otter-service-stdalone 1.0.0__tar.gz → 1.1.1__tar.gz

{otter_service_stdalone-1.0.0 → otter_service_stdalone-1.1.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: otter_service_stdalone
-Version: 1.0.0
+Version: 1.1.1
 Summary: Grading Service for Instructors using Otter Grader
 Home-page: https://github.com/sean-morris/otter-service-stdalone
 Author: Sean Morris

{otter_service_stdalone-1.0.0 → otter_service_stdalone-1.1.1}/setup.cfg

@@ -23,7 +23,7 @@ python_requires = >=3.8
 where = src
 
 [options.package_data]
-otter_service_stdalone = index.html, secrets/*.yaml, static_templates/*.html
+otter_service_stdalone = index.html, secrets/*.yaml, static_templates/*.html, static_files/*, scripts/*
 
 [options.entry_points]
 console_scripts = 

otter_service_stdalone-1.1.1/src/otter_service_stdalone/__init__.py

@@ -0,0 +1 @@
+__version__ = "1.1.1"

{otter_service_stdalone-1.0.0 → otter_service_stdalone-1.1.1}/src/otter_service_stdalone/app.py

@@ -4,10 +4,12 @@ import tornado.web
 import tornado.auth
 import os
 import uuid
+import tornado.websocket
 from otter_service_stdalone import fs_logging as log
 from otter_service_stdalone import user_auth as u_auth
 from otter_service_stdalone import grade_notebooks
 from zipfile import ZipFile, ZIP_DEFLATED
+import queue
 
 
 __UPLOADS__ = "/tmp/uploads"
@@ -16,6 +18,53 @@ log_error = f'{os.environ.get("ENVIRONMENT")}-logs'
 log_http = f'{os.environ.get("ENVIRONMENT")}-http-error'
 
 authorization_states = {}  # used to protect against cross-site request forgery attacks.
+session_queues = {}
+session_messages = {}
+session_callbacks = {}
+
+
+class WebSocketHandler(tornado.websocket.WebSocketHandler):
+    """This handles updates to the application from otter-grader
+    """
+    def open(self):
+        """if logged in, start a callback once a second to see if there messages for the
+            logged in user
+        """
+        if self.get_secure_cookie("user"):
+            user_id = self.get_secure_cookie("user").decode('utf-8')
+            if user_id not in session_callbacks:
+                session_callbacks[user_id] = tornado.ioloop.PeriodicCallback(lambda: self.send_results(user_id), 1000)
+                session_callbacks[user_id].start()
+
+    def on_message(self, message):
+        pass  # No action needed on incoming message
+
+    def on_close(self):
+        """stop the periodic classback on close
+        """
+        if self.get_secure_cookie("user"):
+            user_id = self.get_secure_cookie("user").decode('utf-8')
+            if user_id in session_callbacks and session_callbacks[user_id].callback:
+                session_callbacks[user_id].stop()
+                session_callbacks.pop(user_id)
+
+    def send_results(self, user_id):
+        """if there are messages for this user, send them to application by submission.
+            We save the messages in the session so if refresh on client side they still
+            have the updates
+        """
+        try:
+            if user_id in session_queues:
+                user_queue_dict = session_queues[user_id]
+                user_messages_dict = session_messages[user_id]
+                if user_queue_dict:
+                    for result_id, q in user_queue_dict.items():
+                        if not q.empty():
+                            while not q.empty():
+                                user_messages_dict[result_id].append(q.get())
+                            self.write_message({"messages": user_messages_dict})
+        except tornado.websocket.WebSocketClosedError:
+            log.write_logs("ws-error", "Web Socket Problem", "", "", log_error)
 
 
 class HealthHandler(tornado.web.RequestHandler):
@@ -136,27 +185,26 @@ class Download(BaseHandler):
             msg += "Please check the code or upload your notebooks "
             msg += "and autograder.zip for grading again."
             self.render("index.html",  download_message=msg)
-        elif not os.path.exists(f"{directory}/grading-logs.txt"):
+        elif not os.path.exists(f"{directory}/final_grades.csv"):
             m = "Download: Results Not Ready"
             log.write_logs(download_code, m, f"{download_code}", "debug", log_debug)
             msg = "The results of your download are not ready yet. "
             msg += "Please check back."
             self.render("index.html",  download_message=msg, dcode=download_code)
         else:
-            if not os.path.isfile(f"{directory}/final_grades.csv"):
-                m = "Download: final_grades.csv does not exist"
-                t = "Problem grading notebooks see stack trace"
-                log.write_logs(download_code, m, t, "debug", log_debug)
-                with open(f"{directory}/final_grades.csv", "a") as f:
-                    m = "There was a problem grading your notebooks. Please see grading-logs.txt"
-                    f.write(m)
-                    f.close()
             m = "Download Success: Creating results.zip"
             log.write_logs(download_code, m, "", "debug", log_debug)
             with ZipFile(f"{directory}/results.zip", 'w') as zipF:
-                for file in ["final_grades.csv", "grading-logs.txt"]:
-                    if os.path.isfile(f"{directory}/{file}"):
-                        zipF.write(f"{directory}/{file}", file, compress_type=ZIP_DEFLATED)
+                final_file = "final_grades.csv"
+                if os.path.isfile(f"{directory}/{final_file}"):
+                    zipF.write(f"{directory}/{final_file}", final_file, compress_type=ZIP_DEFLATED)
+                for filename in os.listdir(f"{directory}/grading-summaries"):
+                    file_path = os.path.join(f"{directory}/grading-summaries", filename)
+                    if os.path.isfile(file_path):
+                        f_path = f"grading-summaries-do-not-distribute/{filename}"
+                        zipF.write(f"{file_path}", f_path, compress_type=ZIP_DEFLATED)
+                read_me = os.path.join(os.path.dirname(__file__), "static_files", "README_DO_NOT_DISTRIBUTE.txt")
+                zipF.write(read_me, "README_DO_NOT_DISTRIBUTE.txt", compress_type=ZIP_DEFLATED)
 
             self.set_header('Content-Type', 'application/octet-stream')
             self.set_header("Content-Description", "File Transfer")
@@ -179,7 +227,7 @@ class Upload(BaseHandler):
 
     Args:
         tornado (tornado.web.RequestHandler): The upload request handler
-    """
+    """        
     @tornado.web.authenticated
     def get(self):
         # this just redirects to login and displays main page
@@ -189,6 +237,11 @@ class Upload(BaseHandler):
     async def post(self):
         """this handles the post request and asynchronously launches the grader
         """
+        user = self.get_current_user()
+        user_id = user.decode('utf-8')
+        if user_id not in session_queues:
+            session_queues[user_id] = {}
+            session_messages[user_id] = {}
         g = grade_notebooks.GradeNotebooks()
         files = self.request.files
         results_path = str(uuid.uuid4())
@@ -219,11 +272,13 @@ class Upload(BaseHandler):
             fh.write(notebooks['body'])
             m = "Step 3: Uploaded Files Written to Disk"
             log.write_logs(results_path, m, f"Results Code: {results_path}", "debug", log_debug)
-            m = "Please save this code. You can retrieve your files by submitting this code "
-            m += f"in the \"Results\" section to the right: {results_path}"
+            m = "Please save this code; it appears in the \"Notebook Grading Progress\" section below. You can "
+            m += f"retrieve your files by submitting this code in the \"Results\" section to the right: {results_path}"
             self.render("index.html", message=m)
             try:
-                await g.grade(auto_p, notebooks_path, results_path)
+                session_queues[user_id][results_path] = queue.Queue()
+                session_messages[user_id][results_path] = []
+                await g.grade(auto_p, notebooks_path, results_path, session_queues[user_id].get(results_path))
             except Exception as e:
                 log.write_logs(results_path, "Grading Problem", str(e), "error", log_error)
         else:
@@ -244,8 +299,10 @@ application = tornado.web.Application([
         (r"/login", LoginHandler),
         (r"/upload", Upload),
         (r"/download", Download),
+        (r"/update", WebSocketHandler),
         (r"/oauth_callback", GitHubOAuthHandler),
         (r"/otterhealth", HealthHandler),
+        (r"/scripts/(.*)", tornado.web.StaticFileHandler, {"path": os.path.join(os.path.dirname(__file__), "scripts")}),
         ], **settings, debug=False)
 
 

otter_service_stdalone-1.1.1/src/otter_service_stdalone/grade_notebooks.py

@@ -0,0 +1,75 @@
+import asyncio
+from otter_service_stdalone import fs_logging as log, upload_handle as uh
+import os
+from otter.grade import main as grade
+
+log_debug = f'{os.environ.get("ENVIRONMENT")}-debug'
+log_count = f'{os.environ.get("ENVIRONMENT")}-count'
+log_error = f'{os.environ.get("ENVIRONMENT")}-logs'
+
+
+class GradeNotebooks():
+    """The class contains the async grade method for executing
+        otter grader as well as a function for logging the number of 
+        notebooks to be graded
+    """    
+    def count_ipynb_files(self, directory, extension):
+        """this count the files for logging purposes"""
+        count = 0
+        for filename in os.listdir(directory):
+            if filename.endswith(extension):
+                count += 1
+        return count
+
+    async def grade(self, p, notebooks_path, results_id, user_queue):
+        """Calls otter grade asynchronously and writes the various log files
+        and results of grading generating by otter-grader
+
+        Args:
+            p (str): the path to autograder.zip -- the solutions
+            notebooks_path (str): the path to the folder of notebooks to be graded
+            results_id (str): used for identifying logs
+
+        Raises:
+            Exception: Timeout Exception is raised if async takes longer than 20 min
+
+        Returns:
+            boolean: True is the process completes; otherwise an Exception is thrown
+        """
+        try:
+            notebook_folder = uh.handle_upload(notebooks_path, results_id)
+            notebook_count = self.count_ipynb_files(notebook_folder, ".ipynb")
+            log.write_logs(results_id, f"{notebook_count}",
+                           "",
+                           "info",
+                           f'{os.environ.get("ENVIRONMENT")}-count')
+            log.write_logs(results_id, "Step 5: Notebook Folder configured and grading started",
+                           f"Notebook Folder: {notebook_folder}",
+                           "debug",
+                           log_debug)
+
+            await grade(
+                name='grader',
+                autograder=p,
+                paths=(notebook_folder,),
+                containers=10,
+                timeout=300,
+                ext="ipynb",
+                output_dir=notebook_folder,
+                result_queue=user_queue
+            )
+            user_queue.put("Results available for download")
+
+            log.write_logs(results_id, "Step 6: Grading: Finished",
+                           f"{notebook_folder}",
+                           "debug",
+                           log_debug)
+            log.write_logs(results_id, f"Grading: Finished: {notebook_folder}",
+                           "",
+                           "info",
+                           log_error)
+            return True
+        except asyncio.TimeoutError:
+            raise Exception(f'Grading timed out for {notebook_folder}')
+        except Exception as e:
+            raise e

{otter_service_stdalone-1.0.0 → otter_service_stdalone-1.1.1}/src/otter_service_stdalone/index.html

@@ -4,6 +4,39 @@
 <title>Upload Form</title>
 <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/bulma@0.9.4/css/bulma.min.css">
 <script defer src="https://use.fontawesome.com/releases/v5.3.1/js/all.js"></script>
+<style>
+  /* Styles to make the div scrollable after a certain height */
+  #messages {
+      max-height: 400px;
+      overflow-y: auto; /* Enable vertical scrolling */
+      padding: 10px; 
+      width: auto;
+  }
+  /* Styles for the collapsible div */
+  .collapsible {
+      border: 1px solid #ccc;
+      width: auto; 
+      margin-bottom: 10px; 
+  }
+
+  /* Styles for the header */
+  .header {
+      background-color: #f1f1f1;
+      padding: 10px;
+      cursor: pointer;
+  }
+
+  /* Styles for the content */
+  .content {
+      max-height: 300px;
+      overflow-y: auto; /* Enable vertical scrolling */
+      padding: 10px;
+      display: none;
+  }
+
+
+</style>
+<script src="/scripts/web_socket.js"></script>
 </head>
 <body>
     <section class="container">
@@ -14,7 +47,7 @@
                         Cloudbank Otter Grading - Beta
                     </h1>
                     <h2 class="subtitle">
-                        Upload your notebooks, grade them, and download results.
+                          Upload your notebooks, grade them, and download results.
                     </h2>
                 </div>
             </div>
@@ -84,15 +117,17 @@
                             {% end %}
                         </form>
                     </div>
-                    </div>
+                </div>
+                <div id="messages">
+                  <p class="title is-3">Notebook Grading Progress</p>
+                  <p id="none-msg">No submissions are being graded</p>
+                </div>
             </div>
         </div>
         <div class="hero is-info welcome is-small">
           <div class="hero-body">
               <div class="container">
-                  <h2 class="subtitle">
-                      Questions? Problems? email: sean.smorris at berkeley.edu
-                  </h2>
+                  <span class="has-text-right is-pulled-right">email: sean.smorris@berkeley.edu</span>
               </div>
           </div>
       </div>

otter_service_stdalone-1.1.1/src/otter_service_stdalone/scripts/web_socket.js

@@ -0,0 +1,127 @@
+/**
+ * This is main function of the script. It sets up the web sockets and handles messages
+ * coming from the application. The last line of the script calls this function
+ */
+function connectWebSocket() {
+    var loc = window.location;
+    var wsStart = loc.protocol === "https:" ? "ws://" : "ws://";
+    var wsUrl = wsStart + loc.host + "/update";
+
+    var ws = new WebSocket(wsUrl);
+    submission_divs = {}
+    reconnectInterval = 3000;
+    ws.onopen = function() {
+        console.log("WebSocket is open now.");
+        reconnectInterval = 3000;
+    };
+
+    ws.onmessage = function(event) {
+        var messagesDiv = document.getElementById("messages");
+        var noneMsgP = document.getElementById("none-msg");
+        noneMsgP.style.display = "none"
+        json_msgs = JSON.parse(event.data)["messages"];
+        console.log(json_msgs)
+        Object.entries(json_msgs).forEach(([submission_key, messages], index) => {
+          if (!(submission_key in submission_divs)){
+            messagesDiv.appendChild(_setUpNewSubmission(submission_key, index, messages))
+          } else {
+            _updateSubmission(submission_key, index, messages)
+          }
+          
+          messagesDiv.scrollTop = messagesDiv.scrollHeight;
+        });
+    };
+
+    ws.onclose = function() {
+        //if closes attempts re-connect every few seconds
+        console.log("WebSocket is closed now.");
+        setTimeout(connectWebSocket, 3000);
+    };
+
+    ws.onerror = function(error) {
+        console.error('WebSocket error:', error);
+        ws.close();
+    };
+  };
+
+/**
+ * This function sets up the div that will report progress on the given submission
+ * in the application
+ * @param {*} submission_key doanload code - unique to submission
+ * @param {*} index - the submission number in this session for the user
+ * @param {*} messages - all the messages that need to be added to progress
+ */
+function _setUpNewSubmission(submission_key, index, messages){
+    var newMessage = document.createElement("div");
+    newMessage.id = submission_key
+    var newMessageHeader = document.createElement("div");
+    var newMessageContent = document.createElement("div");
+    newMessageContent.id = "msg-" + submission_key
+    newMessageHeader.id = "header-" + submission_key
+    var toggleSign =  document.createElement("span");
+    var submissionHeader =  document.createElement("span");
+    submissionHeader.innerHTML = " Submission Progress: Submission #" + (index+1)
+    submissionHeader.id = "sub-header-" + submission_key
+    newMessage.className = "collapsible"
+    newMessageHeader.className = "header"
+    toggleSign.innerHTML = '<i class="fas fa-minus-circle"></i>';
+  
+    newMessageHeader.appendChild(toggleSign)
+    newMessageHeader.appendChild(submissionHeader)
+    newMessageContent.className = "content"
+    newMessageContent.style.display = "block"
+    newMessage.appendChild(newMessageHeader)
+    newMessage.appendChild(newMessageContent)
+    submission_divs[submission_key] = newMessage
+    const li = document.createElement('li');
+    li.textContent = "Download Code: " + submission_key;
+    newMessageContent.appendChild(li);
+    for (const m of messages) {
+      const li = document.createElement('li');
+      li.textContent = m;
+      newMessageContent.appendChild(li);
+    }
+    // Toggle the visibility of the scrollable content
+    newMessageHeader.addEventListener('click', () => {
+      if (newMessageContent.style.display == 'none') {
+        newMessageContent.style.display = 'block';
+        toggleSign.innerHTML = '<i class="fas fa-minus-circle"></i>';
+      } else {
+        newMessageContent.style.display = 'none';
+        toggleSign.innerHTML = '<i class="fas fa-plus-circle"></i>';
+      }
+    });
+    return newMessage;
+}
+
+/**
+ * This updates the progress div for this submission
+ * 
+ * @param {*} submission_key doanload code - unique to submission
+ * @param {*} index - the submission number in this session for the user
+ * @param {*} messages - all the messages that need to be added to progress
+ */
+function _updateSubmission(submission_key, index, messages){
+    var newMessageContent = document.getElementById("msg-" + submission_key);
+    var items = newMessageContent.getElementsByTagName("li");
+    var msgs = []
+    for (var i = 0; i < items.length; ++i) {
+        msgs.push(items[i].textContent)
+    }
+    for (const m of messages) {
+      if(!(msgs.includes(m))){
+        const li = document.createElement('li');
+        li.textContent = m;
+        newMessageContent.appendChild(li);
+      }
+    }
+    if(messages.includes("Results available for download")){
+      var header = document.getElementById("header-" + submission_key)
+      header.style.backgroundColor = '#7BAE37';
+      var subheader = document.getElementById("sub-header-" + submission_key)
+      subheader.innerHTML = " Submission Progress: Submission #" + (index+1) + "</br>Download Code: " + submission_key;
+    }
+}
+
+
+connectWebSocket()

otter_service_stdalone-1.1.1/src/otter_service_stdalone/static_files/README_DO_NOT_DISTRIBUTE.txt

@@ -0,0 +1,9 @@
+Please do not distribute the grade summaries in the folder, grading-summaries-do-not-distribute!
+
+These summaries contain the answers to all questions, including the hidden tests
+run by the grader. 
+
+We have included these files so you can see what errors were made by a student
+on their notebook without having to re-run the notebook yourself.
+
+Thanks!

{otter_service_stdalone-1.0.0 → otter_service_stdalone-1.1.1}/src/otter_service_stdalone.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: otter_service_stdalone
-Version: 1.0.0
+Version: 1.1.1
 Summary: Grading Service for Instructors using Otter Grader
 Home-page: https://github.com/sean-morris/otter-service-stdalone
 Author: Sean Morris

{otter_service_stdalone-1.0.0 → otter_service_stdalone-1.1.1}/src/otter_service_stdalone.egg-info/SOURCES.txt

@@ -14,10 +14,12 @@ src/otter_service_stdalone.egg-info/SOURCES.txt
 src/otter_service_stdalone.egg-info/dependency_links.txt
 src/otter_service_stdalone.egg-info/entry_points.txt
 src/otter_service_stdalone.egg-info/top_level.txt
+src/otter_service_stdalone/scripts/web_socket.js
 src/otter_service_stdalone/secrets/gh_key.dev.yaml
 src/otter_service_stdalone/secrets/gh_key.local.yaml
 src/otter_service_stdalone/secrets/gh_key.prod.yaml
 src/otter_service_stdalone/secrets/gh_key.staging.yaml
+src/otter_service_stdalone/static_files/README_DO_NOT_DISTRIBUTE.txt
 src/otter_service_stdalone/static_templates/403.html
 src/otter_service_stdalone/static_templates/500.html
 tests/test_upload_handle.py

otter_service_stdalone-1.0.0/src/otter_service_stdalone/__init__.py

@@ -1 +0,0 @@
-__version__ = "1.0.0"

otter_service_stdalone-1.0.0/src/otter_service_stdalone/grade_notebooks.py

@@ -1,105 +0,0 @@
-import asyncio
-import async_timeout
-from otter_service_stdalone import fs_logging as log, upload_handle as uh
-import os
-
-log_debug = f'{os.environ.get("ENVIRONMENT")}-debug'
-log_count = f'{os.environ.get("ENVIRONMENT")}-count'
-log_error = f'{os.environ.get("ENVIRONMENT")}-logs'
-
-
-class GradeNotebooks():
-    """The class contains the async grade method for executing
-        otter grader as well as a function for logging the number of 
-        notebooks to be graded
-    """
-
-    def count_ipynb_files(self, directory, extension):
-        """this count the files for logging purposes"""
-        count = 0
-        for filename in os.listdir(directory):
-            if filename.endswith(extension):
-                count += 1
-        return count
-
-    async def grade(self, p, notebooks_path, results_id):
-        """Calls otter grade asynchronously and writes the various log files
-        and results of grading generating by otter-grader
-
-        Args:
-            p (str): the path to autograder.zip -- the solutions
-            notebooks_path (str): the path to the folder of notebooks to be graded
-            results_id (str): used for identifying logs
-
-        Raises:
-            Exception: Timeout Exception is raised if async takes longer than 20 min
-
-        Returns:
-            boolean: True is the process completes; otherwise an Exception is thrown
-        """
-        try:
-            notebook_folder = uh.handle_upload(notebooks_path, results_id)
-            notebook_count = self.count_ipynb_files(notebook_folder, ".ipynb")
-            log.write_logs(results_id, f"{notebook_count}",
-                           "",
-                           "info",
-                           f'{os.environ.get("ENVIRONMENT")}-count')
-            log.write_logs(results_id, "Step 5: Notebook Folder configured for grader",
-                           f"Notebook Folder: {notebook_folder}",
-                           "debug",
-                           log_debug)
-            command = [
-                'otter', 'grade',
-                '-n', 'grader',
-                '-a', p,
-                notebook_folder,
-                "--ext", "ipynb",
-                "--containers", "10",
-                "--timeout", "15",
-                "-o", notebook_folder,
-                "-v"
-            ]
-            log.write_logs(results_id, f"Step 6: Grading Start: {notebook_folder}",
-                           " ".join(command),
-                           "debug",
-                           log_debug)
-            process = await asyncio.create_subprocess_exec(
-                *command,
-                stdin=asyncio.subprocess.PIPE,
-                stdout=asyncio.subprocess.PIPE,
-                stderr=asyncio.subprocess.PIPE
-            )
-
-            # this is waiting for communication back from the process
-            # some images are quite big and take some time to build the first
-            # time through - like 20 min for otter-grader
-            async with async_timeout.timeout(2000):
-                stdout, stderr = await process.communicate()
-
-                with open(f"{notebook_folder}/grading-output.txt", "w") as f:
-                    for line in stdout.decode().splitlines():
-                        f.write(line + "\n")
-                log.write_logs(results_id, "Step 7: Grading: Finished: Write: grading-output.txt",
-                               f"{notebook_folder}/grading-output.txt",
-                               "debug",
-                               log_debug)
-                with open(f"{notebook_folder}/grading-logs.txt", "w") as f:
-                    for line in stderr.decode().splitlines():
-                        f.write(line + "\n")
-                log.write_logs(results_id, "Step 8: Grading: Finished: Write grading-logs.txt",
-                               f"{notebook_folder}/grading-logs.txt",
-                               "debug",
-                               log_debug)
-                log.write_logs(results_id, f"Step 9: Grading: Finished: {notebook_folder}",
-                               " ".join(command),
-                               "debug",
-                               log_debug)
-                log.write_logs(results_id, f"Grading: Finished: {notebook_folder}",
-                               " ".join(command),
-                               "info",
-                               log_error)
-                return True
-        except asyncio.TimeoutError:
-            raise Exception(f'Grading timed out for {notebook_folder}')
-        except Exception as e:
-            raise e