removed ScopeProvider.set everywhere
fixed occurrencescall git-svn-id: http://svn.research-infrastructures.eu/public/d4science/gcube/trunk/portlets/user/speciesdiscovery@141544 82a268e6-3cf1-43bd-a215-b396298e98cf
This commit is contained in:
parent
f82797b6f1
commit
2b71b38a8b
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@ -1,20 +1,21 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<classpath>
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<classpathentry kind="lib" path="/home/francesco-mangiacrapa/libraries/asm-5.0.3/lib/asm-5.0.3.jar"/>
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<classpathentry kind="src" output="target/species-discovery-3.8.2-SNAPSHOT/WEB-INF/classes" path="src/main/java">
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<classpathentry kind="src" output="target/species-discovery-3.9.0-SNAPSHOT/WEB-INF/classes" path="src/main/java">
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<attributes>
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<attribute name="optional" value="true"/>
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<attribute name="maven.pomderived" value="true"/>
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</attributes>
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</classpathentry>
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<classpathentry including="**/*.java" kind="src" output="src/main/webapp/WEB-INF/classes" path="src/main/resources"/>
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<classpathentry kind="src" output="target/test-classes" path="src/test/java">
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<classpathentry excluding="log4j/" kind="src" output="target/test-classes" path="src/test/java">
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<attributes>
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<attribute name="optional" value="true"/>
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<attribute name="maven.pomderived" value="true"/>
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</attributes>
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</classpathentry>
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<classpathentry including="**/*.java" kind="src" output="target/test-classes" path="src/test/resources"/>
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<classpathentry including="*.properties" kind="src" path="src/test/java/log4j"/>
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<classpathentry kind="con" path="org.maven.ide.eclipse.MAVEN2_CLASSPATH_CONTAINER">
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<attributes>
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<attribute name="org.eclipse.jst.component.dependency" value="/WEB-INF/lib"/>
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@ -31,5 +32,5 @@
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<attribute name="org.eclipse.jst.component.dependency" value="/WEB-INF/lib"/>
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</attributes>
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</classpathentry>
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<classpathentry kind="output" path="target/species-discovery-3.8.2-SNAPSHOT/WEB-INF/classes"/>
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<classpathentry kind="output" path="target/species-discovery-3.9.0-SNAPSHOT/WEB-INF/classes"/>
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</classpath>
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@ -3,6 +3,8 @@
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<wb-resource deploy-path="/" source-path="/target/m2e-wtp/web-resources"/>
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<wb-resource deploy-path="/" source-path="/src/main/webapp" tag="defaultRootSource"/>
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<wb-resource deploy-path="/WEB-INF/classes" source-path="/src/main/java"/>
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<wb-resource deploy-path="/WEB-INF/classes" source-path="/src/test/java"/>
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<wb-resource deploy-path="/WEB-INF/classes" source-path="/src/test/java/log4j"/>
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<property name="java-output-path" value="/${module}/target/www/WEB-INF/classes"/>
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<property name="context-root" value="species-discovery"/>
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</wb-module>
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@ -41,19 +41,8 @@ import org.gcube.portlets.user.speciesdiscovery.shared.TaxonomyRow;
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*/
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public class TaxonomyRowTable extends HttpServlet {
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/**
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*
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*/
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protected static final String UTF_8 = "UTF-8";
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/**
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*
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*/
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private static final long serialVersionUID = 9157876104914505028L;
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/**
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*
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*/
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public static final String TEXT_HTML = "text/html; charset=UTF-8";
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public static final String DOCTYPE = "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\">";
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@ -68,8 +68,7 @@ public class SessionUtil {
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SpeciesService service = (SpeciesService) session.getAttribute(SPECIES_SERVICE);
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if (service==null) {
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logger.trace("Service not found, creating it");
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String scope = session.getScope();
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service = new SpeciesService(scope, session);
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service = new SpeciesService();
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session.setAttribute(SPECIES_SERVICE, service);
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}
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@ -137,7 +137,6 @@ public class DaoSession {
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Map<String,String> properties = new HashMap<String, String>();
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// properties.put("javax.persistence.jdbc.driver", jdbcDriverH2);
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try{
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properties.put("javax.persistence.jdbc.url", getConnectionUrl(session));
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}
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@ -18,8 +18,6 @@ import java.util.Map.Entry;
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import java.util.concurrent.TimeUnit;
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import org.apache.log4j.Logger;
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import org.gcube.application.framework.core.session.ASLSession;
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import org.gcube.common.scope.api.ScopeProvider;
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import org.gcube.data.spd.client.proxies.ClassificationClient;
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import org.gcube.data.spd.client.proxies.ExecutorClient;
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import org.gcube.data.spd.client.proxies.ManagerClient;
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@ -59,59 +57,24 @@ public class SpeciesService {
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protected Logger logger = Logger.getLogger(SpeciesService.class);
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protected String scope;
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protected ASLSession session;
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protected ManagerClient call;
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protected OccurrenceClient occurrencesCall;
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protected ClassificationClient classificationCall;
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protected ExecutorClient executorCall;
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protected String lastQuery = "";
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/**
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* Instantiates a new species service.
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*
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* @param scope
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* the scope
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* @param session
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* the session
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* @throws Exception
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* the exception
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*/
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public SpeciesService(String scope, ASLSession session)
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throws Exception {
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this(scope);
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this.session = session;
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}
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/**
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* Instantiates a new species service.
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*
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* @param scope
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* the scope
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* @throws Exception
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* the exception
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* @throws Exception the exception
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*/
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public SpeciesService(String scope)
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throws Exception {
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this.scope = scope;
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ScopeProvider.instance.set(scope);
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// this.call = manager().at(
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// URI.create("http://node24.d.d4science.research-infrastructures.eu:9000")).withTimeout(3,
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// TimeUnit.MINUTES).build();
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// this.occurrencesCall = occurrences().at(
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// URI.create("http://node24.d.d4science.research-infrastructures.eu:9000")).withTimeout(3,
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// TimeUnit.MINUTES).build();
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// this.classificationCall = classification().at(
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// URI.create("http://node24.d.d4science.research-infrastructures.eu:9000")).withTimeout(3,
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// TimeUnit.MINUTES).build();
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public SpeciesService() throws Exception {
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System.out.println("CALLING MANAGER ");
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this.call = manager().withTimeout(3, TimeUnit.MINUTES).build();
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this.executorCall = executor().withTimeout(3, TimeUnit.MINUTES).build();
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OccurrenceClient a =
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occurrences().withTimeout(3, TimeUnit.MINUTES).build();
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this.classificationCall =
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classification().withTimeout(3, TimeUnit.MINUTES).build();
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this.occurrencesCall = occurrences().withTimeout(3, TimeUnit.MINUTES).build();
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this.classificationCall = classification().withTimeout(3, TimeUnit.MINUTES).build();
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}
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/**
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@ -129,7 +92,6 @@ public class SpeciesService {
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this.scope = scope;
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if (instanceOnlyOccurrence) {
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ScopeProvider.instance.set(scope);
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System.out.println("CALLING OCCURRENCE MANAGER ");
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this.occurrencesCall = occurrences().withTimeout(3, TimeUnit.MINUTES).build();
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}
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@ -185,7 +147,6 @@ public class SpeciesService {
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logger.trace("retrieveTaxonomyById...");
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try {
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ScopeProvider.instance.set(scope);
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Stream<TaxonomyItem> stream = classificationCall.getTaxaByIds(ids);
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return new StreamIterator<TaxonomyItem>(stream);
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}
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@ -211,7 +172,6 @@ public class SpeciesService {
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logger.trace("retrieveSynonymsById...");
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try {
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ScopeProvider.instance.set(scope);
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Stream<TaxonomyItem> stream =
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classificationCall.getSynonymsById(id);
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return new StreamIterator<TaxonomyItem>(stream);
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@ -239,9 +199,7 @@ public class SpeciesService {
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logger.trace("search by Query - query is: " + query);
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// System.out.println("searchByQuery query: "+query);
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try {
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ScopeProvider.instance.set(scope);
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lastQuery = query;
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// System.err.println("ScopeProvider SCOPE "+ScopeProvider.instance.get());
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logger.trace("call species service search...");
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// System.out.println("call species service search...");
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Stream<ResultElement> stream = call.search(query);
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@ -286,10 +244,7 @@ public class SpeciesService {
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throws SearchServiceException {
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logger.trace("searchByQuery query: " + query);
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// System.out.println("searchByQuery query: "+query);
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try {
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ScopeProvider.instance.set(scope);
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// System.err.println("ScopeProvider SCOPE "+ScopeProvider.instance.get());
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logger.trace("call species service search...");
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System.out.println("call species service search...");
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return call.search(query);
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@ -316,7 +271,6 @@ public class SpeciesService {
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try {
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List<DataSourceModel> listDsModel =
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new ArrayList<DataSourceModel>();
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ScopeProvider.instance.set(scope);
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System.out.println("setting scope " + scope);
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List<PluginDescription> plugin = call.getPluginsDescription();
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if (plugin != null) {
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@ -475,9 +429,6 @@ public class SpeciesService {
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throws SearchServiceException {
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try {
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// Stream<String> keysStream = convert(keys);
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ScopeProvider.instance.set(scope);
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logger.trace("Instancing scope: "+scope);
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logger.trace("Calling occurrencesCall passing keys: "+keys);
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logger.trace("occurrencesCall != null? "+(occurrencesCall==null));
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Stream<OccurrencePoint> stream = occurrencesCall.getByKeys(keys);
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@ -504,7 +455,6 @@ public class SpeciesService {
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try {
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// Stream<String> idsStream = convert(ids);
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ScopeProvider.instance.set(scope);
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Stream<OccurrencePoint> stream = occurrencesCall.getByIds(ids);
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return new StreamIterator<OccurrencePoint>(stream);
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}
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@ -530,7 +480,6 @@ public class SpeciesService {
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try {
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// Stream<String> keysStream = convert(keys);
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ScopeProvider.instance.set(scope);
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return occurrencesCall.createLayer(streamKey);
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}
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catch (Exception e) {
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@ -555,7 +504,6 @@ public class SpeciesService {
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throws Exception {
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try {
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ScopeProvider.instance.set(scope);
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Stream<TaxonomyItem> items =
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classificationCall.getTaxonChildrenById(parentId);
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return new StreamIterator<TaxonomyItem>(items);
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@ -578,7 +526,6 @@ public class SpeciesService {
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*/
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public CompleteJobStatus getTaxonomyJobById(String jobId) {
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ScopeProvider.instance.set(scope);
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CompleteJobStatus status = null;
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try {
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status = this.executorCall.getStatus(jobId);
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@ -609,7 +556,6 @@ public class SpeciesService {
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throws Exception {
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InputStream is = null;
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ScopeProvider.instance.set(scope);
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try {
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String url = this.executorCall.getResultLink(jobIdentifier);
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if (url == null || url.isEmpty()) {
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@ -640,7 +586,6 @@ public class SpeciesService {
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throws Exception {
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InputStream is = null;
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ScopeProvider.instance.set(scope);
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try {
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String url = this.executorCall.getErrorLink(jobIdentifier);
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if (url == null || url.isEmpty()) {
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@ -670,7 +615,6 @@ public class SpeciesService {
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public boolean isAvailableTaxonomyJobErrorFileById(String jobIdentifier)
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throws Exception {
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ScopeProvider.instance.set(scope);
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try {
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String url = this.executorCall.getErrorLink(jobIdentifier);
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if (url == null || url.isEmpty()) {
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@ -700,7 +644,6 @@ public class SpeciesService {
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public String createTaxonomyJobForDWCAByChildren(String taxonomyId)
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throws Exception {
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ScopeProvider.instance.set(scope);
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try {
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return this.executorCall.createDwCAByChildren(taxonomyId);
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}
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@ -722,7 +665,6 @@ public class SpeciesService {
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public String createTaxonomyJobForDWCAByIds(List<String> ids)
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throws Exception {
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ScopeProvider.instance.set(scope);
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try {
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Stream<String> keysStream = convert(ids);
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return executorCall.createDwCAByIds(keysStream);
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@ -744,7 +686,6 @@ public class SpeciesService {
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public void cancelTaxonomyJobById(String jobIdentifier) {
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try {
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ScopeProvider.instance.set(scope);
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this.executorCall.removeJob(jobIdentifier);
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}
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catch (Exception e) {
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@ -763,7 +704,6 @@ public class SpeciesService {
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public CompleteJobStatus getOccurrenceJobById(String jobId) {
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try {
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ScopeProvider.instance.set(scope);
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return this.executorCall.getStatus(jobId); // CHANGE INTO OCCURRENCE
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// JOB
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// **************************************************************************************
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@ -793,7 +733,6 @@ public class SpeciesService {
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throws Exception {
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try {
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ScopeProvider.instance.set(scope);
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return this.executorCall.createCSV(streamKey);
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}
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catch (Exception e) {
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@ -817,7 +756,6 @@ public class SpeciesService {
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throws Exception {
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try {
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ScopeProvider.instance.set(scope);
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return this.executorCall.createDarwincoreFromOccurrenceKeys(streamKey);
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}
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catch (Exception e) {
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@ -841,7 +779,6 @@ public class SpeciesService {
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throws Exception {
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try {
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ScopeProvider.instance.set(scope);
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return this.executorCall.createCSVforOM(streamKey);
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}
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catch (Exception e) {
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@ -863,7 +800,6 @@ public class SpeciesService {
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public void cancelOccurrenceJobById(String jobIdentifier) {
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try {
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ScopeProvider.instance.set(scope);
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this.executorCall.removeJob(jobIdentifier); // CHANGE INTO
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// OCCURRENCE JOB
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// **************************************************************************************
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@ -888,7 +824,6 @@ public class SpeciesService {
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throws Exception {
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InputStream is = null;
|
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ScopeProvider.instance.set(scope);
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try {
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String url = this.executorCall.getResultLink(jobIdentifier); // CHANGE
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// INTO
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@ -925,7 +860,6 @@ public class SpeciesService {
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throws Exception {
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InputStream is = null;
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ScopeProvider.instance.set(scope);
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try {
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String url = this.executorCall.getErrorLink(jobIdentifier);
|
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logger.trace("URL returned by species service is: " + url);
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@ -955,7 +889,6 @@ public class SpeciesService {
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public boolean isAvailableOccurrenceJobErrorFileById(String jobIdentifier)
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throws Exception {
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||||
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||||
ScopeProvider.instance.set(scope);
|
||||
try {
|
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String url = this.executorCall.getErrorLink(jobIdentifier);
|
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if (url == null || url.isEmpty()) {
|
||||
|
|
|
@ -7,7 +7,6 @@ import org.apache.log4j.Logger;
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import org.gcube.application.framework.core.session.ASLSession;
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import org.gcube.common.homelibrary.home.HomeLibrary;
|
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import org.gcube.common.homelibrary.home.workspace.Workspace;
|
||||
import org.gcube.common.scope.api.ScopeProvider;
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||||
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||||
/**
|
||||
* @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
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||||
|
@ -27,16 +26,10 @@ public class GetWorkspaceUtil {
|
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throw new Exception("Scope into ASL session is null");
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||||
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||||
String scope = session.getScope().toString();
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||||
|
||||
logger.trace("Get workspace for scope "+scope);
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||||
|
||||
ScopeProvider.instance.set(scope);
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||||
|
||||
logger.trace("ScopeProvider instancied for scope "+scope);
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||||
|
||||
//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());
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||||
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||||
return HomeLibrary.getUserWorkspace(session.getUsername());
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||||
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||||
}
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||||
}
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|
|
|
@ -10,13 +10,15 @@ import javax.persistence.GeneratedValue;
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|||
import javax.persistence.GenerationType;
|
||||
import javax.persistence.Id;
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||||
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||||
import com.google.gwt.user.client.rpc.IsSerializable;
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||||
|
||||
/**
|
||||
*
|
||||
* @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
|
||||
*
|
||||
*/
|
||||
@Entity
|
||||
public class CommonName implements Serializable {
|
||||
public class CommonName implements IsSerializable, Serializable {
|
||||
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||||
/**
|
||||
*
|
||||
|
|
|
@ -5,11 +5,13 @@ package org.gcube.portlets.user.speciesdiscovery.shared;
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|||
|
||||
import java.io.Serializable;
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||||
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||||
import com.google.gwt.user.client.rpc.IsSerializable;
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||||
|
||||
/**
|
||||
* @author "Federico De Faveri defaveri@isti.cnr.it"
|
||||
*
|
||||
*/
|
||||
public class Coordinate implements Serializable {
|
||||
public class Coordinate implements IsSerializable, Serializable {
|
||||
|
||||
/**
|
||||
*
|
||||
|
|
|
@ -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)
|
||||
|
|
|
@ -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<SpeciesCapability> listFilters;
|
||||
private SpeciesCapability capability;
|
||||
|
||||
|
|
|
@ -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<DataSourceCapability> listCapabilities;
|
||||
private DataSourceRepositoryInfo dataSourceRepositoryInfo;
|
||||
|
||||
|
|
|
@ -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<String, String> properties;
|
||||
|
|
|
@ -2,7 +2,9 @@ package org.gcube.portlets.user.speciesdiscovery.shared;
|
|||
|
||||
import java.io.Serializable;
|
||||
|
||||
public enum DownloadState implements Serializable {
|
||||
import com.google.gwt.user.client.rpc.IsSerializable;
|
||||
|
||||
public enum DownloadState implements IsSerializable, Serializable {
|
||||
PENDING,
|
||||
ONGOING,
|
||||
ONGOINGWITHFAILURES,
|
||||
|
|
|
@ -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
|
||||
|
Reference in New Issue