def add_new_sequence(sequence):
'''
Method called when a new sequence is created on GDV.
It should import fast from JBrowse
'''
print 'add new sequence'
file_url = Assembly(sequence).get_sqlite_url()
print file_url
out = os.path.join(filemanager.temporary_directory(), 'Genes.sql')
fileinfo = filemanager.FileInfo(inputtype='url',
inpath=file_url, trackname='Genes', extension='sql', outpath=out, admin=True)
print fileinfo
user = DBSession.query(User).filter(User.key == constants.admin_user_key()).first()
user_info = {'id': user.id, 'name': user.name, 'email': user.email}
sequence_info = {'id': sequence.id, 'name': sequence.name}
# track
t = Track()
t.name = fileinfo.trackname
t.sequence_id = sequence.id
t.user_id = user.id
DBSession.add(t)
DBSession.flush()
# send task
async = tasks.new_input.delay(user_info, fileinfo, sequence_info, t.id)
t.task_id = async.task_id
DBSession.add(t)
sequence.default_tracks.append(t)
DBSession.add(sequence)
DBSession.flush()
def add_new_sequence(sequence):
'''
Method called when a new sequence is created on GDV.
It should import fast from JBrowse
'''
print 'add new sequence'
file_url = Assembly(sequence).get_sqlite_url()
print file_url
out = os.path.join(filemanager.temporary_directory(), 'Genes.sql')
fileinfo = filemanager.FileInfo(inputtype='url',
inpath=file_url,
trackname='Genes',
extension='sql',
outpath=out,
admin=True)
print fileinfo
user = DBSession.query(User).filter(
User.key == constants.admin_user_key()).first()
user_info = {'id': user.id, 'name': user.name, 'email': user.email}
sequence_info = {'id': sequence.id, 'name': sequence.name}
# track
t = Track()
t.name = fileinfo.trackname
t.sequence_id = sequence.id
t.user_id = user.id
DBSession.add(t)
DBSession.flush()
# send task
async = tasks.new_input.delay(user_info, fileinfo, sequence_info, t.id)
t.task_id = async .task_id
DBSession.add(t)
sequence.default_tracks.append(t)
DBSession.add(sequence)
DBSession.flush()
def bootstrap(command, conf, vars):
"""Place any commands to setup turbotequila here.
Note that you will have to log in the application one before launching the bootstrap."""
try:
print '[pygdv] [DATABASE] Adding default groups and permissions'
print '[pygdv] [bootstrap] Adding default groups and permissions'
# ADMIN GROUP
admins = model.Group()
admins.name = constants.groups['admin']['name']
admins.id = constants.groups['admin']['id']
model.DBSession.add(admins)
# USER GROUP
users = model.Group()
users.name = constants.groups['user']['name']
users.id = constants.groups['user']['id']
model.DBSession.add(users)
# ADMIN PERMISSION
perm = model.Permission()
perm.id = constants.permissions['admin']['id']
perm.name = constants.permissions['admin']['name']
perm.description = constants.permissions['admin']['desc']
perm.groups.append(admins)
model.DBSession.add(perm)
# READ PERMISSION
read = model.Permission()
read.id = constants.permissions['read']['id']
read.name = constants.permissions['read']['name']
read.description = constants.permissions['read']['desc']
read.groups.append(users)
model.DBSession.add(read)
# RIGHTS
write = model.Right()
write.id = constants.rights['upload']['id']
write.name = constants.rights['upload']['name']
write.description = constants.rights['upload']['desc']
model.DBSession.add(write)
execute = model.Right()
execute.id = constants.rights['download']['id']
execute.name = constants.rights['download']['name']
execute.description = constants.rights['download']['desc']
model.DBSession.add(execute)
read = model.Right()
read.id = constants.rights['read']['id']
read.name = constants.rights['read']['name']
read.description = constants.rights['read']['desc']
model.DBSession.add(read)
print '[pygdv] [bootstrap] Adding admin user'
u = model.User()
u.id = constants.admin_user['id']
u.name = constants.admin_user['name']
u.firstname = constants.admin_user['firstname']
u.key = constants.admin_user_key()
u.email = constants.admin_user_email()
admins.users.append(u)
users.users.append(u)
model.DBSession.add(u)
model.DBSession.add(users)
model.DBSession.add(admins)
transaction.commit()
except IntegrityError:
print 'Warning, there was a problem adding your auth data, it may have already been added:'
import traceback
print traceback.format_exc()
transaction.abort()
print 'Ending with bootstrapping...'
def bootstrap(command, conf, vars):
"""Place any commands to setup turbotequila here.
Note that you will have to log in the application one before launching the bootstrap."""
try:
print "[pygdv] [DATABASE] Adding default groups and permissions"
print "[pygdv] [bootstrap] Adding default groups and permissions"
# ADMIN GROUP
admins = model.Group()
admins.name = constants.groups["admin"]["name"]
admins.id = constants.groups["admin"]["id"]
model.DBSession.add(admins)
# USER GROUP
users = model.Group()
users.name = constants.groups["user"]["name"]
users.id = constants.groups["user"]["id"]
model.DBSession.add(users)
# ADMIN PERMISSION
perm = model.Permission()
perm.id = constants.permissions["admin"]["id"]
perm.name = constants.permissions["admin"]["name"]
perm.description = constants.permissions["admin"]["desc"]
perm.groups.append(admins)
model.DBSession.add(perm)
# READ PERMISSION
read = model.Permission()
read.id = constants.permissions["read"]["id"]
read.name = constants.permissions["read"]["name"]
read.description = constants.permissions["read"]["desc"]
read.groups.append(users)
model.DBSession.add(read)
# RIGHTS
write = model.Right()
write.id = constants.rights["upload"]["id"]
write.name = constants.rights["upload"]["name"]
write.description = constants.rights["upload"]["desc"]
model.DBSession.add(write)
execute = model.Right()
execute.id = constants.rights["download"]["id"]
execute.name = constants.rights["download"]["name"]
execute.description = constants.rights["download"]["desc"]
model.DBSession.add(execute)
read = model.Right()
read.id = constants.rights["read"]["id"]
read.name = constants.rights["read"]["name"]
read.description = constants.rights["read"]["desc"]
model.DBSession.add(read)
print "[pygdv] [bootstrap] Adding admin user"
u = model.User()
u.id = constants.admin_user["id"]
u.name = constants.admin_user["name"]
u.firstname = constants.admin_user["firstname"]
u.key = constants.admin_user_key()
u.email = constants.admin_user_email()
admins.users.append(u)
users.users.append(u)
model.DBSession.add(u)
model.DBSession.add(users)
model.DBSession.add(admins)
transaction.commit()
except IntegrityError:
print "Warning, there was a problem adding your auth data, it may have already been added:"
import traceback
print traceback.format_exc()
transaction.abort()
print "Ending with bootstrapping..."
