Update JaCoCo to 0.8.2 and fix wrong imports. Related to IQSS#775.

As JaCoCo has been a direct dependency in *compile* scope.

At a few 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

@@ -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>
 
     <!--Maven checks for dependendies from these repos in the order shown in the pom.xml
@@ -402,11 +403,6 @@
             <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
@@ -644,7 +640,7 @@
             <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>

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;

src/main/java/edu/harvard/iq/dataverse/harvest/client/oai/OaiHandler.java

@@ -23,14 +23,15 @@
 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;
 import java.util.ArrayList;
 import java.util.Date;
 import java.util.Iterator;
 import java.util.List;
-import org.codehaus.plexus.util.StringUtils;
 
 /**
  *

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;
 
 /**
  *

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;

src/test/java/edu/harvard/iq/dataverse/dataaccess/StorageIOTest.java

@@ -5,7 +5,6 @@
  */
 package edu.harvard.iq.dataverse.dataaccess;
 
-import edu.emory.mathcs.backport.java.util.Arrays;
 import edu.harvard.iq.dataverse.DataFile;
 import edu.harvard.iq.dataverse.Dataset;
 import edu.harvard.iq.dataverse.Dataverse;
@@ -18,6 +17,7 @@
 import java.io.OutputStream;
 import java.io.RandomAccessFile;
 import java.nio.channels.Channel;
+import java.util.Arrays;
 import java.util.List;
 import org.apache.commons.httpclient.Header;
 import org.apache.commons.httpclient.methods.GetMethod;

src/test/java/edu/harvard/iq/dataverse/util/json/BriefJsonPrinterTest.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.Dataset;
 import edu.harvard.iq.dataverse.DatasetField;
 import edu.harvard.iq.dataverse.DatasetFieldConstant;
@@ -12,6 +11,9 @@
 import edu.harvard.iq.dataverse.workflow.Workflow;
 import javax.json.JsonObject;
 import org.junit.Test;
+
+import java.util.Collections;
+
 import static org.junit.Assert.*;
 
 /**

src/test/java/edu/harvard/iq/dataverse/validation/PasswordValidatorTest.java

@@ -1,6 +1,5 @@
 package edu.harvard.iq.dataverse.validation;
 
-import edu.emory.mathcs.backport.java.util.Arrays;
 import org.apache.commons.lang.StringUtils;
 import org.junit.Assert;
 import org.junit.BeforeClass;
@@ -10,6 +9,7 @@
 import java.io.FileOutputStream;
 import java.io.IOException;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Date;
 import java.util.List;
 import java.util.logging.Logger;