biostar.sh

#!/bin/bash

while getopts ":e:" opt; do
  case $opt in
    e)
      CONFIG="$OPTARG"
      echo "Using configuration from $CONFIG" >&2
      source $CONFIG
      ;;
    \?)
      echo "Invalid option: -$OPTARG" >&2
      ;;
    :)
      echo "-$OPTARG requires an argument" >&2
      ;;
  esac
done

# Environment variables must be set externally.
if [ -z "$BIOSTAR_HOME" ]; then
    echo "(!) environment variables not set."
    echo "(!) Try: $(basename $0) -e conf/defaults.env"
    exit 1
fi

# Stop on errors or missing environment variables.
set -ue

if [ $# == 0 ]; then
    echo ''
    echo 'Usage:'
    echo ''
    echo "  $ $(basename $0) <command>"
    echo ''
    echo 'Multiple commands may be used on the same line:'
    echo ''
    echo "  $ $(basename $0) init import run"
    echo ''
    echo 'Commands:'
    echo ''
    echo '  init      - initializes the database'
    echo '  run       - runs the development server'
    echo "  index     - initializes the search index"
    echo '  test      - runs all tests'
    echo '  env       - shows all customizable environment variables'
    echo ' '
    echo "  import    - imports the data fixture JSON_DATA_FIXTURE=$JSON_DATA_FIXTURE"
    echo "  dump      - dumps data as JSON_DATA_FIXTURE=$JSON_DATA_FIXTURE"
    echo "  delete    - removes the sqlite database DATABASE_NAME=$DATABASE_NAME"
    echo ''
    echo "  pg_drop   - drops postgres DATABASE_NAME=$DATABASE_NAME"
    echo "  pg_create - creates postgres DATABASE_NAME=$DATABASE_NAME"
    echo "  pg_import sqldump.gz - imports the gzipped filename into postgres DATABASE_NAME=$DATABASE_NAME"
    echo ''
    echo "Use environment variables to customize settings. See the docs."
    echo ' '
    echo "DJANGO_SETTINGS_MODULE=$DJANGO_SETTINGS_MODULE"
    echo "DATABASE_NAME=$DATABASE_NAME"
    echo ''
fi

while (( "$#" )); do

    if [ "$1" = "delete" ]; then
        echo "*** Deleting the sqlite database"
        $PYTHON $DJANGO_ADMIN delete_database --settings=$DJANGO_SETTINGS_MODULE
    fi

    if [ "$1" = "pg_drop" ]; then
        echo "*** Dropping the $DATABASE_NAME=$DATABASE_NAME!"
        dropdb -i $DATABASE_NAME
    fi

    if [ "$1" = "pg_create" ]; then
        # creates the PG database
        echo "*** Creating postgresql database DATABASE_NAME=$DATABASE_NAME"
        createdb $DATABASE_NAME -E utf8 --template template0
    fi

    if [ "$1" = "pg_import" ]; then
        echo "*** Importing into DATABASE_NAME=$DATABASE_NAME"
        gunzip -c $2 | psql $DATABASE_NAME
    fi

    if [ "$1" = "pg_dump" ]; then
        echo "*** Dumping the $DATABASE_NAME database."
        $PYTHON $DJANGO_ADMIN biostar_pg_dump -v $VERBOSITY --settings=$DJANGO_SETTINGS_MODULE
    fi

    if [ "$1" = "run" ]; then
        echo "*** Run the development server with $DJANGO_SETTINGS_MODULE and DATABASE_NAME=$DATABASE_NAME"
        $PYTHON $DJANGO_ADMIN runserver $BIOSTAR_HOSTNAME --settings=$DJANGO_SETTINGS_MODULE
    fi

	if [ "$1" = "waitress" ]; then
        echo "*** Run a waitress server with $DJANGO_SETTINGS_MODULE and DATABASE_NAME=$DATABASE_NAME"
        waitress-serve --port=8080 --call biostar.wsgi:white
    fi

   	if [ "$1" = "testdeploy" ]; then
        echo "*** deploys to the test site"
        fab -f conf/fabs/fabfile.py test_site pull restart
    fi

    if [ "$1" = "init" ]; then
        echo "*** Initializing server on $BIOSTAR_HOSTNAME with $DJANGO_SETTINGS_MODULE"
        echo "*** Running all tests"
        #$PYTHON $DJANGO_ADMIN test --noinput -v $VERBOSITY --settings=$DJANGO_SETTINGS_MODULE
        $PYTHON $DJANGO_ADMIN syncdb -v $VERBOSITY --noinput --settings=$DJANGO_SETTINGS_MODULE

        $PYTHON $DJANGO_ADMIN migrate  biostar.apps.users --settings=$DJANGO_SETTINGS_MODULE
        $PYTHON $DJANGO_ADMIN migrate  biostar.apps.posts --settings=$DJANGO_SETTINGS_MODULE
        $PYTHON $DJANGO_ADMIN migrate  --settings=$DJANGO_SETTINGS_MODULE
        $PYTHON $DJANGO_ADMIN initialize_site --settings=$DJANGO_SETTINGS_MODULE

        $PYTHON $DJANGO_ADMIN collectstatic -v $VERBOSITY --noinput --settings=$DJANGO_SETTINGS_MODULE

    fi

    # Produce the environment variables recognized by Biostar.
    if [ "$1" = "test" ]; then
        echo "*** Running all tests"
        $PYTHON $DJANGO_ADMIN test --noinput --failfast -v $VERBOSITY --settings=$DJANGO_SETTINGS_MODULE
    fi

    # Produce the environment variables recognized by Biostar.
    if [ "$1" = "env" ]; then
        echo "*** Biostar specific environment variables"
        echo BIOSTAR_HOME=$BIOSTAR_HOME
        echo BIOSTAR_ADMIN_EMAIL=$BIOSTAR_ADMIN_EMAIL
        echo BIOSTAR_ADMIN_NAME=$BIOSTAR_ADMIN_NAME
        echo "-"
        echo DJANGO_SETTINGS_MODULE=$DJANGO_SETTINGS_MODULE
        echo DATABASE_NAME=$DATABASE_NAME
        echo DEFAULT_FROM_EMAIL=$DEFAULT_FROM_EMAIL
    fi

    if [ "$1" = "import" ]; then
        echo "*** Importing json data from $JSON_DATA_FIXTURE"
        $PYTHON $DJANGO_ADMIN loaddata $JSON_DATA_FIXTURE --settings=$DJANGO_SETTINGS_MODULE
    fi

    if [ "$1" = "dump" ]; then
        echo "*** Dumping json data into $JSON_DATA_FIXTURE"
        $PYTHON $DJANGO_ADMIN dumpdata users posts messages badges planet --settings=$DJANGO_SETTINGS_MODULE | gzip > $JSON_DATA_FIXTURE
    fi

    if [ "$1" = "index" ]; then
        echo "*** Indexing site content"
        $PYTHON $DJANGO_ADMIN rebuild_index --noinput --settings=$DJANGO_SETTINGS_MODULE
    fi

    if [ "$1" = "update_index" ]; then
        echo "*** Updating site index"
        $PYTHON $DJANGO_ADMIN update_index --age 1 --settings=$DJANGO_SETTINGS_MODULE
    fi

    if [ "$1" = "import_biostar1" ]; then
        echo "*** Migrating from Biostar 1"
        echo "*** BIOSTAR_MIGRATE_DIR=$BIOSTAR_MIGRATE_DIR"
        $PYTHON $DJANGO_ADMIN import_biostar1 -u -p -x
    fi


shift
done