Warning
This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.
Source code for galaxy.files.sources
import abc
import os
import time
from typing import Set
from galaxy.exceptions import (
ConfigurationError,
ItemAccessibilityException,
)
from galaxy.util.bool_expressions import (
BooleanExpressionEvaluator,
TokenContainedEvaluator,
)
from galaxy.util.template import fill_template
DEFAULT_SCHEME = "gxfiles"
DEFAULT_WRITABLE = False
[docs]class FilesSource(metaclass=abc.ABCMeta):
"""
"""
[docs] @abc.abstractmethod
def get_uri_root(self):
"""Return a prefix for the root (e.g. gxfiles://prefix/)."""
[docs] @abc.abstractmethod
def get_scheme(self):
"""Return a prefix for the root (e.g. the gxfiles in gxfiles://prefix/path)."""
[docs] @abc.abstractmethod
def get_writable(self):
"""Return a boolean indicating if this target is writable."""
[docs] @abc.abstractmethod
def user_has_access(self, user_context) -> bool:
"""Return a boolean indicating if the user can access the FileSource."""
# TODO: off-by-default
[docs] @abc.abstractmethod
def list(self, source_path="/", recursive=False, user_context=None):
"""Return dictionary of 'Directory's and 'File's."""
[docs] @abc.abstractmethod
def realize_to(self, source_path, native_path, user_context=None):
"""Realize source path (relative to uri root) to local file system path."""
[docs] def write_from(self, target_path, native_path, user_context=None):
"""Write file at native path to target_path (relative to uri root).
"""
[docs] @abc.abstractmethod
def to_dict(self, for_serialization=False, user_context=None):
"""Return a dictified representation of this FileSource instance.
If ``user_context`` is supplied, properties should be written so user
context doesn't need to be present after the plugin is re-hydrated.
"""
[docs]class BaseFilesSource(FilesSource):
[docs] def user_has_access(self, user_context) -> bool:
if user_context is None and self.user_context_required:
return False
return (
user_context is None
or user_context.is_admin
or (
self._user_has_required_roles(user_context)
and self._user_has_required_groups(user_context)
)
)
@property
def user_context_required(self) -> bool:
return self.requires_roles is not None or self.requires_groups is not None
[docs] def get_uri_root(self):
prefix = self.get_prefix()
scheme = self.get_scheme()
root = f"{scheme}://"
if prefix:
root = uri_join(root, prefix)
return root
[docs] def uri_from_path(self, path):
uri_root = self.get_uri_root()
return uri_join(uri_root, path)
def _parse_common_config_opts(self, kwd: dict):
self._file_sources_config = kwd.pop("file_sources_config")
self.id = kwd.pop("id")
self.label = kwd.pop("label", None) or self.id
self.doc = kwd.pop("doc", None)
self.scheme = kwd.pop("scheme", DEFAULT_SCHEME)
self.writable = kwd.pop("writable", DEFAULT_WRITABLE)
self.requires_roles = kwd.pop("requires_roles", None)
self.requires_groups = kwd.pop("requires_groups", None)
self._validate_security_rules()
# If coming from to_dict, strip API helper values
kwd.pop("uri_root", None)
kwd.pop("type", None)
return kwd
[docs] def to_dict(self, for_serialization=False, user_context=None):
rval = {
"id": self.id,
"type": self.plugin_type,
"uri_root": self.get_uri_root(),
"label": self.label,
"doc": self.doc,
"writable": self.writable,
"requires_roles": self.requires_roles,
"requires_groups": self.requires_groups,
}
if for_serialization:
rval.update(self._serialization_props(user_context=user_context))
return rval
[docs] def to_dict_time(self, ctime):
if ctime is None:
return None
elif isinstance(ctime, (int, float)):
return time.strftime("%m/%d/%Y %I:%M:%S %p", time.localtime(ctime))
else:
return ctime.strftime("%m/%d/%Y %I:%M:%S %p")
@abc.abstractmethod
def _serialization_props(self):
"""Serialize properties needed to recover plugin configuration.
Used in to_dict method if for_serialization is True.
"""
[docs] def list(self, path="/", recursive=False, user_context=None):
self._check_user_access(user_context)
return self._list(path, recursive, user_context)
@abc.abstractmethod
def _list(self, path="/", recursive=False, user_context=None):
pass
[docs] def write_from(self, target_path, native_path, user_context=None):
if not self.get_writable():
raise Exception("Cannot write to a non-writable file source.")
self._check_user_access(user_context)
self._write_from(target_path, native_path, user_context=user_context)
@abc.abstractmethod
def _write_from(self, target_path, native_path, user_context=None):
pass
[docs] def realize_to(self, source_path, native_path, user_context=None):
self._check_user_access(user_context)
self._realize_to(source_path, native_path, user_context)
@abc.abstractmethod
def _realize_to(self, source_path, native_path, user_context=None):
pass
def _check_user_access(self, user_context):
"""Raises an exception if the given user doesn't have the rights to access this file source.
Warning: if the user_context is None, then the check is skipped. This is due to tool executions context
not having access to the user_context. The validation will be done when checking the tool parameters.
"""
if user_context is not None and not self.user_has_access(user_context):
raise ItemAccessibilityException(f"User {user_context.username} has no access to file source.")
def _evaluate_prop(self, prop_val, user_context):
rval = prop_val
if isinstance(prop_val, str) and "$" in prop_val:
template_context = dict(
user=user_context,
environ=os.environ,
config=self._file_sources_config,
)
rval = fill_template(prop_val, context=template_context, futurized=True)
return rval
def _user_has_required_roles(self, user_context) -> bool:
if self.requires_roles:
return self._evaluate_security_rules(self.requires_roles, user_context.role_names)
return True
def _user_has_required_groups(self, user_context) -> bool:
if self.requires_groups:
return self._evaluate_security_rules(self.requires_groups, user_context.group_names)
return True
def _evaluate_security_rules(self, rule_expression: str, user_credentials: Set[str]) -> bool:
token_evaluator = TokenContainedEvaluator(user_credentials)
evaluator = BooleanExpressionEvaluator(token_evaluator)
return evaluator.evaluate_expression(rule_expression)
def _validate_security_rules(self) -> None:
"""Checks if the security rules defined in the plugin configuration are valid boolean expressions or raises
a ConfigurationError exception otherwise."""
def _get_error_msg_for(rule_name: str) -> str:
return f"Invalid boolean expression for '{rule_name}' in {self.label} file source plugin configuration."
if self.requires_roles and not BooleanExpressionEvaluator.is_valid_expression(self.requires_roles):
raise ConfigurationError(_get_error_msg_for("requires_roles"))
if self.requires_groups and not BooleanExpressionEvaluator.is_valid_expression(self.requires_groups):
raise ConfigurationError(_get_error_msg_for("requires_groups"))
[docs]def uri_join(*args):
# url_join doesn't work with non-standard scheme
arg0 = args[0]
if "://" in arg0:
scheme, path = arg0.split("://", 1)
rval = f"{scheme}://{slash_join(path, *args[1:]) if path else slash_join(*args[1:])}"
else:
rval = slash_join(*args)
return rval
[docs]def slash_join(*args):
# https://codereview.stackexchange.com/questions/175421/joining-strings-to-form-a-url
return "/".join(arg.strip("/") for arg in args)