From 07bec0375f9c6c0d730f9a9e5056169a5bb262e3 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Thu, 17 Nov 2016 19:25:34 +0000
Subject: [PATCH] Paths passed to removeDuplicates must exist. Immv/cp scripts
raise error when called programmatically.
---
fsl/scripts/imcp.py | 14 +++++++-------
fsl/scripts/immv.py | 13 ++++++-------
fsl/utils/path.py | 20 ++++++++++++++++----
3 files changed, 29 insertions(+), 18 deletions(-)
diff --git a/fsl/scripts/imcp.py b/fsl/scripts/imcp.py
index 71af0fd86..4ec9887ab 100755
--- a/fsl/scripts/imcp.py
+++ b/fsl/scripts/imcp.py
@@ -58,13 +58,13 @@ def main(argv=None):
fileGroups=fslimage.FILE_GROUPS)
for src in srcs:
- try:
- imcp.imcp(src, dest, useDefaultExt=True)
-
- except Exception as e:
- print(e)
- break
+ imcp.imcp(src, dest, useDefaultExt=True)
if __name__ == '__main__':
- main()
+
+ try:
+ main()
+ except Exception as e:
+ print(e)
+ sys.exit(1)
diff --git a/fsl/scripts/immv.py b/fsl/scripts/immv.py
index 66f57bd49..f5a4843a6 100755
--- a/fsl/scripts/immv.py
+++ b/fsl/scripts/immv.py
@@ -59,13 +59,12 @@ def main(argv=None):
fileGroups=fslimage.FILE_GROUPS)
for src in srcs:
- try:
- imcp.immv(src, dest, useDefaultExt=True)
-
- except Exception as e:
- print(e)
- break
+ imcp.immv(src, dest, useDefaultExt=True)
if __name__ == '__main__':
- main()
+ try:
+ main()
+ except Exception as e:
+ print(e)
+ sys.exit(1)
diff --git a/fsl/utils/path.py b/fsl/utils/path.py
index cbd9fd8bd..32a676cc3 100644
--- a/fsl/utils/path.py
+++ b/fsl/utils/path.py
@@ -246,7 +246,10 @@ def removeDuplicates(paths, allowedExts=None, fileGroups=None):
['001.img', '002.img', '003.img']
- :arg paths: List of paths to reduce.
+ A :exc:`PathError` is raised if any of the paths do not exist.
+
+ :arg paths: List of paths to reduce. If ``allowedExts`` is not
+ ``None``, may be incomplete.
:arg allowedExts: Allowed/recognised file extensions.
@@ -257,10 +260,19 @@ def removeDuplicates(paths, allowedExts=None, fileGroups=None):
for path in paths:
+ path = addExt(path,
+ mustExist=True,
+ allowedExts=allowedExts,
+ fileGroups=fileGroups)
+
groupFiles = getFileGroup(path, allowedExts, fileGroups)
- if not any([g in unique for g in groupFiles]):
- unique.append(path)
+ if len(groupFiles) == 0:
+ if path not in unique:
+ unique.append(path)
+
+ elif not any([p in unique for p in groupFiles]):
+ unique.append(groupFiles[0])
return unique
@@ -320,7 +332,7 @@ def getFileGroup(path, allowedExts=None, fileGroups=None, fullPaths=True):
for group in fileGroups:
- if ext not in group:
+ if ext != '' and ext not in group:
continue
groupFiles = [base + s for s in group]
--
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