diff --git a/fsl/utils/filetree/filetree.py b/fsl/utils/filetree/filetree.py
index 0b97268f2dd82580550e1c1d8ce3fda5498b6cfd..a58744668d07767d477b4021e33fab50c10368e7 100644
--- a/fsl/utils/filetree/filetree.py
+++ b/fsl/utils/filetree/filetree.py
@@ -1,10 +1,11 @@
from pathlib import Path, PurePath
-from typing import Tuple, Optional, List, Dict, Any, Set
+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
+from fsl.utils.deprecated import deprecated
class MissingVariable(KeyError):
@@ -257,12 +258,38 @@ class FileTree(object):
raise IOError("Pickle file did not contain %s object" % cls)
return res
- def exists(self, short_names, on_disk=False, error=False, glob_vars=()):
+ def defines(self, short_names, error=False):
+ """
+ Checks whether templates are defined for all the `short_names`
+
+ :param short_names: sequence of expected short names to exist in the tree
+ :param error: if True raises ValueError if any `short_names` are undefined
+ :return: True if all are defined, False otherwise
+ :raise: ValueError if `error` is set to True and any template is missing
+ """
+ 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 template definitions for {}".format(missing))
+ return False
+ return True
+
+ def on_disk(self, short_names, error=False, glob_vars=()):
"""
- Checks whether the short_names are defined in the tree (and optional exist on the disk)
+ Checks whether at least one file exists for every file in `short_names`
: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.
@@ -271,34 +298,34 @@ class FileTree(object):
- ValueError if error is set and the tree is incomplete
- IOError if error is set and any files are missing from the disk
"""
+ self.defines(short_names, error=error)
+
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
+ 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
-
- 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))
+ raise IOError("Failed to find any files on disk 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
+ @deprecated(rin='2.4', msg='Use FileTree.defines or FileTree.on_disk instead')
+ def exists(self, short_names, on_disk=False, error=False, glob_vars=()):
+ """
+ Deprecated in favor of :meth:`on_disk` and :meth:`defines`.
+ """
+ if on_disk:
+ return self.on_disk(short_names, error=error, glob_vars=glob_vars)
+ else:
+ return self.defines(short_names, error=error, glob_vars=glob_vars)
+
+
@classmethod
def read(cls, tree_name: str, directory='.', **variables) -> "FileTree":
"""
diff --git a/tests/test_filetree/test_read.py b/tests/test_filetree/test_read.py
index cba2625e19601722301e5b3b68f26fa472152637..00bd310106b422fecff8029045c38c44ed943ae9 100644
--- a/tests/test_filetree/test_read.py
+++ b/tests/test_filetree/test_read.py
@@ -34,17 +34,17 @@ def test_complicated_tree():
same_path(tree.update(hemi='L').get('T1w_32k/white'), L_white)
same_path(tree.sub_trees['T1w_32k'].update(hemi='L').get('white'), L_white)
- assert tree.exists(('T1w_32k/white', ))
- assert tree.exists('T1w_32k/white')
- assert not tree.exists(('T1w_32k/white_misspelled', ))
- assert not tree.exists(('T1w_32k/white', 'T1w_32k/white_misspelled', ))
- assert not tree.exists(('T1w_32k_err/white', ))
- assert not tree.exists(('../test'))
+ assert tree.defines(('T1w_32k/white', ))
+ assert tree.defines('T1w_32k/white')
+ assert not tree.defines(('T1w_32k/white_misspelled', ))
+ assert not tree.defines(('T1w_32k/white', 'T1w_32k/white_misspelled', ))
+ assert not tree.defines(('T1w_32k_err/white', ))
+ assert not tree.defines(('../test'))
with pytest.raises(ValueError):
- assert not tree.exists(('../test'), error=True)
+ assert not tree.defines(('../test'), error=True)
with pytest.raises(ValueError):
- tree.exists(('T1w_32k_err/white', ), error=True)
- assert tree.exists(('T1w_32k/white', ), error=True)
+ tree.defines(('T1w_32k_err/white', ), error=True)
+ assert tree.defines(('T1w_32k/white', ), error=True)
def test_parent_tree():
@@ -110,14 +110,14 @@ def test_custom_tree():
assert vars == tree.extract_variables('sub_file', filename)
assert {'opt': None} == tree.extract_variables('sub_file', tree.get('sub_file'))
- assert tree.exists(('sub_file', 'opt_file'), error=True, on_disk=True, glob_vars=['opt'])
- assert tree.exists(('sub_file', 'opt_file'), on_disk=True, glob_vars=['opt'])
- assert not tree.exists(('sub_file', 'opt_file'), error=False, on_disk=True)
+ assert tree.on_disk(('sub_file', 'opt_file'), error=True, glob_vars=['opt'])
+ assert tree.on_disk(('sub_file', 'opt_file'), glob_vars=['opt'])
+ assert not tree.on_disk(('sub_file', 'opt_file'), error=False)
with pytest.raises(KeyError):
- assert tree.exists(('sub_file', 'opt_file'), error=True, on_disk=True)
- assert not tree.update(opt='test2').exists(('sub_file', 'opt_file'), on_disk=True)
+ assert tree.on_disk(('sub_file', 'opt_file'), error=True)
+ assert not tree.update(opt='test2').on_disk(('sub_file', 'opt_file'))
with pytest.raises(IOError):
- tree.update(opt='test2').exists(('sub_file', 'opt_file'), on_disk=True, error=True)
+ tree.update(opt='test2').on_disk(('sub_file', 'opt_file'), error=True)
assert tree.template_variables() == {'opt'}
assert tree.template_variables(optional=False) == {'opt'}