Update woken-messages to 2.4.2

pom.xml

@@ -47,7 +47,7 @@
         <spring-data-jpa.version>1.10.11.RELEASE</spring-data-jpa.version>
         <spring-boot-starter-actuator.version>1.4.7.RELEASE</spring-boot-starter-actuator.version>
         <aspectjweaver.version>1.8.9</aspectjweaver.version>
-        <woken-messages.version>2.3.1</woken-messages.version>
+        <woken-messages.version>2.4.2</woken-messages.version>
         <javax-inject.version>1</javax-inject.version>
         <akka.version>2.5.9</akka.version>
         <spring-context.version>4.3.4.RELEASE</spring-context.version>
@@ -192,7 +192,7 @@
             <version>${aspectjweaver.version}</version>
         </dependency>
         <dependency>
-            <groupId>eu.humanbrainproject.mip</groupId>
+            <groupId>ch.chuv.lren.woken</groupId>
             <artifactId>woken-messages_2.11</artifactId>
             <version>${woken-messages.version}</version>
         </dependency>

src/main/java/eu/hbp/mip/akka/ExperimentActor.java

 package eu.hbp.mip.akka;
 
 import akka.actor.AbstractActor;
-import eu.hbp.mip.woken.messages.query.QueryResult;
+import ch.chuv.lren.woken.messages.query.QueryResult;
 import eu.hbp.mip.model.Experiment;
 import eu.hbp.mip.repositories.ExperimentRepository;
 import org.slf4j.Logger;

src/main/java/eu/hbp/mip/akka/WokenClientController.java

@@ -8,8 +8,8 @@ import akka.cluster.client.ClusterClient;
 import akka.cluster.client.ClusterClientSettings;
 import akka.pattern.Patterns;
 import akka.util.Timeout;
-import eu.hbp.mip.woken.messages.query.Query;
-import eu.hbp.mip.woken.messages.query.QueryResult;
+import ch.chuv.lren.woken.messages.query.Query;
+import ch.chuv.lren.woken.messages.query.QueryResult;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;

src/main/java/eu/hbp/mip/controllers/ExperimentApi.java

@@ -13,7 +13,7 @@ import eu.hbp.mip.repositories.ExperimentRepository;
 import eu.hbp.mip.repositories.ModelRepository;
 import eu.hbp.mip.utils.HTTPUtil;
 import eu.hbp.mip.utils.JSONUtil;
-import eu.hbp.mip.woken.messages.query.QueryResult;
+import ch.chuv.lren.woken.messages.query.QueryResult;
 import io.swagger.annotations.Api;
 import io.swagger.annotations.ApiOperation;
 import io.swagger.annotations.ApiParam;
@@ -258,7 +258,7 @@ public class ExperimentApi extends WokenClientController {
         User user = securityConfiguration.getUser();
 
         // this runs in the background. For future optimization: use a thread pool
-        final eu.hbp.mip.woken.messages.query.ExperimentQuery experimentQuery = experiment.prepareQuery(user.getUsername());
+        final ch.chuv.lren.woken.messages.query.ExperimentQuery experimentQuery = experiment.prepareQuery(user.getUsername());
         final ExecutionContext ec = getExecutor();
 
         Future<Object> response = sendWokenQuery(experimentQuery, 24*3600);

src/main/java/eu/hbp/mip/controllers/MethodsApi.java

@@ -4,8 +4,8 @@ import com.google.gson.Gson;
 import com.google.gson.JsonObject;
 import com.google.gson.JsonParser;
 import eu.hbp.mip.akka.WokenClientController;
-import eu.hbp.mip.woken.messages.query.MethodsQuery$;
-import eu.hbp.mip.woken.messages.query.MethodsResponse;
+import ch.chuv.lren.woken.messages.query.MethodsQuery$;
+import ch.chuv.lren.woken.messages.query.MethodsResponse;
 import io.swagger.annotations.Api;
 import io.swagger.annotations.ApiOperation;
 import org.slf4j.Logger;

src/main/java/eu/hbp/mip/model/Experiment.java

@@ -7,16 +7,15 @@ import com.google.gson.JsonObject;
 import com.google.gson.JsonParser;
 import com.google.gson.annotations.Expose;
 import com.google.gson.reflect.TypeToken;
-import eu.hbp.mip.woken.messages.datasets.DatasetId;
-import eu.hbp.mip.woken.messages.query.ExperimentQuery;
-import eu.hbp.mip.woken.messages.query.*;
+import ch.chuv.lren.woken.messages.datasets.DatasetId;
+import ch.chuv.lren.woken.messages.query.ExperimentQuery;
+import ch.chuv.lren.woken.messages.query.*;
 import eu.hbp.mip.utils.TypesConvert;
-import eu.hbp.mip.woken.messages.query.filters.FilterRule;
-import eu.hbp.mip.woken.messages.variables.FeatureIdentifier;
+import ch.chuv.lren.woken.messages.query.filters.FilterRule;
+import ch.chuv.lren.woken.messages.variables.FeatureIdentifier;
 import org.hibernate.annotations.Cascade;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-import scala.None$;
 import scala.Option;
 import scala.collection.JavaConversions;
 
@@ -98,7 +97,7 @@ public class Experiment {
 
     public ExperimentQuery prepareQuery(String user) {
         if (model == null || model.getQuery() == null)
-            return new ExperimentQuery(null, null, null, null, null, null, null, null, null, null, null);
+            return new ExperimentQuery(null, null, null, null, null, Option.empty(), null, null, null, null, null, null);
 
         List<AlgorithmSpec> algorithms = new LinkedList<>();
         Type algoList = new TypeToken<LinkedList<eu.hbp.mip.model.Algorithm>>(){}.getType();
@@ -132,9 +131,9 @@ public class Experiment {
         Option<FilterRule> filters = conv.toFilterRule(filtersJson);
         UserId userId = new UserId(user);
 
-        return new ExperimentQuery(userId, variablesSeq, covariablesSeq, groupingSeq, filters,
+        return new ExperimentQuery(userId, variablesSeq, covariablesSeq, groupingSeq, filters, Option.empty(),
                 trainingDatasets, testingDatasets, algorithmsSeq, validationDatasets,
-                validationsSeq, None$.empty());
+                validationsSeq, Option.empty());
     }
 
 

src/main/java/eu/hbp/mip/model/MiningQuery.java

@@ -3,11 +3,11 @@ package eu.hbp.mip.model;
 import ch.chuv.lren.mip.portal.WokenConversions;
 import com.google.gson.Gson;
 import eu.hbp.mip.utils.TypesConvert;
-import eu.hbp.mip.woken.messages.datasets.DatasetId;
-import eu.hbp.mip.woken.messages.query.ExecutionPlan;
-import eu.hbp.mip.woken.messages.query.UserId;
-import eu.hbp.mip.woken.messages.query.filters.FilterRule;
-import eu.hbp.mip.woken.messages.variables.FeatureIdentifier;
+import ch.chuv.lren.woken.messages.datasets.DatasetId;
+import ch.chuv.lren.woken.messages.query.ExecutionPlan;
+import ch.chuv.lren.woken.messages.query.UserId;
+import ch.chuv.lren.woken.messages.query.filters.FilterRule;
+import ch.chuv.lren.woken.messages.variables.FeatureIdentifier;
 import scala.Option;
 
 import java.util.LinkedList;
@@ -87,9 +87,9 @@ public class MiningQuery {
         this.algorithm = algorithm;
     }
 
-    public eu.hbp.mip.woken.messages.query.MiningQuery prepareQuery(String user) {
+    public ch.chuv.lren.woken.messages.query.MiningQuery prepareQuery(String user) {
 
-        eu.hbp.mip.woken.messages.query.AlgorithmSpec scalaAlgorithm = new eu.hbp.mip.woken.messages.query.AlgorithmSpec(
+        ch.chuv.lren.woken.messages.query.AlgorithmSpec scalaAlgorithm = new ch.chuv.lren.woken.messages.query.AlgorithmSpec(
                 algorithm.getCode(), TypesConvert.algoParamsToScala(algorithm.getParameters()));
 
         scala.collection.immutable.List<FeatureIdentifier> variablesSeq =
@@ -105,8 +105,8 @@ public class MiningQuery {
         String filtersJson = getFilters();
         Option<FilterRule> filters = conv.toFilterRule(filtersJson);
 
-        return new eu.hbp.mip.woken.messages.query.MiningQuery(userId,
-                variablesSeq, covariablesSeq, groupingSeq, filters, datasets, scalaAlgorithm, Option.<ExecutionPlan>empty());
+        return new ch.chuv.lren.woken.messages.query.MiningQuery(userId,
+                variablesSeq, covariablesSeq, groupingSeq, filters, Option.empty(), datasets, scalaAlgorithm, Option.empty());
     }
 
     @Override

src/main/java/eu/hbp/mip/utils/TypesConvert.java

 package eu.hbp.mip.utils;
 
-import eu.hbp.mip.woken.messages.query.CodeValue;
-import eu.hbp.mip.woken.messages.variables.FeatureIdentifier;
-import eu.hbp.mip.woken.messages.variables.VariableId;
+import ch.chuv.lren.woken.messages.query.CodeValue;
+import ch.chuv.lren.woken.messages.variables.FeatureIdentifier;
+import ch.chuv.lren.woken.messages.variables.VariableId;
 import eu.hbp.mip.model.AlgorithmParam;
 import eu.hbp.mip.model.Variable;
 import scala.collection.JavaConversions;

src/main/resources/application.conf

@@ -15,11 +15,11 @@ akka {
     }
 
     serializers {
-      query-result-serializer = "eu.hbp.mip.woken.messages.query.QueryResultSerializer"
+      query-result-serializer = "ch.chuv.lren.woken.messages.query.QueryResultSerializer"
     }
 
     serialization-bindings {
-      "eu.hbp.mip.woken.messages.query.QueryResult" = query-result-serializer
+      "ch.chuv.lren.woken.messages.query.QueryResult" = query-result-serializer
     }
     enable-additional-serialization-bindings = off
     allow-java-serialization = on

src/main/scala/ch.chuv.lren/mip/portal/WokenConversions.scala

 package ch.chuv.lren.mip.portal
 
 import eu.hbp.mip.model.Variable
-import eu.hbp.mip.woken.messages.datasets.DatasetId
-import eu.hbp.mip.woken.messages.query.filters.FilterRule
-import eu.hbp.mip.woken.messages.query.filters.queryFiltersProtocol._
+import ch.chuv.lren.woken.messages.datasets.DatasetId
+import ch.chuv.lren.woken.messages.query.filters.FilterRule
+import ch.chuv.lren.woken.messages.query.filters.queryFiltersProtocol._
 import org.springframework.stereotype.Component
 import spray.json._