Merge pull request #279 from OHDSI/release-1.17.1

Commons Release 1.17.1
OHDSI · Feb 8, 2021 · 6e58df1 · 6e58df1
2 parents d71f4a6 + 9fe9d9e
commit 6e58df1
Show file tree

Hide file tree

Showing 14 changed files with 81 additions and 89 deletions.
diff --git a/arachne-common-types/pom.xml b/arachne-common-types/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <artifactId>arachne-commons-bundle</artifactId>
         <groupId>com.odysseusinc.arachne</groupId>
-        <version>1.17.0</version>
+        <version>1.17.1</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
     <modelVersion>4.0.0</modelVersion>

diff --git a/arachne-common-utils/pom.xml b/arachne-common-utils/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <artifactId>arachne-commons-bundle</artifactId>
         <groupId>com.odysseusinc.arachne</groupId>
-        <version>1.17.0</version>
+        <version>1.17.1</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
     <modelVersion>4.0.0</modelVersion>
@@ -14,9 +14,10 @@
 
     <properties>
         <java.version>1.8</java.version>
-        <spring.version>5.1.7.RELEASE</spring.version>
-        <handlebars.version>4.0.6</handlebars.version>
-        <commons.io.version>2.5</commons.io.version>
+        <spring.version>5.1.17.RELEASE</spring.version>
+        <handlebars.version>4.2.0</handlebars.version>
+        <commons.io.version>2.8.0</commons.io.version>
+        <commons.lang.version>3.11</commons.lang.version>
     </properties>
 
     <dependencies>
@@ -28,7 +29,10 @@
         <dependency>
             <groupId>commons-io</groupId>
             <artifactId>commons-io</artifactId>
-            <version>${commons.io.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.commons</groupId>
+            <artifactId>commons-lang3</artifactId>
         </dependency>
         <dependency>
             <groupId>junit</groupId>
@@ -43,7 +47,7 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-compiler-plugin</artifactId>
-                <version>3.7.0</version>
+                <version>3.8.1</version>
                 <configuration>
                     <source>${java.version}</source>
                     <target>${java.version}</target>

diff --git a/arachne-commons/pom.xml b/arachne-commons/pom.xml
@@ -7,7 +7,7 @@
     <parent>
         <groupId>com.odysseusinc.arachne</groupId>
         <artifactId>arachne-commons-bundle</artifactId>
-        <version>1.17.0</version>
+        <version>1.17.1</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
@@ -16,11 +16,11 @@
 
     <properties>
         <java.version>1.8</java.version>
-        <commons.io.version>2.8.0</commons.io.version>
-        <springfox.swagger2.version>2.9.2</springfox.swagger2.version>
-        <commons.lang.version>3.11</commons.lang.version>
         <flyway.version>4.2.0</flyway.version>
-        <jackson.version>2.11.2</jackson.version>
+        <activemq.version>5.15.14</activemq.version>
+        <guava.version>30.1-jre</guava.version>
+        <jackson.version>2.10.5</jackson.version>
+        <springfox.swagger2.version>2.9.2</springfox.swagger2.version>
     </properties>
 
     <dependencies>
@@ -34,7 +34,6 @@
         <dependency>
             <groupId>org.apache.commons</groupId>
             <artifactId>commons-lang3</artifactId>
-            <version>${commons.lang.version}</version>
         </dependency>
 
         <dependency>
@@ -50,7 +49,12 @@
         <dependency>
             <groupId>com.fasterxml.jackson.core</groupId>
             <artifactId>jackson-databind</artifactId>
-            <version>${jackson.version}</version>
+            <version>2.10.5.1</version>
+        </dependency>
+        <dependency>
+            <groupId>com.google.guava</groupId>
+            <artifactId>guava</artifactId>
+            <version>${guava.version}</version>
         </dependency>
 
         <!-- Start ActiveMQ -->
@@ -62,12 +66,12 @@
         <dependency>
             <groupId>org.apache.activemq</groupId>
             <artifactId>activemq-broker</artifactId>
-            <version>5.14.5</version>
+            <version>${activemq.version}</version>
         </dependency>
         <dependency>
             <groupId>org.apache.activemq</groupId>
             <artifactId>activemq-kahadb-store</artifactId>
-            <version>5.14.5</version>
+            <version>${activemq.version}</version>
         </dependency>
         <!-- End ActiveMQ -->
 
@@ -84,7 +88,6 @@
         <dependency>
             <groupId>commons-io</groupId>
             <artifactId>commons-io</artifactId>
-            <version>${commons.io.version}</version>
         </dependency>
         <dependency>
             <groupId>io.springfox</groupId>
@@ -124,8 +127,8 @@
         </dependency>
         <dependency>
             <groupId>org.hamcrest</groupId>
-            <artifactId>hamcrest-all</artifactId>
-            <version>1.3</version>
+            <artifactId>hamcrest</artifactId>
+            <version>2.2</version>
             <scope>test</scope>
         </dependency>
     </dependencies>

diff --git a/arachne-commons/src/main/java/com/odysseusinc/arachne/commons/utils/ComparableVersion.java b/arachne-commons/src/main/java/com/odysseusinc/arachne/commons/utils/ComparableVersion.java
@@ -1,6 +1,8 @@
 package com.odysseusinc.arachne.commons.utils;
 
+
 import com.google.common.collect.ImmutableMap;
+
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Iterator;

diff --git a/...ne-commons/src/test/java/com/odysseusinc/arachne/commons/utils/ComparableVersionTest.java b/...ne-commons/src/test/java/com/odysseusinc/arachne/commons/utils/ComparableVersionTest.java
@@ -1,7 +1,7 @@
 package com.odysseusinc.arachne.commons.utils;
 
+import static org.hamcrest.MatcherAssert.assertThat;
 import static org.hamcrest.core.Is.is;
-import static org.junit.Assert.*;
 
 import org.junit.Test;
 

diff --git a/arachne-no-handler-found-exception-util/pom.xml b/arachne-no-handler-found-exception-util/pom.xml
@@ -7,7 +7,7 @@
     <parent>
         <groupId>com.odysseusinc.arachne</groupId>
         <artifactId>arachne-commons-bundle</artifactId>
-        <version>1.17.0</version>
+        <version>1.17.1</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/arachne-scheduler/pom.xml b/arachne-scheduler/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>com.odysseusinc.arachne</groupId>
         <artifactId>arachne-commons-bundle</artifactId>
-        <version>1.17.0</version>
+        <version>1.17.1</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
@@ -68,7 +68,7 @@
         <dependency>
             <groupId>org.springframework</groupId>
             <artifactId>spring-core</artifactId>
-            <version>4.3.21.RELEASE</version>
+            <version>${spring.version}</version>
         </dependency>
     </dependencies>
 

diff --git a/arachne-storage/pom.xml b/arachne-storage/pom.xml
@@ -7,7 +7,7 @@
     <parent>
         <groupId>com.odysseusinc.arachne</groupId>
         <artifactId>arachne-commons-bundle</artifactId>
-        <version>1.17.0</version>
+        <version>1.17.1</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
@@ -17,7 +17,6 @@
     <properties>
         <java.version>1.8</java.version>
         <spring.boot.version>1.5.22.RELEASE</spring.boot.version>
-        <commons.lang3.version>3.11</commons.lang3.version>
         <jackrabbit.version>2.21.3</jackrabbit.version>
     </properties>
 
@@ -40,7 +39,6 @@
         <dependency>
             <groupId>org.apache.commons</groupId>
             <artifactId>commons-lang3</artifactId>
-            <version>${commons.lang3.version}</version>
         </dependency>
         <dependency>
             <groupId>javax.jcr</groupId>

diff --git a/arachne-sys-settings/pom.xml b/arachne-sys-settings/pom.xml
@@ -7,7 +7,7 @@
     <parent>
         <groupId>com.odysseusinc.arachne</groupId>
         <artifactId>arachne-commons-bundle</artifactId>
-        <version>1.17.0</version>
+        <version>1.17.1</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
@@ -17,23 +17,13 @@
     <properties>
         <java.version>1.8</java.version>
         <springfox.swagger2.version>2.9.2</springfox.swagger2.version>
-        <postgresql.version>42.2.1</postgresql.version>
+        <postgresql.version>42.2.15</postgresql.version>
         <flyway.version>4.2.0</flyway.version>
         <spring.jasypt.version>1.18</spring.jasypt.version>
     </properties>
 
     <dependencies>
 
-        <!--<dependency>-->
-            <!--<groupId>org.hibernate</groupId>-->
-            <!--<artifactId>hibernate-validator</artifactId>-->
-            <!--<version>5.2.4.Final</version>-->
-        <!--</dependency>-->
-        <!--<dependency>-->
-            <!--<groupId>com.fasterxml.jackson.core</groupId>-->
-            <!--<artifactId>jackson-annotations</artifactId>-->
-            <!--<version>2.8.3</version>-->
-        <!--</dependency>-->
         <dependency>
             <groupId>org.postgresql</groupId>
             <artifactId>postgresql</artifactId>

diff --git a/.../src/main/java/com/odysseusinc/arachne/system/settings/config/SpringPropertiesConfig.java b/.../src/main/java/com/odysseusinc/arachne/system/settings/config/SpringPropertiesConfig.java
@@ -23,19 +23,16 @@
 package com.odysseusinc.arachne.system.settings.config;
 
 import com.ulisesbocchio.jasyptspringboot.EncryptablePropertyResolver;
-import java.io.IOException;
-import java.net.URI;
+
 import java.sql.Connection;
-import java.sql.Driver;
 import java.sql.DriverManager;
 import java.sql.ResultSet;
 import java.sql.SQLException;
 import java.sql.Statement;
 import java.util.HashMap;
 import java.util.Map;
 import java.util.Properties;
-import javax.sql.DataSource;
-import org.postgresql.ds.PGPoolingDataSource;
+
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.context.annotation.Bean;
@@ -51,59 +48,46 @@ public class SpringPropertiesConfig {
     private static final String SQL = "SELECT * FROM system_settings WHERE value IS NOT NULL";
     private static final Logger LOG = LoggerFactory.getLogger(SpringPropertiesConfig.class);
 
-       private DataSource getDataSource(EncryptablePropertyResolver encryptablePropertyResolver, ConfigurableEnvironment environment)
-               throws IOException, ClassNotFoundException, IllegalAccessException, InstantiationException, SQLException {
-
-            final String datasourceUrl = environment.getProperty("spring.datasource.url");
-            final String datasourceUsername = environment.getProperty("spring.datasource.username");
-            final String datasourcePassword = environment.getProperty("spring.datasource.password");
-            final String connectionUrl = encryptablePropertyResolver.resolvePropertyValue(datasourceUrl);
-            final String user = encryptablePropertyResolver.resolvePropertyValue(datasourceUsername);
-            final String password = encryptablePropertyResolver.resolvePropertyValue(datasourcePassword);
-            DriverManager.registerDriver((Driver) Class.forName("org.postgresql.Driver").newInstance());
-            final String cleanURI = connectionUrl.substring(5);
-            final URI uri = URI.create(cleanURI);
-            final PGPoolingDataSource ds = new PGPoolingDataSource();
-            ds.setServerName(uri.getHost());
-            ds.setPortNumber(uri.getPort());
-            ds.setDatabaseName(uri.getPath().substring(1));
-            ds.setUser(user);
-            ds.setPassword(password);
-            ds.setMaxConnections(10);
-        return ds;
+    private Connection getConnection(EncryptablePropertyResolver encryptablePropertyResolver, ConfigurableEnvironment environment)
+            throws SQLException {
+
+        final String datasourceUrl = environment.getProperty("spring.datasource.url");
+        final String datasourceUsername = environment.getProperty("spring.datasource.username");
+        final String datasourcePassword = environment.getProperty("spring.datasource.password");
+        final String connectionUrl = encryptablePropertyResolver.resolvePropertyValue(datasourceUrl);
+        final String user = encryptablePropertyResolver.resolvePropertyValue(datasourceUsername);
+        final String password = encryptablePropertyResolver.resolvePropertyValue(datasourcePassword);
+        return DriverManager.getConnection(connectionUrl, user, password);
     }
 
-    private Map getDbProperties(DataSource dataSource, EncryptablePropertyResolver encryptablePropertyResolver) {
+    private Map<String, Object> getDbProperties(Connection connection, EncryptablePropertyResolver encryptablePropertyResolver) throws SQLException {
 
         Map<String, Object> loadedProperties = new HashMap<>();
 
-        try {
-            Connection connection = dataSource.getConnection();
-            try (Statement statement = connection.createStatement()) {
-                try (ResultSet rs = statement.executeQuery(SQL)) {
-                    while (rs.next()) {
-                        String name = rs.getString("name");
-                        String value = rs.getString("value");
-                        value = encryptablePropertyResolver.resolvePropertyValue(value);
-                        loadedProperties.put(name, value);
-                    }
+        try (Statement statement = connection.createStatement()) {
+            try (ResultSet rs = statement.executeQuery(SQL)) {
+                while (rs.next()) {
+                    String name = rs.getString("name");
+                    String value = rs.getString("value");
+                    value = encryptablePropertyResolver.resolvePropertyValue(value);
+                    loadedProperties.put(name, value);
                 }
             }
-        } catch (SQLException e) {
-            LOG.error("Error loading properties", e);
         }
-
         return loadedProperties;
     }
 
     @Bean
     public PropertySourcesPlaceholderConfigurer propertySourcesPlaceholderConfigurer(
             EncryptablePropertyResolver encryptablePropertyResolver, ConfigurableEnvironment environment
-    ) throws IOException, ClassNotFoundException, IllegalAccessException, InstantiationException, SQLException {
+    ) throws SQLException {
 
-        DataSource dataSource = getDataSource(encryptablePropertyResolver, environment);
         Properties dbProps = new Properties();
-        dbProps.putAll(getDbProperties(dataSource, encryptablePropertyResolver));
+        try (Connection connection = getConnection(encryptablePropertyResolver, environment)) {
+            dbProps.putAll(getDbProperties(connection, encryptablePropertyResolver));
+        } catch (SQLException e) {
+            LOG.error("Error loading properties", e);
+        }
 
         PropertySourcesPlaceholderConfigurer configurer = new PropertySourcesPlaceholderConfigurer();
 

diff --git a/data-source-manager/pom.xml b/data-source-manager/pom.xml
@@ -29,7 +29,7 @@
     <parent>
         <groupId>com.odysseusinc.arachne</groupId>
         <artifactId>arachne-commons-bundle</artifactId>
-        <version>1.17.0</version>
+        <version>1.17.1</version>
         <relativePath>../</relativePath>
     </parent>
 
@@ -38,7 +38,6 @@
 
     <properties>
         <java.version>1.8</java.version>
-        <commons.lang3.version>3.11</commons.lang3.version>
     </properties>
 
     <dependencies>
@@ -55,7 +54,6 @@
         <dependency>
             <groupId>org.apache.commons</groupId>
             <artifactId>commons-lang3</artifactId>
-            <version>${commons.lang3.version}</version>
         </dependency>
         <dependency>
             <groupId>org.jasypt</groupId>