From eee2c3662323b6743a7d11777e0ce9115254639f Mon Sep 17 00:00:00 2001
From: Michiel Cottaar <MichielCottaar@gmail.com>
Date: Thu, 2 May 2019 13:46:52 +0100
Subject: [PATCH] BUG: check invalid characters in the FileTree
Also made small fixes to trees that contained invalid characters
---
fsl/utils/filetree/parse.py | 20 ++++++++++++++++++++
fsl/utils/filetree/trees/HCP_Surface.tree | 2 +-
fsl/utils/filetree/trees/freesurfer.tree | 4 ++--
3 files changed, 23 insertions(+), 3 deletions(-)
diff --git a/fsl/utils/filetree/parse.py b/fsl/utils/filetree/parse.py
index 11a8f1f22..f76fe9b72 100644
--- a/fsl/utils/filetree/parse.py
+++ b/fsl/utils/filetree/parse.py
@@ -38,6 +38,21 @@ def list_all_trees() -> List[str]:
return trees
+def check_forbidden_characters(text, characters, text_type):
+ """
+ Checks the text for forbidden characters
+
+ raises ValueError if one is found
+
+ :param text: string with the text
+ :param characters: sequence of forbidden characters
+ :param text_type: type of the text to raise in error message
+ """
+ bad = [character for character in characters if character in text]
+ if len(bad) > 0:
+ raise ValueError(f'Invalid character(s) "{"".join(bad)}" in {text_type}: {text}')
+
+
def read_line(line: str) -> Tuple[int, PurePath, str]:
"""
Parses line from the tree file
@@ -54,11 +69,14 @@ def read_line(line: str) -> Tuple[int, PurePath, str]:
match = re.match(r'^(\s*)(\S*)\s*\((\S*)\)\s*$', line)
if match is not None:
gr = match.groups()
+ check_forbidden_characters(gr[1], r'<>"/\|?*', 'file or directory name')
+ check_forbidden_characters(gr[2], r'(){}/', 'short name')
return len(gr[0]), PurePath(gr[1]), gr[2]
match = re.match(r'^(\s*)(\S*)\s*$', line)
if match is not None:
gr = match.groups()
short_name = gr[1].split('.')[0]
+ check_forbidden_characters(gr[1], r'<>"/\|?*', 'file or directory name')
return len(gr[0]), PurePath(gr[1]), short_name
raise ValueError('Unrecognized line %s' % line)
@@ -79,6 +97,8 @@ def read_subtree_line(line: str, directory: str) -> Tuple[int, "filetree.FileTre
if match is None:
raise ValueError("Sub-tree line could not be parsed: {}".format(line.strip()))
spaces, type_name, variables_str, short_name = match.groups()
+ check_forbidden_characters(type_name, r'<>:"/\|?*', 'sub-tree name')
+ check_forbidden_characters(short_name, r'(){}/', 'sub-tree name')
variables = {}
if len(variables_str.strip()) != 0:
diff --git a/fsl/utils/filetree/trees/HCP_Surface.tree b/fsl/utils/filetree/trees/HCP_Surface.tree
index 0d6e02539..9db03d9cc 100644
--- a/fsl/utils/filetree/trees/HCP_Surface.tree
+++ b/fsl/utils/filetree/trees/HCP_Surface.tree
@@ -27,6 +27,6 @@
{subject}.sulc_MSMAll.{space}.dscalar.nii (sulc_msm_cifti)
{subject}.thickness_MSMAll.{space}.dscalar.nii (thick_msm_cifti)
{subject}.curvature_MSMAll.{space}.dscalar.nii (curv_msm_cifti)
-{subject}.BA.32k_fs_LR.dlabel.nii (BA_cifti))
+{subject}.BA.32k_fs_LR.dlabel.nii (BA_cifti)
{subject}.aparc.32k_fs_LR.dlabel.nii (aparc_cifti)
{subject}.aparc.a2009s.32k_fs_LR.dlabel.nii (aparc2009_cifti)
diff --git a/fsl/utils/filetree/trees/freesurfer.tree b/fsl/utils/filetree/trees/freesurfer.tree
index 8a20ac211..cd6df40ba 100644
--- a/fsl/utils/filetree/trees/freesurfer.tree
+++ b/fsl/utils/filetree/trees/freesurfer.tree
@@ -67,10 +67,10 @@
aparc.a2009s+aseg.mgz (aparc_a2009s_aseg)
aseg.mgz
- label/
+ label
{hemi}h.aparc.annot (aparc.annot)
- stats/
+ stats
aseg.stats (aseg_stats)
wmparc.stats (wmparc_stats)
--
GitLab