Fixed concurrent modification exception.

src/main/java/nl/andrewlalis/Main.java

@@ -28,23 +28,20 @@ public class Main {
         // Command executor which will be used by all actions the user can do.
         CommandExecutor executor = new CommandExecutor();
 
-        // Main application model is stored as a static variable that is accessible everywhere.
-        InitializerApp.organization = new Organization();
-
         // Initialize User Interface.
         InitializerApp app = new InitializerApp(executor);
         app.begin();
         app.setAccessToken(userOptions.get("token"));
 
         // Initialize executable commands.
-        executor.registerCommand("read_students", new ReadStudentsFile());
+        executor.registerCommand("read_students", new ReadStudentsFile(app));
         executor.registerCommand("archive_all", new ArchiveRepos());
         executor.registerCommand("generate_assignments", new GenerateAssignmentsRepo());
         executor.registerCommand("define_ta_teams", new DefineTaTeams(app));
-        executor.registerCommand("list_errors", new ListErrors());
+        executor.registerCommand("list_errors", new ListErrors(app));
         executor.registerCommand("delete_repos", new DeleteRepos());
         executor.registerCommand("delegate_student_teams", new DelegateStudentTeams(app));
-        executor.registerCommand("setup_student_repos", new SetupStudentRepos());
+        executor.registerCommand("setup_student_repos", new SetupStudentRepos(app));
 
         logger.info("GithubManager for Github Repositories in Educational Organizations.\n" +
                 "© Andrew Lalis (2018), All rights reserved.\n" +

src/main/java/nl/andrewlalis/git_api/GithubManager.java

@@ -111,7 +111,6 @@ public class GithubManager {
         // Check if the repository already exists.
         GHRepository existingRepo = this.organization.getRepository(assignmentsRepoName);
         if (existingRepo != null) {
-            InitializerApp.organization.addError(new Error(Severity.MINOR, "Assignments repository already existed, deleting it."));
             existingRepo.delete();
             logger.fine("Deleted pre-existing assignments repository.");
         }
@@ -172,7 +171,7 @@ public class GithubManager {
                     repo.delete();
                     logger.info("Deleted repository: " + repo.getName());
                 } catch (IOException e) {
-                    InitializerApp.organization.addError(new Error(Severity.HIGH, "Could not delete repository: " + repo.getName()));
+                    logger.severe("Could not delete repository: " + repo.getName());
                     e.printStackTrace();
                 }
             }
@@ -212,7 +211,8 @@ public class GithubManager {
             }
             logger.info("Archived repository: " + repo.getFullName());
         } catch (IOException e) {
-            InitializerApp.organization.addError(new Error(Severity.HIGH, "Could not archive repository: " + repo.getName()));
+            logger.severe("Could not archive repository: " + repo.getName());
+            e.printStackTrace();
         }
     }
 
@@ -233,8 +233,8 @@ public class GithubManager {
             repo.addCollaborators(users);
             this.assignmentsRepo.addCollaborators(users);
         } catch (IOException e) {
-            InitializerApp.organization.addError(new Error(Severity.HIGH, "Students in team: " + team + " could not be added as collaborators to assignments repo or their repository."));
+            logger.severe("Could not add students as collaborators to assignments or their repo.\n" + team);
-            logger.warning("Could not add students as collaborators to assignments or their repo.");
+            e.printStackTrace();
         }
     }
 
@@ -248,8 +248,8 @@ public class GithubManager {
             taTeam.add(studentRepo, GHOrganization.Permission.ADMIN);
             logger.fine("Added team " + taTeam.getName() + " as admin to repository: " + studentRepo.getName());
         } catch (IOException e) {
-            InitializerApp.organization.addError(new Error(Severity.HIGH, "Could not add TA Team: " + taTeam.getName() + " as ADMIN to repository: " + studentRepo.getName()));
             logger.severe("Could not add TA Team: " + taTeam.getName() + " as admins to repository: " + studentRepo.getName());
+            e.printStackTrace();
         }
     }
 
@@ -269,7 +269,6 @@ public class GithubManager {
             protectionBuilder.enable();
             logger.fine("Protected master branch of repository: " + repo.getName());
         } catch (IOException e) {
-            InitializerApp.organization.addError(new Error(Severity.HIGH, "Could not protect master branch of repository: " + repo.getName()));
             logger.severe("Could not protect master branch of repository: " + repo.getName());
             e.printStackTrace();
         }
@@ -285,8 +284,7 @@ public class GithubManager {
             repo.createRef("refs/heads/development", sha1);
             logger.fine("Created development branch of repository: " + repo.getName());
         } catch (IOException e) {
-            InitializerApp.organization.addError(new Error(Severity.HIGH, "Could not create development branch of repository: " + repo.getName()));
+            logger.severe("Could not create development branch for repository: " + repo.getName());
-            logger.severe("Could not create development branch for repository: " + repo.getName() + '\n' + e.getMessage());
             e.printStackTrace();
         }
     }
@@ -314,8 +312,7 @@ public class GithubManager {
             logger.fine("Created repository: " + repo.getName());
             return repo;
         } catch (IOException e) {
-            logger.severe("Could not create repository: " + name + '\n' + e.getMessage());
+            logger.severe("Could not create repository: " + name);
-            InitializerApp.organization.addError(new Error(Severity.CRITICAL, "Could not create repository: " + name));
             e.printStackTrace();
             return null;
         }

src/main/java/nl/andrewlalis/model/Student.java

@@ -1,9 +1,5 @@
 package nl.andrewlalis.model;
 
-import nl.andrewlalis.model.error.Error;
-import nl.andrewlalis.model.error.Severity;
-import nl.andrewlalis.ui.view.InitializerApp;
-
 import java.util.List;
 import java.util.Map;
 import java.util.logging.Logger;
@@ -49,12 +45,7 @@ public class Student extends Person {
     public StudentTeam getPreferredTeam(Map<Integer, Student> studentMap) {
         StudentTeam t = new StudentTeam();
         for (int partnerNumber : this.getPreferredPartners()) {
-            if (!studentMap.containsKey(partnerNumber)) {
+            t.addMember(studentMap.get(partnerNumber));
-                InitializerApp.organization.addError(new Error(Severity.MEDIUM, "Student " + this.getNumber() + " has non-existent preferred partner with id: " + partnerNumber));
-                logger.warning("Student has non-existent partner id: " + partnerNumber + '\n' + this);
-            } else {
-                t.addMember(studentMap.get(partnerNumber));
-            }
         }
         t.addMember(this);
         return t;

src/main/java/nl/andrewlalis/ui/control/command/executables/DelegateStudentTeams.java

@@ -38,7 +38,7 @@ public class DelegateStudentTeams extends GithubExecutable {
 
     @Override
     protected boolean executeWithManager(GithubManager manager, String[] args) {
-        if (InitializerApp.organization.getStudentTeams().isEmpty()) {
+        if (this.app.getOrganization().getStudentTeams().isEmpty()) {
             JOptionPane.showMessageDialog(this.app, "There are no student teams! Please read some from a CSV file first.", "No Student Teams", JOptionPane.ERROR_MESSAGE);
             return false;
         }
@@ -47,7 +47,7 @@ public class DelegateStudentTeams extends GithubExecutable {
 
         if (dialog.isSuccessful()) {
             Map<TATeam, Integer> results = dialog.getResult();
-            List<StudentTeam> teams = InitializerApp.organization.getStudentTeams();
+            List<StudentTeam> teams = this.app.getOrganization().getStudentTeams();
             int initialTeamsSize = teams.size();
             Stack<StudentTeam> teamsStack = new Stack<>();
             // Randomize the ordering of the student teams here.
@@ -61,7 +61,7 @@ public class DelegateStudentTeams extends GithubExecutable {
                 for (int i = 0; i < entry.getValue(); i++) {
                     team.addStudentTeam(teamsStack.pop());
                 }
-                InitializerApp.organization.getTaTeams().add(team);
+                this.app.getOrganization().getTaTeams().add(team);
             }
         } else {
             return false;

src/main/java/nl/andrewlalis/ui/control/command/executables/ListErrors.java

@@ -11,6 +11,11 @@ import java.util.logging.Logger;
  */
 public class ListErrors implements Executable {
 
+    /**
+     * A reference to the current application.
+     */
+    private InitializerApp app;
+
     /**
      * The logger for outputting debug info.
      */
@@ -19,13 +24,17 @@ public class ListErrors implements Executable {
         logger.setParent(Logger.getGlobal());
     }
 
+    public ListErrors(InitializerApp app) {
+        this.app = app;
+    }
+
     @Override
     public boolean execute(String[] args) {
         StringBuilder sb = new StringBuilder("Runtime Errors:\n");
-        if (InitializerApp.organization.getErrors().isEmpty()) {
+        if (this.app.getOrganization().getErrors().isEmpty()) {
             sb.append("None");
         }
-        for (Error error : InitializerApp.organization.getErrors()) {
+        for (Error error : this.app.getOrganization().getErrors()) {
             sb.append(error).append('\n');
         }
         logger.info(sb.toString());

src/main/java/nl/andrewlalis/ui/control/command/executables/ReadStudentsFile.java

@@ -17,6 +17,15 @@ import java.util.List;
  */
 public class ReadStudentsFile implements Executable {
 
+    /**
+     * A reference to the current application, which contains the model for storing information.
+     */
+    private InitializerApp app;
+
+    public ReadStudentsFile(InitializerApp app) {
+        this.app = app;
+    }
+
     @Override
     public boolean execute(String[] args) {
         if (args.length < 2) {
@@ -28,7 +37,7 @@ public class ReadStudentsFile implements Executable {
         if (teams == null) {
             return false;
         }
-        InitializerApp.organization.setStudentTeams(teams);
+        this.app.getOrganization().setStudentTeams(teams);
         return true;
     }
 }

src/main/java/nl/andrewlalis/ui/control/command/executables/SetupStudentRepos.java

@@ -7,13 +7,26 @@ import nl.andrewlalis.ui.view.InitializerApp;
 
 import java.util.List;
 
+/**
+ * This executable, when run, sets up all student repositories.
+ */
 public class SetupStudentRepos extends GithubExecutable {
+
+    /**
+     * A reference to the current application.
+     */
+    private InitializerApp app;
+
+    public SetupStudentRepos(InitializerApp app) {
+        this.app = app;
+    }
+
     @Override
     protected boolean executeWithManager(GithubManager manager, String[] args) {
         if (args.length < 1) {
             return false;
         }
-        List<TATeam> taTeams = InitializerApp.organization.getTaTeams();
+        List<TATeam> taTeams = this.app.getOrganization().getTaTeams();
         for (TATeam team : taTeams) {
             for (StudentTeam studentTeam : team.getStudentTeams()) {
                 manager.setupStudentRepo(studentTeam, team, args[0]);

src/main/java/nl/andrewlalis/ui/view/InitializerApp.java

@@ -42,7 +42,7 @@ public class InitializerApp extends JFrame {
     /**
      * The organization object, which contains all important state information.
      */
-    public static Organization organization;
+    private Organization organization;
 
     /**
      * Constructs a new instance of the main application frame, with both an executor, and organization model.
@@ -52,6 +52,7 @@ public class InitializerApp extends JFrame {
      */
     public InitializerApp(CommandExecutor executor) {
         this.executor = executor;
+        this.organization = new Organization();
 
         // UI initialization.
         ImageIcon icon = new ImageIcon(getClass().getResource("/image/icon.png"));
@@ -221,6 +222,10 @@ public class InitializerApp extends JFrame {
         return this.accessTokenField.getText().trim();
     }
 
+    public Organization getOrganization() {
+        return this.organization;
+    }
+
     public void setAccessToken(String accessToken) {
         this.accessTokenField.setText(accessToken);
     }

src/main/java/nl/andrewlalis/ui/view/dialogs/delegateStudentTeams/DelegateStudentTeamsDialog.java

@@ -48,7 +48,7 @@ public class DelegateStudentTeamsDialog extends JDialog {
         super(parentApp, "Delegate Student Teams", true);
         this.manager = manager;
         this.teamSpinners = new ArrayList<>();
-        this.totalStudentTeamsCount = InitializerApp.organization.getStudentTeams().size();
+        this.totalStudentTeamsCount = parentApp.getOrganization().getStudentTeams().size();
         this.setDefaultCloseOperation(DISPOSE_ON_CLOSE);
 
         this.initUI();

src/main/java/nl/andrewlalis/util/TeamGenerator.java

@@ -39,7 +39,6 @@ public class TeamGenerator {
         logger.fine("Generating teams of size " + teamSize);
         if (teamSize < 1) {
             logger.severe("Invalid team size.");
-            InitializerApp.organization.addError(new Error(Severity.CRITICAL, "Invalid team size while generating teams from CSV."));
             throw new IllegalArgumentException("StudentTeam size must be greater than or equal to 1. Got " + teamSize);
         }
         logger.fine("Parsing CSV file.");
@@ -51,7 +50,6 @@ public class TeamGenerator {
             studentMap = readAllStudents(records, teamSize);
         } catch (ArrayIndexOutOfBoundsException e) {
             logger.severe("StudentTeam size does not match column count in records.");
-            InitializerApp.organization.addError(new Error(Severity.CRITICAL, "Team size does not match column count in records."));
             throw new IllegalArgumentException("StudentTeam size does not match column count in records.");
         }
 
@@ -156,11 +154,17 @@ public class TeamGenerator {
             }
             Student s = new Student(Integer.parseInt(record.get(3)), record.get(2), record.get(1), record.get(4), preferredIds);
             if (studentMap.containsValue(s)) {
-                InitializerApp.organization.addError(new Error(Severity.HIGH, "Duplicate entries for student:\n" + s + "\nSince records are in chronological order, this more recent duplicate will override the previous value."));
                 logger.warning("Duplicate entry found for student: " + s + "\nOverwriting previous value.");
             }
             studentMap.put(s.getNumber(), s);
         }
+
+        // Perform a safety check to ensure all preferred partners are valid students.
+        for (Map.Entry<Integer, Student> entry : studentMap.entrySet()) {
+            // Remove any ids that don't exist in the whole list of students.
+            entry.getValue().getPreferredPartners().removeIf(partnerId -> !studentMap.containsKey(partnerId));
+        }
+        // At this point, all students are valid, and all preferred partners are valid.
         logger.fine("Read " + studentMap.size() + " students from records.");
         return studentMap;
     }