From a64ad35a68ffec8d6bec942f3bfac46b5e42656c Mon Sep 17 00:00:00 2001
From: Oliver Bertuch <o.bertuch@fz-juelich.de>
Date: Wed, 7 Nov 2018 15:25:29 +0100
Subject: [PATCH] Update JaCoCo to 0.8.2 and fix wrong imports. Related to
 #775.

As JaCoCo has been a direct dependency in *compile* scope, at four places
accidentially some classes from transitive dependencies from JaCoCo have been used
instead of the classes used commonly within the codebase.
Removing the JaCoCo direct dependency as only the plugin is used at build/test time. It is sufficient for Maven to have the
plugin included with its version number - this is handled as a transitive dependency during the build internally by Maven.

Hopefully this created no harm, but better fix this now.
---
 pom.xml                                            |  8 ++------
 .../providers/oauth2/impl/GitHubOAuth2AP.java      |  2 +-
 .../dataverse/harvest/client/oai/OaiHandler.java   |  3 ++-
 .../harvest/server/web/servlet/OAIServlet.java     |  3 ++-
 .../iq/dataverse/util/json/JsonPrinter.java        | 14 ++------------
 5 files changed, 9 insertions(+), 21 deletions(-)

diff --git a/pom.xml b/pom.xml
index 061eafb63bc..9e3ae8a6279 100644
--- a/pom.xml
+++ b/pom.xml
@@ -35,6 +35,7 @@
         <junit.vintage.version>5.3.1</junit.vintage.version>
         <junit.platform.version>1.3.1</junit.platform.version>
         <mockito.version>2.22.0</mockito.version>
+        <jacoco.version>0.8.2</jacoco.version>
     </properties>
 
     <repositories>
@@ -418,11 +419,6 @@
             <version>2.4.0</version>
             <scope>test</scope>
         </dependency>
-        <dependency>
-            <groupId>org.jacoco</groupId>
-            <artifactId>jacoco-maven-plugin</artifactId>
-            <version>0.7.5.201505241946</version>
-        </dependency>
         <!-- Added specific versionf of SLF4J jars; otherwise we end up with
         conflicting versions of slf4j-api and slf4j-log4j12, loaded as
         dependencies for different packages; which was causing some incompatibility
@@ -660,7 +656,7 @@
             <plugin>
                 <groupId>org.jacoco</groupId>
                 <artifactId>jacoco-maven-plugin</artifactId>
-                <version>0.7.5.201505241946</version>
+                <version>${jacoco.version}</version>
                 <configuration>
                     <destfile>${basedir}/target/coverage-reports/jacoco-unit.exec</destfile>
                     <datafile>${basedir}/target/coverage-reports/jacoco-unit.exec</datafile>
diff --git a/src/main/java/edu/harvard/iq/dataverse/authorization/providers/oauth2/impl/GitHubOAuth2AP.java b/src/main/java/edu/harvard/iq/dataverse/authorization/providers/oauth2/impl/GitHubOAuth2AP.java
index f230522a824..895fe80738e 100644
--- a/src/main/java/edu/harvard/iq/dataverse/authorization/providers/oauth2/impl/GitHubOAuth2AP.java
+++ b/src/main/java/edu/harvard/iq/dataverse/authorization/providers/oauth2/impl/GitHubOAuth2AP.java
@@ -2,13 +2,13 @@
 
 import com.github.scribejava.apis.GitHubApi;
 import com.github.scribejava.core.builder.api.BaseApi;
-import edu.emory.mathcs.backport.java.util.Collections;
 import edu.harvard.iq.dataverse.authorization.AuthenticatedUserDisplayInfo;
 import edu.harvard.iq.dataverse.authorization.providers.oauth2.AbstractOAuth2AuthenticationProvider;
 import edu.harvard.iq.dataverse.authorization.providers.shib.ShibUserNameFields;
 import edu.harvard.iq.dataverse.authorization.providers.shib.ShibUtil;
 import edu.harvard.iq.dataverse.util.BundleUtil;
 import java.io.StringReader;
+import java.util.Collections;
 import javax.json.Json;
 import javax.json.JsonObject;
 import javax.json.JsonReader;
diff --git a/src/main/java/edu/harvard/iq/dataverse/harvest/client/oai/OaiHandler.java b/src/main/java/edu/harvard/iq/dataverse/harvest/client/oai/OaiHandler.java
index 0fc38a27011..e4642fe0a4d 100644
--- a/src/main/java/edu/harvard/iq/dataverse/harvest/client/oai/OaiHandler.java
+++ b/src/main/java/edu/harvard/iq/dataverse/harvest/client/oai/OaiHandler.java
@@ -23,6 +23,8 @@
 import java.io.Serializable;
 import java.io.UnsupportedEncodingException;
 import javax.xml.parsers.ParserConfigurationException;
+
+import org.apache.commons.lang.StringUtils;
 import org.xml.sax.SAXException;
 import javax.xml.transform.TransformerException;
 import java.net.URLEncoder;
@@ -30,7 +32,6 @@
 import java.util.Date;
 import java.util.Iterator;
 import java.util.List;
-import org.codehaus.plexus.util.StringUtils;
 
 /**
  *
diff --git a/src/main/java/edu/harvard/iq/dataverse/harvest/server/web/servlet/OAIServlet.java b/src/main/java/edu/harvard/iq/dataverse/harvest/server/web/servlet/OAIServlet.java
index 447d97ee80a..05d34250fd6 100644
--- a/src/main/java/edu/harvard/iq/dataverse/harvest/server/web/servlet/OAIServlet.java
+++ b/src/main/java/edu/harvard/iq/dataverse/harvest/server/web/servlet/OAIServlet.java
@@ -39,6 +39,8 @@
 import edu.harvard.iq.dataverse.harvest.server.xoai.XlistRecords;
 import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
 import edu.harvard.iq.dataverse.util.SystemConfig;
+import org.apache.commons.lang.StringUtils;
+
 import java.io.ByteArrayOutputStream;
 
 import java.io.IOException;
@@ -57,7 +59,6 @@
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 import javax.xml.stream.XMLStreamException;
-import org.codehaus.plexus.util.StringUtils;
 
 /**
  *
diff --git a/src/main/java/edu/harvard/iq/dataverse/util/json/JsonPrinter.java b/src/main/java/edu/harvard/iq/dataverse/util/json/JsonPrinter.java
index a79072d18ae..3209a7cac0d 100644
--- a/src/main/java/edu/harvard/iq/dataverse/util/json/JsonPrinter.java
+++ b/src/main/java/edu/harvard/iq/dataverse/util/json/JsonPrinter.java
@@ -1,6 +1,5 @@
 package edu.harvard.iq.dataverse.util.json;
 
-import edu.emory.mathcs.backport.java.util.Collections;
 import edu.harvard.iq.dataverse.ControlledVocabularyValue;
 import edu.harvard.iq.dataverse.DataFile;
 import edu.harvard.iq.dataverse.DataFileTag;
@@ -41,20 +40,11 @@
 import static edu.harvard.iq.dataverse.util.json.NullSafeJsonBuilder.jsonObjectBuilder;
 import edu.harvard.iq.dataverse.workflow.Workflow;
 import edu.harvard.iq.dataverse.workflow.step.WorkflowStepData;
-import java.util.ArrayList;
-import java.util.Set;
+
+import java.util.*;
 import javax.json.Json;
 import javax.json.JsonArrayBuilder;
 import javax.json.JsonObjectBuilder;
-import java.util.Date;
-import java.util.List;
-import java.util.TreeSet;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Deque;
-import java.util.EnumSet;
-import java.util.LinkedList;
-import java.util.Map;
 import java.util.function.BiConsumer;
 import java.util.function.BinaryOperator;
 import java.util.function.Function;