from pathlib import Path, PurePath
from typing import Tuple, Optional, Dict, Any, Set
from copy import deepcopy
from . import parse
import pickle
import os.path as op
from . import utils
class MissingVariable(KeyError):
"""
Returned when the variables of a tree or its parents do not contain a given variable
"""
pass
class FileTree(object):
"""
Contains the input/output filename tree
Properties:
- ``templates``: dictionary mapping short names to filename templates
- ``variables``: dictionary mapping variables in the templates to specific values (variables set to None are explicitly unset)
- ``sub_trees``: filename trees describing specific sub-directories
- ``parent``: parent FileTree, of which this sub-tree is a sub-directory
"""
def __init__(self,
templates: Dict[str, str],
variables: Dict[str, Any],
sub_trees: Dict[str, "FileTree"]=None,
parent: Optional["FileTree"]=None):
"""
Creates a new filename tree.
"""
self.templates = templates
self.variables = variables
if sub_trees is None:
sub_trees = {}
self.sub_trees = sub_trees
self._parent = parent
@property
def parent(self, ):
"""
Parent FileTree, of which this sub-tree is a sub-directory
"""
return self._parent
@property
def all_variables(self, ):
"""
All tree variables including those inherited from the parent tree
"""
if self.parent is None:
return dict(self.variables)
res = self.parent.all_variables
res.update(self.variables)
return res
def get_variable(self, name: str, default=None) -> str:
"""
Gets a variable used to fill out the template
:param name: variable name
:param default: default variables (if not set a MissingVariable error is raised if a variable is missing)
:return: value of the variable
"""
variables = self.all_variables
if name in variables and variables[name] is not None:
return variables[name]
if default is None:
raise MissingVariable('Variable {} not found in sub-tree or parents'.format(name))
return default
def _get_template_tree(self, short_name: str) -> Tuple["FileTree", str]:
"""
Retrieves template text from this tree, parent tree or sub_tree
:param short_name: filename reference name
:return: tuple with the containing tree and the template text
"""
if '/' in short_name:
sub_tree, sub_name = short_name.split('/', maxsplit=1)
if sub_tree == '..':
if self.parent is None:
raise KeyError("Tried to access the parent of the top-level tree")
return self.parent._get_template_tree(sub_name)
return self.sub_trees[sub_tree]._get_template_tree(sub_name)
return self, self.templates[short_name]
def get_template(self, short_name: str) -> Tuple[str, Dict[str, str]]:
"""
Returns the sub-tree that defines a given short name
- '/' characters in short_name refer to sub-trees
- '../' characters in short_name refer to parents
For example:
- "eddy/output" refers to the "output" in the "eddy" sub_tree (i.e. ``self.sub_trees['eddy'].templates['output']``)
- "../other/name" refers to the "other" sub-tree of the parent tree (i.e., ``self.parent.sub_trees['other'].templates['name']``)
:param short_name: name of the template
:return: tuple with the template and the variables corresponding to the template
"""
tree, text = self._get_template_tree(short_name)
return text, tree.all_variables
def template_variables(self, short_name: Optional[str]=None, optional=True, required=True) -> Set[str]:
"""
Returns the variables needed to define a template
:param short_name: name of the template (defaults to all)
:param optional: if set to False don't include the optional variables
:param required: if set to False don't include the required variables
:return: set of variable names
"""
if not optional and not required:
return set()
if short_name is None:
all_vars = set()
required_vars = set()
for short_name in self.templates.keys():
all_vars.update(self.template_variables(short_name))
if required or optional:
required_vars.update(self.template_variables(short_name, optional=False))
for sub_tree in self.sub_trees.values():
all_vars.update(sub_tree.template_variables())
if required or optional:
required_vars.update(sub_tree.template_variables(optional=False))
if optional and required:
return all_vars
if required:
return required_vars
if optional:
return all_vars.difference(required_vars)
else:
_, text = self._get_template_tree(short_name)
all_vars = set(utils.find_variables(text))
if optional and required:
return all_vars
opt_vars = set(utils.optional_variables(text))
if optional:
return opt_vars
if required:
return all_vars.difference(opt_vars)
def get(self, short_name, make_dir=False) -> str:
"""
Gets a full filename based on its short name
:param short_name: identifier in the tree
:param make_dir: if True make sure that the directory leading to this file exists
:return: full filename
"""
text, variables = self.get_template(short_name)
res = Path(utils.resolve(text, variables))
if make_dir:
res.parents[0].mkdir(parents=True, exist_ok=True)
return str(res)
def get_all(self, short_name: str, glob_vars=()) -> Tuple[str]:
"""
Gets all existing directory/file names matching a specific pattern
:param short_name: short name of the path template
:param glob_vars: sequence of undefined variables that can take any possible values when looking for matches on the disk.
Any defined variables in `glob_vars` will be ignored.
If glob_vars is set to 'all', all undefined variables will be used to look up matches.
:return: sorted sequence of paths
"""
text, variables = self.get_template(short_name)
return tuple(str(Path(fn)) for fn in utils.get_all(text, variables, glob_vars=glob_vars))
def get_all_vars(self, short_name: str, glob_vars=()) -> Tuple[Dict[str, str]]:
"""
Gets all the parameters that generate existing filenames
:param short_name: short name of the path template
:param glob_vars: sequence of undefined variables that can take any possible values when looking for matches on the disk.
Any defined variables in `glob_vars` will be ignored.
If glob_vars is set to 'all', all undefined variables will be used to look up matches.
:return: sequence of dictionaries with the variables settings used to generate each filename
"""
return tuple(self.extract_variables(short_name, fn) for fn in self.get_all(short_name, glob_vars=glob_vars))
def update(self, **variables) -> "FileTree":
"""
Creates a new FileTree with updated variables
:param variables: new values for the variables
Setting a variable to None will cause the variable to be unset
:return: New FileTree with same templates for directory names and filenames, but updated variables
"""
new_tree = deepcopy(self)
new_tree.variables.update(variables)
for key, value in variables.items():
if value is None:
del new_tree.variables[key]
return new_tree
def extract_variables(self, short_name: str, filename: str) -> Dict[str, str]:
"""
Extracts the variables from the given filename
:param short_name: short name of the path template
:param filename: filename matching the template
:return: variables needed to get to the given filename
Variables with None value are optional variables in the template that were not used
"""
text, _ = self.get_template(short_name)
return utils.extract_variables(text, filename, self.variables)
def save_pickle(self, filename):
"""
Saves the Filetree to a pickle file
:param filename: filename to store the file tree (usually ending with .pck)
"""
with open(filename, 'wb') as f:
pickle.dump(self, f)
@classmethod
def load_pickle(cls, filename):
"""
Loads the Filetree from a pickle file
:param filename: filename produced from Filetree.save
:return: stored Filetree
"""
with open(filename, 'rb') as f:
res = pickle.load(f)
if not isinstance(res, cls):
raise IOError("Pickle file did not contain %s object" % cls)
return res
def exists(self, short_names, on_disk=False, error=False, glob_vars=()):
"""
Checks whether the short_names are defined in the tree (and optional exist on the disk)
:param short_names: list of expected short names to exist in the tree
:param on_disk: if True checks whether the files exist on disk
:param error: if True raises a helpful error when the check fails
:param glob_vars: sequence of undefined variables that can take any possible values when looking for matches on the disk
If `glob_vars` contains any defined variables, it will be ignored.
:return: True if short names exist and optionally exist on disk (False otherwise)
:raise:
- ValueError if error is set and the tree is incomplete
- IOError if error is set and any files are missing from the disk
"""
if isinstance(short_names, str):
short_names = (short_names, )
def single_test(short_name):
try:
self._get_template_tree(short_name)
except KeyError:
return True
return False
missing = tuple(name for name in short_names if single_test(name))
if len(missing) > 0:
if error:
raise ValueError("Provided Filetree is missing file definitions for {}".format(missing))
return False
if on_disk:
try:
missing = tuple(name for name in short_names if len(self.get_all(name, glob_vars=glob_vars)) == 0)
except KeyError:
if error:
raise
return False
if len(missing) > 0:
if error:
raise IOError("Failed to find any files existing for {}".format(missing))
return False
return True
@classmethod
def read(cls, tree_name: str, directory='.', **variables) -> "FileTree":
"""
Reads a FileTree from a specific file
The return type is ``cls`` unless the tree_name has been previously registered.
The return type of any sub-tree is ``FileTree`` unless the tree_name has been previously registered.
:param tree_name: file containing the filename tree.
Can provide the filename of a tree file or the name for a tree in the ``filetree.tree_directories``.
:param directory: parent directory of the full tree (defaults to current directory)
:param variables: variable settings
:return: dictionary from specifier to filename
"""
if op.exists(tree_name):
filename = tree_name
elif op.exists(tree_name + '.tree'):
filename = tree_name + '.tree'
else:
filename = parse.search_tree(tree_name)
filename = Path(filename)
templates = {}
nspaces_level = []
sub_trees = {}
file_variables = {}
with open(str(filename), 'r') as f:
for full_line in f:
# ignore anything behind the first #-character
line = full_line.split('#')[0]
if len(line.strip()) == 0:
continue
if line.strip()[:2] == '->':
nspaces = line.index('->')
if len(nspaces_level) == 0:
sub_dir = directory
elif nspaces > nspaces_level[-1]:
sub_dir = current_filename
elif nspaces < nspaces_level[-1]:
if nspaces not in nspaces_level:
raise ValueError('line %s dropped to a non-existent level' % line)
new_level = nspaces_level.index(nspaces)
current_filename = current_filename.parents[len(nspaces_level) - new_level - 1] / filename
nspaces_level = nspaces_level[:new_level + 1]
sub_dir = current_filename.parents[0]
else:
sub_dir = current_filename.parents[0]
_, sub_tree, short_name = parse.read_subtree_line(line, sub_dir)
if short_name in sub_trees:
raise ValueError("Name of sub_tree {short_name} used multiple times in {tree_name}.tree".format(**locals()))
sub_trees[short_name] = sub_tree
elif '=' in line:
key, value = line.split('=')
if len(key.split()) != 1:
raise ValueError("Variable assignment could not be parsed: {line}".format(**locals()))
file_variables[key.strip()] = value.strip()
else:
nspaces, filename, short_name = parse.read_line(line)
if short_name in templates:
raise ValueError("Name of directory/file {short_name} used multiple times in {tree_name}.tree".format(**locals()))
if len(nspaces_level) == 0:
current_filename = PurePath(directory) / filename
nspaces_level.append(nspaces)
elif nspaces > nspaces_level[-1]:
# increase the level
current_filename = current_filename / filename
nspaces_level.append(nspaces)
elif nspaces < nspaces_level[-1]:
# decreased the level
if nspaces not in nspaces_level:
raise ValueError('line %s dropped to a non-existent level' % full_line)
new_level = nspaces_level.index(nspaces)
current_filename = current_filename.parents[len(nspaces_level) - new_level - 1] / filename
nspaces_level = nspaces_level[:new_level + 1]
else:
current_filename = current_filename.parents[0] / filename
templates[short_name] = str(current_filename)
file_variables.update(variables)
res = get_registered(tree_name, cls)(templates, variables=file_variables, sub_trees=sub_trees)
for tree in sub_trees.values():
tree._parent = res
return res
_registered_subtypes = {}
def register_tree(name: str, tree_subtype: type):
"""
Registers a tree_subtype under name
Loading a tree with given name will lead to the `tree_subtype` rather than FileTree to be returned
:param name: name of tree filename
:param tree_subtype: tree subtype
"""
global _registered_subtypes
if not issubclass(tree_subtype, FileTree):
raise ValueError("Only sub-classes of FileTree can be registered")
_registered_subtypes[name] = tree_subtype
def get_registered(name, default=FileTree) -> type:
"""
Get the previously registered subtype for ``name``
:param name: name of the sub-tree
:param default: type to return if the name has not been registered
:return: FileTree or sub-type thereof
"""
if name in _registered_subtypes:
return _registered_subtypes[name]
name = op.split(name)[1]
if name in _registered_subtypes:
return _registered_subtypes[name]
while name.endswith('.tree'):
name = name[:-5]
if name in _registered_subtypes:
return _registered_subtypes[name]
return default