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

    # Load the environment variables.
source conf/defaults.env

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

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

The default admin is foo@bar.com password foobar. 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

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:

• Create Authentication App: http://developers.facebook.com/setup/
• More information: Facebook Developer Resources: http://developers.facebook.com/docs/authentication/

Adding Google authentication:

• Google Developer Console: https://cloud.google.com/console/project
• Create new project and copy data from credentials
• Callback must be http://domain/accounts/google/login/callback/

Twitter:

• Add your application at Twitter Apps Interface: http://twitter.com/apps/

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.