[#2119] Implement Proper Deep Cloning for RepoConfiguration and CliArguments

src/main/java/reposense/model/Author.java

@@ -10,7 +10,7 @@
 /**
  * Represents a Git Author.
  */
-public class Author {
+public class Author implements Cloneable {
     public static final String NAME_NO_AUTHOR_WITH_COMMITS_FOUND =
             "NO AUTHOR WITH COMMITS FOUND WITHIN THIS PERIOD OF TIME";
     private static final String UNKNOWN_AUTHOR_GIT_ID = "-";
@@ -208,5 +208,14 @@ private void addStandardGitHostEmails(List<String> emails) {
             emails.add(standardGitLabEmail);
         }
     }
+
+    @Override
+    public Author clone() throws CloneNotSupportedException {
+        Author clone = (Author) super.clone();
+        clone.emails = new ArrayList<>(this.emails);
+        clone.authorAliases = new ArrayList<>(this.authorAliases);
+        clone.ignoreGlobList = new ArrayList<>(this.ignoreGlobList);
+        return clone;
+    }
 }
 

src/main/java/reposense/model/AuthorConfiguration.java

@@ -13,7 +13,7 @@
 /**
  * Represents author configuration information from CSV config file for a single repository.
  */
-public class AuthorConfiguration {
+public class AuthorConfiguration implements Cloneable {
     public static final String DEFAULT_BRANCH = "HEAD";
     public static final boolean DEFAULT_HAS_AUTHOR_CONFIG_FILE = false;
     private static final Logger logger = LogsManager.getLogger(AuthorConfiguration.class);
@@ -336,4 +336,38 @@ public void setHasAuthorConfigFile(boolean hasAuthorConfigFile) {
     public boolean hasAuthorConfigFile() {
         return hasAuthorConfigFile;
     }
+
+    /**
+     * Creates an identical deep copy of this {@code AuthorConfiguration} object.
+     *
+     * @return Deep copy of this {@code AuthorConfiguration} object.
+     * @throws CloneNotSupportedException if the cloning operation fails.
+     */
+    @Override
+    public AuthorConfiguration clone() throws CloneNotSupportedException {
+        AuthorConfiguration clone = (AuthorConfiguration) super.clone();
+        clone.location = this.location.clone();
+        clone.authorNamesToAuthorMap = new HashMap<>();
+        clone.authorEmailsToAuthorMap = new HashMap<>();
+        clone.authorDisplayNameMap = new HashMap<>();
+        clone.authorList = new ArrayList<>();
+
+        for (Author a : this.authorList) {
+            clone.authorList.add(a.clone());
+        }
+
+        for (Map.Entry<String, Author> entry : this.authorNamesToAuthorMap.entrySet()) {
+            clone.authorNamesToAuthorMap.put(entry.getKey(), entry.getValue().clone());
+        }
+
+        for (Map.Entry<String, Author> entry : this.authorEmailsToAuthorMap.entrySet()) {
+            clone.authorEmailsToAuthorMap.put(entry.getKey(), entry.getValue().clone());
+        }
+
+        for (Map.Entry<Author, String> entry : this.authorDisplayNameMap.entrySet()) {
+            clone.authorDisplayNameMap.put(entry.getKey().clone(), entry.getValue());
+        }
+
+        return clone;
+    }
 }

src/main/java/reposense/model/CliArguments.java

@@ -4,19 +4,21 @@
 import java.nio.file.Paths;
 import java.time.LocalDateTime;
 import java.time.ZoneId;
+import java.util.ArrayList;
 import java.util.List;
 import java.util.Objects;
 
 import reposense.parser.ArgsParser;
 import reposense.parser.AuthorConfigCsvParser;
+import reposense.parser.ConfigurationBuildException;
 import reposense.parser.GroupConfigCsvParser;
 import reposense.parser.RepoConfigCsvParser;
 import reposense.parser.ReportConfigJsonParser;
 
 /**
  * Represents command line arguments user supplied when running the program.
  */
-public class CliArguments {
+public class CliArguments implements Cloneable {
     private static final Path EMPTY_PATH = Paths.get("");
 
     private final Path outputFilePath;
@@ -25,7 +27,7 @@ public class CliArguments {
     private final LocalDateTime untilDate;
     private final boolean isSinceDateProvided;
     private final boolean isUntilDateProvided;
-    private final List<FileType> formats;
+    private List<FileType> formats;
     private final boolean isLastModifiedDateIncluded;
     private final boolean isShallowCloningPerformed;
     private final boolean isAutomaticallyLaunching;
@@ -229,6 +231,36 @@ public boolean equals(Object other) {
                 && Objects.equals(this.reportConfigFilePath, otherCliArguments.reportConfigFilePath);
     }
 
+    /**
+     * Clones the current instance of {@code CliArguments}. This method will only explicitly clone
+     * objects that are not immutable (e.g. List, Lists of mutable objects, other ordinary mutable
+     * objects).
+     *
+     * @return {@code CliArguments} instance that is semantically identical to this instance of
+     *     {@code CliArguments}.
+     * @throws CloneNotSupportedException if cloning for certain objects is not permitted.
+     */
+    @Override
+    public CliArguments clone() throws CloneNotSupportedException {
+        CliArguments clone = (CliArguments) super.clone();
+
+        // clone the formats, each FileType object needs to be individually cloned
+        clone.formats = new ArrayList<>();
+        for (FileType ft : this.formats) {
+            clone.formats.add(ft.clone());
+        }
+
+        // clone the string list; its ok to do a shallow copy since strings are mutable
+        clone.locations = this.locations == null ? clone.locations : new ArrayList<>(this.locations);
+
+        // clone the report config; use the clone method to clone the object for us
+        clone.reportConfiguration = this.reportConfiguration == null
+                ? clone.reportConfiguration
+                : this.reportConfiguration.clone();
+
+        return clone;
+    }
+
     /**
      * Builder used to build CliArguments.
      */
@@ -506,6 +538,7 @@ public Builder reportConfiguration(ReportConfiguration reportConfiguration) {
          * Builds CliArguments.
          *
          * @return CliArguments
+         * @throws ConfigurationBuildException if the object cannot be cloned
          */
         public CliArguments build() {
             return new CliArguments(this);

src/main/java/reposense/model/CommitHash.java

@@ -10,7 +10,7 @@
 /**
  * Represents a git commit hash in {@code RepoConfiguration}.
  */
-public class CommitHash {
+public class CommitHash implements Cloneable {
     private static final String COMMIT_HASH_REGEX = "^[0-9a-f]+$";
     private static final String COMMIT_RANGED_HASH_REGEX = "^[0-9a-f]+\\.\\.[0-9a-f]+$";
     private static final String INVALID_COMMIT_HASH_MESSAGE =
@@ -109,5 +109,16 @@ private static void validateCommit(String commitHash) throws IllegalArgumentExce
             throw new IllegalArgumentException(String.format(INVALID_COMMIT_HASH_MESSAGE, commitHash));
         }
     }
+
+    /**
+     * Creates a deep copy of this {@code CommitHash} object.
+     *
+     * @return Deep copy of this {@code CommitHash} object.
+     * @throws CloneNotSupportedException if the cloning operation fails.
+     */
+    @Override
+    public CommitHash clone() throws CloneNotSupportedException {
+        return (CommitHash) super.clone();
+    }
 }
 

src/main/java/reposense/model/FileType.java

@@ -4,6 +4,7 @@
 import java.nio.file.FileSystems;
 import java.nio.file.PathMatcher;
 import java.nio.file.Paths;
+import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
 import java.util.regex.Pattern;
@@ -17,7 +18,7 @@
 /**
  * Represents a file type for use in {@link FileTypeManager}.
  */
-public class FileType {
+public class FileType implements Cloneable {
     private static final Pattern FILE_FORMAT_VALIDATION_PATTERN = Pattern.compile("^\\w+$");
     private static final String MESSAGE_ILLEGAL_FILE_FORMAT = "The provided file format, %s, contains illegal "
             + "characters.";
@@ -110,6 +111,22 @@ public boolean equals(Object other) {
         return this.label.equals(otherFileType.label) && this.paths.equals(otherFileType.paths);
     }
 
+    /**
+     * Clones this instance of {@code FileType}.
+     *
+     * @return New instance of {@code FileType} that is semantically similar to this instance
+     *     of {@code FileType}.
+     * @throws CloneNotSupportedException if there are any objects that cannot be cloned.
+     */
+    @Override
+    public FileType clone() throws CloneNotSupportedException {
+        // it suffices to do a shallow clone since strings are immutable
+        FileType clone = (FileType) super.clone();
+        clone.paths = new ArrayList<>(this.paths);
+
+        return clone;
+    }
+
     /**
      * Overrides the Gson serializer to serialize only the label of each file type instead on the entire object.
      */

src/main/java/reposense/model/FileTypeManager.java

@@ -8,7 +8,7 @@
  * Holds a list of whitelisted formats and user-specified custom
  * groupings.
  */
-public class FileTypeManager {
+public class FileTypeManager implements Cloneable {
     private static final String DEFAULT_GROUP = "other";
     private static final FileType DEFAULT_GROUP_TYPE = new FileType(DEFAULT_GROUP, Collections.singletonList("**"));
 
@@ -126,4 +126,15 @@ public boolean equals(Object other) {
         FileTypeManager otherFileType = (FileTypeManager) other;
         return this.groups.equals(otherFileType.groups) && this.formats.equals(otherFileType.formats);
     }
+
+    @Override
+    public FileTypeManager clone() throws CloneNotSupportedException {
+        FileTypeManager clone = (FileTypeManager) super.clone();
+
+        // do a shallow copy since strings are immutable
+        clone.formats = new ArrayList<>(this.formats);
+        clone.groups = new ArrayList<>(this.groups);
+
+        return clone;
+    }
 }

src/main/java/reposense/model/RepoConfiguration.java

@@ -20,7 +20,7 @@
 /**
  * Represents configuration information from CSV config file for a single repository.
  */
-public class RepoConfiguration {
+public class RepoConfiguration implements Cloneable {
     public static final String DEFAULT_BRANCH = "HEAD";
     public static final String DEFAULT_EXTRA_OUTPUT_FOLDER_NAME = "";
     public static final long DEFAULT_FILE_SIZE_LIMIT = 500000;
@@ -60,6 +60,29 @@
      */
     private RepoConfiguration() {}
 
+    /**
+     * Creates a deep copy of this {@code RepoConfiguration} object.
+     *
+     * @return Deep copy of this {@code RepoConfiguration} object.
+     * @throws CloneNotSupportedException if the cloning operation fails.
+     */
+    @Override
+    public RepoConfiguration clone() throws CloneNotSupportedException {
+        RepoConfiguration clone = (RepoConfiguration) super.clone();
+        clone.location = this.location == null ? clone.location : this.location.clone();
+        clone.fileTypeManager = this.fileTypeManager == null ? clone.fileTypeManager : this.fileTypeManager.clone();
+        clone.ignoreGlobList = new ArrayList<>(this.ignoreGlobList);
+        clone.ignoredAuthorsList = new ArrayList<>(this.ignoredAuthorsList);
+        clone.authorConfig = this.authorConfig == null ? clone.authorConfig : this.authorConfig.clone();
+        clone.ignoreCommitList = new ArrayList<>();
+
+        for (CommitHash hash : this.ignoreCommitList) {
+            clone.ignoreCommitList.add(hash.clone());
+        }
+
+        return clone;
+    }
+
     /**
      * Builds the necessary configurations for RepoConfiguration.
      * Obeys the Builder pattern as described in {@link CliArguments}.
@@ -68,7 +91,7 @@
         private String displayName;
         private String outputFolderName;
         private String repoFolderName;
-        private RepoConfiguration repoConfiguration;
+        private final RepoConfiguration repoConfiguration;
 
         /**
          * Returns an empty instance of the RepoConfiguration Builder.
@@ -426,13 +449,11 @@
             this.processNames();
 
             // save a reference to the current built object
-            RepoConfiguration toReturn = this.repoConfiguration;
-
-            // reset the internal reference to avoid aliasing
-            this.repoConfiguration = new RepoConfiguration();
-
-            // return the reference to the built RepoConfiguration object
-            return toReturn;
+            try {
+                return this.repoConfiguration.clone();
+            } catch (CloneNotSupportedException ex) {
+                throw new ConfigurationBuildException();
+            }
         }
 
         /**

src/main/java/reposense/model/RepoLocation.java

@@ -20,7 +20,7 @@
 /**
  * Represents a repository location.
  */
-public class RepoLocation {
+public class RepoLocation implements Cloneable {
     protected static final String UNSUPPORTED_DOMAIN_NAME = "NOT_RECOGNIZED";
 
     private static final String MESSAGE_INVALID_LOCATION = "%s is an invalid location.";
@@ -269,4 +269,18 @@ public boolean equals(Object other) {
     public int hashCode() {
         return location.hashCode();
     }
+
+    /**
+     * Clones this {@code RepoLocation} instance.
+     *
+     * @return A new instance of {@code RepoLocation} that is sematically identical to this
+     *     {@code RepoLocation} instance.
+     * @throws CloneNotSupportedException if there is a problem when cloning this
+     *     {@code RepoLocation} object.
+     */
+    @Override
+    public RepoLocation clone() throws CloneNotSupportedException {
+        // regular shallow clone will suffice since strings are immutable
+        return (RepoLocation) super.clone();
+    }
 }

src/main/java/reposense/model/ReportConfiguration.java

@@ -3,11 +3,16 @@
 /**
  * Represents configuration information from JSON config file for generated report.
  */
-public class ReportConfiguration {
+public class ReportConfiguration implements Cloneable {
     private static final String DEFAULT_TITLE = "RepoSense Report";
     private String title;
 
     public String getTitle() {
         return (title == null) ? DEFAULT_TITLE : title;
     }
+
+    @Override
+    public ReportConfiguration clone() throws CloneNotSupportedException {
+        return (ReportConfiguration) super.clone();
+    }
 }