Cleanup

docker/README.md

@@ -52,10 +52,6 @@ To use this image, you need a running instance of PostgreSQL and to configure th
 
 ### ENDPOINTS
 
-* WOKEN_PORT_8088_TCP_ADDR: default value is "woken".
-* WOKEN_PORT_8088_TCP_PORT default value is "8088".
-* WOKEN_AKKA_PATH default value is "/user/entrypoint".
-
 * EXAREME_URL: URL to Exareme server, default value is "http://hbps2.chuv.ch:9090".
 * WORKFLOW_URL: URL to Workflow server
 * JWT_SECRET: "secret"

docker/config/application.tmpl

@@ -8,12 +8,6 @@ spring:
     username: {{ default .Env.PORTAL_DB_USER "postgres" }}
     password: {{ .Env.PORTAL_DB_PASSWORD }}
     driver-class-name: org.postgresql.Driver
-  metaDatasource:
-    url: {{ default .Env.META_DB_URL "jdbc:postgresql://172.22.0.1:5432/meta" }}
-    schema: {{ default .Env.META_DB_SCHEMA "public" }}
-    username: {{ default .Env.META_DB_USER "postgres" }}
-    password: {{ .Env.META_DB_PASSWORD }}
-    driver-class-name: org.postgresql.Driver
 
   data:
     jpa:

pom.xml

@@ -47,7 +47,6 @@
         <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>3.0.14</woken-messages.version>
         <javax-inject.version>1</javax-inject.version>
         <akka.version>2.5.22</akka.version>
         <spring-context.version>4.3.4.RELEASE</spring-context.version>
@@ -225,11 +224,7 @@
             <artifactId>aspectjweaver</artifactId>
             <version>${aspectjweaver.version}</version>
         </dependency>
-        <dependency>
-            <groupId>ch.chuv.lren.woken</groupId>
-            <artifactId>woken-messages_2.11</artifactId>
-            <version>${woken-messages.version}</version>
-        </dependency>
+        
         <dependency>
             <groupId>javax.inject</groupId>
             <artifactId>javax.inject</artifactId>

src/main/java/eu/hbp/mip/configuration/PersistenceConfiguration.java

 package eu.hbp.mip.configuration;
 
 import org.flywaydb.core.Flyway;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.beans.factory.annotation.Qualifier;
-import org.springframework.beans.factory.annotation.Value;
 import org.springframework.boot.autoconfigure.jdbc.DataSourceBuilder;
 import org.springframework.boot.context.properties.ConfigurationProperties;
 import org.springframework.boot.orm.jpa.EntityScan;
 import org.springframework.context.annotation.*;
 import org.springframework.data.jpa.repository.config.EnableJpaRepositories;
-import org.springframework.jdbc.core.JdbcTemplate;
 import org.springframework.orm.jpa.JpaVendorAdapter;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
 import org.springframework.orm.jpa.vendor.HibernateJpaVendorAdapter;
@@ -32,18 +28,6 @@ public class PersistenceConfiguration {
         return DataSourceBuilder.create().build();
     }
 
-    @Bean(name = "metaDatasource")
-    @ConfigurationProperties(prefix="spring.metaDatasource")
-    public DataSource metaDataSource() {
-        return DataSourceBuilder.create().build();
-    }
-
-    @Bean
-    @Autowired
-    @Qualifier("metaJdbcTemplate")
-    public JdbcTemplate metaJdbcTemplate() {
-        return new JdbcTemplate(metaDataSource());
-    }
 
     @Bean(name = "entityManagerFactory")
     @DependsOn("flyway")

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

 package eu.hbp.mip.controllers;
 
-import akka.dispatch.OnSuccess;
 import com.google.gson.*;
 import com.google.common.collect.Lists;
 import com.google.gson.Gson;
@@ -10,7 +9,6 @@ import eu.hbp.mip.model.*;
 import eu.hbp.mip.repositories.ExperimentRepository;
 import eu.hbp.mip.repositories.ModelRepository;
 import eu.hbp.mip.utils.HTTPUtil;
-import ch.chuv.lren.woken.messages.query.QueryResult;
 import io.swagger.annotations.Api;
 import io.swagger.annotations.ApiOperation;
 import io.swagger.annotations.ApiParam;
@@ -21,8 +19,6 @@ import org.springframework.beans.factory.annotation.Value;
 import org.springframework.http.HttpStatus;
 import org.springframework.http.ResponseEntity;
 import org.springframework.web.bind.annotation.*;
-import scala.concurrent.ExecutionContext;
-import scala.concurrent.Future;
 import eu.hbp.mip.utils.JWTUtil;
 
 import java.io.IOException;

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

@@ -4,10 +4,7 @@
 
 package eu.hbp.mip.controllers;
 
-import ch.chuv.lren.woken.messages.query.filters.FilterRule;
 import com.github.slugify.Slugify;
-import com.google.gson.Gson;
-import com.google.gson.JsonObject;
 import eu.hbp.mip.model.Model;
 import eu.hbp.mip.model.User;
 import eu.hbp.mip.model.UserInfo;
@@ -17,11 +14,9 @@ import io.swagger.annotations.*;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.beans.factory.annotation.Qualifier;
 import org.springframework.http.HttpStatus;
 import org.springframework.http.ResponseEntity;
 import org.springframework.web.bind.annotation.*;
-import scala.Option;
 
 import java.io.IOException;
 import java.util.*;

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

@@ -2,21 +2,11 @@ package eu.hbp.mip.model;
 
 import com.google.gson.*;
 import com.google.gson.annotations.Expose;
-import com.google.gson.reflect.TypeToken;
-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 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.Option;
-import scala.collection.JavaConversions;
 
 import javax.persistence.*;
-import java.lang.reflect.Type;
 import java.util.*;
 
 /**

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

 package eu.hbp.mip.model;
 
 import com.google.gson.Gson;
-import eu.hbp.mip.utils.TypesConvert;
-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;
 import java.util.List;
 

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

-package eu.hbp.mip.utils;
-
-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;
-
-import java.util.LinkedList;
-import java.util.List;
-import java.util.stream.Collectors;
-
-/**
- * Created by mirco on 06.01.17.
- */
-public class TypesConvert {
-
-    public static scala.collection.immutable.List<FeatureIdentifier> variablesToIdentifiers(List<Variable> vars) {
-        List<FeatureIdentifier> varIds = new LinkedList<>();
-        for (Variable v: vars) {
-            if (!v.getCode().isEmpty()) {
-                varIds.add(new VariableId(v.getCode()));
-            }
-        }
-        return JavaConversions.asScalaBuffer(varIds).toList();
-    }
-
-    public static scala.collection.immutable.List<CodeValue> algoParamsToScala(List<AlgorithmParam> aps) {
-        List<CodeValue> cvs = aps.stream().map(p -> new CodeValue(p.getCode(), p.getValue())).collect(Collectors.toList());
-        return JavaConversions.asScalaBuffer(cvs).toList();
-    }
-
-}