From 22aba33af7ae3a3851f5a0da5f53f7645e7e5254 Mon Sep 17 00:00:00 2001
From: Michael Manis <electricpyrotechnic@gmail.com>
Date: Thu, 7 Sep 2017 18:11:09 -0400
Subject: [PATCH 01/40] Initial commit + tests

---
 pycanvasgrader/pycanvasgrader.py | 70 ++++++++++++++++++++++++++++++++
 pycanvasgrader/test_grader.py    | 32 +++++++++++++++
 2 files changed, 102 insertions(+)
 create mode 100644 pycanvasgrader/pycanvasgrader.py
 create mode 100644 pycanvasgrader/test_grader.py

diff --git a/pycanvasgrader/pycanvasgrader.py b/pycanvasgrader/pycanvasgrader.py
new file mode 100644
index 0000000..484f992
--- /dev/null
+++ b/pycanvasgrader/pycanvasgrader.py
@@ -0,0 +1,70 @@
+#!
+"""
+Automates the grading of programming assignments on Canvas.
+MUST create an 'access.token' file in the same directory as this file with a valid Canvas OAuth2 token
+"""
+
+# built-ins
+import py
+import json
+
+# 3rd-party
+import requests
+
+# globals
+RUN_WITH_TESTS = True
+
+
+class PyCanvasGrader:
+    """
+    A PyCanvasGrader object; responsible for communicating with the Canvas API
+    """
+    def __init__(self):
+        self.token = self.authenticate()
+        if self.token == 'none':
+            print('Unable to retrieve OAuth2 token')
+            exit()
+
+        self.session = requests.Session()
+        self.session.headers.update({'Authorization': 'Bearer ' + self.token})
+
+    @staticmethod
+    def authenticate() -> str:
+        """
+        Responsible for retrieving the OAuth2 token for the session.
+        :return: The OAuth2 token
+
+        TODO Talk about "proper" OAuth2 authentication
+        """
+
+        with open('access.token', 'r', encoding='UTF-8') as access_file:
+            for line in access_file:
+                token = line.strip()
+                if isinstance(token, str) and len(token) > 2:
+                    return token
+        return 'none'
+
+    def courses(self, enrollment_type: str=None) -> list:
+        """
+
+        :param enrollment_type: teacher, student, ta, observer, designer
+        :return: A list of the user's courses as dictionaries, optionally filtered by enrollment_type
+        """
+        url = 'https://canvas.instructure.com/api/v1/courses'
+        if enrollment_type is not None:
+            url += '?enrollment_type=' + enrollment_type
+
+        r = self.session.get(url)
+        response = json.loads(r.text)
+        return response
+
+
+def main():
+    g = PyCanvasGrader()
+    print(g.courses('ta'))
+
+
+if __name__ == '__main__':
+    if RUN_WITH_TESTS:
+        py.test.cmdline.main()
+    main()
diff --git a/pycanvasgrader/test_grader.py b/pycanvasgrader/test_grader.py
new file mode 100644
index 0000000..fdd0e04
--- /dev/null
+++ b/pycanvasgrader/test_grader.py
@@ -0,0 +1,32 @@
+"""
+Unit tests for PyCanvasGrader
+"""
+# built-ins
+import json
+
+# 3rd-party
+import requests
+from requests_oauthlib import OAuth2
+
+# package-specific
+from .pycanvasgrader import PyCanvasGrader
+
+
+class TestGrader:
+    def test_authenticate(self):
+        """
+        Make sure the authentication function returns a valid key
+        """
+        token = PyCanvasGrader().authenticate()
+        s = requests.Session()
+        r = s.get('https://canvas.instructure.com/api/v1/courses', headers={'Authorization': 'Bearer ' + token})
+        resp = json.loads(r.text)
+        assert type(resp) == list and resp[0].get('id') is not None
+
+    def test_courses(self):
+        """
+        Make sure that courses always returns a list
+        """
+        g = PyCanvasGrader()
+        courses = g.courses('designer')
+        assert type(courses) == list

From 46cc1c6a1ed6793e054c4f13d7ccf549953d9902 Mon Sep 17 00:00:00 2001
From: Michael Manis <electricpyrotechnic@gmail.com>
Date: Thu, 7 Sep 2017 18:37:59 -0400
Subject: [PATCH 02/40] added requirements.txt

---
 pycanvasgrader/requirements.txt | 10 ++++++++++
 1 file changed, 10 insertions(+)
 create mode 100644 pycanvasgrader/requirements.txt

diff --git a/pycanvasgrader/requirements.txt b/pycanvasgrader/requirements.txt
new file mode 100644
index 0000000..a925c1e
--- /dev/null
+++ b/pycanvasgrader/requirements.txt
@@ -0,0 +1,10 @@
+certifi==2017.7.27.1
+chardet==3.0.4
+colorama==0.3.9
+idna==2.6
+oauthlib==2.0.3
+py==1.4.34
+pytest==3.2.2
+requests==2.18.4
+requests-oauthlib==0.8.0
+urllib3==1.22

From 4aac6e10380a9f59bcab6b211e6f32bb732ef757 Mon Sep 17 00:00:00 2001
From: Michael Manis <electricpyrotechnic@gmail.com>
Date: Thu, 7 Sep 2017 19:39:15 -0400
Subject: [PATCH 03/40] updated requirements.txt

---
 pycanvasgrader/requirements.txt | 3 ---
 pycanvasgrader/test_grader.py   | 1 -
 2 files changed, 4 deletions(-)

diff --git a/pycanvasgrader/requirements.txt b/pycanvasgrader/requirements.txt
index a925c1e..ba79371 100644
--- a/pycanvasgrader/requirements.txt
+++ b/pycanvasgrader/requirements.txt
@@ -1,10 +1,7 @@
 certifi==2017.7.27.1
 chardet==3.0.4
-colorama==0.3.9
 idna==2.6
-oauthlib==2.0.3
 py==1.4.34
 pytest==3.2.2
 requests==2.18.4
-requests-oauthlib==0.8.0
 urllib3==1.22
diff --git a/pycanvasgrader/test_grader.py b/pycanvasgrader/test_grader.py
index fdd0e04..a68bc8f 100644
--- a/pycanvasgrader/test_grader.py
+++ b/pycanvasgrader/test_grader.py
@@ -6,7 +6,6 @@
 
 # 3rd-party
 import requests
-from requests_oauthlib import OAuth2
 
 # package-specific
 from .pycanvasgrader import PyCanvasGrader

From 673aec5f52e2d37b7061d320a694f5c2643d6e59 Mon Sep 17 00:00:00 2001
From: Michael Manis <electricpyrotechnic@gmail.com>
Date: Thu, 7 Sep 2017 19:43:50 -0400
Subject: [PATCH 04/40] added __init__.py

---
 pycanvasgrader/__init__.py | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 pycanvasgrader/__init__.py

diff --git a/pycanvasgrader/__init__.py b/pycanvasgrader/__init__.py
new file mode 100644
index 0000000..e69de29

From bec9e16aad98a8c3b343d40f7fdbc986f88844fd Mon Sep 17 00:00:00 2001
From: Michael Manis <electricpyrotechnic@gmail.com>
Date: Fri, 8 Sep 2017 01:46:43 -0400
Subject: [PATCH 05/40] Created skeleton of command line

---
 pycanvasgrader/pycanvasgrader.py | 165 +++++++++++++++++++++++++++++--
 pycanvasgrader/test_grader.py    |  19 +++-
 2 files changed, 176 insertions(+), 8 deletions(-)

diff --git a/pycanvasgrader/pycanvasgrader.py b/pycanvasgrader/pycanvasgrader.py
index 484f992..27c758d 100644
--- a/pycanvasgrader/pycanvasgrader.py
+++ b/pycanvasgrader/pycanvasgrader.py
@@ -7,6 +7,8 @@
 # built-ins
 import py
 import json
+import os
+from zipfile import ZipFile
 
 # 3rd-party
 import requests
@@ -44,24 +46,173 @@ def authenticate() -> str:
                     return token
         return 'none'
 
+    def close(self):
+        self.session.close()
+
     def courses(self, enrollment_type: str=None) -> list:
         """
-
-        :param enrollment_type: teacher, student, ta, observer, designer
+        :param enrollment_type: (Optional) teacher, student, ta, observer, designer
         :return: A list of the user's courses as dictionaries, optionally filtered by enrollment_type
         """
         url = 'https://canvas.instructure.com/api/v1/courses'
         if enrollment_type is not None:
             url += '?enrollment_type=' + enrollment_type
 
-        r = self.session.get(url)
-        response = json.loads(r.text)
-        return response
+        response = self.session.get(url)
+        return json.loads(response.text)
+
+    def assignments(self, course_id: int, ungraded: bool=True) -> list:
+        """
+        :param course_id: Course ID to filter by
+        :param ungraded: Whether to filter assignments by only those that have ungraded work. Default: True
+        :return: A list of the course's assignments
+        """
+        url = 'https://canvas.instructure.com/api/v1/courses/' + str(course_id) + '/assignments'
+        if ungraded:
+            url += '?bucket=ungraded'
+
+        response = self.session.get(url)
+        return json.loads(response.text)
+
+    def submissions(self, course_id: int, assignment_id: int) -> list:
+        """
+        :param course_id: The ID of the course containing the assignment
+        :param assignment_id: The ID of the assignment
+        :return: A list of the assignment's submissions
+        """
+        url = 'https://canvas.instructure.com/api/v1/courses/' + str(course_id) + '/assignments/' + str(assignment_id) + '/submissions'
+
+        response = self.session.get(url)
+        return json.loads(response.text)
+
+    def user(self, user_id: int) -> dict:
+        """
+        :param user_id: The ID of the user
+        :return: A dictionary with the user's information
+        """
+        url = 'https://canvas.instructure.com/api/v1/users/' + str(user_id)
+
+        response = self.session.get(url)
+        return json.loads(response.text)
+
+
+def parse_zip(zip_file: str) -> dict:
+    """
+    Maps file names to user IDs from a zip of downloaded Canvas submissions
+    :param zip_file: The name of the zip file to parse
+    :return: if the zip can be parsed, a dictionary containing the user ID's mapped to the parsed file name, otherwise an empty dict
+    """
+    user_dict = {}
+
+    with ZipFile('zips/' + zip_file, 'r') as z:
+        for name in z.namelist():
+            if name.count('_') < 3:
+                print('Skipping file: ' + name + '. Invalid filename')
+            else:
+                (name, user_id, unknown, file) = name.split('_', maxsplit=3)
+                user_dict[user_id] = file
+    if len(user_dict) < 1:
+        print('Unable to read any files from the zip. Please check the file and try again')
+    return user_dict
+
+
+def choose_val(hi_num: int) -> int:
+    val = 'none'
+    while not str.isdigit(val) or (int(val) > hi_num or int(val) <= 0):
+        val = input()
+    return int(val)
+
+
+def choose_bool() -> bool:
+    val = 'none'
+    while not str.lower(val) in ['y', 'n', 'yes', 'no']:
+        val = input()
+    if val in ['y', 'yes']:
+        return True
+    else:
+        return False
+
+
+def choose_zip() -> str:
+    name = input()
+    if name[-4:] != '.zip':
+        name += '.zip'
+    if not os.path.isfile('zips/' + name):
+        print('Could not find the file. Make sure it is in the zips directory and try again:')
+        return choose_zip()
+    else:
+        return name
 
 
 def main():
-    g = PyCanvasGrader()
-    print(g.courses('ta'))
+    grader = PyCanvasGrader()
+    course_list = grader.courses('teacher')
+
+    print('Choose a course from the following list:')
+    for count, course in enumerate(course_list):
+        print('%i.\t%s (%s)' % (count + 1, course.get('name'), course.get('course_code')))
+
+    course_choice = choose_val(len(course_list)) - 1
+
+    print('Show only ungraded assignments? (y or n):')
+    ungraded = choose_bool()
+
+    course_id = course_list[course_choice].get('id')
+    assignment_list = grader.assignments(course_list[course_choice].get('id'), ungraded=ungraded)
+
+    print('Choose an assignment to grade:')
+    for count, assignment in enumerate(assignment_list):
+        print('%i.\t%s' % (count + 1, assignment.get('name')))
+
+    assignment_choice = choose_val(len(assignment_list)) - 1
+    assignment_id = assignment_list[assignment_choice].get('id')
+    print('If you haven\'t already, please download the most current submissions.zip for this assignment:\n' +
+          assignment_list[assignment_choice].get('submissions_download_url'))
+
+    invalid_zip = True
+    user_file_dict = {}
+    while invalid_zip:
+        print('Place the zip in the \'zips\' directory, and then enter the zip\'s name here:')
+        zip_file = choose_zip()
+
+        user_file_dict = parse_zip(zip_file)
+        if len(user_file_dict) > 0:
+            invalid_zip = False
+
+    submission_list = grader.submissions(course_id, assignment_id)
+    if len(submission_list) < 1:
+        print('There are no submissions for this assignment.')
+        grader.close()
+        main()
+        exit(0)
+
+    user_submission_dict = {}
+    for user_id, filename in user_file_dict.items():
+        for submission in submission_list:
+            if user_id in str(submission.get('user_id')):
+                user_submission_dict['user_id'] = submission['id']
+
+    if len(user_submission_dict) < 1:
+        print('Could not match any file names in the zip to any online submissions.')
+        grader.close()
+        main()
+        exit(0)
+
+    print('Successfully matched %i submission(s) to files in the zip file. Is this correct? (y or n):' % len(user_submission_dict))
+    correct = choose_bool()
+    if not correct:
+        grader.close()
+        main()
+        exit(0)
+
+    print('Students to grade: [Name (email)]')
+    for user_id in user_submission_dict:
+        user_data = grader.user(user_id)
+        print(str(user_data.get('name')) + '(%s)' % user_data.get('email'))
+
+    input('Press enter to begin grading')
+
+    print('done')
 
 
 if __name__ == '__main__':
diff --git a/pycanvasgrader/test_grader.py b/pycanvasgrader/test_grader.py
index a68bc8f..970fdfc 100644
--- a/pycanvasgrader/test_grader.py
+++ b/pycanvasgrader/test_grader.py
@@ -24,8 +24,25 @@ def test_authenticate(self):
 
     def test_courses(self):
         """
-        Make sure that courses always returns a list
+        Make sure that courses() always returns a list
         """
         g = PyCanvasGrader()
         courses = g.courses('designer')
         assert type(courses) == list
+
+    def test_assignments(self):
+        """
+        Make sure that assignments() always returns a list
+        """
+        g = PyCanvasGrader()
+        course_id = g.courses('teacher')[0].get('id')
+        assert type(g.assignments(course_id, ungraded=False)) == list
+
+    def test_submissions(self):
+        """
+        Make sure that submissions() always returns a list
+        """
+        g = PyCanvasGrader()
+        course_id = g.courses('teacher')[0].get('id')
+        assignment_id = g.assignments(course_id, ungraded=False)[0].get('id')
+        assert type(g.submissions(course_id, assignment_id)) == list

From 06520a29774a223e470eca2acf841478b4431990 Mon Sep 17 00:00:00 2001
From: Michael Manis <electricpyrotechnic@gmail.com>
Date: Fri, 8 Sep 2017 02:17:42 -0400
Subject: [PATCH 06/40] Better zip file experience, added comments to main
 function

---
 pycanvasgrader/pycanvasgrader.py | 44 +++++++++++++++++++-------------
 1 file changed, 26 insertions(+), 18 deletions(-)

diff --git a/pycanvasgrader/pycanvasgrader.py b/pycanvasgrader/pycanvasgrader.py
index 27c758d..b143c74 100644
--- a/pycanvasgrader/pycanvasgrader.py
+++ b/pycanvasgrader/pycanvasgrader.py
@@ -133,52 +133,59 @@ def choose_bool() -> bool:
         return False
 
 
-def choose_zip() -> str:
-    name = input()
-    if name[-4:] != '.zip':
-        name += '.zip'
-    if not os.path.isfile('zips/' + name):
-        print('Could not find the file. Make sure it is in the zips directory and try again:')
-        return choose_zip()
-    else:
-        return name
-
-
 def main():
+    # Initialize grading session and fetch courses
     grader = PyCanvasGrader()
     course_list = grader.courses('teacher')
 
+    # Have user select course
     print('Choose a course from the following list:')
     for count, course in enumerate(course_list):
         print('%i.\t%s (%s)' % (count + 1, course.get('name'), course.get('course_code')))
-
-    course_choice = choose_val(len(course_list)) - 1
+    course_choice = choose_val(len(course_list)) - 1  # the plus and minus 1 are to hide the 0-based numbering
 
     print('Show only ungraded assignments? (y or n):')
     ungraded = choose_bool()
-
     course_id = course_list[course_choice].get('id')
     assignment_list = grader.assignments(course_list[course_choice].get('id'), ungraded=ungraded)
 
+    # Have user choose assignment
     print('Choose an assignment to grade:')
     for count, assignment in enumerate(assignment_list):
         print('%i.\t%s' % (count + 1, assignment.get('name')))
-
     assignment_choice = choose_val(len(assignment_list)) - 1
     assignment_id = assignment_list[assignment_choice].get('id')
+
+    # Remind user to get latest zip file
     print('If you haven\'t already, please download the most current submissions.zip for this assignment:\n' +
           assignment_list[assignment_choice].get('submissions_download_url'))
 
+    input('\nPress enter when this you have placed this zip file into the /zips/ directory')
+
+    # Have user choose zip
     invalid_zip = True
     user_file_dict = {}
     while invalid_zip:
-        print('Place the zip in the \'zips\' directory, and then enter the zip\'s name here:')
-        zip_file = choose_zip()
+        zip_list = []
+        print('Choose a zip file to use:')
+        sub = 0 # This is to keep indices visually correct while excluding non-zip files
+        for count, zip_name in enumerate(os.listdir('zips')):
+            if zip_name.split('.')[-1] != 'zip':
+                sub += 1
+                continue
+            zip_list.append(zip_name)
+            print('%i.\t%s' % (count - sub + 1, zip_name))  # Again, the plus and minus 1 are to hide the 0-based numbering
+
+        selection = choose_val(len(zip_list)) - 1
+        zip_file = zip_list[selection]
 
         user_file_dict = parse_zip(zip_file)
         if len(user_file_dict) > 0:
             invalid_zip = False
+        else:
+            print('This zip is invalid. Make sure you do not change the names inside the zip and try again')
 
+    # Get list of submissions for this assignment
     submission_list = grader.submissions(course_id, assignment_id)
     if len(submission_list) < 1:
         print('There are no submissions for this assignment.')
@@ -186,6 +193,7 @@ def main():
         main()
         exit(0)
 
+    # Match the user IDs found in the zip with the IDs who submitted the assignment online
     user_submission_dict = {}
     for user_id, filename in user_file_dict.items():
         for submission in submission_list:
@@ -208,7 +216,7 @@ def main():
     print('Students to grade: [Name (email)]')
     for user_id in user_submission_dict:
         user_data = grader.user(user_id)
-        print(str(user_data.get('name')) + '(%s)' % user_data.get('email'))
+        print(str(user_data.get('name')) + '\t(%s)' % user_data.get('email'))
 
     input('Press enter to begin grading')
 

From 8bc7a8b479769bcd4c48fdd30eb395a707248caf Mon Sep 17 00:00:00 2001
From: Michael Manis <electricpyrotechnic@gmail.com>
Date: Fri, 8 Sep 2017 03:30:15 -0400
Subject: [PATCH 07/40] Created backbone of file testing

---
 pycanvasgrader/pycanvasgrader.py | 72 +++++++++++++++++++++++++++++++-
 1 file changed, 70 insertions(+), 2 deletions(-)

diff --git a/pycanvasgrader/pycanvasgrader.py b/pycanvasgrader/pycanvasgrader.py
index b143c74..99148c8 100644
--- a/pycanvasgrader/pycanvasgrader.py
+++ b/pycanvasgrader/pycanvasgrader.py
@@ -7,16 +7,84 @@
 # built-ins
 import py
 import json
+import re
 import os
+import subprocess
 from zipfile import ZipFile
 
 # 3rd-party
 import requests
 
 # globals
-RUN_WITH_TESTS = True
+RUN_WITH_TESTS = False
 
 
+class TestSkeleton:
+    """
+    An abstract skeleton to handle testing of a specific group of files
+    """
+    def __init__(self, commands: list, extensions: str=None, file_regex: str=None):
+        """
+        :param commands: A list of Command objects. These will be run in the order that they are added.
+        :param extensions: Which file extensions this skeleton applies to
+        :param file_regex: A regular expression to match files for this skeleton. Combines with extensions
+        """
+        if not any((extensions, file_regex)):
+            raise ValueError('Either extensions or file_regex must be defined')
+        self.commands = commands
+        self.extensions = extensions
+        self.file_regex = file_regex
+
+    # TODO Create tests
+    class Command:
+        """
+        An abstract command to be run in a console
+        """
+        def __init__(self, command: str, args: str, print_output: bool=True, output_match: str=None, output_regex: str=None, timeout: int=None):
+            """
+            :param command: The command to be run.
+            :param args: The arguments to pass to the command. Use %s to denote the file name
+            :param print_output: Whether to visibly print the output
+            :param output_match: An exact string that the output should match. If this and output_regex are None, then this Command always 'matches'
+            :param output_regex: A regular expression that the string should match. Combines with output_match.
+            If this and output_match are None, then this Command always 'matches'
+            :param timeout: Time, in seconds, that this Command should run for before timing out
+
+            """
+            self.command = command
+            self.args = args
+            self.output_match = output_match
+            self.output_regex = re.compile(output_regex)
+            self.print_output = print_output
+            self.timeout = timeout
+
+        def run(self):
+            """
+            Runs the Command
+            :return: A dictonary containing its return code, stdout, and stderr
+            """
+            proc = subprocess.run([self.command, self.args], stdout=subprocess.PIPE, stderr=subprocess.STDOUT, timeout=self.timeout, encoding='UTF-8')
+            return {'returncode': proc.returncode, 'stdout': proc.stdout, 'stderr': proc.stderr}
+
+        def run_and_match(self):
+            """
+            Runs the command and matches the output to the output_match/regex. If neither are defined then this always returns true
+            :return: Whether the output matched or not
+            """
+            result = self.run()
+            if self.print_output:
+                print(result['stdout'])
+
+            if not any((self.output_match, self.output_regex)):
+                return True
+
+            if self.output_match and self.output_match in result['stdout']:
+                return True
+
+            if self.output_regex.match(result['stdout']):
+                return True
+            return False
+
 class PyCanvasGrader:
     """
     A PyCanvasGrader object; responsible for communicating with the Canvas API
@@ -168,7 +236,7 @@ def main():
     while invalid_zip:
         zip_list = []
         print('Choose a zip file to use:')
-        sub = 0 # This is to keep indices visually correct while excluding non-zip files
+        sub = 0  # This is to keep indices visually correct while excluding non-zip files
         for count, zip_name in enumerate(os.listdir('zips')):
             if zip_name.split('.')[-1] != 'zip':
                 sub += 1

From c81cabb7b6861fd5bee1f80b5ed1821997f09491 Mon Sep 17 00:00:00 2001
From: Michael Manis <electricpyrotechnic@gmail.com>
Date: Fri, 8 Sep 2017 03:30:40 -0400
Subject: [PATCH 08/40] type-o

---
 pycanvasgrader/pycanvasgrader.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pycanvasgrader/pycanvasgrader.py b/pycanvasgrader/pycanvasgrader.py
index 99148c8..260d976 100644
--- a/pycanvasgrader/pycanvasgrader.py
+++ b/pycanvasgrader/pycanvasgrader.py
@@ -61,7 +61,7 @@ def __init__(self, command: str, args: str, print_output: bool=True, output_matc
         def run(self):
             """
             Runs the Command
-            :return: A dictonary containing its return code, stdout, and stderr
+            :return: A dictionary containing its return code, stdout, and stderr
             """
             proc = subprocess.run([self.command, self.args], stdout=subprocess.PIPE, stderr=subprocess.STDOUT, timeout=self.timeout, encoding='UTF-8')
             return {'returncode': proc.returncode, 'stdout': proc.stdout, 'stderr': proc.stderr}

From 7f3339b544bfb49c8d9c0af02a5aa5d51356650f Mon Sep 17 00:00:00 2001
From: Michael Manis <electricpyrotechnic@gmail.com>
Date: Fri, 8 Sep 2017 03:31:01 -0400
Subject: [PATCH 09/40] spacing

---
 pycanvasgrader/pycanvasgrader.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pycanvasgrader/pycanvasgrader.py b/pycanvasgrader/pycanvasgrader.py
index 260d976..8a652e5 100644
--- a/pycanvasgrader/pycanvasgrader.py
+++ b/pycanvasgrader/pycanvasgrader.py
@@ -85,6 +85,7 @@ def run_and_match(self):
                 return True
             return False
 
+
 class PyCanvasGrader:
     """
     A PyCanvasGrader object; responsible for communicating with the Canvas API

From 03db78c8f33289bac12930a2feb1ea2eb6e0d80e Mon Sep 17 00:00:00 2001
From: Michael Manis <electricpyrotechnic@gmail.com>
Date: Fri, 8 Sep 2017 18:04:11 -0400
Subject: [PATCH 10/40] First release

---
 pycanvasgrader/pycanvasgrader.py    | 302 ++++++++++++++++++++++------
 pycanvasgrader/skeletons/java.json  |  26 +++
 pycanvasgrader/temp/git_include.dir |   0
 pycanvasgrader/zips/submissions.zip | Bin 0 -> 1028 bytes
 4 files changed, 268 insertions(+), 60 deletions(-)
 create mode 100644 pycanvasgrader/skeletons/java.json
 create mode 100644 pycanvasgrader/temp/git_include.dir
 create mode 100644 pycanvasgrader/zips/submissions.zip

diff --git a/pycanvasgrader/pycanvasgrader.py b/pycanvasgrader/pycanvasgrader.py
index 8a652e5..ef3834b 100644
--- a/pycanvasgrader/pycanvasgrader.py
+++ b/pycanvasgrader/pycanvasgrader.py
@@ -2,6 +2,14 @@
 """
 Automates the grading of programming assignments on Canvas.
 MUST create an 'access.token' file in the same directory as this file with a valid Canvas OAuth2 token
+MUST clear temp directory before running program (TODO will fix this)
+REQUIRED File structure:
+- pycanvasgrader
+  -- skeletons
+  -- temp
+  -- zips
+  access.token
+  pycanvasgrader.py
 """
 
 # built-ins
@@ -23,67 +31,184 @@ class TestSkeleton:
     """
     An abstract skeleton to handle testing of a specific group of files
     """
-    def __init__(self, commands: list, extensions: str=None, file_regex: str=None):
+    def __init__(self, descriptor: str, commands: list, extensions: str=None, file_regex: str=None):
         """
+        :param descriptor: The description of this TestSkeleton
         :param commands: A list of Command objects. These will be run in the order that they are added.
-        :param extensions: Which file extensions this skeleton applies to
-        :param file_regex: A regular expression to match files for this skeleton. Combines with extensions
+        :param extensions: Which file extensions this skeleton applies to (Unimplemented)
+        :param file_regex: A regular expression to match files for this skeleton. Combines with extensions (Unimplemented)
         """
         if not any((extensions, file_regex)):
             raise ValueError('Either extensions or file_regex must be defined')
+        self.descriptor = descriptor
         self.commands = commands
         self.extensions = extensions
         self.file_regex = file_regex
 
-    # TODO Create tests
-    class Command:
+    @classmethod
+    def from_file(cls, filename):
+        with open('skeletons/' + filename) as skeleton_file:
+            data = json.load(skeleton_file)
+            try:
+                descriptor = data['descriptor']
+                commands = data['commands']
+                extensions = data.get('extensions')
+                file_regex = data.get('file_regex')
+                if not any((extensions, file_regex)):
+                    raise KeyError
+            except KeyError:
+                return None
+            else:
+                command_list = []
+                for json_dict in commands:
+                    command = Command.from_json_dict(commands[json_dict])
+                    if command is not None:
+                        command_list.append(command)
+
+                return TestSkeleton(descriptor, command_list, extensions, file_regex)
+
+    def run_tests(self) -> int:
+        total_score = 0
+        for count, command in enumerate(self.commands):
+            print('\n--Running command %i--' % count)
+            if command.run_and_match():
+                total_score += command.point_val
+            print('Current score: %i' % total_score)
+        return total_score
+
+
+# TODO Create tests
+class Command:
+    """
+    An abstract command to be run in a console
+    """
+    def __init__(self, command: str, args: str=None, target_file: str=None, ask_for_target: bool=False,
+                 include_filetype: bool=True, print_output: bool=True, output_match: str=None, output_regex: str=None,
+                 negate_match: bool=False, timeout: int=None, point_val: int=0):
         """
-        An abstract command to be run in a console
+        :param command: The command to be run.
+        :param args: The arguments to pass to the command. Use %s to denote a file name
+        :param target_file: The file to replace %s with
+        :param ask_for_target: Whether to prompt for a file in the current directory. Overrides file_target
+        :param include_filetype: Whether to include the filetype in the %s substitution
+        :param print_output: Whether to visibly print the output
+        :param output_match: An exact string that the output should match. If this and output_regex are None, then this Command always 'matches'
+        :param output_regex: A regular expression that the string should match. Combines with output_match.
+        If this and output_match are None, then this Command always 'matches'
+        :param negate_match: Whether to negate the result of checking output_match and output_regex
+        :param timeout: Time, in seconds, that this Command should run for before timing out
+        :param point_val: Amount of points that a successful match is worth (Can be negative)
         """
-        def __init__(self, command: str, args: str, print_output: bool=True, output_match: str=None, output_regex: str=None, timeout: int=None):
-            """
-            :param command: The command to be run.
-            :param args: The arguments to pass to the command. Use %s to denote the file name
-            :param print_output: Whether to visibly print the output
-            :param output_match: An exact string that the output should match. If this and output_regex are None, then this Command always 'matches'
-            :param output_regex: A regular expression that the string should match. Combines with output_match.
-            If this and output_match are None, then this Command always 'matches'
-            :param timeout: Time, in seconds, that this Command should run for before timing out
-
-            """
-            self.command = command
-            self.args = args
-            self.output_match = output_match
+        self.command = command
+        self.args = args
+        self.target_file = target_file
+        self.ask_for_target = ask_for_target
+        self.include_filetype = include_filetype
+        self.output_match = output_match
+        if output_regex is not None:
             self.output_regex = re.compile(output_regex)
-            self.print_output = print_output
-            self.timeout = timeout
-
-        def run(self):
-            """
-            Runs the Command
-            :return: A dictionary containing its return code, stdout, and stderr
-            """
-            proc = subprocess.run([self.command, self.args], stdout=subprocess.PIPE, stderr=subprocess.STDOUT, timeout=self.timeout, encoding='UTF-8')
-            return {'returncode': proc.returncode, 'stdout': proc.stdout, 'stderr': proc.stderr}
-
-        def run_and_match(self):
-            """
-            Runs the command and matches the output to the output_match/regex. If neither are defined then this always returns true
-            :return: Whether the output matched or not
-            """
-            result = self.run()
-            if self.print_output:
-                print(result['stdout'])
-
-            if not any((self.output_match, self.output_regex)):
-                return True
+        else:
+            self.output_regex = None
+        self.negate_match = negate_match
+        self.print_output = print_output
+        self.timeout = timeout
+        self.point_val = point_val
+
+    @classmethod
+    def from_json_dict(cls, json_dict: dict):
+        try:
+            command = json_dict['command']
+        except KeyError:
+            return None
+        else:
+            args = json_dict.get('args')
+            target_file = json_dict.get('target_file')
+            ask_for_target = json_dict.get('ask_for_target')
+            include_filetype = json_dict.get('include_filetype')
+            print_output = json_dict.get('print_output')
+            output_match = json_dict.get('output_match')
+            output_regex = json_dict.get('output_regex')
+            negate_match = json_dict.get('negate_match')
+            timeout = json_dict.get('timeout')
+            point_val = json_dict.get('point_val')
+
+            vars_dict = {'command': command, 'args': args, 'target_file': target_file,
+                         'ask_for_target': ask_for_target, 'include_filetype': include_filetype,
+                         'print_output': print_output, 'output_match': output_match, 'output_regex': output_regex,
+                         'negate_match': negate_match, 'timeout': timeout, 'point_val': point_val}
+            args_dict = {}
+            for var_name, val in vars_dict.items():
+                if val is not None:
+                    args_dict[var_name] = val
+            return Command(**args_dict)
+
+    @classmethod
+    def target_prompt(cls, command: str):
+        sub = 0
+        file_list = []
+        if len(os.listdir(os.getcwd())) < 1:
+            print('This directory is empty, unable to choose a file for "%s" command' % command)
+            return None
+
+        print('Select a file for the "%s" command:' % command)
+        for count, file_name in enumerate(os.listdir(os.getcwd())):
+            if os.path.isdir(file_name):
+                sub += 1
+                continue
+            file_list.append(file_name)
+            print('%i.\t%s' % (count - sub + 1, file_name))  # The plus and minus 1 are to hide the 0-based numbering
 
-            if self.output_match and self.output_match in result['stdout']:
-                return True
+        selection = choose_val(len(file_list)) - 1
+        return file_list[selection]
+
+    def run(self) -> dict:
+        """
+        Runs the Command
+        :return: A dictionary containing the command's return code, stdout, and stderr
+        """
+        command = self.command
+        args = self.args
+        filename = self.target_file
+        if self.ask_for_target:
+            filename = Command.target_prompt(self.command)
+        if not self.include_filetype:
+            filename = os.path.splitext(filename)[0]
+        if filename is not None:
+            command = self.command.replace('%s', filename)
+            args = self.args.replace('%s', filename)
+        elif '%s' in self.command + '|' + self.args:
+            print('No filename given, but this command contains filename wildcards (%s). This command will probably fail')
+
+        proc = subprocess.run([command, args], stdout=subprocess.PIPE, stderr=subprocess.STDOUT, timeout=self.timeout, encoding='UTF-8', shell=True)
+        return {'returncode': proc.returncode, 'stdout': proc.stdout, 'stderr': proc.stderr}
+
+    def run_and_match(self) -> bool:
+        """
+        Runs the command and matches the output to the output_match/regex. If neither are defined then this always returns true
+        :return: Whether the output matched or not
+        """
+        result = self.run()
+        if self.print_output:
+            print(result['stdout'])
+
+        if not any((self.output_match, self.output_regex)):
+            return True
 
+        if self.output_regex:
             if self.output_regex.match(result['stdout']):
+                if self.negate_match:
+                    return False
                 return True
-            return False
+
+        if self.output_match:
+            if self.output_match in result['stdout']:
+                if self.negate_match:
+                    return False
+                return True
+
+        if self.negate_match:
+            return True
+        return False
 
 
 class PyCanvasGrader:
@@ -165,24 +290,30 @@ def user(self, user_id: int) -> dict:
         return json.loads(response.text)
 
 
-def parse_zip(zip_file: str) -> dict:
+def parse_zip(zip_file: str) -> set:
     """
     Maps file names to user IDs from a zip of downloaded Canvas submissions
     :param zip_file: The name of the zip file to parse
     :return: if the zip can be parsed, a dictionary containing the user ID's mapped to the parsed file name, otherwise an empty dict
     """
-    user_dict = {}
+    user_ids = set()
 
     with ZipFile('zips/' + zip_file, 'r') as z:
         for name in z.namelist():
             if name.count('_') < 3:
                 print('Skipping file: ' + name + '. Invalid filename')
             else:
-                (name, user_id, unknown, file) = name.split('_', maxsplit=3)
-                user_dict[user_id] = file
-    if len(user_dict) < 1:
+                (username, user_id, unknown, file) = name.split('_', maxsplit=3)
+                user_ids.add(user_id)
+
+                file_path = 'temp/%s/' % user_id
+                os.makedirs(os.path.dirname('temp/%s/' % user_id), exist_ok=True)
+                z.extract(name, path=file_path)
+                os.replace(file_path + name, file_path + file)
+
+    if len(user_ids) < 1:
         print('Unable to read any files from the zip. Please check the file and try again')
-    return user_dict
+    return user_ids
 
 
 def choose_val(hi_num: int) -> int:
@@ -202,11 +333,19 @@ def choose_bool() -> bool:
         return False
 
 
+def parse_skeletons() -> list:
+    skeleton_list = []
+    for skeleton_file in os.listdir('skeletons'):
+        skeleton = TestSkeleton.from_file(skeleton_file)
+        if skeleton is not None:
+            skeleton_list.append(skeleton)
+    return skeleton_list
+
+
 def main():
     # Initialize grading session and fetch courses
     grader = PyCanvasGrader()
     course_list = grader.courses('teacher')
-
     # Have user select course
     print('Choose a course from the following list:')
     for count, course in enumerate(course_list):
@@ -233,7 +372,7 @@ def main():
 
     # Have user choose zip
     invalid_zip = True
-    user_file_dict = {}
+    user_ids = []
     while invalid_zip:
         zip_list = []
         print('Choose a zip file to use:')
@@ -248,8 +387,8 @@ def main():
         selection = choose_val(len(zip_list)) - 1
         zip_file = zip_list[selection]
 
-        user_file_dict = parse_zip(zip_file)
-        if len(user_file_dict) > 0:
+        user_ids = parse_zip(zip_file)
+        if len(user_ids) > 0:
             invalid_zip = False
         else:
             print('This zip is invalid. Make sure you do not change the names inside the zip and try again')
@@ -262,12 +401,15 @@ def main():
         main()
         exit(0)
 
-    # Match the user IDs found in the zip with the IDs who submitted the assignment online
+    # Match the user IDs found in the zip with the IDs in the online submission
     user_submission_dict = {}
-    for user_id, filename in user_file_dict.items():
+    for user_id in user_ids:
         for submission in submission_list:
-            if user_id in str(submission.get('user_id')):
-                user_submission_dict['user_id'] = submission['id']
+            long_id = submission.get('user_id')
+            if str(user_id) in str(long_id):
+                file_path = os.path.join(os.getcwd(), 'temp')
+                os.rename(os.path.join(file_path, str(user_id)), os.path.join(file_path, str(long_id)))
+                user_submission_dict[long_id] = submission['id']
 
     if len(user_submission_dict) < 1:
         print('Could not match any file names in the zip to any online submissions.')
@@ -275,19 +417,59 @@ def main():
         main()
         exit(0)
 
-    print('Successfully matched %i submission(s) to files in the zip file. Is this correct? (y or n):' % len(user_submission_dict))
+    s = ''
+    if len(user_submission_dict) > 1:
+        s = 's'
+    print('Successfully matched %i submission%s to files in the zip file. Is this correct? (y or n):' % (len(user_submission_dict), s))
     correct = choose_bool()
     if not correct:
         grader.close()
         main()
         exit(0)
 
+    skeleton_list = parse_skeletons()
+    if len(skeleton_list) < 1:
+        print('Could not find any skeleton files in the skeletons directory. Would you like to create one now? (y or n):')
+        if choose_bool():
+            print('unimplemented')
+        else:
+            pass
+        grader.close()
+        main()
+        exit(0)
+
+    print('Choose a skeleton to use for grading this assignment:')
+    for count, skeleton in enumerate(skeleton_list):
+        print('%i.\t%s' % (count + 1, skeleton.descriptor))
+    skeleton_choice = choose_val(len(skeleton_list)) - 1
+    selected_skeleton = skeleton_list[skeleton_choice]
+
     print('Students to grade: [Name (email)]')
     for user_id in user_submission_dict:
         user_data = grader.user(user_id)
         print(str(user_data.get('name')) + '\t(%s)' % user_data.get('email'))
 
     input('Press enter to begin grading')
+    for cur_user_id in user_submission_dict:
+        try:
+            os.chdir('temp/' + str(cur_user_id))
+        except (WindowsError, OSError):
+            print('Could not access files for user %i. Skipping' % cur_user_id)
+            continue
+
+        print('Grading user %i...' % cur_user_id)
+        score = selected_skeleton.run_tests()
+
+        if score < 0:
+            score = 0
+        action_list = ['Submit this grade', 'Modify this grade', 'Skip this submission', 'Re-grade this submission']
+
+        print('Grade for this assignment: %i' % score)
+        print('Choose an action:')
+        for count, action in enumerate(action_list):
+            print('%i.\t%s' % (count + 1, action))
+        action_choice = choose_val(len(action_list)) - 1
+        selected_action = action_list[skeleton_choice]
 
     print('done')
 
diff --git a/pycanvasgrader/skeletons/java.json b/pycanvasgrader/skeletons/java.json
new file mode 100644
index 0000000..52100b9
--- /dev/null
+++ b/pycanvasgrader/skeletons/java.json
@@ -0,0 +1,26 @@
+{
+  "descriptor": "Example Java skeleton",
+  "extensions": ".java",
+
+  "commands": {
+
+    "command_1": {
+      "command": "C:\\Program Files\\Java\\jdk1.8.0_92\\bin\\javac.exe",
+      "args": "%s",
+      "print_output": true,
+      "point_val": 25,
+      "output_match": "error",
+      "negate_match": true,
+      "ask_for_target": true
+    },
+    "command_2": {
+      "command": "java",
+      "args": "%s",
+      "print_output": true,
+      "output_match": "Variable Value :2",
+      "point_val": 75,
+      "ask_for_target": true,
+      "include_filetype": false
+    }
+  }
+}
\ No newline at end of file
diff --git a/pycanvasgrader/temp/git_include.dir b/pycanvasgrader/temp/git_include.dir
new file mode 100644
index 0000000..e69de29
diff --git a/pycanvasgrader/zips/submissions.zip b/pycanvasgrader/zips/submissions.zip
new file mode 100644
index 0000000000000000000000000000000000000000..92df292a1d0f05ed9b9a45dbfb2cd63f40cc532d
GIT binary patch
literal 1028
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literal 0
HcmV?d00001


From d5297392f16beb342f6f928ab245debefda61356 Mon Sep 17 00:00:00 2001
From: Michael Manis <electricpyrotechnic@gmail.com>
Date: Sat, 9 Sep 2017 14:15:59 -0400
Subject: [PATCH 11/40] Fixed name output, a lot of formatting

---
 pycanvasgrader/pycanvasgrader.py   | 44 ++++++++++++++++++++----------
 pycanvasgrader/skeletons/java.json |  4 +--
 2 files changed, 31 insertions(+), 17 deletions(-)

diff --git a/pycanvasgrader/pycanvasgrader.py b/pycanvasgrader/pycanvasgrader.py
index ef3834b..b66c351 100644
--- a/pycanvasgrader/pycanvasgrader.py
+++ b/pycanvasgrader/pycanvasgrader.py
@@ -25,6 +25,7 @@
 
 # globals
 RUN_WITH_TESTS = False
+ONLY_RUN_TESTS = False
 
 
 class TestSkeleton:
@@ -70,10 +71,16 @@ def from_file(cls, filename):
     def run_tests(self) -> int:
         total_score = 0
         for count, command in enumerate(self.commands):
-            print('\n--Running command %i--' % count)
+            print('\n--Running test %i--' % (count + 1))
             if command.run_and_match():
+                if command.point_val > 0:
+                    print('--Adding %i points--' % command.point_val)
+                elif command.point_val == 0:
+                    print('--No points set for this test--')
+                else:
+                    print('--Subtracting %i points--' % abs(command.point_val))
                 total_score += command.point_val
-            print('Current score: %i' % total_score)
+            print('--Current score: %i--' % total_score)
         return total_score
 
 
@@ -189,19 +196,22 @@ def run_and_match(self) -> bool:
         """
         result = self.run()
         if self.print_output:
+            print('\t--OUTPUT--')
             print(result['stdout'])
-
+            print('\t--END OUTPUT--')
         if not any((self.output_match, self.output_regex)):
             return True
 
         if self.output_regex:
             if self.output_regex.match(result['stdout']):
+                print('--Matched regular expression--')
                 if self.negate_match:
                     return False
                 return True
 
         if self.output_match:
             if self.output_match in result['stdout']:
+                print('--Matched string comparison--')
                 if self.negate_match:
                     return False
                 return True
@@ -279,12 +289,13 @@ def submissions(self, course_id: int, assignment_id: int) -> list:
         response = self.session.get(url)
         return json.loads(response.text)
 
-    def user(self, user_id: int) -> dict:
+    def user(self, course_id: int, user_id: int) -> dict:
         """
+        :param course_id: The class to search
         :param user_id: The ID of the user
         :return: A dictionary with the user's information
         """
-        url = 'https://canvas.instructure.com/api/v1/users/' + str(user_id)
+        url = 'https://canvas.instructure.com/api/v1/courses/%i/users/%i' % (course_id, user_id)
 
         response = self.session.get(url)
         return json.loads(response.text)
@@ -444,27 +455,29 @@ def main():
     skeleton_choice = choose_val(len(skeleton_list)) - 1
     selected_skeleton = skeleton_list[skeleton_choice]
 
-    print('Students to grade: [Name (email)]')
+    name_dict = {}
+    print('Students to grade: [Name (email)]\n----')
     for user_id in user_submission_dict:
-        user_data = grader.user(user_id)
+        user_data = grader.user(course_id, user_id)
+        if user_data.get('name') is not None:
+            name_dict[user_id] = user_data['name']
         print(str(user_data.get('name')) + '\t(%s)' % user_data.get('email'))
-
-    input('Press enter to begin grading')
+    print('----\n')
+    input('Press enter to begin grading\n')
     for cur_user_id in user_submission_dict:
         try:
             os.chdir('temp/' + str(cur_user_id))
         except (WindowsError, OSError):
-            print('Could not access files for user %i. Skipping' % cur_user_id)
+            print('Could not access files for user "%i". Skipping' % cur_user_id)
             continue
-
-        print('Grading user %i...' % cur_user_id)
+        print('--Grading user "%s"--' % name_dict.get(cur_user_id))
         score = selected_skeleton.run_tests()
 
         if score < 0:
             score = 0
         action_list = ['Submit this grade', 'Modify this grade', 'Skip this submission', 'Re-grade this submission']
 
-        print('Grade for this assignment: %i' % score)
+        print('\n--All tests completed--\nGrade for this assignment: %i' % score)
         print('Choose an action:')
         for count, action in enumerate(action_list):
             print('%i.\t%s' % (count + 1, action))
@@ -475,6 +488,7 @@ def main():
 
 
 if __name__ == '__main__':
-    if RUN_WITH_TESTS:
+    if RUN_WITH_TESTS or ONLY_RUN_TESTS:
         py.test.cmdline.main()
-    main()
+    if not ONLY_RUN_TESTS:
+        main()
diff --git a/pycanvasgrader/skeletons/java.json b/pycanvasgrader/skeletons/java.json
index 52100b9..3c26ec9 100644
--- a/pycanvasgrader/skeletons/java.json
+++ b/pycanvasgrader/skeletons/java.json
@@ -4,7 +4,7 @@
 
   "commands": {
 
-    "command_1": {
+    "test_1": {
       "command": "C:\\Program Files\\Java\\jdk1.8.0_92\\bin\\javac.exe",
       "args": "%s",
       "print_output": true,
@@ -13,7 +13,7 @@
       "negate_match": true,
       "ask_for_target": true
     },
-    "command_2": {
+    "test_2": {
       "command": "java",
       "args": "%s",
       "print_output": true,

From abcb5c1ec49577d5f49d50e3e0c13f655c65dd62 Mon Sep 17 00:00:00 2001
From: Michael Manis <electricpyrotechnic@gmail.com>
Date: Sat, 9 Sep 2017 18:21:23 -0400
Subject: [PATCH 12/40] renamed Command class to AssignmentTest, added exact
 match option, added ability to grade submissions, made file handling more
 robust, properly clean temp directory, simplified various logic,

---
 pycanvasgrader/pycanvasgrader.py    | 193 +++++++++++++++++-----------
 pycanvasgrader/skeletons/java.json  |   2 +-
 pycanvasgrader/temp/git_include.dir |   0
 3 files changed, 120 insertions(+), 75 deletions(-)
 delete mode 100644 pycanvasgrader/temp/git_include.dir

diff --git a/pycanvasgrader/pycanvasgrader.py b/pycanvasgrader/pycanvasgrader.py
index b66c351..991a234 100644
--- a/pycanvasgrader/pycanvasgrader.py
+++ b/pycanvasgrader/pycanvasgrader.py
@@ -13,13 +13,15 @@
 """
 
 # built-ins
-import py
+import glob
 import json
-import re
 import os
+import shutil
+import re
 import subprocess
 from zipfile import ZipFile
 
+import py
 # 3rd-party
 import requests
 
@@ -32,19 +34,14 @@ class TestSkeleton:
     """
     An abstract skeleton to handle testing of a specific group of files
     """
-    def __init__(self, descriptor: str, commands: list, extensions: str=None, file_regex: str=None):
+
+    def __init__(self, descriptor: str, tests: list):
         """
         :param descriptor: The description of this TestSkeleton
-        :param commands: A list of Command objects. These will be run in the order that they are added.
-        :param extensions: Which file extensions this skeleton applies to (Unimplemented)
-        :param file_regex: A regular expression to match files for this skeleton. Combines with extensions (Unimplemented)
+        :param tests: A list of AssignmentTest objects. These will be run in the order that they are added.
         """
-        if not any((extensions, file_regex)):
-            raise ValueError('Either extensions or file_regex must be defined')
         self.descriptor = descriptor
-        self.commands = commands
-        self.extensions = extensions
-        self.file_regex = file_regex
+        self.tests = tests
 
     @classmethod
     def from_file(cls, filename):
@@ -52,46 +49,43 @@ def from_file(cls, filename):
             data = json.load(skeleton_file)
             try:
                 descriptor = data['descriptor']
-                commands = data['commands']
-                extensions = data.get('extensions')
-                file_regex = data.get('file_regex')
-                if not any((extensions, file_regex)):
-                    raise KeyError
+                tests = data['tests']
             except KeyError:
                 return None
             else:
-                command_list = []
-                for json_dict in commands:
-                    command = Command.from_json_dict(commands[json_dict])
-                    if command is not None:
-                        command_list.append(command)
+                test_list = []
+                for json_dict in tests:
+                    test = AssignmentTest.from_json_dict(tests[json_dict])
+                    if test is not None:
+                        test_list.append(test)
 
-                return TestSkeleton(descriptor, command_list, extensions, file_regex)
+                return TestSkeleton(descriptor, test_list)
 
     def run_tests(self) -> int:
         total_score = 0
-        for count, command in enumerate(self.commands):
+        for count, test in enumerate(self.tests):
             print('\n--Running test %i--' % (count + 1))
-            if command.run_and_match():
-                if command.point_val > 0:
-                    print('--Adding %i points--' % command.point_val)
-                elif command.point_val == 0:
+            if test.run_and_match():
+                if test.point_val > 0:
+                    print('--Adding %i points--' % test.point_val)
+                elif test.point_val == 0:
                     print('--No points set for this test--')
                 else:
-                    print('--Subtracting %i points--' % abs(command.point_val))
-                total_score += command.point_val
+                    print('--Subtracting %i points--' % abs(test.point_val))
+                total_score += test.point_val
             print('--Current score: %i--' % total_score)
         return total_score
 
 
 # TODO Create tests
-class Command:
+class AssignmentTest:
     """
-    An abstract command to be run in a console
+    An abstract test to be run on an assignment submission
     """
-    def __init__(self, command: str, args: str=None, target_file: str=None, ask_for_target: bool=False,
-                 include_filetype: bool=True, print_output: bool=True, output_match: str=None, output_regex: str=None,
-                 negate_match: bool=False, timeout: int=None, point_val: int=0):
+
+    def __init__(self, command: str, args: str = None, target_file: str = None, ask_for_target: bool = False,
+                 include_filetype: bool = True, print_output: bool = True, output_match: str = None, output_regex: str = None,
+                 negate_match: bool = False, exact_match: bool = False, timeout: int = None, point_val: int = 0):
         """
         :param command: The command to be run.
         :param args: The arguments to pass to the command. Use %s to denote a file name
@@ -103,6 +97,7 @@ def __init__(self, command: str, args: str=None, target_file: str=None, ask_for_
         :param output_regex: A regular expression that the string should match. Combines with output_match.
         If this and output_match are None, then this Command always 'matches'
         :param negate_match: Whether to negate the result of checking output_match and output_regex
+        :param exact_match: Whether the naive string match (output_match) should be an exact check or a substring check
         :param timeout: Time, in seconds, that this Command should run for before timing out
         :param point_val: Amount of points that a successful match is worth (Can be negative)
         """
@@ -117,6 +112,7 @@ def __init__(self, command: str, args: str=None, target_file: str=None, ask_for_
         else:
             self.output_regex = None
         self.negate_match = negate_match
+        self.exact_match = exact_match
         self.print_output = print_output
         self.timeout = timeout
         self.point_val = point_val
@@ -136,18 +132,19 @@ def from_json_dict(cls, json_dict: dict):
             output_match = json_dict.get('output_match')
             output_regex = json_dict.get('output_regex')
             negate_match = json_dict.get('negate_match')
+            exact_match = json_dict.get('exact_match')
             timeout = json_dict.get('timeout')
             point_val = json_dict.get('point_val')
 
             vars_dict = {'command': command, 'args': args, 'target_file': target_file,
                          'ask_for_target': ask_for_target, 'include_filetype': include_filetype,
                          'print_output': print_output, 'output_match': output_match, 'output_regex': output_regex,
-                         'negate_match': negate_match, 'timeout': timeout, 'point_val': point_val}
+                         'negate_match': negate_match, 'exact_match': exact_match, 'timeout': timeout, 'point_val': point_val}
             args_dict = {}
             for var_name, val in vars_dict.items():
                 if val is not None:
                     args_dict[var_name] = val
-            return Command(**args_dict)
+            return AssignmentTest(**args_dict)
 
     @classmethod
     def target_prompt(cls, command: str):
@@ -177,7 +174,7 @@ def run(self) -> dict:
         args = self.args
         filename = self.target_file
         if self.ask_for_target:
-            filename = Command.target_prompt(self.command)
+            filename = AssignmentTest.target_prompt(self.command)
         if not self.include_filetype:
             filename = os.path.splitext(filename)[0]
         if filename is not None:
@@ -210,21 +207,25 @@ def run_and_match(self) -> bool:
                 return True
 
         if self.output_match:
-            if self.output_match in result['stdout']:
+            if self.exact_match:
+                condition = self.output_match == result['stdout']
+            else:
+                condition = self.output_match in result['stdout']
+
+            if condition:
                 print('--Matched string comparison--')
                 if self.negate_match:
                     return False
                 return True
 
-        if self.negate_match:
-            return True
-        return False
+        return self.negate_match
 
 
 class PyCanvasGrader:
     """
     A PyCanvasGrader object; responsible for communicating with the Canvas API
     """
+
     def __init__(self):
         self.token = self.authenticate()
         if self.token == 'none':
@@ -253,7 +254,7 @@ def authenticate() -> str:
     def close(self):
         self.session.close()
 
-    def courses(self, enrollment_type: str=None) -> list:
+    def courses(self, enrollment_type: str = None) -> list:
         """
         :param enrollment_type: (Optional) teacher, student, ta, observer, designer
         :return: A list of the user's courses as dictionaries, optionally filtered by enrollment_type
@@ -265,7 +266,7 @@ def courses(self, enrollment_type: str=None) -> list:
         response = self.session.get(url)
         return json.loads(response.text)
 
-    def assignments(self, course_id: int, ungraded: bool=True) -> list:
+    def assignments(self, course_id: int, ungraded: bool = True) -> list:
         """
         :param course_id: Course ID to filter by
         :param ungraded: Whether to filter assignments by only those that have ungraded work. Default: True
@@ -300,6 +301,13 @@ def user(self, course_id: int, user_id: int) -> dict:
         response = self.session.get(url)
         return json.loads(response.text)
 
+    def grade_submission(self, course_id, assignment_id, user_id, grade):
+        url = 'https://canvas.instructure.com/api/v1/courses/%i/assignments/%i/submissions/%i/?submission[posted_grade]=%i' \
+              % (course_id, assignment_id, user_id, grade)
+
+        response = self.session.put(url)
+        return json.loads(response.text)
+
 
 def parse_zip(zip_file: str) -> set:
     """
@@ -309,7 +317,7 @@ def parse_zip(zip_file: str) -> set:
     """
     user_ids = set()
 
-    with ZipFile('zips/' + zip_file, 'r') as z:
+    with ZipFile(os.path.join('zips', zip_file), 'r') as z:
         for name in z.namelist():
             if name.count('_') < 3:
                 print('Skipping file: ' + name + '. Invalid filename')
@@ -317,19 +325,23 @@ def parse_zip(zip_file: str) -> set:
                 (username, user_id, unknown, file) = name.split('_', maxsplit=3)
                 user_ids.add(user_id)
 
-                file_path = 'temp/%s/' % user_id
-                os.makedirs(os.path.dirname('temp/%s/' % user_id), exist_ok=True)
+                file_path = os.path.join('temp', user_id, '')
+                os.makedirs(os.path.dirname(file_path), exist_ok=True)
                 z.extract(name, path=file_path)
-                os.replace(file_path + name, file_path + file)
+                os.replace(os.path.join(file_path, name), os.path.join(file_path + file))
 
     if len(user_ids) < 1:
         print('Unable to read any files from the zip. Please check the file and try again')
     return user_ids
 
 
-def choose_val(hi_num: int) -> int:
+def choose_val(hi_num: int, allow_zero: bool = False) -> int:
     val = 'none'
-    while not str.isdigit(val) or (int(val) > hi_num or int(val) <= 0):
+
+    while True:
+        if str.isdigit(val) and int(val) <= hi_num:
+            if (allow_zero and int(val) >= 0) or (not allow_zero and int(val) > 0):
+                break
         val = input()
     return int(val)
 
@@ -338,10 +350,7 @@ def choose_bool() -> bool:
     val = 'none'
     while not str.lower(val) in ['y', 'n', 'yes', 'no']:
         val = input()
-    if val in ['y', 'yes']:
-        return True
-    else:
-        return False
+    return val in ['y', 'yes']
 
 
 def parse_skeletons() -> list:
@@ -353,25 +362,47 @@ def parse_skeletons() -> list:
     return skeleton_list
 
 
+def restart_program(grader: PyCanvasGrader):
+    grader.close()
+    clear_tempdir()
+    main()
+    exit(0)
+
+
+def clear_tempdir():
+    try:
+        shutil.rmtree(os.path.join(os.path.dirname(os.path.abspath(__file__)), 'temp'))
+    except Exception:
+        print('An error occurred while removing the "temp" directory. Please delete the directory manually and re-run the program')
+        exit(1)
+
+
 def main():
+    clear_tempdir()
     # Initialize grading session and fetch courses
     grader = PyCanvasGrader()
     course_list = grader.courses('teacher')
     # Have user select course
     print('Choose a course from the following list:')
-    for count, course in enumerate(course_list):
-        print('%i.\t%s (%s)' % (count + 1, course.get('name'), course.get('course_code')))
-    course_choice = choose_val(len(course_list)) - 1  # the plus and minus 1 are to hide the 0-based numbering
+    for count, course in enumerate(course_list, 1):
+        print('%i.\t%s (%s)' % (count, course.get('name'), course.get('course_code')))
+    course_choice = choose_val(len(course_list)) - 1  # the minus 1 is to hide the 0-based numbering
 
     print('Show only ungraded assignments? (y or n):')
     ungraded = choose_bool()
     course_id = course_list[course_choice].get('id')
     assignment_list = grader.assignments(course_list[course_choice].get('id'), ungraded=ungraded)
 
+    if len(assignment_list) < 1:
+        input('No assignments were found. Press enter to restart')
+        grader.close()
+        main()
+        exit(0)
+
     # Have user choose assignment
     print('Choose an assignment to grade:')
-    for count, assignment in enumerate(assignment_list):
-        print('%i.\t%s' % (count + 1, assignment.get('name')))
+    for count, assignment in enumerate(assignment_list, 1):
+        print('%i.\t%s' % (count, assignment.get('name')))
     assignment_choice = choose_val(len(assignment_list)) - 1
     assignment_id = assignment_list[assignment_choice].get('id')
 
@@ -379,7 +410,7 @@ def main():
     print('If you haven\'t already, please download the most current submissions.zip for this assignment:\n' +
           assignment_list[assignment_choice].get('submissions_download_url'))
 
-    input('\nPress enter when this you have placed this zip file into the /zips/ directory')
+    input('\nPress enter when this you have placed this zip file into the "zips" directory')
 
     # Have user choose zip
     invalid_zip = True
@@ -387,13 +418,10 @@ def main():
     while invalid_zip:
         zip_list = []
         print('Choose a zip file to use:')
-        sub = 0  # This is to keep indices visually correct while excluding non-zip files
-        for count, zip_name in enumerate(os.listdir('zips')):
-            if zip_name.split('.')[-1] != 'zip':
-                sub += 1
-                continue
+        for count, zip_name in enumerate(glob.glob(os.path.join('zips', '*.zip')), 1):
+            zip_name = os.path.basename(zip_name)
             zip_list.append(zip_name)
-            print('%i.\t%s' % (count - sub + 1, zip_name))  # Again, the plus and minus 1 are to hide the 0-based numbering
+            print('%i.\t%s' % (count, zip_name))  # Again, the plus and minus 1 are to hide the 0-based numbering
 
         selection = choose_val(len(zip_list)) - 1
         zip_file = zip_list[selection]
@@ -412,10 +440,14 @@ def main():
         main()
         exit(0)
 
+    print('Only grade currently ungraded submissions? (y or n):')
+    ungraded_only = choose_bool()
     # Match the user IDs found in the zip with the IDs in the online submission
     user_submission_dict = {}
     for user_id in user_ids:
         for submission in submission_list:
+            if ungraded_only and submission.get('grader_id') is not None:  # Skip assignments that have been graded already
+                continue
             long_id = submission.get('user_id')
             if str(user_id) in str(long_id):
                 file_path = os.path.join(os.getcwd(), 'temp')
@@ -450,8 +482,8 @@ def main():
         exit(0)
 
     print('Choose a skeleton to use for grading this assignment:')
-    for count, skeleton in enumerate(skeleton_list):
-        print('%i.\t%s' % (count + 1, skeleton.descriptor))
+    for count, skeleton in enumerate(skeleton_list, 1):
+        print('%i.\t%s' % (count, skeleton.descriptor))
     skeleton_choice = choose_val(len(skeleton_list)) - 1
     selected_skeleton = skeleton_list[skeleton_choice]
 
@@ -466,7 +498,7 @@ def main():
     input('Press enter to begin grading\n')
     for cur_user_id in user_submission_dict:
         try:
-            os.chdir('temp/' + str(cur_user_id))
+            os.chdir(os.path.join('temp', str(cur_user_id)))
         except (WindowsError, OSError):
             print('Could not access files for user "%i". Skipping' % cur_user_id)
             continue
@@ -477,12 +509,25 @@ def main():
             score = 0
         action_list = ['Submit this grade', 'Modify this grade', 'Skip this submission', 'Re-grade this submission']
 
-        print('\n--All tests completed--\nGrade for this assignment: %i' % score)
-        print('Choose an action:')
-        for count, action in enumerate(action_list):
-            print('%i.\t%s' % (count + 1, action))
-        action_choice = choose_val(len(action_list)) - 1
-        selected_action = action_list[skeleton_choice]
+        while True:
+            print('\n--All tests completed--\nGrade for this assignment: %i' % score)
+            print('Choose an action:')
+            for count, action in enumerate(action_list, 1):
+                print('%i.\t%s' % (count, action))
+            action_choice = choose_val(len(action_list)) - 1
+            selected_action = action_list[action_choice]
+
+            if selected_action == 'Submit this grade':
+                grader.grade_submission(course_id, assignment_id, cur_user_id, score)
+                print('Grade submitted')
+                break
+            elif selected_action == 'Modify this grade':
+                print('Enter a new grade for this submission:')
+                score = choose_val(1000, allow_zero=True)
+            elif selected_action == 'Skip this submission':
+                break
+            elif selected_action == 'Re-grade this submission':
+                score = selected_skeleton.run_tests()
 
     print('done')
 
diff --git a/pycanvasgrader/skeletons/java.json b/pycanvasgrader/skeletons/java.json
index 3c26ec9..0b30816 100644
--- a/pycanvasgrader/skeletons/java.json
+++ b/pycanvasgrader/skeletons/java.json
@@ -2,7 +2,7 @@
   "descriptor": "Example Java skeleton",
   "extensions": ".java",
 
-  "commands": {
+  "tests": {
 
     "test_1": {
       "command": "C:\\Program Files\\Java\\jdk1.8.0_92\\bin\\javac.exe",
diff --git a/pycanvasgrader/temp/git_include.dir b/pycanvasgrader/temp/git_include.dir
deleted file mode 100644
index e69de29..0000000

From 5e6be8b52ebd96c70dfa2d0bce3922e3bac8ca2a Mon Sep 17 00:00:00 2001
From: Michael Manis <electricpyrotechnic@gmail.com>
Date: Sat, 9 Sep 2017 18:23:39 -0400
Subject: [PATCH 13/40] Use restart_program function where required

---
 pycanvasgrader/pycanvasgrader.py | 21 +++++----------------
 1 file changed, 5 insertions(+), 16 deletions(-)

diff --git a/pycanvasgrader/pycanvasgrader.py b/pycanvasgrader/pycanvasgrader.py
index 991a234..1a3d8e8 100644
--- a/pycanvasgrader/pycanvasgrader.py
+++ b/pycanvasgrader/pycanvasgrader.py
@@ -2,7 +2,6 @@
 """
 Automates the grading of programming assignments on Canvas.
 MUST create an 'access.token' file in the same directory as this file with a valid Canvas OAuth2 token
-MUST clear temp directory before running program (TODO will fix this)
 REQUIRED File structure:
 - pycanvasgrader
   -- skeletons
@@ -395,9 +394,7 @@ def main():
 
     if len(assignment_list) < 1:
         input('No assignments were found. Press enter to restart')
-        grader.close()
-        main()
-        exit(0)
+        restart_program(grader)
 
     # Have user choose assignment
     print('Choose an assignment to grade:')
@@ -436,9 +433,7 @@ def main():
     submission_list = grader.submissions(course_id, assignment_id)
     if len(submission_list) < 1:
         print('There are no submissions for this assignment.')
-        grader.close()
-        main()
-        exit(0)
+        restart_program(grader)
 
     print('Only grade currently ungraded submissions? (y or n):')
     ungraded_only = choose_bool()
@@ -456,9 +451,7 @@ def main():
 
     if len(user_submission_dict) < 1:
         print('Could not match any file names in the zip to any online submissions.')
-        grader.close()
-        main()
-        exit(0)
+        restart_program(grader)
 
     s = ''
     if len(user_submission_dict) > 1:
@@ -466,9 +459,7 @@ def main():
     print('Successfully matched %i submission%s to files in the zip file. Is this correct? (y or n):' % (len(user_submission_dict), s))
     correct = choose_bool()
     if not correct:
-        grader.close()
-        main()
-        exit(0)
+        restart_program(grader)
 
     skeleton_list = parse_skeletons()
     if len(skeleton_list) < 1:
@@ -477,9 +468,7 @@ def main():
             print('unimplemented')
         else:
             pass
-        grader.close()
-        main()
-        exit(0)
+        restart_program(grader)
 
     print('Choose a skeleton to use for grading this assignment:')
     for count, skeleton in enumerate(skeleton_list, 1):

From 6c1664098e2c3b0c269acbfd814823414ce13007 Mon Sep 17 00:00:00 2001
From: Michael Manis <electricpyrotechnic@gmail.com>
Date: Sat, 9 Sep 2017 18:27:55 -0400
Subject: [PATCH 14/40] Use proper exception type

---
 pycanvasgrader/pycanvasgrader.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pycanvasgrader/pycanvasgrader.py b/pycanvasgrader/pycanvasgrader.py
index 1a3d8e8..3fec810 100644
--- a/pycanvasgrader/pycanvasgrader.py
+++ b/pycanvasgrader/pycanvasgrader.py
@@ -371,7 +371,7 @@ def restart_program(grader: PyCanvasGrader):
 def clear_tempdir():
     try:
         shutil.rmtree(os.path.join(os.path.dirname(os.path.abspath(__file__)), 'temp'))
-    except Exception:
+    except BaseException:
         print('An error occurred while removing the "temp" directory. Please delete the directory manually and re-run the program')
         exit(1)
 

From cc05b60f5e229816b5eece4d477b19a7e1551c1d Mon Sep 17 00:00:00 2001
From: Michael Manis <electricpyrotechnic@gmail.com>
Date: Sat, 9 Sep 2017 21:38:06 -0400
Subject: [PATCH 15/40] Update comments

---
 pycanvasgrader/pycanvasgrader.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pycanvasgrader/pycanvasgrader.py b/pycanvasgrader/pycanvasgrader.py
index 3fec810..f5f5664 100644
--- a/pycanvasgrader/pycanvasgrader.py
+++ b/pycanvasgrader/pycanvasgrader.py
@@ -159,7 +159,7 @@ def target_prompt(cls, command: str):
                 sub += 1
                 continue
             file_list.append(file_name)
-            print('%i.\t%s' % (count - sub + 1, file_name))  # The plus and minus 1 are to hide the 0-based numbering
+            print('%i.\t%s' % (count - sub + 1, file_name))  # The minus 1 is to hide the 0-based numbering
 
         selection = choose_val(len(file_list)) - 1
         return file_list[selection]
@@ -418,7 +418,7 @@ def main():
         for count, zip_name in enumerate(glob.glob(os.path.join('zips', '*.zip')), 1):
             zip_name = os.path.basename(zip_name)
             zip_list.append(zip_name)
-            print('%i.\t%s' % (count, zip_name))  # Again, the plus and minus 1 are to hide the 0-based numbering
+            print('%i.\t%s' % (count, zip_name))  # Again, the minus 1 is to hide the 0-based numbering
 
         selection = choose_val(len(zip_list)) - 1
         zip_file = zip_list[selection]

From d11c4714bdb4de223e10a05c1bc247ff04d4717a Mon Sep 17 00:00:00 2001
From: Michael Manis <electricpyrotechnic@gmail.com>
Date: Tue, 12 Sep 2017 16:47:55 -0400
Subject: [PATCH 16/40] Updated temp directory handling

---
 pycanvasgrader/pycanvasgrader.py | 18 ++++++++++--------
 1 file changed, 10 insertions(+), 8 deletions(-)

diff --git a/pycanvasgrader/pycanvasgrader.py b/pycanvasgrader/pycanvasgrader.py
index f5f5664..e900253 100644
--- a/pycanvasgrader/pycanvasgrader.py
+++ b/pycanvasgrader/pycanvasgrader.py
@@ -363,21 +363,23 @@ def parse_skeletons() -> list:
 
 def restart_program(grader: PyCanvasGrader):
     grader.close()
-    clear_tempdir()
+    init_tempdir()
     main()
     exit(0)
 
 
-def clear_tempdir():
-    try:
-        shutil.rmtree(os.path.join(os.path.dirname(os.path.abspath(__file__)), 'temp'))
-    except BaseException:
-        print('An error occurred while removing the "temp" directory. Please delete the directory manually and re-run the program')
-        exit(1)
+def init_tempdir():
+        try:
+            if os.path.exists('temp'):
+                shutil.rmtree(os.path.join(os.path.dirname(os.path.abspath(__file__)), 'temp'))
+            os.makedirs('temp', exist_ok=True)
+        except BaseException as e:
+            print('An error occurred while initializing the "temp" directory. Please delete/create the directory manually and re-run the program')
+            exit(1)
 
 
 def main():
-    clear_tempdir()
+    init_tempdir()
     # Initialize grading session and fetch courses
     grader = PyCanvasGrader()
     course_list = grader.courses('teacher')

From a5ecb19cb2ba7e2c3fe6ba86faa19eef479d9ee4 Mon Sep 17 00:00:00 2001
From: Michael Manis <electricpyrotechnic@gmail.com>
Date: Tue, 12 Sep 2017 18:52:08 -0400
Subject: [PATCH 17/40] submissions are now downloaded directly from canvas,
 rather than taken from the submissions.zip

---
 pycanvasgrader/pycanvasgrader.py | 119 ++++++++++++++++++-------------
 1 file changed, 71 insertions(+), 48 deletions(-)

diff --git a/pycanvasgrader/pycanvasgrader.py b/pycanvasgrader/pycanvasgrader.py
index e900253..53a0af9 100644
--- a/pycanvasgrader/pycanvasgrader.py
+++ b/pycanvasgrader/pycanvasgrader.py
@@ -9,10 +9,12 @@
   -- zips
   access.token
   pycanvasgrader.py
+
+  TODO test temp directory deletion timing on Windows
+  TODO implement skeleton creation wizard
 """
 
 # built-ins
-import glob
 import json
 import os
 import shutil
@@ -80,6 +82,7 @@ def run_tests(self) -> int:
 class AssignmentTest:
     """
     An abstract test to be run on an assignment submission
+    TODO 'sequential' command requirement
     """
 
     def __init__(self, command: str, args: str = None, target_file: str = None, ask_for_target: bool = False,
@@ -258,7 +261,7 @@ def courses(self, enrollment_type: str = None) -> list:
         :param enrollment_type: (Optional) teacher, student, ta, observer, designer
         :return: A list of the user's courses as dictionaries, optionally filtered by enrollment_type
         """
-        url = 'https://canvas.instructure.com/api/v1/courses'
+        url = 'https://sit.instructure.com/api/v1/courses'
         if enrollment_type is not None:
             url += '?enrollment_type=' + enrollment_type
 
@@ -271,7 +274,7 @@ def assignments(self, course_id: int, ungraded: bool = True) -> list:
         :param ungraded: Whether to filter assignments by only those that have ungraded work. Default: True
         :return: A list of the course's assignments
         """
-        url = 'https://canvas.instructure.com/api/v1/courses/' + str(course_id) + '/assignments'
+        url = 'https://sit.instructure.com/api/v1/courses/' + str(course_id) + '/assignments'
         if ungraded:
             url += '?bucket=ungraded'
 
@@ -284,24 +287,52 @@ def submissions(self, course_id: int, assignment_id: int) -> list:
         :param assignment_id: The ID of the assignment
         :return: A list of the assignment's submissions
         """
-        url = 'https://canvas.instructure.com/api/v1/courses/' + str(course_id) + '/assignments/' + str(assignment_id) + '/submissions'
+        url = 'https://sit.instructure.com/api/v1/courses/' + str(course_id) + '/assignments/' + str(assignment_id) + '/submissions'
 
         response = self.session.get(url)
         return json.loads(response.text)
 
+    def download_submission(self, submission: dict, filepath: str) -> bool:
+        """
+        Attempts to download the attachments for a given submission into the requested directory. Creates the directory if it does not exist.
+        :param submission: The submission dictionary
+        :param filepath: the path where the submission attachments will be placed
+        :return: True if the request succeeded, False otherwise
+        """
+        try:
+            user_id = submission['user_id']
+            attachments = submission['attachments']
+        except ValueError:
+            return False
+
+        for attachment in attachments:
+            try:
+                url = attachment['url']
+                filename = attachment['filename']
+            except ValueError:
+                return False
+
+            os.makedirs(os.path.join('temp', str(user_id)), exist_ok=True)
+            r = self.session.get(url, stream=True)
+            with open(os.path.join(filepath, filename), 'wb') as f:
+                for chunk in r.iter_content(chunk_size=1024):
+                    if chunk:
+                        f.write(chunk)
+        return True
+
     def user(self, course_id: int, user_id: int) -> dict:
         """
         :param course_id: The class to search
         :param user_id: The ID of the user
         :return: A dictionary with the user's information
         """
-        url = 'https://canvas.instructure.com/api/v1/courses/%i/users/%i' % (course_id, user_id)
+        url = 'https://sit.instructure.com/api/v1/courses/%i/users/%i' % (course_id, user_id)
 
         response = self.session.get(url)
         return json.loads(response.text)
 
     def grade_submission(self, course_id, assignment_id, user_id, grade):
-        url = 'https://canvas.instructure.com/api/v1/courses/%i/assignments/%i/submissions/%i/?submission[posted_grade]=%i' \
+        url = 'https://sit.instructure.com/api/v1/courses/%i/assignments/%i/submissions/%i/?submission[posted_grade]=%i' \
               % (course_id, assignment_id, user_id, grade)
 
         response = self.session.put(url)
@@ -353,6 +384,10 @@ def choose_bool() -> bool:
 
 
 def parse_skeletons() -> list:
+    """
+    Responsible for validating and parsing the skeleton files in the "skeletons" directory
+    :return: A list of valid skeletons
+    """
     skeleton_list = []
     for skeleton_file in os.listdir('skeletons'):
         skeleton = TestSkeleton.from_file(skeleton_file)
@@ -371,9 +406,10 @@ def restart_program(grader: PyCanvasGrader):
 def init_tempdir():
         try:
             if os.path.exists('temp'):
-                shutil.rmtree(os.path.join(os.path.dirname(os.path.abspath(__file__)), 'temp'))
+                os.rename('temp', 'old-temp')
+                shutil.rmtree(os.path.join(os.path.dirname(os.path.abspath(__file__)), 'old-temp'))
             os.makedirs('temp', exist_ok=True)
-        except BaseException as e:
+        except BaseException:
             print('An error occurred while initializing the "temp" directory. Please delete/create the directory manually and re-run the program')
             exit(1)
 
@@ -382,7 +418,20 @@ def main():
     init_tempdir()
     # Initialize grading session and fetch courses
     grader = PyCanvasGrader()
-    course_list = grader.courses('teacher')
+
+    action_list = ['teacher', 'ta']
+
+    print('Choose a class role to filter by:')
+    for count, action in enumerate(action_list, 1):
+        print('%i.\t%s' % (count, action))
+    action_choice = choose_val(len(action_list)) - 1
+    selected_role = action_list[action_choice]
+
+    course_list = grader.courses(selected_role)
+    if len(course_list) < 1:
+        input('No courses were found. Press enter to restart')
+        restart_program(grader)
+
     # Have user select course
     print('Choose a course from the following list:')
     for count, course in enumerate(course_list, 1):
@@ -405,60 +454,34 @@ def main():
     assignment_choice = choose_val(len(assignment_list)) - 1
     assignment_id = assignment_list[assignment_choice].get('id')
 
-    # Remind user to get latest zip file
-    print('If you haven\'t already, please download the most current submissions.zip for this assignment:\n' +
-          assignment_list[assignment_choice].get('submissions_download_url'))
-
-    input('\nPress enter when this you have placed this zip file into the "zips" directory')
-
-    # Have user choose zip
-    invalid_zip = True
-    user_ids = []
-    while invalid_zip:
-        zip_list = []
-        print('Choose a zip file to use:')
-        for count, zip_name in enumerate(glob.glob(os.path.join('zips', '*.zip')), 1):
-            zip_name = os.path.basename(zip_name)
-            zip_list.append(zip_name)
-            print('%i.\t%s' % (count, zip_name))  # Again, the minus 1 is to hide the 0-based numbering
-
-        selection = choose_val(len(zip_list)) - 1
-        zip_file = zip_list[selection]
-
-        user_ids = parse_zip(zip_file)
-        if len(user_ids) > 0:
-            invalid_zip = False
-        else:
-            print('This zip is invalid. Make sure you do not change the names inside the zip and try again')
-
     # Get list of submissions for this assignment
     submission_list = grader.submissions(course_id, assignment_id)
     if len(submission_list) < 1:
-        print('There are no submissions for this assignment.')
+        input('There are no submissions for this assignment. Press enter to restart')
         restart_program(grader)
 
     print('Only grade currently ungraded submissions? (y or n):')
     ungraded_only = choose_bool()
     # Match the user IDs found in the zip with the IDs in the online submission
     user_submission_dict = {}
-    for user_id in user_ids:
-        for submission in submission_list:
-            if ungraded_only and submission.get('grader_id') is not None:  # Skip assignments that have been graded already
-                continue
-            long_id = submission.get('user_id')
-            if str(user_id) in str(long_id):
-                file_path = os.path.join(os.getcwd(), 'temp')
-                os.rename(os.path.join(file_path, str(user_id)), os.path.join(file_path, str(long_id)))
-                user_submission_dict[long_id] = submission['id']
+    for submission in submission_list:
+        if ungraded_only and submission.get('grader_id') is not None:  # Skip assignments that have been graded already
+            continue
+        user_id = submission.get('user_id')
+        if submission.get('attachments') is not None:
+            if grader.download_submission(submission, os.path.join('temp', str(user_id))):
+                user_submission_dict[user_id] = submission['id']
+            else:
+                print('There was a problem downloading this user\'s submission. Skipping.')
 
     if len(user_submission_dict) < 1:
-        print('Could not match any file names in the zip to any online submissions.')
+        input('Could not download any submissions. Press enter to restart')
         restart_program(grader)
 
     s = ''
     if len(user_submission_dict) > 1:
         s = 's'
-    print('Successfully matched %i submission%s to files in the zip file. Is this correct? (y or n):' % (len(user_submission_dict), s))
+    print('Successfully retrieved %i submission%s. Is this correct? (y or n):' % (len(user_submission_dict), s))
     correct = choose_bool()
     if not correct:
         restart_program(grader)
@@ -470,7 +493,7 @@ def main():
             print('unimplemented')
         else:
             pass
-        restart_program(grader)
+        exit(0)
 
     print('Choose a skeleton to use for grading this assignment:')
     for count, skeleton in enumerate(skeleton_list, 1):

From cf353388b9943dfc929933efe16a8094bcc00100 Mon Sep 17 00:00:00 2001
From: Michael Manis <electricpyrotechnic@gmail.com>
Date: Tue, 12 Sep 2017 20:08:04 -0400
Subject: [PATCH 18/40] removed unused parse_zip

---
 pycanvasgrader/pycanvasgrader.py | 28 +---------------------------
 1 file changed, 1 insertion(+), 27 deletions(-)

diff --git a/pycanvasgrader/pycanvasgrader.py b/pycanvasgrader/pycanvasgrader.py
index 53a0af9..6aba5c1 100644
--- a/pycanvasgrader/pycanvasgrader.py
+++ b/pycanvasgrader/pycanvasgrader.py
@@ -21,8 +21,8 @@
 import re
 import subprocess
 from zipfile import ZipFile
-
 import py
+
 # 3rd-party
 import requests
 
@@ -339,32 +339,6 @@ def grade_submission(self, course_id, assignment_id, user_id, grade):
         return json.loads(response.text)
 
 
-def parse_zip(zip_file: str) -> set:
-    """
-    Maps file names to user IDs from a zip of downloaded Canvas submissions
-    :param zip_file: The name of the zip file to parse
-    :return: if the zip can be parsed, a dictionary containing the user ID's mapped to the parsed file name, otherwise an empty dict
-    """
-    user_ids = set()
-
-    with ZipFile(os.path.join('zips', zip_file), 'r') as z:
-        for name in z.namelist():
-            if name.count('_') < 3:
-                print('Skipping file: ' + name + '. Invalid filename')
-            else:
-                (username, user_id, unknown, file) = name.split('_', maxsplit=3)
-                user_ids.add(user_id)
-
-                file_path = os.path.join('temp', user_id, '')
-                os.makedirs(os.path.dirname(file_path), exist_ok=True)
-                z.extract(name, path=file_path)
-                os.replace(os.path.join(file_path, name), os.path.join(file_path + file))
-
-    if len(user_ids) < 1:
-        print('Unable to read any files from the zip. Please check the file and try again')
-    return user_ids
-
-
 def choose_val(hi_num: int, allow_zero: bool = False) -> int:
     val = 'none'
 

From 6e7f60da90cab1c1ef572aae8261d7d8b10ca62a Mon Sep 17 00:00:00 2001
From: ThePyrotechnic <electricpyrotechnic@gmail.com>
Date: Wed, 13 Sep 2017 17:36:00 -0400
Subject: [PATCH 19/40] started numeric matching & more automation options

---
 pycanvasgrader/pycanvasgrader.py  | 47 +++++++++++++++++++++++++------
 pycanvasgrader/skeletons/C++.json | 11 ++++++++
 2 files changed, 50 insertions(+), 8 deletions(-)
 create mode 100644 pycanvasgrader/skeletons/C++.json

diff --git a/pycanvasgrader/pycanvasgrader.py b/pycanvasgrader/pycanvasgrader.py
index 6aba5c1..a168d46 100644
--- a/pycanvasgrader/pycanvasgrader.py
+++ b/pycanvasgrader/pycanvasgrader.py
@@ -6,12 +6,12 @@
 - pycanvasgrader
   -- skeletons
   -- temp
-  -- zips
   access.token
   pycanvasgrader.py
 
   TODO test temp directory deletion timing on Windows
   TODO implement skeleton creation wizard
+  TODO test/implement visual grading (ask for grade after test runs)
 """
 
 # built-ins
@@ -20,10 +20,9 @@
 import shutil
 import re
 import subprocess
-from zipfile import ZipFile
-import py
 
 # 3rd-party
+import py
 import requests
 
 # globals
@@ -36,13 +35,15 @@ class TestSkeleton:
     An abstract skeleton to handle testing of a specific group of files
     """
 
-    def __init__(self, descriptor: str, tests: list):
+    def __init__(self, descriptor: str, automation_level: str, tests: list):
         """
         :param descriptor: The description of this TestSkeleton
         :param tests: A list of AssignmentTest objects. These will be run in the order that they are added.
+        :param automation_level: How many questions the grader should ask
         """
         self.descriptor = descriptor
         self.tests = tests
+        self.automation_level = automation_level
 
     @classmethod
     def from_file(cls, filename):
@@ -85,12 +86,14 @@ class AssignmentTest:
     TODO 'sequential' command requirement
     """
 
-    def __init__(self, command: str, args: str = None, target_file: str = None, ask_for_target: bool = False,
-                 include_filetype: bool = True, print_output: bool = True, output_match: str = None, output_regex: str = None,
+    def __init__(self, command: str, args: str = None, single_file: bool = False, target_file: str = None,
+                 ask_for_target: bool = False, include_filetype: bool = True, print_output: bool = True,
+                 output_match: str = None, output_regex: str = None, numeric_match: list = None,
                  negate_match: bool = False, exact_match: bool = False, timeout: int = None, point_val: int = 0):
         """
         :param command: The command to be run.
         :param args: The arguments to pass to the command. Use %s to denote a file name
+        :param single_file: Whether to assume the assignment is a single file and use the first file found as %s
         :param target_file: The file to replace %s with
         :param ask_for_target: Whether to prompt for a file in the current directory. Overrides file_target
         :param include_filetype: Whether to include the filetype in the %s substitution
@@ -98,6 +101,7 @@ def __init__(self, command: str, args: str = None, target_file: str = None, ask_
         :param output_match: An exact string that the output should match. If this and output_regex are None, then this Command always 'matches'
         :param output_regex: A regular expression that the string should match. Combines with output_match.
         If this and output_match are None, then this Command always 'matches'
+        :param numeric_match: Enables numeric matching. This overrides string and regex matching
         :param negate_match: Whether to negate the result of checking output_match and output_regex
         :param exact_match: Whether the naive string match (output_match) should be an exact check or a substring check
         :param timeout: Time, in seconds, that this Command should run for before timing out
@@ -105,6 +109,7 @@ def __init__(self, command: str, args: str = None, target_file: str = None, ask_
         """
         self.command = command
         self.args = args
+        self.single_file = single_file
         self.target_file = target_file
         self.ask_for_target = ask_for_target
         self.include_filetype = include_filetype
@@ -113,6 +118,7 @@ def __init__(self, command: str, args: str = None, target_file: str = None, ask_
             self.output_regex = re.compile(output_regex)
         else:
             self.output_regex = None
+        self.numeric_match = numeric_match
         self.negate_match = negate_match
         self.exact_match = exact_match
         self.print_output = print_output
@@ -127,21 +133,24 @@ def from_json_dict(cls, json_dict: dict):
             return None
         else:
             args = json_dict.get('args')
+            single_file = json_dict.get('single_file')
             target_file = json_dict.get('target_file')
             ask_for_target = json_dict.get('ask_for_target')
             include_filetype = json_dict.get('include_filetype')
             print_output = json_dict.get('print_output')
             output_match = json_dict.get('output_match')
             output_regex = json_dict.get('output_regex')
+            numeric_match = json_dict.get('numeric_match')
             negate_match = json_dict.get('negate_match')
             exact_match = json_dict.get('exact_match')
             timeout = json_dict.get('timeout')
             point_val = json_dict.get('point_val')
 
-            vars_dict = {'command': command, 'args': args, 'target_file': target_file,
+            vars_dict = {'command': command, 'args': args, 'single_file': single_file, 'target_file': target_file,
                          'ask_for_target': ask_for_target, 'include_filetype': include_filetype,
                          'print_output': print_output, 'output_match': output_match, 'output_regex': output_regex,
-                         'negate_match': negate_match, 'exact_match': exact_match, 'timeout': timeout, 'point_val': point_val}
+                         'numeric_match': numeric_match, 'negate_match': negate_match, 'exact_match': exact_match,
+                         'timeout': timeout, 'point_val': point_val}
             args_dict = {}
             for var_name, val in vars_dict.items():
                 if val is not None:
@@ -201,6 +210,28 @@ def run_and_match(self) -> bool:
         if not any((self.output_match, self.output_regex)):
             return True
 
+        if self.numeric_match is not None:
+            numeric_match = list(self.numeric_match)  # Clone the list
+            extracted_nums = []
+            for t in result['stdout'].split():
+                try:
+                    extracted_nums.append(float(t))
+                except ValueError:
+                    pass
+            if len(extracted_nums) == 0:
+                return False
+
+            for num in numeric_match:
+                for number in extracted_nums:
+                    if isinstance(num, list):
+                        if num[0] <= number <= num[1]:
+                            numeric_match.remove(num)
+                    elif isinstance(num, (int, float)):
+                        if number == num:
+                            numeric_match.remove(num)
+
+            return len(numeric_match) == 0
+
         if self.output_regex:
             if self.output_regex.match(result['stdout']):
                 print('--Matched regular expression--')
diff --git a/pycanvasgrader/skeletons/C++.json b/pycanvasgrader/skeletons/C++.json
new file mode 100644
index 0000000..f9c4721
--- /dev/null
+++ b/pycanvasgrader/skeletons/C++.json
@@ -0,0 +1,11 @@
+{
+  "descriptor": "C++ high automation",
+  "automation_level": 3,
+  "tests": {
+    "compile_test": {
+      "command": "g++ -std=c++11",
+      "numeric_match": [[8.98,9],[9.98,10], 12],
+      "single_file": true
+    }
+  }
+}
\ No newline at end of file

From 1e7cedb2a30cca201e0de193a6b67f9ec5cacf93 Mon Sep 17 00:00:00 2001
From: ThePyrotechnic <electricpyrotechnic@gmail.com>
Date: Wed, 13 Sep 2017 22:33:08 -0400
Subject: [PATCH 20/40] started numeric matching & more automation options

---
 pycanvasgrader/pycanvasgrader.py   | 87 +++++++++++++++++++-----------
 pycanvasgrader/skeletons/C++.json  | 19 +++++--
 pycanvasgrader/skeletons/java.json |  2 -
 3 files changed, 70 insertions(+), 38 deletions(-)

diff --git a/pycanvasgrader/pycanvasgrader.py b/pycanvasgrader/pycanvasgrader.py
index a168d46..23bbc8f 100644
--- a/pycanvasgrader/pycanvasgrader.py
+++ b/pycanvasgrader/pycanvasgrader.py
@@ -28,14 +28,16 @@
 # globals
 RUN_WITH_TESTS = False
 ONLY_RUN_TESTS = False
-
+NUM_REGEX = re.compile(r'[+-]?\d+\.\d+|\d+')
+#r'[+-]?\d+\.\d+|\d+'
+#r'[-+]?\d+(\.\d+)?'
 
 class TestSkeleton:
     """
     An abstract skeleton to handle testing of a specific group of files
     """
 
-    def __init__(self, descriptor: str, automation_level: str, tests: list):
+    def __init__(self, descriptor: str, tests: list, automation_level: int = 0):
         """
         :param descriptor: The description of this TestSkeleton
         :param tests: A list of AssignmentTest objects. These will be run in the order that they are added.
@@ -48,20 +50,27 @@ def __init__(self, descriptor: str, automation_level: str, tests: list):
     @classmethod
     def from_file(cls, filename):
         with open('skeletons/' + filename) as skeleton_file:
-            data = json.load(skeleton_file)
+            try:
+                data = json.load(skeleton_file)
+            except json.JSONDecodeError:
+                print('There is an error in the %s skeleton file. This skeleton will not be available' % filename)
+                return None
             try:
                 descriptor = data['descriptor']
                 tests = data['tests']
             except KeyError:
                 return None
             else:
+                automation_level = data.get('automation_level')
+                if automation_level is None:
+                    automation_level = 0
                 test_list = []
                 for json_dict in tests:
                     test = AssignmentTest.from_json_dict(tests[json_dict])
                     if test is not None:
                         test_list.append(test)
 
-                return TestSkeleton(descriptor, test_list)
+                return TestSkeleton(descriptor, test_list, automation_level)
 
     def run_tests(self) -> int:
         total_score = 0
@@ -79,7 +88,6 @@ def run_tests(self) -> int:
         return total_score
 
 
-# TODO Create tests
 class AssignmentTest:
     """
     An abstract test to be run on an assignment submission
@@ -184,7 +192,11 @@ def run(self) -> dict:
         command = self.command
         args = self.args
         filename = self.target_file
-        if self.ask_for_target:
+        if self.single_file and len(os.listdir(os.getcwd())) > 0:
+            filename = os.listdir(os.getcwd())[0]
+        elif len(os.listdir(os.getcwd())) == 1:
+            filename = os.listdir(os.getcwd()[0])
+        elif self.ask_for_target:
             filename = AssignmentTest.target_prompt(self.command)
         if not self.include_filetype:
             filename = os.path.splitext(filename)[0]
@@ -202,27 +214,29 @@ def run_and_match(self) -> bool:
         Runs the command and matches the output to the output_match/regex. If neither are defined then this always returns true
         :return: Whether the output matched or not
         """
+        global NUM_REGEX
+
         result = self.run()
         if self.print_output:
             print('\t--OUTPUT--')
             print(result['stdout'])
             print('\t--END OUTPUT--')
-        if not any((self.output_match, self.output_regex)):
+        if not any((self.output_match, self.output_regex, self.numeric_match)):
             return True
 
         if self.numeric_match is not None:
             numeric_match = list(self.numeric_match)  # Clone the list
-            extracted_nums = []
-            for t in result['stdout'].split():
-                try:
-                    extracted_nums.append(float(t))
-                except ValueError:
-                    pass
-            if len(extracted_nums) == 0:
-                return False
-
-            for num in numeric_match:
-                for number in extracted_nums:
+            extracted_nums = map(float, re.findall(NUM_REGEX, result['stdout']))
+
+            for number in extracted_nums:
+                for num in numeric_match:
+                    if isinstance(num, str):
+                        numeric_match.remove(num)
+                        range_vals = list(map(float, re.findall(NUM_REGEX, num)))
+                        if len(range_vals) != 2:
+                            continue
+                        num = [range_vals[0] - range_vals[1], range_vals[0] + range_vals[1]]
+                        numeric_match.append(num)
                     if isinstance(num, list):
                         if num[0] <= number <= num[1]:
                             numeric_match.remove(num)
@@ -514,6 +528,10 @@ def main():
             name_dict[user_id] = user_data['name']
         print(str(user_data.get('name')) + '\t(%s)' % user_data.get('email'))
     print('----\n')
+
+    print('Require confirmation before submitting grades? (y or n)')
+    grade_conf = choose_bool()
+
     input('Press enter to begin grading\n')
     for cur_user_id in user_submission_dict:
         try:
@@ -530,23 +548,28 @@ def main():
 
         while True:
             print('\n--All tests completed--\nGrade for this assignment: %i' % score)
-            print('Choose an action:')
-            for count, action in enumerate(action_list, 1):
-                print('%i.\t%s' % (count, action))
-            action_choice = choose_val(len(action_list)) - 1
-            selected_action = action_list[action_choice]
-
-            if selected_action == 'Submit this grade':
+            if not grade_conf:
                 grader.grade_submission(course_id, assignment_id, cur_user_id, score)
                 print('Grade submitted')
                 break
-            elif selected_action == 'Modify this grade':
-                print('Enter a new grade for this submission:')
-                score = choose_val(1000, allow_zero=True)
-            elif selected_action == 'Skip this submission':
-                break
-            elif selected_action == 'Re-grade this submission':
-                score = selected_skeleton.run_tests()
+            else:
+                print('Choose an action:')
+                for count, action in enumerate(action_list, 1):
+                    print('%i.\t%s' % (count, action))
+                action_choice = choose_val(len(action_list)) - 1
+                selected_action = action_list[action_choice]
+
+                if selected_action == 'Submit this grade':
+                    grader.grade_submission(course_id, assignment_id, cur_user_id, score)
+                    print('Grade submitted')
+                    break
+                elif selected_action == 'Modify this grade':
+                    print('Enter a new grade for this submission:')
+                    score = choose_val(1000, allow_zero=True)
+                elif selected_action == 'Skip this submission':
+                    break
+                elif selected_action == 'Re-grade this submission':
+                    score = selected_skeleton.run_tests()
 
     print('done')
 
diff --git a/pycanvasgrader/skeletons/C++.json b/pycanvasgrader/skeletons/C++.json
index f9c4721..e4840b3 100644
--- a/pycanvasgrader/skeletons/C++.json
+++ b/pycanvasgrader/skeletons/C++.json
@@ -1,11 +1,22 @@
 {
-  "descriptor": "C++ high automation",
-  "automation_level": 3,
+  "descriptor": "Java high automation",
   "tests": {
     "compile_test": {
-      "command": "g++ -std=c++11",
-      "numeric_match": [[8.98,9],[9.98,10], 12],
+      "command": "C:\\Program Files\\Java\\jdk1.8.0_92\\bin\\javac.exe",
+      "args": "%s",
+      "print_output": false,
+      "point_val": 25,
+      "output_match": "error",
+      "negate_match": true,
       "single_file": true
+    },
+    "run_test": {
+      "command": "java",
+      "args": "%s",
+      "numeric_match": ["2|0.1"],
+      "single_file": true,
+      "include_filetype": false,
+      "point_val": 75
     }
   }
 }
\ No newline at end of file
diff --git a/pycanvasgrader/skeletons/java.json b/pycanvasgrader/skeletons/java.json
index 0b30816..b53d82c 100644
--- a/pycanvasgrader/skeletons/java.json
+++ b/pycanvasgrader/skeletons/java.json
@@ -1,7 +1,5 @@
 {
   "descriptor": "Example Java skeleton",
-  "extensions": ".java",
-
   "tests": {
 
     "test_1": {

From 2758f625ba34734e5173461349d013b0e2636faf Mon Sep 17 00:00:00 2001
From: Michael Manis <electricpyrotechnic@gmail.com>
Date: Mon, 18 Sep 2017 12:24:52 -0400
Subject: [PATCH 21/40] fixed file handling bugs, added print file option, made
 args a proper list

---
 pycanvasgrader/pycanvasgrader.py   | 46 +++++++++++++++++++----------
 pycanvasgrader/skeletons/C++.json  | 22 --------------
 pycanvasgrader/skeletons/HW1c.json | 23 +++++++++++++++
 pycanvasgrader/skeletons/HW2e.json | 21 +++++++++++++
 pycanvasgrader/skeletons/java.json | 24 ---------------
 pycanvasgrader/test_files/HW1c.cpp | 25 ++++++++++++++++
 pycanvasgrader/test_files/HW2e.cpp | 47 ++++++++++++++++++++++++++++++
 7 files changed, 146 insertions(+), 62 deletions(-)
 delete mode 100644 pycanvasgrader/skeletons/C++.json
 create mode 100644 pycanvasgrader/skeletons/HW1c.json
 create mode 100644 pycanvasgrader/skeletons/HW2e.json
 delete mode 100644 pycanvasgrader/skeletons/java.json
 create mode 100644 pycanvasgrader/test_files/HW1c.cpp
 create mode 100644 pycanvasgrader/test_files/HW2e.cpp

diff --git a/pycanvasgrader/pycanvasgrader.py b/pycanvasgrader/pycanvasgrader.py
index 23bbc8f..c3d102a 100644
--- a/pycanvasgrader/pycanvasgrader.py
+++ b/pycanvasgrader/pycanvasgrader.py
@@ -20,6 +20,7 @@
 import shutil
 import re
 import subprocess
+import sys
 
 # 3rd-party
 import py
@@ -29,8 +30,9 @@
 RUN_WITH_TESTS = False
 ONLY_RUN_TESTS = False
 NUM_REGEX = re.compile(r'[+-]?\d+\.\d+|\d+')
-#r'[+-]?\d+\.\d+|\d+'
-#r'[-+]?\d+(\.\d+)?'
+# r'[+-]?\d+\.\d+|\d+'
+# r'[-+]?\d+(\.\d+)?'
+
 
 class TestSkeleton:
     """
@@ -94,13 +96,14 @@ class AssignmentTest:
     TODO 'sequential' command requirement
     """
 
-    def __init__(self, command: str, args: str = None, single_file: bool = False, target_file: str = None,
+    def __init__(self, command: str, args: list = None, print_file: bool = False, single_file: bool = False, target_file: str = None,
                  ask_for_target: bool = False, include_filetype: bool = True, print_output: bool = True,
                  output_match: str = None, output_regex: str = None, numeric_match: list = None,
                  negate_match: bool = False, exact_match: bool = False, timeout: int = None, point_val: int = 0):
         """
         :param command: The command to be run.
-        :param args: The arguments to pass to the command. Use %s to denote a file name
+        :param args: List of arguments to pass to the command. Use %s to denote a file name
+        :param print_file: Whether to print the contents of the target_file being tested (Does nothing if no file is selected)
         :param single_file: Whether to assume the assignment is a single file and use the first file found as %s
         :param target_file: The file to replace %s with
         :param ask_for_target: Whether to prompt for a file in the current directory. Overrides file_target
@@ -117,6 +120,7 @@ def __init__(self, command: str, args: str = None, single_file: bool = False, ta
         """
         self.command = command
         self.args = args
+        self.print_file = print_file
         self.single_file = single_file
         self.target_file = target_file
         self.ask_for_target = ask_for_target
@@ -141,6 +145,7 @@ def from_json_dict(cls, json_dict: dict):
             return None
         else:
             args = json_dict.get('args')
+            print_file = json_dict.get('print_file')
             single_file = json_dict.get('single_file')
             target_file = json_dict.get('target_file')
             ask_for_target = json_dict.get('ask_for_target')
@@ -154,7 +159,7 @@ def from_json_dict(cls, json_dict: dict):
             timeout = json_dict.get('timeout')
             point_val = json_dict.get('point_val')
 
-            vars_dict = {'command': command, 'args': args, 'single_file': single_file, 'target_file': target_file,
+            vars_dict = {'command': command, 'args': args, 'print_file': print_file, 'single_file': single_file, 'target_file': target_file,
                          'ask_for_target': ask_for_target, 'include_filetype': include_filetype,
                          'print_output': print_output, 'output_match': output_match, 'output_regex': output_regex,
                          'numeric_match': numeric_match, 'negate_match': negate_match, 'exact_match': exact_match,
@@ -192,21 +197,30 @@ def run(self) -> dict:
         command = self.command
         args = self.args
         filename = self.target_file
-        if self.single_file and len(os.listdir(os.getcwd())) > 0:
-            filename = os.listdir(os.getcwd())[0]
-        elif len(os.listdir(os.getcwd())) == 1:
-            filename = os.listdir(os.getcwd()[0])
-        elif self.ask_for_target:
-            filename = AssignmentTest.target_prompt(self.command)
-        if not self.include_filetype:
+        if filename is None:
+            if self.single_file and len(os.listdir(os.getcwd())) > 0:
+                filename = os.listdir(os.getcwd())[0]
+            elif len(os.listdir(os.getcwd())) == 1:
+                filename = os.listdir(os.getcwd())[0]
+            elif self.ask_for_target:
+                filename = AssignmentTest.target_prompt(self.command)
+
+        if not self.include_filetype and filename is not None:
             filename = os.path.splitext(filename)[0]
         if filename is not None:
+            if self.print_file:
+                print('--FILE--')
+                with open(filename, "r") as f:
+                    shutil.copyfileobj(f, sys.stdout)
+                print('--END FILE--')
             command = self.command.replace('%s', filename)
-            args = self.args.replace('%s', filename)
-        elif '%s' in self.command + '|' + self.args:
-            print('No filename given, but this command contains filename wildcards (%s). This command will probably fail')
+            if args is not None:
+                args = [arg.replace('%s', filename) for arg in args]
 
-        proc = subprocess.run([command, args], stdout=subprocess.PIPE, stderr=subprocess.STDOUT, timeout=self.timeout, encoding='UTF-8', shell=True)
+        if args is not None:
+            proc = subprocess.run([command] + args, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, timeout=self.timeout, encoding='UTF-8', shell=True)
+        else:
+            proc = subprocess.run(command, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, timeout=self.timeout, encoding='UTF-8', shell=True)
         return {'returncode': proc.returncode, 'stdout': proc.stdout, 'stderr': proc.stderr}
 
     def run_and_match(self) -> bool:
diff --git a/pycanvasgrader/skeletons/C++.json b/pycanvasgrader/skeletons/C++.json
deleted file mode 100644
index e4840b3..0000000
--- a/pycanvasgrader/skeletons/C++.json
+++ /dev/null
@@ -1,22 +0,0 @@
-{
-  "descriptor": "Java high automation",
-  "tests": {
-    "compile_test": {
-      "command": "C:\\Program Files\\Java\\jdk1.8.0_92\\bin\\javac.exe",
-      "args": "%s",
-      "print_output": false,
-      "point_val": 25,
-      "output_match": "error",
-      "negate_match": true,
-      "single_file": true
-    },
-    "run_test": {
-      "command": "java",
-      "args": "%s",
-      "numeric_match": ["2|0.1"],
-      "single_file": true,
-      "include_filetype": false,
-      "point_val": 75
-    }
-  }
-}
\ No newline at end of file
diff --git a/pycanvasgrader/skeletons/HW1c.json b/pycanvasgrader/skeletons/HW1c.json
new file mode 100644
index 0000000..2776232
--- /dev/null
+++ b/pycanvasgrader/skeletons/HW1c.json
@@ -0,0 +1,23 @@
+{
+  "descriptor": "HW1c Grader",
+  "tests": {
+
+    "test_1": {
+      "command": "g++",
+      "args": ["%s", "-o", "out"],
+      "single_file": true,
+      "print_output": true,
+      "print_file": true,
+      "output_match": "error",
+      "negate_match": true,
+      "point_val": 25
+    },
+    "test_2": {
+      "command": "out.exe",
+      "print_output": true,
+      "output_match": "5050\n5050\n",
+      "exact_match": false,
+      "point_val": 75
+    }
+  }
+}
diff --git a/pycanvasgrader/skeletons/HW2e.json b/pycanvasgrader/skeletons/HW2e.json
new file mode 100644
index 0000000..c5af1b5
--- /dev/null
+++ b/pycanvasgrader/skeletons/HW2e.json
@@ -0,0 +1,21 @@
+{
+  "descriptor": "HW2e Grader",
+  "tests": {
+
+    "test_1": {
+      "command": "g++",
+      "args": ["%s", "-o", "out"],
+      "print_output": true,
+      "point_val": 25,
+      "output_match": "error",
+      "negate_match": true
+    },
+    "test_2": {
+      "command": "out.exe",
+      "print_output": true,
+      "output_match": "120 120\n2004310016 2004310016\n5 5\n233 233\n20358520\n",
+      "exact_match": true,
+      "point_val": 75
+    }
+  }
+}
diff --git a/pycanvasgrader/skeletons/java.json b/pycanvasgrader/skeletons/java.json
deleted file mode 100644
index b53d82c..0000000
--- a/pycanvasgrader/skeletons/java.json
+++ /dev/null
@@ -1,24 +0,0 @@
-{
-  "descriptor": "Example Java skeleton",
-  "tests": {
-
-    "test_1": {
-      "command": "C:\\Program Files\\Java\\jdk1.8.0_92\\bin\\javac.exe",
-      "args": "%s",
-      "print_output": true,
-      "point_val": 25,
-      "output_match": "error",
-      "negate_match": true,
-      "ask_for_target": true
-    },
-    "test_2": {
-      "command": "java",
-      "args": "%s",
-      "print_output": true,
-      "output_match": "Variable Value :2",
-      "point_val": 75,
-      "ask_for_target": true,
-      "include_filetype": false
-    }
-  }
-}
\ No newline at end of file
diff --git a/pycanvasgrader/test_files/HW1c.cpp b/pycanvasgrader/test_files/HW1c.cpp
new file mode 100644
index 0000000..a22849c
--- /dev/null
+++ b/pycanvasgrader/test_files/HW1c.cpp
@@ -0,0 +1,25 @@
+#include <iostream>
+
+using namespace std;
+
+int sum(int);
+int sum2(int);
+
+int main()
+{
+    cout << sum(100) << '\n';
+    cout << sum2(100) << '\n';
+    return 0;
+}
+
+int sum(int n) {
+    int total = 0;
+    for (int a = 1; a <= n; a++)
+        total += a;
+
+    return total;
+}
+
+int sum2(int n) {
+    return n * (n + 1) / 2;
+}
diff --git a/pycanvasgrader/test_files/HW2e.cpp b/pycanvasgrader/test_files/HW2e.cpp
new file mode 100644
index 0000000..6106105
--- /dev/null
+++ b/pycanvasgrader/test_files/HW2e.cpp
@@ -0,0 +1,47 @@
+#include <iostream>
+
+using namespace std;
+
+int fact(int);
+int fibo(int);
+unsigned choose(unsigned, unsigned);
+
+int main()
+{
+    cout << fact(5) << ' ' << fact(5) << '\n';
+    cout << fact(15) << ' ' << fact(15) << '\n';
+    cout << fibo(5) << ' ' << fibo(5) << '\n';
+    cout << fibo(13) << ' ' << fibo(13) << '\n';
+    cout << choose(52,6) << '\n';
+
+    return 0;
+}
+
+unsigned choose( unsigned n, unsigned k )
+{
+    if (k > n) return 0;
+    if (k * 2 > n) k = n-k;
+    if (k == 0) return 1;
+
+    int result = n;
+    for( int i = 2; i <= k; ++i ) {
+        result *= (n-i+1);
+        result /= i;
+    }
+    return result;
+}
+
+int fibo(int n)
+{
+   if (n <= 1)
+      return n;
+   return fibo(n-1) + fibo(n-2);
+}
+
+int fact(int n)
+{
+    if(n > 1)
+        return n * fact(n - 1);
+    else
+        return 1;
+}

From 686168aac7f5d278195c339c41170e62c6e67d75 Mon Sep 17 00:00:00 2001
From: Michael Manis <electricpyrotechnic@gmail.com>
Date: Mon, 18 Sep 2017 12:51:52 -0400
Subject: [PATCH 22/40] added message user JSON + API endpoint, still need to
 hook it up

---
 pycanvasgrader/pycanvasgrader.py   | 12 ++++++++++++
 pycanvasgrader/skeletons/HW1c.json | 21 ++++++++++++++++++---
 2 files changed, 30 insertions(+), 3 deletions(-)

diff --git a/pycanvasgrader/pycanvasgrader.py b/pycanvasgrader/pycanvasgrader.py
index c3d102a..73c3ea8 100644
--- a/pycanvasgrader/pycanvasgrader.py
+++ b/pycanvasgrader/pycanvasgrader.py
@@ -397,6 +397,18 @@ def grade_submission(self, course_id, assignment_id, user_id, grade):
         response = self.session.put(url)
         return json.loads(response.text)
 
+    def message_user(self, recipient_id: int, body: str, subject: str = None):
+        url = 'https://sit.instructure.com/api/v1/conversations/'
+
+        data = {
+            'recipients[]': recipient_id,
+            'body': body,
+            'subject': subject
+        }
+
+        response = self.session.post(url, data)
+        return json.loads(response.text)
+
 
 def choose_val(hi_num: int, allow_zero: bool = False) -> int:
     val = 'none'
diff --git a/pycanvasgrader/skeletons/HW1c.json b/pycanvasgrader/skeletons/HW1c.json
index 2776232..1668654 100644
--- a/pycanvasgrader/skeletons/HW1c.json
+++ b/pycanvasgrader/skeletons/HW1c.json
@@ -5,19 +5,34 @@
     "test_1": {
       "command": "g++",
       "args": ["%s", "-o", "out"],
+
       "single_file": true,
       "print_output": true,
       "print_file": true,
+
       "output_match": "error",
       "negate_match": true,
-      "point_val": 25
+
+      "point_val": 25,
+
+      "fail_notification": {
+        "subject": "HW1c compilation failed",
+        "body": "This is an automated message to inform you that compilation of your submission for HW1chas failed\nPlease resbumit this assigment or your grade will remain a 0."
+      }
     },
     "test_2": {
       "command": "out.exe",
       "print_output": true,
-      "output_match": "5050\n5050\n",
+
+      "output_match": "5050\n5050",
       "exact_match": false,
-      "point_val": 75
+
+      "point_val": 75,
+
+      "fail_notification": {
+        "subject": "HW1c testing failed",
+        "body": "This is an automated message to inform you that testing of your submission for HW1c has failed.\nCheck to make sure your output conforms exactly to what is expected on Canvas."
+      }
     }
   }
 }

From 9803c3b6f0a425203a76a8c27b4b7284b951057b Mon Sep 17 00:00:00 2001
From: ThePyrotechnic <electricpyrotechnic@gmail.com>
Date: Mon, 18 Sep 2017 13:47:30 -0400
Subject: [PATCH 23/40] messages implemented

---
 pycanvasgrader/pycanvasgrader.py   | 43 +++++++++++++++++++++++-------
 pycanvasgrader/skeletons/HW1c.json |  2 +-
 2 files changed, 35 insertions(+), 10 deletions(-)

diff --git a/pycanvasgrader/pycanvasgrader.py b/pycanvasgrader/pycanvasgrader.py
index 73c3ea8..9c3145b 100644
--- a/pycanvasgrader/pycanvasgrader.py
+++ b/pycanvasgrader/pycanvasgrader.py
@@ -9,7 +9,6 @@
   access.token
   pycanvasgrader.py
 
-  TODO test temp directory deletion timing on Windows
   TODO implement skeleton creation wizard
   TODO test/implement visual grading (ask for grade after test runs)
 """
@@ -27,6 +26,10 @@
 import requests
 
 # globals
+DISARM_ALL = False
+DISARM_MESSAGER = True
+DISARM_GRADER = False
+
 RUN_WITH_TESTS = False
 ONLY_RUN_TESTS = False
 NUM_REGEX = re.compile(r'[+-]?\d+\.\d+|\d+')
@@ -74,7 +77,7 @@ def from_file(cls, filename):
 
                 return TestSkeleton(descriptor, test_list, automation_level)
 
-    def run_tests(self) -> int:
+    def run_tests(self, grader: PyCanvasGrader, user_id: int) -> int:
         total_score = 0
         for count, test in enumerate(self.tests):
             print('\n--Running test %i--' % (count + 1))
@@ -86,6 +89,15 @@ def run_tests(self) -> int:
                 else:
                     print('--Subtracting %i points--' % abs(test.point_val))
                 total_score += test.point_val
+            elif test.fail_notif:
+                try:
+                    body = test.fail_notif['body']
+                except ValueError:
+                    pass
+                else:
+                    subject = test.fail_notif.get('subject')
+                    grader.message_user(user_id, body, subject)
+
             print('--Current score: %i--' % total_score)
         return total_score
 
@@ -99,7 +111,7 @@ class AssignmentTest:
     def __init__(self, command: str, args: list = None, print_file: bool = False, single_file: bool = False, target_file: str = None,
                  ask_for_target: bool = False, include_filetype: bool = True, print_output: bool = True,
                  output_match: str = None, output_regex: str = None, numeric_match: list = None,
-                 negate_match: bool = False, exact_match: bool = False, timeout: int = None, point_val: int = 0):
+                 negate_match: bool = False, exact_match: bool = False, timeout: int = None, fail_notif: dict = None, point_val: int = 0):
         """
         :param command: The command to be run.
         :param args: List of arguments to pass to the command. Use %s to denote a file name
@@ -116,6 +128,7 @@ def __init__(self, command: str, args: list = None, print_file: bool = False, si
         :param negate_match: Whether to negate the result of checking output_match and output_regex
         :param exact_match: Whether the naive string match (output_match) should be an exact check or a substring check
         :param timeout: Time, in seconds, that this Command should run for before timing out
+        :param fail_notif: Message to be sent to user when test fails
         :param point_val: Amount of points that a successful match is worth (Can be negative)
         """
         self.command = command
@@ -135,6 +148,7 @@ def __init__(self, command: str, args: list = None, print_file: bool = False, si
         self.exact_match = exact_match
         self.print_output = print_output
         self.timeout = timeout
+        self.fail_notif = fail_notif
         self.point_val = point_val
 
     @classmethod
@@ -157,13 +171,14 @@ def from_json_dict(cls, json_dict: dict):
             negate_match = json_dict.get('negate_match')
             exact_match = json_dict.get('exact_match')
             timeout = json_dict.get('timeout')
+            fail_notif = json_dict.get('fail_notification')
             point_val = json_dict.get('point_val')
 
             vars_dict = {'command': command, 'args': args, 'print_file': print_file, 'single_file': single_file, 'target_file': target_file,
                          'ask_for_target': ask_for_target, 'include_filetype': include_filetype,
                          'print_output': print_output, 'output_match': output_match, 'output_regex': output_regex,
                          'numeric_match': numeric_match, 'negate_match': negate_match, 'exact_match': exact_match,
-                         'timeout': timeout, 'point_val': point_val}
+                         'timeout': timeout, 'fail_notif': fail_notif, 'point_val': point_val}
             args_dict = {}
             for var_name, val in vars_dict.items():
                 if val is not None:
@@ -391,13 +406,19 @@ def user(self, course_id: int, user_id: int) -> dict:
         return json.loads(response.text)
 
     def grade_submission(self, course_id, assignment_id, user_id, grade):
+        global DISARM_ALL, DISARM_GRADER
         url = 'https://sit.instructure.com/api/v1/courses/%i/assignments/%i/submissions/%i/?submission[posted_grade]=%i' \
               % (course_id, assignment_id, user_id, grade)
 
-        response = self.session.put(url)
-        return json.loads(response.text)
+        if DISARM_ALL or DISARM_GRADER:
+            print('Dummy: Grade submitted')
+            return 'dummy success'
+        else:
+            response = self.session.put(url)
+            return json.loads(response.text)
 
     def message_user(self, recipient_id: int, body: str, subject: str = None):
+        global DISARM_ALL, DISARM_MESSAGER
         url = 'https://sit.instructure.com/api/v1/conversations/'
 
         data = {
@@ -406,8 +427,12 @@ def message_user(self, recipient_id: int, body: str, subject: str = None):
             'subject': subject
         }
 
-        response = self.session.post(url, data)
-        return json.loads(response.text)
+        if DISARM_ALL or DISARM_MESSAGER:
+            print('Dummy: user messaged')
+            return 'dummy success'
+        else:
+            response = self.session.post(url, data)
+            return json.loads(response.text)
 
 
 def choose_val(hi_num: int, allow_zero: bool = False) -> int:
@@ -566,7 +591,7 @@ def main():
             print('Could not access files for user "%i". Skipping' % cur_user_id)
             continue
         print('--Grading user "%s"--' % name_dict.get(cur_user_id))
-        score = selected_skeleton.run_tests()
+        score = selected_skeleton.run_tests(grader, cur_user_id)
 
         if score < 0:
             score = 0
diff --git a/pycanvasgrader/skeletons/HW1c.json b/pycanvasgrader/skeletons/HW1c.json
index 1668654..93e2aeb 100644
--- a/pycanvasgrader/skeletons/HW1c.json
+++ b/pycanvasgrader/skeletons/HW1c.json
@@ -17,7 +17,7 @@
 
       "fail_notification": {
         "subject": "HW1c compilation failed",
-        "body": "This is an automated message to inform you that compilation of your submission for HW1chas failed\nPlease resbumit this assigment or your grade will remain a 0."
+        "body": "This is an automated message to inform you that compilation of your submission for HW1c has failed\nPlease resbumit this assigment or your grade will remain a 0."
       }
     },
     "test_2": {

From db71de51b3bfa943185227f85cc74c883f75f737 Mon Sep 17 00:00:00 2001
From: ThePyrotechnic <electricpyrotechnic@gmail.com>
Date: Wed, 20 Sep 2017 15:04:29 -0400
Subject: [PATCH 24/40] string updates

---
 .idea/codeStyleSettings.xml                   |   9 +
 .idea/grading.iml                             |  11 +
 .idea/misc.xml                                |   4 +
 .idea/modules.xml                             |   8 +
 .idea/vcs.xml                                 |   6 +
 .idea/workspace.xml                           | 593 ++++++++++++++++++
 .../__pycache__/__init__.cpython-36.pyc       | Bin 0 -> 148 bytes
 .../__pycache__/pycanvasgrader.cpython-36.pyc | Bin 0 -> 2886 bytes
 .../test_grader.cpython-36-PYTEST.pyc         | Bin 0 -> 2785 bytes
 pycanvasgrader/access.token                   |   1 +
 pycanvasgrader/pycanvasgrader.py              | 287 +++++----
 pycanvasgrader/skeletons/HW1c.json            |   4 +-
 pycanvasgrader/temp/27592/HW1c.cpp            |  25 +
 13 files changed, 800 insertions(+), 148 deletions(-)
 create mode 100644 .idea/codeStyleSettings.xml
 create mode 100644 .idea/grading.iml
 create mode 100644 .idea/misc.xml
 create mode 100644 .idea/modules.xml
 create mode 100644 .idea/vcs.xml
 create mode 100644 .idea/workspace.xml
 create mode 100644 pycanvasgrader/__pycache__/__init__.cpython-36.pyc
 create mode 100644 pycanvasgrader/__pycache__/pycanvasgrader.cpython-36.pyc
 create mode 100644 pycanvasgrader/__pycache__/test_grader.cpython-36-PYTEST.pyc
 create mode 100644 pycanvasgrader/access.token
 create mode 100644 pycanvasgrader/temp/27592/HW1c.cpp

diff --git a/.idea/codeStyleSettings.xml b/.idea/codeStyleSettings.xml
new file mode 100644
index 0000000..5555dd2
--- /dev/null
+++ b/.idea/codeStyleSettings.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectCodeStyleSettingsManager">
+    <option name="PER_PROJECT_SETTINGS">
+      <value />
+    </option>
+    <option name="PREFERRED_PROJECT_CODE_STYLE" value="Default" />
+  </component>
+</project>
\ No newline at end of file
diff --git a/.idea/grading.iml b/.idea/grading.iml
new file mode 100644
index 0000000..e6258db
--- /dev/null
+++ b/.idea/grading.iml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<module type="PYTHON_MODULE" version="4">
+  <component name="NewModuleRootManager">
+    <content url="file://$MODULE_DIR$" />
+    <orderEntry type="jdk" jdkName="Python 3.6.2 virtualenv at C:\Users\elect\pycanvasgrader" jdkType="Python SDK" />
+    <orderEntry type="sourceFolder" forTests="false" />
+  </component>
+  <component name="TestRunnerService">
+    <option name="PROJECT_TEST_RUNNER" value="Unittests" />
+  </component>
+</module>
\ No newline at end of file
diff --git a/.idea/misc.xml b/.idea/misc.xml
new file mode 100644
index 0000000..fe7494e
--- /dev/null
+++ b/.idea/misc.xml
@@ -0,0 +1,4 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectRootManager" version="2" project-jdk-name="Python 3.6.2 virtualenv at C:\Users\elect\pycanvasgrader" project-jdk-type="Python SDK" />
+</project>
\ No newline at end of file
diff --git a/.idea/modules.xml b/.idea/modules.xml
new file mode 100644
index 0000000..0b6948b
--- /dev/null
+++ b/.idea/modules.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectModuleManager">
+    <modules>
+      <module fileurl="file://$PROJECT_DIR$/.idea/grading.iml" filepath="$PROJECT_DIR$/.idea/grading.iml" />
+    </modules>
+  </component>
+</project>
\ No newline at end of file
diff --git a/.idea/vcs.xml b/.idea/vcs.xml
new file mode 100644
index 0000000..94a25f7
--- /dev/null
+++ b/.idea/vcs.xml
@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="VcsDirectoryMappings">
+    <mapping directory="$PROJECT_DIR$" vcs="Git" />
+  </component>
+</project>
\ No newline at end of file
diff --git a/.idea/workspace.xml b/.idea/workspace.xml
new file mode 100644
index 0000000..69244b1
--- /dev/null
+++ b/.idea/workspace.xml
@@ -0,0 +1,593 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ChangeListManager">
+    <list default="true" id="54d8ef13-2d7a-46b2-af83-82b82d6627c0" name="Default" comment="messages implemented">
+      <change type="MODIFICATION" beforePath="$PROJECT_DIR$/pycanvasgrader/pycanvasgrader.py" afterPath="$PROJECT_DIR$/pycanvasgrader/pycanvasgrader.py" />
+      <change type="MODIFICATION" beforePath="$PROJECT_DIR$/pycanvasgrader/skeletons/HW1c.json" afterPath="$PROJECT_DIR$/pycanvasgrader/skeletons/HW1c.json" />
+    </list>
+    <option name="EXCLUDED_CONVERTED_TO_IGNORED" value="true" />
+    <option name="TRACKING_ENABLED" value="true" />
+    <option name="SHOW_DIALOG" value="false" />
+    <option name="HIGHLIGHT_CONFLICTS" value="true" />
+    <option name="HIGHLIGHT_NON_ACTIVE_CHANGELIST" value="false" />
+    <option name="LAST_RESOLUTION" value="IGNORE" />
+  </component>
+  <component name="CoverageDataManager">
+    <SUITE FILE_PATH="coverage/grading$pycanvasgrader.coverage" NAME="pycanvasgrader Coverage Results" MODIFIED="1505933985744" SOURCE_PROVIDER="com.intellij.coverage.DefaultCoverageFileProvider" RUNNER="coverage.py" COVERAGE_BY_TEST_ENABLED="true" COVERAGE_TRACING_ENABLED="false" WORKING_DIRECTORY="$PROJECT_DIR$/pycanvasgrader" />
+  </component>
+  <component name="FileEditorManager">
+    <leaf SIDE_TABS_SIZE_LIMIT_KEY="375">
+      <file leaf-file-name="access.token" pinned="false" current-in-tab="false">
+        <entry file="file://$PROJECT_DIR$/pycanvasgrader/access.token">
+          <provider selected="true" editor-type-id="text-editor">
+            <state relative-caret-position="0">
+              <caret line="0" column="69" lean-forward="false" selection-start-line="0" selection-start-column="69" selection-end-line="0" selection-end-column="69" />
+              <folding />
+            </state>
+          </provider>
+        </entry>
+      </file>
+      <file leaf-file-name="pycanvasgrader.py" pinned="false" current-in-tab="true">
+        <entry file="file://$PROJECT_DIR$/pycanvasgrader/pycanvasgrader.py">
+          <provider selected="true" editor-type-id="text-editor">
+            <state relative-caret-position="73">
+              <caret line="142" column="41" lean-forward="true" selection-start-line="142" selection-start-column="41" selection-end-line="142" selection-end-column="41" />
+              <folding>
+                <element signature="e#401#412#0" expanded="true" />
+                <element signature="e#8191#17454#0" expanded="false" />
+              </folding>
+            </state>
+          </provider>
+        </entry>
+      </file>
+      <file leaf-file-name="HW1c.json" pinned="false" current-in-tab="false">
+        <entry file="file://$PROJECT_DIR$/pycanvasgrader/skeletons/HW1c.json">
+          <provider selected="true" editor-type-id="text-editor">
+            <state relative-caret-position="294">
+              <caret line="14" column="0" lean-forward="true" selection-start-line="14" selection-start-column="0" selection-end-line="14" selection-end-column="0" />
+              <folding />
+            </state>
+          </provider>
+        </entry>
+      </file>
+      <file leaf-file-name="HW1c.cpp" pinned="false" current-in-tab="false">
+        <entry file="file://$PROJECT_DIR$/pycanvasgrader/test_files/HW1c.cpp">
+          <provider selected="true" editor-type-id="text-editor">
+            <state relative-caret-position="210">
+              <caret line="10" column="30" lean-forward="false" selection-start-line="10" selection-start-column="30" selection-end-line="10" selection-end-column="30" />
+              <folding />
+            </state>
+          </provider>
+        </entry>
+      </file>
+      <file leaf-file-name="HW2e.json" pinned="false" current-in-tab="false">
+        <entry file="file://$PROJECT_DIR$/pycanvasgrader/skeletons/HW2e.json">
+          <provider selected="true" editor-type-id="text-editor">
+            <state relative-caret-position="378">
+              <caret line="18" column="5" lean-forward="false" selection-start-line="18" selection-start-column="5" selection-end-line="18" selection-end-column="5" />
+              <folding />
+            </state>
+          </provider>
+        </entry>
+      </file>
+      <file leaf-file-name="test_grader.py" pinned="false" current-in-tab="false">
+        <entry file="file://$PROJECT_DIR$/pycanvasgrader/test_grader.py">
+          <provider selected="true" editor-type-id="text-editor">
+            <state relative-caret-position="882">
+              <caret line="48" column="0" lean-forward="false" selection-start-line="48" selection-start-column="0" selection-end-line="48" selection-end-column="0" />
+              <folding>
+                <element signature="e#50#61#0" expanded="true" />
+              </folding>
+            </state>
+          </provider>
+        </entry>
+      </file>
+    </leaf>
+  </component>
+  <component name="FileTemplateManagerImpl">
+    <option name="RECENT_TEMPLATES">
+      <list>
+        <option value="Python Script" />
+      </list>
+    </option>
+  </component>
+  <component name="FindInProjectRecents">
+    <findStrings>
+      <find>run_tests</find>
+      <find>automat</find>
+      <find>message_user</find>
+      <find>Grade Submitted</find>
+    </findStrings>
+  </component>
+  <component name="Git.Settings">
+    <option name="RECENT_GIT_ROOT_PATH" value="$PROJECT_DIR$" />
+  </component>
+  <component name="IdeDocumentHistory">
+    <option name="CHANGED_PATHS">
+      <list>
+        <option value="$PROJECT_DIR$/pycanvasgrader/access.token" />
+        <option value="$PROJECT_DIR$/pycanvasgrader/__init__.py" />
+        <option value="$PROJECT_DIR$/pycanvasgrader/test_grader.py" />
+        <option value="$PROJECT_DIR$/pycanvasgrader/skeletons/java.json" />
+        <option value="$PROJECT_DIR$/pycanvasgrader/skeletons/C++.json" />
+        <option value="$PROJECT_DIR$/pycanvasgrader/skeletons/HW1c.json" />
+        <option value="$PROJECT_DIR$/pycanvasgrader/pycanvasgrader.py" />
+      </list>
+    </option>
+  </component>
+  <component name="JsBuildToolGruntFileManager" detection-done="true" sorting="DEFINITION_ORDER" />
+  <component name="JsBuildToolPackageJson" detection-done="true" sorting="DEFINITION_ORDER" />
+  <component name="JsGulpfileManager">
+    <detection-done>true</detection-done>
+    <sorting>DEFINITION_ORDER</sorting>
+  </component>
+  <component name="ProjectFrameBounds" extendedState="6">
+    <option name="x" value="-9" />
+    <option name="y" value="-9" />
+    <option name="width" value="1938" />
+    <option name="height" value="1060" />
+  </component>
+  <component name="ProjectInspectionProfilesVisibleTreeState">
+    <entry key="Project Default">
+      <profile-state>
+        <expanded-state>
+          <State>
+            <id />
+          </State>
+        </expanded-state>
+        <selected-state>
+          <State>
+            <id>Python</id>
+          </State>
+        </selected-state>
+      </profile-state>
+    </entry>
+  </component>
+  <component name="ProjectView">
+    <navigator currentView="ProjectPane" proportions="" version="1">
+      <flattenPackages />
+      <showMembers />
+      <showModules />
+      <showLibraryContents />
+      <hideEmptyPackages />
+      <abbreviatePackageNames />
+      <autoscrollToSource />
+      <autoscrollFromSource />
+      <sortByType />
+      <manualOrder />
+      <foldersAlwaysOnTop value="true" />
+    </navigator>
+    <panes>
+      <pane id="Scope" />
+      <pane id="Scratches" />
+      <pane id="ProjectPane">
+        <subPane>
+          <expand>
+            <path>
+              <item name="grading" type="b2602c69:ProjectViewProjectNode" />
+              <item name="grading" type="462c0819:PsiDirectoryNode" />
+            </path>
+            <path>
+              <item name="grading" type="b2602c69:ProjectViewProjectNode" />
+              <item name="grading" type="462c0819:PsiDirectoryNode" />
+              <item name="pycanvasgrader" type="462c0819:PsiDirectoryNode" />
+            </path>
+            <path>
+              <item name="grading" type="b2602c69:ProjectViewProjectNode" />
+              <item name="grading" type="462c0819:PsiDirectoryNode" />
+              <item name="pycanvasgrader" type="462c0819:PsiDirectoryNode" />
+              <item name="skeletons" type="462c0819:PsiDirectoryNode" />
+            </path>
+            <path>
+              <item name="grading" type="b2602c69:ProjectViewProjectNode" />
+              <item name="grading" type="462c0819:PsiDirectoryNode" />
+              <item name="pycanvasgrader" type="462c0819:PsiDirectoryNode" />
+              <item name="test_files" type="462c0819:PsiDirectoryNode" />
+            </path>
+          </expand>
+          <select />
+        </subPane>
+      </pane>
+    </panes>
+  </component>
+  <component name="PropertiesComponent">
+    <property name="nodejs_interpreter_path" value="C:/Program Files/nodejs/node" />
+    <property name="WebServerToolWindowFactoryState" value="false" />
+    <property name="settings.editor.selected.configurable" value="application.passwordSafe" />
+    <property name="last_opened_file_path" value="$USER_HOME$/AppData/Local/Programs/Python/Python36/python.exe" />
+  </component>
+  <component name="RunDashboard">
+    <option name="ruleStates">
+      <list>
+        <RuleState>
+          <option name="name" value="ConfigurationTypeDashboardGroupingRule" />
+        </RuleState>
+        <RuleState>
+          <option name="name" value="StatusDashboardGroupingRule" />
+        </RuleState>
+      </list>
+    </option>
+  </component>
+  <component name="RunManager" selected="Python.pycanvasgrader">
+    <configuration name="pycanvasgrader" type="PythonConfigurationType" factoryName="Python" temporary="true">
+      <option name="INTERPRETER_OPTIONS" value="" />
+      <option name="PARENT_ENVS" value="true" />
+      <envs>
+        <env name="PYTHONUNBUFFERED" value="1" />
+      </envs>
+      <option name="SDK_HOME" value="" />
+      <option name="WORKING_DIRECTORY" value="$PROJECT_DIR$/pycanvasgrader" />
+      <option name="IS_MODULE_SDK" value="true" />
+      <option name="ADD_CONTENT_ROOTS" value="true" />
+      <option name="ADD_SOURCE_ROOTS" value="true" />
+      <module name="grading" />
+      <EXTENSION ID="PythonCoverageRunConfigurationExtension" enabled="false" sample_coverage="true" runner="coverage.py" />
+      <option name="SCRIPT_NAME" value="$PROJECT_DIR$/pycanvasgrader/pycanvasgrader.py" />
+      <option name="PARAMETERS" value="" />
+      <option name="SHOW_COMMAND_LINE" value="false" />
+      <option name="EMULATE_TERMINAL" value="false" />
+    </configuration>
+    <recent_temporary>
+      <list size="1">
+        <item index="0" class="java.lang.String" itemvalue="Python.pycanvasgrader" />
+      </list>
+    </recent_temporary>
+  </component>
+  <component name="ShelveChangesManager" show_recycled="false">
+    <option name="remove_strategy" value="false" />
+  </component>
+  <component name="TaskManager">
+    <task active="true" id="Default" summary="Default task">
+      <changelist id="54d8ef13-2d7a-46b2-af83-82b82d6627c0" name="Default" comment="" />
+      <created>1504822670108</created>
+      <option name="number" value="Default" />
+      <option name="presentableId" value="Default" />
+      <updated>1504822670108</updated>
+    </task>
+    <task id="LOCAL-00001" summary="started numeric matching &amp; more automation options">
+      <created>1505338560843</created>
+      <option name="number" value="00001" />
+      <option name="presentableId" value="LOCAL-00001" />
+      <option name="project" value="LOCAL" />
+      <updated>1505338560843</updated>
+    </task>
+    <task id="LOCAL-00002" summary="started numeric matching &amp; more automation options">
+      <created>1505356388316</created>
+      <option name="number" value="00002" />
+      <option name="presentableId" value="LOCAL-00002" />
+      <option name="project" value="LOCAL" />
+      <updated>1505356388317</updated>
+    </task>
+    <task id="LOCAL-00003" summary="messages implemented">
+      <created>1505756850892</created>
+      <option name="number" value="00003" />
+      <option name="presentableId" value="LOCAL-00003" />
+      <option name="project" value="LOCAL" />
+      <updated>1505756850892</updated>
+    </task>
+    <option name="localTasksCounter" value="4" />
+    <servers />
+  </component>
+  <component name="ToolWindowManager">
+    <frame x="-9" y="-9" width="1938" height="1060" extended-state="6" />
+    <layout>
+      <window_info id="Project" active="true" anchor="left" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="true" show_stripe_button="true" weight="0.25725028" sideWeight="0.5" order="1" side_tool="false" content_ui="combo" />
+      <window_info id="TODO" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="8" side_tool="false" content_ui="tabs" />
+      <window_info id="Event Log" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.32921347" sideWeight="0.5042965" order="0" side_tool="true" content_ui="tabs" />
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new file mode 100644
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diff --git a/pycanvasgrader/access.token b/pycanvasgrader/access.token
new file mode 100644
index 0000000..ec325d6
--- /dev/null
+++ b/pycanvasgrader/access.token
@@ -0,0 +1 @@
+1030~v7wtqrohOlMXdfVU1sBGEJWPm3IsTubOVH02BQTB9T2rRoltJ2QdmMcdAmxHME8x
\ No newline at end of file
diff --git a/pycanvasgrader/pycanvasgrader.py b/pycanvasgrader/pycanvasgrader.py
index 9c3145b..1e79e9f 100644
--- a/pycanvasgrader/pycanvasgrader.py
+++ b/pycanvasgrader/pycanvasgrader.py
@@ -26,7 +26,7 @@
 import requests
 
 # globals
-DISARM_ALL = False
+DISARM_ALL = True
 DISARM_MESSAGER = True
 DISARM_GRADER = False
 
@@ -37,20 +37,156 @@
 # r'[-+]?\d+(\.\d+)?'
 
 
+class PyCanvasGrader:
+    """
+    A PyCanvasGrader object; responsible for communicating with the Canvas API
+    """
+
+    def __init__(self):
+        self.token = self.authenticate()
+        if self.token == 'none':
+            print('Unable to retrieve OAuth2 token')
+            exit()
+
+        self.session = requests.Session()
+        self.session.headers.update({'Authorization': 'Bearer ' + self.token})
+
+    @staticmethod
+    def authenticate() -> str:
+        """
+        Responsible for retrieving the OAuth2 token for the session.
+        :return: The OAuth2 token
+
+        TODO Talk about "proper" OAuth2 authentication
+        """
+
+        with open('access.token', 'r', encoding='UTF-8') as access_file:
+            for line in access_file:
+                token = line.strip()
+                if isinstance(token, str) and len(token) > 2:
+                    return token
+        return 'none'
+
+    def close(self):
+        self.session.close()
+
+    def courses(self, enrollment_type: str = None) -> list:
+        """
+        :param enrollment_type: (Optional) teacher, student, ta, observer, designer
+        :return: A list of the user's courses as dictionaries, optionally filtered by enrollment_type
+        """
+        url = 'https://sit.instructure.com/api/v1/courses'
+        if enrollment_type is not None:
+            url += '?enrollment_type=' + enrollment_type
+
+        response = self.session.get(url)
+        return json.loads(response.text)
+
+    def assignments(self, course_id: int, ungraded: bool = True) -> list:
+        """
+        :param course_id: Course ID to filter by
+        :param ungraded: Whether to filter assignments by only those that have ungraded work. Default: True
+        :return: A list of the course's assignments
+        """
+        url = 'https://sit.instructure.com/api/v1/courses/' + str(course_id) + '/assignments'
+        if ungraded:
+            url += '?bucket=ungraded'
+
+        response = self.session.get(url)
+        return json.loads(response.text)
+
+    def submissions(self, course_id: int, assignment_id: int) -> list:
+        """
+        :param course_id: The ID of the course containing the assignment
+        :param assignment_id: The ID of the assignment
+        :return: A list of the assignment's submissions
+        """
+        url = 'https://sit.instructure.com/api/v1/courses/' + str(course_id) + '/assignments/' + str(assignment_id) + '/submissions'
+
+        response = self.session.get(url)
+        return json.loads(response.text)
+
+    def download_submission(self, submission: dict, filepath: str) -> bool:
+        """
+        Attempts to download the attachments for a given submission into the requested directory. Creates the directory if it does not exist.
+        :param submission: The submission dictionary
+        :param filepath: the path where the submission attachments will be placed
+        :return: True if the request succeeded, False otherwise
+        """
+        try:
+            user_id = submission['user_id']
+            attachments = submission['attachments']
+        except ValueError:
+            return False
+
+        for attachment in attachments:
+            try:
+                url = attachment['url']
+                filename = attachment['filename']
+            except ValueError:
+                return False
+
+            os.makedirs(os.path.join('temp', str(user_id)), exist_ok=True)
+            r = self.session.get(url, stream=True)
+            with open(os.path.join(filepath, filename), 'wb') as f:
+                for chunk in r.iter_content(chunk_size=1024):
+                    if chunk:
+                        f.write(chunk)
+        return True
+
+    def user(self, course_id: int, user_id: int) -> dict:
+        """
+        :param course_id: The class to search
+        :param user_id: The ID of the user
+        :return: A dictionary with the user's information
+        """
+        url = 'https://sit.instructure.com/api/v1/courses/%i/users/%i' % (course_id, user_id)
+
+        response = self.session.get(url)
+        return json.loads(response.text)
+
+    def grade_submission(self, course_id, assignment_id, user_id, grade):
+        global DISARM_ALL, DISARM_GRADER
+        url = 'https://sit.instructure.com/api/v1/courses/%i/assignments/%i/submissions/%i/?submission[posted_grade]=%i' \
+              % (course_id, assignment_id, user_id, grade)
+
+        if DISARM_ALL or DISARM_GRADER:
+            print('Grader disarmed; grade not actually submitted')
+            return 'dummy success'
+        else:
+            response = self.session.put(url)
+            return json.loads(response.text)
+
+    def message_user(self, recipient_id: int, body: str, subject: str = None):
+        global DISARM_ALL, DISARM_MESSAGER
+        url = 'https://sit.instructure.com/api/v1/conversations/'
+
+        data = {
+            'recipients[]': recipient_id,
+            'body': body,
+            'subject': subject
+        }
+
+        if DISARM_ALL or DISARM_MESSAGER:
+            print('Messenger disarmed; user was not messaged')
+            return 'dummy success'
+        else:
+            response = self.session.post(url, data)
+            return json.loads(response.text)
+
+
 class TestSkeleton:
     """
     An abstract skeleton to handle testing of a specific group of files
     """
 
-    def __init__(self, descriptor: str, tests: list, automation_level: int = 0):
+    def __init__(self, descriptor: str, tests: list):
         """
         :param descriptor: The description of this TestSkeleton
         :param tests: A list of AssignmentTest objects. These will be run in the order that they are added.
-        :param automation_level: How many questions the grader should ask
         """
         self.descriptor = descriptor
         self.tests = tests
-        self.automation_level = automation_level
 
     @classmethod
     def from_file(cls, filename):
@@ -66,16 +202,13 @@ def from_file(cls, filename):
             except KeyError:
                 return None
             else:
-                automation_level = data.get('automation_level')
-                if automation_level is None:
-                    automation_level = 0
                 test_list = []
                 for json_dict in tests:
                     test = AssignmentTest.from_json_dict(tests[json_dict])
                     if test is not None:
                         test_list.append(test)
 
-                return TestSkeleton(descriptor, test_list, automation_level)
+                return TestSkeleton(descriptor, test_list)
 
     def run_tests(self, grader: PyCanvasGrader, user_id: int) -> int:
         total_score = 0
@@ -297,144 +430,6 @@ def run_and_match(self) -> bool:
         return self.negate_match
 
 
-class PyCanvasGrader:
-    """
-    A PyCanvasGrader object; responsible for communicating with the Canvas API
-    """
-
-    def __init__(self):
-        self.token = self.authenticate()
-        if self.token == 'none':
-            print('Unable to retrieve OAuth2 token')
-            exit()
-
-        self.session = requests.Session()
-        self.session.headers.update({'Authorization': 'Bearer ' + self.token})
-
-    @staticmethod
-    def authenticate() -> str:
-        """
-        Responsible for retrieving the OAuth2 token for the session.
-        :return: The OAuth2 token
-
-        TODO Talk about "proper" OAuth2 authentication
-        """
-
-        with open('access.token', 'r', encoding='UTF-8') as access_file:
-            for line in access_file:
-                token = line.strip()
-                if isinstance(token, str) and len(token) > 2:
-                    return token
-        return 'none'
-
-    def close(self):
-        self.session.close()
-
-    def courses(self, enrollment_type: str = None) -> list:
-        """
-        :param enrollment_type: (Optional) teacher, student, ta, observer, designer
-        :return: A list of the user's courses as dictionaries, optionally filtered by enrollment_type
-        """
-        url = 'https://sit.instructure.com/api/v1/courses'
-        if enrollment_type is not None:
-            url += '?enrollment_type=' + enrollment_type
-
-        response = self.session.get(url)
-        return json.loads(response.text)
-
-    def assignments(self, course_id: int, ungraded: bool = True) -> list:
-        """
-        :param course_id: Course ID to filter by
-        :param ungraded: Whether to filter assignments by only those that have ungraded work. Default: True
-        :return: A list of the course's assignments
-        """
-        url = 'https://sit.instructure.com/api/v1/courses/' + str(course_id) + '/assignments'
-        if ungraded:
-            url += '?bucket=ungraded'
-
-        response = self.session.get(url)
-        return json.loads(response.text)
-
-    def submissions(self, course_id: int, assignment_id: int) -> list:
-        """
-        :param course_id: The ID of the course containing the assignment
-        :param assignment_id: The ID of the assignment
-        :return: A list of the assignment's submissions
-        """
-        url = 'https://sit.instructure.com/api/v1/courses/' + str(course_id) + '/assignments/' + str(assignment_id) + '/submissions'
-
-        response = self.session.get(url)
-        return json.loads(response.text)
-
-    def download_submission(self, submission: dict, filepath: str) -> bool:
-        """
-        Attempts to download the attachments for a given submission into the requested directory. Creates the directory if it does not exist.
-        :param submission: The submission dictionary
-        :param filepath: the path where the submission attachments will be placed
-        :return: True if the request succeeded, False otherwise
-        """
-        try:
-            user_id = submission['user_id']
-            attachments = submission['attachments']
-        except ValueError:
-            return False
-
-        for attachment in attachments:
-            try:
-                url = attachment['url']
-                filename = attachment['filename']
-            except ValueError:
-                return False
-
-            os.makedirs(os.path.join('temp', str(user_id)), exist_ok=True)
-            r = self.session.get(url, stream=True)
-            with open(os.path.join(filepath, filename), 'wb') as f:
-                for chunk in r.iter_content(chunk_size=1024):
-                    if chunk:
-                        f.write(chunk)
-        return True
-
-    def user(self, course_id: int, user_id: int) -> dict:
-        """
-        :param course_id: The class to search
-        :param user_id: The ID of the user
-        :return: A dictionary with the user's information
-        """
-        url = 'https://sit.instructure.com/api/v1/courses/%i/users/%i' % (course_id, user_id)
-
-        response = self.session.get(url)
-        return json.loads(response.text)
-
-    def grade_submission(self, course_id, assignment_id, user_id, grade):
-        global DISARM_ALL, DISARM_GRADER
-        url = 'https://sit.instructure.com/api/v1/courses/%i/assignments/%i/submissions/%i/?submission[posted_grade]=%i' \
-              % (course_id, assignment_id, user_id, grade)
-
-        if DISARM_ALL or DISARM_GRADER:
-            print('Dummy: Grade submitted')
-            return 'dummy success'
-        else:
-            response = self.session.put(url)
-            return json.loads(response.text)
-
-    def message_user(self, recipient_id: int, body: str, subject: str = None):
-        global DISARM_ALL, DISARM_MESSAGER
-        url = 'https://sit.instructure.com/api/v1/conversations/'
-
-        data = {
-            'recipients[]': recipient_id,
-            'body': body,
-            'subject': subject
-        }
-
-        if DISARM_ALL or DISARM_MESSAGER:
-            print('Dummy: user messaged')
-            return 'dummy success'
-        else:
-            response = self.session.post(url, data)
-            return json.loads(response.text)
-
-
 def choose_val(hi_num: int, allow_zero: bool = False) -> int:
     val = 'none'
 
diff --git a/pycanvasgrader/skeletons/HW1c.json b/pycanvasgrader/skeletons/HW1c.json
index 93e2aeb..742e6fe 100644
--- a/pycanvasgrader/skeletons/HW1c.json
+++ b/pycanvasgrader/skeletons/HW1c.json
@@ -8,7 +8,7 @@
 
       "single_file": true,
       "print_output": true,
-      "print_file": true,
+      "print_file": false,
 
       "output_match": "error",
       "negate_match": true,
@@ -24,7 +24,7 @@
       "command": "out.exe",
       "print_output": true,
 
-      "output_match": "5050\n5050",
+      "output_match": "5050\n5050\n",
       "exact_match": false,
 
       "point_val": 75,
diff --git a/pycanvasgrader/temp/27592/HW1c.cpp b/pycanvasgrader/temp/27592/HW1c.cpp
new file mode 100644
index 0000000..a22849c
--- /dev/null
+++ b/pycanvasgrader/temp/27592/HW1c.cpp
@@ -0,0 +1,25 @@
+#include <iostream>
+
+using namespace std;
+
+int sum(int);
+int sum2(int);
+
+int main()
+{
+    cout << sum(100) << '\n';
+    cout << sum2(100) << '\n';
+    return 0;
+}
+
+int sum(int n) {
+    int total = 0;
+    for (int a = 1; a <= n; a++)
+        total += a;
+
+    return total;
+}
+
+int sum2(int n) {
+    return n * (n + 1) / 2;
+}

From 17bdb86056fc80660a9862b77cbf963f51e60765 Mon Sep 17 00:00:00 2001
From: ThePyrotechnic <electricpyrotechnic@gmail.com>
Date: Wed, 20 Sep 2017 22:04:30 -0400
Subject: [PATCH 25/40] added documentation, disarming, fixed output_regex and
 timeout

---
 pycanvasgrader/pycanvasgrader.py            |  38 ++-
 pycanvasgrader/skeletons/HW1c.json          |   1 -
 pycanvasgrader/skeletons/documentation.html | 324 ++++++++++++++++++++
 3 files changed, 351 insertions(+), 12 deletions(-)
 create mode 100644 pycanvasgrader/skeletons/documentation.html

diff --git a/pycanvasgrader/pycanvasgrader.py b/pycanvasgrader/pycanvasgrader.py
index 1e79e9f..cfe5d57 100644
--- a/pycanvasgrader/pycanvasgrader.py
+++ b/pycanvasgrader/pycanvasgrader.py
@@ -26,8 +26,8 @@
 import requests
 
 # globals
-DISARM_ALL = True
-DISARM_MESSAGER = True
+DISARM_ALL = False
+DISARM_MESSAGER = False
 DISARM_GRADER = False
 
 RUN_WITH_TESTS = False
@@ -151,7 +151,7 @@ def grade_submission(self, course_id, assignment_id, user_id, grade):
               % (course_id, assignment_id, user_id, grade)
 
         if DISARM_ALL or DISARM_GRADER:
-            print('Grader disarmed; grade not actually submitted')
+            print('Grader disarmed; grade will not actually be submitted')
             return 'dummy success'
         else:
             response = self.session.put(url)
@@ -168,7 +168,7 @@ def message_user(self, recipient_id: int, body: str, subject: str = None):
         }
 
         if DISARM_ALL or DISARM_MESSAGER:
-            print('Messenger disarmed; user was not messaged')
+            print('Messenger disarmed; user wil not actually be messaged')
             return 'dummy success'
         else:
             response = self.session.post(url, data)
@@ -180,13 +180,15 @@ class TestSkeleton:
     An abstract skeleton to handle testing of a specific group of files
     """
 
-    def __init__(self, descriptor: str, tests: list):
+    def __init__(self, descriptor: str, tests: list, disarm: bool = False):
         """
         :param descriptor: The description of this TestSkeleton
         :param tests: A list of AssignmentTest objects. These will be run in the order that they are added.
+        :param disarm: Whether to actually submit grades/send messages
         """
         self.descriptor = descriptor
         self.tests = tests
+        self.disarm = disarm
 
     @classmethod
     def from_file(cls, filename):
@@ -202,15 +204,21 @@ def from_file(cls, filename):
             except KeyError:
                 return None
             else:
+                disarm = data.get('disarm')
+                if disarm is None:
+                    disarm = False
                 test_list = []
                 for json_dict in tests:
                     test = AssignmentTest.from_json_dict(tests[json_dict])
                     if test is not None:
                         test_list.append(test)
 
-                return TestSkeleton(descriptor, test_list)
+                return TestSkeleton(descriptor, test_list, disarm)
 
     def run_tests(self, grader: PyCanvasGrader, user_id: int) -> int:
+        global DISARM_ALL
+        DISARM_ALL = self.disarm
+
         total_score = 0
         for count, test in enumerate(self.tests):
             print('\n--Running test %i--' % (count + 1))
@@ -273,7 +281,7 @@ def __init__(self, command: str, args: list = None, print_file: bool = False, si
         self.include_filetype = include_filetype
         self.output_match = output_match
         if output_regex is not None:
-            self.output_regex = re.compile(output_regex)
+            self.output_regex = re.compile(re.escape(output_regex))
         else:
             self.output_regex = None
         self.numeric_match = numeric_match
@@ -365,10 +373,14 @@ def run(self) -> dict:
             if args is not None:
                 args = [arg.replace('%s', filename) for arg in args]
 
-        if args is not None:
-            proc = subprocess.run([command] + args, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, timeout=self.timeout, encoding='UTF-8', shell=True)
-        else:
-            proc = subprocess.run(command, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, timeout=self.timeout, encoding='UTF-8', shell=True)
+        try:
+
+            if args is not None:
+                proc = subprocess.run([command] + args, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, timeout=self.timeout, encoding='UTF-8', shell=True)
+            else:
+                proc = subprocess.run(command, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, timeout=self.timeout, encoding='UTF-8', shell=True)
+        except subprocess.TimeoutExpired:
+            return {'timeout': True}
         return {'returncode': proc.returncode, 'stdout': proc.stdout, 'stderr': proc.stderr}
 
     def run_and_match(self) -> bool:
@@ -379,6 +391,10 @@ def run_and_match(self) -> bool:
         global NUM_REGEX
 
         result = self.run()
+
+        if result.get('timeout'):
+            return False
+
         if self.print_output:
             print('\t--OUTPUT--')
             print(result['stdout'])
diff --git a/pycanvasgrader/skeletons/HW1c.json b/pycanvasgrader/skeletons/HW1c.json
index 742e6fe..ac47b2a 100644
--- a/pycanvasgrader/skeletons/HW1c.json
+++ b/pycanvasgrader/skeletons/HW1c.json
@@ -1,7 +1,6 @@
 {
   "descriptor": "HW1c Grader",
   "tests": {
-
     "test_1": {
       "command": "g++",
       "args": ["%s", "-o", "out"],
diff --git a/pycanvasgrader/skeletons/documentation.html b/pycanvasgrader/skeletons/documentation.html
new file mode 100644
index 0000000..d401118
--- /dev/null
+++ b/pycanvasgrader/skeletons/documentation.html
@@ -0,0 +1,324 @@
+<!DOCTYPE html>
+<html lang="en">
+<style>
+    h1 {
+        font-size: xx-large;
+        font-family: sans-serif;
+    }
+
+    h2 {
+        font-family: sans-serif;
+    }
+
+    h4 {
+        font-family: sans-serif;
+        margin: 5px 4em;
+    }
+
+    .container {
+        margin: 10px 10px;
+        padding-bottom: 10px;
+        border-bottom: dashed;
+        border-color: #aaaaaa;
+    }
+
+    .item {
+        font-size: larger;
+        font-weight: bold;
+        font-family: sans-serif
+    }
+
+    .desc {
+        margin: 5px 2em;
+    }
+
+    .example {
+        display: inline;
+        margin-left: 4em;
+        padding: 1px 2px;
+        color: white;
+        background-color: dimgray;
+        font-family: Consolas, monospace;
+    }
+
+    .example-multiline {
+        display: flex;
+    }
+
+    .opt {
+        color: orange;
+    }
+
+    .none {
+        color: darkgoldenrod;
+    }
+
+    .false {
+        color: darkred;
+    }
+
+    .true {
+        color: darkgreen;
+    }
+
+</style>
+<head>
+    <meta charset="UTF-8">
+    <title>Title</title>
+</head>
+<body>
+<h1>Skeleton JSON file format</h1>
+
+<h2>Every Skeleton contains:</h2>
+<div class="container">
+    <div class="item">
+        "descriptor" - String
+    </div>
+    <div class="desc">
+        The name for this skeleton. Displayed when choosing a skeleton for an assignment.
+    </div>
+    <h4>Example:</h4>
+    <div class="example">
+        "descriptor": "HW1 Grader"
+    </div>
+</div>
+<div class="container">
+    <div class="item">
+        "disarm" - Boolean <span class="opt">(Optional)</span> Default: <span class="false">false</span>
+    </div>
+    <div class="desc">
+        Whether to "disarm" this skeleton. A disarmed skeleton does not actually upload grades to Canvas, and does not send messages to users.
+    </div>
+    <h4>Example:</h4>
+    <div class="example">
+        "disarm": true
+    </div>
+</div>
+<div class="container">
+    <div class="item">
+        "tests" - Dictionary
+    </div>
+    <div class="desc">
+        The list of tests that this skeleton should run. See below for how to write tests.
+    </div>
+    <h4>Example:</h4>
+    <div class="example">
+        "tests": {
+        ...
+        }
+    </div>
+</div>
+
+<h2>Every Test contains:</h2>
+<div class="container">
+    <div class="item">
+        "command" - String
+    </div>
+    <div class="desc">
+        The command to be run, surrounded by quotes (""). Do NOT include arguments! See below for how to include arguments.
+    </div>
+    <h4>Example:</h4>
+    <div class="example">
+        "command": "g++"
+    </div>
+</div>
+<div class="container">
+    <div class="item">
+        "args" - List <span class="opt">(Optional)</span> Default: <span class="none">none</span>
+    </div>
+    <div class="desc">
+        A list of arguments to be passed to the command for this test. Can use the filename wildcard
+    </div>
+    <h4>Example:</h4>
+    <div class="example">
+        "args": ["%s", "-o", "out"]
+    </div>
+</div>
+<div class="container">
+    <div class="item">
+        "print_file" - Boolean <span class="opt">(Optional)</span> Default: <span class="false">false</span>
+    </div>
+    <div class="desc">
+        Whether to print the student's file to the console.
+    </div>
+    <h4>Example:</h4>
+    <div class="example">
+        "print_file": true
+    </div>
+</div>
+<div class="container">
+    <div class="item">
+        "single_file" - Boolean <span class="opt">(Optional)</span> Default: <span class="false">false</span>
+    </div>
+    <div class="desc">
+        Whether to assume that the user's submission is a single file or not.<br/>
+        For information on how this is used, see "About the filename wildcard"
+    </div>
+    <h4>Example:</h4>
+    <div class="example">
+        "single_file": true
+    </div>
+</div>
+<div class="container">
+    <div class="item">
+        "target_file" - String <span class="opt">(Optional)</span> Default: <span class="none">none</span>
+    </div>
+    <div class="desc">
+        The filename that "%s" will be replaced with, if it is found in the arguments list.
+    </div>
+    <h4>Example:</h4>
+    <div class="example">
+        "target_file": "MyClass.java"
+    </div>
+</div>
+<div class="container">
+    <div class="item">
+        "ask_for_target" - Boolean <span class="opt">(Optional)</span> Default: <span class="false">false</span>
+    </div>
+    <div class="desc">
+        Whether to prompt for a file to replace %s" with.<br/>
+        This will ask the grader to choose from the files submitted buy the student.
+    </div>
+    <h4>Example:</h4>
+    <div class="example">
+        "ask_for_target": true
+    </div>
+</div>
+<div class="container">
+    <div class="item">
+        "include_filetype" - Boolean <span class="opt">(Optional)</span> Default: <span class="true">true</span>
+    </div>
+    <div class="desc">
+        Whether to include or chop off the filetype extension when replacing the wildcard ("%s") with the student's file.
+    </div>
+    <h4>Example:</h4>
+    <div class="example">
+        "include_filetype: false
+    </div>
+</div>
+<div class="container">
+    <div class="item">
+        print_output - Boolean <span class="opt">(Optional)</span> Default: <span class="false">false</span>
+    </div>
+    <div class="desc">
+        Whether to print the output of this test's command into the console.
+    </div>
+    <h4>Example:</h4>
+    <div class="example">
+        "print_output": true
+    </div>
+</div>
+<div class="container">
+    <div class="item">
+        output_match - String <span class="opt">(Optional)</span> Default: <span class="none">none</span>
+    </div>
+    <div class="desc">
+        If "exact_match" is set, this string must exactly match the output of the command, or the test will fail.<br/>
+        Note: If "output_regex" or "numeric_match" is set, this argument has no effect.
+    </div>
+    <h4>Example:</h4>
+    <div class="example">
+        "output_match": "Hawaii is the youngest state.\nThe sky is blue.\n"
+    </div>
+</div>
+<div class="container">
+    <div class="item">
+        "output_regex" - String <span class="opt">(Optional)</span> Default: <span class="none">none</span>
+    </div>
+    <div class="desc">
+        A regular expression that the output should satisfy for the test to pass.<br/>
+        Note: This overrides "output_match". If "numeric_match" is set, this argument has no effect.
+    </div>
+    <h4>Example:</h4>
+    <div class="example-multiline">
+        <div class="example">
+            //match output with an even number of a's and an odd number of b's<br/>
+            "output_regex": "^(aa)*(bb)*b$"
+        </div>
+    </div>
+</div>
+<div class="container">
+    <div class="item">
+        "numeric_match" - Array <span class="opt">(Optional)</span> Default: <span class="none">none</span>
+    </div>
+    <div class="desc">
+        A list of numbers that must ALL be found somewhere in the command's output for the test to pass.<br>
+        Numbers can be duplicated if they must be found more than once.
+        A number can be denoted in three ways:<br>
+        <ol>
+            <li>As an exact number (2, 3.333)</li>
+            <li>As an array denoting a range ([2, 2.5])</li>
+            <li>As a string denoting a number plus/minus the second number ("10,0.0001")</li>
+        </ol>
+        Note: This overrides "outut_regex" and "output_match".
+    </div>
+    <h4>Example:</h4>
+    <div class="example">
+        "numeric_match": [200, [8.5, 9], "50,0.5"]
+    </div>
+</div>
+<div class="container">
+    <div class="item">
+        "negate_match" - Boolean <span class="opt">(Optional)</span> Default: <span class="falsse">false</span>
+    </div>
+    <div class="desc">
+        Whether to negate the result of the output comparison ("numeric_match", "output_regex", or "output_match; whichever was specified)<br/>
+        In other words: if the output comparison fails, the test passes. If the comparison succeeds, the test fails.
+    </div>
+    <h4>Example:</h4>
+    <div class="example">
+        "negate_match": true
+    </div>
+</div>
+<div class="container">
+    <div class="item">
+        "exact_match" - Boolean <span class="opt">(Optional)</span> Default: <span class="false">false</span>
+    </div>
+    <div class="desc">
+        Only used with "output_match". Whether the string must be an exact match, or if it just needs to be found somewhere in the output.
+    </div>
+    <h4>Example:</h4>
+    <div class="example">
+        "exact_match": true
+    </div>
+</div>
+<div class="container">
+    <div class="item">
+        "timeout" - Integer <span class="opt">(Optional)</span> Default: <span class="none">none</span>
+    </div>
+    <div class="desc">
+        An optional timeout, in seconds, to be set for this test's command. If the command times out, then the test fails.
+    </div>
+    <h4>Example:</h4>
+    <div class="example">
+        "timeout": 5
+    </div>
+</div>
+
+<h3>About the filename wildcard ("%s"):</h3>
+<p>
+    The filename wildcard ("%s") can be used to denote a filename in the current student's submission.<br/>
+    If no filename is explicitly given with the "target_file" parameter, the following logic is used to replace "%s":<br/>
+</p>
+<ol>
+    <li>If the "single_file" parameter is <span class="true">true</span>, then the first file which the user submitted will be chosen to replace "%s", regardless of how many files they submitted.</li>
+    <li>If the "single_file" parameter is not set or is <span class="false">false</span>, but the user has only submitted one file, then that file is chosen to replace "%s".</li>
+    <li>If "ask_for_target" is set then the program will ask the grader to chose a file from a list of all the files that the current user submitted.</li>
+    <li>Finally, if none of these conditions can be satisfied, "%s" is left as-is and the command will probably not work as expected.</li>
+</ol>
+</body>
+</html>
+<!--
+<div class="container">
+    <div class="item">
+        <span class="opt">(Optional)</span> Default: <span class=""></span>
+    </div>
+    <div class="desc">
+
+    </div>
+    <h4>Example:</h4>
+    <div class="example">
+
+    </div>
+</div>
+-->
\ No newline at end of file

From 4953fea3779b13e6903f5a9581c96ce9ed9fb2a6 Mon Sep 17 00:00:00 2001
From: Michael Manis <electricpyrotechnic@gmail.com>
Date: Thu, 21 Sep 2017 15:57:57 -0400
Subject: [PATCH 26/40] fixed

---
 pycanvasgrader/access.token         |   1 -
 pycanvasgrader/zips/submissions.zip | Bin 1028 -> 0 bytes
 2 files changed, 1 deletion(-)
 delete mode 100644 pycanvasgrader/access.token
 delete mode 100644 pycanvasgrader/zips/submissions.zip

diff --git a/pycanvasgrader/access.token b/pycanvasgrader/access.token
deleted file mode 100644
index ec325d6..0000000
--- a/pycanvasgrader/access.token
+++ /dev/null
@@ -1 +0,0 @@
-1030~v7wtqrohOlMXdfVU1sBGEJWPm3IsTubOVH02BQTB9T2rRoltJ2QdmMcdAmxHME8x
\ No newline at end of file
diff --git a/pycanvasgrader/zips/submissions.zip b/pycanvasgrader/zips/submissions.zip
deleted file mode 100644
index 92df292a1d0f05ed9b9a45dbfb2cd63f40cc532d..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 1028
zcmWIWW@Zs#U|`^25Y*G~c8V<JjbUV9P+(?YPyvb-mz1WY=9QGB7MH{unVVV~#Ty%#
zm|Gee#RrrY6jbVEC6*<&2A$42Y#^|Q{S$w;zVD?+4*k5AQ|{e%@>(!O&g|5+u!*Y5
zYm<FW?hl`~_DCkr)ua4p&-A5*gjuVya<ra1m>oKe_m7V{gMz8^%{u$EEwlU%?cc=A
zek12_*ef0rF_ZU}b-L3(O!H<xlyQ8UP>#-%7Y8z$gx0bf-`st`OF8|r#WE#R(dA38
zrz}lBxtYD;M6WV$+&jg_+YU`XwJ!8cpT_6*?x0}x=FJJR#{9OoyVM&?cN=S6+_Wh!
z@qmo6IMa^8L=ThlSr??goE8cX;}705@0En*Fa3a560eV|-#WwF9DCsOyV)$w8=hFY
z9Zr%o-~Fg-S@k-{;Je#dIA<@)n3Ryc;A@N5*R{XBiZ-*G<u=T{{V(S^<K7Y}<$dy3
zopUYJtC!CHySkd|U(naPAqoM^T#j*pzpPuM1Y|CF-O*&K-@LCUXj$3YY~OoFB5T&{
z%1y}&480O6?)zu$h49iptN}P<M;lM<7(-%5L07>!e>9Tl5J`+oA`G}Q5iq707#S2m
t6c7-Tr2@Qhn+S?{5P+CC513hTnTRDB1bDNufiyD#;c6i549w>Y3;+m|jy?bY


From bbb4f5ba9cf6baa1f60c09026fced455773970f4 Mon Sep 17 00:00:00 2001
From: Michael Manis <electricpyrotechnic@gmail.com>
Date: Thu, 21 Sep 2017 16:11:54 -0400
Subject: [PATCH 27/40] finished documentation

---
 pycanvasgrader/skeletons/documentation.html | 30 +++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/pycanvasgrader/skeletons/documentation.html b/pycanvasgrader/skeletons/documentation.html
index d401118..f1d5662 100644
--- a/pycanvasgrader/skeletons/documentation.html
+++ b/pycanvasgrader/skeletons/documentation.html
@@ -134,6 +134,18 @@ <h4>Example:</h4>
         "args": ["%s", "-o", "out"]
     </div>
 </div>
+<div class="container">
+    <div class="item">
+        "point_val" - Integer<span class="opt">(Optional)</span> Default: <span class="none">none</span>
+    </div>
+    <div class="desc">
+        A point value to be added to the student's total if the test passes. Can be negative.
+    </div>
+    <h4>Example:</h4>
+    <div class="example">
+        "point_val": 25
+    </div>
+</div>
 <div class="container">
     <div class="item">
         "print_file" - Boolean <span class="opt">(Optional)</span> Default: <span class="false">false</span>
@@ -294,6 +306,24 @@ <h4>Example:</h4>
         "timeout": 5
     </div>
 </div>
+<div class="container">
+    <div class="item">
+        "fail_notif" - Dictionary <span class="opt">(Optional)</span> Default: <span class="none">none</span>
+    </div>
+    <div class="desc">
+        This message will be sent to the student if the fest fails.<br/>
+        Consists of a dictionary containing a "body" string and an optional "subject" string.
+    </div>
+    <h4>Example:</h4>
+    <div class="example-multiline">
+        <div class="example">
+            "fail_notif": {<br/>
+              &nbsp;&nbsp;"subject": "Test failed"<br/>
+              &nbsp;&nbsp;"body": "Your submission failed a test!\nYou may re-submit this assignment"<br/>
+            }
+        </div>
+    </div>
+</div>
 
 <h3>About the filename wildcard ("%s"):</h3>
 <p>

From 156876f30258ac1270d1f0ed2bdae7e5634f67a7 Mon Sep 17 00:00:00 2001
From: Michael Manis <electricpyrotechnic@gmail.com>
Date: Tue, 26 Sep 2017 11:43:15 -0400
Subject: [PATCH 28/40] Corrected regex to include negative sign for integers,
 added stdin input option to tests, cleaned up test runner, made temp dir
 handling more robust, updated output

---
 .../{skeletons => }/documentation.html        | 16 ++++++-
 pycanvasgrader/pycanvasgrader.py              | 44 ++++++++++--------
 pycanvasgrader/skeletons/HW1a.json            | 27 +++++++++++
 pycanvasgrader/skeletons/HW1d.json            | 35 +++++++++++++++
 pycanvasgrader/skeletons/HW1e.json            | 45 +++++++++++++++++++
 pycanvasgrader/temp/27592/HW1c.cpp            | 25 -----------
 pycanvasgrader/test_files/HW1a.cpp            | 24 ++++++++++
 pycanvasgrader/test_files/HW1d.cpp            | 28 ++++++++++++
 pycanvasgrader/test_files/HW1e.cpp            | 22 +++++++++
 9 files changed, 221 insertions(+), 45 deletions(-)
 rename pycanvasgrader/{skeletons => }/documentation.html (95%)
 create mode 100644 pycanvasgrader/skeletons/HW1a.json
 create mode 100644 pycanvasgrader/skeletons/HW1d.json
 create mode 100644 pycanvasgrader/skeletons/HW1e.json
 delete mode 100644 pycanvasgrader/temp/27592/HW1c.cpp
 create mode 100644 pycanvasgrader/test_files/HW1a.cpp
 create mode 100644 pycanvasgrader/test_files/HW1d.cpp
 create mode 100644 pycanvasgrader/test_files/HW1e.cpp

diff --git a/pycanvasgrader/skeletons/documentation.html b/pycanvasgrader/documentation.html
similarity index 95%
rename from pycanvasgrader/skeletons/documentation.html
rename to pycanvasgrader/documentation.html
index f1d5662..ccc2f7b 100644
--- a/pycanvasgrader/skeletons/documentation.html
+++ b/pycanvasgrader/documentation.html
@@ -134,6 +134,18 @@ <h4>Example:</h4>
         "args": ["%s", "-o", "out"]
     </div>
 </div>
+<div class="container">
+    <div class="item">
+        "input" - String <span class="opt">(Optional)</span> Default: <span class="none">none</span>
+    </div>
+    <div class="desc">
+        An input string to be passed to stdin for this test.
+    </div>
+    <h4>Example:</h4>
+    <div class="example">
+        "input": "25"
+    </div>
+</div>
 <div class="container">
     <div class="item">
         "point_val" - Integer<span class="opt">(Optional)</span> Default: <span class="none">none</span>
@@ -210,7 +222,7 @@ <h4>Example:</h4>
 </div>
 <div class="container">
     <div class="item">
-        print_output - Boolean <span class="opt">(Optional)</span> Default: <span class="false">false</span>
+        "print_output" - Boolean <span class="opt">(Optional)</span> Default: <span class="false">false</span>
     </div>
     <div class="desc">
         Whether to print the output of this test's command into the console.
@@ -222,7 +234,7 @@ <h4>Example:</h4>
 </div>
 <div class="container">
     <div class="item">
-        output_match - String <span class="opt">(Optional)</span> Default: <span class="none">none</span>
+        "output_match" - String <span class="opt">(Optional)</span> Default: <span class="none">none</span>
     </div>
     <div class="desc">
         If "exact_match" is set, this string must exactly match the output of the command, or the test will fail.<br/>
diff --git a/pycanvasgrader/pycanvasgrader.py b/pycanvasgrader/pycanvasgrader.py
index cfe5d57..e5d3fec 100644
--- a/pycanvasgrader/pycanvasgrader.py
+++ b/pycanvasgrader/pycanvasgrader.py
@@ -32,7 +32,7 @@
 
 RUN_WITH_TESTS = False
 ONLY_RUN_TESTS = False
-NUM_REGEX = re.compile(r'[+-]?\d+\.\d+|\d+')
+NUM_REGEX = re.compile(r'-?\d+\.\d+|-?\d+')
 # r'[+-]?\d+\.\d+|\d+'
 # r'[-+]?\d+(\.\d+)?'
 
@@ -230,14 +230,16 @@ def run_tests(self, grader: PyCanvasGrader, user_id: int) -> int:
                 else:
                     print('--Subtracting %i points--' % abs(test.point_val))
                 total_score += test.point_val
-            elif test.fail_notif:
-                try:
-                    body = test.fail_notif['body']
-                except ValueError:
-                    pass
-                else:
-                    subject = test.fail_notif.get('subject')
-                    grader.message_user(user_id, body, subject)
+            else:
+                print('--Test failed--')
+                if test.fail_notif:
+                    try:
+                        body = test.fail_notif['body']
+                    except ValueError:
+                        pass
+                    else:
+                        subject = test.fail_notif.get('subject')
+                        grader.message_user(user_id, body, subject)
 
             print('--Current score: %i--' % total_score)
         return total_score
@@ -249,13 +251,14 @@ class AssignmentTest:
     TODO 'sequential' command requirement
     """
 
-    def __init__(self, command: str, args: list = None, print_file: bool = False, single_file: bool = False, target_file: str = None,
+    def __init__(self, command: str, args: list = None, input_str: str = None, print_file: bool = False, single_file: bool = False, target_file: str = None,
                  ask_for_target: bool = False, include_filetype: bool = True, print_output: bool = True,
                  output_match: str = None, output_regex: str = None, numeric_match: list = None,
                  negate_match: bool = False, exact_match: bool = False, timeout: int = None, fail_notif: dict = None, point_val: int = 0):
         """
         :param command: The command to be run.
         :param args: List of arguments to pass to the command. Use %s to denote a file name
+        :param input_str: String to send to stdin
         :param print_file: Whether to print the contents of the target_file being tested (Does nothing if no file is selected)
         :param single_file: Whether to assume the assignment is a single file and use the first file found as %s
         :param target_file: The file to replace %s with
@@ -274,6 +277,7 @@ def __init__(self, command: str, args: list = None, print_file: bool = False, si
         """
         self.command = command
         self.args = args
+        self.input_str = input_str
         self.print_file = print_file
         self.single_file = single_file
         self.target_file = target_file
@@ -300,6 +304,7 @@ def from_json_dict(cls, json_dict: dict):
             return None
         else:
             args = json_dict.get('args')
+            input_str = json_dict.get('input')
             print_file = json_dict.get('print_file')
             single_file = json_dict.get('single_file')
             target_file = json_dict.get('target_file')
@@ -315,7 +320,7 @@ def from_json_dict(cls, json_dict: dict):
             fail_notif = json_dict.get('fail_notification')
             point_val = json_dict.get('point_val')
 
-            vars_dict = {'command': command, 'args': args, 'print_file': print_file, 'single_file': single_file, 'target_file': target_file,
+            vars_dict = {'command': command, 'args': args, 'input_str': input_str, 'print_file': print_file, 'single_file': single_file, 'target_file': target_file,
                          'ask_for_target': ask_for_target, 'include_filetype': include_filetype,
                          'print_output': print_output, 'output_match': output_match, 'output_regex': output_regex,
                          'numeric_match': numeric_match, 'negate_match': negate_match, 'exact_match': exact_match,
@@ -374,11 +379,13 @@ def run(self) -> dict:
                 args = [arg.replace('%s', filename) for arg in args]
 
         try:
-
-            if args is not None:
-                proc = subprocess.run([command] + args, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, timeout=self.timeout, encoding='UTF-8', shell=True)
+            if args:
+                command_to_send = [command] + args
             else:
-                proc = subprocess.run(command, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, timeout=self.timeout, encoding='UTF-8', shell=True)
+                command_to_send = command
+
+            proc = subprocess.run(command_to_send, input=self.input, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, timeout=self.timeout, encoding='UTF-8', shell=True)
+
         except subprocess.TimeoutExpired:
             return {'timeout': True}
         return {'returncode': proc.returncode, 'stdout': proc.stdout, 'stderr': proc.stderr}
@@ -487,8 +494,9 @@ def restart_program(grader: PyCanvasGrader):
 def init_tempdir():
         try:
             if os.path.exists('temp'):
+                if os.path.exists('old-temp'):
+                    shutil.rmtree(os.path.join(os.path.dirname(os.path.abspath(__file__)), 'old-temp'))
                 os.rename('temp', 'old-temp')
-                shutil.rmtree(os.path.join(os.path.dirname(os.path.abspath(__file__)), 'old-temp'))
             os.makedirs('temp', exist_ok=True)
         except BaseException:
             print('An error occurred while initializing the "temp" directory. Please delete/create the directory manually and re-run the program')
@@ -631,9 +639,9 @@ def main():
                 elif selected_action == 'Skip this submission':
                     break
                 elif selected_action == 'Re-grade this submission':
-                    score = selected_skeleton.run_tests()
+                    score = selected_skeleton.run_tests(grader, cur_user_id)
 
-    print('done')
+    print('Finished grading all submissions for this assignment')
 
 
 if __name__ == '__main__':
diff --git a/pycanvasgrader/skeletons/HW1a.json b/pycanvasgrader/skeletons/HW1a.json
new file mode 100644
index 0000000..6a242ac
--- /dev/null
+++ b/pycanvasgrader/skeletons/HW1a.json
@@ -0,0 +1,27 @@
+{
+  "descriptor": "HW1a Grader",
+  "tests": {
+
+    "compile": {
+      "command": "g++",
+      "args": ["%s", "-o", "out"],
+      "single_file": true,
+      "print_output": true,
+      "point_val": 50,
+      "output_match": "error",
+      "negate_match": true
+    },
+    "test_5": {
+      "command": "out.exe",
+      "print_output": true,
+      "numeric_match": [16, 8, 4, 2 ,1],
+      "point_val": 25
+    },
+    "test_25": {
+      "command": "out.exe",
+      "print_output": true,
+      "numeric_match": [76, 38, 19, 58, 29, 88, 44, 22, 11, 34, 17, 52, 26, 13, 40, 20, 10, 5, 16, 8, 4, 2, 1],
+      "point_val": 25
+    }
+  }
+}
diff --git a/pycanvasgrader/skeletons/HW1d.json b/pycanvasgrader/skeletons/HW1d.json
new file mode 100644
index 0000000..6a69cd0
--- /dev/null
+++ b/pycanvasgrader/skeletons/HW1d.json
@@ -0,0 +1,35 @@
+{
+  "descriptor": "HW1d Grader",
+  "tests": {
+
+    "compile": {
+      "command": "g++",
+      "args": ["%s", "-o", "out"],
+      "single_file": true,
+      "print_output": false,
+      "point_val": 50,
+      "output_match": "error",
+      "negate_match": true
+    },
+    "test_sums": {
+      "command": "out.exe",
+      "print_output": true,
+      "numeric_match": [5.18738, 5.18738, 5.18738, 5.18738],
+      "point_val": 10
+    },
+    "test_float": {
+      "command": "out.exe",
+      "print_output": true,
+      "numeric_match": [9.53674, 7],
+      "exact_match": false,
+      "point_val": 20
+    },
+    "test_double": {
+      "command": "out.exe",
+      "print_output": true,
+      "numeric_match": [-8.88178, 16],
+      "exact_match": false,
+      "point_val": 20
+    }
+  }
+}
diff --git a/pycanvasgrader/skeletons/HW1e.json b/pycanvasgrader/skeletons/HW1e.json
new file mode 100644
index 0000000..dc87bf9
--- /dev/null
+++ b/pycanvasgrader/skeletons/HW1e.json
@@ -0,0 +1,45 @@
+{
+  "descriptor": "HW1e Grader",
+  "tests": {
+
+    "compile": {
+      "command": "g++",
+      "args": ["%s", "-o", "out"],
+      "single_file": true,
+      "print_output": false,
+      "point_val": 50,
+      "output_match": "error",
+      "negate_match": true
+    },
+    "test_5": {
+      "command": "out.exe",
+      "input": "5",
+      "print_output": true,
+      "numeric_match": [120],
+      "point_val": 12.5
+    },
+    "test_10": {
+      "command": "out.exe",
+      "input": "10",
+      "print_output": true,
+      "numeric_match": [3628800],
+      "point_val": 12.5
+    },
+    "test_20": {
+      "command": "out.exe",
+      "input": "20",
+      "print_output": true,
+      "numeric_match": [-2102132736],
+      "exact_match": false,
+      "point_val": 12.5
+    },
+    "test_30": {
+      "command": "out.exe",
+      "input": "30",
+      "print_output": true,
+      "numeric_match": [1409286144],
+      "exact_match": false,
+      "point_val": 12.5
+    }
+  }
+}
diff --git a/pycanvasgrader/temp/27592/HW1c.cpp b/pycanvasgrader/temp/27592/HW1c.cpp
deleted file mode 100644
index a22849c..0000000
--- a/pycanvasgrader/temp/27592/HW1c.cpp
+++ /dev/null
@@ -1,25 +0,0 @@
-#include <iostream>
-
-using namespace std;
-
-int sum(int);
-int sum2(int);
-
-int main()
-{
-    cout << sum(100) << '\n';
-    cout << sum2(100) << '\n';
-    return 0;
-}
-
-int sum(int n) {
-    int total = 0;
-    for (int a = 1; a <= n; a++)
-        total += a;
-
-    return total;
-}
-
-int sum2(int n) {
-    return n * (n + 1) / 2;
-}
diff --git a/pycanvasgrader/test_files/HW1a.cpp b/pycanvasgrader/test_files/HW1a.cpp
new file mode 100644
index 0000000..61945da
--- /dev/null
+++ b/pycanvasgrader/test_files/HW1a.cpp
@@ -0,0 +1,24 @@
+#include <iostream>
+
+using namespace std;
+void collatz(int);
+
+int main()
+{
+    int n = 0;
+    cout << "Enter a number: ";
+    cin >> n;
+    collatz(n);
+
+    return 0;
+}
+
+void collatz(int n) {
+    if (n == 1) cout << endl;
+    else {
+        if (n % 2 == 1) n = 3*n + 1;
+        else n = n/2;
+        cout << n << ", ";
+        collatz(n);
+    }
+}
diff --git a/pycanvasgrader/test_files/HW1d.cpp b/pycanvasgrader/test_files/HW1d.cpp
new file mode 100644
index 0000000..7decd02
--- /dev/null
+++ b/pycanvasgrader/test_files/HW1d.cpp
@@ -0,0 +1,28 @@
+#include <iostream>
+
+using namespace std;
+
+int main()
+{
+    float sum1_float, sum2_float = 0;
+    double sum1_double, sum2_double = 0;
+
+    for(int a = 1; a <= 100; a++) {
+        sum1_float += 1/(float)a;
+        sum1_double += 1/(double)a;
+    }
+
+    for(int a = 100; a > 0; a--) {
+        sum2_float += 1/(float)a;
+        sum2_double += 1/(double)a;
+    }
+    float diff_float = sum1_float - sum2_float;
+    double diff_double = sum1_double - sum2_double;
+
+    cout << "float sum1: " << sum1_float << " | float sum2: " << sum2_float << endl;
+    cout << "float diff: " << diff_float << endl;
+    cout << "double sum1: " << sum1_double << " | double sum2: " << sum2_double << endl;
+    cout << "double diff: " << diff_double << endl;
+
+    return 0;
+}
diff --git a/pycanvasgrader/test_files/HW1e.cpp b/pycanvasgrader/test_files/HW1e.cpp
new file mode 100644
index 0000000..b500d28
--- /dev/null
+++ b/pycanvasgrader/test_files/HW1e.cpp
@@ -0,0 +1,22 @@
+#include <iostream>
+
+using namespace std;
+
+int fact(int);
+
+int main()
+{
+    int n = 0;
+    cout << "Enter a number: ";
+    cin >> n;
+    cout << fact(n);
+
+    return 0;
+}
+
+int fact(int n) {
+    int total = 1;
+    while (n > 0)
+        total *= n--;
+    return total;
+}

From 43b9635bea864cee8ebba39bd4cfa436d3761d84 Mon Sep 17 00:00:00 2001
From: Michael Manis <electricpyrotechnic@gmail.com>
Date: Tue, 26 Sep 2017 12:06:42 -0400
Subject: [PATCH 29/40] Re-organized and updated documentation

---
 pycanvasgrader/documentation.html | 88 ++++++++++++++++---------------
 1 file changed, 45 insertions(+), 43 deletions(-)

diff --git a/pycanvasgrader/documentation.html b/pycanvasgrader/documentation.html
index ccc2f7b..95c9ab5 100644
--- a/pycanvasgrader/documentation.html
+++ b/pycanvasgrader/documentation.html
@@ -84,28 +84,28 @@ <h4>Example:</h4>
 </div>
 <div class="container">
     <div class="item">
-        "disarm" - Boolean <span class="opt">(Optional)</span> Default: <span class="false">false</span>
+        "tests" - Dictionary
     </div>
     <div class="desc">
-        Whether to "disarm" this skeleton. A disarmed skeleton does not actually upload grades to Canvas, and does not send messages to users.
+        The list of tests that this skeleton should run. See below for how to write tests.
     </div>
     <h4>Example:</h4>
     <div class="example">
-        "disarm": true
+        "tests": {
+        ...
+        }
     </div>
 </div>
 <div class="container">
     <div class="item">
-        "tests" - Dictionary
+        "disarm" - Boolean <span class="opt">(Optional)</span> Default: <span class="false">false</span>
     </div>
     <div class="desc">
-        The list of tests that this skeleton should run. See below for how to write tests.
+        Whether to "disarm" this skeleton. A disarmed skeleton does not actually upload grades to Canvas, and does not send messages to users.
     </div>
     <h4>Example:</h4>
     <div class="example">
-        "tests": {
-        ...
-        }
+        "disarm": true
     </div>
 </div>
 
@@ -146,6 +146,18 @@ <h4>Example:</h4>
         "input": "25"
     </div>
 </div>
+<div class="container">
+    <div class="item">
+        "timeout" - Integer <span class="opt">(Optional)</span> Default: <span class="none">none</span>
+    </div>
+    <div class="desc">
+        An optional timeout, in seconds, to be set for this test's command. If the command times out, then the test fails.
+    </div>
+    <h4>Example:</h4>
+    <div class="example">
+        "timeout": 5
+    </div>
+</div>
 <div class="container">
     <div class="item">
         "point_val" - Integer<span class="opt">(Optional)</span> Default: <span class="none">none</span>
@@ -160,14 +172,14 @@ <h4>Example:</h4>
 </div>
 <div class="container">
     <div class="item">
-        "print_file" - Boolean <span class="opt">(Optional)</span> Default: <span class="false">false</span>
+        "target_file" - String <span class="opt">(Optional)</span> Default: <span class="none">none</span>
     </div>
     <div class="desc">
-        Whether to print the student's file to the console.
+        The filename that "%s" will be replaced with, if "%s" is found in the arguments list.
     </div>
     <h4>Example:</h4>
     <div class="example">
-        "print_file": true
+        "target_file": "MyClass.java"
     </div>
 </div>
 <div class="container">
@@ -185,39 +197,39 @@ <h4>Example:</h4>
 </div>
 <div class="container">
     <div class="item">
-        "target_file" - String <span class="opt">(Optional)</span> Default: <span class="none">none</span>
+        "ask_for_target" - Boolean <span class="opt">(Optional)</span> Default: <span class="false">false</span>
     </div>
     <div class="desc">
-        The filename that "%s" will be replaced with, if it is found in the arguments list.
+        Whether to prompt for a file to replace %s" with.<br/>
+        This will ask the grader to choose from the files submitted by the student.
     </div>
     <h4>Example:</h4>
     <div class="example">
-        "target_file": "MyClass.java"
+        "ask_for_target": true
     </div>
 </div>
 <div class="container">
     <div class="item">
-        "ask_for_target" - Boolean <span class="opt">(Optional)</span> Default: <span class="false">false</span>
+        "include_filetype" - Boolean <span class="opt">(Optional)</span> Default: <span class="true">true</span>
     </div>
     <div class="desc">
-        Whether to prompt for a file to replace %s" with.<br/>
-        This will ask the grader to choose from the files submitted buy the student.
+        Whether to include or chop off the filetype extension when replacing the wildcard ("%s") with the student's file.
     </div>
     <h4>Example:</h4>
     <div class="example">
-        "ask_for_target": true
+        "include_filetype: false
     </div>
 </div>
 <div class="container">
     <div class="item">
-        "include_filetype" - Boolean <span class="opt">(Optional)</span> Default: <span class="true">true</span>
+        "print_file" - Boolean <span class="opt">(Optional)</span> Default: <span class="false">false</span>
     </div>
     <div class="desc">
-        Whether to include or chop off the filetype extension when replacing the wildcard ("%s") with the student's file.
+        Whether to print the student's file to the console.
     </div>
     <h4>Example:</h4>
     <div class="example">
-        "include_filetype: false
+        "print_file": true
     </div>
 </div>
 <div class="container">
@@ -237,7 +249,8 @@ <h4>Example:</h4>
         "output_match" - String <span class="opt">(Optional)</span> Default: <span class="none">none</span>
     </div>
     <div class="desc">
-        If "exact_match" is set, this string must exactly match the output of the command, or the test will fail.<br/>
+        A string that must be in the output of the command for the test to pass.<br/>
+        If "exact_match" is <span class="true">true</span>, this string must exactly match the output of the command, or the test will fail.<br/>
         Note: If "output_regex" or "numeric_match" is set, this argument has no effect.
     </div>
     <h4>Example:</h4>
@@ -256,7 +269,7 @@ <h4>Example:</h4>
     <h4>Example:</h4>
     <div class="example-multiline">
         <div class="example">
-            //match output with an even number of a's and an odd number of b's<br/>
+            //match an output string consisting of an even number of a's and an odd number of b's<br/>
             "output_regex": "^(aa)*(bb)*b$"
         </div>
     </div>
@@ -266,19 +279,19 @@ <h4>Example:</h4>
         "numeric_match" - Array <span class="opt">(Optional)</span> Default: <span class="none">none</span>
     </div>
     <div class="desc">
-        A list of numbers that must ALL be found somewhere in the command's output for the test to pass.<br>
-        Numbers can be duplicated if they must be found more than once.
-        A number can be denoted in three ways:<br>
+        A list of numbers that must ALL be found somewhere in the command's output for the test to pass.<br/    >
+        Numbers can be duplicated if they must be found more than once.<br/>
+        A number can be denoted in three ways:<br/>
         <ol>
-            <li>As an exact number (2, 3.333)</li>
-            <li>As an array denoting a range ([2, 2.5])</li>
-            <li>As a string denoting a number plus/minus the second number ("10,0.0001")</li>
+            <li>As an exact number (e.g. 3.14)</li>
+            <li>As an array denoting a range (e.g. [2, 2.5])</li>
+            <li>As a string denoting a number plus/minus the second number (e.g. "10, 0.0001" is the same as [9.9999, 10.0001])</li>
         </ol>
         Note: This overrides "outut_regex" and "output_match".
     </div>
     <h4>Example:</h4>
     <div class="example">
-        "numeric_match": [200, [8.5, 9], "50,0.5"]
+        "numeric_match": [200, -33.333, [8.5, 9], "-50,0.5"]
     </div>
 </div>
 <div class="container">
@@ -306,25 +319,14 @@ <h4>Example:</h4>
         "exact_match": true
     </div>
 </div>
-<div class="container">
-    <div class="item">
-        "timeout" - Integer <span class="opt">(Optional)</span> Default: <span class="none">none</span>
-    </div>
-    <div class="desc">
-        An optional timeout, in seconds, to be set for this test's command. If the command times out, then the test fails.
-    </div>
-    <h4>Example:</h4>
-    <div class="example">
-        "timeout": 5
-    </div>
-</div>
 <div class="container">
     <div class="item">
         "fail_notif" - Dictionary <span class="opt">(Optional)</span> Default: <span class="none">none</span>
     </div>
     <div class="desc">
         This message will be sent to the student if the fest fails.<br/>
-        Consists of a dictionary containing a "body" string and an optional "subject" string.
+        Consists of a dictionary containing a "body" string and an optional "subject" string.<br/>
+        The message will be sent from your Canvas account, as though you had manually started a conversation with the student.
     </div>
     <h4>Example:</h4>
     <div class="example-multiline">

From b3540a9cb346d9cab075671f6352222470c7a180 Mon Sep 17 00:00:00 2001
From: Michael Manis <electricpyrotechnic@gmail.com>
Date: Fri, 29 Sep 2017 10:44:53 -0400
Subject: [PATCH 30/40] Re-organized and updated documentation

---
 pycanvasgrader/pycanvasgrader.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/pycanvasgrader/pycanvasgrader.py b/pycanvasgrader/pycanvasgrader.py
index e5d3fec..531a500 100644
--- a/pycanvasgrader/pycanvasgrader.py
+++ b/pycanvasgrader/pycanvasgrader.py
@@ -9,7 +9,6 @@
   access.token
   pycanvasgrader.py
 
-  TODO implement skeleton creation wizard
   TODO test/implement visual grading (ask for grade after test runs)
 """
 

From 5c231201a8c254649d165f9b7fc6db82f98b084d Mon Sep 17 00:00:00 2001
From: Michael Manis <electricpyrotechnic@gmail.com>
Date: Fri, 29 Sep 2017 10:50:54 -0400
Subject: [PATCH 31/40] delete some text

---
 pycanvasgrader/pycanvasgrader.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pycanvasgrader/pycanvasgrader.py b/pycanvasgrader/pycanvasgrader.py
index e5d3fec..2ccca0b 100644
--- a/pycanvasgrader/pycanvasgrader.py
+++ b/pycanvasgrader/pycanvasgrader.py
@@ -10,7 +10,7 @@
   pycanvasgrader.py
 
   TODO implement skeleton creation wizard
-  TODO test/implement visual grading (ask for grade after test runs)
+  TODO test/implement visual grading
 """
 
 # built-ins

From 023cb08a937e0435db36843a430e716f3834248c Mon Sep 17 00:00:00 2001
From: Michael Manis <electricpyrotechnic@gmail.com>
Date: Fri, 29 Sep 2017 10:55:22 -0400
Subject: [PATCH 32/40] added text

---
 pycanvasgrader/pycanvasgrader.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pycanvasgrader/pycanvasgrader.py b/pycanvasgrader/pycanvasgrader.py
index 2ccca0b..7ee4520 100644
--- a/pycanvasgrader/pycanvasgrader.py
+++ b/pycanvasgrader/pycanvasgrader.py
@@ -11,6 +11,7 @@
 
   TODO implement skeleton creation wizard
   TODO test/implement visual grading
+  test branch
 """
 
 # built-ins

From 7597634857c101b96d152007e9d3032fe3b5e166 Mon Sep 17 00:00:00 2001
From: Michael Manis <electricpyrotechnic@gmail.com>
Date: Fri, 29 Sep 2017 11:11:10 -0400
Subject: [PATCH 33/40] delete some text

---
 pycanvasgrader/pycanvasgrader.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pycanvasgrader/pycanvasgrader.py b/pycanvasgrader/pycanvasgrader.py
index 7ee4520..4a31649 100644
--- a/pycanvasgrader/pycanvasgrader.py
+++ b/pycanvasgrader/pycanvasgrader.py
@@ -11,7 +11,7 @@
 
   TODO implement skeleton creation wizard
   TODO test/implement visual grading
-  test branch
+  test branch 3 adds text
 """
 
 # built-ins

From 95ba4ba36b095cab47a39cda265d0b9309624076 Mon Sep 17 00:00:00 2001
From: Michael Manis <electricpyrotechnic@gmail.com>
Date: Fri, 29 Sep 2017 11:12:13 -0400
Subject: [PATCH 34/40] remove all added text

---
 pycanvasgrader/pycanvasgrader.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/pycanvasgrader/pycanvasgrader.py b/pycanvasgrader/pycanvasgrader.py
index 4a31649..2ccca0b 100644
--- a/pycanvasgrader/pycanvasgrader.py
+++ b/pycanvasgrader/pycanvasgrader.py
@@ -11,7 +11,6 @@
 
   TODO implement skeleton creation wizard
   TODO test/implement visual grading
-  test branch 3 adds text
 """
 
 # built-ins

From 89c74edaacf60b75d5bb9b8a8b8d7e914e987f8e Mon Sep 17 00:00:00 2001
From: root <root@localhost.localdomain>
Date: Thu, 12 Oct 2017 19:00:23 -0400
Subject: [PATCH 35/40] Better access.token handling

---
 pycanvasgrader/pycanvasgrader.py | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/pycanvasgrader/pycanvasgrader.py b/pycanvasgrader/pycanvasgrader.py
index 2ccca0b..7fe3f27 100644
--- a/pycanvasgrader/pycanvasgrader.py
+++ b/pycanvasgrader/pycanvasgrader.py
@@ -59,13 +59,15 @@ def authenticate() -> str:
 
         TODO Talk about "proper" OAuth2 authentication
         """
-
-        with open('access.token', 'r', encoding='UTF-8') as access_file:
-            for line in access_file:
-                token = line.strip()
-                if isinstance(token, str) and len(token) > 2:
-                    return token
-        return 'none'
+        try:
+            with open('access.token', 'r', encoding='UTF-8') as access_file:
+                for line in access_file:
+                    token = line.strip()
+                    if isinstance(token, str) and len(token) > 2:
+                        return token
+        except FileNotFoundError:
+            print("Could not find an access.token file. You must place your Canvas OAuth token in a file named 'access.token', in this directory.")
+            exit(1)
 
     def close(self):
         self.session.close()

From 16dc48273562a3a75ba3fb82be9ca78efad01754 Mon Sep 17 00:00:00 2001
From: root <root@localhost.localdomain>
Date: Thu, 12 Oct 2017 19:23:52 -0400
Subject: [PATCH 36/40] fixed type-o

---
 pycanvasgrader/old-temp/27592/HW1e.cpp | 22 ++++++++++++++++++++++
 pycanvasgrader/pycanvasgrader.py       |  2 +-
 pycanvasgrader/temp/27592/HW1e.cpp     | 22 ++++++++++++++++++++++
 pycanvasgrader/virtenv/bin/python      |  1 +
 pycanvasgrader/virtenv/bin/python3     |  1 +
 pycanvasgrader/virtenv/bin/python3.6   |  1 +
 pycanvasgrader/virtenv/lib64           |  1 +
 pycanvasgrader/virtenv/pyvenv.cfg      |  3 +++
 8 files changed, 52 insertions(+), 1 deletion(-)
 create mode 100644 pycanvasgrader/old-temp/27592/HW1e.cpp
 create mode 100644 pycanvasgrader/temp/27592/HW1e.cpp
 create mode 120000 pycanvasgrader/virtenv/bin/python
 create mode 120000 pycanvasgrader/virtenv/bin/python3
 create mode 120000 pycanvasgrader/virtenv/bin/python3.6
 create mode 120000 pycanvasgrader/virtenv/lib64
 create mode 100644 pycanvasgrader/virtenv/pyvenv.cfg

diff --git a/pycanvasgrader/old-temp/27592/HW1e.cpp b/pycanvasgrader/old-temp/27592/HW1e.cpp
new file mode 100644
index 0000000..f95225c
--- /dev/null
+++ b/pycanvasgrader/old-temp/27592/HW1e.cpp
@@ -0,0 +1,22 @@
+#include <iostream>
+
+using namespace std;
+
+int fact(int);
+
+int main()
+{
+    int n = 0;
+    cout << "Enter a number: ";
+    cin >> n;
+    cout << fact(n);
+
+    return 0;
+}
+
+int fact(int n) {
+    int total = 1;
+    while (n > 0)
+        total *= n--;
+    return total;
+}
diff --git a/pycanvasgrader/pycanvasgrader.py b/pycanvasgrader/pycanvasgrader.py
index 7fe3f27..b5abc57 100644
--- a/pycanvasgrader/pycanvasgrader.py
+++ b/pycanvasgrader/pycanvasgrader.py
@@ -386,7 +386,7 @@ def run(self) -> dict:
             else:
                 command_to_send = command
 
-            proc = subprocess.run(command_to_send, input=self.input, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, timeout=self.timeout, encoding='UTF-8', shell=True)
+            proc = subprocess.run(command_to_send, input=self.input_str, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, timeout=self.timeout, encoding='UTF-8', shell=True)
 
         except subprocess.TimeoutExpired:
             return {'timeout': True}
diff --git a/pycanvasgrader/temp/27592/HW1e.cpp b/pycanvasgrader/temp/27592/HW1e.cpp
new file mode 100644
index 0000000..f95225c
--- /dev/null
+++ b/pycanvasgrader/temp/27592/HW1e.cpp
@@ -0,0 +1,22 @@
+#include <iostream>
+
+using namespace std;
+
+int fact(int);
+
+int main()
+{
+    int n = 0;
+    cout << "Enter a number: ";
+    cin >> n;
+    cout << fact(n);
+
+    return 0;
+}
+
+int fact(int n) {
+    int total = 1;
+    while (n > 0)
+        total *= n--;
+    return total;
+}
diff --git a/pycanvasgrader/virtenv/bin/python b/pycanvasgrader/virtenv/bin/python
new file mode 120000
index 0000000..039b719
--- /dev/null
+++ b/pycanvasgrader/virtenv/bin/python
@@ -0,0 +1 @@
+python3.6
\ No newline at end of file
diff --git a/pycanvasgrader/virtenv/bin/python3 b/pycanvasgrader/virtenv/bin/python3
new file mode 120000
index 0000000..039b719
--- /dev/null
+++ b/pycanvasgrader/virtenv/bin/python3
@@ -0,0 +1 @@
+python3.6
\ No newline at end of file
diff --git a/pycanvasgrader/virtenv/bin/python3.6 b/pycanvasgrader/virtenv/bin/python3.6
new file mode 120000
index 0000000..6270541
--- /dev/null
+++ b/pycanvasgrader/virtenv/bin/python3.6
@@ -0,0 +1 @@
+/usr/bin/python3.6
\ No newline at end of file
diff --git a/pycanvasgrader/virtenv/lib64 b/pycanvasgrader/virtenv/lib64
new file mode 120000
index 0000000..7951405
--- /dev/null
+++ b/pycanvasgrader/virtenv/lib64
@@ -0,0 +1 @@
+lib
\ No newline at end of file
diff --git a/pycanvasgrader/virtenv/pyvenv.cfg b/pycanvasgrader/virtenv/pyvenv.cfg
new file mode 100644
index 0000000..1c9b80d
--- /dev/null
+++ b/pycanvasgrader/virtenv/pyvenv.cfg
@@ -0,0 +1,3 @@
+home = /usr/bin
+include-system-site-packages = false
+version = 3.6.2

From 99f13739a504952bc9ae09ff0d99d32b7d7d5b95 Mon Sep 17 00:00:00 2001
From: root <root@localhost.localdomain>
Date: Thu, 12 Oct 2017 19:26:13 -0400
Subject: [PATCH 37/40] removed temp

---
 pycanvasgrader/old-temp/27592/HW1e.cpp | 22 ----------------------
 pycanvasgrader/temp/27592/HW1e.cpp     | 22 ----------------------
 2 files changed, 44 deletions(-)
 delete mode 100644 pycanvasgrader/old-temp/27592/HW1e.cpp
 delete mode 100644 pycanvasgrader/temp/27592/HW1e.cpp

diff --git a/pycanvasgrader/old-temp/27592/HW1e.cpp b/pycanvasgrader/old-temp/27592/HW1e.cpp
deleted file mode 100644
index f95225c..0000000
--- a/pycanvasgrader/old-temp/27592/HW1e.cpp
+++ /dev/null
@@ -1,22 +0,0 @@
-#include <iostream>
-
-using namespace std;
-
-int fact(int);
-
-int main()
-{
-    int n = 0;
-    cout << "Enter a number: ";
-    cin >> n;
-    cout << fact(n);
-
-    return 0;
-}
-
-int fact(int n) {
-    int total = 1;
-    while (n > 0)
-        total *= n--;
-    return total;
-}
diff --git a/pycanvasgrader/temp/27592/HW1e.cpp b/pycanvasgrader/temp/27592/HW1e.cpp
deleted file mode 100644
index f95225c..0000000
--- a/pycanvasgrader/temp/27592/HW1e.cpp
+++ /dev/null
@@ -1,22 +0,0 @@
-#include <iostream>
-
-using namespace std;
-
-int fact(int);
-
-int main()
-{
-    int n = 0;
-    cout << "Enter a number: ";
-    cin >> n;
-    cout << fact(n);
-
-    return 0;
-}
-
-int fact(int n) {
-    int total = 1;
-    while (n > 0)
-        total *= n--;
-    return total;
-}

From 6e30eb387c71ff26554bd55cdf964aa7ad94e95d Mon Sep 17 00:00:00 2001
From: ThePyrotechnic <electricpyrotechnic@gmail.com>
Date: Fri, 13 Oct 2017 12:26:16 -0400
Subject: [PATCH 38/40] added shebang

---
 pycanvasgrader/pycanvasgrader.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pycanvasgrader/pycanvasgrader.py b/pycanvasgrader/pycanvasgrader.py
index b5abc57..6821573 100644
--- a/pycanvasgrader/pycanvasgrader.py
+++ b/pycanvasgrader/pycanvasgrader.py
@@ -1,4 +1,4 @@
-#!
+#!/usr/bin/env python3.6
 """
 Automates the grading of programming assignments on Canvas.
 MUST create an 'access.token' file in the same directory as this file with a valid Canvas OAuth2 token

From 5f9cf12f895e27c37bf21fce15f15854b7dbf081 Mon Sep 17 00:00:00 2001
From: ThePyrotechnic <electricpyrotechnic@gmail.com>
Date: Fri, 13 Oct 2017 14:23:03 -0400
Subject: [PATCH 39/40] Updated urls, fixed directory handling

---
 pycanvasgrader/pycanvasgrader.py   | 26 +++++++++++++++++++-------
 pycanvasgrader/skeletons/HW1c.json | 17 ++++-------------
 2 files changed, 23 insertions(+), 20 deletions(-)

diff --git a/pycanvasgrader/pycanvasgrader.py b/pycanvasgrader/pycanvasgrader.py
index 6821573..8e229ee 100644
--- a/pycanvasgrader/pycanvasgrader.py
+++ b/pycanvasgrader/pycanvasgrader.py
@@ -77,9 +77,9 @@ def courses(self, enrollment_type: str = None) -> list:
         :param enrollment_type: (Optional) teacher, student, ta, observer, designer
         :return: A list of the user's courses as dictionaries, optionally filtered by enrollment_type
         """
-        url = 'https://sit.instructure.com/api/v1/courses'
+        url = 'https://sit.instructure.com/api/v1/courses?per_page=100'
         if enrollment_type is not None:
-            url += '?enrollment_type=' + enrollment_type
+            url += '&enrollment_type=' + enrollment_type
 
         response = self.session.get(url)
         return json.loads(response.text)
@@ -90,9 +90,9 @@ def assignments(self, course_id: int, ungraded: bool = True) -> list:
         :param ungraded: Whether to filter assignments by only those that have ungraded work. Default: True
         :return: A list of the course's assignments
         """
-        url = 'https://sit.instructure.com/api/v1/courses/' + str(course_id) + '/assignments'
+        url = 'https://sit.instructure.com/api/v1/courses/' + str(course_id) + '/assignments?per_page=100'
         if ungraded:
-            url += '?bucket=ungraded'
+            url += '&bucket=ungraded'
 
         response = self.session.get(url)
         return json.loads(response.text)
@@ -103,7 +103,7 @@ def submissions(self, course_id: int, assignment_id: int) -> list:
         :param assignment_id: The ID of the assignment
         :return: A list of the assignment's submissions
         """
-        url = 'https://sit.instructure.com/api/v1/courses/' + str(course_id) + '/assignments/' + str(assignment_id) + '/submissions'
+        url = 'https://sit.instructure.com/api/v1/courses/' + str(course_id) + '/assignments/' + str(assignment_id) + '/submissions?per_page=100'
 
         response = self.session.get(url)
         return json.loads(response.text)
@@ -385,8 +385,11 @@ def run(self) -> dict:
                 command_to_send = [command] + args
             else:
                 command_to_send = command
+            if sys.version_info[1] == 5:
+                proc = subprocess.run(command_to_send, input=self.input_str, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, timeout=self.timeout, shell=True)
 
-            proc = subprocess.run(command_to_send, input=self.input_str, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, timeout=self.timeout, encoding='UTF-8', shell=True)
+            else:
+                proc = subprocess.run(command_to_send, input=self.input_str, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, timeout=self.timeout, encoding='UTF-8', shell=True)
 
         except subprocess.TimeoutExpired:
             return {'timeout': True}
@@ -506,6 +509,11 @@ def init_tempdir():
 
 
 def main():
+    version_info = sys.version_info
+    if version_info[0] != 3 and version_info[1] < 5:
+        print("Python 3.5+ is required")
+        exit(1)
+
     init_tempdir()
     # Initialize grading session and fetch courses
     grader = PyCanvasGrader()
@@ -642,7 +650,11 @@ def main():
                     break
                 elif selected_action == 'Re-grade this submission':
                     score = selected_skeleton.run_tests(grader, cur_user_id)
-
+        try:
+            os.chdir(os.path.join('..', '..'))
+        except (WindowsError, OSError):
+            print("Unable to leave current directory")
+            exit(1)
     print('Finished grading all submissions for this assignment')
 
 
diff --git a/pycanvasgrader/skeletons/HW1c.json b/pycanvasgrader/skeletons/HW1c.json
index ac47b2a..9a809d9 100644
--- a/pycanvasgrader/skeletons/HW1c.json
+++ b/pycanvasgrader/skeletons/HW1c.json
@@ -1,5 +1,6 @@
 {
   "descriptor": "HW1c Grader",
+  "disarm": true,
   "tests": {
     "test_1": {
       "command": "g++",
@@ -12,12 +13,7 @@
       "output_match": "error",
       "negate_match": true,
 
-      "point_val": 25,
-
-      "fail_notification": {
-        "subject": "HW1c compilation failed",
-        "body": "This is an automated message to inform you that compilation of your submission for HW1c has failed\nPlease resbumit this assigment or your grade will remain a 0."
-      }
+      "point_val": 25
     },
     "test_2": {
       "command": "out.exe",
@@ -25,13 +21,8 @@
 
       "output_match": "5050\n5050\n",
       "exact_match": false,
-
-      "point_val": 75,
-
-      "fail_notification": {
-        "subject": "HW1c testing failed",
-        "body": "This is an automated message to inform you that testing of your submission for HW1c has failed.\nCheck to make sure your output conforms exactly to what is expected on Canvas."
-      }
+      "timeout": 5,
+      "point_val": 75
     }
   }
 }

From 1a74332470170a30c8feed3c4cb3671c52530676 Mon Sep 17 00:00:00 2001
From: Michael Manis <electricpyrotechnic@gmail.com>
Date: Thu, 1 Feb 2018 12:22:08 -0500
Subject: [PATCH 40/40] paginate submission downloading.

---
 pycanvasgrader/pycanvasgrader.py   | 7 ++++++-
 pycanvasgrader/skeletons/HW1d.json | 4 ++--
 2 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/pycanvasgrader/pycanvasgrader.py b/pycanvasgrader/pycanvasgrader.py
index 8e229ee..c3afc15 100644
--- a/pycanvasgrader/pycanvasgrader.py
+++ b/pycanvasgrader/pycanvasgrader.py
@@ -106,7 +106,12 @@ def submissions(self, course_id: int, assignment_id: int) -> list:
         url = 'https://sit.instructure.com/api/v1/courses/' + str(course_id) + '/assignments/' + str(assignment_id) + '/submissions?per_page=100'
 
         response = self.session.get(url)
-        return json.loads(response.text)
+        final_response = json.loads(response.text)
+        while response.links.get("next"):
+            response = self.session.get(response.links['next']['url'])
+            final_response.extend(json.loads(response.text))
+
+        return final_response
 
     def download_submission(self, submission: dict, filepath: str) -> bool:
         """
diff --git a/pycanvasgrader/skeletons/HW1d.json b/pycanvasgrader/skeletons/HW1d.json
index 6a69cd0..6853228 100644
--- a/pycanvasgrader/skeletons/HW1d.json
+++ b/pycanvasgrader/skeletons/HW1d.json
@@ -20,14 +20,14 @@
     "test_float": {
       "command": "out.exe",
       "print_output": true,
-      "numeric_match": [9.53674, 7],
+      "numeric_match": [9.53674, -7],
       "exact_match": false,
       "point_val": 20
     },
     "test_double": {
       "command": "out.exe",
       "print_output": true,
-      "numeric_match": [-8.88178, 16],
+      "numeric_match": [-8.88178, -16],
       "exact_match": false,
       "point_val": 20
     }