Passenger apps gateway tutorial

.github/workflows/publish.yml

@@ -16,7 +16,7 @@ jobs:
 
     steps:
       - name: checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Make Html
         run: |

source/installation/modify-system-security.rst

@@ -36,6 +36,7 @@ The custom SELinux booleans provided by the OnDemand SELinux policy:
 * ``ondemand_use_kubernetes`` (**default=off**): Allow OnDemand to interact with Kubernetes.
 * ``ondemand_use_ldap`` (**default=off**): Allows OnDemand to interact with remote LDAP servers. This does not affect Apache LDAP authentication. This is only necessary if the PUN is interacting with LDAP ports.
 * ``ondemand_use_kerberos`` (**default=off**): Allow OnDemand to interact with Kerberos.
+* ``ondemand_use_smtp`` (**default=off**): Allow OnDemand to interact with SMTP for sending emails.
 
 The following SELinux booleans are enabled by the ``ondemand-selinux`` package:
 

source/reference/files/ondemand-d-ymls.rst

@@ -728,3 +728,56 @@ Configuration Properties
     .. code-block:: yaml
 
       hide_app_version: true
+
+.. describe:: globus_endpoints (Array<Object>, null)
+
+  Add a Globus button to the file browser that opens the current directory
+  in the Globus transfer web app.
+
+  Default
+    Null, do not enable the Globus button
+
+  Example
+    Use a single endpoint for the whole filesystem.
+
+    .. code-block:: yaml
+
+       globus_endpoints:
+         - path "/"
+           endpoint: "716de4ac-xxxx-xxxx-xxxx-xxxxxxxxxxxx"
+           endpoint_path "/"
+
+  Example
+    Use multiple endpoints.
+
+    .. code-block:: yaml
+
+       globus_endpoints:
+         - path: "/home"
+           endpoint: "716de4ac-xxxx-xxxx-xxxx-xxxxxxxxxxxx"
+           endpoint_path: "/home"
+
+         - path: "/project"
+           endpoint: "9f1fe759-xxxx-xxxx-xxxx-xxxxxxxxxxxx"
+           endpoint_path: "/project"
+
+  Example
+    When pathnames differ between the filesystem and endpoint.
+
+    .. code-block:: yaml
+
+       globus_endpoints:
+         - path: "/project"
+           endpoint: "9f1fe759-xxxx-xxxx-xxxx-xxxxxxxxxxxx"
+           endpoint_path: "/"
+
+  Example
+    Reference the home directory of the current user.
+
+    .. code-block:: yaml
+
+      globus_endpoints:
+        - path: "<%=  Etc.getpwnam(Etc.getlogin).dir %>"
+          endpoint: "9f1fe759-xxxx-xxxx-xxxx-xxxxxxxxxxxx"
+          endpoint_path: "/"
+

source/tutorials/tutorials-passenger-apps.rst

@@ -12,3 +12,4 @@ At the bottom of the page is a list of tutorials for developing Passenger apps f
    :caption: Tutorials
 
    tutorials-passenger-apps/ps-to-quota
+   tutorials-passenger-apps/science-gateway

source/tutorials/tutorials-passenger-apps/science-gateway.rst

@@ -0,0 +1,130 @@
+.. _app-development-tutorials-passenger-apps-science-gateway:
+
+Creating a Science Gateway App
+==============================
+
+Overview of App
+---------------
+
+We will make a science gateway that displays information retrieved, 
+processed, and rendered in the browser using phusion passenger and 
+the python programming language.
+
+The app we will be copying is: https://github.com/OSC/ood-example-science-gateway. Running
+this app at the start you should only see:
+
+.. figure:: /images/passenger-python-flask-app.png
+   :align: center
+
+   Initial state of app after launch.
+
+And by the end of this tutorial the app will look like the following:
+
+.. figure:: /images/app-sharing-2.png
+   :align: center
+
+   Final state of app after tutorial.
+
+This **assumes** you have followed the directions to :ref:`enabling-development-mode` in the
+Dashboard.
+
+Our app will use and have the following:
+
+#. Bootstrap 5 for nice views.
+#. The navbar in the app will contain a link back to the ood dashboard.
+#. The app will make requests for us which are then processed and returned for our view.
+#. It is built using `Python's Flask <https://github.com/pallets/flask>`__ which 
+   is similar to the `Sinatra framework <https://github.com/sinatra/sinatra>`__, 
+   or `Node.js's Express <https://github.com/expressjs/express>`__ .
+
+Benefits
+........
+
+This will provide users with an example of how to build their own 
+science gateway in OnDemand and hosted through OnDemand. 
+
+By doing so, we will se that OnDemand provides great flexibility in 
+allowing you to work in either ``ruby``, ``node.js``, or 
+``python`` which all integrate easily with Passenger Phusion.
+
+But *any* language can now be supported as of **Passenger Phusion 6**, as long 
+as your app:
+
+#. Speaks ``http``.
+#. Binds to a ``port``.
+#. Runs in the foreground.
+#. **And The language of your choice and its build tools are available on your system.**
+
+The App's Packages and Code
+...........................
+
+For any app we develop, the key thing here will be that we can use our *own packages* and code 
+to build what we are trying to do, **assuming your cluster has the language and tooling in place.**
+
+We will be using ``python3`` in this example with a combination of ``venv`` and ``pip`` to build our project.
+
+This will enable us to login to OnDemand and then work within our development sandbox to use 
+code from *our own* python modules. This could just as easily be our own ``gems`` if we used 
+``ruby`` or packages if we used ``node``.
+
+This means we will have to do some setup to ensure our app uses our own designated packages and 
+not OnDemand's or the system packages. This gives users a great deal of flexibility in how they develop.
+
+Phusion Passenger Project Structure
+...................................
+
+The project structure is simply following a common pattern used when developing a phusion passenger app.
+
+This mainly consists of an entrypoint file for passenger phusion, and then various files to be used by our 
+webserver to be served or executed by the app.
+
+You can see this explanation and the various forms of the files and their names in 
+the `Passenger project structure documentation <https://www.phusionpassenger.com/docs/tutorials/fundamental_concepts/python/>`__
+
+Files and Their Purpose
+.......................
+
+.. list-table:: Initial Skeleton Files
+   :header-rows: 1
+
+   * - File
+     - Description
+   * - ``passenger_wsgi.py``
+     - Entry point of the Phusion Passenger app which expects the file to be named ``passenger_wsgi.py``. The contents and file name will depend on the application and the web framework used.
+   * - ``app.rb``
+     - Flask app config and routes.
+   * - ``templates/index.html``
+     - the main section of the html page template using ``render_template()`` commands from ``app.py``.
+       which auto-escapes output of ERB tags by default (for security)
+   * - ``teamplates/layout.html``
+     - the rendered HTML from ``views/index.html`` is inserted into this layout,
+       where css and javascript files are included.
+   * - ``tmp/always_restart.txt``
+     - A Phusion Passenger convention to restart our server each request to see our code changes. The file should be empty.
+
+Build From Scratch
+..................
+
+#. ``cd`` into you dev directory, which should have already been setup as per prereqs above.
+#. ``mkdir science_gateway_app`` and ``cd`` into it.
+#. Initialize our environment with ``python3 -m venv .venv``.
+#. ``touch passenger_wsgi.py``. Thise creates a WSGI file in the app's root directory. 
+#. ``touch app.py``
+#. ``mkdir -p tmp/always_restart.txt``. No content needed as this is a passenger convention to reload our changes each request.
+#. ``mkdir -p templates/index.html``
+
+Build From GitHub
+-----------------
+There are going to be 2 branches for this repo. The ``completed`` branch has all the code we are going to write and the 
+completed app.
+
+The ``master`` branch is what will have the initial project skeleton files we need to begin in order to follow the steps below.
+
+Development
+-----------
+
+Brand App
+---------
+
+Publish App
+-----------