diff --git a/.classpath b/.classpath index 5402ac0..7de8e04 100644 --- a/.classpath +++ b/.classpath @@ -1,20 +1,21 @@ - + - + + @@ -31,5 +32,5 @@ - + diff --git a/.settings/org.eclipse.wst.common.component b/.settings/org.eclipse.wst.common.component index d81dc60..b77a9a0 100644 --- a/.settings/org.eclipse.wst.common.component +++ b/.settings/org.eclipse.wst.common.component @@ -3,6 +3,8 @@ + + diff --git a/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/TaxonomyRowTable.java b/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/TaxonomyRowTable.java index ea24db0..022b766 100644 --- a/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/TaxonomyRowTable.java +++ b/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/TaxonomyRowTable.java @@ -41,19 +41,8 @@ import org.gcube.portlets.user.speciesdiscovery.shared.TaxonomyRow; */ public class TaxonomyRowTable extends HttpServlet { - /** - * - */ protected static final String UTF_8 = "UTF-8"; - - /** - * - */ private static final long serialVersionUID = 9157876104914505028L; - - /** - * - */ public static final String TEXT_HTML = "text/html; charset=UTF-8"; public static final String DOCTYPE = ""; diff --git a/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/asl/SessionUtil.java b/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/asl/SessionUtil.java index a46f66e..a92fce2 100644 --- a/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/asl/SessionUtil.java +++ b/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/asl/SessionUtil.java @@ -1,5 +1,5 @@ /** - * + * */ package org.gcube.portlets.user.speciesdiscovery.server.asl; @@ -27,12 +27,12 @@ import org.gcube.portlets.user.speciesdiscovery.shared.cluster.ClusterCommonName import org.gcube.portlets.user.speciesdiscovery.shared.cluster.ClusterCommonNameDataSourceForTaxonomyRow; /** - * + * * @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it * */ public class SessionUtil { - + public static final String SPECIES_SERVICE = "SPECIES_SERVICE"; public static final String SEARCH_SESSION = "SEARCH_SESSION"; public static final String TAXONOMY_OCCURRENCE = "TAXONOMY_OCCURRENCE"; @@ -51,10 +51,10 @@ public class SessionUtil { private static final String CACHE_HASH_MAP_CHILDREN_TAXONOMY = "CACHE_HASH_MAP_CHILDREN_TAXONOMY"; private static final String CACHE_HASH_MAP_SYNONYMS_TAXONOMY = "CACHE_HASH_MAP_SYNONYMS_TAXONOMY"; private static final String CACHE_HASH_MAP_TAXONOMYID_TAXONOMY = "CACHE_HASH_MAP_TAXONOMYID_TAXONOMY"; - + protected static Logger logger = Logger.getLogger(SessionUtil.class); - - + + public static EntityManagerFactory getEntityManagerFactory(ASLSession session) { return (EntityManagerFactory) session.getAttribute(ENTITY_FACTORY); } @@ -62,41 +62,40 @@ public class SessionUtil { public static void setEntityManagerFactory(ASLSession session, EntityManagerFactory factory) { session.setAttribute(ENTITY_FACTORY, factory); } - + public static SpeciesService getService(ASLSession session) throws Exception { SpeciesService service = (SpeciesService) session.getAttribute(SPECIES_SERVICE); if (service==null) { logger.trace("Service not found, creating it"); - String scope = session.getScope(); - service = new SpeciesService(scope, session); + service = new SpeciesService(); session.setAttribute(SPECIES_SERVICE, service); } - + return service; } - + @SuppressWarnings("unchecked") public static FetchingSession getCurrentSearchSession(ASLSession session) { return (FetchingSession) session.getAttribute(SEARCH_SESSION); } - + public static void setCurrentSearchSession(ASLSession session, FetchingSession searchSession){ session.setAttribute(SEARCH_SESSION, searchSession); } - - + + @SuppressWarnings("unchecked") public static FetchingSession getCurrentOccurrenceSession(ASLSession session){ return (FetchingSession) session.getAttribute(TAXONOMY_OCCURRENCE); } - - + + public static void setCurrentOccurrenceSession(ASLSession session, FetchingSession searchSession){ session.setAttribute(TAXONOMY_OCCURRENCE, searchSession); } - + // public static void setCurrentTaxonomyChildrenSession(ASLSession session, FetchingSession searchSession) // { // session.setAttribute(TAXONOMY_CHILD, searchSession); @@ -114,10 +113,10 @@ public class SessionUtil { // user = "lucio.lelii"; // user = "pasquale.pagano"; // user = "francesco.mangiacrapa"; - + String scope = "/gcube/devsec"; //Development // String scope = "/d4science.research-infrastructures.eu/gCubeApps/BiodiversityResearchEnvironment"; //Production - + httpSession.setAttribute(USERNAME_ATTRIBUTE, user); ASLSession session = SessionManager.getInstance().getASLSession(sessionID, user); session.setScope(scope); @@ -125,7 +124,7 @@ public class SessionUtil { logger.warn("TaxonomySearchServiceImpl STARTING IN TEST MODE - NO USER FOUND"); logger.warn("Created fake Asl session for user "+user + " with scope "+scope); // session.setScope("/gcube/devsec"); - + return session; } @@ -133,12 +132,12 @@ public class SessionUtil { } //MODIFIED****************************************************************************************** - + public static void setCurrentEJBResultRow(ASLSession session, ResultRowPersistence resultRowPersistence) { session.setAttribute(EJB_RESULT_ROW, resultRowPersistence); } - + public static ResultRowPersistence getCurrentEJBResultRow(ASLSession session) { return (ResultRowPersistence) session.getAttribute(EJB_RESULT_ROW); } @@ -146,39 +145,39 @@ public class SessionUtil { public static void setCurrentEJBTaxonRow(ASLSession session,TaxonRowPersistence taxonRowPersistence) { session.setAttribute(EJB_TAXON_ROW, taxonRowPersistence); } - + public static TaxonRowPersistence getCurrentEJBTaxonRow(ASLSession session) { return (TaxonRowPersistence) session.getAttribute(EJB_TAXON_ROW); } - + public static void setCurrentEJBOccurrence(ASLSession session, OccurrenceRowPersistence occurrenceRowPersistence) { session.setAttribute(EJB_OCCURENCE, occurrenceRowPersistence); } - + public static OccurrenceRowPersistence getCurrentEJBOccurrence(ASLSession session) { return (OccurrenceRowPersistence) session.getAttribute(EJB_OCCURENCE); } - + @SuppressWarnings("unchecked") public static TaxonomyRowPersistence getCurrentEJBTaxonomyItem(ASLSession session) { return (TaxonomyRowPersistence) session.getAttribute(EJB_TAXONOMY); } - + public static void setCurrentEJBTaxonomyItem(ASLSession session, TaxonomyRowPersistence taxonomyItemDAO) { session.setAttribute(EJB_TAXONOMY, taxonomyItemDAO); - + } public static void setCurrentEJBOccurrencesJob(ASLSession session, OccurrenceJobPersistence occurrenceJobPersistence) { session.setAttribute(EJB_OCCURRENCES_JOB, occurrenceJobPersistence); - + } - + @SuppressWarnings("unchecked") public static OccurrenceJobPersistence getCurrentDaoOccurrencesJob(ASLSession session) { return (OccurrenceJobPersistence) session.getAttribute(EJB_OCCURRENCES_JOB); } - + @SuppressWarnings("unchecked") public static TaxonomyJobPersistence getCurrentDAOTaxonomyJob(ASLSession session) { return (TaxonomyJobPersistence) session.getAttribute(EJB_TAXONOMY_JOB); @@ -195,17 +194,17 @@ public class SessionUtil { public static void setCurrentQuery(ASLSession aslSession, String lastQuery) { logger.trace("Last query in session: "+lastQuery); aslSession.setAttribute(CURRENT_SPD_QUERY, lastQuery); - + } - + /** - * + * * @param aslSession */ public static String getCurrentQuery(ASLSession aslSession) { return (String) aslSession.getAttribute(CURRENT_SPD_QUERY); - + } /** @@ -213,89 +212,89 @@ public class SessionUtil { */ public static void setCurrentClusterCommonNameForResultRow(ASLSession session, HashMap hashClusterCommonNameDataSource) { session.setAttribute(CLUSTER_COMMONNAME_FOR_RESULTROW, hashClusterCommonNameDataSource); - + } - + /** * @param hashClusterCommonNameDataSource - * @return + * @return */ public static HashMap getCurrentClusterCommonNameForResultRow(ASLSession session) { return (HashMap) session.getAttribute(CLUSTER_COMMONNAME_FOR_RESULTROW); - + } - - + + /** * @param hashClusterCommonNameDataSource */ public static void setCurrentClusterCommonNameForTaxonomyRow(ASLSession session, HashMap hashClusterCommonNameDataSource) { session.setAttribute(CLUSTER_COMMONNAME_FOR_TAXONOMYROW, hashClusterCommonNameDataSource); - - } - - /** - * @param hashClusterCommonNameDataSource - * @return - */ - public static HashMap getCurrentClusterCommonNameForTaxonomyRow(ASLSession session) { - return (HashMap) session.getAttribute(CLUSTER_COMMONNAME_FOR_TAXONOMYROW); - + } /** - * @return - * + * @param hashClusterCommonNameDataSource + * @return + */ + public static HashMap getCurrentClusterCommonNameForTaxonomyRow(ASLSession session) { + return (HashMap) session.getAttribute(CLUSTER_COMMONNAME_FOR_TAXONOMYROW); + + } + + /** + * @return + * */ public static HashMap getHashMapChildrenTaxonomyCache(ASLSession session) { return (HashMap) session.getAttribute(CACHE_HASH_MAP_CHILDREN_TAXONOMY); - + } - + /** - * @return - * + * @return + * */ public static void setHashMapChildrenTaxonomyCache(ASLSession session, Map list) { session.setAttribute(CACHE_HASH_MAP_CHILDREN_TAXONOMY, list); - + } - - + + /** - * @return - * + * @return + * */ public static HashMap getHashMapSynonymsTaxonomyCache(ASLSession session) { return (HashMap) session.getAttribute(CACHE_HASH_MAP_SYNONYMS_TAXONOMY); - + } - + /** - * @return - * + * @return + * */ public static void setHashMapSynonymsTaxonomyCache(ASLSession session, Map list) { session.setAttribute(CACHE_HASH_MAP_SYNONYMS_TAXONOMY, list); - + } - - + + /** - * @return - * + * @return + * */ public static HashMap getHashMapTaxonomyByIdsCache(ASLSession session) { return (HashMap) session.getAttribute(CACHE_HASH_MAP_TAXONOMYID_TAXONOMY); - + } - + /** - * @return - * + * @return + * */ public static void setHashMapTaxonomyByIdsCache(ASLSession session, Map list) { session.setAttribute(CACHE_HASH_MAP_TAXONOMYID_TAXONOMY, list); - + } } diff --git a/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/DaoSession.java b/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/DaoSession.java index 2533add..ef21d44 100644 --- a/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/DaoSession.java +++ b/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/DaoSession.java @@ -23,44 +23,44 @@ import org.gcube.portlets.user.speciesdiscovery.shared.DatabaseServiceException; * */ public class DaoSession { - + protected static final String PROPERTY_CATALINA_HOME = "catalina.home"; protected static final String CATALINA_HOME = "CATALINA_HOME"; protected static final String PERSISTENCE_H2DBSPECIES_H2 = "persistence/h2dbspecies/h2"; public static Logger logger = Logger.getLogger(DaoSession.class); private static final String JDBCDRIVER = "jdbc:h2:"; - - + + public static String getUsernameScopeValue(String username, String scope){ - + scope = scope.replaceAll("/",""); username = username.replaceAll("\\.",""); return username+scope; } - - - + + + /** - * + * * @return $CATALINA_HOME - * @throws Exception + * @throws Exception */ public static String getTomcatFolder(){ - + String catalinaHome = System.getenv(CATALINA_HOME) != null ? System.getenv(CATALINA_HOME) : System.getProperty(PROPERTY_CATALINA_HOME); - + if(catalinaHome == null || catalinaHome.isEmpty()) logger.error("CATALINA_HOME ENVIROMENT NOT FOUND - RETURNED / PATH"); - - + + return catalinaHome.endsWith("/") ? catalinaHome : catalinaHome+"/"; } - - + + public static String getConnectionUrl(ASLSession session){ - + String username = session.getUsername(); String scope = session.getScopeName(); return JDBCDRIVER +getTomcatFolder()+PERSISTENCE_H2DBSPECIES_H2+getUsernameScopeValue(username,scope)+";create=true"; @@ -82,26 +82,26 @@ public class DaoSession { } } - + //MODIFIED**************************************************************************************+ - - - + + + public static EntityManager newEntityManager(ASLSession session){ - + return getEntityManagerFactory(session).createEntityManager(); } - + public static EntityManagerFactory getEntityManagerFactory(ASLSession session){ - + EntityManagerFactory factory = SessionUtil.getEntityManagerFactory(session); - + if(factory==null){ factory = createEntityManagerFactory(session); SessionUtil.setEntityManagerFactory(session, factory); } - + return factory; } @@ -109,22 +109,22 @@ public class DaoSession { { OccurrenceJobPersistence occurrencesJobDao = SessionUtil.getCurrentDaoOccurrencesJob(session); - + if(occurrencesJobDao==null){ occurrencesJobDao = initOccurrencesJobsDao(session); SessionUtil.setCurrentEJBOccurrencesJob(session, occurrencesJobDao); } - + return occurrencesJobDao; } - + public static TaxonomyJobPersistence getTaxonomyJobDAO(ASLSession session) throws Exception { TaxonomyJobPersistence taxonomyJobPeristence = SessionUtil.getCurrentDAOTaxonomyJob(session); - + if(taxonomyJobPeristence==null){ taxonomyJobPeristence = initTaxonomyJobsDao(session); SessionUtil.setCurrentDAOTaxonomyJob(session, taxonomyJobPeristence); @@ -132,12 +132,11 @@ public class DaoSession { return taxonomyJobPeristence; } - + public static EntityManagerFactory createEntityManagerFactory(ASLSession session){ - + Map properties = new HashMap(); // properties.put("javax.persistence.jdbc.driver", jdbcDriverH2); - try{ properties.put("javax.persistence.jdbc.url", getConnectionUrl(session)); } @@ -149,19 +148,19 @@ public class DaoSession { } //emf = Persistence.createEntityManagerFactory("jpablogPUnit"); return Persistence.createEntityManagerFactory("SPD_PERSISTENCE_FACTORY",properties); - + } - - + + public static OccurrenceJobPersistence initOccurrencesJobsDao(ASLSession session) throws Exception { - + String username = session.getUsername(); String scope = session.getScopeName(); return createOccurrencesJobDao(username, scope, session); - + } - + public static TaxonomyJobPersistence initTaxonomyJobsDao(ASLSession session) throws Exception{ TaxonomyJobPersistence occurrenceJobPersistence = new TaxonomyJobPersistence(getEntityManagerFactory(session)); @@ -169,34 +168,34 @@ public class DaoSession { return occurrenceJobPersistence; } - + public static OccurrenceJobPersistence createOccurrencesJobDao(String username, String scope, ASLSession session) throws Exception{ - + OccurrenceJobPersistence occurrenceJobPersistence = new OccurrenceJobPersistence(getEntityManagerFactory(session)); SessionUtil.setCurrentEJBOccurrencesJob(session, occurrenceJobPersistence); - + // logger.trace("ResultRow Dao IS READY AT CONNECTION URL: " + jdbcDriver + " table name "+ resultRowDAO.getTableInfo().getTableName()); - + return occurrenceJobPersistence; } - + public static ResultRowPersistence initResultRowDao(ASLSession session) throws Exception { - + ResultRowPersistence resultRowPersistence = new ResultRowPersistence(getEntityManagerFactory(session)); SessionUtil.setCurrentEJBResultRow(session, resultRowPersistence); - + // logger.trace("ResultRow Dao IS READY AT CONNECTION URL: " + jdbcDriver + " table name "+ resultRowDAO.getTableInfo().getTableName()); - + return resultRowPersistence; } - + public static OccurrenceRowPersistence getOccurrenceDAO(ASLSession session) throws Exception { OccurrenceRowPersistence occurrenceEJB = SessionUtil.getCurrentEJBOccurrence(session); - + if(occurrenceEJB==null){ occurrenceEJB = initOccurrenceDao(session); SessionUtil.setCurrentEJBOccurrence(session, occurrenceEJB); @@ -207,60 +206,60 @@ public class DaoSession { public static TaxonRowPersistence initTaxonDao(ASLSession session) throws Exception { - + TaxonRowPersistence taxonRowPersistence = new TaxonRowPersistence(getEntityManagerFactory(session)); SessionUtil.setCurrentEJBTaxonRow(session, taxonRowPersistence); - + // logger.trace("ResultRow Dao IS READY AT CONNECTION URL: " + jdbcDriver + " table name "+ resultRowDAO.getTableInfo().getTableName()); - + return taxonRowPersistence; } - + private static OccurrenceRowPersistence initOccurrenceDao(ASLSession session) throws Exception { OccurrenceRowPersistence occurrenceRowPersistence = new OccurrenceRowPersistence(getEntityManagerFactory(session)); SessionUtil.setCurrentEJBOccurrence(session, occurrenceRowPersistence); - + // logger.trace("ResultRow Dao IS READY AT CONNECTION URL: " + jdbcDriver + " table name "+ resultRowDAO.getTableInfo().getTableName()); - + return occurrenceRowPersistence; - + } - + public static TaxonRowPersistence getTaxonDAO(ASLSession session) throws Exception { TaxonRowPersistence taxonDao = SessionUtil.getCurrentEJBTaxonRow(session); - + if(taxonDao==null){ taxonDao = initTaxonDao(session); SessionUtil.setCurrentEJBTaxonRow(session, taxonDao); } - + // System.out.println("Return taxon Dao : " + taxonDao + " table name: " + taxonDao.getTableConfig().getTableName()); // System.out.println("session id: " + session.getExternalSessionID() + " sessione username: " +session.getUsername() + " session scope: "+session.getScopeName()); return taxonDao; } - + public static TaxonomyRowPersistence getTaxonomyDAO(ASLSession session) throws Exception { logger.trace("In getTaxonomyDAO..."); - + TaxonomyRowPersistence taxonItemDAO = SessionUtil.getCurrentEJBTaxonomyItem(session); - + if(taxonItemDAO==null){ taxonItemDAO = initTaxonomyItemDao(session, "taxonomyrow"); SessionUtil.setCurrentEJBTaxonomyItem(session, taxonItemDAO); } - + // logger.trace("Return taxonomy row Dao : " + taxonItemDAO + " table name: " + taxonItemDAO.getTableConfig().getTableName()); // logger.trace("session id: " + session.getExternalSessionID() + " sessione username: " +session.getUsername() + " session scope: "+session.getScopeName()); return taxonItemDAO; } - + private static TaxonomyRowPersistence initTaxonomyItemDao(ASLSession session, String tableName) throws Exception{ TaxonomyRowPersistence taxonomyRP = new TaxonomyRowPersistence(getEntityManagerFactory(session)); @@ -268,26 +267,26 @@ public class DaoSession { return taxonomyRP; } - + public static ResultRowPersistence getResultRowDAO(ASLSession session) throws Exception - { - + { + logger.trace("In getResultRowDAO..."); - + ResultRowPersistence resultRowEJB = SessionUtil.getCurrentEJBResultRow(session); - + if(resultRowEJB==null){ resultRowEJB = initResultRowDao(session); SessionUtil.setCurrentEJBResultRow(session, resultRowEJB); } - + // logger.trace("Return result row Dao : " + resultRowEJB + " table name: " + resultRowDAO.getTableConfig().getTableName()); // logger.trace("session id: " + session.getExternalSessionID() + " sessione username: " +session.getUsername() + " session scope: "+session.getScopeName()); return resultRowEJB; } - - - + + + } diff --git a/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/service/SpeciesService.java b/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/service/SpeciesService.java index 583edd7..5d706ad 100644 --- a/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/service/SpeciesService.java +++ b/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/service/SpeciesService.java @@ -18,8 +18,6 @@ import java.util.Map.Entry; import java.util.concurrent.TimeUnit; import org.apache.log4j.Logger; -import org.gcube.application.framework.core.session.ASLSession; -import org.gcube.common.scope.api.ScopeProvider; import org.gcube.data.spd.client.proxies.ClassificationClient; import org.gcube.data.spd.client.proxies.ExecutorClient; import org.gcube.data.spd.client.proxies.ManagerClient; @@ -59,59 +57,24 @@ public class SpeciesService { protected Logger logger = Logger.getLogger(SpeciesService.class); protected String scope; - protected ASLSession session; protected ManagerClient call; protected OccurrenceClient occurrencesCall; protected ClassificationClient classificationCall; protected ExecutorClient executorCall; protected String lastQuery = ""; - /** - * Instantiates a new species service. - * - * @param scope - * the scope - * @param session - * the session - * @throws Exception - * the exception - */ - public SpeciesService(String scope, ASLSession session) - throws Exception { - - this(scope); - this.session = session; - } /** * Instantiates a new species service. * - * @param scope - * the scope - * @throws Exception - * the exception + * @throws Exception the exception */ - public SpeciesService(String scope) - throws Exception { - - this.scope = scope; - ScopeProvider.instance.set(scope); - // this.call = manager().at( - // URI.create("http://node24.d.d4science.research-infrastructures.eu:9000")).withTimeout(3, - // TimeUnit.MINUTES).build(); - // this.occurrencesCall = occurrences().at( - // URI.create("http://node24.d.d4science.research-infrastructures.eu:9000")).withTimeout(3, - // TimeUnit.MINUTES).build(); - // this.classificationCall = classification().at( - // URI.create("http://node24.d.d4science.research-infrastructures.eu:9000")).withTimeout(3, - // TimeUnit.MINUTES).build(); + public SpeciesService() throws Exception { System.out.println("CALLING MANAGER "); this.call = manager().withTimeout(3, TimeUnit.MINUTES).build(); this.executorCall = executor().withTimeout(3, TimeUnit.MINUTES).build(); - OccurrenceClient a = - occurrences().withTimeout(3, TimeUnit.MINUTES).build(); - this.classificationCall = - classification().withTimeout(3, TimeUnit.MINUTES).build(); + this.occurrencesCall = occurrences().withTimeout(3, TimeUnit.MINUTES).build(); + this.classificationCall = classification().withTimeout(3, TimeUnit.MINUTES).build(); } /** @@ -129,7 +92,6 @@ public class SpeciesService { this.scope = scope; if (instanceOnlyOccurrence) { - ScopeProvider.instance.set(scope); System.out.println("CALLING OCCURRENCE MANAGER "); this.occurrencesCall = occurrences().withTimeout(3, TimeUnit.MINUTES).build(); } @@ -185,7 +147,6 @@ public class SpeciesService { logger.trace("retrieveTaxonomyById..."); try { - ScopeProvider.instance.set(scope); Stream stream = classificationCall.getTaxaByIds(ids); return new StreamIterator(stream); } @@ -211,7 +172,6 @@ public class SpeciesService { logger.trace("retrieveSynonymsById..."); try { - ScopeProvider.instance.set(scope); Stream stream = classificationCall.getSynonymsById(id); return new StreamIterator(stream); @@ -239,9 +199,7 @@ public class SpeciesService { logger.trace("search by Query - query is: " + query); // System.out.println("searchByQuery query: "+query); try { - ScopeProvider.instance.set(scope); lastQuery = query; - // System.err.println("ScopeProvider SCOPE "+ScopeProvider.instance.get()); logger.trace("call species service search..."); // System.out.println("call species service search..."); Stream stream = call.search(query); @@ -286,10 +244,7 @@ public class SpeciesService { throws SearchServiceException { logger.trace("searchByQuery query: " + query); - // System.out.println("searchByQuery query: "+query); try { - ScopeProvider.instance.set(scope); - // System.err.println("ScopeProvider SCOPE "+ScopeProvider.instance.get()); logger.trace("call species service search..."); System.out.println("call species service search..."); return call.search(query); @@ -316,7 +271,6 @@ public class SpeciesService { try { List listDsModel = new ArrayList(); - ScopeProvider.instance.set(scope); System.out.println("setting scope " + scope); List plugin = call.getPluginsDescription(); if (plugin != null) { @@ -475,9 +429,6 @@ public class SpeciesService { throws SearchServiceException { try { - // Stream keysStream = convert(keys); - ScopeProvider.instance.set(scope); - logger.trace("Instancing scope: "+scope); logger.trace("Calling occurrencesCall passing keys: "+keys); logger.trace("occurrencesCall != null? "+(occurrencesCall==null)); Stream stream = occurrencesCall.getByKeys(keys); @@ -504,7 +455,6 @@ public class SpeciesService { try { // Stream idsStream = convert(ids); - ScopeProvider.instance.set(scope); Stream stream = occurrencesCall.getByIds(ids); return new StreamIterator(stream); } @@ -530,7 +480,6 @@ public class SpeciesService { try { // Stream keysStream = convert(keys); - ScopeProvider.instance.set(scope); return occurrencesCall.createLayer(streamKey); } catch (Exception e) { @@ -555,7 +504,6 @@ public class SpeciesService { throws Exception { try { - ScopeProvider.instance.set(scope); Stream items = classificationCall.getTaxonChildrenById(parentId); return new StreamIterator(items); @@ -578,7 +526,6 @@ public class SpeciesService { */ public CompleteJobStatus getTaxonomyJobById(String jobId) { - ScopeProvider.instance.set(scope); CompleteJobStatus status = null; try { status = this.executorCall.getStatus(jobId); @@ -609,7 +556,6 @@ public class SpeciesService { throws Exception { InputStream is = null; - ScopeProvider.instance.set(scope); try { String url = this.executorCall.getResultLink(jobIdentifier); if (url == null || url.isEmpty()) { @@ -640,7 +586,6 @@ public class SpeciesService { throws Exception { InputStream is = null; - ScopeProvider.instance.set(scope); try { String url = this.executorCall.getErrorLink(jobIdentifier); if (url == null || url.isEmpty()) { @@ -670,7 +615,6 @@ public class SpeciesService { public boolean isAvailableTaxonomyJobErrorFileById(String jobIdentifier) throws Exception { - ScopeProvider.instance.set(scope); try { String url = this.executorCall.getErrorLink(jobIdentifier); if (url == null || url.isEmpty()) { @@ -700,7 +644,6 @@ public class SpeciesService { public String createTaxonomyJobForDWCAByChildren(String taxonomyId) throws Exception { - ScopeProvider.instance.set(scope); try { return this.executorCall.createDwCAByChildren(taxonomyId); } @@ -722,7 +665,6 @@ public class SpeciesService { public String createTaxonomyJobForDWCAByIds(List ids) throws Exception { - ScopeProvider.instance.set(scope); try { Stream keysStream = convert(ids); return executorCall.createDwCAByIds(keysStream); @@ -744,7 +686,6 @@ public class SpeciesService { public void cancelTaxonomyJobById(String jobIdentifier) { try { - ScopeProvider.instance.set(scope); this.executorCall.removeJob(jobIdentifier); } catch (Exception e) { @@ -763,7 +704,6 @@ public class SpeciesService { public CompleteJobStatus getOccurrenceJobById(String jobId) { try { - ScopeProvider.instance.set(scope); return this.executorCall.getStatus(jobId); // CHANGE INTO OCCURRENCE // JOB // ************************************************************************************** @@ -793,7 +733,6 @@ public class SpeciesService { throws Exception { try { - ScopeProvider.instance.set(scope); return this.executorCall.createCSV(streamKey); } catch (Exception e) { @@ -817,7 +756,6 @@ public class SpeciesService { throws Exception { try { - ScopeProvider.instance.set(scope); return this.executorCall.createDarwincoreFromOccurrenceKeys(streamKey); } catch (Exception e) { @@ -841,7 +779,6 @@ public class SpeciesService { throws Exception { try { - ScopeProvider.instance.set(scope); return this.executorCall.createCSVforOM(streamKey); } catch (Exception e) { @@ -863,7 +800,6 @@ public class SpeciesService { public void cancelOccurrenceJobById(String jobIdentifier) { try { - ScopeProvider.instance.set(scope); this.executorCall.removeJob(jobIdentifier); // CHANGE INTO // OCCURRENCE JOB // ************************************************************************************** @@ -888,7 +824,6 @@ public class SpeciesService { throws Exception { InputStream is = null; - ScopeProvider.instance.set(scope); try { String url = this.executorCall.getResultLink(jobIdentifier); // CHANGE // INTO @@ -925,7 +860,6 @@ public class SpeciesService { throws Exception { InputStream is = null; - ScopeProvider.instance.set(scope); try { String url = this.executorCall.getErrorLink(jobIdentifier); logger.trace("URL returned by species service is: " + url); @@ -955,7 +889,6 @@ public class SpeciesService { public boolean isAvailableOccurrenceJobErrorFileById(String jobIdentifier) throws Exception { - ScopeProvider.instance.set(scope); try { String url = this.executorCall.getErrorLink(jobIdentifier); if (url == null || url.isEmpty()) { diff --git a/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/util/GetWorkspaceUtil.java b/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/util/GetWorkspaceUtil.java index d9b85b1..894e917 100644 --- a/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/util/GetWorkspaceUtil.java +++ b/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/util/GetWorkspaceUtil.java @@ -1,5 +1,5 @@ /** - * + * */ package org.gcube.portlets.user.speciesdiscovery.server.util; @@ -7,7 +7,6 @@ import org.apache.log4j.Logger; import org.gcube.application.framework.core.session.ASLSession; import org.gcube.common.homelibrary.home.HomeLibrary; import org.gcube.common.homelibrary.home.workspace.Workspace; -import org.gcube.common.scope.api.ScopeProvider; /** * @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it @@ -17,26 +16,20 @@ import org.gcube.common.scope.api.ScopeProvider; public class GetWorkspaceUtil { protected static Logger logger = Logger.getLogger(GetWorkspaceUtil.class); - + public static Workspace getWorskspace(ASLSession session) throws Exception { - + if(session==null) throw new Exception("ASL session is null"); - + if(session.getScope()==null) throw new Exception("Scope into ASL session is null"); - + String scope = session.getScope().toString(); - - logger.trace("Get workspace for scope "+scope); - - ScopeProvider.instance.set(scope); - - logger.trace("ScopeProvider instancied for scope "+scope); - + //logger.trace("Get workspace for scope "+scope); + //ScopeProvider.instance.set(scope); + //logger.trace("ScopeProvider instancied for scope "+scope); logger.trace("retuning workspace for username "+session.getUsername()); - return HomeLibrary.getUserWorkspace(session.getUsername()); - } } diff --git a/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/CommonName.java b/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/CommonName.java index b034246..944de2b 100644 --- a/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/CommonName.java +++ b/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/CommonName.java @@ -1,5 +1,5 @@ /** - * + * */ package org.gcube.portlets.user.speciesdiscovery.shared; @@ -10,16 +10,18 @@ import javax.persistence.GeneratedValue; import javax.persistence.GenerationType; import javax.persistence.Id; +import com.google.gwt.user.client.rpc.IsSerializable; + /** - * + * * @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it * */ @Entity -public class CommonName implements Serializable { +public class CommonName implements IsSerializable, Serializable { /** - * + * */ private static final long serialVersionUID = 1140787822064828769L; @@ -27,22 +29,22 @@ public class CommonName implements Serializable { public final static String NAME= "name"; public final static String LANGUAGE= "language"; public final static String REFERENCE_RESULTROW_ID = "resultRowId"; - + @Id @GeneratedValue(strategy = GenerationType.IDENTITY) private int internalId; - - + + protected int id; - + private int resultRowId; protected String name; protected String language; - + public CommonName(){} - + /** * @param name * @param language @@ -97,5 +99,5 @@ public class CommonName implements Serializable { public int getResultRowId() { return resultRowId; } - + } diff --git a/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/Coordinate.java b/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/Coordinate.java index b832714..a538dc3 100644 --- a/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/Coordinate.java +++ b/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/Coordinate.java @@ -1,26 +1,28 @@ /** - * + * */ package org.gcube.portlets.user.speciesdiscovery.shared; import java.io.Serializable; +import com.google.gwt.user.client.rpc.IsSerializable; + /** * @author "Federico De Faveri defaveri@isti.cnr.it" * */ -public class Coordinate implements Serializable { - +public class Coordinate implements IsSerializable, Serializable { + /** - * + * */ private static final long serialVersionUID = -2357675565732391317L; - + protected float latitude; protected float longitude; - + public Coordinate(){} - + /** * @param latitude * @param longitude @@ -29,35 +31,35 @@ public class Coordinate implements Serializable { this.latitude = latitude; this.longitude = longitude; } - + /** * @return the latitude */ public float getLatitude() { return latitude; } - + /** * @param latitude the latitude to set */ public void setLatitude(float latitude) { this.latitude = latitude; } - + /** * @return the longitude */ public float getLongitude() { return longitude; } - + /** * @param longitude the longitude to set */ public void setLongitude(float longitude) { this.longitude = longitude; } - + /** * {@inheritDoc} */ diff --git a/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/DataSource.java b/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/DataSource.java index 25cec0c..14e2688 100644 --- a/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/DataSource.java +++ b/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/DataSource.java @@ -1,5 +1,7 @@ package org.gcube.portlets.user.speciesdiscovery.shared; +import java.io.Serializable; + import javax.persistence.Entity; import javax.persistence.GeneratedValue; import javax.persistence.GenerationType; @@ -15,7 +17,12 @@ import com.google.gwt.user.client.rpc.IsSerializable; * Jan 10, 2017 */ @Entity -public class DataSource implements IsSerializable{ +public class DataSource implements IsSerializable, Serializable{ + + /** + * + */ + private static final long serialVersionUID = -7978955895523864898L; @Id @GeneratedValue(strategy = GenerationType.IDENTITY) diff --git a/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/DataSourceCapability.java b/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/DataSourceCapability.java index 6ddffc9..28b6489 100644 --- a/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/DataSourceCapability.java +++ b/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/DataSourceCapability.java @@ -1,5 +1,6 @@ package org.gcube.portlets.user.speciesdiscovery.shared; +import java.io.Serializable; import java.util.ArrayList; import com.google.gwt.user.client.rpc.IsSerializable; @@ -12,8 +13,12 @@ import com.google.gwt.user.client.rpc.IsSerializable; * @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it * Jan 10, 2017 */ -public class DataSourceCapability implements IsSerializable{ +public class DataSourceCapability implements IsSerializable, Serializable{ + /** + * + */ + private static final long serialVersionUID = 844266531985842984L; private ArrayList listFilters; private SpeciesCapability capability; diff --git a/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/DataSourceModel.java b/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/DataSourceModel.java index d39b7df..05b84d6 100644 --- a/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/DataSourceModel.java +++ b/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/DataSourceModel.java @@ -1,7 +1,10 @@ package org.gcube.portlets.user.speciesdiscovery.shared; +import java.io.Serializable; import java.util.ArrayList; +import com.google.gwt.user.client.rpc.IsSerializable; + /** * The Class DataSourceModel. @@ -9,8 +12,12 @@ import java.util.ArrayList; * @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it * Jan 10, 2017 */ -public class DataSourceModel extends DataSource { +public class DataSourceModel extends DataSource implements IsSerializable, Serializable{ + /** + * + */ + private static final long serialVersionUID = -8314335099130160226L; private ArrayList listCapabilities; private DataSourceRepositoryInfo dataSourceRepositoryInfo; diff --git a/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/DataSourceRepositoryInfo.java b/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/DataSourceRepositoryInfo.java index 7ac4d25..dae9191 100644 --- a/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/DataSourceRepositoryInfo.java +++ b/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/DataSourceRepositoryInfo.java @@ -1,5 +1,6 @@ package org.gcube.portlets.user.speciesdiscovery.shared; +import java.io.Serializable; import java.util.Map; import com.google.gwt.user.client.rpc.IsSerializable; @@ -11,8 +12,12 @@ import com.google.gwt.user.client.rpc.IsSerializable; * @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it * Jan 10, 2017 */ -public class DataSourceRepositoryInfo implements IsSerializable{ +public class DataSourceRepositoryInfo implements IsSerializable, Serializable{ + /** + * + */ + private static final long serialVersionUID = -2778021508260771963L; private String logoUrl; private String pageUrl; private Map properties; diff --git a/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/DownloadState.java b/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/DownloadState.java index 2546e4d..ba3924e 100644 --- a/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/DownloadState.java +++ b/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/DownloadState.java @@ -2,13 +2,15 @@ package org.gcube.portlets.user.speciesdiscovery.shared; import java.io.Serializable; -public enum DownloadState implements Serializable { - PENDING, - ONGOING, - ONGOINGWITHFAILURES, - FAILED, - COMPLETED, - COMPLETEDWITHFAILURES, +import com.google.gwt.user.client.rpc.IsSerializable; + +public enum DownloadState implements IsSerializable, Serializable { + PENDING, + ONGOING, + ONGOINGWITHFAILURES, + FAILED, + COMPLETED, + COMPLETEDWITHFAILURES, SAVING, SAVED, SERVICE_UNKNOWN diff --git a/src/test/java/log4j/log4j.properties b/src/test/java/log4j/log4j.properties new file mode 100644 index 0000000..7983f47 --- /dev/null +++ b/src/test/java/log4j/log4j.properties @@ -0,0 +1,33 @@ +# Set root category priority to WARN and its only appender to A1. +log4j.rootCategory=ERROR, A1 + +log4j.appender.A1=org.apache.log4j.ConsoleAppender + + +# A1 uses PatternLayout. +log4j.appender.A1.layout=org.apache.log4j.PatternLayout +log4j.appender.A1.layout.ConversionPattern=%d{ISO8601} %-5p %c{2} [%t,%M:%L] %m%n + + +# Display any warnings generated by our code +#log4j.category.org.gcube=trace +#log4j.category.org.globus=trace +#log4j.category.isclient=INFO +#log4j.category.org.gcube.common.homelibrary.jcr=TRACE + + +log4j.category.org.gcube.portlets.user.workspace=TRACE + + + +log4j.logger.org.gcube=TRACE +log4j.logger.org.gcube.application.framework.core.session=INFO +log4j.logger.org.gcube.contentmanager=ERROR +log4j.logger.org.gcube.common.scope=ERROR +log4j.logger.org.gcube.contentmanagement=ERROR +log4j.logger.org.gcube.resources.discovery.icclient=ERROR +log4j.logger.org.gcube.common.clients=ERROR +#log4j.logger.org.gcube.common.homelibrary.jcr=TRACE +log4j.logger.org.gcube.application.framework.accesslogger=ERROR +log4j.logger.org.apache.pdfbox.util.PDFStreamEngine=ERROR +