The biostar.sh manager¶

The biostar.sh shell command automatizes a number of commonly used tasks. Run it with no parameters to get help on a typical usage::

Usage:

  $ biostar.sh <command>

Multiple commands may be used on the same line:

  $ biostar.sh init import run

Commands:

  init      - initializes the database
  run       - runs the development server
  index     - initializes the search index
  test      - runs all tests
  env       - shows all customizable environment variables

  import    - imports the data fixture JSON_DATA_FIXTURE=import/default-fixture.json.gz
  dump      - dumps data as JSON_DATA_FIXTURE=import/default-fixture.json.gz
  delete    - removes the sqlite database DATABASE_NAME=biostar.db

  pg_drop        - drops postgres DATABASE_NAME=biostar.db
  pg_create      - creates postgres DATABASE_NAME=biostar.db
  pg_import f.gz - imports the gzipped filename into postgres DATABASE_NAME=biostar.db

Use environment variables to customize settings. See the docs.

DJANGO_SETTINGS_MODULE=biostar.settings.base

Subcommands¶

In addition there are a number of data management commands that are implemented for the each app. Run::

python manage.py help

And look for the output for the app [server], these commands will look like::

[server]
    biostar_pg_dump
    delete_database
    import_biostar1
    import_mbox
    initialize_site
    prune_data
    usermod
    sqlfix
    sitemap
    user_crawl
    test_email
    test_task
    patch

You can run each of these subcommands with the -h flag to get more information on them.

Command line tagging¶

There is a command line tool to perform content tagging based on a regular expression. The invocation is::

workon biostar
source live/deploy.env
python manage.py patch --tag "regexp:tag1,tag2,tag3"

Where the regular expression regexp will be searched against the content and when found matching tags tag1, tag2, tag3 will be applied. Example::

python manage.py patch --tag "gff:gff,interval"

To detect what posts would be tagged but not actually perform the tagging pass the --dry command. In that case only the post titles will be listed::

python manage.py patch --tag "gff:gff,interval" --dry

This command will navigate through all questions in the database.

Example commands¶

Frequently used commands::

# Set the password for a user identified by their userid
python manage.py usermod -u 2 -p abcde

# Set the password for a user identified by their email
python manage.py usermod -e foo@bar -p abcde

# Rebuild the entire search index
python manage.py rebuild_index

# Reindex only what has changed in the last hour
python manage.py update_index --age 1

# Import 100 posts from a mbox file into biostar
python manage.py import_mbox -f filename -l 100

# Create a postgres database dump
python manage.py biostar_pg_dump

Merging Users¶

Create a space separated text file that contains the emails in the form::

master_email alias_email1 alias_email2 ...

Then run the command::

python manage.py patch --merge_users yourfile.txt

The command will move all content, votes and accounts associated with users identified by the aliases into the master email. It then deletes the alias users. The effect of this command cannot be reverted other than loading up a backup database dump.