#247: upgrade dependencies

Dockerfile

@@ -1,11 +1,11 @@
-FROM sismics/ubuntu-jetty:9.3.11
+FROM sismics/ubuntu-jetty:9.4.12
 MAINTAINER b.gamard@sismics.com
 
 RUN apt-get update && apt-get -y -q install ffmpeg mediainfo tesseract-ocr tesseract-ocr-fra tesseract-ocr-ita tesseract-ocr-kor tesseract-ocr-rus tesseract-ocr-ukr tesseract-ocr-spa tesseract-ocr-ara tesseract-ocr-hin tesseract-ocr-deu tesseract-ocr-pol tesseract-ocr-jpn tesseract-ocr-por tesseract-ocr-tha tesseract-ocr-jpn tesseract-ocr-chi-sim tesseract-ocr-chi-tra && \
     apt-get clean && rm -rf /var/lib/apt/lists/*
 
 # Remove the embedded javax.mail jar from Jetty
-RUN rm -f /opt/jetty/lib/jndi/javax.mail.glassfish-*.jar
+RUN rm -f /opt/jetty/lib/mail/javax.mail.glassfish-*.jar
 
 ADD docs.xml /opt/jetty/webapps/docs.xml
 ADD docs-web/target/docs-web-*.war /opt/jetty/webapps/docs.war

docs-core/src/main/java/com/sismics/docs/core/util/indexing/LuceneIndexingHandler.java

@@ -39,7 +39,6 @@ import org.apache.lucene.store.Directory;
 import org.apache.lucene.store.NoLockFactory;
 import org.apache.lucene.store.RAMDirectory;
 import org.apache.lucene.store.SimpleFSDirectory;
-import org.apache.lucene.util.Version;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -110,13 +109,7 @@ public class LuceneIndexingHandler implements IndexingHandler {
             log.info("Checking index health and version");
             try (CheckIndex checkIndex = new CheckIndex(directory)) {
                 CheckIndex.Status status = checkIndex.checkIndex();
-                if (status.clean) {
+                if (!status.clean) {
-                    for (CheckIndex.Status.SegmentInfoStatus segmentInfo : status.segmentInfos) {
-                        if (!segmentInfo.version.onOrAfter(Version.LATEST)) {
-                            throw new Exception("Index is old (" + segmentInfo.version + ")");
-                        }
-                    }
-                } else {
                     throw new Exception("Index is dirty");
                 }
             }
@@ -352,7 +345,7 @@ public class LuceneIndexingHandler implements IndexingHandler {
             return;
         }
 
-        FuzzySuggester suggester = new FuzzySuggester(new StandardAnalyzer());
+        FuzzySuggester suggester = new FuzzySuggester(directory, "", new StandardAnalyzer());
         LuceneDictionary dictionary = new LuceneDictionary(directoryReader, "title");
         suggester.build(dictionary);
         int lastIndex = search.lastIndexOf(' ');

docs-core/src/main/java/com/sismics/util/ImageUtil.java

@@ -73,11 +73,12 @@ public class ImageUtil {
      * @param email Email
      * @return Gravatar hash
      */
+    @SuppressWarnings("deprecation") // Gravatar uses MD5, nothing we can do about it
     public static String computeGravatar(String email) {
         if (email == null) {
             return null;
         }
-        
+
         return Hashing.md5().hashString(
                 email.trim().toLowerCase(), Charsets.UTF_8)
                 .toString();

docs-web-common/src/main/java/com/sismics/security/AnonymousPrincipal.java

@@ -1,10 +1,9 @@
 package com.sismics.security;
 
-import java.util.Set;
+import com.google.common.collect.Sets;
-
 import org.joda.time.DateTimeZone;
 
-import jersey.repackaged.com.google.common.collect.Sets;
+import java.util.Set;
 
 /**
  * Anonymous principal.

docs-web-common/src/main/java/com/sismics/util/filter/SecurityFilter.java

@@ -1,5 +1,6 @@
 package com.sismics.util.filter;
 
+import com.google.common.collect.Sets;
 import com.sismics.docs.core.constant.Constants;
 import com.sismics.docs.core.dao.GroupDao;
 import com.sismics.docs.core.dao.RoleBaseFunctionDao;
@@ -8,7 +9,6 @@ import com.sismics.docs.core.dao.dto.GroupDto;
 import com.sismics.docs.core.model.jpa.User;
 import com.sismics.security.AnonymousPrincipal;
 import com.sismics.security.UserPrincipal;
-import jersey.repackaged.com.google.common.collect.Sets;
 import org.joda.time.DateTimeZone;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;

docs-web/pom.xml

@@ -41,6 +41,11 @@
       <groupId>org.glassfish.jersey.media</groupId>
       <artifactId>jersey-media-multipart</artifactId>
     </dependency>
+
+    <dependency>
+      <groupId>org.glassfish.jersey.inject</groupId>
+      <artifactId>jersey-hk2</artifactId>
+    </dependency>
       
     <!-- Other external dependencies -->
     <dependency>

pom.xml

@@ -16,52 +16,50 @@
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
 
     <!-- Dependencies version (external) -->
-    <org.apache.commons.commons-compress.version>1.10</org.apache.commons.commons-compress.version>
+    <org.apache.commons.commons-compress.version>1.18</org.apache.commons.commons-compress.version>
     <commons-lang.commons-lang.version>2.6</commons-lang.commons-lang.version>
-    <commons-io.commons-io.version>2.4</commons-io.commons-io.version>
+    <commons-io.commons-io.version>2.6</commons-io.commons-io.version>
     <org.apache.commons.commons-email.version>1.5</org.apache.commons.commons-email.version>
-    <org.freemarker.freemarker.version>2.3.23</org.freemarker.freemarker.version>
+    <org.freemarker.freemarker.version>2.3.28</org.freemarker.freemarker.version>
     <commons-dbcp.version>1.4</commons-dbcp.version>
-    <com.google.guava.guava.version>19.0</com.google.guava.guava.version>
+    <com.google.guava.guava.version>26.0-jre</com.google.guava.guava.version>
     <log4j.log4j.version>1.2.16</log4j.log4j.version>
     <org.slf4j.version>1.6.4</org.slf4j.version>
     <org.slf4j.jcl-over-slf4j.version>1.6.6</org.slf4j.jcl-over-slf4j.version>
     <junit.junit.version>4.12</junit.junit.version>
-    <com.h2database.h2.version>1.4.191</com.h2database.h2.version>
+    <com.h2database.h2.version>1.4.197</com.h2database.h2.version>
-    <org.glassfish.jersey.version>2.22.2</org.glassfish.jersey.version>
+    <org.glassfish.jersey.version>2.27</org.glassfish.jersey.version>
-    <org.glassfish.javax.json.version>1.1.2</org.glassfish.javax.json.version>
+    <org.glassfish.javax.json.version>1.1.3</org.glassfish.javax.json.version>
     <org.mindrot.jbcrypt>0.3m</org.mindrot.jbcrypt>
-    <org.apache.lucene.version>5.5.0</org.apache.lucene.version>
+    <org.apache.lucene.version>7.5.0</org.apache.lucene.version>
     <org.imgscalr.imgscalr-lib.version>4.2</org.imgscalr.imgscalr-lib.version>
     <org.apache.pdfbox.pdfbox.version>2.0.12</org.apache.pdfbox.pdfbox.version>
     <org.bouncycastle.bcprov-jdk15on.version>1.54</org.bouncycastle.bcprov-jdk15on.version>
-    <joda-time.joda-time.version>2.9.2</joda-time.joda-time.version>
+    <joda-time.joda-time.version>2.10</joda-time.joda-time.version>
-    <org.hibernate.hibernate.version>5.1.0.Final</org.hibernate.hibernate.version>
+    <org.hibernate.hibernate.version>5.3.7.Final</org.hibernate.hibernate.version>
-    <javax.servlet.javax.servlet-api.version>3.1.0</javax.servlet.javax.servlet-api.version>
+    <javax.servlet.javax.servlet-api.version>4.0.1</javax.servlet.javax.servlet-api.version>
     <fr.opensagres.xdocreport.version>2.0.1</fr.opensagres.xdocreport.version>
     <net.java.dev.jna.jna.version>4.2.1</net.java.dev.jna.jna.version>
     <com.twelvemonkeys.imageio.version>3.3.2</com.twelvemonkeys.imageio.version>
     <com.levigo.jbig2.levigo-jbig2-imageio.version>1.6.5</com.levigo.jbig2.levigo-jbig2-imageio.version>
     <com.github.jai-imageio.jai-imageio-jpeg2000.version>1.3.0</com.github.jai-imageio.jai-imageio-jpeg2000.version>
-    <org.postgresql.postgresql.version>42.2.2</org.postgresql.postgresql.version>
+    <org.postgresql.postgresql.version>42.2.5</org.postgresql.postgresql.version>
     <org.subethamail.subethasmtp-wiser.version>1.2</org.subethamail.subethasmtp-wiser.version>
-    <com.icegreen.greenmail.version>1.5.7</com.icegreen.greenmail.version>
+    <com.icegreen.greenmail.version>1.5.8</com.icegreen.greenmail.version>
-    <com.sun.mail.javax.mail.version>1.5.6</com.sun.mail.javax.mail.version>
+    <com.sun.mail.javax.mail.version>1.6.2</com.sun.mail.javax.mail.version>
-    <org.jsoup.jsoup.version>1.11.2</org.jsoup.jsoup.version>
+    <org.jsoup.jsoup.version>1.11.3</org.jsoup.jsoup.version>
     <com.squareup.okhttp3.okhttp.version>3.11.0</com.squareup.okhttp3.okhttp.version>
 
-    <org.eclipse.jetty.jetty-server.version>9.3.11.v20160721</org.eclipse.jetty.jetty-server.version>
+    <org.eclipse.jetty.jetty-server.version>9.4.12.v20180830</org.eclipse.jetty.jetty-server.version>
-    <org.eclipse.jetty.jetty-webapp.version>9.3.11.v20160721</org.eclipse.jetty.jetty-webapp.version>
+    <org.eclipse.jetty.jetty-webapp.version>9.4.12.v20180830</org.eclipse.jetty.jetty-webapp.version>
-    <org.eclipse.jetty.jetty-servlet.version>9.3.11.v20160721</org.eclipse.jetty.jetty-servlet.version>
+    <org.eclipse.jetty.jetty-servlet.version>9.4.12.v20180830</org.eclipse.jetty.jetty-servlet.version>
     
     <!-- Plugins version -->
     <org.apache.maven.plugins.maven-antrun-plugin.version>1.8</org.apache.maven.plugins.maven-antrun-plugin.version>
-    <org.apache.maven.plugins.maven-dependency-plugin.version>2.10</org.apache.maven.plugins.maven-dependency-plugin.version>
+    <org.apache.maven.plugins.maven-jar-plugin.version>3.1.0</org.apache.maven.plugins.maven-jar-plugin.version>
-    <org.apache.maven.plugins.maven-jar-plugin.version>2.6</org.apache.maven.plugins.maven-jar-plugin.version>
+    <org.apache.maven.plugins.maven-war-plugin.version>3.2.2</org.apache.maven.plugins.maven-war-plugin.version>
-    <org.apache.maven.plugins.maven-resources-plugin.version>2.7</org.apache.maven.plugins.maven-resources-plugin.version>
+    <org.apache.maven.plugins.maven-surefire-plugin.version>2.22.1</org.apache.maven.plugins.maven-surefire-plugin.version>
-    <org.apache.maven.plugins.maven-war-plugin.version>2.6</org.apache.maven.plugins.maven-war-plugin.version>
+    <org.eclipse.jetty.jetty-maven-plugin.version>9.4.12.v20180830</org.eclipse.jetty.jetty-maven-plugin.version>
-    <org.apache.maven.plugins.maven-surefire-plugin.version>2.19.1</org.apache.maven.plugins.maven-surefire-plugin.version>
-    <org.eclipse.jetty.jetty-maven-plugin.version>9.3.11.v20160721</org.eclipse.jetty.jetty-maven-plugin.version>
   </properties>
   
   <scm>
@@ -92,28 +90,16 @@
 
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>
-        <artifactId>maven-dependency-plugin</artifactId>
+        <artifactId>maven-war-plugin</artifactId>
-        <version>${org.apache.maven.plugins.maven-dependency-plugin.version}</version>
+        <version>${org.apache.maven.plugins.maven-war-plugin.version}</version>
       </plugin>
-
+      
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>
         <artifactId>maven-jar-plugin</artifactId>
         <version>${org.apache.maven.plugins.maven-jar-plugin.version}</version>
       </plugin>
-      
+
-      <plugin>
-        <groupId>org.apache.maven.plugins</groupId>
-        <artifactId>maven-resources-plugin</artifactId>
-        <version>${org.apache.maven.plugins.maven-resources-plugin.version}</version>
-      </plugin>
-      
-      <plugin>
-        <groupId>org.apache.maven.plugins</groupId>
-        <artifactId>maven-war-plugin</artifactId>
-        <version>${org.apache.maven.plugins.maven-war-plugin.version}</version>
-      </plugin>
-      
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>
         <artifactId>maven-surefire-plugin</artifactId>
@@ -285,6 +271,12 @@
         <version>${org.glassfish.jersey.version}</version>
       </dependency>
       
+      <dependency>
+        <groupId>org.glassfish.jersey.inject</groupId>
+        <artifactId>jersey-hk2</artifactId>
+        <version>${org.glassfish.jersey.version}</version>
+      </dependency>
+
       <dependency>
         <groupId>org.glassfish.jersey.core</groupId>
         <artifactId>jersey-client</artifactId>