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The following commit(s) were added to refs/heads/master by this push:
new 8782ddb Gateways19 tutorial: various edits
8782ddb is described below
commit 8782ddbecc9398a1a601c6c47e4321b7a6664f12
Author: Marcus Christie <[email protected]>
AuthorDate: Fri Sep 20 21:56:04 2019 -0400
Gateways19 tutorial: various edits
---
docs/tutorial/gateways2019_tutorial.md | 119 +++++++++++++++++----------------
1 file changed, 63 insertions(+), 56 deletions(-)
diff --git a/docs/tutorial/gateways2019_tutorial.md
b/docs/tutorial/gateways2019_tutorial.md
index c6988f2..d762400 100644
--- a/docs/tutorial/gateways2019_tutorial.md
+++ b/docs/tutorial/gateways2019_tutorial.md
@@ -28,7 +28,7 @@ tutorial.
## Hands on: run a Gaussian computational experiment in the Django portal
-### Create a portal user account
+### Log into gateways19.scigap.org
First, you'll need a user account. For the in person tutorial we'll have a set
of pre-created usernames and passwords to use. If you are unable to attend the
@@ -39,6 +39,9 @@ the CILogon institution selection page. If you don't find
your institution
listed here, go back to the _Create Account_ page and fill out the form to
create an account with a username, password, etc.
+Once you have an account,
+[log into the Gateways19 portal](https://gateways19.scigap.org/auth/login).
+
After you've logged in, an administrator can grant you access to run the
Gaussian application. During the tutorial we'll grant you access right away and
let you know. If you're at the in person tutorial and using a pre-created
@@ -134,8 +137,8 @@ we'll just create a dummy deployment so that we can invoke
it from the Workspace
Dashboard.
8. Click on the **Deployments** tab.
-9. Click on the **New Deployment** button. Select the first compute resource in
- the drop down list and click **OK**.
+9. Click on the **New Deployment** button. Select the _mike.hpc.lsu.edu_
compute
+ resource in the drop down list and click **OK**.
10. For the _Application Executable Path_, provide the value `/usr/bin/true`.
This is the only required field.
11. Click **Save** at the bottom of the screen.
@@ -338,6 +341,7 @@ use as a development environment.
tutorial files and clone <https://github.com/machristie/gateways19-tutorial>
```bash
+cd $HOME
git clone https://github.com/machristie/gateways19-tutorial.git
```
@@ -352,6 +356,7 @@ unzip gateways19-tutorial/airavata-django-portal.zip
4. Create a virtual environment.
```bash
+cd $HOME/airavata-django-portal
python3 -m venv venv
```
@@ -364,7 +369,6 @@ source venv/bin/activate
6. Install the airavata-django-portal dependencies in the virtual environment.
```
-cd airavata-django-portal
pip install -r requirements.txt
```
@@ -382,6 +386,7 @@ python manage.py runserver
2. Run
```
+cd $HOME
git clone https://github.com/machristie/gateways19-tutorial.git
cd gateways19-tutorial
docker run --name gateways19-tutorial -p 8000:8000 -v $PWD:/code
machristie/gateways19-tutorial
@@ -400,8 +405,8 @@ for now by typing `Control-C` in the console.
1. We've defined a custom output view provider, called
GaussianEigenvaluesViewProvider, in `output_views.py`. Open
- `gateways19-tutorial/gateways19_tutorial/output_views.py` in your editor and
- we'll look at how it is implemented. First we add some imports
+ `$HOME/gateways19-tutorial/gateways19_tutorial/output_views.py` in your
+ editor and we'll look at how it is implemented. First we add some imports
```python
import io
@@ -590,7 +595,7 @@ Django portal virtual environment isn't activated, see step
5 in the previous
section. We'll also use pip to install the output viewer's dependencies.
```bash
-cd ../gateways19-tutorial
+cd $HOME/gateways19-tutorial
pip install -r requirements.txt
python setup.py develop
```
@@ -604,7 +609,6 @@ $ cd /code
$ pip install -r requirements.txt
$ python setup.py develop
$ exit
-docker stop gateways19-tutorial
```
### Use the GaussianEigenvaluesViewProvider with the Gaussian log output file
@@ -618,7 +622,7 @@ additional output view of the file.
**Running Django locally**
```
-cd ../airavata-django-portal/
+cd $HOME/airavata-django-portal/
python manage.py runserver
```
@@ -628,7 +632,7 @@ python manage.py runserver
docker start -a gateways19-tutorial
```
-2. Log into your local Django Portal instance.
+2. Log into your local Django Portal instance at <http://localhost:8000>.
3. In the menu at the top, select **Settings**.
4. Click on the **Gaussian16** application.
5. Click on the **Interface** tab.
@@ -671,14 +675,25 @@ This is an intentionally simple example to demonstrate
the general principle of
using custom REST APIs and UI to setup, execute and post-process/visualize the
output of a computational experiment.
+We've already registered the _Echo_ application with the portal, meaning we
+registered its interface and on which compute resource it is deployed.
+
+A
+[Django _application_ or
_app_](https://docs.djangoproject.com/en/2.2/ref/applications/)
+is a Python package that may include Django views, url mappings, models, etc.
+It's a way of creating a kind of plug-in that integrates with a Django server.
+We'll create this custom user interface by developing a Django app that uses
the
+Django framework as well as the Airavata Django Portal REST APIs and JS
library.
+
### Setting up the Django app
To start, we'll just create a simple "Hello World" page for the Django app and
get it properly registered with the local Django Portal instance.
1. In the `gateways19-tutorial` directory, open
- `gateways19_tutorial/templates/gateways19_tutorial/hello.html`. Some of the
- HTML view is commented out. The following is the uncommented content:
+
`$HOME/gateways19-tutorial/gateways19_tutorial/templates/gateways19_tutorial/hello.html`.
+ Some of the HTML view is commented out. The following is the uncommented
+ content:
```xml
{% extends 'base.html' %}
@@ -694,7 +709,7 @@ get it properly registered with the local Django Portal
instance.
{% endblock content %}
```
-2. Open the file `gateways19_tutorial/apps.py`:
+2. Open the file `$HOME/gateways19-tutorial/gateways19_tutorial/apps.py`:
```python
from django.apps import AppConfig
@@ -711,7 +726,7 @@ This the main metadata for this custom Django app. Besides
the normal metadata
that the Django framework expects, this also defines a display name
(`verbose_name`) and an icon (`fa_icon_class`) to use for this custom app.
-3. Open the file `gateways19_tutorial/views.py`:
+3. Open the file `$HOME/gateways19-tutorial/gateways19_tutorial/views.py`:
```python
from django.shortcuts import render
@@ -725,7 +740,7 @@ def hello_world(request):
This view will simply display the template created in the previous step.
-4. Open the file `gateways19_tutorial/urls.py`:
+4. Open the file `$HOME/gateways19-tutorial/gateways19_tutorial/urls.py`:
```python
from django.conf.urls import url, include
@@ -757,35 +772,7 @@ gateways19_tutorial =
gateways19_tutorial.apps:Gateways19TutorialAppConfig
)
```
-6. When we update the metadata, we need to install it again into the Django
- Portal's virtual environment. Since the metadata was already there in the
- file, we don't need to reinstall this Python package, but keep in mind you
- would need to reinstall it if you are creating one of these from scratch.
- Here's how you would reinstall it:
-
-**Running Django locally**
-
-Make sure that the Django Portal's virtual environment is activated and run:
-
-```bash
-cd ../gateways19-tutorial
-# Activate the airavata-django-portal virtual environment if not already
activated
-source ../venv/bin/activate
-python setup.py develop
-```
-
-**Running Docker container**
-
-```bash
-docker start gateways19-tutorial
-docker exec -it gateways19-tutorial /bin/bash -l
-$ cd /code
-$ python setup.py develop
-$ exit
-docker stop gateways19-tutorial
-```
-
-7. Start the Django Portal server again:
+6. Start the Django Portal server again:
**Running Django locally**
@@ -801,16 +788,17 @@ python manage.py runserver
docker start -a gateways19-tutorial
```
-Now you should be able to log into the portal locally and see **Gateways 19
-Tutorial** in the drop down menu in the header (click on **Workspace** then you
-should see it in that menu).
+Now you should be able to [log into the portal locally](http://localhost:8000)
+and see **Gateways 19 Tutorial** in the drop down menu in the header (click on
+**Workspace** then you should see it in that menu).
### Adding a list of "Hello" greetings
Now we'll create a REST endpoint in our custom Django app that will return
greetings in several languages.
-1. In the `views.py` file, we add the following import:
+1. In the `$HOME/gatewways19-tutorial/gateways19_tutorial/views.py` file, we
add
+ the following import:
```python
from django.http import JsonResponse
@@ -842,7 +830,8 @@ def languages(request):
}]})
```
-3. In `urls.py` we add a url mapping for the `languages` view:
+3. In `$HOME/gateways19-tutorial/gateways19_tutorial/urls.py` we add a url
+ mapping for the `languages` view:
```python
urlpatterns = [
@@ -851,10 +840,12 @@ urlpatterns = [
]
```
-4. In `hello.html`, uncomment the comment that starts
- `<!-- Adding a list of "Hello" greetings` on line 11 and ends on line 21.
- That is, just delete lines 11 and 21. This adds a `<select>` element to the
- template which will be used to display the greeting options:
+4. In
+
`$HOME/gateways19-tutorial/gateways19_tutorial/templates/gateways19_tutorial/hello.html`,
+ uncomment the comment that starts `<!-- Adding a list of "Hello" greetings`
+ on line 11 and ends on line 21. That is, just delete lines 11 and 21. This
+ adds a `<select>` element to the template which will be used to display the
+ greeting options:
```html
...
@@ -915,7 +906,9 @@ you should see a dropdown of greetings in several
languages, like so:
Now we'll use the `AiravataAPI` library to load the user's recent experiments.
-1. In `hello.html`, uncomment the comment that begins with
+1. In
+
`$HOME/gateways19-tutorial/gateways19_tutorial/templates/gateways19_tutorial/hello.html`,
+ uncomment the comment that begins with
`<!-- Displaying a list of recent experiments` on line 21 or so and ends on
line 45. This adds table to display recent experiments to the bottom of
`hello.html`:
@@ -958,7 +951,7 @@ Now we'll use the `AiravataAPI` library to load the user's
recent experiments.
{% endblock content %}
```
-2. Now we'll use the ExperimentServiceService to load the user's most recent 5
+2. Now we'll use the ExperimentSearchService to load the user's most recent 5
_Echo_ experiments and display them in the table. We add the following to
the
end of the _scripts_ block in `hello.html`:
@@ -1004,7 +997,9 @@ The user interface should now look something like:
Now we'll use `AiravataAPI` to submit an Echo job.
-1. We add a click handler to the _Run_ button that gets the selected greeting
+1. In
+
`$HOME/gateways19-tutorial/gateways19_tutorial/templates/gateways19_tutorial/hello.html`
+ we add a click handler to the _Run_ button that gets the selected greeting
value:
```javascript
@@ -1234,3 +1229,15 @@ function loadExperiments() {
You can try out this custom Django app in the deployed instance of the tutorial
portal where it really does download and parse the standard out.
+
+## Resources
+
+You can browser the final version of the _gateways19-tutorial_ code at
+<https://github.com/machristie/gateways19-tutorial/tree/solution>. If you get
+stuck at some point with the tutorial you can skip to the solution by running
+the following git command in your _gateways19-tutorial_ repo:
+
+```bash
+cd $HOME/gateways19-tutorial
+git reset --hard origin/solution
+```
