/
fabfile.py
executable file
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fabfile.py
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#from fabric.api import *
# from fabric.api import run,local
# from invoke import run
from fabric.api import run
from subprocess import check_output
#comment
# env.user = 'raony'
# env.hosts = ['localhost']
def install():
# local('pip install cython')
# local('pip install pynnotator')
local('pip install -r requirements.txt')
# local('pynnotator install')
# local('python manage.py migrate auth')#bug with version 1.8
# local('python manage.py migrate')
def backup_users():
local('python3 manage.py dumpdata --indent=4 --format=json auth account allauth > fixtures/users.json')
# local('python3 manage.py dumpdata --indent=4 --format=json individuals > fixtures/individuals.json')
# local('python3 manage.py dumpdata --indent=4 --format=json individuals.usergroup > fixtures/usergroups.json')
# local('python manage.py dumpdata users allauth > initial_data.json')
def reset_migrations():
models = ['cases', 'projects', 'individuals', 'databases', 'variants',
'diseases', 'genes', 'files', 'filter_analysis', 'samples', 'analyses',
'tasks', 'workers', 'upload', 'settings', 'projects', 'mapps', 'pathway_analysis', 'mapps', 'analyses']
for model in models:
local('rm -rf %s/migrations' % (model))
for model in models:
local('python manage.py makemigrations %s' % (model))
local('python manage.py migrate')
def resetdb():
# local('rm db.sqlite3')
# local('psql -d template1 -c "DROP DATABASE rockbio_prod;"')
# local('psql -d template1 -c "CREATE DATABASE rockbio_prod;"')
# local('python manage.py syncdb')
local('dropdb rockbio')
local('createdb rockbio')
local('./manage.py migrate')
# local('python manage.py loaddata fixtures/users.json')
# local('python manage.py loaddata fixtures/usergroups.json')
#load genes, diseases, pathways
# local('python manage.py createsuperuser')
#local('python manage.py runserver mendel.medicina.ufmg.br:8001')
def import_samples():
local('./manage.py import_files')
local('python ../scripts/import_samples.py')
local('python ../scripts/update_sample_files.py')
def make_doc():
with lcd('../docs'):
local('make html')
local('cp -rf _build/html/* /var/www/rockbio_static/docs/')
def backup():
command = 'python3 manage.py dumpdata --indent=4 --format=json auth.user account allauth > fixtures/users.json'
check_output(command,shell=True)
command = 'python3 manage.py dumpdata --indent=4 --format=json keys > fixtures/keys.json'
check_output(command, shell = True)
# run(' mysqldump -u root -p rockbio14 | gzip > db_backup/rockbio151012.sql.gz ')
def restore():
# command = 'python3 manage.py loaddata fixtures/users.json'
# check_output(command, shell=True)
command = 'python3 manage.py loaddata fixtures/keys.json'
check_output(command, shell=True)
def create_sample_data():
#backup all users
# with cd('/projects/www/rockbio14'):
#
# run('mysqldump -u root -p rockbio14 auth_user account_account profiles_profile | gzip > db_backup/users.sql.gz')
# #get sample from individuals
# run('mysqldump -u root -p --where="individual_id < 16" rockbio14 individuals_variant | gzip > db_backup/individual_variants_sample.sql.gz')
# run('mysqldump -u root -p --where="id < 16" rockbio14 individuals_individual | gzip > db_backup/individuals_sample.sql.gz')
get('/projects/www/rockbio14/db_backup/users.sql.gz', '/home/raony/sites/rockbio14/db_backup/')
get('/projects/www/rockbio14/db_backup/individual_variants_sample.sql.gz', '/home/raony/sites/rockbio14/db_backup/')
get('/projects/www/rockbio14/db_backup/individuals_sample.sql.gz', '/home/raony/sites/rockbio14/db_backup/')
def copy_sample_from_server():
local('scp 150.164.199.43:/projects/www/rockbio14/db_backup/rockbio040113_withoutvariants.zip .')
def make_sample_data():
# local('pg_dump -U raony rockbio -T individuals_variant > db_sample/rockbio_sample_variants.sql')
# local('zip db_sample/samples.sql.zip db_sample/rockbio_sample_variants.sql')
# local('rm db_sample/rockbio_sample_variants.sql')
local('python manage.py makefixture --format=json --indent=4 rockbio.individuals.variant[1:101] > fixtures/individuals_variant.json')
def load_sample_data():
local('psql -U raony -d rockbio < db_sample/rockbio210313_sample.sql')
local('psql -U raony -d rockbio -f db_sample/restore_db.sql')
def loaddata():
#Load user and sample from individuals
local('gunzip < db_backup/users.sql.gz | mysql -u root -p rockbio')
local('gunzip < db_backup/individual_variants_sample.sql.gz | mysql -u root -p rockbio ')
local('gunzip < db_backup/individuals_sample.sql.gz | mysql -u root -p rockbio ')
# run(' gunzip < db_backup/rockbio151012.sql.gz | mysql -u root -p rockbio14 ')
# local("""python manage.py loaddata db_backup/all_without_individuals.json.gz""")
def local_reset():
#delete database
# local("sudo su - postgres")
# local("""psql -c 'DROP DATABASE rockbio_dev;'""")
# local("""psql -c 'CREATE DATABASE rockbio_dev;'""")
#sync and migrate
local('python manage.py sqlclear individuals | python manage.py dbshell')
local('python manage.py syncdb --migrate')
local('python manage.py createsuperuser')
local('python manage.py runserver mendel.medicina.ufmg.br:8002')
#load user data
# local('python manage.py loaddata user_data.json')
#ready to go!
#backup db?
#python manage.py dumpdata -v 2 --format=json users auth account > user_data.json
#
# local('python manage.py flush --noinput')
#local('python manage.py syncdb --noinput')
# local('python manage.py runserver')
def requirements():
local('pip install -r requirements.txt')
#local('python filetransfers/setup.py install')
#local('python wikitools-1.1.1/setup.py install')
#local('easy_install fisher')
def backup_diseases():
local('python manage.py dumpdata ')
def run_local():
# local('pkill python')
local('python manage.py celeryd &')
local('python manage.py runserver mendel.medicina.ufmg.br:8002')
# local('pkill python')
def deploy(message="changes (fabric)"):
local('git add .; git commit -m "%s";git push' % (message))
with cd('/projects/www/rockbio'):
# run('git reset --hard HEAD')
run('git pull')
# run('source virtualenvwrapper.sh && workon genome_research && python manage.py syncdb --noinput')
run('sudo /etc/init.d/apache2 restart')
def clean_individuals():
local('python manage.py sqlclear individuals | python manage.py dbshell')
def clean_variants():
local('python manage.py sqlclear variants | python manage.py dbshell')
local('python manage.py migrate')
def docs():
with lcd('../docs'):
local('make html')
local('cp -r _build/html/* ../static/docs/')