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Source code for galaxy.files

import logging
import os
from collections import (
from typing import (

from galaxy import exceptions
from galaxy.util import plugin_config
from galaxy.util.dictifiable import Dictifiable

log = logging.getLogger(__name__)

FileSourcePath = namedtuple("FileSourcePath", ["file_source", "path"])

[docs]class ConfiguredFileSources: """Load plugins and resolve Galaxy URIs to FileSource objects."""
[docs] def __init__( self, file_sources_config: "ConfiguredFileSourcesConfig", conf_file=None, conf_dict=None, load_stock_plugins=False, ): self._file_sources_config = file_sources_config self._plugin_classes = self._file_source_plugins_dict() file_sources = [] if conf_file is not None: file_sources = self._load_plugins_from_file(conf_file) elif conf_dict is not None: plugin_source = plugin_config.plugin_source_from_dict(conf_dict) file_sources = self._parse_plugin_source(plugin_source) else: file_sources = [] custom_sources_configured = len(file_sources) > 0 if load_stock_plugins: stock_file_source_conf_dict = [] def _ensure_loaded(plugin_type): for file_source in file_sources: if file_source.plugin_type == plugin_type: return stock_file_source_conf_dict.append({"type": plugin_type}) if file_sources_config.ftp_upload_dir is not None: _ensure_loaded("gxftp") if file_sources_config.library_import_dir is not None: _ensure_loaded("gximport") if file_sources_config.user_library_import_dir is not None: _ensure_loaded("gxuserimport") if stock_file_source_conf_dict: stock_plugin_source = plugin_config.plugin_source_from_dict(stock_file_source_conf_dict) # insert at begining instead of append so FTP and library import appear # at the top of the list (presumably the most common options). Admins can insert # these explicitly for greater control. file_sources = self._parse_plugin_source(stock_plugin_source) + file_sources self._file_sources = file_sources self.custom_sources_configured = custom_sources_configured
def _load_plugins_from_file(self, conf_file): plugin_source = plugin_config.plugin_source_from_path(conf_file) return self._parse_plugin_source(plugin_source) def _file_source_plugins_dict(self): import galaxy.files.sources return plugin_config.plugins_dict(galaxy.files.sources, "plugin_type") def _parse_plugin_source(self, plugin_source): extra_kwds = { "file_sources_config": self._file_sources_config, } return plugin_config.load_plugins( self._plugin_classes, plugin_source, extra_kwds, dict_to_list_key="id", )
[docs] def get_file_source_path(self, uri): """Parse uri into a FileSource object and a path relative to its base.""" if "://" not in uri: raise exceptions.RequestParameterInvalidException(f"Invalid uri [{uri}]") scheme, rest = uri.split("://", 1) if scheme not in self.get_schemes(): raise exceptions.RequestParameterInvalidException(f"Unsupported URI scheme [{scheme}]") if scheme != "gxfiles": # prefix unused id_prefix = None path = rest else: if "/" in rest: id_prefix, path = rest.split("/", 1) else: id_prefix, path = rest, "/" file_source = self.get_file_source(id_prefix, scheme) return FileSourcePath(file_source, path)
[docs] def validate_uri_root(self, uri, user_context): # validate a URI against Galaxy's configuration, environment, and the current # user. Throw appropriate exception if there is a problem with the files source # referenced by the URI. if uri.startswith("gxuserimport://"): user_login = user_context.email user_base_dir = self._file_sources_config.user_library_import_dir if user_base_dir is None: raise exceptions.ConfigDoesNotAllowException( "The configuration of this Galaxy instance does not allow upload from user directories." ) full_import_dir = os.path.join(user_base_dir, user_login) if not os.path.exists(full_import_dir): raise exceptions.ObjectNotFound("Your user import directory does not exist.") elif uri.startswith("gximport://"): base_dir = self._file_sources_config.library_import_dir if base_dir is None: raise exceptions.ConfigDoesNotAllowException( "The configuration of this Galaxy instance does not allow usage of import directory." ) elif uri.startswith("gxftp://"): user_ftp_base_dir = self._file_sources_config.ftp_upload_dir if user_ftp_base_dir is None: raise exceptions.ConfigDoesNotAllowException( "The configuration of this Galaxy instance does not allow upload from FTP directories." ) user_ftp_dir = user_context.ftp_dir if not user_ftp_dir or not os.path.exists(user_ftp_dir): raise exceptions.ObjectNotFound( "Your FTP directory does not exist, attempting to upload files to it may cause it to be created." )
[docs] def get_file_source(self, id_prefix, scheme): for file_source in self._file_sources: # gxfiles uses prefix to find plugin, other scheme are assumed to have # at most one file_source. if scheme != file_source.get_scheme(): continue prefix_match = scheme != "gxfiles" or file_source.get_prefix() == id_prefix if prefix_match: return file_source
[docs] def looks_like_uri(self, path_or_uri): # is this string a URI this object understands how to realize if path_or_uri.startswith("gx") and "://" in path_or_uri: for scheme in self.get_schemes(): if path_or_uri.startswith(f"{scheme}://"): return True return False
[docs] def get_schemes(self): schemes = set() for file_source in self._file_sources: schemes.add(file_source.get_scheme()) return schemes
[docs] def plugins_to_dict( self, for_serialization: bool = False, user_context: Optional["FileSourceDictifiable"] = None ) -> List[Dict[str, Any]]: rval = [] for file_source in self._file_sources: if not file_source.user_has_access(user_context): continue el = file_source.to_dict(for_serialization=for_serialization, user_context=user_context) rval.append(el) return rval
[docs] def to_dict( self, for_serialization: bool = False, user_context: Optional["FileSourceDictifiable"] = None ) -> Dict[str, Any]: return { "file_sources": self.plugins_to_dict(for_serialization=for_serialization, user_context=user_context), "config": self._file_sources_config.to_dict(), }
[docs] @staticmethod def from_app_config(config): config_file = config.file_sources_config_file config_dict = None if not config_file or not os.path.exists(config_file): config_file = None config_dict = config.file_sources file_sources_config = ConfiguredFileSourcesConfig.from_app_config(config) return ConfiguredFileSources( file_sources_config, conf_file=config_file, conf_dict=config_dict, load_stock_plugins=True )
[docs] @staticmethod def from_dict(as_dict): if as_dict is not None: sources_as_dict = as_dict["file_sources"] config_as_dict = as_dict["config"] file_sources_config = ConfiguredFileSourcesConfig.from_dict(config_as_dict) else: sources_as_dict = [] file_sources_config = ConfiguredFileSourcesConfig() return ConfiguredFileSources(file_sources_config, conf_dict=sources_as_dict)
[docs]class NullConfiguredFileSources(ConfiguredFileSources):
[docs] def __init__( self, ): super().__init__(ConfiguredFileSourcesConfig())
[docs]class ConfiguredFileSourcesConfig:
[docs] def __init__( self, symlink_allowlist=None, fetch_url_allowlist=None, library_import_dir=None, user_library_import_dir=None, ftp_upload_dir=None, ftp_upload_purge=True, ): symlink_allowlist = symlink_allowlist or [] fetch_url_allowlist = fetch_url_allowlist or [] self.symlink_allowlist = symlink_allowlist self.fetch_url_allowlist = fetch_url_allowlist self.library_import_dir = library_import_dir self.user_library_import_dir = user_library_import_dir self.ftp_upload_dir = ftp_upload_dir self.ftp_upload_purge = ftp_upload_purge
[docs] @staticmethod def from_app_config(config): # Formalize what we read in from config to create a more clear interface # for this component. kwds = {} kwds["symlink_allowlist"] = getattr(config, "user_library_import_symlink_allowlist", []) kwds["fetch_url_allowlist"] = getattr(config, "fetch_url_allowlist", []) kwds["library_import_dir"] = getattr(config, "library_import_dir", None) kwds["user_library_import_dir"] = getattr(config, "user_library_import_dir", None) kwds["ftp_upload_dir"] = getattr(config, "ftp_upload_dir", None) kwds["ftp_upload_purge"] = getattr(config, "ftp_upload_purge", True) return ConfiguredFileSourcesConfig(**kwds)
[docs] def to_dict(self): return { "symlink_allowlist": self.symlink_allowlist, "fetch_url_allowlist": self.fetch_url_allowlist, "library_import_dir": self.library_import_dir, "user_library_import_dir": self.user_library_import_dir, "ftp_upload_dir": self.ftp_upload_dir, "ftp_upload_purge": self.ftp_upload_purge, }
[docs] @staticmethod def from_dict(as_dict): return ConfiguredFileSourcesConfig( symlink_allowlist=as_dict["symlink_allowlist"], fetch_url_allowlist=as_dict["fetch_url_allowlist"], library_import_dir=as_dict["library_import_dir"], user_library_import_dir=as_dict["user_library_import_dir"], ftp_upload_dir=as_dict["ftp_upload_dir"], ftp_upload_purge=as_dict["ftp_upload_purge"], )
[docs]class FileSourceDictifiable(Dictifiable): dict_collection_visible_keys = ("email", "username", "ftp_dir", "preferences", "is_admin")
[docs] def to_dict(self, view="collection", value_mapper=None): rval = super().to_dict(view=view, value_mapper=value_mapper) rval["role_names"] = list(self.role_names) rval["group_names"] = list(self.group_names) return rval
@property def role_names(self) -> Set[str]: raise NotImplementedError @property def group_names(sefl) -> Set[str]: raise NotImplementedError
[docs]class ProvidesUserFileSourcesUserContext(FileSourceDictifiable): """Implement a FileSourcesUserContext from a Galaxy ProvidesUserContext (e.g. trans)."""
[docs] def __init__(self, trans): self.trans = trans
@property def email(self): user = self.trans.user return user and user.email @property def username(self): user = self.trans.user return user and user.username @property def ftp_dir(self): return self.trans.user_ftp_dir @property def preferences(self): user = self.trans.user return user and user.extra_preferences or defaultdict(lambda: None) @property def role_names(self) -> Set[str]: """The set of role names of this user.""" user = self.trans.user return {ura.role.name for ura in user.roles} if user else set() @property def group_names(self) -> Set[str]: """The set of group names to which this user belongs.""" user = self.trans.user return {ugr.group.name for ugr in user.groups} if user else set() @property def is_admin(self): """Whether this user is an administrator.""" return self.trans.user_is_admin @property def user_vault(self): """User vault namespace""" user_vault = self.trans.user_vault return user_vault or defaultdict(lambda: None) @property def app_vault(self): """App vault namespace""" vault = self.trans.app.vault return vault or defaultdict(lambda: None)
[docs]class DictFileSourcesUserContext(FileSourceDictifiable):
[docs] def __init__(self, **kwd): self._kwd = kwd
@property def email(self): return self._kwd.get("email") @property def username(self): return self._kwd.get("username") @property def ftp_dir(self): return self._kwd.get("user_ftp_dir") @property def preferences(self): return self._kwd.get("preferences") @property def role_names(self): return set(self._kwd.get("role_names", [])) @property def group_names(self): return set(self._kwd.get("group_names", [])) @property def is_admin(self): return self._kwd.get("is_admin") @property def user_vault(self): return self._kwd.get("user_vault") @property def app_vault(self): return self._kwd.get("app_vault")