From d7322712d0c68858800e96ec5bdb38e344a3cf5c Mon Sep 17 00:00:00 2001
From: Manuel Spuhler <manuel.spuhler@chuv.ch>
Date: Wed, 30 Oct 2019 14:18:46 +0100
Subject: [PATCH] Cleanup
---
docker/README.md | 4 ---
docker/config/application.tmpl | 6 ----
pom.xml | 7 +---
.../PersistenceConfiguration.java | 16 ---------
.../eu/hbp/mip/controllers/ExperimentApi.java | 4 ---
.../eu/hbp/mip/controllers/ModelsApi.java | 5 ---
.../java/eu/hbp/mip/model/Experiment.java | 10 ------
.../java/eu/hbp/mip/model/MiningQuery.java | 8 -----
.../java/eu/hbp/mip/utils/TypesConvert.java | 34 -------------------
9 files changed, 1 insertion(+), 93 deletions(-)
delete mode 100644 src/main/java/eu/hbp/mip/utils/TypesConvert.java
diff --git a/docker/README.md b/docker/README.md
index 6bf2610ac..faedc351e 100644
--- a/docker/README.md
+++ b/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"
diff --git a/docker/config/application.tmpl b/docker/config/application.tmpl
index 10be575a2..3321fea84 100644
--- a/docker/config/application.tmpl
+++ b/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:
diff --git a/pom.xml b/pom.xml
index 2eb3508d2..f887da821 100644
--- a/pom.xml
+++ b/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>
diff --git a/src/main/java/eu/hbp/mip/configuration/PersistenceConfiguration.java b/src/main/java/eu/hbp/mip/configuration/PersistenceConfiguration.java
index 20b6fb7dc..5c03ec4eb 100644
--- a/src/main/java/eu/hbp/mip/configuration/PersistenceConfiguration.java
+++ b/src/main/java/eu/hbp/mip/configuration/PersistenceConfiguration.java
@@ -1,15 +1,11 @@
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")
diff --git a/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java b/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
index 40a2f064f..40d12eab8 100644
--- a/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
@@ -1,6 +1,5 @@
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;
diff --git a/src/main/java/eu/hbp/mip/controllers/ModelsApi.java b/src/main/java/eu/hbp/mip/controllers/ModelsApi.java
index f01076181..56bc1ce10 100644
--- a/src/main/java/eu/hbp/mip/controllers/ModelsApi.java
+++ b/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.*;
diff --git a/src/main/java/eu/hbp/mip/model/Experiment.java b/src/main/java/eu/hbp/mip/model/Experiment.java
index 7149063be..a15b575c9 100644
--- a/src/main/java/eu/hbp/mip/model/Experiment.java
+++ b/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.*;
/**
diff --git a/src/main/java/eu/hbp/mip/model/MiningQuery.java b/src/main/java/eu/hbp/mip/model/MiningQuery.java
index cf33a4ecb..6ced26503 100644
--- a/src/main/java/eu/hbp/mip/model/MiningQuery.java
+++ b/src/main/java/eu/hbp/mip/model/MiningQuery.java
@@ -1,14 +1,6 @@
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;
diff --git a/src/main/java/eu/hbp/mip/utils/TypesConvert.java b/src/main/java/eu/hbp/mip/utils/TypesConvert.java
deleted file mode 100644
index 2e473997b..000000000
--- a/src/main/java/eu/hbp/mip/utils/TypesConvert.java
+++ /dev/null
@@ -1,34 +0,0 @@
-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();
- }
-
-}
--
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