def get_conf_dict(self):
"""
Build up a configuration dictionary that is standard for ALL IEs.
TODO: replace hashed password with plaintext.
"""
trans = self.trans
request = trans.request
api_key = api_keys.ApiKeyManager(trans.app).get_or_create_api_key(trans.user)
conf_file = {
'history_id': self.attr.history_id,
'api_key': api_key,
'remote_host': request.remote_addr,
# DOCKER_PORT is NO LONGER AVAILABLE. All IEs must update.
'cors_origin': request.host_url,
'user_email': self.trans.user.email,
'proxy_prefix': self.attr.proxy_prefix,
}
web_port = self.attr.galaxy_config.galaxy_infrastructure_web_port
conf_file['galaxy_web_port'] = web_port or self.attr.galaxy_config.guess_galaxy_port()
if self.attr.viz_config.has_option("docker", "galaxy_url"):
conf_file['galaxy_url'] = self.attr.viz_config.get("docker", "galaxy_url")
elif self.attr.galaxy_config.galaxy_infrastructure_url_set:
conf_file['galaxy_url'] = self.attr.galaxy_config.galaxy_infrastructure_url.rstrip('/') + '/'
else:
conf_file['galaxy_url'] = request.application_url.rstrip('/') + '/'
# Galaxy paster port is deprecated
conf_file['galaxy_paster_port'] = conf_file['galaxy_web_port']
return conf_file
def create_api_key(self, user):
"""
Create and return an API key for `user`.
"""
# TODO: seems like this should return the model
# Also TODO: seems unused? drop and see what happens? -John
return api_keys.ApiKeyManager(self.app).create_api_key(user)
def __build_environment_variables(self):
param_dict = self.param_dict
environment_variables = []
for environment_variable_def in self.tool.environment_variables:
directory = self.local_working_directory
environment_variable = environment_variable_def.copy()
environment_variable_template = environment_variable_def[
"template"]
inject = environment_variable_def.get("inject")
if inject == "api_key":
if self._user:
from galaxy.managers import api_keys
environment_variable_template = api_keys.ApiKeyManager(
self.app).get_or_create_api_key(self._user)
else:
environment_variable_template = ""
is_template = False
else:
is_template = True
with tempfile.NamedTemporaryFile(dir=directory,
prefix="tool_env_",
delete=False) as temp:
config_filename = temp.name
self.__write_workdir_file(config_filename,
environment_variable_template,
param_dict,
is_template=is_template,
strip=environment_variable_def.get(
"strip", False))
config_file_basename = os.path.basename(config_filename)
# environment setup in job file template happens before `cd $working_directory`
environment_variable["value"] = '`cat "%s/%s"`' % (
self.compute_environment.env_config_directory(),
config_file_basename)
environment_variable["raw"] = True
environment_variable["job_directory_path"] = config_filename
environment_variables.append(environment_variable)
home_dir = self.compute_environment.home_directory()
tmp_dir = self.compute_environment.tmp_directory()
if home_dir:
environment_variable = dict(name="HOME",
value='"%s"' % home_dir,
raw=True)
environment_variables.append(environment_variable)
if tmp_dir:
for tmp_directory_var in self.tool.tmp_directory_vars:
environment_variable = dict(name=tmp_directory_var,
value='"%s"' % tmp_dir,
raw=True)
environment_variables.append(environment_variable)
self.environment_variables = environment_variables
return environment_variables
def write_conf_file(self, output_directory, extra={}):
"""
Build up a configuration file that is standard for ALL IEs.
TODO: replace hashed password with plaintext.
"""
trans = self.trans
request = trans.request
api_key = api_keys.ApiKeyManager(trans.app).get_or_create_api_key(
trans.user)
conf_file = {
'history_id': self.attr.history_id,
'api_key': api_key,
'remote_host': request.remote_addr,
'docker_port': self.attr.PORT,
'cors_origin': request.host_url,
}
if self.attr.viz_config.has_option("docker", "galaxy_url"):
conf_file['galaxy_url'] = self.attr.viz_config.get(
"docker", "galaxy_url")
elif self.attr.galaxy_config.galaxy_infrastructure_url_set:
conf_file[
'galaxy_url'] = self.attr.galaxy_config.galaxy_infrastructure_url.rstrip(
'/') + '/'
else:
conf_file['galaxy_url'] = request.application_url.rstrip('/') + '/'
web_port = self.attr.galaxy_config.galaxy_infrastructure_web_port
conf_file[
'galaxy_paster_port'] = web_port or self.attr.galaxy_config.guess_galaxy_port(
)
if self.attr.PASSWORD_AUTH:
# Generate a random password + salt
notebook_pw_salt = self.generate_password(length=12)
notebook_pw = self.generate_password(length=24)
m = hashlib.sha1()
m.update(notebook_pw + notebook_pw_salt)
conf_file['notebook_password'] = '******' % (notebook_pw_salt,
m.hexdigest())
# Should we use password based connection or "default" connection style in galaxy
else:
notebook_pw = "None"
# Some will need to pass extra data
for extra_key in extra:
conf_file[extra_key] = extra[extra_key]
self.attr.notebook_pw = notebook_pw
# Write conf
with open(os.path.join(output_directory, 'conf.yaml'), 'wb') as handle:
handle.write(yaml.dump(conf_file, default_flow_style=False))
def get_api_key():
return api_keys.ApiKeyManager(trans.app).get_or_create_api_key(
trans.user)
def __init__(self, app):
super().__init__(app)
self.user_manager = users.UserManager(app)
self.user_serializer = users.UserSerializer(app)
self.user_deserializer = users.UserDeserializer(app)
self.api_key_manager = api_keys.ApiKeyManager(app)
def create_api_key(self, user):
"""
Create and return an API key for `user`.
"""
# TODO: seems like this should return the model
return api_keys.ApiKeyManager(self.app).create_api_key(user)
def __init__(self, app):
super(AuthenticationController, self).__init__(app)
self.api_keys_manager = api_keys.ApiKeyManager(app)
def __init__(self, app):
super().__init__(app)
self.user_manager = users.UserManager(app)
self.api_keys_manager = api_keys.ApiKeyManager(app)
