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Install

The sourcecode can be obtained via::

git clone https://github.com/ialbert/biostar-central.git

Getting started

Get the source and switch to the source directory. The recommended installation is via virtualenv and pip::

# Install the requirements.
pip install --upgrade -r conf/requirements/base.txt

# Initialize, import test data and run the site.
./biostar.sh init import run

Visit http://localhost:8080 to see the site loaded with default settings.

The default admin is 1@lvh.me password 1@lvh.me. The default email handler will print to the console. You can reset the password for any user then copy paste the password reset url into the browser.

Run the manager on its own to see all the commands at your disposal::

./biostar.sh

To enable searching you must the content with::

./biostar.sh index

Blog Aggregation

Biostar has the ability to aggregate blog feeds and allow searching and linking to them. List the RSS feeds in a file then::

# Initialize with new feed urls (see example)
python manage.py planet --add biostar/apps/planet/example-feeds.txt

# Download all feeds (usually performed daily)
python manage.py planet --download

# Add one new blog entry for each feed the downloaded file (if there is any)
python manage.py planet --update 1

Sending Emails

By default Biostar can send email via the standard email facilities that Django provides see https://docs.djangoproject.com/en/dev/topics/email/

Biostar offers a few helper functions that allow emailing via Amazon SES::

# Amazon SES email settings.
EMAIL_USE_TLS = True
EMAIL_BACKEND = 'biostar.mailer.SSLEmailBackend'

Note: sending an email blocks the server thread! This means that the server process allocated to sending email will stop serving other users while the email is being sent. For low traffic sites this may not be a problem but for higher traffic sites the approach is not feasible.

To address that Biostar also implements a Celery based email backend that queues up and sends emails as separate worker processes, independently of the main server. Setting that up is very simple via the settings::

# Amazon SES email sent asynchronously.
EMAIL_USE_TLS = True
EMAIL_BACKEND = 'biostar.mailer.CeleryEmailBackend'
CELERY_EMAIL_BACKEND = 'biostar.mailer.SSLEmailBackend'

Receiving Emails

Biostar can be set up to receive emails and deposit them into threads. This allows users to use emails to post to Biostar.

To enable this functionality the site admins need to set up an email system that can, when a matching and address can perform a POST action to a predetermined URL. For example when delivering email via postmaster utility on linux the etc/alias file would need to contain::

reply: "| curl -F key='123' -F body='<-' https://www.mybiostar.org/local/email/

The above line will trigger a submit action every time that an email is received that matches the address words reply. For example: reply@server.org

Important: Biostar will send emails as reply+1238429283+code@server.org. The segment between the two + signs is unique to the user and post and are required for the post to be inserted in the correct location. The email server will have to properly interpret the + signs and route this email via the reply@server.org address. Now the default installations of postmaster already work this way, and it is an internal settings to postmaster. This pattern that routes the email must match the EMAIL_REPLY_PATTERN setting in Biostar.

The key=123 parameter is just an additional measure that prevent someone flooding the email service. The value is set via the EMAIL_REPLY_SECRET_KEY settings.

The default settings that govern the email reply service are the following::

# What address pattern will handle the replies.
EMAIL_REPLY_PATTERN = "reply+%s+code@biostars.io"

# The format of the email address that is sent
EMAIL_FROM_PATTERN = u'''"%s on Biostar" <%s>'''

# The secret key that is required to parse the email
EMAIL_REPLY_SECRET_KEY = "abc"

# The subject of the reply goes here
EMAIL_REPLY_SUBJECT = u"[biostar] %s"

Note: when you set the alias remember to restart the services::

sudo postalias /etc/alias
sudo service postmaster restart

A simpler setup that requires no local SMTP servers could reply on commercial services such as mailgun and others.

Social authentication

The social logins settings will need to be initialized with the proper authentication parameters. Typically this involves creating an application at the provider and obtaining the credentials.

See the conf/defaults.env for the proper variable naming.

Adding Facebook authentication:

Adding Google authentication:

Twitter:

ORCID:

External authentication

Other domains can provide authentication for Biostar by setting a cookie with a certain value. For this to work Biostar will have to be set to run as a subdomain of the hosting site.

Cookie settings ^^^^^^^^^^^^^^^

The cookie value needs to contain the email:hash as value. For exampl if the EXTERNAL_AUTH django settings are::

# Cookie name, cookie secret key pair
EXTERNAL_AUTH = [
    ("foo.bar.com", "ABC"),
]

If an unauthenticated user sends a cookie named foo.bar.com with the value::

foo@bar.com:d46d8c07777e3adf739cfc0c432759b0

then Biostar will automatically log in the user. It will automatically create an account for the user if the email does not already exist.

Setting the EXTERNAL_LOGIN_URL and EXTERNAL_LOGOUT_URL settings will also perform the redirects to the external site login and logout urls::

EXTERNAL_LOGIN_URL = "http://some.site.com/login"
EXTERNAL_LOGOUT_URL = "http://some.site.com/logout"

Generating the value is simple like so::

email = "foo@bar.com"
digest = hmac.new(key, email).hexdigest()
value = "%s:%s" % (email, digest)

Prefill post ^^^^^^^^^^^^

Set the title, tag_val, content and category fields of a get request to pre-populate a question::

http://localhost:8080/p/new/post/?title=Need+help+with+bwa&tag_val=bwa+samtools&content=What+does+it+do?&category=SNP-Calling

Migrating from Biostar 1.X

Due to the complete rework there is no database schema migration.

Instead users of Biostar 1 site are expected to export their data with a script provided in Biostar 1 then import it with a management command provided with Biostar 2.

The migration will take the following steps:

  1. Set the BIOSTAR_MIGRATE_DIR environment variable to point to a work directory that will hold the temporary data, for example export BIOSTAR_MIGRATE_DIR="~/tmp/biostar_export"

  2. Load the environment variables for the Biostar 1 site then run python -m main.bin.export -u -p -v. This will dump the contents of the site into the directory that BIOSTAR_MIGRATE_DIR points to.

  3. Load the environment variables for you Biostar 2 site then run the ./biostar.sh import_biostar1 command.

Some caveats, depending how you set the variables you may need to be located in the root of your site. This applies for the default settings that both sites come with, as the root is determined relative to the directory that the command is run in.