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

@@ -31,21 +31,23 @@ public class Main {
         // Command executor which will be used by all actions the user can do.
         CommandExecutor executor = new CommandExecutor();
 
-        // Main application model.
+        // Main application model is stored as a static variable that is accessible everywhere.
-        Organization organization = new Organization();
+        InitializerApp.organization = new Organization();
 
         // Initialize User Interface.
-        InitializerApp app = new InitializerApp(executor, organization);
+        InitializerApp app = new InitializerApp(executor);
         app.begin();
         app.setAccessToken(userOptions.get("token"));
 
         // Initialize executable commands.
-        executor.registerCommand("read_students", new ReadStudentsFile(organization));
+        executor.registerCommand("read_students", new ReadStudentsFile(InitializerApp.organization));
         executor.registerCommand("archive_all", new ArchiveRepos());
         executor.registerCommand("generate_assignments", new GenerateAssignmentsRepo());
         executor.registerCommand("define_ta_teams", new DefineTaTeams(app));
 
-        logger.info("GithubManager for Github Repositories in Educational Organizations. Program initialized.");
+        logger.info("GithubManager for Github Repositories in Educational Organizations.\n" +
+                "© Andrew Lalis (2018), All rights reserved.\n" +
+                "Program initialized.");
     }
 
 }

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

@@ -2,7 +2,13 @@ package nl.andrewlalis.git_api;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.fasterxml.jackson.databind.node.ObjectNode;
-import nl.andrewlalis.model.*;
+import nl.andrewlalis.model.Student;
+import nl.andrewlalis.model.StudentTeam;
+import nl.andrewlalis.model.TATeam;
+import nl.andrewlalis.model.TeachingAssistant;
+import nl.andrewlalis.model.error.Error;
+import nl.andrewlalis.model.error.Severity;
+import nl.andrewlalis.ui.view.InitializerApp;
 import org.apache.http.HttpResponse;
 import org.apache.http.client.methods.HttpPatch;
 import org.apache.http.entity.StringEntity;
@@ -81,7 +87,7 @@ public class GithubManager {
     public List<TeachingAssistant> getMembers() {
         List<TeachingAssistant> teachingAssistants = new ArrayList<>();
         try {
-            for (GHUser member : this.organization.getMembers()) {
+            for (GHUser member : this.organization.listMembers().asList()) {
                 teachingAssistants.add(new TeachingAssistant(-1, member.getName(), member.getEmail(), member.getLogin()));
             }
         } catch (IOException e) {
@@ -91,34 +97,6 @@ public class GithubManager {
         return teachingAssistants;
     }
 
-    /**
-     * Initializes the github repository for all studentTeams given.
-     *
-     * Creates for the entire organization:
-     * - an assignments repository with protected master branch and TA permissions.
-     * Creates for each team:
-     * - a repository
-     * - protected master branch
-     * - development branch
-     * - adds students to repository
-     * - adds all students to assignments repository.
-     * @param studentTeams The list of student studentTeams.
-     * @param teamAll The team of all teaching assistants.
-     * @param assignmentsRepoName The name of the assignments repo.
-     * @throws Exception If an error occurs while initializing the github repositories.
-     */
-    public void initializeGithubRepos(List<StudentTeam> studentTeams, TATeam teamAll, String assignmentsRepoName) throws Exception {
-        this.setupAssignmentsRepo(assignmentsRepoName, "fuck the police", teamAll.getName());
-
-        StudentTeam t = new StudentTeam();
-        Student s = new Student(3050831, "Andrew Lalis", "andrewlalisofficial@gmail.com", "andrewlalis", null);
-        t.addMember(s);
-        t.setId(42);
-
-        this.setupStudentTeam(t, teamAll.getGithubTeam(), "advoop_2018");
-        // TODO: Finish this method.
-    }
-
     /**
      * Sets up the organization's assignments repository, and grants permissions to all teaching assistants.
      * @param assignmentsRepoName The name of the assignments repository.
@@ -131,6 +109,7 @@ 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.");
         }
@@ -155,46 +134,45 @@ public class GithubManager {
      * @param team The student team to set up.
      * @param taTeam The team of teaching assistants that is responsible for these students.
      * @param prefix The prefix to append to the front of the repo name.
-     * @throws IOException If an HTTP request fails.
      */
-    public void setupStudentTeam(StudentTeam team, GHTeam taTeam, String prefix) throws IOException {
+    public void setupStudentTeam(StudentTeam team, TATeam taTeam, String prefix) {
         // First check that the assignments repo exists, otherwise no invitations can be sent.
         if (this.assignmentsRepo == null) {
             logger.warning("Assignments repository must be created before student repositories.");
             return;
         }
 
-        GHRepository repo = this.createRepository(team.generateUniqueName(prefix), taTeam, team.generateRepoDescription(), false, true, false);
+        GHRepository repo = this.createRepository(team.generateUniqueName(prefix), taTeam.getGithubTeam(), team.generateRepoDescription(), false, true, false);
 
         if (repo == null) {
             logger.severe("Repository for student team " + team.getId() + " could not be created.");
             return;
         }
 
-        this.protectMasterBranch(repo, taTeam);
+        this.protectMasterBranch(repo, taTeam.getGithubTeam());
         this.createDevelopmentBranch(repo);
+        this.addTATeamAsAdmin(repo, taTeam.getGithubTeam());
+        this.inviteStudentsToRepos(team, repo);
 
-        taTeam.add(repo, GHOrganization.Permission.ADMIN);
+        team.setRepository(repo);
-        logger.fine("Added team " + taTeam.getName() + " as admin to repository: " + repo.getName());
+        team.setTaTeam(taTeam);
-
-        List<GHUser> users = new ArrayList<>();
-        for (Student student : team.getStudents()) {
-            GHUser user = this.github.getUser(student.getGithubUsername());
-            users.add(user);
-        }
-
-        repo.addCollaborators(users);
-        this.assignmentsRepo.addCollaborators(users);
     }
 
     /**
      * Deletes all repositories in the organization.
-     * @throws IOException if an error occurs with sending requests.
+     * @param substring The substring which repository names should contain to be deleted.
      */
-    public void deleteAllRepositories() throws IOException {
+    public void deleteAllRepositories(String substring) {
         List<GHRepository> repositories = this.organization.listRepositories().asList();
         for (GHRepository repo : repositories) {
-            repo.delete();
+            if (repo.getName().contains(substring)) {
+                try {
+                    repo.delete();
+                } catch (IOException e) {
+                    InitializerApp.organization.addError(new Error(Severity.HIGH, "Could not delete repository: " + repo.getName()));
+                    e.printStackTrace();
+                }
+            }
         }
     }
 
@@ -202,7 +180,7 @@ public class GithubManager {
      * Archives all repositories whose name contains the given substring.
      * @param sub Any repository containing this substring will be archived.
      */
-    public void archiveAllRepositories(String sub) throws IOException {
+    public void archiveAllRepositories(String sub) {
         List<GHRepository> repositories = this.organization.listRepositories().asList();
         for (GHRepository repo : repositories) {
             if (repo.getName().contains(sub)) {
@@ -215,21 +193,61 @@ public class GithubManager {
      * Archives a repository so that it can no longer be manipulated.
      * TODO: Change to using Github API instead of Apache HttpUtils.
      * @param repo The repository to archive.
-     * @throws IOException If an error occurs with the HTTP request.
      */
-    public void archiveRepository(GHRepository repo) throws IOException {
+    private void archiveRepository(GHRepository repo) {
-        HttpPatch patch = new HttpPatch("https://api.github.com/repos/" + repo.getFullName() + "?access_token=" + this.accessToken);
+        try {
-        CloseableHttpClient client = HttpClientBuilder.create().build();
+            HttpPatch patch = new HttpPatch("https://api.github.com/repos/" + repo.getFullName() + "?access_token=" + this.accessToken);
-        ObjectMapper mapper = new ObjectMapper();
+            CloseableHttpClient client = HttpClientBuilder.create().build();
-        ObjectNode root = mapper.createObjectNode();
+            ObjectMapper mapper = new ObjectMapper();
-        root.put("archived", true);
+            ObjectNode root = mapper.createObjectNode();
-        String json = mapper.writeValueAsString(root);
+            root.put("archived", true);
-        patch.setEntity(new StringEntity(json));
+            String json = mapper.writeValueAsString(root);
-        HttpResponse response = client.execute(patch);
+            patch.setEntity(new StringEntity(json));
-        if (response.getStatusLine().getStatusCode() != 200) {
+            HttpResponse response = client.execute(patch);
-            throw new IOException("Could not archive repository: " + repo.getName() + ". Code: " + response.getStatusLine().getStatusCode());
+            if (response.getStatusLine().getStatusCode() != 200) {
+                throw new IOException("Could not archive repository: " + repo.getName() + ". Code: " + response.getStatusLine().getStatusCode());
+            }
+            logger.info("Archived repository: " + repo.getFullName());
+        } catch (IOException e) {
+            InitializerApp.organization.addError(new Error(Severity.HIGH, "Could not archive repository: " + repo.getName()));
+        }
+    }
+
+    /**
+     * Invites students in a team to their repository, and the assignments repository.
+     * @param team The team of students to invite as collaborators.
+     * @param repo The repository created for the students.
+     */
+    private void inviteStudentsToRepos(StudentTeam team, GHRepository repo) {
+        try {
+            logger.finest("Adding students from team: " + team.getId() + " as collaborators.");
+            List<GHUser> users = new ArrayList<>();
+            for (Student student : team.getStudents()) {
+                GHUser user = this.github.getUser(student.getGithubUsername());
+                users.add(user);
+            }
+
+            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.warning("Could not add students as collaborators to assignments or their repo.");
+        }
+    }
+
+    /**
+     * Adds a teaching assistant team as admins to a particular student repository.
+     * @param studentRepo The student repository.
+     * @param taTeam The team to give admin rights.
+     */
+    private void addTATeamAsAdmin(GHRepository studentRepo, GHTeam taTeam) {
+        try {
+            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());
         }
-        logger.info("Archived repository: " + repo.getFullName());
     }
 
     /**
@@ -248,6 +266,7 @@ 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();
         }
@@ -263,6 +282,7 @@ 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() + '\n' + e.getMessage());
             e.printStackTrace();
         }
@@ -276,7 +296,7 @@ public class GithubManager {
      * @param hasWiki Whether the repo has a wiki enabled.
      * @param hasIssues Whether the repo has issues enabled.
      * @param isPrivate Whether or not the repository is private.
-     * @return The repository that was created, or
+     * @return The repository that was created, or null if it could not be created.
      */
     private GHRepository createRepository(String name, GHTeam taTeam, String description, boolean hasWiki, boolean hasIssues, boolean isPrivate){
         try {
@@ -286,12 +306,13 @@ public class GithubManager {
             builder.issues(hasIssues);
             builder.description(description);
             builder.gitignoreTemplate("Java");
-            builder.private_(isPrivate); // TODO: Change this to true for production
+            builder.private_(isPrivate);
             GHRepository repo = builder.create();
             logger.fine("Created repository: " + repo.getName());
             return repo;
         } catch (IOException e) {
             logger.severe("Could not create repository: " + name + '\n' + e.getMessage());
+            InitializerApp.organization.addError(new Error(Severity.CRITICAL, "Could not create repository: " + name));
             e.printStackTrace();
             return null;
         }

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

@@ -1,16 +1,17 @@
 package nl.andrewlalis.model;
 
-import com.sun.org.apache.xpath.internal.operations.Or;
+import nl.andrewlalis.model.error.Error;
 
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Observable;
 
 /**
  * This class represents the overarching model container for the entire application, and holds in memory all student
  * teams created, teaching assistant teams, and any other state information that would be needed by the user interface
  * or runtime executables.
  */
-public class Organization {
+public class Organization extends Observable {
 
     /**
      * A list of all student teams in this organization. This is generated from a CSV file supplied after many students
@@ -18,11 +19,18 @@ public class Organization {
      */
     private List<StudentTeam> studentTeams;
 
+    /**
+     * A queue of errors that accumulates as the program runs. These will be output to the user after execution of
+     * critical sections, so that inevitable errors due to input imperfections are not overlooked.
+     */
+    private List<Error> errors;
+
     /**
      * Constructs a new Organization object with all instance variables initialized to empty values.
      */
     public Organization() {
         this.studentTeams = new ArrayList<>();
+        this.errors = new ArrayList<>();
     }
 
     /**
@@ -38,9 +46,25 @@ public class Organization {
         return this.studentTeams;
     }
 
+    public List<Error> getErrors() {
+        return this.errors;
+    }
+
     // SETTERS
     public void setStudentTeams(List<StudentTeam> teams) {
         this.studentTeams = teams;
+        this.setChanged();
+        this.notifyObservers();
+    }
+
+    /**
+     * Adds an error to the list of accumulated errors.
+     * @param newError The newly generated error to add.
+     */
+    public void addError(Error newError) {
+        this.errors.add(newError);
+        this.setChanged();
+        this.notifyObservers();
     }
 
 }

src/main/java/nl/andrewlalis/model/error/Error.java

@@ -0,0 +1,45 @@
+package nl.andrewlalis.model.error;
+
+import java.text.DateFormat;
+import java.text.SimpleDateFormat;
+import java.util.Date;
+
+/**
+ * Represents an error that occurs, but does not stop the application while running. Different from an exception in that
+ * errors are meant to be added to a list and processed at a later time, and not hinder the operations in the present.
+ */
+public class Error {
+
+    /**
+     * The time at which this error occurred.
+     */
+    private long timestamp;
+
+    /**
+     * The severity of the error.
+     */
+    private Severity severity;
+
+    /**
+     * A custom error message generated at the time of the error.
+     */
+    private String message;
+
+    /**
+     * Constructs a new Error with a severity and message.
+     * @param severity The severity of the message.
+     * @param message The custom generated error message for this error.
+     */
+    public Error(Severity severity, String message) {
+        this.timestamp = System.currentTimeMillis();
+        this.severity = severity;
+        this.message = message;
+    }
+
+    @Override
+    public String toString() {
+        DateFormat df = new SimpleDateFormat("dd/MM/yyyy HH:mm:ss");
+        String dateString = df.format(new Date(this.timestamp));
+        return dateString + ' ' + this.severity.toString() + ": " + this.message;
+    }
+}

src/main/java/nl/andrewlalis/model/error/Severity.java

@@ -0,0 +1,12 @@
+package nl.andrewlalis.model.error;
+
+/**
+ * Represents the different levels of severity for errors.
+ */
+public enum Severity {
+    CRITICAL,       // Anything which happens and could have serious side-effects or massive implications system-wide.
+    HIGH,           // Errors which should be at the top of priority to sort out after a procedure is executed.
+    MEDIUM,         // Medium errors are, as the name implies, of a medium priority.
+    LOW,            // Low severity errors are the smallest errors that should be processed soon to avoid issues.
+    MINOR           // Minor errors are so insignificant that they may not even require user intervention.
+}

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

@@ -2,6 +2,10 @@ package nl.andrewlalis.ui.control.command.executables;
 
 import nl.andrewlalis.git_api.GithubManager;
 
+/**
+ * An executable which opens up a dialog to allow a user to delegate how many student teams each TATeam gets to manage,
+ * and actually generate the student repositories using the manager.
+ */
 public class GenerateStudentRepos extends GithubExecutable {
 
     @Override

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

@@ -2,7 +2,10 @@ package nl.andrewlalis.ui.control.command.executables;
 
 import nl.andrewlalis.model.Organization;
 import nl.andrewlalis.model.StudentTeam;
+import nl.andrewlalis.model.error.Error;
+import nl.andrewlalis.model.error.Severity;
 import nl.andrewlalis.ui.control.command.Executable;
+import nl.andrewlalis.ui.view.InitializerApp;
 import nl.andrewlalis.util.FileUtils;
 
 import java.util.List;
@@ -17,15 +20,6 @@ import java.util.List;
  */
 public class ReadStudentsFile implements Executable {
 
-    /**
-     * A reference to the application's organization model.
-     */
-    private Organization organization;
-
-    public ReadStudentsFile(Organization organization) {
-        this.organization = organization;
-    }
-
     @Override
     public boolean execute(String[] args) {
         if (args.length < 2) {
@@ -37,7 +31,7 @@ public class ReadStudentsFile implements Executable {
         if (teams == null) {
             return false;
         }
-        this.organization.setStudentTeams(teams);
+        InitializerApp.organization.setStudentTeams(teams);
         return true;
     }
 }

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

@@ -1,15 +1,12 @@
 package nl.andrewlalis.ui.view;
 
-import com.sun.org.apache.xpath.internal.operations.Or;
 import nl.andrewlalis.model.Organization;
-import nl.andrewlalis.model.StudentTeam;
 import nl.andrewlalis.ui.control.OutputTextHandler;
 import nl.andrewlalis.ui.control.command.CommandExecutor;
 import nl.andrewlalis.ui.control.listeners.*;
 
 import javax.swing.*;
 import java.awt.*;
-import java.util.List;
 import java.util.logging.Level;
 import java.util.logging.Logger;
 
@@ -44,19 +41,16 @@ public class InitializerApp extends JFrame {
     /**
      * The organization object, which contains all important state information.
      */
-    private Organization organization;
+    public static Organization organization;
 
     /**
      * Constructs a new instance of the main application frame, with both an executor, and organization model.
      *
      * @param executor The command executor, which is passed to any action listeners, so that buttons in this interface
      *                 may execute commands in the same way that the command line can.
-     * @param organization A reference to the application's organization model, which holds all important runtime state
-     *                     information.
      */
-    public InitializerApp(CommandExecutor executor, Organization organization) {
+    public InitializerApp(CommandExecutor executor) {
         this.executor = executor;
-        this.organization = organization;
 
         // UI initialization.
         ImageIcon icon = new ImageIcon(getClass().getResource("/image/icon.png"));

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

@@ -2,6 +2,9 @@ package nl.andrewlalis.util;
 
 import nl.andrewlalis.model.Student;
 import nl.andrewlalis.model.StudentTeam;
+import nl.andrewlalis.model.error.Error;
+import nl.andrewlalis.model.error.Severity;
+import nl.andrewlalis.ui.view.InitializerApp;
 import org.apache.commons.csv.CSVFormat;
 import org.apache.commons.csv.CSVRecord;
 
@@ -36,6 +39,7 @@ 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.");
@@ -47,6 +51,7 @@ 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.");
         }