SciPost

This repository carries the entire codebase for the scipost.org scientific publication portal.

Project organization

Development work for SciPost is headed by Jean-Sébastien Caux and Jorran de Wit. Bug reports, issues, suggestions and ideas can be emailed to techsupport@scipost.org.

If you are competent in web development and would like to join our core development team, please email your credentials to jscaux@scipost.org.

License

This codebase is released under the terms of the GNU Affero General Public License (Version 3, 19 November 2007).

Dependencies

SciPost is written in Python 3.5 using Django 1.11 and requires PostgreSQL 9.4 or higher. Python dependencies are listed in requirements.txt. Frontend dependencies are managed by NPM in package.json.

Getting started

Database

Make sure that PostgreSQL is installed and running and that a database with user is set up. A good guide how to do this can be found here (NOTE: stop before the 'Update settings' part).

Python version

Make sure you're using Python 3.5. You are strongly encouraged to use a virtual environment.

$ pyvenv scipostenv
$ source scipostenv/bin/activate

Now install dependencies:

(scipostenv) $ pip install -r requirements.txt

Frontend dependencies

NPM (version 5.x; tested on v5.3.0) will take care of frontend dependencies. To install all packages now run:

(scipostenv) $ npm install

Settings

In this project, many settings are not sensitive and are thus tracked using Git. Some settings are however secret. These settings may be saved into the secrets.json file in the root of the project. The minimum required structure is as follows (please mind the non-empty, but still invalid SECRET_KEY):

{
  "SECRET_KEY": "<key>",
  "DB_NAME": "",
  "DB_USER": "",
  "DB_PWD": ""
}

The settings file itself is saved into SciPost_v1/settings/local_<name>.py. Be sure to wildcard import the base.py file in the top of your settings file. To run the server, use one of two ways. Either:

(scipostenv) $ ./manage.py runserver --settings=SciPost_v1.settings.local_<name>

... or for convenience, export the same settingsfile path to the DJANGO_SETTINGS_MODULE variable, so that one can run the django commands by default:

(scipostenv) $ export DJANGO_SETTINGS_MODULE="SciPost_v1.settings.local_<name>"

One can of course also add this variable to the ~/.bash_profile for convenience.

Mail

In the mails application a special Email Backend is defined. This will write all emails to the database. To use this backend, in the settings set the the variable EMAIL_BACKEND as:

# settings.py
EMAIL_BACKEND = 'mails.backends.filebased.ModelEmailBackend'
EMAIL_BACKEND_ORIGINAL = 'mails.backends.filebased.EmailBackend'

A management command is defined to send the unsent mails in the database. This management command uses the Email Backend defined in the settings under variable EMAIL_BACKEND_ORIGINAL. If not defined, this defaults to the Django default: django.core.mail.backends.smtp.EmailBackend.

(scipostenv) $ ./manage.py send_mails

Check, double check

To make sure everything is set up and correctly configured, run:

(scipostenv) $ ./manage.py check

Module bundler

Webpack takes care of assets in the scipost/static/scipost/assets folder. To (re)compile all assets into the static_bundles folder, simply run:

(scipostenv) $ npm run webpack

While editing assets, it may be helpful to put Webpack in watch mode. This will recompile your assets in real time. To do so, instead of the above command, run:

(scipostenv) $ npm run webpack-live

Sass and Bootstrap

Styling will mainly be configured using .scss files in the scipost/static/scipost/scss/preconfig.scss file, relying on Bootstrap v4.0.0-beta. A full list of variables available by default can be found here. All modules are configured in the .bootstraprc file. All modules are disabled by default.

Collectstatic

In order to collect static files from all INSTALLED_APPS (i.e. the assets managed by Webpack), run:

(scipostenv) $ ./manage.py collectstatic

This will put all static files in the STATIC_ROOT folder defined in your settings file. If needed, you can remove stale static files through:

(scipostenv) $ ./manage.py collectstatic --clear

Create and run migrations

Now that everything is set up, we can create the relevant tables in the database:

(scipostenv) $ ./manage.py migrate

Create a superuser

In order to use the admin site, you'll need a superuser account, which can be created using:

(scipostenv) $ ./manage.py createsuperuser

Create groups and permissions

Groups and their respective permissions are set using the management command:

(scipostenv) $ ./manage.py add_groups_and_permissions

Run server

You are now ready to run the server:

(scipostenv) $ ./manage.py runserver

Contributors

Users of the SciPost portal are known as Contributors and are created through the registration form accessible from the home page.

You can create a number of users, and use the admin site to give them various permissions through memberships of certain groups. For example, you'll want members of the SciPost Administrators and Editorial Administrators groups in order to access the internal management and editorial tools.

Initial data

If you're working on an (almost) empty test database, you can easily fill it using one of the built-in commands. To create a few instances for each available object, simply run:

(scipostenv) $ ./manage.py populate_db --all

Run the same command with the --help argument to find arguments to create instances for individual models:

(scipostenv) $ ./manage.py populate_db --help

Maintaining database migrations

Every time fields in any of the models change, a database migration needs to be created and applied. The first documents a database change and its inverse, the second actually changes the database.

Make sure to commit the migration to Git after applying it, so other developers can use them.

(scipostenv) $ ./manage.py makemigrations
(scipostenv) $ ./manage.py migrate

Search engine

Django Haystack is used to handle search queries. The search engine needs indexing before you can use it:

(scipostenv) $ ./manage.py update_index -u default

Models involved in searches are re-indexed using post_save signals.

Scheduled tasks

The tasks that involve large requests from CR are supposed to run in the background. For this to work, Celery is required. The following commands assume that you are in the scipost_v1 main folder, inside the right virtual environment.

Celery depends on a broker, for which we use RabbitMQ. Start it with

nohup rabbitmq-server > ../logs/rabbitmq.log 2>&1 &

Then the Celery worker itself:

nohup celery -A SciPost_v1 worker --loglevel=info -E > ../logs/celery_worker.log 2>&1 &

And finally beat, which enables setting up periodic tasks:

nohup celery -A SciPost_v1 beat --loglevel=info --scheduler django_celery_beat.schedulers:DatabaseScheduler > ../logs/celery_beat.log 2>&1 &

Documentation

All project documentation is gathered from .rst files and code-embedded docstrings. The documentation for the codebase can be found in docs/codebase.

Sphinxdoc

The documentation is saved in the local database as a Project with name SciPost Codebase, with slug codebase and path /docs/codebase (this project should be manually created in the admin under the Sphinxdoc app).

To update the docs, simply run

(scipostenv) $ ./manage.py updatedoc -b codebase

The documentation is then viewable by navigating to docs/codebase.

There are also other Projects containing information about SciPost, user guides etc. The list can be found on by viewing docs in the browser.

Locally-served documentation

The documentation can be rendered using Sphinx. Note that rendering documentation is only available from the virtual environment - and only when the host settings have been configured.

To build the documentation, run:

(scipostenv) $ cd docs/[project slug]
(scipostenv) $ make html

for each of the documentation projects. After this, generated documentation are available in docs/[project slug]/_build/html.

Templated emails

The mails app is used as the (templated) mailing processor of SciPost. Each email is defined using two files: the template and the configuration file.

Each mail is defined using certain general configuration possibilities. These options are defined in the json configuration file or are overwritten in the methods described below. These fields are:

• subject {string}

The subject of the mail.

• recipient_list and bcc {list}

Both fields are lists of strings. Each string may be either a plain mail address, eg. example@scipost.org, or it may represent a certain relation to the central object. For example, one may define:

>>> sub_1 = Submission.objects.first()
>>> mail_util = DirectMailUtil([...], object=sub_1, recipient_list=['example@scipost.org', 'submitted_by.user.email'])

• from_email {string}

For this field, the same flexibility and functionality exists as for the recipient_list and bcc fields. However, this field should always be a single string entry.

>>> mail_util = DirectMailUtil([...], from_email='noreply@scipost.org')

• from_name {string}

The representation of the mail sender.

Central object

Using a single Model instance

The "central object" is a django.db.models.Model instance that will be used for the email fields if needed and in the template. The mail engine will try to automatically detect a possible Model instance and save this in the template context as <Model.verbose_name> and object. The keyword you use to send it to the mail engine is not relevant for this method, but will be copied to be used in the template as well.

Example

>>> sub_1 = Submission.object.first()
>>> mail_util = DirectMailUtil([...], weird_keyword=sub_1)

Now, in the template, the variables weird_keyword, submission and object will all represent the sub_1 instance. For example:

<h1>Dear {{ weird_keyword.submitted_by.get_title_display }} {{ object.submitted_by.user.last_name }},</h1>
<p>Thank you for your submission: {{ submission.title }}.</p>

Using multiple Model instances

If a certain mail requires more than one Model instance, it is required to pass either a instance or object parameter for the mail engine to determine the central object.

Example

>>> sub_1 = Submission.object.first()
>>> report_1 = Report.object.first()
>>> mail_util = DirectMailUtil([...], submission=sub_1, report=report_1)
ValueError: "Multiple db instances are given."

Here, it is required to pass either the instance or object parameter, eg.:

>>> mail_util = DirectMailUtil([...], object=sub_1, report=report_1)

Configuration file

File: templates/email/<mail_code>.json

Each mail is configured with a json file, which at least contains a subject and recipient_list value. The other fields are optional. An example of all available configuration fields are shown:

{
    "subject": "Foo subject",
    "recipient_list": [
        "noreply@scipost.org"
    ],
    "bcc": [
        "secret@scipost.org"
    ],
    "from_email": "server@scipost.org",
    "from_name": "SciPost Techsupport"
}

Template file

File: templates/email/<mail_code>.html

Any mail will be defined in the html file using the conventions as per Django's default template processor.

Direct mail utility

The fastest, easiest way to use templated emails is using the DirectMailUtil class.

class mails.utils.DirectMailUtil(*mail_code, delayed_processing=True, subject='', recipient_list=[], bcc=[], from_email='', from_name='', *template_variables)

Attributes

• mail_code {string}

The unique code refereeing to a template and configuration file.

• delayed_processing {boolean, optional}

Execute template rendering in a cronjob to reduce executing time.

• subject {string, optional}

Overwrite the subject field defined in the configuration field.

• recipient_list {list, optional}

Overwrite the recipient_list field defined in the configuration field.

• bcc {list, optional}

Overwrite the bcc field defined in the configuration field.

• from_email {string, optional}

Overwrite the from_email field defined in the configuration field.

• from_name {string, optional}

Overwrite the from_name field defined in the configuration field.

• **template_variables

Append any keyword argument that may be used in the email template.

Methods

• send_mail()

Send the mail as defined on initialization.

Basic example

>>> from mails.utils import DirectMailUtil
>>> mail_util = DirectMailUtil('test_mail_code_1')
>>> mail_util.send_mail()

This utility is protected to prevent double sending. So now, the following has no effect anymore:

>>> mail_util.send_mail()

Class-based view editor

This acts like a regular Django class-based view, but will intercept the post request to load the email form and submit when positively validated.

This view may be used as a generic editing view or DetailView.

class mails.views.MailView

This view is a basic class-based view, which may be used as basic editor for a specific templated email.

Attributes

• mail_code {string}

The unique code refereeing to a template and configuration file.

• mail_config {dict, optional}

Overwrite any of the configuration fields of the configuration file: * subject {string} * recipient_list {list} * bcc {list} * from_email {string} * from_name {string}

• mail_variables {dict, optional}

Append extra variables to the mail template.

• fail_silently {boolean, optional}

If set to False, raise PermissionDenied is can_send_mail() returns False on POST request.

Methods

• can_send_mail()

Control permission to actually send the mail. Return a boolean, returns True by default.

• get_mail_config()

Return an optional explicit mail configuration. Return a dictionary, returns mail_config by default.

class mails.views.MailFormView

This view may be used as a generic editing view, and will intercept the POST request to let the user edit the email before saving the original form and sending the templated mail.

Attributes

• form_class {django.forms.ModelForm | django.forms.Form}

The original form to use as in any regular Django editing view.

• mail_code {string}

The unique code refereeing to a template and configuration file.

• mail_config {dict, optional}

Overwrite any of the configuration fields of the configuration file: * subject {string} * recipient_list {list} * bcc {list} * from_email {string} * from_name {string}

• mail_variables {dict, optional}

Append extra variables to the mail template.

• fail_silently {boolean, optional}

If set to False, raise PermissionDenied is can_send_mail() returns False on POST request.

Methods

• can_send_mail()

Control permission to actually send the mail. Return a boolean, returns True by default.

• get_mail_config()

Return an optional explicit mail configuration. Return a dictionary, returns mail_config by default.

Basic example

# <app>/views.py
from mails.views import MailView

class FooView(MailView):
    mail_code = 'test_mail_code_1'

# <app>/urls.py
from django.conf.urls import url

from .views import FooView

urlpatterns = [
    url(r'^$', FooView.as_view(), name='foo'),
]

Function-based view editor

Similar as to the MailView it is possible to have the user edit a templated email before sending in function-based views, using the MailEditorSubview.

class mails.views.MailEditorSubview(*request, mail_code, header_template='', context={}, subject='', recipient_list=[], bcc=[], from_email='', from_name='', *template_variables)

Attributes

• request {django.http.HttpResponse}

The HttpResponse which is typically the first parameter in a function-based view.

• mail_code {string}

The unique code refereeing to a template and configuration file.

• header_template {string, optional}

Any template that may be used in the header of the edit form.

• context {dict, optional}

A context dictionary as in any usual Django view, which may be useful combined with header_template.

• subject {string, optional}

Overwrite the subject field defined in the configuration field.

• recipient_list {list, optional}

Overwrite the recipient_list field defined in the configuration field.

• bcc {list, optional}

Overwrite the bcc field defined in the configuration field.

• from_email {string, optional}

Overwrite the from_email field defined in the configuration field.

• from_name {string, optional}

Overwrite the from_name field defined in the configuration field.

• **template_variables

Append any keyword argument that may be used in the email template.

Methods

• is_valid()

See if data is returned and valid, similar to Django forms. Returns a boolean.

• interrupt()

Interrupt request by rendering the templated email form. Returns a HttpResponse.

• send_mail()

Send email as edited by the user in the template.

Basic example

from submissions.models import Submission
from mails.views import MailEditorSubview

def any_method_based_view(request):
    submission = Submission.objects.first()
    mail_request = MailEditorSubview(request, 'test_mail_code_1', object=submission)
    if mail_request.is_valid():
        mail_request.send_mail()
        return redirect('reverse:url')
    else:
        return mail_request.interrupt()

Important epilogue

Every templated mail defined in the templates/email/ folder will be tested for proper configuration. This tests includes tests on the configuration file and existence of the template. Important note: it does not test the content of the templates (read: the variables used in the template). To run these, and all other mail-related unit tests, simple run the following:

(scipostenv) $ ./manage.py test mails.tests -k

A successful test ends by printing "OK". In any other case, errors will be raised.

Django-extensions

django-extensions provide added commands like ./manage.py shell_plus, which preloads all models in a shell session. Additional imports may be specified in settings.py as follows:

SHELL_PLUS_POST_IMPORTS = (
    ('theses.factories', ('ThesisLinkFactory')),
    ('comments.factories', ('CommentFactory')),
)

Scheduled tasks

The tasks that involve large requests from CR are supposed to run in the background. For this to work, Celery is required. The following commands assume that you are in the scipost_v1 main folder, inside the right virtual environment.

Celery depends on a broker, for which we use RabbitMQ. On MacOS one may simply install this by executing:

$ brew update
$ brew install rabbitmq

To start the RabbitMQ broker:

nohup nice rabbitmq-server > ../logs/rabbitmq.log 2>&1 &

Then the Celery worker itself:

nohup nice celery -A SciPost_v1 worker --loglevel=info -E > ../logs/celery_worker.log 2>&1 &

And finally beat, which enables setting up periodic tasks:

nohup nice celery -A SciPost_v1 beat --loglevel=info --scheduler django_celery_beat.schedulers:DatabaseScheduler > ../logs/celery_beat.log 2>&1 &

Note: on the staging server, these commands are contained in two shell scripts in the scipoststg home folder. Just run

./start_celery.sh