + "\"");
- } else {
- String params = tmp[0];
- String url = tmp[1];
- try {
- result = connector.getNodesFromServer(params, url);
- } catch (Exception e) {
- throw new SourceNotAvailable(e);
- }
- }
- } else {
- throw new InvalidArgumentException("Don't know what to do with string \"" + query + "\"");
- }
- } else {
- throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
- }
- return result;
- }
-
- /**
- * Default constructor.
- */
- public ReactomeConnector() {
- super(ReactomeConnector.class);
- }
-
- /**
- * Determines if only one object instance should be created for single
- * reactome database identifier.
- */
- private boolean oneInstancePerId = true;
-
- /**
- * Map of all reactome objects retrieved by this connector.
- */
- private Map<Integer, ReactomeDatabaseObject> objectMap = new HashMap<Integer, ReactomeDatabaseObject>();
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(ReactomeConnector.class);
- /**
- * Url used for accessing Reactome RestFULL API.
- */
- private static final String REACTOME_URL = "http://reactome.org/ReactomeRESTfulAPI/RESTfulWS/";
-
- @Override
- public List<ReactomePhysicalEntity> getEntitiesForName(String name) throws IOException {
- return getEntitiesForName(name, true);
- }
-
- @Override
- public List<ReactomePhysicalEntity> getEntitiesForName(String name, boolean full) throws IOException {
- List<ReactomePhysicalEntity> result = new ArrayList<ReactomePhysicalEntity>();
-
- String query = "name=" + name;
- List<ReactomeDatabaseObject> objects = getSimpleObjectListByQuery(query, ReactomePhysicalEntity.class);
-
- for (ReactomeDatabaseObject object : objects) {
- if (full) {
- ReactomePhysicalEntity fullEntity = (ReactomePhysicalEntity) getFullObjectForDbId(object.getDbId());
- result.add(fullEntity);
- } else {
- result.add((ReactomePhysicalEntity) object);
- }
- }
- return result;
- }
-
- @Override
- public List<ReactomePhysicalEntity> getEntitiesForChebiId(Set<MiriamData> ids, boolean deepSearch) throws IOException {
- Set<ReactomePhysicalEntity> set = new HashSet<ReactomePhysicalEntity>();
- List<ReactomePhysicalEntity> result = new ArrayList<ReactomePhysicalEntity>();
- if (ids == null) {
- return result;
- }
- for (MiriamData md : ids) {
- if (md == null) {
- return result;
- }
- String id = md.getResource().replace("CHEBI:", "");
-
- String query = "identifier=" + id;
- List<ReactomeDatabaseObject> objects = getSimpleObjectListByQuery(query, ReactomeReferenceMolecule.class);
-
- for (ReactomeDatabaseObject object : objects) {
- ReactomeReferenceMolecule reference = (ReactomeReferenceMolecule) getFullObjectForDbId(object.getDbId());
- List<ReactomeSimpleEntity> list = getSimpleEntitiesByReferenceMolecule(reference);
- set.addAll(list);
- }
- if (deepSearch) {
- int lastSize = 0;
- do {
- lastSize = set.size();
- Set<ReactomePhysicalEntity> complexes = getComplexesContainingOneOfElements(set);
- set.addAll(complexes);
- Set<ReactomePhysicalEntity> sets = getSetsContainingOneOfElements(set);
- set.addAll(sets);
- } while (lastSize != set.size());
- }
- result.addAll(set);
- }
- return result;
- }
-
- @Override
- public List<ReactomePhysicalEntity> getEntitiesForUniprotId(Collection<MiriamData> uniprot) throws IOException {
- Set<ReactomePhysicalEntity> set = new HashSet<ReactomePhysicalEntity>();
-
- for (MiriamData md : uniprot) {
- if (!MiriamType.UNIPROT.equals(md.getDataType())) {
- throw new InvalidArgumentException("Only uniprot miriam are acceptable");
- }
- String id = md.getResource();
- int lastSize = set.size();
- do {
- lastSize = set.size();
-
- String query = "identifier=" + id;
- List<ReactomeDatabaseObject> objects = getSimpleObjectListByQuery(query, ReactomeReferenceSequence.class);
-
- for (ReactomeDatabaseObject object : objects) {
- ReactomeReferenceSequence reference = (ReactomeReferenceSequence) getFullObjectForDbId(object.getDbId());
- List<ReactomePhysicalEntity> list = getPhysicalEnitiesForReferenceSequence(reference);
- set.addAll(list);
- }
- query = "secondaryIdentifier=" + id;
- objects = getSimpleObjectListByQuery(query, ReactomeReferenceSequence.class);
-
- for (ReactomeDatabaseObject object : objects) {
- ReactomeReferenceSequence reference = (ReactomeReferenceSequence) getFullObjectForDbId(object.getDbId());
- List<ReactomePhysicalEntity> list = getPhysicalEnitiesForReferenceSequence(reference);
- set.addAll(list);
- }
-
- Set<ReactomePhysicalEntity> complexes = getComplexesContainingOneOfElements(set);
- set.addAll(complexes);
- Set<ReactomePhysicalEntity> sets = getSetsContainingOneOfElements(set);
- set.addAll(sets);
- } while (lastSize != set.size());
- }
- List<ReactomePhysicalEntity> result = new ArrayList<ReactomePhysicalEntity>();
- result.addAll(set);
- return result;
- }
-
- /**
- * Returns list of ReactomeComplex that contain one of the elements given in
- * the parameter.
- *
- * @param objects
- * list of objects for which we want to retrieve complexes
- * @return list of ReactomeComplex that contain one of the elements given in
- * the parameter
- * @throws IOException
- * thrown when there is a problem with connection to reactome
- * database
- */
- private Set<ReactomePhysicalEntity> getComplexesContainingOneOfElements(Collection<ReactomePhysicalEntity> objects) throws IOException {
- Set<ReactomePhysicalEntity> result = new HashSet<ReactomePhysicalEntity>();
- for (ReactomeDatabaseObject obj : objects) {
- String query = "hasComponent=" + obj.getDbId();
- List<ReactomeDatabaseObject> complexes = getSimpleObjectListByQuery(query, ReactomeComplex.class);
- for (ReactomeDatabaseObject complex : complexes) {
- result.add((ReactomePhysicalEntity) getFullObjectForDbId(complex.getDbId()));
- }
- }
- return result;
- }
-
- /**
- * Returns list of ReactomeEntitySet that contain one of the elements given in
- * the parameter.
- *
- * @param objects
- * list of objects for which we want to retrieve sets
- * @return list of ReactomeEntitySet that contain one of the elements given in
- * the parameter
- * @throws IOException
- * thrown when there is a problem with connection to reactome
- * database
- */
- private Set<ReactomePhysicalEntity> getSetsContainingOneOfElements(Collection<ReactomePhysicalEntity> objects) throws IOException {
-
- Set<ReactomePhysicalEntity> result = new HashSet<ReactomePhysicalEntity>();
- for (ReactomeDatabaseObject obj : objects) {
- String query = "hasMember=" + obj.getDbId();
- List<ReactomeDatabaseObject> complexes = getSimpleObjectListByQuery(query, ReactomeEntitySet.class);
- for (ReactomeDatabaseObject complex : complexes) {
- result.add((ReactomeEntitySet) getFullObjectForDbId(complex.getDbId()));
- }
- query = "hasCandidate=" + obj.getDbId();
- complexes = getSimpleObjectListByQuery(query, ReactomeCandidateSet.class);
- for (ReactomeDatabaseObject complex : complexes) {
- result.add((ReactomeCandidateSet) getFullObjectForDbId(complex.getDbId()));
- }
- }
- return result;
- }
-
- /**
- * Returns list of ReactomeEntityWithAccessionedSequence that refers to
- * parameter reference.
- *
- * @param reference
- * object to which result should refer to
- * @return list of ReactomeEntityWithAccessionedSequence that contain one of
- * the elements given in the parameter
- * @throws IOException
- * thrown when there is a problem with connection to reactome
- * database
- */
- private List<ReactomePhysicalEntity> getPhysicalEnitiesForReferenceSequence(ReactomeReferenceSequence reference) throws IOException {
- List<ReactomePhysicalEntity> result = new ArrayList<ReactomePhysicalEntity>();
-
- String query = "referenceEntity=" + reference.getDbId();
- List<ReactomeDatabaseObject> objects = getSimpleObjectListByQuery(query, ReactomeEntityWithAccessionedSequence.class);
-
- for (ReactomeDatabaseObject object : objects) {
- result.add((ReactomePhysicalEntity) getFullObjectForDbId(object.getDbId()));
- }
- return result;
- }
-
- /**
- * Returns list of ReactomeSimpleEntity that refers to parameter reference.
- *
- * @param reference
- * object to which result should refer to
- * @return list of ReactomeSimpleEntity that contain one of the elements given
- * in the parameter
- * @throws IOException
- * thrown when there is a problem with connection to reactome
- * database
- */
- private List<ReactomeSimpleEntity> getSimpleEntitiesByReferenceMolecule(ReactomeReferenceMolecule reference) throws IOException {
- List<ReactomeSimpleEntity> result = new ArrayList<ReactomeSimpleEntity>();
-
- String query = "referenceEntity=" + reference.getDbId();
- List<ReactomeDatabaseObject> objects = getSimpleObjectListByQuery(query, ReactomeSimpleEntity.class);
-
- for (ReactomeDatabaseObject object : objects) {
- result.add((ReactomeSimpleEntity) getFullObjectForDbId(object.getDbId()));
- }
- return result;
- }
-
- /**
- * Ges list of reactions that interact with object given in the parameter.
- *
- * @param id
- * identifier of the object that should be included in the result
- * reactions
- * @return list of reactions that interact with object given in the parameter
- * @throws IOException
- * thrown when there is a problem with connection to reactome
- * database
- */
- public List<ReactomeReactionlikeEvent> getReactionsForEntityId(Integer id) throws IOException {
- List<ReactomeReactionlikeEvent> result = new ArrayList<ReactomeReactionlikeEvent>();
-
- String query = "input=" + id;
- List<ReactomeDatabaseObject> objects = getSimpleObjectListByQuery(query, ReactomeReactionlikeEvent.class);
-
- for (ReactomeDatabaseObject object : objects) {
- ReactomeDatabaseObject entity = getFullObjectForDbId(object.getDbId());
- if (entity instanceof ReactomeReactionlikeEvent) {
- result.add((ReactomeReactionlikeEvent) entity);
- }
- }
-
- query = "output=" + id;
- objects = getSimpleObjectListByQuery(query, ReactomeReactionlikeEvent.class);
-
- for (ReactomeDatabaseObject object : objects) {
- ReactomeDatabaseObject entity = getFullObjectForDbId(object.getDbId());
- if (entity instanceof ReactomeReactionlikeEvent) {
- result.add((ReactomeReactionlikeEvent) entity);
- }
- }
-
- // and now find reaction with apropriate catalyst
- query = "physicalEntity=" + id;
- List<ReactomeDatabaseObject> catalysts = getSimpleObjectListByQuery(query, ReactomeCatalystActivity.class);
- for (ReactomeDatabaseObject catalyst : catalysts) {
- query = "catalystActivity=" + catalyst.getDbId();
- objects = getSimpleObjectListByQuery(query, ReactomeReactionlikeEvent.class);
- for (ReactomeDatabaseObject object : objects) {
- ReactomeDatabaseObject entity = getFullObjectForDbId(object.getDbId());
- if (entity instanceof ReactomeReactionlikeEvent) {
- result.add((ReactomeReactionlikeEvent) entity);
- }
- }
- }
-
- return result;
- }
-
- @Override
- public Class<?> getTypeForDbId(Integer id) throws ClassNotFoundException, InvalidXmlSchemaException {
- Node node = getFullNodeForDbId(id);
- Class<?> result = getTypeForNode(node);
- return result;
- }
-
- /**
- * Returns class type of the data represented in the xml node.
- *
- * @param node
- * xml node
- * @return class type of the data represented in the xml node
- * @throws ClassNotFoundException
- * thrown when there is a problem with finding apropriate class
- */
- protected Class<?> getTypeForNode(Node node) throws ClassNotFoundException {
- Class<?> result = null;
- for (int i = 0; i < node.getChildNodes().getLength(); i++) {
- Node child = node.getChildNodes().item(i);
- if (child.getNodeName().equals("schemaClass")) {
- // our classes aren't exactly the same as reactome names, change what is
- // different
- String shortName = child.getTextContent().replaceAll("GO_", "Go");
- String className = ReactomeDatabaseObject.class.getPackage().getName() + ".Reactome" + shortName;
- result = Class.forName(className);
- }
- }
- return result;
- }
-
- @Override
- public ReactomeDatabaseObject getFullObjectForDbId(Integer id) {
- try {
- ReactomeDatabaseObject result = null;
- if (oneInstancePerId) {
- result = objectMap.get(id);
- if (result != null) {
- return result;
- }
- }
- Class<?> classType;
- Node node = getFullNodeForDbId(id);
- classType = getTypeForNode(node);
- ReactomeNodeParser<?> parser = ReactomeParserFactory.getParserForClass(classType);
- result = parser.parseObject(node);
- if (oneInstancePerId) {
- objectMap.put(id, result);
- }
- return result;
- } catch (ClassNotFoundException e) {
- throw new InvalidArgumentException("Unknown class type: " + e.getMessage());
- } catch (InvalidXmlSchemaException e) {
- logger.error(e, e);
- return null;
- }
- }
-
- @Override
- @SuppressWarnings("unchecked")
- public void updateOnlyIdFields(ReactomeDatabaseObject object) {
- DataSourceUpdater dsu = this;
- for (Method method : object.getClass().getMethods()) {
-
- if (Modifier.isPublic(method.getModifiers()) && method.getParameterTypes().length == 0
- && (method.getName().startsWith("get") || method.getName().startsWith("is"))) {
-
- if (ReactomeDatabaseObject.class.isAssignableFrom(method.getReturnType())) {
- try {
- ReactomeDatabaseObject value = (ReactomeDatabaseObject) method.invoke(object);
- if (value != null) {
- if (value.getStatus().equals(ReactomeStatus.ONLY_ID)) {
- ReactomeDatabaseObject newValue = dsu.getFullObjectForDbId(value.getDbId());
- String setterName = method.getName();
- if (setterName.startsWith("get")) {
- setterName = setterName.replaceFirst("get", "set");
- } else {
- setterName = setterName.replaceFirst("is", "set");
- }
- try {
- Method setterMethod = object.getClass().getMethod(setterName, method.getReturnType());
- setterMethod.invoke(object, newValue);
- } catch (NoSuchMethodException e) {
- e.printStackTrace();
- } catch (IllegalArgumentException e) {
- logger.error(
- "Cannot assign " + newValue.getClass() + " (id: " + value.getDbId() + ") to field: " + setterName.replace("set", "") + " ("
- + method.getReturnType() + ")");
- } catch (SecurityException e) {
-
- e.printStackTrace();
- // ignore it - however this would be strange
- }
- }
- }
- } catch (IllegalAccessException e) {
- e.printStackTrace();
- } catch (IllegalArgumentException e) {
- e.printStackTrace();
- } catch (InvocationTargetException e) {
- e.printStackTrace();
- // ignore it
- }
-
- } else if (List.class.isAssignableFrom(method.getReturnType())) {
- try {
- @SuppressWarnings("rawtypes")
- List list = (List) method.invoke(object);
- for (int i = 0; i < list.size(); i++) {
- Object obj = list.get(i);
- if (obj instanceof ReactomeDatabaseObject) {
- if (((ReactomeDatabaseObject) obj).getStatus().equals(ReactomeStatus.ONLY_ID)) {
- ReactomeDatabaseObject newValue = dsu.getFullObjectForDbId(((ReactomeDatabaseObject) obj).getDbId());
- list.set(i, newValue);
- }
- }
- }
- } catch (IllegalAccessException e) {
- e.printStackTrace();
- } catch (IllegalArgumentException e) {
- e.printStackTrace();
- } catch (InvocationTargetException e) {
- e.printStackTrace();
- // ignore it
- }
- }
- }
- }
- }
-
- @Override
- public ReactomeDatabaseObject getFullObjectForStableIdentifier(String stableIdentifier) throws IOException {
- if (stableIdentifier == null) {
- return null;
- }
- String[] tmp = stableIdentifier.split("\\.");
- String identifier = tmp[0];
- String version = "0";
- if (tmp.length > 1) {
- version = tmp[1];
- }
- return getFullObjectForStableIdentifier(identifier, version);
- }
-
- @Override
- public ReactomeDatabaseObject getFullObjectForStableIdentifier(String identifier, String version) throws IOException {
- String stableIdentifierQuery = "identifier=" + identifier;
-
- List<ReactomeDatabaseObject> stableIdentifiers = getSimpleObjectListByQuery(stableIdentifierQuery, ReactomeStableIdentifier.class);
-
- ReactomeStableIdentifier newestIdentifier = null;
- ReactomeStableIdentifier matchedIdentifier = null;
-
- for (ReactomeDatabaseObject object : stableIdentifiers) {
- ReactomeStableIdentifier entity = (ReactomeStableIdentifier) getFullObjectForDbId(object.getDbId());
- if (newestIdentifier == null) {
- newestIdentifier = entity;
- } else {
- try {
- Integer id1 = Integer.parseInt(newestIdentifier.getIdentifierVersion());
- Integer id2 = Integer.parseInt(entity.getIdentifierVersion());
- if (id2 > id1) {
- newestIdentifier = entity;
- }
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- }
- }
- if (entity.getDisplayName().equals(identifier + "." + version) || entity.getIdentifierVersion().equalsIgnoreCase(version)) {
- matchedIdentifier = entity;
- }
- }
- if (matchedIdentifier == null) {
- if (newestIdentifier != null) {
- logger.warn(
- "Invalid REACTOME stable identifier: \"" + identifier + "." + version + "\". Using another similar: " + newestIdentifier.getIdentifier() + "."
- + newestIdentifier.getIdentifierVersion());
- }
- matchedIdentifier = newestIdentifier;
- }
- if (matchedIdentifier != null) {
- String query = "stableIdentifier=" + matchedIdentifier.getDbId();
- List<ReactomeDatabaseObject> objects = getSimpleObjectListByQuery(query, ReactomeDatabaseObject.class);
-
- for (ReactomeDatabaseObject object : objects) {
- return getFullObjectForDbId(object.getDbId());
- }
-
- }
- return null;
- }
-
- // ------------------------------------------------
-
- // Methods that directly connect to reactome database (via restfull API)
-
- // ------------------------------------------------
-
- /**
- * This method get content of the page of the url (and post content).
- *
- * @param url
- * url address to connect
- * @param postParam
- * params of the post method
- * @param type
- * MIME type of the result
- * @param method
- * request method (POST/GET)
- * @return return the string with the content of the webpage
- * @throws IOException
- * thrown when there are some problem with network connection
- */
- protected String getResponse(String url, String postParam, MimeType type, HttpConnectionMethodType method) throws IOException {
- URL obj = new URL(url);
- HttpURLConnection con = (HttpURLConnection) obj.openConnection();
-
- // add reuqest header
- con.setRequestMethod(method.name());
- con.setRequestProperty("Accept", type.getTextRepresentation());
- con.setRequestProperty("Content-Type", type.getTextRepresentation());
- con.setConnectTimeout(CONNECTION_TIMEOUT);
- con.setReadTimeout(CONNECTION_TIMEOUT);
-
- String urlParameters = postParam;
-
- logger.debug("Sending '" + method + "' request to URL : " + url);
- if (method.name().equals("POST")) {
- logger.debug("Parameters : " + urlParameters);
- }
-
- // Send post request
- con.setDoOutput(true);
- if (method.name().equalsIgnoreCase("POST")) {
- DataOutputStream wr = new DataOutputStream(con.getOutputStream());
- wr.writeBytes(urlParameters);
- wr.flush();
- wr.close();
- }
-
- int responseCode = con.getResponseCode();
- logger.debug("Response Code : " + responseCode);
-
- String result = IOUtils.toString(con.getInputStream());
- logger.debug(result);
- return result;
- }
-
- @Override
- public List<ReactomeDatabaseObject> getSimpleObjectListByQuery(String query, Class<? extends ReactomeDatabaseObject> clazz) throws IOException {
- if (query.contains("\n")) {
- throw new InvalidArgumentException("Query cannot contain new line character");
- }
- ReactomeNodeParser<?> parser = ReactomeParserFactory.getParserForClass(clazz);
- List<ReactomeDatabaseObject> result = new ArrayList<ReactomeDatabaseObject>();
-
- String url = REACTOME_URL + "listByQuery/" + clazz.getSimpleName().replaceFirst("Reactome", "").replaceAll("Go", "GO_");
-
- String key = query + "\n" + url;
-
- Node node = getCacheNode(key);
- NodeList nodes = null;
- if (node != null) {
- nodes = node.getChildNodes();
- } else {
- try {
- nodes = getNodesFromServer(query, url);
- } catch (InvalidXmlSchemaException e) {
- throw new IOException(e);
- }
- setCacheNode(key, nodes.item(0));
- nodes = nodes.item(0).getChildNodes();
- }
- for (int i = 0; i < nodes.getLength(); i++) {
- if (nodes.item(i).getNodeType() != Node.ELEMENT_NODE) {
- continue;
- }
- ReactomeDatabaseObject object = parser.parseSimplifiedObject(nodes.item(i));
- result.add(object);
- }
- return result;
- }
-
- /**
- * Returns list of nodes from the server identified by the query and POST
- * params.
- *
- * @param query
- * string query to the database sent by POST method
- * @param url
- * direct url to the API
- * @return list of nodes from the server identified by the query and POST
- * params.
- * @throws IOException
- * thrown when there are some problem with network connection
- * @throws InvalidXmlSchemaException
- * thrown when there is a problem with xml
- */
- private NodeList getNodesFromServer(String query, String url) throws IOException, InvalidXmlSchemaException {
- String response = getResponse(url, query, MimeType.XML, HttpConnectionMethodType.POST);
- logger.debug(response);
- Node node = getXmlDocumentFromString(response);
- NodeList nodes = node.getChildNodes();
- if (nodes.getLength() < 1) {
- throw new InvalidArgumentException("Problem with xml document");
- }
- return nodes;
- }
-
- /**
- * This method returns xml NODE for object identified by id (identifier in
- * reactome database). However if object is in local cache then local copy is
- * returned. If object doesn't exist in local cache then after retrieving it
- * from reactome is put to the cache.
- *
- * @param id
- * identifier in reactome database
- * @return xml node for the id given reactome id
- * @throws InvalidXmlSchemaException
- * thrown when there is a problem with xml
- */
- @Override
- public Node getFullNodeForDbId(Integer id) throws InvalidXmlSchemaException {
- Node result = getCacheNode(IDENTIFIER_QUERY_PREFIX + id);
- if (result != null) {
- return result;
- }
-
- String response;
- String url = REACTOME_URL + "queryById/DatabaseObject/" + id;
- try {
- response = getResponse(url, "", MimeType.XML, HttpConnectionMethodType.GET);
- Document doc = getXmlDocumentFromString(response);
- NodeList nodes = doc.getChildNodes();
- result = nodes.item(0);
- setCacheNode(IDENTIFIER_QUERY_PREFIX + id, result);
- return result;
- } catch (IOException e) {
- logger.error(e.getMessage(), e);
- return null;
- }
- }
-
- @Override
- public Map<Integer, ReactomeDatabaseObject> getFullObjectsForDbIds(List<Integer> ids) throws ClassNotFoundException, IOException {
- Map<Integer, ReactomeDatabaseObject> result = new HashMap<Integer, ReactomeDatabaseObject>();
- for (Integer integer : ids) {
- result.put(integer, getFullObjectForDbId(integer));
- }
-
- return result;
-
- }
-
- @Override
- public List<ReactomePhysicalEntity> getEntitiesForSetOfIds(Set<MiriamData> identifiers) throws IOException {
- return getEntitiesForUniprotId(identifiers);
- }
-
- @Override
- public ExternalServiceStatus getServiceStatus() {
- ExternalServiceStatus status = new ExternalServiceStatus(
- "Reactome RESTful API", "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html");
-
- GeneralCacheInterface cacheCopy = getCache();
- this.setCache(null);
-
- try {
- ReactomeDatabaseObject obj = getFullObjectForDbId(CHECK_SERVICE_STATUS_EXAMPLE);
- status.setStatus(ExternalServiceStatusType.OK);
- if (obj == null) {
- status.setStatus(ExternalServiceStatusType.DOWN);
- } else if (obj.getClass().equals(ReactomeDatabaseObject.class)) {
- status.setStatus(ExternalServiceStatusType.CHANGED);
- }
- } catch (Exception e) {
- logger.error(status.getName() + " is down", e);
- status.setStatus(ExternalServiceStatusType.DOWN);
- }
- this.setCache(cacheCopy);
- return status;
- }
-
-}
+package lcsb.mapviewer.reactome.utils;
+
+import java.io.DataOutputStream;
+import java.io.IOException;
+import java.lang.reflect.InvocationTargetException;
+import java.lang.reflect.Method;
+import java.lang.reflect.Modifier;
+import java.net.HttpURLConnection;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import lcsb.mapviewer.common.XmlParser;
+import org.apache.commons.io.IOUtils;
+import org.apache.log4j.Logger;
+import org.springframework.stereotype.Service;
+import org.springframework.transaction.annotation.Transactional;
+import org.w3c.dom.Document;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+
+import lcsb.mapviewer.annotation.cache.CachableInterface;
+import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
+import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
+import lcsb.mapviewer.annotation.services.ExternalServiceStatus;
+import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
+import lcsb.mapviewer.common.HttpConnectionMethodType;
+import lcsb.mapviewer.common.MimeType;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.reactome.model.ReactomeCandidateSet;
+import lcsb.mapviewer.reactome.model.ReactomeCatalystActivity;
+import lcsb.mapviewer.reactome.model.ReactomeComplex;
+import lcsb.mapviewer.reactome.model.ReactomeDatabaseObject;
+import lcsb.mapviewer.reactome.model.ReactomeEntitySet;
+import lcsb.mapviewer.reactome.model.ReactomeEntityWithAccessionedSequence;
+import lcsb.mapviewer.reactome.model.ReactomePhysicalEntity;
+import lcsb.mapviewer.reactome.model.ReactomeReactionlikeEvent;
+import lcsb.mapviewer.reactome.model.ReactomeReferenceMolecule;
+import lcsb.mapviewer.reactome.model.ReactomeReferenceSequence;
+import lcsb.mapviewer.reactome.model.ReactomeSimpleEntity;
+import lcsb.mapviewer.reactome.model.ReactomeStableIdentifier;
+import lcsb.mapviewer.reactome.model.ReactomeStatus;
+import lcsb.mapviewer.reactome.xml.ReactomeNodeParser;
+import lcsb.mapviewer.reactome.xml.ReactomeParserFactory;
+
+/**
+ * Data access object for reactome data.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Transactional
+@Service
+public class ReactomeConnector extends CachableInterface implements DataSourceUpdater {
+
+ /**
+ * Identifier of the object in reactome database used for testing connection.
+ */
+ private static final int CHECK_SERVICE_STATUS_EXAMPLE = 109581;
+
+ /**
+ * Default timeout of http connection (in miliseconds).
+ */
+ private static final int CONNECTION_TIMEOUT = 10000;
+
+ /**
+ * Prefix used in cache entries for objects queried by the identifier.
+ */
+ private static final String IDENTIFIER_QUERY_PREFIX = "ID: ";
+
+ @Override
+ public Object refreshCacheQuery(Object query) throws SourceNotAvailable {
+ ReactomeConnector connector = new ReactomeConnector();
+
+ String name;
+ Object result = null;
+ if (query instanceof String) {
+ name = (String) query;
+ if (name.startsWith(IDENTIFIER_QUERY_PREFIX)) {
+ String strId = name.substring(IDENTIFIER_QUERY_PREFIX.length());
+ Integer id = Integer.valueOf(strId);
+ try {
+ return connector.getFullNodeForDbId(id);
+ } catch (InvalidXmlSchemaException e) {
+ throw new SourceNotAvailable(e);
+ }
+ } else if (name.contains("\n")) {
+ String[] tmp = name.split("\n");
+ if (tmp.length != 2) {
+ throw new InvalidArgumentException("Don't know what to do with string \"" + query + "\"");
+ } else {
+ String params = tmp[0];
+ String url = tmp[1];
+ try {
+ result = connector.getNodesFromServer(params, url);
+ } catch (Exception e) {
+ throw new SourceNotAvailable(e);
+ }
+ }
+ } else {
+ throw new InvalidArgumentException("Don't know what to do with string \"" + query + "\"");
+ }
+ } else {
+ throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
+ }
+ return result;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public ReactomeConnector() {
+ super(ReactomeConnector.class);
+ }
+
+ /**
+ * Determines if only one object instance should be created for single
+ * reactome database identifier.
+ */
+ private boolean oneInstancePerId = true;
+
+ /**
+ * Map of all reactome objects retrieved by this connector.
+ */
+ private Map<Integer, ReactomeDatabaseObject> objectMap = new HashMap<Integer, ReactomeDatabaseObject>();
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(ReactomeConnector.class);
+ /**
+ * Url used for accessing Reactome RestFULL API.
+ */
+ private static final String REACTOME_URL = "http://reactome.org/ReactomeRESTfulAPI/RESTfulWS/";
+
+ @Override
+ public List<ReactomePhysicalEntity> getEntitiesForName(String name) throws IOException {
+ return getEntitiesForName(name, true);
+ }
+
+ @Override
+ public List<ReactomePhysicalEntity> getEntitiesForName(String name, boolean full) throws IOException {
+ List<ReactomePhysicalEntity> result = new ArrayList<ReactomePhysicalEntity>();
+
+ String query = "name=" + name;
+ List<ReactomeDatabaseObject> objects = getSimpleObjectListByQuery(query, ReactomePhysicalEntity.class);
+
+ for (ReactomeDatabaseObject object : objects) {
+ if (full) {
+ ReactomePhysicalEntity fullEntity = (ReactomePhysicalEntity) getFullObjectForDbId(object.getDbId());
+ result.add(fullEntity);
+ } else {
+ result.add((ReactomePhysicalEntity) object);
+ }
+ }
+ return result;
+ }
+
+ @Override
+ public List<ReactomePhysicalEntity> getEntitiesForChebiId(Set<MiriamData> ids, boolean deepSearch) throws IOException {
+ Set<ReactomePhysicalEntity> set = new HashSet<ReactomePhysicalEntity>();
+ List<ReactomePhysicalEntity> result = new ArrayList<ReactomePhysicalEntity>();
+ if (ids == null) {
+ return result;
+ }
+ for (MiriamData md : ids) {
+ if (md == null) {
+ return result;
+ }
+ String id = md.getResource().replace("CHEBI:", "");
+
+ String query = "identifier=" + id;
+ List<ReactomeDatabaseObject> objects = getSimpleObjectListByQuery(query, ReactomeReferenceMolecule.class);
+
+ for (ReactomeDatabaseObject object : objects) {
+ ReactomeReferenceMolecule reference = (ReactomeReferenceMolecule) getFullObjectForDbId(object.getDbId());
+ List<ReactomeSimpleEntity> list = getSimpleEntitiesByReferenceMolecule(reference);
+ set.addAll(list);
+ }
+ if (deepSearch) {
+ int lastSize = 0;
+ do {
+ lastSize = set.size();
+ Set<ReactomePhysicalEntity> complexes = getComplexesContainingOneOfElements(set);
+ set.addAll(complexes);
+ Set<ReactomePhysicalEntity> sets = getSetsContainingOneOfElements(set);
+ set.addAll(sets);
+ } while (lastSize != set.size());
+ }
+ result.addAll(set);
+ }
+ return result;
+ }
+
+ @Override
+ public List<ReactomePhysicalEntity> getEntitiesForUniprotId(Collection<MiriamData> uniprot) throws IOException {
+ Set<ReactomePhysicalEntity> set = new HashSet<ReactomePhysicalEntity>();
+
+ for (MiriamData md : uniprot) {
+ if (!MiriamType.UNIPROT.equals(md.getDataType())) {
+ throw new InvalidArgumentException("Only uniprot miriam are acceptable");
+ }
+ String id = md.getResource();
+ int lastSize = set.size();
+ do {
+ lastSize = set.size();
+
+ String query = "identifier=" + id;
+ List<ReactomeDatabaseObject> objects = getSimpleObjectListByQuery(query, ReactomeReferenceSequence.class);
+
+ for (ReactomeDatabaseObject object : objects) {
+ ReactomeReferenceSequence reference = (ReactomeReferenceSequence) getFullObjectForDbId(object.getDbId());
+ List<ReactomePhysicalEntity> list = getPhysicalEnitiesForReferenceSequence(reference);
+ set.addAll(list);
+ }
+ query = "secondaryIdentifier=" + id;
+ objects = getSimpleObjectListByQuery(query, ReactomeReferenceSequence.class);
+
+ for (ReactomeDatabaseObject object : objects) {
+ ReactomeReferenceSequence reference = (ReactomeReferenceSequence) getFullObjectForDbId(object.getDbId());
+ List<ReactomePhysicalEntity> list = getPhysicalEnitiesForReferenceSequence(reference);
+ set.addAll(list);
+ }
+
+ Set<ReactomePhysicalEntity> complexes = getComplexesContainingOneOfElements(set);
+ set.addAll(complexes);
+ Set<ReactomePhysicalEntity> sets = getSetsContainingOneOfElements(set);
+ set.addAll(sets);
+ } while (lastSize != set.size());
+ }
+ List<ReactomePhysicalEntity> result = new ArrayList<ReactomePhysicalEntity>();
+ result.addAll(set);
+ return result;
+ }
+
+ /**
+ * Returns list of ReactomeComplex that contain one of the elements given in
+ * the parameter.
+ *
+ * @param objects
+ * list of objects for which we want to retrieve complexes
+ * @return list of ReactomeComplex that contain one of the elements given in
+ * the parameter
+ * @throws IOException
+ * thrown when there is a problem with connection to reactome
+ * database
+ */
+ private Set<ReactomePhysicalEntity> getComplexesContainingOneOfElements(Collection<ReactomePhysicalEntity> objects) throws IOException {
+ Set<ReactomePhysicalEntity> result = new HashSet<ReactomePhysicalEntity>();
+ for (ReactomeDatabaseObject obj : objects) {
+ String query = "hasComponent=" + obj.getDbId();
+ List<ReactomeDatabaseObject> complexes = getSimpleObjectListByQuery(query, ReactomeComplex.class);
+ for (ReactomeDatabaseObject complex : complexes) {
+ result.add((ReactomePhysicalEntity) getFullObjectForDbId(complex.getDbId()));
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Returns list of ReactomeEntitySet that contain one of the elements given in
+ * the parameter.
+ *
+ * @param objects
+ * list of objects for which we want to retrieve sets
+ * @return list of ReactomeEntitySet that contain one of the elements given in
+ * the parameter
+ * @throws IOException
+ * thrown when there is a problem with connection to reactome
+ * database
+ */
+ private Set<ReactomePhysicalEntity> getSetsContainingOneOfElements(Collection<ReactomePhysicalEntity> objects) throws IOException {
+
+ Set<ReactomePhysicalEntity> result = new HashSet<ReactomePhysicalEntity>();
+ for (ReactomeDatabaseObject obj : objects) {
+ String query = "hasMember=" + obj.getDbId();
+ List<ReactomeDatabaseObject> complexes = getSimpleObjectListByQuery(query, ReactomeEntitySet.class);
+ for (ReactomeDatabaseObject complex : complexes) {
+ result.add((ReactomeEntitySet) getFullObjectForDbId(complex.getDbId()));
+ }
+ query = "hasCandidate=" + obj.getDbId();
+ complexes = getSimpleObjectListByQuery(query, ReactomeCandidateSet.class);
+ for (ReactomeDatabaseObject complex : complexes) {
+ result.add((ReactomeCandidateSet) getFullObjectForDbId(complex.getDbId()));
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Returns list of ReactomeEntityWithAccessionedSequence that refers to
+ * parameter reference.
+ *
+ * @param reference
+ * object to which result should refer to
+ * @return list of ReactomeEntityWithAccessionedSequence that contain one of
+ * the elements given in the parameter
+ * @throws IOException
+ * thrown when there is a problem with connection to reactome
+ * database
+ */
+ private List<ReactomePhysicalEntity> getPhysicalEnitiesForReferenceSequence(ReactomeReferenceSequence reference) throws IOException {
+ List<ReactomePhysicalEntity> result = new ArrayList<ReactomePhysicalEntity>();
+
+ String query = "referenceEntity=" + reference.getDbId();
+ List<ReactomeDatabaseObject> objects = getSimpleObjectListByQuery(query, ReactomeEntityWithAccessionedSequence.class);
+
+ for (ReactomeDatabaseObject object : objects) {
+ result.add((ReactomePhysicalEntity) getFullObjectForDbId(object.getDbId()));
+ }
+ return result;
+ }
+
+ /**
+ * Returns list of ReactomeSimpleEntity that refers to parameter reference.
+ *
+ * @param reference
+ * object to which result should refer to
+ * @return list of ReactomeSimpleEntity that contain one of the elements given
+ * in the parameter
+ * @throws IOException
+ * thrown when there is a problem with connection to reactome
+ * database
+ */
+ private List<ReactomeSimpleEntity> getSimpleEntitiesByReferenceMolecule(ReactomeReferenceMolecule reference) throws IOException {
+ List<ReactomeSimpleEntity> result = new ArrayList<ReactomeSimpleEntity>();
+
+ String query = "referenceEntity=" + reference.getDbId();
+ List<ReactomeDatabaseObject> objects = getSimpleObjectListByQuery(query, ReactomeSimpleEntity.class);
+
+ for (ReactomeDatabaseObject object : objects) {
+ result.add((ReactomeSimpleEntity) getFullObjectForDbId(object.getDbId()));
+ }
+ return result;
+ }
+
+ /**
+ * Ges list of reactions that interact with object given in the parameter.
+ *
+ * @param id
+ * identifier of the object that should be included in the result
+ * reactions
+ * @return list of reactions that interact with object given in the parameter
+ * @throws IOException
+ * thrown when there is a problem with connection to reactome
+ * database
+ */
+ public List<ReactomeReactionlikeEvent> getReactionsForEntityId(Integer id) throws IOException {
+ List<ReactomeReactionlikeEvent> result = new ArrayList<ReactomeReactionlikeEvent>();
+
+ String query = "input=" + id;
+ List<ReactomeDatabaseObject> objects = getSimpleObjectListByQuery(query, ReactomeReactionlikeEvent.class);
+
+ for (ReactomeDatabaseObject object : objects) {
+ ReactomeDatabaseObject entity = getFullObjectForDbId(object.getDbId());
+ if (entity instanceof ReactomeReactionlikeEvent) {
+ result.add((ReactomeReactionlikeEvent) entity);
+ }
+ }
+
+ query = "output=" + id;
+ objects = getSimpleObjectListByQuery(query, ReactomeReactionlikeEvent.class);
+
+ for (ReactomeDatabaseObject object : objects) {
+ ReactomeDatabaseObject entity = getFullObjectForDbId(object.getDbId());
+ if (entity instanceof ReactomeReactionlikeEvent) {
+ result.add((ReactomeReactionlikeEvent) entity);
+ }
+ }
+
+ // and now find reaction with apropriate catalyst
+ query = "physicalEntity=" + id;
+ List<ReactomeDatabaseObject> catalysts = getSimpleObjectListByQuery(query, ReactomeCatalystActivity.class);
+ for (ReactomeDatabaseObject catalyst : catalysts) {
+ query = "catalystActivity=" + catalyst.getDbId();
+ objects = getSimpleObjectListByQuery(query, ReactomeReactionlikeEvent.class);
+ for (ReactomeDatabaseObject object : objects) {
+ ReactomeDatabaseObject entity = getFullObjectForDbId(object.getDbId());
+ if (entity instanceof ReactomeReactionlikeEvent) {
+ result.add((ReactomeReactionlikeEvent) entity);
+ }
+ }
+ }
+
+ return result;
+ }
+
+ @Override
+ public Class<?> getTypeForDbId(Integer id) throws ClassNotFoundException, InvalidXmlSchemaException {
+ Node node = getFullNodeForDbId(id);
+ Class<?> result = getTypeForNode(node);
+ return result;
+ }
+
+ /**
+ * Returns class type of the data represented in the xml node.
+ *
+ * @param node
+ * xml node
+ * @return class type of the data represented in the xml node
+ * @throws ClassNotFoundException
+ * thrown when there is a problem with finding apropriate class
+ */
+ protected Class<?> getTypeForNode(Node node) throws ClassNotFoundException {
+ Class<?> result = null;
+ for (int i = 0; i < node.getChildNodes().getLength(); i++) {
+ Node child = node.getChildNodes().item(i);
+ if (child.getNodeName().equals("schemaClass")) {
+ // our classes aren't exactly the same as reactome names, change what is
+ // different
+ String shortName = child.getTextContent().replaceAll("GO_", "Go");
+ String className = ReactomeDatabaseObject.class.getPackage().getName() + ".Reactome" + shortName;
+ result = Class.forName(className);
+ }
+ }
+ return result;
+ }
+
+ @Override
+ public ReactomeDatabaseObject getFullObjectForDbId(Integer id) {
+ try {
+ ReactomeDatabaseObject result = null;
+ if (oneInstancePerId) {
+ result = objectMap.get(id);
+ if (result != null) {
+ return result;
+ }
+ }
+ Class<?> classType;
+ Node node = getFullNodeForDbId(id);
+ classType = getTypeForNode(node);
+ ReactomeNodeParser<?> parser = ReactomeParserFactory.getParserForClass(classType);
+ result = parser.parseObject(node);
+ if (oneInstancePerId) {
+ objectMap.put(id, result);
+ }
+ return result;
+ } catch (ClassNotFoundException e) {
+ throw new InvalidArgumentException("Unknown class type: " + e.getMessage());
+ } catch (InvalidXmlSchemaException e) {
+ logger.error(e, e);
+ return null;
+ }
+ }
+
+ @Override
+ @SuppressWarnings("unchecked")
+ public void updateOnlyIdFields(ReactomeDatabaseObject object) {
+ DataSourceUpdater dsu = this;
+ for (Method method : object.getClass().getMethods()) {
+
+ if (Modifier.isPublic(method.getModifiers()) && method.getParameterTypes().length == 0
+ && (method.getName().startsWith("get") || method.getName().startsWith("is"))) {
+
+ if (ReactomeDatabaseObject.class.isAssignableFrom(method.getReturnType())) {
+ try {
+ ReactomeDatabaseObject value = (ReactomeDatabaseObject) method.invoke(object);
+ if (value != null) {
+ if (value.getStatus().equals(ReactomeStatus.ONLY_ID)) {
+ ReactomeDatabaseObject newValue = dsu.getFullObjectForDbId(value.getDbId());
+ String setterName = method.getName();
+ if (setterName.startsWith("get")) {
+ setterName = setterName.replaceFirst("get", "set");
+ } else {
+ setterName = setterName.replaceFirst("is", "set");
+ }
+ try {
+ Method setterMethod = object.getClass().getMethod(setterName, method.getReturnType());
+ setterMethod.invoke(object, newValue);
+ } catch (NoSuchMethodException e) {
+ e.printStackTrace();
+ } catch (IllegalArgumentException e) {
+ logger.error(
+ "Cannot assign " + newValue.getClass() + " (id: " + value.getDbId() + ") to field: " + setterName.replace("set", "") + " ("
+ + method.getReturnType() + ")");
+ } catch (SecurityException e) {
+
+ e.printStackTrace();
+ // ignore it - however this would be strange
+ }
+ }
+ }
+ } catch (IllegalAccessException e) {
+ e.printStackTrace();
+ } catch (IllegalArgumentException e) {
+ e.printStackTrace();
+ } catch (InvocationTargetException e) {
+ e.printStackTrace();
+ // ignore it
+ }
+
+ } else if (List.class.isAssignableFrom(method.getReturnType())) {
+ try {
+ @SuppressWarnings("rawtypes")
+ List list = (List) method.invoke(object);
+ for (int i = 0; i < list.size(); i++) {
+ Object obj = list.get(i);
+ if (obj instanceof ReactomeDatabaseObject) {
+ if (((ReactomeDatabaseObject) obj).getStatus().equals(ReactomeStatus.ONLY_ID)) {
+ ReactomeDatabaseObject newValue = dsu.getFullObjectForDbId(((ReactomeDatabaseObject) obj).getDbId());
+ list.set(i, newValue);
+ }
+ }
+ }
+ } catch (IllegalAccessException e) {
+ e.printStackTrace();
+ } catch (IllegalArgumentException e) {
+ e.printStackTrace();
+ } catch (InvocationTargetException e) {
+ e.printStackTrace();
+ // ignore it
+ }
+ }
+ }
+ }
+ }
+
+ @Override
+ public ReactomeDatabaseObject getFullObjectForStableIdentifier(String stableIdentifier) throws IOException {
+ if (stableIdentifier == null) {
+ return null;
+ }
+ String[] tmp = stableIdentifier.split("\\.");
+ String identifier = tmp[0];
+ String version = "0";
+ if (tmp.length > 1) {
+ version = tmp[1];
+ }
+ return getFullObjectForStableIdentifier(identifier, version);
+ }
+
+ @Override
+ public ReactomeDatabaseObject getFullObjectForStableIdentifier(String identifier, String version) throws IOException {
+ String stableIdentifierQuery = "identifier=" + identifier;
+
+ List<ReactomeDatabaseObject> stableIdentifiers = getSimpleObjectListByQuery(stableIdentifierQuery, ReactomeStableIdentifier.class);
+
+ ReactomeStableIdentifier newestIdentifier = null;
+ ReactomeStableIdentifier matchedIdentifier = null;
+
+ for (ReactomeDatabaseObject object : stableIdentifiers) {
+ ReactomeStableIdentifier entity = (ReactomeStableIdentifier) getFullObjectForDbId(object.getDbId());
+ if (newestIdentifier == null) {
+ newestIdentifier = entity;
+ } else {
+ try {
+ Integer id1 = Integer.parseInt(newestIdentifier.getIdentifierVersion());
+ Integer id2 = Integer.parseInt(entity.getIdentifierVersion());
+ if (id2 > id1) {
+ newestIdentifier = entity;
+ }
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ }
+ }
+ if (entity.getDisplayName().equals(identifier + "." + version) || entity.getIdentifierVersion().equalsIgnoreCase(version)) {
+ matchedIdentifier = entity;
+ }
+ }
+ if (matchedIdentifier == null) {
+ if (newestIdentifier != null) {
+ logger.warn(
+ "Invalid REACTOME stable identifier: \"" + identifier + "." + version + "\". Using another similar: " + newestIdentifier.getIdentifier() + "."
+ + newestIdentifier.getIdentifierVersion());
+ }
+ matchedIdentifier = newestIdentifier;
+ }
+ if (matchedIdentifier != null) {
+ String query = "stableIdentifier=" + matchedIdentifier.getDbId();
+ List<ReactomeDatabaseObject> objects = getSimpleObjectListByQuery(query, ReactomeDatabaseObject.class);
+
+ for (ReactomeDatabaseObject object : objects) {
+ return getFullObjectForDbId(object.getDbId());
+ }
+
+ }
+ return null;
+ }
+
+ // ------------------------------------------------
+
+ // Methods that directly connect to reactome database (via restfull API)
+
+ // ------------------------------------------------
+
+ /**
+ * This method get content of the page of the url (and post content).
+ *
+ * @param url
+ * url address to connect
+ * @param postParam
+ * params of the post method
+ * @param type
+ * MIME type of the result
+ * @param method
+ * request method (POST/GET)
+ * @return return the string with the content of the webpage
+ * @throws IOException
+ * thrown when there are some problem with network connection
+ */
+ protected String getResponse(String url, String postParam, MimeType type, HttpConnectionMethodType method) throws IOException {
+ URL obj = new URL(url);
+ HttpURLConnection con = (HttpURLConnection) obj.openConnection();
+
+ // add reuqest header
+ con.setRequestMethod(method.name());
+ con.setRequestProperty("Accept", type.getTextRepresentation());
+ con.setRequestProperty("Content-Type", type.getTextRepresentation());
+ con.setConnectTimeout(CONNECTION_TIMEOUT);
+ con.setReadTimeout(CONNECTION_TIMEOUT);
+
+ String urlParameters = postParam;
+
+ logger.debug("Sending '" + method + "' request to URL : " + url);
+ if (method.name().equals("POST")) {
+ logger.debug("Parameters : " + urlParameters);
+ }
+
+ // Send post request
+ con.setDoOutput(true);
+ if (method.name().equalsIgnoreCase("POST")) {
+ DataOutputStream wr = new DataOutputStream(con.getOutputStream());
+ wr.writeBytes(urlParameters);
+ wr.flush();
+ wr.close();
+ }
+
+ int responseCode = con.getResponseCode();
+ logger.debug("Response Code : " + responseCode);
+
+ String result = IOUtils.toString(con.getInputStream());
+ logger.debug(result);
+ return result;
+ }
+
+ @Override
+ public List<ReactomeDatabaseObject> getSimpleObjectListByQuery(String query, Class<? extends ReactomeDatabaseObject> clazz) throws IOException {
+ if (query.contains("\n")) {
+ throw new InvalidArgumentException("Query cannot contain new line character");
+ }
+ ReactomeNodeParser<?> parser = ReactomeParserFactory.getParserForClass(clazz);
+ List<ReactomeDatabaseObject> result = new ArrayList<ReactomeDatabaseObject>();
+
+ String url = REACTOME_URL + "listByQuery/" + clazz.getSimpleName().replaceFirst("Reactome", "").replaceAll("Go", "GO_");
+
+ String key = query + "\n" + url;
+
+ Node node = getCacheNode(key);
+ NodeList nodes = null;
+ if (node != null) {
+ nodes = node.getChildNodes();
+ } else {
+ try {
+ nodes = getNodesFromServer(query, url);
+ } catch (InvalidXmlSchemaException e) {
+ throw new IOException(e);
+ }
+ setCacheNode(key, nodes.item(0));
+ nodes = nodes.item(0).getChildNodes();
+ }
+ for (int i = 0; i < nodes.getLength(); i++) {
+ if (nodes.item(i).getNodeType() != Node.ELEMENT_NODE) {
+ continue;
+ }
+ ReactomeDatabaseObject object = parser.parseSimplifiedObject(nodes.item(i));
+ result.add(object);
+ }
+ return result;
+ }
+
+ /**
+ * Returns list of nodes from the server identified by the query and POST
+ * params.
+ *
+ * @param query
+ * string query to the database sent by POST method
+ * @param url
+ * direct url to the API
+ * @return list of nodes from the server identified by the query and POST
+ * params.
+ * @throws IOException
+ * thrown when there are some problem with network connection
+ * @throws InvalidXmlSchemaException
+ * thrown when there is a problem with xml
+ */
+ private NodeList getNodesFromServer(String query, String url) throws IOException, InvalidXmlSchemaException {
+ String response = getResponse(url, query, MimeType.XML, HttpConnectionMethodType.POST);
+ logger.debug(response);
+ Node node = XmlParser.getXmlDocumentFromString(response);
+ NodeList nodes = node.getChildNodes();
+ if (nodes.getLength() < 1) {
+ throw new InvalidArgumentException("Problem with xml document");
+ }
+ return nodes;
+ }
+
+ /**
+ * This method returns xml NODE for object identified by id (identifier in
+ * reactome database). However if object is in local cache then local copy is
+ * returned. If object doesn't exist in local cache then after retrieving it
+ * from reactome is put to the cache.
+ *
+ * @param id
+ * identifier in reactome database
+ * @return xml node for the id given reactome id
+ * @throws InvalidXmlSchemaException
+ * thrown when there is a problem with xml
+ */
+ @Override
+ public Node getFullNodeForDbId(Integer id) throws InvalidXmlSchemaException {
+ Node result = getCacheNode(IDENTIFIER_QUERY_PREFIX + id);
+ if (result != null) {
+ return result;
+ }
+
+ String response;
+ String url = REACTOME_URL + "queryById/DatabaseObject/" + id;
+ try {
+ response = getResponse(url, "", MimeType.XML, HttpConnectionMethodType.GET);
+ Document doc = XmlParser.getXmlDocumentFromString(response);
+ NodeList nodes = doc.getChildNodes();
+ result = nodes.item(0);
+ setCacheNode(IDENTIFIER_QUERY_PREFIX + id, result);
+ return result;
+ } catch (IOException e) {
+ logger.error(e.getMessage(), e);
+ return null;
+ }
+ }
+
+ @Override
+ public Map<Integer, ReactomeDatabaseObject> getFullObjectsForDbIds(List<Integer> ids) throws ClassNotFoundException, IOException {
+ Map<Integer, ReactomeDatabaseObject> result = new HashMap<Integer, ReactomeDatabaseObject>();
+ for (Integer integer : ids) {
+ result.put(integer, getFullObjectForDbId(integer));
+ }
+
+ return result;
+
+ }
+
+ @Override
+ public List<ReactomePhysicalEntity> getEntitiesForSetOfIds(Set<MiriamData> identifiers) throws IOException {
+ return getEntitiesForUniprotId(identifiers);
+ }
+
+ @Override
+ public ExternalServiceStatus getServiceStatus() {
+ ExternalServiceStatus status = new ExternalServiceStatus(
+ "Reactome RESTful API", "http://reactome.org/ReactomeRESTfulAPI/ReactomeRESTFulAPI.html");
+
+ GeneralCacheInterface cacheCopy = getCache();
+ this.setCache(null);
+
+ try {
+ ReactomeDatabaseObject obj = getFullObjectForDbId(CHECK_SERVICE_STATUS_EXAMPLE);
+ status.setStatus(ExternalServiceStatusType.OK);
+ if (obj == null) {
+ status.setStatus(ExternalServiceStatusType.DOWN);
+ } else if (obj.getClass().equals(ReactomeDatabaseObject.class)) {
+ status.setStatus(ExternalServiceStatusType.CHANGED);
+ }
+ } catch (Exception e) {
+ logger.error(status.getName() + " is down", e);
+ status.setStatus(ExternalServiceStatusType.DOWN);
+ }
+ this.setCache(cacheCopy);
+ return status;
+ }
+
+}