From bf800e909be20e09c932103444f6fa28a1519eab Mon Sep 17 00:00:00 2001
From: Brian Drawert <brian@drawert.net>
Date: Wed, 8 Sep 2021 08:53:31 -0700
Subject: [PATCH 01/60] launching webbrowser now has a timeout

---
 launch_webbrowser.py | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/launch_webbrowser.py b/launch_webbrowser.py
index e9f892e27b..0cf64c63a0 100755
--- a/launch_webbrowser.py
+++ b/launch_webbrowser.py
@@ -4,6 +4,9 @@
 import sys
 import time
 import webbrowser
+
+MAX_WAIT_TIME = 60
+
 try:
     import docker
 except ImportError:
@@ -25,11 +28,15 @@
 #time.sleep(10)
 print("Checking for running StochSS container: stochss-lab")
 container_started = False
+poll_start_time = time.time()
 while not container_started:
+    if (time.time() - MAX_WAIT_TIME) > poll_start_time:
+        print(f"Stopped checking for running StochSS container after {MAX_WAIT_TIME}s")
+        sys.exit(1)
     time.sleep(1)
     try:
         stochss_container=docker_client.containers.get("stochss-lab")
-        print("Generating StochSS webpage...")
+        print("Checking to see if the server is active.")
         jupyter_url_generator=stochss_container.exec_run("jupyter notebook list", demux=False)
         url_regex = r"(?i)\b((?:https?://|www\d{0,3}[.]|[a-z0-9.\-]+[.][a-z]{2,4}/)(?:[^\s()<>]+|\(([^\s()<>]+|(\([^\s()<>]+\)))*\))+(?:\(([^\s()<>]+|(\([^\s()<>]+\)))*\)|[^\s`!()\[\]{};:'\".,<>?«»“”‘’]))"
         jupyter_url_bytes = jupyter_url_generator.output

From 6f11e63795cce780d9bf415e3f9b5f0bb8f31e74 Mon Sep 17 00:00:00 2001
From: Brian Drawert <brian@drawert.net>
Date: Tue, 14 Sep 2021 12:54:12 -0700
Subject: [PATCH 02/60] adding a 1 second pause before opening the broswer

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

diff --git a/launch_webbrowser.py b/launch_webbrowser.py
index 0cf64c63a0..9524b9c75e 100755
--- a/launch_webbrowser.py
+++ b/launch_webbrowser.py
@@ -47,6 +47,7 @@
         jupyter_url=jupyter_url_sequence[0]
         jupyter_url=jupyter_url.replace('0.0.0.0','127.0.0.1')
         print(f"Opening StochSS webpage...\n")
+        time.sleep(1)
         webbrowser.open_new_tab(jupyter_url)
         print("Welcome to StochSS!\n\nYou can access your local StochSS service with this URL:\n\n")
         print(jupyter_url+"\n")

From 5bbe5d83f77a69769cf4b4dbcadf768b86109dbf Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 22 Sep 2021 13:14:37 -0400
Subject: [PATCH 03/60] Fixed issue with the notebook context menu in projects.

---
 client/project-config.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/project-config.js b/client/project-config.js
index edf1cef1b0..9c0629e0ff 100644
--- a/client/project-config.js
+++ b/client/project-config.js
@@ -151,7 +151,7 @@ let getNotebookContext = (view, node) => {
     open: open,
     publish: view.getPublishNotebookContext(node),
     download: download, rename: rename,
-    duplicate: duplicate, delete: deleteFile
+    duplicate: duplicate, moveToTrash: moveToTrash
   }
 }
 

From 8429294ffe898125d1c71b8eb20c782d43fa2318 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 22 Sep 2021 13:29:20 -0400
Subject: [PATCH 04/60] Fixed issue with the copy button for notebook
 presentations.

---
 client/views/jstree-view.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/views/jstree-view.js b/client/views/jstree-view.js
index 5bed5b9f8b..1fe55f6ab8 100644
--- a/client/views/jstree-view.js
+++ b/client/views/jstree-view.js
@@ -900,7 +900,7 @@ module.exports = View.extend({
             msg.html(reason);
             msg.css("display", "inline-block");
           }
-          app.copyToClipboard(links.presentation, onFulfilled, onReject);
+          app.copyToClipboard(body.links.presentation, onFulfilled, onReject);
         });
       },
       error: (err, response, body) => {

From 6ec07363a6300e3268ec6efbc6624ca68fa20e79 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 22 Sep 2021 13:39:20 -0400
Subject: [PATCH 05/60] Updated the version number.

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

diff --git a/__version__.py b/__version__.py
index 93d8b3f6da..06125f64be 100644
--- a/__version__.py
+++ b/__version__.py
@@ -5,7 +5,7 @@
 # @website https://github.com/stochss/stochss
 # =============================================================================
 
-__version__ = '2.4.1'
+__version__ = '2.4.2'
 __title__ = 'StochSS'
 __description__ = 'StochSS is an integrated development environment (IDE) \
                     for simulation of biochemical networks.'

From 1792dfbb383d1f2dd9337ef3e7afda0837eead5b Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 22 Sep 2021 16:00:57 -0400
Subject: [PATCH 06/60] Added the creation date for presentations to the
 presentation data and replaced the file name with the presentation name.

---
 stochss/handlers/util/stochss_folder.py | 43 +++++++++++++++++++++++--
 1 file changed, 41 insertions(+), 2 deletions(-)

diff --git a/stochss/handlers/util/stochss_folder.py b/stochss/handlers/util/stochss_folder.py
index 3c49af47e1..c7ec6f384e 100644
--- a/stochss/handlers/util/stochss_folder.py
+++ b/stochss/handlers/util/stochss_folder.py
@@ -21,6 +21,7 @@
 import shutil
 import string
 import zipfile
+import datetime
 import traceback
 
 import requests
@@ -98,6 +99,21 @@ def __build_jstree_node(self, path, file):
         return node
 
 
+    @classmethod
+    def __get_presentation_model_name(cls, file_path):
+        with open(file_path, "r") as model_file:
+            name = json.load(model_file)['name']
+        return name
+
+
+    @classmethod
+    def __get_presentation_notebook_name(cls, file_path):
+        with open(file_path, "r") as nb_file:
+            file = json.load(nb_file)['file']
+            name = cls.get_name(cls, path=file)
+        return name
+
+
     @classmethod
     def __overwrite(cls, path, ext):
         if ext == "zip":
@@ -363,10 +379,17 @@ def get_presentations(cls):
         presentations = []
         if not os.path.isdir(path):
             return presentations
+        if os.path.exists(os.path.join(path, ".presentation_names.json")):
+            with open(os.path.join(path, ".presentation_names.json"), "r") as names_file:
+                names = json.load(names_file)
+        else:
+            names = {}
+        need_names = not bool(names)
         safe_chars = set(string.ascii_letters + string.digits)
         hostname = escape(os.environ.get('JUPYTERHUB_USER'), safe=safe_chars)
         for file in os.listdir(path):
             file_path = os.path.join(path, file)
+            ctime = os.path.getctime(file_path)
             query_str = f"?owner={hostname}&file={file}"
             routes = {
                 "smdl": "present-model",
@@ -374,10 +397,26 @@ def get_presentations(cls):
                 "job": "present-job",
                 "ipynb": "present-notebook"
             }
-            route = routes[file.split('.').pop()]
+            ext = file.split('.').pop()
+            if file in names.keys():
+                name = names[file]
+            else:
+                if ext in ("mdl", "smdl"):
+                    name = cls.__get_presentation_model_name(file_path)
+                elif ext == "job":
+                    name = cls.__get_presentation_job_name(file_path)
+                elif ext == "ipynb":
+                    name = cls.__get_presentation_notebook_name(file_path)
+                names[file] = name
+            if need_names:
+                with open(os.path.join(path, ".presentation_names.json"), "w") as names_file:
+                    json.dump(names, names_file)
+            route = routes[ext]
             link = f"/stochss/{route}{query_str}"
             presentation = {
-                "file": file, "link": link, "size": os.path.getsize(file_path)
+                "file": file, "link": link, "name": name,
+                "size": os.path.getsize(file_path),
+                "ctime": datetime.datetime.fromtimestamp(ctime).strftime("%b %d, %Y")
             }
             presentations.append(presentation)
         return presentations

From 0ca9d6b1aa710d9ad6c08a7ae29b428ea2371fd0 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 22 Sep 2021 16:28:49 -0400
Subject: [PATCH 07/60] Added helper function to get the name of a job
 presentation if the presentation names file does not exist.

---
 stochss/handlers/util/stochss_folder.py | 15 +++++++++++----
 1 file changed, 11 insertions(+), 4 deletions(-)

diff --git a/stochss/handlers/util/stochss_folder.py b/stochss/handlers/util/stochss_folder.py
index c7ec6f384e..48f1e13571 100644
--- a/stochss/handlers/util/stochss_folder.py
+++ b/stochss/handlers/util/stochss_folder.py
@@ -18,6 +18,7 @@
 
 import os
 import json
+import pickle
 import shutil
 import string
 import zipfile
@@ -99,6 +100,14 @@ def __build_jstree_node(self, path, file):
         return node
 
 
+    @classmethod
+    def __get_presentation_job_name(cls, file_path):
+        with open(file_path, "rb") as job_file:
+            job = pickle.load(job_file)
+            name = job['name']
+        return name
+
+
     @classmethod
     def __get_presentation_model_name(cls, file_path):
         with open(file_path, "r") as model_file:
@@ -390,7 +399,6 @@ def get_presentations(cls):
         for file in os.listdir(path):
             file_path = os.path.join(path, file)
             ctime = os.path.getctime(file_path)
-            query_str = f"?owner={hostname}&file={file}"
             routes = {
                 "smdl": "present-model",
                 "mdl": "present-model",
@@ -411,10 +419,9 @@ def get_presentations(cls):
             if need_names:
                 with open(os.path.join(path, ".presentation_names.json"), "w") as names_file:
                     json.dump(names, names_file)
-            route = routes[ext]
-            link = f"/stochss/{route}{query_str}"
             presentation = {
-                "file": file, "link": link, "name": name,
+                "file": f"{name}.{ext}",
+                "link": f"/stochss/{routes[ext]}?owner={hostname}&file={file}",
                 "size": os.path.getsize(file_path),
                 "ctime": datetime.datetime.fromtimestamp(ctime).strftime("%b %d, %Y")
             }

From 8c23672c844cfaa00206bfc792c670206740ef54 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 22 Sep 2021 16:30:56 -0400
Subject: [PATCH 08/60] Added function to handle adding and removing names from
 the presentation names file.

---
 stochss/handlers/util/stochss_base.py | 39 +++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)

diff --git a/stochss/handlers/util/stochss_base.py b/stochss/handlers/util/stochss_base.py
index 43a5b73ea8..f8727ad40b 100644
--- a/stochss/handlers/util/stochss_base.py
+++ b/stochss/handlers/util/stochss_base.py
@@ -46,6 +46,28 @@ def __init__(self, path):
         self.logs = []
 
 
+    def add_presentation_name(self, file, name):
+        '''
+        Add a new presentation to the presentation names file.
+
+        Attributes
+        ----------
+        file : str
+            Name of the presentation file
+        name : str
+            Name of the presentation
+        '''
+        path = os.path.join(self.user_dir, ".presentations", ".presentation_names.json")
+        if os.path.exists(path):
+            with open(path, "r") as names_file:
+                names = json.load(names_file)
+        else:
+            names = {}
+        names[file] = name
+        with open(path, "w") as names_file:
+            json.dump(names, names_file)
+
+
     @classmethod
     def check_project_format(cls, path):
         '''
@@ -87,6 +109,23 @@ def check_workflow_format(cls, path):
         return True
 
 
+    def delete_presentation_name(self, file):
+        '''
+        Remove a presentation name from the presentation names file.
+
+        Attributes
+        ----------
+        file : str
+            Name of the presentation file to remove
+        '''
+        path = os.path.join(self.user_dir, ".presentations", ".presentation_names.json")
+        with open(path, "r") as names_file:
+            names = json.load(names_file)
+        del names[file]
+        with open(path, "w") as names_file:
+            json.dump(names, names_file)
+
+
     @classmethod
     def get_new_path(cls, dst_path):
         '''

From 24dbd225b5bd3e77959749cacb282001e50eddff Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 22 Sep 2021 16:39:53 -0400
Subject: [PATCH 09/60] Added function calls to add names of presentations to
 the presentation names file for new presentations.

---
 stochss/handlers/util/stochss_job.py           | 1 +
 stochss/handlers/util/stochss_model.py         | 1 +
 stochss/handlers/util/stochss_notebook.py      | 1 +
 stochss/handlers/util/stochss_spatial_model.py | 1 +
 4 files changed, 4 insertions(+)

diff --git a/stochss/handlers/util/stochss_job.py b/stochss/handlers/util/stochss_job.py
index 61663da1b4..11dd944084 100644
--- a/stochss/handlers/util/stochss_job.py
+++ b/stochss/handlers/util/stochss_job.py
@@ -746,6 +746,7 @@ def publish_presentation(self, name=None):
             else:
                 exists = False
                 name = self.get_file() if name is None else name
+                self.add_presentation_name(file, name)
                 path = os.path.join(self.__get_results_path(), "results.p")
                 with open(path, "rb") as results_file:
                     results = pickle.load(results_file)
diff --git a/stochss/handlers/util/stochss_model.py b/stochss/handlers/util/stochss_model.py
index 3bfe947995..48c196916b 100644
--- a/stochss/handlers/util/stochss_model.py
+++ b/stochss/handlers/util/stochss_model.py
@@ -485,6 +485,7 @@ def publish_presentation(self):
             if os.path.exists(dst):
                 data = None
             else:
+                self.add_presentation_name(file, self.model['name'])
                 data = {"path": dst, "new":True, "model":self.model}
             query_str = f"?owner={hostname}&file={file}"
             present_link = f"/stochss/present-model{query_str}"
diff --git a/stochss/handlers/util/stochss_notebook.py b/stochss/handlers/util/stochss_notebook.py
index bc0731e057..fffdead4bd 100644
--- a/stochss/handlers/util/stochss_notebook.py
+++ b/stochss/handlers/util/stochss_notebook.py
@@ -604,6 +604,7 @@ def publish_presentation(self):
             if os.path.exists(dst):
                 exists = True
             else:
+                self.add_presentation_name(file, self.get_name())
                 exists = False
                 with open(dst, "w") as presentation_file:
                     json.dump(notebook_pres, presentation_file)
diff --git a/stochss/handlers/util/stochss_spatial_model.py b/stochss/handlers/util/stochss_spatial_model.py
index 6e2ea225f9..75422c62c3 100644
--- a/stochss/handlers/util/stochss_spatial_model.py
+++ b/stochss/handlers/util/stochss_spatial_model.py
@@ -615,6 +615,7 @@ def publish_presentation(self):
             if os.path.exists(dst):
                 data = None
             else:
+                self.add_presentation_name(file, self.model['name'])
                 data = {"path": dst, "new":True, "model":self.model}
             query_str = f"?owner={hostname}&file={file}"
             present_link = f"/stochss/present-model{query_str}"

From 49bc850d0a86d682dd8efc1e7dabccd2ef37e736 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 22 Sep 2021 16:46:51 -0400
Subject: [PATCH 10/60] Added function call to remove a presentation name from
 the presentation names file when a presentation is deleted.

---
 stochss/handlers/util/stochss_file.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/stochss/handlers/util/stochss_file.py b/stochss/handlers/util/stochss_file.py
index 2c621494fc..2e7cb3f815 100644
--- a/stochss/handlers/util/stochss_file.py
+++ b/stochss/handlers/util/stochss_file.py
@@ -60,6 +60,8 @@ def delete(self):
         '''
         path = self.get_path(full=True)
         try:
+            if ".presentations" in path:
+                self.delete_presentation_name(self.get_file())
             os.remove(path)
             return "The file {0} was successfully deleted.".format(self.get_file())
         except FileNotFoundError as err:

From 451e3d29ea68ebb7eeb84bc433bc6dfa5c8150d2 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 22 Sep 2021 17:07:52 -0400
Subject: [PATCH 11/60] Fixed bugs.

---
 stochss/handlers/util/stochss_folder.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/stochss/handlers/util/stochss_folder.py b/stochss/handlers/util/stochss_folder.py
index 48f1e13571..391e9e37c9 100644
--- a/stochss/handlers/util/stochss_folder.py
+++ b/stochss/handlers/util/stochss_folder.py
@@ -396,7 +396,7 @@ def get_presentations(cls):
         need_names = not bool(names)
         safe_chars = set(string.ascii_letters + string.digits)
         hostname = escape(os.environ.get('JUPYTERHUB_USER'), safe=safe_chars)
-        for file in os.listdir(path):
+        for file in [file for file in os.listdir(path) if not file.startswith('.')]:
             file_path = os.path.join(path, file)
             ctime = os.path.getctime(file_path)
             routes = {
@@ -416,16 +416,16 @@ def get_presentations(cls):
                 elif ext == "ipynb":
                     name = cls.__get_presentation_notebook_name(file_path)
                 names[file] = name
-            if need_names:
-                with open(os.path.join(path, ".presentation_names.json"), "w") as names_file:
-                    json.dump(names, names_file)
             presentation = {
-                "file": f"{name}.{ext}",
+                "file": file, "name": f"{name}.{ext}",
                 "link": f"/stochss/{routes[ext]}?owner={hostname}&file={file}",
                 "size": os.path.getsize(file_path),
                 "ctime": datetime.datetime.fromtimestamp(ctime).strftime("%b %d, %Y")
             }
             presentations.append(presentation)
+        if need_names:
+            with open(os.path.join(path, ".presentation_names.json"), "w") as names_file:
+                json.dump(names, names_file)
         return presentations
 
 

From 02de6ed4ee63a5a3fdeac131151d0c99e0e74164 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Fri, 24 Sep 2021 13:51:36 -0400
Subject: [PATCH 12/60] Added the creation time and name properties to the
 presentations model.

---
 client/models/presentation.js | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/client/models/presentation.js b/client/models/presentation.js
index 17a07f2295..3e027ade20 100644
--- a/client/models/presentation.js
+++ b/client/models/presentation.js
@@ -20,8 +20,10 @@ let State = require('ampersand-state');
 
 module.exports = State.extend({
   session: {
+    ctime: 'string',
     file: 'string',
     link: 'string',
+    name: 'string',
     size: 'number',
     tag: 'string'
   },

From 585a5bb62dd152bbe2a7be58f52f6f5e4de00e12 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Fri, 24 Sep 2021 14:51:02 -0400
Subject: [PATCH 13/60] Changed the file name for presentations to the
 presentation name.  Added the creation date to the presentations listing.

---
 client/templates/includes/presentationView.pug | 8 ++++++--
 client/templates/pages/browser.pug             | 4 +++-
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/client/templates/includes/presentationView.pug b/client/templates/includes/presentationView.pug
index 113ec43540..9b14ffa957 100644
--- a/client/templates/includes/presentationView.pug
+++ b/client/templates/includes/presentationView.pug
@@ -5,14 +5,18 @@ div.mx-1
 
   div.row
 
-    div.col-sm-6
+    div.col-sm-4
 
-      a.pl-2(href=this.model.link)=this.model.file
+      a.pl-2(href=this.model.link)=this.model.name
 
     div.col-sm-2
 
       button.btn.btn-outline-secondary.box-shadow(data-hook="copy-link") Copy Link
 
+    div.col-sm-2
+
+      div=this.model.ctime
+
     div.col-sm-2
 
       div=this.model.size + " " + this.model.tag
diff --git a/client/templates/pages/browser.pug b/client/templates/pages/browser.pug
index a634614fe5..a0b9dc16eb 100644
--- a/client/templates/pages/browser.pug
+++ b/client/templates/pages/browser.pug
@@ -36,7 +36,9 @@ section.page
 
         div.mx-1.row.head.align-items-baseline
 
-          div.col-sm-8: h6 <b>File</b>
+          div.col-sm-6: h6 <b>File</b>
+
+          div.col-sm-2: h6 <b>Date</b>
 
           div.col-sm-2: h6 <b>Size</b>
 

From bd826076d88e3db4ab8c5e7c0c5354394b270e5f Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Mon, 27 Sep 2021 14:32:52 -0400
Subject: [PATCH 14/60] Added tests for new functions.

---
 stochss/tests/test_stochss_base.py | 37 ++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

diff --git a/stochss/tests/test_stochss_base.py b/stochss/tests/test_stochss_base.py
index 11e2f1f920..89cbc2e068 100644
--- a/stochss/tests/test_stochss_base.py
+++ b/stochss/tests/test_stochss_base.py
@@ -59,6 +59,30 @@ def tearDown(self):
         if StochSSBase.user_dir != os.path.expanduser("~"):
             StochSSBase.user_dir = os.path.expanduser("~")
 
+    ################################################################################################
+    # Unit tests for the StochSS base class add_presentation_name function.
+    ################################################################################################
+
+    def test_add_presentation_name__file_exists(self):
+        ''' Check if the presentation name is add to the presentation names file. '''
+        StochSSBase.user_dir = self.tempdir.name
+        test_base = StochSSBase(path="")
+        with mock.patch("os.path.exists", return_value=True):
+            with mock.patch("builtins.open", mock.mock_open(read_data="{}")):
+                with mock.patch("json.dump") as mock_json_dump:
+                    test_base.add_presentation_name("foo", "bar")
+                    mock_json_dump.assert_called_once_with({'foo': 'bar'}, mock.ANY)
+
+
+    def test_add_presentation_name__file_does_not_exists(self):
+        ''' Check if the presentation names file was created with the given entry. '''
+        StochSSBase.user_dir = self.tempdir.name
+        test_base = StochSSBase(path="")
+        with mock.patch("builtins.open", mock.mock_open()):
+            with mock.patch("json.dump") as mock_json_dump:
+                test_base.add_presentation_name("foo", "bar")
+                mock_json_dump.assert_called_once_with({'foo': 'bar'}, mock.ANY)
+
     ################################################################################################
     # Unit tests for the StochSS base class check_project_format function.
     ################################################################################################
@@ -130,6 +154,19 @@ def test_check_workflow_format__new(self):
         ''' Check if the workflow is identified as old. '''
         self.assertTrue(StochSSBase.check_workflow_format(path=self.test_folderpath))
 
+    ################################################################################################
+    # Unit tests for the StochSS base class delete_presentation_name function.
+    ################################################################################################
+
+    def test_delete_presentation_name(self):
+        ''' Check if the target presentation was removed from the presentation names file. '''
+        StochSSBase.user_dir = self.tempdir.name
+        test_base = StochSSBase(path="")
+        with mock.patch("builtins.open", mock.mock_open(read_data='{"foo": "bar"}')):
+            with mock.patch("json.dump") as mock_json_dump:
+                test_base.delete_presentation_name("foo")
+                mock_json_dump.assert_called_once_with({}, mock.ANY)
+
     ################################################################################################
     # Unit tests for the StochSS base class get_new_path function.
     ################################################################################################

From 364a6d0b5e9155e5edbcd76049035642cffc2c24 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Mon, 27 Sep 2021 15:18:26 -0400
Subject: [PATCH 15/60] Added checks to ensure the names file remains in sync
 with the presentations.

---
 stochss/handlers/util/stochss_folder.py | 52 ++++++++++++++++---------
 1 file changed, 33 insertions(+), 19 deletions(-)

diff --git a/stochss/handlers/util/stochss_folder.py b/stochss/handlers/util/stochss_folder.py
index 391e9e37c9..fc3329f0c0 100644
--- a/stochss/handlers/util/stochss_folder.py
+++ b/stochss/handlers/util/stochss_folder.py
@@ -115,6 +115,33 @@ def __get_presentation_model_name(cls, file_path):
         return name
 
 
+    @classmethod
+    def __get_presentation_name(cls, names, file, file_path):
+        ext = file.split('.').pop()
+        if file in names.keys():
+            name = names[file]
+        else:
+            if ext in ("mdl", "smdl"):
+                name = cls.__get_presentation_model_name(file_path)
+            elif ext == "job":
+                name = cls.__get_presentation_job_name(file_path)
+            elif ext == "ipynb":
+                name = cls.__get_presentation_notebook_name(file_path)
+            names[file] = name
+        return name, ext
+
+
+    @classmethod
+    def __get_names_from_file(cls, path, files):
+        if not os.path.exists(os.path.join(path, ".presentation_names.json")):
+            return {}
+        with open(os.path.join(path, ".presentation_names.json"), "r") as names_file:
+            names = json.load(names_file)
+        if len(names.keys()) != len(files):
+            return {}
+        return names
+
+
     @classmethod
     def __get_presentation_notebook_name(cls, file_path):
         with open(file_path, "r") as nb_file:
@@ -385,18 +412,15 @@ def get_presentations(cls):
         ----------
         '''
         path = os.path.join(cls.user_dir, ".presentations")
+        files = [file for file in os.listdir(path) if not file.startswith('.')]
         presentations = []
-        if not os.path.isdir(path):
+        if not files:
             return presentations
-        if os.path.exists(os.path.join(path, ".presentation_names.json")):
-            with open(os.path.join(path, ".presentation_names.json"), "r") as names_file:
-                names = json.load(names_file)
-        else:
-            names = {}
+        names = cls.__get_names_from_file(path, files)
         need_names = not bool(names)
         safe_chars = set(string.ascii_letters + string.digits)
         hostname = escape(os.environ.get('JUPYTERHUB_USER'), safe=safe_chars)
-        for file in [file for file in os.listdir(path) if not file.startswith('.')]:
+        for file in files:
             file_path = os.path.join(path, file)
             ctime = os.path.getctime(file_path)
             routes = {
@@ -405,17 +429,7 @@ def get_presentations(cls):
                 "job": "present-job",
                 "ipynb": "present-notebook"
             }
-            ext = file.split('.').pop()
-            if file in names.keys():
-                name = names[file]
-            else:
-                if ext in ("mdl", "smdl"):
-                    name = cls.__get_presentation_model_name(file_path)
-                elif ext == "job":
-                    name = cls.__get_presentation_job_name(file_path)
-                elif ext == "ipynb":
-                    name = cls.__get_presentation_notebook_name(file_path)
-                names[file] = name
+            name, ext = cls.__get_presentation_name(names, file, file_path)
             presentation = {
                 "file": file, "name": f"{name}.{ext}",
                 "link": f"/stochss/{routes[ext]}?owner={hostname}&file={file}",
@@ -423,7 +437,7 @@ def get_presentations(cls):
                 "ctime": datetime.datetime.fromtimestamp(ctime).strftime("%b %d, %Y")
             }
             presentations.append(presentation)
-        if need_names:
+        if need_names or len(names.keys()) != len(files):
             with open(os.path.join(path, ".presentation_names.json"), "w") as names_file:
                 json.dump(names, names_file)
         return presentations

From 53d64a40d2a681c1ba46a4a1f96dbd4ccedec0dd Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Mon, 27 Sep 2021 15:39:46 -0400
Subject: [PATCH 16/60] Updated the gillespy2 version.

---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index a5b7759e21..d58cc96aff 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -2,7 +2,7 @@ python-libsbml==5.18.0
 python-libsedml==2.0.9
 python-libcombine==0.2.7
 escapism==1.0.1
-gillespy2==1.6.3
+gillespy2==1.6.4
 sciope==0.4
 pygmsh==5.0.2
 meshio==2.3.10

From 870d0ded32bbb314853d80aff91f23a7fb32ea4f Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 29 Sep 2021 09:51:32 -0400
Subject: [PATCH 17/60] Added live graphing to preview.

---
 stochss/handlers/util/ensemble_simulation.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/stochss/handlers/util/ensemble_simulation.py b/stochss/handlers/util/ensemble_simulation.py
index 949fe70b36..d07a754d19 100644
--- a/stochss/handlers/util/ensemble_simulation.py
+++ b/stochss/handlers/util/ensemble_simulation.py
@@ -104,7 +104,8 @@ def run(self, preview=False, verbose=True):
         if preview:
             if verbose:
                 log.info(f"Running {self.g_model.name} preview simulation")
-            results = self.g_model.run(timeout=5)
+            options = {"file_path": f".{self.g_model.name}-preview.json"}
+            results = self.g_model.run(timeout=5, live_output="graph", live_output_options=options)
             if verbose:
                 log.info(f"{self.g_model.name} preview simulation has completed")
                 log.info(f"Generate result plot for {self.g_model.name} preview")

From 7206de19fda26e92c252495eacddc96fd5210885 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 29 Sep 2021 10:15:58 -0400
Subject: [PATCH 18/60] Added function to get the live output figure from the
 file.

---
 stochss/handlers/util/stochss_model.py | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/stochss/handlers/util/stochss_model.py b/stochss/handlers/util/stochss_model.py
index 3bfe947995..00f632303e 100644
--- a/stochss/handlers/util/stochss_model.py
+++ b/stochss/handlers/util/stochss_model.py
@@ -406,6 +406,25 @@ def convert_to_spatial(self):
         return {"Message":message, "File":s_file}, {"spatial":model, "path":s_path}
 
 
+    def get_live_results(self):
+        '''
+        Get the live output figure for the preview.
+
+        Attributes
+        ----------
+        '''
+        file_name = f".{self.get_name()}-preview.json"
+        if not os.path.exists(file_name):
+            return ""
+        with open(file_name, "r") as live_fig:
+            fig = json.load(live_fig)
+            fig["config"] = {
+                "displayModeBar": True,
+                "responsive": True
+            }
+        return {"results": fig, "timeout":False}
+
+
     def get_notebook_data(self):
         '''
         Get the needed data for converting to notebook

From 777ca1e76778245fef2b76c279e16401cc094557 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 29 Sep 2021 10:17:01 -0400
Subject: [PATCH 19/60] Added live output figure to the run model api handler
 response.

---
 stochss/handlers/models.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/stochss/handlers/models.py b/stochss/handlers/models.py
index 5c4152c8f7..b0cab6d728 100644
--- a/stochss/handlers/models.py
+++ b/stochss/handlers/models.py
@@ -229,6 +229,7 @@ async def get(self):
             log.debug(f"Results for the model preview: {results}")
             if results is None:
                 resp['Running'] = True
+                resp['Results'] = model.get_live_results()
                 log.info("The preview is still running")
             else:
                 resp['Results'] = results

From 72a60b79aef671fd09b2c4ec9384fdc47b61f123 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 29 Sep 2021 10:32:10 -0400
Subject: [PATCH 20/60] Added block to render the live output figure.

---
 client/pages/model-editor.js | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/client/pages/model-editor.js b/client/pages/model-editor.js
index 850b8a9946..fcb2e630a9 100644
--- a/client/pages/model-editor.js
+++ b/client/pages/model-editor.js
@@ -197,11 +197,16 @@ let ModelEditor = PageView.extend({
             errorCB(err, response, body);
           }
           else if(!body.Running){
+            Plotly.purge(this.queryByHook('preview-plot-container'));
             if(body.Results.timeout){
               $(this.queryByHook('model-timeout-message')).collapse('show');
             }
             this.plotResults(body.Results.results);
           }else{
+            if(body.Results) {
+              Plotly.purge(this.queryByHook('preview-plot-container'));
+              this.plotResults(body.Results.results);
+            }
             this.getResults();
           }
         },

From d82363ae4cfdbc5e84b4c548b0c7a695399c2d43 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 29 Sep 2021 10:34:25 -0400
Subject: [PATCH 21/60] Added line to cleanup the live figure file.

---
 stochss/handlers/util/ensemble_simulation.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/stochss/handlers/util/ensemble_simulation.py b/stochss/handlers/util/ensemble_simulation.py
index d07a754d19..72ead6f0be 100644
--- a/stochss/handlers/util/ensemble_simulation.py
+++ b/stochss/handlers/util/ensemble_simulation.py
@@ -106,6 +106,7 @@ def run(self, preview=False, verbose=True):
                 log.info(f"Running {self.g_model.name} preview simulation")
             options = {"file_path": f".{self.g_model.name}-preview.json"}
             results = self.g_model.run(timeout=5, live_output="graph", live_output_options=options)
+            os.remove(f".{self.g_model.name}-preview.json")
             if verbose:
                 log.info(f"{self.g_model.name} preview simulation has completed")
                 log.info(f"Generate result plot for {self.g_model.name} preview")

From d29c4be390712ccf1dc2381999d0472e2f79a687 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 29 Sep 2021 10:36:42 -0400
Subject: [PATCH 22/60] Added race condition catch.

---
 stochss/handlers/util/stochss_model.py | 17 ++++++++++-------
 1 file changed, 10 insertions(+), 7 deletions(-)

diff --git a/stochss/handlers/util/stochss_model.py b/stochss/handlers/util/stochss_model.py
index 00f632303e..2194f7a83f 100644
--- a/stochss/handlers/util/stochss_model.py
+++ b/stochss/handlers/util/stochss_model.py
@@ -416,13 +416,16 @@ def get_live_results(self):
         file_name = f".{self.get_name()}-preview.json"
         if not os.path.exists(file_name):
             return ""
-        with open(file_name, "r") as live_fig:
-            fig = json.load(live_fig)
-            fig["config"] = {
-                "displayModeBar": True,
-                "responsive": True
-            }
-        return {"results": fig, "timeout":False}
+        try:
+            with open(file_name, "r") as live_fig:
+                fig = json.load(live_fig)
+                fig["config"] = {
+                    "displayModeBar": True,
+                    "responsive": True
+                }
+            return {"results": fig, "timeout":False}
+        except json.decoder.JSONDecodeError:
+            return ""
 
 
     def get_notebook_data(self):

From 7b5e635a2b831cc66a24db902173ac98c580d90f Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 29 Sep 2021 10:54:31 -0400
Subject: [PATCH 23/60] Updated the interval at which stochss checks for
 preview results.

---
 client/pages/model-editor.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/pages/model-editor.js b/client/pages/model-editor.js
index fcb2e630a9..78a13d5d68 100644
--- a/client/pages/model-editor.js
+++ b/client/pages/model-editor.js
@@ -212,7 +212,7 @@ let ModelEditor = PageView.extend({
         },
         error: errorCB
       });
-    }, 2000);
+    }, 1000);
   },
   handlePresentationClick: function (e) {
     let errorMsg = $(this.queryByHook("error-detected-msg"));

From 56342b47a49603a0111f3cedaec36e1c866f7e5b Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Mon, 4 Oct 2021 12:13:00 -0400
Subject: [PATCH 24/60] Refactored the checkout for the live output file to
 happen as part of the try catch block.

---
 stochss/handlers/util/stochss_model.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/stochss/handlers/util/stochss_model.py b/stochss/handlers/util/stochss_model.py
index 2194f7a83f..65bbeb76ad 100644
--- a/stochss/handlers/util/stochss_model.py
+++ b/stochss/handlers/util/stochss_model.py
@@ -414,8 +414,6 @@ def get_live_results(self):
         ----------
         '''
         file_name = f".{self.get_name()}-preview.json"
-        if not os.path.exists(file_name):
-            return ""
         try:
             with open(file_name, "r") as live_fig:
                 fig = json.load(live_fig)
@@ -424,6 +422,8 @@ def get_live_results(self):
                     "responsive": True
                 }
             return {"results": fig, "timeout":False}
+        except FileNotFoundError:
+            return ""
         except json.decoder.JSONDecodeError:
             return ""
 

From 45fe541425b39c37531a304fb2e5046b89a79ecf Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Mon, 4 Oct 2021 12:40:21 -0400
Subject: [PATCH 25/60] Refactored the preview block to cleanup the live output
 file prior to running a new preview.

---
 stochss/handlers/util/ensemble_simulation.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/stochss/handlers/util/ensemble_simulation.py b/stochss/handlers/util/ensemble_simulation.py
index 72ead6f0be..3958da422e 100644
--- a/stochss/handlers/util/ensemble_simulation.py
+++ b/stochss/handlers/util/ensemble_simulation.py
@@ -104,9 +104,11 @@ def run(self, preview=False, verbose=True):
         if preview:
             if verbose:
                 log.info(f"Running {self.g_model.name} preview simulation")
-            options = {"file_path": f".{self.g_model.name}-preview.json"}
+            live_file = f".{self.g_model.name}-preview.json"
+            if os.path.exists(live_file):
+                os.remove(live_file)
+            options = {"file_path": live_file}
             results = self.g_model.run(timeout=5, live_output="graph", live_output_options=options)
-            os.remove(f".{self.g_model.name}-preview.json")
             if verbose:
                 log.info(f"{self.g_model.name} preview simulation has completed")
                 log.info(f"Generate result plot for {self.g_model.name} preview")

From ed6833edf0dfc4803db0558f95d20487eb4264bd Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Mon, 25 Oct 2021 12:47:05 -0400
Subject: [PATCH 26/60] Spaces are now removed when generating the class name
 for models.

---
 stochss/handlers/util/stochss_notebook.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/stochss/handlers/util/stochss_notebook.py b/stochss/handlers/util/stochss_notebook.py
index bc0731e057..214ef3a551 100644
--- a/stochss/handlers/util/stochss_notebook.py
+++ b/stochss/handlers/util/stochss_notebook.py
@@ -564,7 +564,7 @@ def get_class_name(self):
             return f"M{name}"
         if l_char in string.ascii_lowercase:
             return name.replace(l_char, l_char.upper(), 1)
-        return name
+        return name.replace(" ", "")
 
 
     def get_gillespy2_solver_name(self):

From d1d2b82846e4ce6a2ed9219daa02caa36e8f7f78 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Mon, 25 Oct 2021 13:17:15 -0400
Subject: [PATCH 27/60] Fixed issue with upload file call in project manager,

---
 client/pages/project-manager.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/pages/project-manager.js b/client/pages/project-manager.js
index ccae2200b1..80f26819b1 100644
--- a/client/pages/project-manager.js
+++ b/client/pages/project-manager.js
@@ -314,7 +314,7 @@ let ProjectManager = PageView.extend({
     }
   },
   handleUploadModelClick: function (e) {
-    this.projectFileBrowser.uploadFile(undefined, "model")
+    this.projectFileBrowser.uploadFile(null, this.model.directory, "model", true)
   },
   renderArchiveCollection: function () {
     if(this.archiveCollectionView) {

From 838562070de149d42fe30f9fb36bc9bef5544809 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Tue, 26 Oct 2021 10:38:29 -0400
Subject: [PATCH 28/60] Fixed issue with projects add existing model option.

---
 client/pages/project-manager.js | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/client/pages/project-manager.js b/client/pages/project-manager.js
index ccae2200b1..cffd25f7b4 100644
--- a/client/pages/project-manager.js
+++ b/client/pages/project-manager.js
@@ -92,8 +92,8 @@ let ProjectManager = PageView.extend({
       always: function (err, response, body) {
         let modal = $(modals.importModelHtml(body.files)).modal();
         let okBtn = document.querySelector('#importModelModal .ok-model-btn');
-        let select = document.querySelector('#importModelModal #modelFileInput');
-        let location = document.querySelector('#importModelModal #modelPathInput');
+        let select = document.querySelector('#importModelModal #modelFileSelect');
+        let location = document.querySelector('#importModelModal #modelPathSelect');
         select.addEventListener("change", function (e) {
           okBtn.disabled = e.target.value && body.paths[e.target.value].length >= 2;
           if(body.paths[e.target.value].length >= 2) {

From 0d6f1b00dd079f42907b0495ee2e42311a1ceb96 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Tue, 26 Oct 2021 11:07:58 -0400
Subject: [PATCH 29/60] Refactored the exclusion test to exclude model
 presentations form the add existing model drop down.

---
 stochss/handlers/project.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/stochss/handlers/project.py b/stochss/handlers/project.py
index db3d3d44e0..ccb04bb69f 100644
--- a/stochss/handlers/project.py
+++ b/stochss/handlers/project.py
@@ -171,7 +171,8 @@ def get(self):
             folder = StochSSFolder(path="")
             # file will be excluded if test passes
             test = lambda ext, root, file: bool(".wkfl" in root or f"{path}" in root or \
-                                                "trash" in root.split("/"))
+                                                "trash" in root.split("/") or \
+                                                ".presentations" in root)
             data = folder.get_file_list(ext=[".mdl", ".smdl"], test=test)
             log.debug(f"List of models: {data}")
             self.write(data)

From 4847dd7277747bc7e33a4552de304f52b1e9f5e6 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Tue, 26 Oct 2021 11:26:20 -0400
Subject: [PATCH 30/60] Added button to allow users to be able to clear their
 user logs.

---
 client/templates/body.pug | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/client/templates/body.pug b/client/templates/body.pug
index 7cab6d1365..a2ab6c0467 100644
--- a/client/templates/body.pug
+++ b/client/templates/body.pug
@@ -64,6 +64,8 @@ body
 
                 button.my-0.btn.btn-outline-collapse.inline(data-hook="user-logs-collapse") +
 
+                button.my-0.btn.btn-light.inline(data-hook="clear-user-logs" style="float: right;") clear
+
               div.pl-1.overflow-auto(id="user-logs")
 
       main.col-sm-12.col-md-10.col-xl-9.col-xxl-6.body(role="main" data-hook="page-main")

From ddb8265cf5442fd36bdc4d213cf85d1558a6aedd Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Tue, 26 Oct 2021 11:27:14 -0400
Subject: [PATCH 31/60] Added event listener to fire the clear logs function
 when clicked.

---
 client/views/main.js | 68 ++++----------------------------------------
 1 file changed, 5 insertions(+), 63 deletions(-)

diff --git a/client/views/main.js b/client/views/main.js
index c77d0ce9ce..d907c8d1a2 100644
--- a/client/views/main.js
+++ b/client/views/main.js
@@ -38,67 +38,6 @@ String.prototype.toHtmlEntities = function() {
   });
 };
 
-let operationInfoModalHtml = (infoKey) => {
-  let fileBrowserInfo = `
-    <p>In StochSS we use custom file extensions for a number of files we work with.  Here is a list of our extentions with the files they are associated with:</p>
-    <table style="margin-left: 2em;">
-      <tr>
-        <td width=200> StochSS Model </td>
-        <td> .mdl </td>
-      </tr>
-      <tr>
-        <td width=200> StochSS Spatial Model </td>
-        <td> .smdl </td>
-      </tr>
-      <tr>
-        <td width=200> SBML Model </td>
-        <td> .sbml </td>
-      </tr>
-      <tr>
-        <td width=200> Workflows </td>
-        <td> .wkfl </td>
-      </tr>
-    </table>
-    <br>
-    <p>Other useful file extensions include the following:</p>
-    <table style="margin-left: 2em;">
-      <tr>
-        <td width=200> Jupyter Notebook </td>
-        <td> .ipynb </td>
-      </tr>
-    </table>
-  `;
-  let modelInfo = `
-    Model Information
-  `;
-  let workflowInfo = `
-    Workflow Information
-  `;
-
-  let infoList = {"File Browser":fileBrowserInfo, "Models":modelInfo, "Workflows":workflowInfo}
-  
-  return `
-    <div id="operationInfoModal" class="modal" tabindex="-1" role="dialog">
-      <div class="modal-dialog" role="document">
-        <div class="modal-content info">
-          <div class="modal-header">
-            <h5 class="modal-title"> Working with ${infoKey} </h5>
-            <button type="button" class="close" data-dismiss="modal" aria-label="Close">
-              <span aria-hidden="true">&times;</span>
-            </button>
-          </div>
-          <div class="modal-body">
-            <p> ${infoList[infoKey]} </p>
-          </div>
-          <div class="modal-footer">
-            <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
-          </div>
-        </div>
-      </div>
-    </div>
-  ` 
-}
-
 module.exports = View.extend({
   template: bodyTemplate,
   autoRender: true,
@@ -109,8 +48,8 @@ module.exports = View.extend({
   },
   events: {
     'click [data-hook=registration-link-button]' : 'handleRegistrationLinkClick',
-    'click [data-hook=user-logs-collapse]' : 'collapseExpandLogs'
-    //'click a[href]': 'handleLinkClick'
+    'click [data-hook=user-logs-collapse]' : 'collapseExpandLogs',
+    'click [data-hook=clear-user-logs]' : 'clearUserLogs'
   },
   render: function () {
 
@@ -172,6 +111,9 @@ module.exports = View.extend({
     });
     this.addNewLogBlock();
   },
+  clearUserLogs: function (e) {
+    console.log("Clearing the user logs");
+  },
   collapseExpandLogs: function (e) {
     let logs = $("#user-logs");
     let classes = logs.attr("class").split(/\s+/);

From b53b01794248e739d1d62723543f74ad5a104ff5 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Tue, 26 Oct 2021 11:37:46 -0400
Subject: [PATCH 32/60] Added an api handler and route to clear user logs.

---
 stochss/handlers/__init__.py |  1 +
 stochss/handlers/pages.py    | 18 ++++++++++++++++++
 2 files changed, 19 insertions(+)

diff --git a/stochss/handlers/__init__.py b/stochss/handlers/__init__.py
index 30adcddd42..512ece0016 100644
--- a/stochss/handlers/__init__.py
+++ b/stochss/handlers/__init__.py
@@ -53,6 +53,7 @@ def get_page_handlers(route_start):
         ## API Handlers
         #
         (r'/stochss/api/user-logs\/?', UserLogsAPIHandler),
+        (r'/stochss/api/clear-user-logs\/?', ClearUserLogsAPIHandler),
         (r"/stochss/api/file/browser-list\/?", ModelBrowserFileList),
         (r"/stochss/api/file/upload\/?", UploadFileAPIHandler),
         (r"/stochss/api/file/upload-from-link\/?", UploadFileFromLinkAPIHandler),
diff --git a/stochss/handlers/pages.py b/stochss/handlers/pages.py
index 7ca148a5c0..fc1c5d660b 100644
--- a/stochss/handlers/pages.py
+++ b/stochss/handlers/pages.py
@@ -274,3 +274,21 @@ async def get(self):
             logs = []
         self.write({"logs":logs})
         self.finish()
+
+
+class ClearUserLogsAPIHandler(APIHandler):
+    '''
+    ################################################################################################
+    Handler for clearing the user logs
+    ################################################################################################
+    '''
+    @web.authenticated
+    async def get(self):
+        '''
+        Clear contents of the user log file.
+
+        Attributes
+        ----------
+        '''
+        open(os.path.join(os.path.expanduser("~"), ".user-logs.txt"), "w").close()
+        self.finish()

From a8523ae656d7266d59e3761a9fec165857717e94 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Tue, 26 Oct 2021 11:56:41 -0400
Subject: [PATCH 33/60] Added an xhr request to link client and server
 functions.

---
 client/views/main.js | 35 ++++++++++++++++++++++-------------
 1 file changed, 22 insertions(+), 13 deletions(-)

diff --git a/client/views/main.js b/client/views/main.js
index d907c8d1a2..22a5f4a9cd 100644
--- a/client/views/main.js
+++ b/client/views/main.js
@@ -71,18 +71,7 @@ module.exports = View.extend({
     if(app.getBasePath() === "/") {
       $("#presentation-nav-link").css("display", "none");
     }
-    let self = this;
-    let message = app.getBasePath() === "/" ? "Welcome to StochSS!" : "Welcome to StochSS Live!";
-    $("#user-logs").html(message)
-    this.logBlock = [];
-    this.logs = [];
-    this.getUserLogs();
-    this.scrolled = false;
-    this.scrollCount = 0;
-    $("#user-logs").on("mousewheel", function(e) {
-      self.scrolled = true;
-      self.scrollCount = 0;
-    });
+    this.setupUserLogs();
     return this;
   },
   addNewLogBlock: function () {
@@ -112,7 +101,12 @@ module.exports = View.extend({
     this.addNewLogBlock();
   },
   clearUserLogs: function (e) {
-    console.log("Clearing the user logs");
+    let endpoint = path.join(app.getApiPath(), "clear-user-logs");
+    app.getXHR(endpoint, {
+      success: (err, response, body) => {
+        this.setupUserLogs({getLogs: false});
+      }
+    });
   },
   collapseExpandLogs: function (e) {
     let logs = $("#user-logs");
@@ -191,6 +185,21 @@ module.exports = View.extend({
   navigate: function (page) {
     window.location = url;
   },
+  setupUserLogs: function ({getLogs = true}={}) {
+    let message = app.getBasePath() === "/" ? "Welcome to StochSS!" : "Welcome to StochSS Live!";
+    $("#user-logs").html(message)
+    this.logBlock = [];
+    this.logs = [];
+    this.scrolled = false;
+    this.scrollCount = 0;
+    if(getLogs) {
+      this.getUserLogs();
+      $("#user-logs").on("mousewheel", (e) => {
+        this.scrolled = true;
+        this.scrollCount = 0;
+      });
+    }
+  },
   updateUserLogs: function () {
     setTimeout(_.bind(this.getUserLogs, this), 1000);
   }

From bf371baf6651fcecc80710a5e1fb3c7ad067dfc8 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Tue, 26 Oct 2021 13:20:10 -0400
Subject: [PATCH 34/60] Fixed issue with tokens in file names.  Files issue
 with 404 errors being written as file bodies.

---
 stochss/handlers/util/stochss_folder.py | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/stochss/handlers/util/stochss_folder.py b/stochss/handlers/util/stochss_folder.py
index fc3329f0c0..1e21d5afd6 100644
--- a/stochss/handlers/util/stochss_folder.py
+++ b/stochss/handlers/util/stochss_folder.py
@@ -539,6 +539,13 @@ def upload_from_link(self, remote_path, overwrite=False):
                 body = json.dumps(json.loads(body)['notebook'])
         else:
             file = self.get_file(path=remote_path)
+        if "404: Not Found" in body.decode():
+            message = f"Could not upload this file as {file} was not found."
+            if "?token=" in file:
+                message += "  The token for this file may be out of date."
+            return {"message": message, "reason":"File Not Found"}
+        if "?token=" in file:
+            file = file.split("?token=")[0]
         path = self.get_new_path(dst_path=file)
         if os.path.exists(path):
             if not overwrite:
@@ -575,6 +582,8 @@ def validate_upload_link(self, remote_path):
                 body = json.dumps(json.loads(body)['notebook'])
         else:
             file = self.get_file(path=remote_path)
+        if "?token=" in file:
+            file = file.split("?token=")[0]
         path = self.get_new_path(dst_path=file)
         if ext == "zip":
             with zipfile.ZipFile(path, "r") as zip_file:

From 72d613776fdfe1804416c6b75dcb39ef890d6313 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Tue, 26 Oct 2021 13:20:53 -0400
Subject: [PATCH 35/60] Fixed issue with homelink navigation.

---
 client/pages/loading-page.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/pages/loading-page.js b/client/pages/loading-page.js
index 1b553faef3..be496cdced 100644
--- a/client/pages/loading-page.js
+++ b/client/pages/loading-page.js
@@ -91,7 +91,7 @@ let LoadingPage = PageView.extend({
         $(self.queryByHook("loading-spinner")).css("display", "none");
         let modal = $(modals.errorHtml(body.reason, body.message)).modal();
         modal.on('hidden.bs.modal', function (e) {
-          window.location.href = this.homeLink;
+          window.location.href = self.homeLink;
         });
       }
       app.getXHR(endpoint, {

From b71bee665d21031e7d45c60348d1386fdb049afa Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 27 Oct 2021 08:52:58 -0400
Subject: [PATCH 36/60] Switch the logging FileHandler to RotatingFileHandler
 to allow for log file size control.  Moved the location of the log files to
 /var/log.

---
 stochss/handlers/log.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/stochss/handlers/log.py b/stochss/handlers/log.py
index b8717443c2..a7a6b2fe77 100644
--- a/stochss/handlers/log.py
+++ b/stochss/handlers/log.py
@@ -57,7 +57,8 @@ def setup_file_handler():
     Attributes
     ----------
     '''
-    handler = logging.FileHandler(".user-logs.txt")
+    handler = logging.RotatingFileHandler("/var/log/.user-logs.txt",
+                                          maxBytes=500000, backupCount=1)
     fmt = '%(asctime)s$ %(message)s'
     formatter = LogFormatter(fmt=fmt, datefmt="%b %d, %Y  %I:%M %p UTC")
     handler.setFormatter(formatter)

From 3e4221c6f42a43af7a4793964397f22c1ce7574b Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 27 Oct 2021 10:58:08 -0400
Subject: [PATCH 37/60] Added function to relocate old log file to the new
 location and with the proper file size constraints.

---
 stochss/handlers/log.py | 34 ++++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/stochss/handlers/log.py b/stochss/handlers/log.py
index a7a6b2fe77..e635f509d4 100644
--- a/stochss/handlers/log.py
+++ b/stochss/handlers/log.py
@@ -28,12 +28,46 @@ def init_log():
     Attributes
     ----------
     '''
+    relocate_old_logs()
     setup_stream_handler()
     setup_file_handler()
     log.setLevel(logging.DEBUG)
     log.propagate = False
 
 
+def relocate_old_logs():
+    '''
+    Move the user log file to its new location (/var/log).
+    '''
+    src = os.path.join(os.path.expanduser("~"), ".user-logs.txt")
+    if not os.path.exists(src):
+        return
+    
+    src_size = os.path.getsize(src)
+    if src_size < 500000:
+        os.rename(src, "/var/log/user-logs.txt")
+        return
+    
+    with open(src, "r") as log_file:
+        logs = log_file.read().rstrip().split('\n')
+    os.remove(src)
+    
+    mlog_size = src_size % 500000
+    mlogs = [logs.pop()]
+    while sys.getsizeof("\n".join(mlogs)) < mlog_size:
+        mlogs.insert(0, logs.pop())
+    with open("/var/log/.user-logs.txt", "w") as main_log_file:
+        main_log_file.write("\n".join(mlogs))
+
+    blogs = [logs.pop()]
+    nlog_size = sys.getsizeof(f"\n{logs[-1]}")
+    while logs and sys.getsizeof("\n".join(blogs)) + nlog_size < 500000:
+        blogs.insert(0, logs.pop())
+        nlog_size = sys.getsizeof(f"\n{logs[-1]}")
+    with open("/var/log/.user-logs.txt.bak", "w") as backup_log_file:
+        backup_log_file.write("\n".join(blogs))
+
+
 def setup_stream_handler():
     '''
     Initialize the StochSS stream handler

From f86bffc40719baa26cc7f3d10cdfb192cadd4df1 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 27 Oct 2021 11:01:55 -0400
Subject: [PATCH 38/60] Refactored the user logs api handler to pull from the
 new log file locations.

---
 stochss/handlers/pages.py | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/stochss/handlers/pages.py b/stochss/handlers/pages.py
index fc1c5d660b..b5fe1e1947 100644
--- a/stochss/handlers/pages.py
+++ b/stochss/handlers/pages.py
@@ -264,11 +264,15 @@ async def get(self):
         '''
         self.set_header('Content-Type', 'application/json')
         log_num = self.get_query_arguments(name="logNum")[0]
-        user_dir = os.path.expanduser("~")
-        path = os.path.join(user_dir, ".user-logs.txt")
+        path = os.path.join("/var/logs/.user-logs.txt")
         try:
+            if os.path.exists(f"{path}.bak"):
+                with open(path, "r") as log_file:
+                    logs = log_file.read().strip().split("\n")
+            else:
+                logs = []
             with open(path, "r") as log_file:
-                logs = log_file.read().strip().split("\n")[int(log_num):]
+                logs = logs.extend(log_file.read().strip().split("\n"))[int(log_num):]
         except FileNotFoundError:
             open(path, "w").close()
             logs = []

From 2fb17ad5e95d173fc7a080c3a4bf2c4af896715b Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 27 Oct 2021 11:13:00 -0400
Subject: [PATCH 39/60] Added custom namer and rotator functions.

---
 stochss/handlers/log.py | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/stochss/handlers/log.py b/stochss/handlers/log.py
index e635f509d4..80424fb30c 100644
--- a/stochss/handlers/log.py
+++ b/stochss/handlers/log.py
@@ -91,8 +91,37 @@ def setup_file_handler():
     Attributes
     ----------
     '''
+    def namer(name):
+        '''
+        Namer function for the RotatingFileHandler
+
+        Attributes
+        ----------
+        name : str
+            Default name of the log file.
+        '''
+        return f"{name}.bak"
+
+    def rotator(src, dst):
+        '''
+        Rotator function for the RotatingFileHandler
+
+        Attributes
+        ----------
+        src : str
+            Path to the main log file.
+        dst : str
+            Path to the backup log file.
+        '''
+        if os.path.exists(dst):
+            os.remove(dst)
+        os.rename(src, dst)
+        os.remove(src)
+
     handler = logging.RotatingFileHandler("/var/log/.user-logs.txt",
                                           maxBytes=500000, backupCount=1)
+    handler.namer = namer
+    handler.rotator = rotator
     fmt = '%(asctime)s$ %(message)s'
     formatter = LogFormatter(fmt=fmt, datefmt="%b %d, %Y  %I:%M %p UTC")
     handler.setFormatter(formatter)

From f9b8fcd012f702b0f6bccb35e21dc05bdb829034 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 27 Oct 2021 11:44:38 -0400
Subject: [PATCH 40/60] Refactored the clear user logs api handler to remove
 the files in their new location.

---
 stochss/handlers/pages.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/stochss/handlers/pages.py b/stochss/handlers/pages.py
index b5fe1e1947..59f3e7b10f 100644
--- a/stochss/handlers/pages.py
+++ b/stochss/handlers/pages.py
@@ -294,5 +294,7 @@ async def get(self):
         Attributes
         ----------
         '''
-        open(os.path.join(os.path.expanduser("~"), ".user-logs.txt"), "w").close()
+        if os.path.exists("/var/log/.user-logs.txt.bak"):
+            os.remove("/var/log/.user-logs.txt.bak")
+        open("/var/log/.user-logs.txt", "w").close()
         self.finish()

From d5410488dfa457030d6b4d6c11179c701b6cc109 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 27 Oct 2021 11:46:08 -0400
Subject: [PATCH 41/60] Added missing imports.  Added missing handlers
 reference.

---
 stochss/handlers/log.py | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/stochss/handlers/log.py b/stochss/handlers/log.py
index 80424fb30c..84760427d8 100644
--- a/stochss/handlers/log.py
+++ b/stochss/handlers/log.py
@@ -16,6 +16,8 @@
 along with this program.  If not, see <http://www.gnu.org/licenses/>.
 '''
 
+import os
+import sys
 import logging
 from tornado.log import LogFormatter
 
@@ -42,16 +44,16 @@ def relocate_old_logs():
     src = os.path.join(os.path.expanduser("~"), ".user-logs.txt")
     if not os.path.exists(src):
         return
-    
+
     src_size = os.path.getsize(src)
     if src_size < 500000:
         os.rename(src, "/var/log/user-logs.txt")
         return
-    
+
     with open(src, "r") as log_file:
         logs = log_file.read().rstrip().split('\n')
     os.remove(src)
-    
+
     mlog_size = src_size % 500000
     mlogs = [logs.pop()]
     while sys.getsizeof("\n".join(mlogs)) < mlog_size:
@@ -118,8 +120,8 @@ def rotator(src, dst):
         os.rename(src, dst)
         os.remove(src)
 
-    handler = logging.RotatingFileHandler("/var/log/.user-logs.txt",
-                                          maxBytes=500000, backupCount=1)
+    handler = logging.handlers.RotatingFileHandler("/var/log/.user-logs.txt",
+                                                   maxBytes=500000, backupCount=1)
     handler.namer = namer
     handler.rotator = rotator
     fmt = '%(asctime)s$ %(message)s'

From 69fd1a1787ced402d617c2c4ae05dd69a2958c95 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 27 Oct 2021 12:39:36 -0400
Subject: [PATCH 42/60] Moved the log location back to the users home directory
 to fix permission errors.  Fixed TypeError.

---
 stochss/handlers/log.py   | 15 +++++++--------
 stochss/handlers/pages.py | 12 +++++++-----
 2 files changed, 14 insertions(+), 13 deletions(-)

diff --git a/stochss/handlers/log.py b/stochss/handlers/log.py
index 84760427d8..c082d97c90 100644
--- a/stochss/handlers/log.py
+++ b/stochss/handlers/log.py
@@ -41,24 +41,23 @@ def relocate_old_logs():
     '''
     Move the user log file to its new location (/var/log).
     '''
-    src = os.path.join(os.path.expanduser("~"), ".user-logs.txt")
+    user_dir = os.path.expanduser("~")
+    src = os.path.join(user_dir, ".user-logs.txt")
     if not os.path.exists(src):
         return
 
     src_size = os.path.getsize(src)
     if src_size < 500000:
-        os.rename(src, "/var/log/user-logs.txt")
         return
 
     with open(src, "r") as log_file:
         logs = log_file.read().rstrip().split('\n')
-    os.remove(src)
-
+    
     mlog_size = src_size % 500000
     mlogs = [logs.pop()]
     while sys.getsizeof("\n".join(mlogs)) < mlog_size:
         mlogs.insert(0, logs.pop())
-    with open("/var/log/.user-logs.txt", "w") as main_log_file:
+    with open(os.path.join(user_dir, ".user-logs.txt"), "w") as main_log_file:
         main_log_file.write("\n".join(mlogs))
 
     blogs = [logs.pop()]
@@ -66,7 +65,7 @@ def relocate_old_logs():
     while logs and sys.getsizeof("\n".join(blogs)) + nlog_size < 500000:
         blogs.insert(0, logs.pop())
         nlog_size = sys.getsizeof(f"\n{logs[-1]}")
-    with open("/var/log/.user-logs.txt.bak", "w") as backup_log_file:
+    with open(os.path.join(user_dir, ".user-logs.txt.bak"), "w") as backup_log_file:
         backup_log_file.write("\n".join(blogs))
 
 
@@ -120,8 +119,8 @@ def rotator(src, dst):
         os.rename(src, dst)
         os.remove(src)
 
-    handler = logging.handlers.RotatingFileHandler("/var/log/.user-logs.txt",
-                                                   maxBytes=500000, backupCount=1)
+    path = os.path.join(os.path.expanduser("~"), ".user-logs.txt")
+    handler = logging.handlers.RotatingFileHandler(path, maxBytes=500000, backupCount=1)
     handler.namer = namer
     handler.rotator = rotator
     fmt = '%(asctime)s$ %(message)s'
diff --git a/stochss/handlers/pages.py b/stochss/handlers/pages.py
index 59f3e7b10f..ba03c27060 100644
--- a/stochss/handlers/pages.py
+++ b/stochss/handlers/pages.py
@@ -264,7 +264,7 @@ async def get(self):
         '''
         self.set_header('Content-Type', 'application/json')
         log_num = self.get_query_arguments(name="logNum")[0]
-        path = os.path.join("/var/logs/.user-logs.txt")
+        path = os.path.join(os.path.expanduser("~"), ".user-logs.txt")
         try:
             if os.path.exists(f"{path}.bak"):
                 with open(path, "r") as log_file:
@@ -272,7 +272,8 @@ async def get(self):
             else:
                 logs = []
             with open(path, "r") as log_file:
-                logs = logs.extend(log_file.read().strip().split("\n"))[int(log_num):]
+                logs.extend(log_file.read().strip().split("\n"))
+                logs = logs[int(log_num):]
         except FileNotFoundError:
             open(path, "w").close()
             logs = []
@@ -294,7 +295,8 @@ async def get(self):
         Attributes
         ----------
         '''
-        if os.path.exists("/var/log/.user-logs.txt.bak"):
-            os.remove("/var/log/.user-logs.txt.bak")
-        open("/var/log/.user-logs.txt", "w").close()
+        path = os.path.join(os.path.expanduser("~"), ".user-logs.txt")
+        if os.path.exists(f'{path}.bak'):
+            os.remove(f'{path}.bak')
+        open(path, "w").close()
         self.finish()

From 97c87840d500fe70fe9db297037ab841fe1db78b Mon Sep 17 00:00:00 2001
From: seanebum <smatthe2@unca.edu>
Date: Wed, 27 Oct 2021 13:37:32 -0400
Subject: [PATCH 43/60] added directory of GillesPy2 and SpatialPy examples

---
 EXAMPLE_DIRECTORY.md | 90 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 90 insertions(+)
 create mode 100644 EXAMPLE_DIRECTORY.md

diff --git a/EXAMPLE_DIRECTORY.md b/EXAMPLE_DIRECTORY.md
new file mode 100644
index 0000000000..973c55f43c
--- /dev/null
+++ b/EXAMPLE_DIRECTORY.md
@@ -0,0 +1,90 @@
+#Example Directory
+
+This file contains a directory to all GillesPy2 and SpatialPy example notebooks.
+
+##GillesPy2
+
+["Start Here" Model](https://github.com/StochSS/GillesPy2/blob/main/examples/StartHere.ipynb)
+
+###Starting Models
+
+- [Michaelis Menten](https://github.com/StochSS/GillesPy2/tree/main/examples/StartingModels/MichaelisMenten)
+    - [SSA C Solver](https://github.com/StochSS/GillesPy2/blob/main/examples/StartingModels/MichaelisMenten/Michaelis-Menten_SSA_C.ipynb)
+    - [SSA NumPy Solver](https://github.com/StochSS/GillesPy2/blob/main/examples/StartingModels/MichaelisMenten/Michaelis-Menten_NumPy_SSA.ipynb)
+    - [Tau Leaping NumPy](https://github.com/StochSS/GillesPy2/blob/main/examples/StartingModels/MichaelisMenten/Michaelis-Menten_Basic_Tau_Leaping.ipynb)
+    - [Tau Hybrid NumPy](https://github.com/StochSS/GillesPy2/blob/main/examples/StartingModels/MichaelisMenten/Michaelis-Menten_Basic_Tau_Hybrid.ipynb)
+
+- [Vilar Oscillator](https://github.com/StochSS/GillesPy2/tree/main/examples/StartingModels/VilarOscillator)
+    - [SSA](https://github.com/StochSS/GillesPy2/blob/main/examples/StartingModels/VilarOscillator/VilarOscillator_SSA.ipynb)
+    - [Tau Leaping](https://github.com/StochSS/GillesPy2/blob/main/examples/StartingModels/VilarOscillator/VilarOscillator_Tau_Leaping.ipynb)
+    - [Tau Hybrid](https://github.com/StochSS/GillesPy2/blob/main/examples/StartingModels/VilarOscillator/VilarOscillator_Tau_Hybrid.ipynb)
+
+
+###Results Management
+
+- [Basic Results Management](https://github.com/StochSS/GillesPy2/blob/main/examples/ResultsManagement/basic-results-management.ipynb)
+- [Single Trajectory to CSV](https://github.com/StochSS/GillesPy2/blob/main/examples/ResultsManagement/to_csv-single-trajectory.ipynb)
+- [Multiple Trajectories to CSV](https://github.com/StochSS/GillesPy2/blob/main/examples/ResultsManagement/to_csv-multi-trajectory.ipynb)
+- [Using Pickle](https://github.com/StochSS/GillesPy2/blob/main/examples/ResultsManagement/using-pickle.ipynb)
+
+
+###Data Visualization
+
+- [Data Visualization](https://github.com/StochSS/GillesPy2/blob/main/examples/DataVisualization/DataVisualization.ipynb)
+- [Live Output](https://github.com/StochSS/GillesPy2/blob/main/examples/DataVisualization/LiveOutput.ipynb)
+
+
+###Advanced Features
+
+- [Events](https://github.com/StochSS/GillesPy2/blob/main/examples/AdvancedFeatures/Events.ipynb)
+- [Kinetic Model for Styrene Polymerization](https://github.com/StochSS/GillesPy2/blob/main/examples/AdvancedFeatures/KineticModelForStyrenePolymerization.ipynb)
+- [Photosynthesis](https://github.com/StochSS/GillesPy2/blob/main/examples/AdvancedFeatures/Photosynthesis.ipynb)
+- [GillesPy2 in Parallel](https://github.com/StochSS/GillesPy2/blob/main/examples/AdvancedFeatures/Run%20GillesPy2%20Simulations%20in%20Parallel.ipynb)
+- [SBML Import](https://github.com/StochSS/GillesPy2/blob/main/examples/AdvancedFeatures/SBML_Import_Test.ipynb)
+- [Variable Inputs (SSA)](https://github.com/StochSS/GillesPy2/blob/main/examples/AdvancedFeatures/Variable_SSA_C_Example.ipynb)
+- [Volume Test](https://github.com/StochSS/GillesPy2/blob/main/examples/AdvancedFeatures/Volume_test.py)
+- [Hybrid Continuous Species](https://github.com/StochSS/GillesPy2/blob/main/examples/AdvancedFeatures/hybrid_continuous_species.ipynb)
+- [Hybrid Switching](https://github.com/StochSS/GillesPy2/blob/main/examples/AdvancedFeatures/hybrid_switching_example.ipynb)
+- [Parameter Changing](https://github.com/StochSS/GillesPy2/blob/main/examples/AdvancedFeatures/parameter_changing.py)
+
+
+###Extra Models
+
+- [Brusselator](https://github.com/StochSS/GillesPy2/blob/main/examples/ExtraModels/Brusselator.ipynb)
+- [Genetic Toggle Switch](https://github.com/StochSS/GillesPy2/blob/main/examples/ExtraModels/GeneticToggleSwitch.ipynb)
+- [Opioid Model](https://github.com/StochSS/GillesPy2/blob/main/examples/ExtraModels/Opioid_Model.ipynb)
+- [Oregonator](https://github.com/StochSS/GillesPy2/blob/main/examples/ExtraModels/Oregonator.ipynb)
+- [Tyson Oscillator](https://github.com/StochSS/GillesPy2/blob/main/examples/ExtraModels/Tyson%20Oscillator.ipynb)
+- [Degradation Model](https://github.com/StochSS/GillesPy2/blob/main/examples/ExtraModels/degradation_example.py)
+- [Dimer Model](https://github.com/StochSS/GillesPy2/blob/main/examples/ExtraModels/dimer_example.py)
+- [Tyson Oscillator](https://github.com/StochSS/GillesPy2/blob/main/examples/ExtraModels/tyson_oscillator.py)
+
+
+
+##SpatialPy
+
+###General Examples
+
+- [Bistable Elf Ehrenberg](https://github.com/StochSS/SpatialPy/blob/develop/examples/Bistable_Biochem_Elf_Ehrenberg/Bistable_Biochem_Elf_Ehrenberg.ipynb)
+- [Boundary Conditions](https://github.com/StochSS/SpatialPy/blob/develop/examples/BoundaryCondition/BoundaryCondition.ipynb)
+- [SpatialPy Gravity](https://github.com/StochSS/SpatialPy/blob/develop/examples/Gravity/Spatialpy_gravity.ipynb)
+- [Coral Reef](https://github.com/StochSS/SpatialPy/blob/develop/examples/coral_reef/CoralModel.ipynb)
+- [3D Cylinder Diffusion](https://github.com/StochSS/SpatialPy/blob/develop/examples/cylinderDemo/SpatialPy_cylinderDemo3D.ipynb)
+- [hes1](https://github.com/StochSS/SpatialPy/blob/develop/examples/hes1/hes1.ipynb)
+- [Lid Driven Cavity](https://github.com/StochSS/SpatialPy/blob/develop/examples/lid_driven_cavity/Lid%20driven%20cavity.ipynb)
+- [MinCDE](https://github.com/StochSS/SpatialPy/blob/develop/examples/mincde/mincde.ipynb)
+- [Turing Pattern (Old)](https://github.com/StochSS/SpatialPy/blob/develop/examples/turing_pattern/turing_pattern.ipynb)
+- [Turing Pattern (New)](https://github.com/StochSS/SpatialPy/blob/develop/examples/turing_pattern/new_turing_pattern.ipynb)
+- [Weir](https://github.com/StochSS/SpatialPy/blob/develop/examples/weir/weir.ipynb)
+- [Yeast Polarization](https://github.com/StochSS/SpatialPy/tree/develop/examples/yeast_polarization)
+    - [G-Protein 1D](https://github.com/StochSS/SpatialPy/blob/develop/examples/yeast_polarization/G-Protein_1D.ipynb)
+    - [Polarisome 1D](https://github.com/StochSS/SpatialPy/blob/develop/examples/yeast_polarization/Polarisome_1D.ipynb)
+    - [cdc42](https://github.com/StochSS/SpatialPy/blob/develop/examples/yeast_polarization/cdc42.ipynb)
+
+###Tests
+
+- [Diffusion Validation](https://github.com/StochSS/SpatialPy/blob/develop/examples/tests/Diffusion_validation.ipynb)
+- [Spatial Birth-Death](https://github.com/StochSS/SpatialPy/blob/develop/examples/tests/Spatial_Birth_Death.ipynb)
+- [Compile Time Test](https://github.com/StochSS/SpatialPy/blob/develop/examples/tests/compile_time_comparison.ipynb)
+- [Read Meshes](https://github.com/StochSS/SpatialPy/blob/develop/examples/tests/read_meshes.ipynb)
+

From d630ec01b2f3aa41692d5cb75497b89ec8e8b78f Mon Sep 17 00:00:00 2001
From: Sean Matthew <smatthe2@unca.edu>
Date: Wed, 27 Oct 2021 13:41:27 -0400
Subject: [PATCH 44/60] fixed some spacing

---
 EXAMPLE_DIRECTORY.md | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/EXAMPLE_DIRECTORY.md b/EXAMPLE_DIRECTORY.md
index 973c55f43c..03713a95fc 100644
--- a/EXAMPLE_DIRECTORY.md
+++ b/EXAMPLE_DIRECTORY.md
@@ -1,12 +1,12 @@
-#Example Directory
+# Example Directory
 
 This file contains a directory to all GillesPy2 and SpatialPy example notebooks.
 
-##GillesPy2
+## GillesPy2
 
 ["Start Here" Model](https://github.com/StochSS/GillesPy2/blob/main/examples/StartHere.ipynb)
 
-###Starting Models
+### Starting Models
 
 - [Michaelis Menten](https://github.com/StochSS/GillesPy2/tree/main/examples/StartingModels/MichaelisMenten)
     - [SSA C Solver](https://github.com/StochSS/GillesPy2/blob/main/examples/StartingModels/MichaelisMenten/Michaelis-Menten_SSA_C.ipynb)
@@ -20,7 +20,7 @@ This file contains a directory to all GillesPy2 and SpatialPy example notebooks.
     - [Tau Hybrid](https://github.com/StochSS/GillesPy2/blob/main/examples/StartingModels/VilarOscillator/VilarOscillator_Tau_Hybrid.ipynb)
 
 
-###Results Management
+### Results Management
 
 - [Basic Results Management](https://github.com/StochSS/GillesPy2/blob/main/examples/ResultsManagement/basic-results-management.ipynb)
 - [Single Trajectory to CSV](https://github.com/StochSS/GillesPy2/blob/main/examples/ResultsManagement/to_csv-single-trajectory.ipynb)
@@ -28,13 +28,13 @@ This file contains a directory to all GillesPy2 and SpatialPy example notebooks.
 - [Using Pickle](https://github.com/StochSS/GillesPy2/blob/main/examples/ResultsManagement/using-pickle.ipynb)
 
 
-###Data Visualization
+### Data Visualization
 
 - [Data Visualization](https://github.com/StochSS/GillesPy2/blob/main/examples/DataVisualization/DataVisualization.ipynb)
 - [Live Output](https://github.com/StochSS/GillesPy2/blob/main/examples/DataVisualization/LiveOutput.ipynb)
 
 
-###Advanced Features
+### Advanced Features
 
 - [Events](https://github.com/StochSS/GillesPy2/blob/main/examples/AdvancedFeatures/Events.ipynb)
 - [Kinetic Model for Styrene Polymerization](https://github.com/StochSS/GillesPy2/blob/main/examples/AdvancedFeatures/KineticModelForStyrenePolymerization.ipynb)
@@ -48,7 +48,7 @@ This file contains a directory to all GillesPy2 and SpatialPy example notebooks.
 - [Parameter Changing](https://github.com/StochSS/GillesPy2/blob/main/examples/AdvancedFeatures/parameter_changing.py)
 
 
-###Extra Models
+### Extra Models
 
 - [Brusselator](https://github.com/StochSS/GillesPy2/blob/main/examples/ExtraModels/Brusselator.ipynb)
 - [Genetic Toggle Switch](https://github.com/StochSS/GillesPy2/blob/main/examples/ExtraModels/GeneticToggleSwitch.ipynb)
@@ -61,9 +61,9 @@ This file contains a directory to all GillesPy2 and SpatialPy example notebooks.
 
 
 
-##SpatialPy
+## SpatialPy
 
-###General Examples
+### General Examples
 
 - [Bistable Elf Ehrenberg](https://github.com/StochSS/SpatialPy/blob/develop/examples/Bistable_Biochem_Elf_Ehrenberg/Bistable_Biochem_Elf_Ehrenberg.ipynb)
 - [Boundary Conditions](https://github.com/StochSS/SpatialPy/blob/develop/examples/BoundaryCondition/BoundaryCondition.ipynb)
@@ -81,7 +81,7 @@ This file contains a directory to all GillesPy2 and SpatialPy example notebooks.
     - [Polarisome 1D](https://github.com/StochSS/SpatialPy/blob/develop/examples/yeast_polarization/Polarisome_1D.ipynb)
     - [cdc42](https://github.com/StochSS/SpatialPy/blob/develop/examples/yeast_polarization/cdc42.ipynb)
 
-###Tests
+### Tests
 
 - [Diffusion Validation](https://github.com/StochSS/SpatialPy/blob/develop/examples/tests/Diffusion_validation.ipynb)
 - [Spatial Birth-Death](https://github.com/StochSS/SpatialPy/blob/develop/examples/tests/Spatial_Birth_Death.ipynb)

From 3a348cd12182ad04db3e13ec61a3be71959c5c4e Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Tue, 2 Nov 2021 08:51:35 -0400
Subject: [PATCH 45/60] Updated the GillesPy2 version.  Switched Sciope to the
 github master branch.  Switched SpatialPy to the github develop branch.

---
 requirements.txt | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/requirements.txt b/requirements.txt
index a5b7759e21..ef68e8a1a7 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -2,8 +2,8 @@ python-libsbml==5.18.0
 python-libsedml==2.0.9
 python-libcombine==0.2.7
 escapism==1.0.1
-gillespy2==1.6.3
-sciope==0.4
+gillespy2==1.6.5
+git+https://github.com/StochSS/sciope.git@master
 pygmsh==5.0.2
 meshio==2.3.10
-git+https://github.com/spatialpy/SpatialPy.git@main
+git+https://github.com/StochSS/SpatialPy.git@develop

From f4f74719fc76dcaa993ef09d2cccfa928713a648 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Tue, 2 Nov 2021 09:16:18 -0400
Subject: [PATCH 46/60] Replaced uses of deprecated
 'Parameter.set_expression()' with 'Parameter.expression = '.

---
 stochss/handlers/util/parameter_scan.py           | 2 +-
 stochss/handlers/util/parameter_sweep_1d.py       | 2 +-
 stochss/handlers/util/parameter_sweep_2d.py       | 4 ++--
 stochss/handlers/util/parameter_sweep_notebook.py | 6 +++---
 stochss/handlers/util/sciope_notebook.py          | 2 +-
 5 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/stochss/handlers/util/parameter_scan.py b/stochss/handlers/util/parameter_scan.py
index f1871b6138..a3c914b277 100644
--- a/stochss/handlers/util/parameter_scan.py
+++ b/stochss/handlers/util/parameter_scan.py
@@ -86,7 +86,7 @@ def __setup_model(self, variables):
             return self.model
         tmp_mdl = copy.deepcopy(self.model)
         for name, value in variables.items():
-            tmp_mdl.listOfParameters[name].set_expression(value)
+            tmp_mdl.listOfParameters[name].expression = value
         return tmp_mdl
 
 
diff --git a/stochss/handlers/util/parameter_sweep_1d.py b/stochss/handlers/util/parameter_sweep_1d.py
index 14e0d2b3df..f93feaa49b 100644
--- a/stochss/handlers/util/parameter_sweep_1d.py
+++ b/stochss/handlers/util/parameter_sweep_1d.py
@@ -150,7 +150,7 @@ def run(self, job_id, verbose=False):
                 self.settings['variables'] = {self.param['parameter']:val}
             else:
                 tmp_mdl = copy.deepcopy(self.model)
-                tmp_mdl.listOfParameters[self.param['parameter']].set_expression(val)
+                tmp_mdl.listOfParameters[self.param['parameter']].expression = val
             if verbose:
                 log.info(f"{job_id} --> running: {self.param['parameter']}={val}")
             try:
diff --git a/stochss/handlers/util/parameter_sweep_2d.py b/stochss/handlers/util/parameter_sweep_2d.py
index f4cd173d57..abbee80cfd 100644
--- a/stochss/handlers/util/parameter_sweep_2d.py
+++ b/stochss/handlers/util/parameter_sweep_2d.py
@@ -153,8 +153,8 @@ def run(self, job_id, verbose=False):
                     self.settings['variables'] = variables
                 else:
                     tmp_mdl = copy.deepcopy(self.model)
-                    tmp_mdl.listOfParameters[self.params[0]['parameter']].set_expression(val1)
-                    tmp_mdl.listOfParameters[self.params[1]['parameter']].set_expression(val2)
+                    tmp_mdl.listOfParameters[self.params[0]['parameter']].expression = val1
+                    tmp_mdl.listOfParameters[self.params[1]['parameter']].expression = val2
                 if verbose:
                     message = f"{job_id} --> running: {self.params[0]['parameter']}={val1}, "
                     message += f"{self.params[1]['parameter']}={val2}"
diff --git a/stochss/handlers/util/parameter_sweep_notebook.py b/stochss/handlers/util/parameter_sweep_notebook.py
index 75f586e1c3..165790df63 100644
--- a/stochss/handlers/util/parameter_sweep_notebook.py
+++ b/stochss/handlers/util/parameter_sweep_notebook.py
@@ -128,7 +128,7 @@ def __create_1d_run_str(self):
         else:
             res_str += "tmp_model.run(**kwargs)"
             run_strs.extend([f"{pad*3}tmp_model = c.ps_class()",
-                             f"{pad*3}tmp_model.listOfParameters[c.p1].set_expression(v1)"])
+                             f"{pad*3}tmp_model.listOfParameters[c.p1].expression = v1"])
         run_strs.extend([f"{pad*3}if c.verbose:",
                          pad * 4 + "print(f'running {c.p1}={v1}')",
                          f"{pad*3}if(c.number_of_trajectories > 1):",
@@ -252,8 +252,8 @@ def __create_2d_run_str(self):
         else:
             res_str += "tmp_model.run(**kwargs)"
             run_strs.extend([f"{pad*4}tmp_model = c.ps_class()",
-                             f"{pad*4}tmp_model.listOfParameters[c.p1].set_expression(v1)",
-                             f"{pad*4}tmp_model.listOfParameters[c.p2].set_expression(v2)"])
+                             f"{pad*4}tmp_model.listOfParameters[c.p1].expression = v1",
+                             f"{pad*4}tmp_model.listOfParameters[c.p2].expression = v2"])
         run_strs.extend([f"{pad*4}if c.verbose:",
                          pad * 5 + "print(f'running {c.p1}={v1}, {c.p2}={v2}')",
                          f"{pad*4}if(c.number_of_trajectories > 1):",
diff --git a/stochss/handlers/util/sciope_notebook.py b/stochss/handlers/util/sciope_notebook.py
index a3ec3b7625..ecfbc87234 100644
--- a/stochss/handlers/util/sciope_notebook.py
+++ b/stochss/handlers/util/sciope_notebook.py
@@ -141,7 +141,7 @@ def __create_mi_simulator_cell(self):
             run = f"{pad}res = model.run(**kwargs, variables=variables)"
         else:
             func_def = "def set_model_parameters(params, model):"
-            body = f"{pad*2}model.get_parameter(pname).set_expression(params[e])"
+            body = f"{pad*2}model.get_parameter(pname).expression = params[e]"
             return_str = f"{pad}return model"
             call = f"{pad}model_update = set_model_parameters(params, model)"
             run = f"{pad}res = model_update.run(**kwargs)"

From 88b20a482db9360cf7734e821ac5bac6f06d70a6 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Tue, 2 Nov 2021 09:45:53 -0400
Subject: [PATCH 47/60] Updated the 'Mesh' to 'Domain' and added 'rho' and 'c'
 to the domain builder function .

---
 .../handlers/util/stochss_spatial_model.py    | 46 +++++++++++--------
 1 file changed, 28 insertions(+), 18 deletions(-)

diff --git a/stochss/handlers/util/stochss_spatial_model.py b/stochss/handlers/util/stochss_spatial_model.py
index 75422c62c3..d16f7979ef 100644
--- a/stochss/handlers/util/stochss_spatial_model.py
+++ b/stochss/handlers/util/stochss_spatial_model.py
@@ -26,7 +26,7 @@
 import numpy
 import plotly
 from escapism import escape
-from spatialpy import Model, Species, Parameter, Reaction, Mesh, MeshError, BoundaryCondition, \
+from spatialpy import Model, Species, Parameter, Reaction, Domain, DomainError, BoundaryCondition, \
                       PlaceInitialCondition, UniformInitialCondition, ScatterInitialCondition
 
 from .stochss_base import StochSSBase
@@ -163,9 +163,9 @@ def __convert_domain(self, model):
             gravity = self.model['domain']['gravity']
             if gravity == [0, 0, 0]:
                 gravity = None
-            mesh = Mesh(0, xlim, ylim, zlim, rho0=rho0, c0=c_0, P0=p_0, gravity=gravity)
-            self.__convert_particles(mesh=mesh)
-            model.add_mesh(mesh)
+            domain = Domain(0, xlim, ylim, zlim, rho0=rho0, c0=c_0, P0=p_0, gravity=gravity)
+            self.__convert_particles(domain=domain)
+            model.add_domain(domain)
             model.staticDomain = self.model['domain']['static']
         except KeyError as err:
             message = "Spatial model domain properties are not properly formatted or "
@@ -221,11 +221,12 @@ def __convert_parameters(self, model):
             raise StochSSModelFormatError(message, traceback.format_exc()) from err
 
 
-    def __convert_particles(self, mesh):
+    def __convert_particles(self, domain):
         try:
             for particle in self.model['domain']['particles']:
-                mesh.add_point(particle['point'], particle['volume'], particle['mass'],
-                               particle['type'], particle['nu'], particle['fixed'])
+                domain.add_point(particle['point'], particle['volume'], particle['mass'],
+                                 particle['type'], particle['nu'], particle['fixed'],
+                                 particle['rho'], particle['c'])
         except KeyError as err:
             message = "Spatial model domain particle properties are not properly formatted or "
             message += f"are referenced incorrectly: {str(err)}"
@@ -321,7 +322,7 @@ def __load_domain_from_file(self, path):
             if path.endswith(".domn"):
                 with open(path, "r") as domain_file:
                     return json.load(domain_file)
-            s_domain = Mesh.read_xml_mesh(filename=path)
+            s_domain = Domain.read_xml_mesh(filename=path)
             return self.__build_stochss_domain(s_domain=s_domain)
         except FileNotFoundError as err:
             message = f"Could not find the domain file: {str(err)}"
@@ -329,7 +330,7 @@ def __load_domain_from_file(self, path):
         except json.decoder.JSONDecodeError as err:
             message = f"The domain file is not JSON decobable: {str(err)}"
             raise FileNotJSONFormatError(message, traceback.format_exc()) from err
-        except MeshError as err:
+        except DomainError as err:
             message = f"The domain file is not in proper format: {str(err)}"
             raise DomainFormatError(message, traceback.format_exc()) from err
 
@@ -346,6 +347,18 @@ def __read_model_file(self):
             raise FileNotJSONFormatError(message, traceback.format_exc()) from err
 
 
+    def __update_domain(self):
+        if "domain" not in self.model.keys() or len(self.model['domain'].keys()) < 6:
+            self.model['domain'] = self.get_model_template()['domain']
+        elif "static" not in self.model['domain'].keys():
+            self.model['domain']['static'] = True
+        if "rho" not in self.model['domain']['particles'][0].keys() or \
+                    "c" not in self.model['domain']['particles'][0].keys():
+            for particle in self.model['domain']['particles']:
+                particle['rho'] = particle['mass']/particle['vol']
+                particle['c'] = 10
+
+
     def convert_to_model(self):
         '''
         Convert a spatial model to a non_spatial model
@@ -490,8 +503,8 @@ def get_particles_from_3d_domain(cls, data):
             xlim = [coord + data['transformation'][0] for coord in data['xLim']]
             ylim = [coord + data['transformation'][1] for coord in data['yLim']]
             zlim = [coord + data['transformation'][2] for coord in data['zLim']]
-        s_domain = Mesh.create_3D_domain(xlim=xlim, ylim=ylim, zlim=zlim, nx=data['nx'],
-                                         ny=data['ny'], nz=data['nz'], **data['type'])
+        s_domain = Domain.create_3D_domain(xlim=xlim, ylim=ylim, zlim=zlim, nx=data['nx'],
+                                           ny=data['ny'], nz=data['nz'], **data['type'])
         domain = cls.__build_stochss_domain(s_domain=s_domain)
         limits = {"x_lim":domain['x_lim'], "y_lim":domain['y_lim'], "z_lim":domain['z_lim']}
         return {"particles":domain['particles'], "limits":limits}
@@ -512,9 +525,9 @@ def get_particles_from_remote(cls, mesh, data, types):
             List of type discriptions (lines from an uploaded file)
         '''
         file = tempfile.NamedTemporaryFile()
-        with open(file.name, "w") as mesh_file:
-            mesh_file.write(mesh)
-        s_domain = Mesh.read_xml_mesh(filename=file.name)
+        with open(file.name, "w") as domain_file:
+            domain_file.write(mesh)
+        s_domain = Domain.read_xml_mesh(filename=file.name)
         domain = cls.__build_stochss_domain(s_domain=s_domain, data=data)
         if types is not None:
             type_data = cls.get_types_from_file(lines=types)
@@ -576,10 +589,7 @@ def load(self):
             self.model['defaultMode'] = "discrete"
         if "timestepSize" not in self.model['modelSettings'].keys():
             self.model['modelSettings']['timestepSize'] = 1e-5
-        if "domain" not in self.model.keys() or len(self.model['domain'].keys()) < 6:
-            self.model['domain'] = self.get_model_template()['domain']
-        elif "static" not in self.model['domain'].keys():
-            self.model['domain']['static'] = True
+        self.__update_domain()
         if "boundaryConditions" not in self.model.keys():
             self.model['boundaryConditions'] = []
         for species in self.model['species']:

From a67726d18cb4b5f22768fbabbeb5d62e25821490 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Tue, 2 Nov 2021 09:48:04 -0400
Subject: [PATCH 48/60] Replaced the 'mesh' reference with 'domain' in docs.

---
 stochss/handlers/models.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/stochss/handlers/models.py b/stochss/handlers/models.py
index 5c4152c8f7..acd9986323 100644
--- a/stochss/handlers/models.py
+++ b/stochss/handlers/models.py
@@ -265,7 +265,7 @@ async def get(self):
 class ImportMeshAPIHandler(APIHandler):
     '''
     ################################################################################################
-    Handler for importing mesh particles from remote file.
+    Handler for importing domain particles from remote file.
     ################################################################################################
     '''
     @web.authenticated

From ef776765062d4909291c04351d1e1119e0f32e3b Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Tue, 2 Nov 2021 09:53:51 -0400
Subject: [PATCH 49/60] Updated notebook class to use 'Domain', instead of
 'Mesh'.

---
 stochss/handlers/util/stochss_notebook.py | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/stochss/handlers/util/stochss_notebook.py b/stochss/handlers/util/stochss_notebook.py
index 5403f9da5d..cfd722dd0d 100644
--- a/stochss/handlers/util/stochss_notebook.py
+++ b/stochss/handlers/util/stochss_notebook.py
@@ -222,8 +222,8 @@ def __create_import_cell(self):
             imports = ["import numpy as np"]
             if self.s_model['is_spatial']:
                 imports.append("import spatialpy")
-                imports.append("from spatialpy import Model, Species, Parameter, Reaction, Mesh,\\")
-                imports.append("                      PlaceInitialCondition, \\")
+                imports.append("from spatialpy import Model, Species, Parameter, Reaction,\\")
+                imports.append("                      Domain, PlaceInitialCondition, \\")
                 imports.append("                      UniformInitialCondition, \\")
                 imports.append("                      ScatterInitialCondition")
                 return nbf.new_code_cell("\n".join(imports))
@@ -275,12 +275,12 @@ def __create_initial_condition_strings(self, model, pad):
                 raise StochSSModelFormatError(message, traceback.format_exc()) from err
 
 
-    def __create_mesh_string(self, model, pad):
-        mesh = ["", f"{pad}# Domain",
-                f"{pad}mesh = Mesh.read_stochss_domain('{self.s_model['path']}')",
-                f"{pad}self.add_mesh(mesh)",
-                "", f"{pad}self.staticDomain = {self.s_model['domain']['static']}"]
-        model.extend(mesh)
+    def __create_domain_string(self, model, pad):
+        domain = ["", f"{pad}# Domain",
+                  f"{pad}domain = Domain.read_stochss_domain('{self.s_model['path']}')",
+                  f"{pad}self.add_mesh(domain)",
+                  "", f"{pad}self.staticDomain = {self.s_model['domain']['static']}"]
+        model.extend(domain)
 
 
     def __create_model_cell(self):
@@ -289,7 +289,7 @@ def __create_model_cell(self):
             model = [f"class {self.get_class_name()}(Model):",
                      "    def __init__(self):",
                      f'{pad}Model.__init__(self, name="{self.get_name()}")']
-            self.__create_mesh_string(model=model, pad=pad)
+            self.__create_domain_string(model=model, pad=pad)
             self.__create_boundary_condition_string(model=model, pad=pad)
             self.__create_species_strings(model=model, pad=pad)
             self.__create_initial_condition_strings(model=model, pad=pad)

From f0ce895655b0ce704740b8440b4db187dc27b4d4 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Tue, 2 Nov 2021 10:02:38 -0400
Subject: [PATCH 50/60] Additional updates to domain.

---
 .../handlers/util/stochss_spatial_model.py    | 35 +++++++------------
 1 file changed, 13 insertions(+), 22 deletions(-)

diff --git a/stochss/handlers/util/stochss_spatial_model.py b/stochss/handlers/util/stochss_spatial_model.py
index d16f7979ef..f4b7f84279 100644
--- a/stochss/handlers/util/stochss_spatial_model.py
+++ b/stochss/handlers/util/stochss_spatial_model.py
@@ -93,7 +93,7 @@ def expression(self): # pylint: disable=no-self-use
     def __build_stochss_domain(cls, s_domain, data=None):
         particles = cls.__build_stochss_domain_particles(s_domain=s_domain, data=data)
         gravity = [0] * 3 if s_domain.gravity is None else s_domain.gravity
-        domain = {"size":s_domain.mesh_size,
+        domain = {"size":s_domain.domain_size,
                   "rho_0":s_domain.rho0, # density
                   "c_0":s_domain.c0, # approx./artificial speed of sound
                   "p_0":s_domain.P0, # atmos/background pressure
@@ -136,6 +136,8 @@ def __build_stochss_domain_particles(cls, s_domain, data=None):
                         "mass":s_domain.mass[i],
                         "type":type_id,
                         "nu":viscosity,
+                        "rho":s_domain.rho[i],
+                        "c":s_domain[i],
                         "fixed":fixed}
             particles.append(particle)
         return particles
@@ -438,37 +440,26 @@ def get_domain(self, path=None, new=False):
         return self.__load_domain_from_file(path=path)
 
 
-    def get_domain_plot(self, domain=None, path=None, new=False):
+    def get_domain_plot(self, path=None, new=False):
         '''
         Get a plotly plot of the models domain or a prospective domain
 
         Attributes
         ----------
-        domain : dict
-            The domain to be plotted
         path : str
             Path to a prospective domain
         new : bool
             Indicates whether or not to load an new domain
         '''
-        if domain is None:
-            domain = self.get_domain(path=path, new=new)
-        trace_list = []
-        for i, d_type in enumerate(domain['types']):
-            if len(domain['types']) > 1:
-                particles = list(filter(lambda particle, key=i: particle['type'] == key,
-                                        domain['particles']))
-            else:
-                particles = domain['particles']
-            trace = self.__get_trace_data(particles=particles, name=d_type['name'])
-            trace_list.append(trace)
-        layout = {"scene":{"aspectmode":'data'}, "autosize":True}
-        if len(domain['x_lim']) == 2:
-            layout["xaxis"] = {"range":domain['x_lim']}
-        if len(domain['y_lim']) == 2:
-            layout["yaxis"] = {"range":domain['y_lim']}
-        return json.dumps({"data":trace_list, "layout":layout, "config":{"responsive":True}},
-                          cls=plotly.utils.PlotlyJSONEncoder)
+        if new:
+            path = '/stochss/stochss_templates/nonSpatialModelTemplate.json'
+        elif path is None:
+            path = self.path
+        domain = Domain.read_stochss_domain(path)
+        fig = domain.plot_types(return_plotly_figure=True)
+        fig['layout']['autosize'] = True
+        fig['config'] = {"responsive":True}
+        return json.dumps(fig, cls=plotly.utils.PlotlyJSONEncoder)
 
 
     def get_notebook_data(self):

From b946366130fa1480aa11e946304fd11b05f06f61 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Tue, 2 Nov 2021 10:30:35 -0400
Subject: [PATCH 51/60] Fixed domain plot issue.

---
 stochss/handlers/util/stochss_spatial_model.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/stochss/handlers/util/stochss_spatial_model.py b/stochss/handlers/util/stochss_spatial_model.py
index f4b7f84279..76de0c5a60 100644
--- a/stochss/handlers/util/stochss_spatial_model.py
+++ b/stochss/handlers/util/stochss_spatial_model.py
@@ -357,7 +357,7 @@ def __update_domain(self):
         if "rho" not in self.model['domain']['particles'][0].keys() or \
                     "c" not in self.model['domain']['particles'][0].keys():
             for particle in self.model['domain']['particles']:
-                particle['rho'] = particle['mass']/particle['vol']
+                particle['rho'] = particle['mass']/particle['volume']
                 particle['c'] = 10
 
 
@@ -457,6 +457,8 @@ def get_domain_plot(self, path=None, new=False):
             path = self.path
         domain = Domain.read_stochss_domain(path)
         fig = domain.plot_types(return_plotly_figure=True)
+        if not fig['data']:
+            self.__get_trace_data(particles=[], name="Un-Assigned")
         fig['layout']['autosize'] = True
         fig['config'] = {"responsive":True}
         return json.dumps(fig, cls=plotly.utils.PlotlyJSONEncoder)

From 90ba7719f4f43a899c5e7dbb15b064fa605442a4 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Tue, 2 Nov 2021 10:34:34 -0400
Subject: [PATCH 52/60] Fixed domain plot issue take two.

---
 stochss/handlers/util/stochss_spatial_model.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/stochss/handlers/util/stochss_spatial_model.py b/stochss/handlers/util/stochss_spatial_model.py
index 76de0c5a60..bb57535bea 100644
--- a/stochss/handlers/util/stochss_spatial_model.py
+++ b/stochss/handlers/util/stochss_spatial_model.py
@@ -458,7 +458,9 @@ def get_domain_plot(self, path=None, new=False):
         domain = Domain.read_stochss_domain(path)
         fig = domain.plot_types(return_plotly_figure=True)
         if not fig['data']:
-            self.__get_trace_data(particles=[], name="Un-Assigned")
+            fig['data'].append(self.__get_trace_data(particles=[], name="Un-Assigned"))
+        fig['width'] = None
+        fig['height'] = None
         fig['layout']['autosize'] = True
         fig['config'] = {"responsive":True}
         return json.dumps(fig, cls=plotly.utils.PlotlyJSONEncoder)

From 68b9899d601d974b164aa720a632aee1dc20003d Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Tue, 2 Nov 2021 10:37:24 -0400
Subject: [PATCH 53/60] Fixed domain plot layout issue.

---
 stochss/handlers/util/stochss_spatial_model.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/stochss/handlers/util/stochss_spatial_model.py b/stochss/handlers/util/stochss_spatial_model.py
index bb57535bea..422ac5f7db 100644
--- a/stochss/handlers/util/stochss_spatial_model.py
+++ b/stochss/handlers/util/stochss_spatial_model.py
@@ -459,8 +459,8 @@ def get_domain_plot(self, path=None, new=False):
         fig = domain.plot_types(return_plotly_figure=True)
         if not fig['data']:
             fig['data'].append(self.__get_trace_data(particles=[], name="Un-Assigned"))
-        fig['width'] = None
-        fig['height'] = None
+        fig['layout']['width'] = None
+        fig['layout']['height'] = None
         fig['layout']['autosize'] = True
         fig['config'] = {"responsive":True}
         return json.dumps(fig, cls=plotly.utils.PlotlyJSONEncoder)

From 1762aecff207069f6bb6ca21c9ded833bb7fd4b5 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Tue, 2 Nov 2021 10:40:55 -0400
Subject: [PATCH 54/60] Fixed issue with per particle speed of sound ref.

---
 stochss/handlers/util/stochss_spatial_model.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/stochss/handlers/util/stochss_spatial_model.py b/stochss/handlers/util/stochss_spatial_model.py
index 422ac5f7db..86ce8237b7 100644
--- a/stochss/handlers/util/stochss_spatial_model.py
+++ b/stochss/handlers/util/stochss_spatial_model.py
@@ -137,7 +137,7 @@ def __build_stochss_domain_particles(cls, s_domain, data=None):
                         "type":type_id,
                         "nu":viscosity,
                         "rho":s_domain.rho[i],
-                        "c":s_domain[i],
+                        "c":s_domain.c[i],
                         "fixed":fixed}
             particles.append(particle)
         return particles

From 75320f5b5f2aa55c94d292a0a997b098df9ba830 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Tue, 2 Nov 2021 13:07:37 -0400
Subject: [PATCH 55/60] Fixed species init function.

---
 stochss/handlers/util/stochss_notebook.py      | 2 +-
 stochss/handlers/util/stochss_spatial_model.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/stochss/handlers/util/stochss_notebook.py b/stochss/handlers/util/stochss_notebook.py
index cfd722dd0d..3d3bcae94a 100644
--- a/stochss/handlers/util/stochss_notebook.py
+++ b/stochss/handlers/util/stochss_notebook.py
@@ -403,7 +403,7 @@ def __create_species_strings(self, model, pad):
                     if self.s_model['is_spatial']:
                         names.append(spec["name"])
                         spec_str = f'{pad}{spec["name"]} = Species(name="{spec["name"]}", '
-                        spec_str += f"diffusion_constant={spec['diffusionConst']})"
+                        spec_str += f"diffusion_coefficient={spec['diffusionConst']})"
                         if len(spec['types']) < len(self.s_model['domain']['types']) - 1:
                             type_str = f"{pad}self.restrict({spec['name']}, {str(spec['types'])})"
                             types_str.append(type_str)
diff --git a/stochss/handlers/util/stochss_spatial_model.py b/stochss/handlers/util/stochss_spatial_model.py
index 86ce8237b7..4641d38d1f 100644
--- a/stochss/handlers/util/stochss_spatial_model.py
+++ b/stochss/handlers/util/stochss_spatial_model.py
@@ -267,7 +267,7 @@ def __convert_species(self, model):
         try:
             for species in self.model['species']:
                 name = species['name']
-                s_species = Species(name=name, diffusion_constant=species['diffusionConst'])
+                s_species = Species(name=name, diffusion_coefficient=species['diffusionConst'])
                 model.add_species(s_species)
                 model.restrict(s_species, species['types'])
         except KeyError as err:

From ce00a819f7a00e408928422c0af33edb6967e5a4 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 10 Nov 2021 09:14:31 -0500
Subject: [PATCH 56/60] Moved the preview.json cleanup block to the handler to
 fix incorrect results from being loaded as a result of a race condition.

---
 stochss/handlers/models.py                   | 3 +++
 stochss/handlers/util/ensemble_simulation.py | 2 --
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/stochss/handlers/models.py b/stochss/handlers/models.py
index 292a732874..406595e0c3 100644
--- a/stochss/handlers/models.py
+++ b/stochss/handlers/models.py
@@ -212,6 +212,9 @@ async def get(self):
         target = self.get_query_argument(name="target", default=None)
         resp = {"Running":False, "Outfile":outfile, "Results":""}
         if run_cmd == "start":
+            model = StochSSModel(path=path)
+            if os.path.exists(f".{model.get_name()}-preview.json"):
+                os.remove(f".{model.get_name()}-preview.json")
             exec_cmd = ['/stochss/stochss/handlers/util/scripts/run_preview.py',
                         f'{path}', f'{outfile}']
             if target is not None:
diff --git a/stochss/handlers/util/ensemble_simulation.py b/stochss/handlers/util/ensemble_simulation.py
index 3958da422e..ef57e8e16d 100644
--- a/stochss/handlers/util/ensemble_simulation.py
+++ b/stochss/handlers/util/ensemble_simulation.py
@@ -105,8 +105,6 @@ def run(self, preview=False, verbose=True):
             if verbose:
                 log.info(f"Running {self.g_model.name} preview simulation")
             live_file = f".{self.g_model.name}-preview.json"
-            if os.path.exists(live_file):
-                os.remove(live_file)
             options = {"file_path": live_file}
             results = self.g_model.run(timeout=5, live_output="graph", live_output_options=options)
             if verbose:

From d75bb6647733697674345558ea193027643cee37 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 10 Nov 2021 10:28:40 -0500
Subject: [PATCH 57/60] Fixed issues with updating domain.  Added 2D domain
 creation to allow for custom 2D domains.

---
 .../handlers/util/stochss_spatial_model.py    | 22 +++++++++++++------
 1 file changed, 15 insertions(+), 7 deletions(-)

diff --git a/stochss/handlers/util/stochss_spatial_model.py b/stochss/handlers/util/stochss_spatial_model.py
index 4641d38d1f..395347856b 100644
--- a/stochss/handlers/util/stochss_spatial_model.py
+++ b/stochss/handlers/util/stochss_spatial_model.py
@@ -354,11 +354,12 @@ def __update_domain(self):
             self.model['domain'] = self.get_model_template()['domain']
         elif "static" not in self.model['domain'].keys():
             self.model['domain']['static'] = True
-        if "rho" not in self.model['domain']['particles'][0].keys() or \
-                    "c" not in self.model['domain']['particles'][0].keys():
-            for particle in self.model['domain']['particles']:
-                particle['rho'] = particle['mass']/particle['volume']
-                particle['c'] = 10
+        if self.model['domain']['particles']:
+            if "rho" not in self.model['domain']['particles'][0].keys() or \
+                        "c" not in self.model['domain']['particles'][0].keys():
+                for particle in self.model['domain']['particles']:
+                    particle['rho'] = particle['mass']/particle['volume']
+                    particle['c'] = 10
 
 
     def convert_to_model(self):
@@ -498,8 +499,15 @@ def get_particles_from_3d_domain(cls, data):
             xlim = [coord + data['transformation'][0] for coord in data['xLim']]
             ylim = [coord + data['transformation'][1] for coord in data['yLim']]
             zlim = [coord + data['transformation'][2] for coord in data['zLim']]
-        s_domain = Domain.create_3D_domain(xlim=xlim, ylim=ylim, zlim=zlim, nx=data['nx'],
-                                           ny=data['ny'], nz=data['nz'], **data['type'])
+        dimensions = bool(xlim[1] - xlim[0])
+        dimensions += bool(ylim[1] - ylim[0])
+        dimensions += bool(zlim[1] - zlim[0])
+        if dimensions > 2:
+            s_domain = Domain.create_3D_domain(xlim=xlim, ylim=ylim, zlim=zlim, nx=data['nx'],
+                                               ny=data['ny'], nz=data['nz'], **data['type'])
+        else:
+            s_domain = Domain.create_2D_domain(xlim=xlim, ylim=ylim,
+                                               nx=data['nx'], ny=data['ny'], **data['type'])
         domain = cls.__build_stochss_domain(s_domain=s_domain)
         limits = {"x_lim":domain['x_lim'], "y_lim":domain['y_lim'], "z_lim":domain['z_lim']}
         return {"particles":domain['particles'], "limits":limits}

From b94c52e0df78bd17056aad0c46a5ae7b355d89d6 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 10 Nov 2021 11:41:20 -0500
Subject: [PATCH 58/60] Fixed issue with particle ids missing from plot figs.

---
 stochss/handlers/util/stochss_spatial_model.py | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/stochss/handlers/util/stochss_spatial_model.py b/stochss/handlers/util/stochss_spatial_model.py
index 395347856b..552c765eaf 100644
--- a/stochss/handlers/util/stochss_spatial_model.py
+++ b/stochss/handlers/util/stochss_spatial_model.py
@@ -460,6 +460,20 @@ def get_domain_plot(self, path=None, new=False):
         fig = domain.plot_types(return_plotly_figure=True)
         if not fig['data']:
             fig['data'].append(self.__get_trace_data(particles=[], name="Un-Assigned"))
+        else:
+            s_domain = self.load()['domain']
+            for i, d_type in enumerate(s_domain['types']):
+                if len(s_domain['types']) > 1:
+                    particles = list(filter(lambda partictle, key=i: particle['type'] == key,
+                                            s_domain['particles']))
+                else:
+                    particles = s_domain['particles']
+                ids = list(map(lambda particle: particle['particle_id'], particles))
+                index = fig['data'].index(
+                    list(filter(lambda trace: trace['name'].endswith(str(d_type['typeID'])), fig['data']))[0]
+                )
+                fig['data'][index]['name'] = d_type['name']
+                fig['data'][index]['ids'] = ids
         fig['layout']['width'] = None
         fig['layout']['height'] = None
         fig['layout']['autosize'] = True

From edc2c4055a5db2ae0628444900a0b96802c04fb9 Mon Sep 17 00:00:00 2001
From: BryanRumsey <44621966+BryanRumsey@users.noreply.github.com>
Date: Wed, 10 Nov 2021 14:27:45 -0500
Subject: [PATCH 59/60] Addressed review comment

---
 stochss/handlers/util/stochss_notebook.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/stochss/handlers/util/stochss_notebook.py b/stochss/handlers/util/stochss_notebook.py
index 3d3bcae94a..9db45a860d 100644
--- a/stochss/handlers/util/stochss_notebook.py
+++ b/stochss/handlers/util/stochss_notebook.py
@@ -278,7 +278,7 @@ def __create_initial_condition_strings(self, model, pad):
     def __create_domain_string(self, model, pad):
         domain = ["", f"{pad}# Domain",
                   f"{pad}domain = Domain.read_stochss_domain('{self.s_model['path']}')",
-                  f"{pad}self.add_mesh(domain)",
+                  f"{pad}self.add_domain(domain)",
                   "", f"{pad}self.staticDomain = {self.s_model['domain']['static']}"]
         model.extend(domain)
 

From eafbfd2ff1dea21b382f6cccf6c5947fa8dc9094 Mon Sep 17 00:00:00 2001
From: BryanRumsey <44621966+BryanRumsey@users.noreply.github.com>
Date: Wed, 10 Nov 2021 14:29:38 -0500
Subject: [PATCH 60/60] Increased time to 60 seconds

---
 stochss/handlers/util/ensemble_simulation.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/stochss/handlers/util/ensemble_simulation.py b/stochss/handlers/util/ensemble_simulation.py
index ef57e8e16d..31ed2c8253 100644
--- a/stochss/handlers/util/ensemble_simulation.py
+++ b/stochss/handlers/util/ensemble_simulation.py
@@ -106,7 +106,7 @@ def run(self, preview=False, verbose=True):
                 log.info(f"Running {self.g_model.name} preview simulation")
             live_file = f".{self.g_model.name}-preview.json"
             options = {"file_path": live_file}
-            results = self.g_model.run(timeout=5, live_output="graph", live_output_options=options)
+            results = self.g_model.run(timeout=60, live_output="graph", live_output_options=options)
             if verbose:
                 log.info(f"{self.g_model.name} preview simulation has completed")
                 log.info(f"Generate result plot for {self.g_model.name} preview")