Merge pull request #485 from OHDSI/merge_qa_1.8.0_to_master

Merge qa 1.8.0 to master
OHDSI · Aug 10, 2021 · a1bf389 · a1bf389
2 parents b7d357b + c5b7497
commit a1bf389
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Showing 28 changed files with 281 additions and 451 deletions.
diff --git a/pom.xml b/pom.xml
@@ -6,14 +6,14 @@
 
     <artifactId>datanode</artifactId>
     <groupId>com.odysseusinc.arachne</groupId>
-    <version>1.17.1</version>
+    <version>1.18.0</version>
     <packaging>jar</packaging>
 
 
     <parent>
         <groupId>org.springframework.boot</groupId>
         <artifactId>spring-boot-starter-parent</artifactId>
-        <version>1.5.22.RELEASE</version>
+        <version>2.1.18.RELEASE</version>
         <relativePath/>
     </parent>
 
@@ -27,31 +27,19 @@
         <java.version>1.8</java.version>
         <jjwt.version>0.10.8</jjwt.version>
         <postgresql.version>42.2.15</postgresql.version>
-        <flywayVersion>4.2.0</flywayVersion>
         <javaDockerVersion>3.2.7</javaDockerVersion>
         <springRetryVersion>1.2.4.RELEASE</springRetryVersion>
-        <hikaricp.version>2.6.3</hikaricp.version>
         <build.number>${BUILD_NUMBER}</build.number>
         <build.id>${BUILD_TIMESTAMP}</build.id>
         <dockerImagePrefix>hub.odysseusinc.com</dockerImagePrefix>
         <jackson.version>2.10.5.20201202</jackson.version>
         <!-- Overrides SpringBoot defaults to conform Hydra -->
         <json.version>20170516</json.version>
-        <feign.version>10.11</feign.version>
+        <feign.version>10.7.4</feign.version>
         <assertj.version>3.18.1</assertj.version>
         <bcprov-jdk15on.version>1.67</bcprov-jdk15on.version>
     </properties>
 
-    <dependencyManagement>
-        <dependencies>
-            <dependency>
-                <groupId>org.flywaydb</groupId>
-                <artifactId>flyway-core</artifactId>
-                <version>${flywayVersion}</version>
-            </dependency>
-        </dependencies>
-    </dependencyManagement>
-
     <dependencies>
         <dependency>
             <groupId>com.odysseusinc.arachne</groupId>
@@ -85,6 +73,11 @@
             <groupId>com.odysseusinc.arachne</groupId>
             <version>${project.version}</version>
         </dependency>
+        <dependency>
+            <groupId>javax.jms</groupId>
+            <artifactId>javax.jms-api</artifactId>
+            <version>2.0.1</version>
+        </dependency>
         <dependency>
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-starter-web</artifactId>
@@ -132,7 +125,6 @@
         <dependency>
             <groupId>org.flywaydb</groupId>
             <artifactId>flyway-core</artifactId>
-            <version>${flywayVersion}</version>
         </dependency>
         <dependency>
             <groupId>com.google.code.gson</groupId>
@@ -220,12 +212,6 @@
             <version>3.8.0</version>
         </dependency>
 
-        <dependency>
-            <groupId>com.zaxxer</groupId>
-            <artifactId>HikariCP</artifactId>
-            <version>${hikaricp.version}</version>
-        </dependency>
-
         <dependency>
             <groupId>org.ohdsi.sql</groupId>
             <artifactId>SqlRender</artifactId>
@@ -241,13 +227,6 @@
             <artifactId>hydra</artifactId>
             <version>0.0.11</version>
         </dependency>
-        <!--
-                <dependency>
-                    <groupId>org.json</groupId>
-                    <artifactId>json</artifactId>
-                    <version>20170516</version>
-                </dependency>
-        -->
         <dependency>
             <groupId>org.ohdsi</groupId>
             <artifactId>standardized-analysis-specs</artifactId>
@@ -277,12 +256,6 @@
             <version>${assertj.version}</version>
             <scope>test</scope>
         </dependency>
-        <dependency>
-            <groupId>org.hamcrest</groupId>
-            <artifactId>hamcrest</artifactId>
-            <version>2.1</version>
-            <scope>test</scope>
-        </dependency>
         <dependency>
             <groupId>org.testinfected.hamcrest-matchers</groupId>
             <artifactId>validation-matchers</artifactId>
@@ -411,6 +384,7 @@
                 <artifactId>spring-boot-maven-plugin</artifactId>
                 <executions>
                     <execution>
+                        <id>repackage</id>
                         <goals>
                             <goal>repackage</goal>
                         </goals>
@@ -447,7 +421,7 @@
             <plugin>
                 <groupId>com.spotify</groupId>
                 <artifactId>docker-maven-plugin</artifactId>
-                <version>0.4.13</version>
+                <version>1.2.2</version>
                 <configuration>
                     <imageName>${dockerImagePrefix}/${project.artifactId}</imageName>
                     <imageTags>
@@ -591,8 +565,8 @@
 
     <repositories>
         <repository>
-            <id>odysseus.community.snapshots</id>
-            <name>Odysseus community snapshots</name>
+            <id>community-libs-snapshot-local</id>
+            <name>community-libs-snapshot-local</name>
             <releases>
                 <enabled>false</enabled>
                 <updatePolicy>always</updatePolicy>
@@ -601,11 +575,11 @@
                 <enabled>true</enabled>
                 <updatePolicy>always</updatePolicy>
             </snapshots>
-            <url>http://repo.odysseusinc.com/artifactory/community-libs-snapshot-local</url>
+            <url>https://nexus.odysseusinc.com/repository/community-libs-snapshot-local</url>
         </repository>
         <repository>
-            <id>odysseus.community.releases</id>
-            <name>Odysseus community releases</name>
+            <id>community-libs-release-local</id>
+            <name>community-libs-release-local</name>
             <releases>
                 <enabled>true</enabled>
                 <updatePolicy>always</updatePolicy>
@@ -614,7 +588,7 @@
                 <enabled>false</enabled>
                 <updatePolicy>always</updatePolicy>
             </snapshots>
-            <url>http://repo.odysseusinc.com/artifactory/community-libs-release-local</url>
+            <url>https://nexus.odysseusinc.com/repository/community-libs-release-local</url>
         </repository>
         <repository>
             <id>ohdsi</id>
@@ -660,14 +634,14 @@
 
     <distributionManagement>
         <snapshotRepository>
-            <id>artifactory</id>
-            <name>Odysseus community snapshots</name>
-            <url>http://repo.odysseusinc.com/artifactory/community-libs-snapshot-local</url>
+            <id>community-libs-snapshot-local</id>
+            <name>community-libs-snapshot-local</name>
+            <url>https://nexus.odysseusinc.com/repository/community-libs-snapshot-local</url>
         </snapshotRepository>
         <repository>
-            <id>artifactory</id>
-            <name>Odysseus community releases</name>
-            <url>http://repo.odysseusinc.com/artifactory/community-libs-release-local</url>
+            <id>community-libs-release-local</id>
+            <name>community-libs-release-local</name>
+            <url>https://nexus.odysseusinc.com/repository/community-libs-release-local</url>
         </repository>
     </distributionManagement>
 

diff --git a/src/main/java/com/odysseusinc/arachne/datanode/WebApplicationStarter.java b/src/main/java/com/odysseusinc/arachne/datanode/WebApplicationStarter.java
@@ -23,6 +23,7 @@
 package com.odysseusinc.arachne.datanode;
 
 import com.fasterxml.jackson.databind.DeserializationFeature;
+import com.ulisesbocchio.jasyptspringboot.annotation.EnableEncryptableProperties;
 import org.springframework.boot.SpringApplication;
 import org.springframework.boot.autoconfigure.EnableAutoConfiguration;
 import org.springframework.boot.autoconfigure.domain.EntityScan;
@@ -37,13 +38,14 @@
 import org.springframework.security.core.context.SecurityContextHolder;
 
 @Configuration
-@ComponentScan(basePackages = {"com.odysseusinc.arachne.*", "org.ohdsi.authenticator.*"})
-@EnableAutoConfiguration
 @EnableAsync
 @EnableScheduling
 @EnableJpaRepositories(basePackages = {"com.odysseusinc.arachne.*"})
 @EntityScan(basePackages = {"com.odysseusinc.arachne.*"})
 @EnableAspectJAutoProxy
+@EnableEncryptableProperties
+@EnableAutoConfiguration
+@ComponentScan(basePackages = {"com.odysseusinc.arachne.*", "org.ohdsi.authenticator.*"})
 public class WebApplicationStarter {
 
     public static void main(String... argc) {

diff --git a/src/main/java/com/odysseusinc/arachne/datanode/config/DataSourceConfig.java b/src/main/java/com/odysseusinc/arachne/datanode/config/DataSourceConfig.java
@@ -1,6 +1,6 @@
 /*
  *
- * Copyright 2018 Odysseus Data Services, inc.
+ * Copyright 2021 Odysseus Data Services, inc.
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * You may obtain a copy of the License at
@@ -15,16 +15,14 @@
  *
  * Company: Odysseus Data Services, Inc.
  * Product Owner/Architecture: Gregory Klebanov
- * Authors: Pavel Grafkin, Alexandr Ryabokon, Vitaly Koulakov, Anton Gackovka, Maria Pozhidaeva, Mikhail Mironov
- * Created: June 26, 2017
+ * Authors: Alexandr Cumarav
+ * Created: April 10, 2021
  *
  */
-
 package com.odysseusinc.arachne.datanode.config;
 
 import com.zaxxer.hikari.HikariConfig;
 import com.zaxxer.hikari.HikariDataSource;
-import javax.sql.DataSource;
 import org.bouncycastle.jce.provider.BouncyCastleProvider;
 import org.jasypt.encryption.pbe.StandardPBEStringEncryptor;
 import org.jasypt.hibernate5.encryptor.HibernatePBEEncryptorRegistry;
@@ -36,6 +34,8 @@
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Primary;
 
+import javax.annotation.PostConstruct;
+import javax.sql.DataSource;
 
 @Configuration
 @ConfigurationProperties(prefix = "spring.datasource")
@@ -47,8 +47,8 @@ public class DataSourceConfig extends HikariConfig {
     private String driverClassName;
     @Value("${jasypt.encryptor.password}")
     private String password;
-    @Value("${jasypt.encryptor.database.algorithm}")
-    private String algorythm;
+    @Value("${jasypt.encryptor.algorithm}")
+    private String algorithm;
 
     @Primary
     @Bean
@@ -60,12 +60,13 @@ public DataSource primaryDataSource() {
         return new HikariDataSource(this);
     }
 
-    public PasswordEncryptor defaultStringEncryptor(){
+    @PostConstruct
+    public PasswordEncryptor defaultStringEncryptor() {
 
         StandardPBEStringEncryptor encryptor = new StandardPBEStringEncryptor();
         encryptor.setProvider(new BouncyCastleProvider());
         encryptor.setProviderName("BC");
-        encryptor.setAlgorithm(algorythm);
+        encryptor.setAlgorithm(algorithm);
         encryptor.setKeyObtentionIterations(1000);
         encryptor.setPassword(password);
         HibernatePBEEncryptorRegistry.getInstance()

diff --git a/src/main/java/com/odysseusinc/arachne/datanode/config/FlywayConfig.java b/src/main/java/com/odysseusinc/arachne/datanode/config/FlywayConfig.java
diff --git a/src/main/java/com/odysseusinc/arachne/datanode/config/HibernateValidatorJpaConfig.java b/src/main/java/com/odysseusinc/arachne/datanode/config/HibernateValidatorJpaConfig.java