Updating dependencies to the latest versions (OHDSI, a few third-party libraries) (#2013)

Author: alex-odysseus

pom.xml

@@ -23,7 +23,7 @@
     <shiro.version>1.8.0</shiro.version>
     <dom4j.version>2.1.3</dom4j.version>
     <hydra.version>0.2.0</hydra.version>
-    <featureExtraction.version>3.1.0</featureExtraction.version>
+    <featureExtraction.version>3.2.0</featureExtraction.version>
 
     <commons-fileupload.version>1.3.3</commons-fileupload.version>
 
@@ -604,6 +604,13 @@
         </exclusion>
       </exclusions>
     </dependency>
+    <!-- It is overriding a transitive dependency from the dependency above -->
+    <!-- After migrating to Spring Boot 2.x we should get rid of it -->
+    <dependency>
+      <groupId>org.yaml</groupId>
+      <artifactId>snakeyaml</artifactId>
+      <version>1.26</version>
+    </dependency>
     <dependency>
       <groupId>org.springframework.boot</groupId>
       <artifactId>spring-boot-starter-web</artifactId>
@@ -631,6 +638,13 @@
       <groupId>org.springframework.boot</groupId>
       <artifactId>spring-boot-starter-batch</artifactId>
     </dependency>
+    <!-- It is overriding a transitive dependency from the dependency above -->
+    <!-- After migrating to Spring Boot 2.x we should get rid of it -->
+    <dependency>
+      <groupId>com.thoughtworks.xstream</groupId>
+      <artifactId>xstream</artifactId>
+      <version>1.4.19</version>
+    </dependency>
     <dependency>
       <groupId>org.springframework.boot</groupId>
       <artifactId>spring-boot-starter-jdbc</artifactId>
@@ -739,6 +753,13 @@
             </exclusion>
         </exclusions>
     </dependency>
+    <!-- It is overriding a transitive dependency from the dependency above -->
+    <!-- After migrating to Spring Boot 2.x we should get rid of it -->
+    <dependency>
+      <groupId>net.minidev</groupId>
+      <artifactId>json-smart</artifactId>
+      <version>2.4.8</version>
+    </dependency>
     <dependency>
       <groupId>org.apache.commons</groupId>
       <artifactId>commons-lang3</artifactId>
@@ -979,6 +1000,7 @@
     <dependency>
       <groupId>com.google.code.gson</groupId>
       <artifactId>gson</artifactId>
+      <version>2.8.9</version>
     </dependency>
     <dependency>
       <groupId>org.jasypt</groupId>
@@ -1078,7 +1100,7 @@
     <dependency>
       <groupId>org.ohdsi</groupId>
       <artifactId>standardized-analysis-specs</artifactId>
-      <version>1.3.1</version>
+      <version>1.4.0</version>
       <exclusions>
         <exclusion>
           <groupId>com.fasterxml.jackson.core</groupId>
@@ -1089,7 +1111,7 @@
     <dependency>
       <groupId>org.ohdsi</groupId>
       <artifactId>standardized-analysis-utils</artifactId>
-      <version>1.3.0</version>
+      <version>1.3.2</version>
       <exclusions>
         <exclusion>
           <groupId>com.fasterxml.jackson.core</groupId>