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Commit a3c38e7f authored by Paul McCarthy's avatar Paul McCarthy :mountain_bicyclist:
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TEST: Make tests work: 

 - hdr now takes priority over img
 - immv/imcp scripts now return exit code rather than raising an error
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tests/test_fsl_utils_path.py
+ 130
− 135
View file @ a3c38e7f
......@@ -18,14 +18,9 @@ import fsl.utils.path as fslpath
import fsl.data.image as fslimage
real_print = print
def print(*a, **kwa):
pass
def make_dummy_file(path):
with open(path, 'wt') as f:
f.write('{}\n'.format(op.basename(path)))
f.write('{}\n'.format(op.basename(path)))
def make_dummy_image_file(path):
......@@ -46,14 +41,14 @@ def cleardir(dir):
for f in os.listdir(dir):
f = op.join(dir, f)
if op.isfile(f):
os.remove(f)
os.remove(f)
def test_deepest():
# path, suffixes, output
tests = [
('/blah.feat/foo.ica/fum.gfeat/moo.ica', ['.feat'], '/blah.feat'),
('/blah.feat/foo.ica/fum.gfeat/moo.ica', ['.feat', '.gfeat'], '/blah.feat/foo.ica/fum.gfeat'),
('/blah.feat/foo.ica/fum.gfeat/moo.ica', ['.gfeat'], '/blah.feat/foo.ica/fum.gfeat'),
......@@ -68,7 +63,7 @@ def test_deepest():
( 'blah.feat/foo.ica/fum.gfeat/moo.ica', ['.bob'], None),
( 'blah.feat/foo.ica/fum.gfeat/moo.bob', ['.ica'], 'blah.feat/foo.ica'),
( 'blah.feat/foo.ica/fum.gfeat/moo.bob', ['.ica', '.bob'], 'blah.feat/foo.ica/fum.gfeat/moo.bob'),
('/', [], None),
('', [], None),
('///', [], None),
......@@ -84,7 +79,7 @@ def test_deepest():
def test_shallowest():
# path, suffixes, output
tests = [
('/blah.feat/foo.ica/fum.gfeat/moo.ica', ['.feat'], '/blah.feat'),
('/blah.feat/foo.ica/fum.gfeat/moo.ica', ['.feat', '.gfeat'], '/blah.feat'),
('/blah.feat/foo.ica/fum.gfeat/moo.ica', ['.gfeat'], '/blah.feat/foo.ica/fum.gfeat'),
......@@ -100,7 +95,7 @@ def test_shallowest():
( 'blah.feat/foo.ica/fum.gfeat/moo.bob', ['.ica'], 'blah.feat/foo.ica'),
( 'blah.feat/foo.ica/fum.gfeat/moo.bob', ['.ica', '.bob'], 'blah.feat/foo.ica'),
(' blah.feat/foo.ica/fum.gfeat/moo.bob', ['.ica', '.bob'], 'blah.feat/foo.ica'),
('/', [], None),
('', [], None),
('///', [], None),
......@@ -108,7 +103,7 @@ def test_shallowest():
('', ['blah'], None),
('///', ['blah'], None),
]
for path, suffixes, output in tests:
assert fslpath.shallowest(path, suffixes) == output
......@@ -126,13 +121,13 @@ def test_addExt_imageFiles_mustExist_shouldPass():
# Single files
('file.nii', 'file', 'file.nii'),
('file.nii', 'file.nii', 'file.nii'),
('file.nii', 'file.nii', 'file.nii'),
('file.nii.gz', 'file', 'file.nii.gz'),
('file.nii.gz', 'file.nii.gz', 'file.nii.gz'),
('file.img', 'file', 'file.img'),
('file.img', 'file', 'file.hdr'),
('file.img', 'file.hdr', 'file.hdr'),
('file.img', 'file.img', 'file.img'),
('file.img.gz', 'file', 'file.img.gz'),
('file.img.gz', 'file', 'file.hdr.gz'),
('file.img.gz', 'file.hdr.gz', 'file.hdr.gz'),
('file.img.gz', 'file.img.gz', 'file.img.gz'),
......@@ -141,16 +136,16 @@ def test_addExt_imageFiles_mustExist_shouldPass():
('file.blob.nii', 'file.blob.nii', 'file.blob.nii'),
('file.blob.nii.gz', 'file.blob', 'file.blob.nii.gz'),
('file.blob.nii.gz', 'file.blob.nii.gz', 'file.blob.nii.gz'),
('file.blob.img', 'file.blob', 'file.blob.img'),
('file.blob.img', 'file.blob', 'file.blob.hdr'),
('file.blob.hdr', 'file.blob.hdr', 'file.blob.hdr'),
('file.blob.img', 'file.blob.img', 'file.blob.img'),
('file.blob.img.gz', 'file.blob', 'file.blob.img.gz'),
('file.blob.img.gz', 'file.blob', 'file.blob.hdr.gz'),
('file.blob.hdr.gz', 'file.blob.hdr.gz', 'file.blob.hdr.gz'),
('file.blob.img.gz', 'file.blob.img.gz', 'file.blob.img.gz'),
# Even if that suffix is a itself supported
('file.blob.img.gz', 'file.blob.img.gz', 'file.blob.img.gz'),
# Even if that suffix is a itself supported
# suffix (as long as the path is unambiguous)
('file.img.nii', 'file.img.nii', 'file.img.nii'),
('file.img.nii.gz', 'file.img.nii.gz', 'file.img.nii.gz'),
('file.img.hdr', 'file.img.hdr', 'file.img.hdr'),
......@@ -158,16 +153,16 @@ def test_addExt_imageFiles_mustExist_shouldPass():
('file.img.hdr.gz', 'file.img.hdr.gz', 'file.img.hdr.gz'),
('file.img.img.gz', 'file.img.img.gz', 'file.img.img.gz'),
# Multiple files exist, but prefix is unambiguous
('file.nii file.nii.gz', 'file.nii', 'file.nii'),
('file.nii file.nii.gz', 'file.nii.gz', 'file.nii.gz'),
('file1.nii file2.nii.gz', 'file1', 'file1.nii'),
('file1.nii file2.nii.gz', 'file1.nii', 'file1.nii'),
('file1.nii file2.nii.gz', 'file2', 'file2.nii.gz'),
('file1.nii file2.nii.gz', 'file2.nii.gz', 'file2.nii.gz'),
('file.nii file.img', 'file.nii', 'file.nii'),
('file.nii file.img', 'file.img', 'file.img'),
('file.nii file.img', 'file.hdr', 'file.hdr'),
......@@ -177,25 +172,25 @@ def test_addExt_imageFiles_mustExist_shouldPass():
('file.img.gz file.img', 'file.img.gz', 'file.img.gz'),
('file.img.gz file.img', 'file.hdr.gz', 'file.hdr.gz'),
('file1.img.gz file2.img', 'file2', 'file2.img'),
('file1.img.gz file2.img', 'file2', 'file2.hdr'),
('file1.img.gz file2.img', 'file2.img', 'file2.img'),
('file1.img.gz file2.img', 'file2.hdr', 'file2.hdr'),
('file1.img.gz file2.img', 'file1', 'file1.img.gz'),
('file1.img.gz file2.img', 'file1', 'file1.hdr.gz'),
('file1.img.gz file2.img', 'file1.img.gz', 'file1.img.gz'),
('file1.img.gz file2.img', 'file1.hdr.gz', 'file1.hdr.gz'),
('file1.img.gz file2.img', 'file1.hdr.gz', 'file1.hdr.gz'),
('file1.nii file2.img', 'file1', 'file1.nii'),
('file1.nii file2.img', 'file1.nii', 'file1.nii'),
('file1.nii file2.img', 'file2', 'file2.img'),
('file1.nii file2.img', 'file2', 'file2.hdr'),
('file1.nii file2.img', 'file2.hdr', 'file2.hdr'),
('file1.nii file2.img', 'file2.img', 'file2.img'),
('file1.img file2.img', 'file1', 'file1.img'),
('file1.img file2.img', 'file1', 'file1.hdr'),
('file1.img file2.img', 'file1.hdr', 'file1.hdr'),
('file1.img file2.img', 'file1.img', 'file1.img'),
('file1.img file2.img', 'file2', 'file2.img'),
('file1.img file2.img', 'file2', 'file2.hdr'),
('file1.img file2.img', 'file2.hdr', 'file2.hdr'),
('file1.img file2.img', 'file2.img', 'file2.img'),
('file1.img file2.img', 'file2.img', 'file2.img'),
]
workdir = tempfile.mkdtemp()
......@@ -223,10 +218,10 @@ def test_addExt_imageFiles_mustExist_shouldPass():
assert result == op.join(workdir, expected)
cleardir(workdir)
finally:
shutil.rmtree(workdir)
def test_addExt_otherFiles_mustExist_shouldPass():
......@@ -260,7 +255,7 @@ def test_addExt_otherFiles_mustExist_shouldPass():
('file.a file.b', 'file.a', '.a .b', ['.a .b'], 'file.a'),
('file.a file.b', 'file.b', '.a .b', ['.a .b'], 'file.b'),
('file.a file.b', 'file.a', '.a .b', ['.b .a'], 'file.a'),
('file.a file.b', 'file.b', '.a .b', ['.b .a'], 'file.b'),
('file.a file.b', 'file.b', '.a .b', ['.b .a'], 'file.b'),
('file.a file.b file.c file.d', 'file', '.a .b', ['.a .b'], 'file.a'),
('file.a file.b file.c file.d', 'file', '.a .b', ['.b .a'], 'file.b'),
......@@ -279,7 +274,7 @@ def test_addExt_otherFiles_mustExist_shouldPass():
('file1.a file1.b file2.c file2.d', 'file1.b', '.a .b .c .d', ['.a .b', '.c .d'], 'file1.b'),
('file1.a file1.b file2.c file2.d', 'file2', '.a .b .c .d', ['.a .b', '.c .d'], 'file2.c'),
('file1.a file1.b file2.c file2.d', 'file2.c', '.a .b .c .d', ['.a .b', '.c .d'], 'file2.c'),
('file1.a file1.b file2.c file2.d', 'file2.d', '.a .b .c .d', ['.a .b', '.c .d'], 'file2.d'),
('file1.a file1.b file2.c file2.d', 'file2.d', '.a .b .c .d', ['.a .b', '.c .d'], 'file2.d'),
]
try:
......@@ -292,7 +287,7 @@ def test_addExt_otherFiles_mustExist_shouldPass():
if len(allowedExts) == 0: allowedExts = None
if len(fileGroups) == 0: fileGroups = None
for f in files_to_create:
make_dummy_file(op.join(workdir, f))
......@@ -337,7 +332,7 @@ def test_addExt_imageFiles_mustExist_shouldFail():
('file.hdr.gz file.img.gz', 'file.img'),
('file.hdr file.img', 'file1'),
('file.hdr file.img', 'file1.im'),
('file.hdr file.img', 'filehdr'),
('file.hdr file.img', 'fileimg'),
('filehdr fileimg', 'file.hdr'),
......@@ -345,7 +340,7 @@ def test_addExt_imageFiles_mustExist_shouldFail():
('file.hdr fileimg', 'filehdr'),
('file.hdr fileimg', 'file.img'),
('filehdr file.img', 'fileimg'),
('filehdr file.img', 'file.hdr'),
('filehdr file.img', 'file.hdr'),
# Unsupported type/invalid path
('file.blob', 'file'),
......@@ -359,8 +354,8 @@ def test_addExt_imageFiles_mustExist_shouldFail():
# Incomplete file pairs
('file.hdr', 'file.img'),
('file.img', 'file.hdr'),
('file1.hdr file2.img', 'file1.img'),
('file.img', 'file.hdr'),
('file1.hdr file2.img', 'file1.img'),
('file1.hdr file2.img', 'file2.hdr'),
# Stupid file names
......@@ -385,7 +380,7 @@ def test_addExt_imageFiles_mustExist_shouldFail():
print('files_to_create: ', files_to_create)
print('prefix: ', prefix)
print('workdir: ', os.listdir(workdir))
with pytest.raises(fslpath.PathError):
result = fslpath.addExt(op.join(workdir, prefix),
......@@ -398,7 +393,7 @@ def test_addExt_imageFiles_mustExist_shouldFail():
finally:
shutil.rmtree(workdir)
def test_addExt_otherFiles_mustExist_shouldFail():
workdir = tempfile.mkdtemp()
......@@ -425,7 +420,7 @@ def test_addExt_otherFiles_mustExist_shouldFail():
# Multiple groups, ambiguous path
('file.a file.b file.c file.d', 'file', '.a .b .c .d', ['.a .b', '.c .d']),
]
try:
for files_to_create, prefix, allowedExts, fileGroups in tests:
......@@ -434,7 +429,7 @@ def test_addExt_otherFiles_mustExist_shouldFail():
files_to_create = files_to_create.split()
allowedExts = allowedExts.split()
fileGroups = [g.split() for g in fileGroups]
if len(allowedExts) == 0: allowedExts = None
if len(fileGroups) == 0: fileGroups = None
......@@ -443,7 +438,7 @@ def test_addExt_otherFiles_mustExist_shouldFail():
print('files_to_create: ', files_to_create)
print('prefix: ', prefix)
print('workdir: ', os.listdir(workdir))
print('workdir: ', os.listdir(workdir))
with pytest.raises(fslpath.PathError):
......@@ -453,19 +448,19 @@ def test_addExt_otherFiles_mustExist_shouldFail():
fileGroups=fileGroups)
print('result: ', result)
finally:
shutil.rmtree(workdir)
pass
def test_addExt_noExist():
allowedExts = fslimage.ALLOWED_EXTENSIONS
# When mustExist=False, the addExt
# function does not consult fileGroups.
# When mustExist=False, the addExt
# function does not consult fileGroups.
# So we are not bothering with them
# here.
......@@ -481,15 +476,15 @@ def test_addExt_noExist():
('file.img.gz', None, allowedExts, 'file.img.gz'),
('file.hdr.gz', None, allowedExts, 'file.hdr.gz'),
('file.blob.img', '.img', allowedExts, 'file.blob.img'),
('file.blob.img', '.img', None, 'file.blob.img'),
('file.blob.img', '.img', None, 'file.blob.img'),
# If the file does not have a prefix,
# it should be given the default prefix
('file', 'img', allowedExts, 'fileimg'),
('file', '.img', allowedExts, 'file.img'),
('file', 'img', None, 'fileimg'),
('file', '.img', None, 'file.img'),
('file', '.img', None, 'file.img'),
# Unrecognised prefixes should be ignored
('file.blob', 'img', allowedExts, 'file.blobimg'),
......@@ -499,7 +494,7 @@ def test_addExt_noExist():
]
for prefix, defaultExt, allowedExts, expected in tests:
assert fslpath.addExt(prefix,
allowedExts,
defaultExt=defaultExt,
......@@ -509,7 +504,7 @@ def test_addExt_noExist():
def test_removeExt():
allowedExts = fslimage.ALLOWED_EXTENSIONS
# If len(test) == 2, allowedExts is set from above
# Otherwise, it is set from the test tuple
tests = [
......@@ -530,7 +525,7 @@ def test_removeExt():
]
for test in tests:
path = test[0]
output = test[1]
......@@ -576,13 +571,13 @@ def test_getExt():
print(filename, '==', output)
assert fslpath.getExt(filename, allowed) == output
def test_splitExt():
allowedExts = fslimage.ALLOWED_EXTENSIONS
# len(test) == 2 -> allowedExts set from above
# Otherwise, allowedExts set from test tuple
# Otherwise, allowedExts set from test tuple
tests = [
('blah', ('blah', '')),
('blah.blah', ('blah.blah', '')),
......@@ -614,7 +609,7 @@ def test_splitExt():
('blah', ('blah', '')),
('blah.blah', ('blah.blah', '')),
('blah.blah', ('blah.blah', ''), ['bla']),
('blah.nii.gz', ('blah.nii.gz', ''), ['.nii']),
('blah.nii.gz', ('blah.nii.gz', ''), ['.nii']),
]
for test in tests:
......@@ -626,9 +621,9 @@ def test_splitExt():
print(filename, '==', (outbase, outext))
assert fslpath.splitExt(filename, allowed) == (outbase, outext)
def test_getFileGroup_imageFiles_shouldPass():
allowedExts = fslimage.ALLOWED_EXTENSIONS
......@@ -678,14 +673,14 @@ def test_getFileGroup_imageFiles_shouldPass():
('file.hdr file.img file.nii', 'file.nii', 'file.nii', True),
('file.hdr file.img file.nii', 'file.hdr', 'file.hdr file.img', True),
('file.hdr file.img file.nii', 'file.img', 'file.hdr file.img', True),
]
# TODO You need to add passing tests for unambiguous=True
workdir = tempfile.mkdtemp()
try:
try:
for test in tests:
......@@ -741,7 +736,7 @@ def test_getFileGroup_otherFiles_shouldPass():
('file.a file.b', '', '', 'file.b', 'file.b'),
('file.a file.b', '', ['.a .b'], 'file.a', 'file.a file.b'),
('file.a file.b', '', ['.a .b'], 'file.b', 'file.a file.b'),
('file.a file.b file.c', '', ['.a .b .c'], 'file.a', 'file.a file.b file.c'),
('file.a file.b file.c', '', ['.a .b .c'], 'file.b', 'file.a file.b file.c'),
('file.a file.b file.c', '', ['.a .b .c'], 'file.c', 'file.a file.b file.c'),
......@@ -749,9 +744,9 @@ def test_getFileGroup_otherFiles_shouldPass():
('file.a file.b file.c file.d', '', ['.a .b', '.c .d'], 'file.a', 'file.a file.b'),
('file.a file.b file.c file.d', '', ['.a .b', '.c .d'], 'file.b', 'file.a file.b'),
('file.a file.b file.c file.d', '', ['.a .b', '.c .d'], 'file.c', 'file.c file.d'),
('file.a file.b file.c file.d', '', ['.a .b', '.c .d'], 'file.d', 'file.c file.d'),
('file.a file.b file.c file.d', '', ['.a .b', '.c .d'], 'file.d', 'file.c file.d'),
# allowedExts != None - incomplete paths
# allowedExts != None - incomplete paths
# allowed, but must be unambiguous
('file.a', '.a', '', 'file', 'file.a'),
('file.a', '.a', '', 'file.a', 'file.a'),
......@@ -759,12 +754,12 @@ def test_getFileGroup_otherFiles_shouldPass():
('file.a file.b', '.a .b', '', 'file.b', 'file.b'),
('file1.a file2.b', '.a .b', '', 'file1', 'file1.a'),
('file1.a file2.b', '.a .b', '', 'file1.a', 'file1.a'),
('file1.a file2.b', '.a .b', '', 'file2', 'file2.b'),
('file1.a file2.b', '.a .b', '', 'file2.b', 'file2.b'),
('file1.a file2.b', '.a .b', '', 'file2', 'file2.b'),
('file1.a file2.b', '.a .b', '', 'file2.b', 'file2.b'),
('file.a file.b', '.a .b', ['.a .b'], 'file', 'file.a file.b'),
('file.a file.b', '.a .b', ['.a .b'], 'file.a', 'file.a file.b'),
('file.a file.b', '.a .b', ['.a .b'], 'file.b', 'file.a file.b'),
('file.a file.b', '.a .b', ['.a .b'], 'file.b', 'file.a file.b'),
('file.a file.b file.c', '.a .b .c', ['.a .b .c'], 'file', 'file.a file.b file.c'),
('file.a file.b file.c', '.a .b .c', ['.a .b .c'], 'file.a', 'file.a file.b file.c'),
......@@ -782,13 +777,13 @@ def test_getFileGroup_otherFiles_shouldPass():
('file1.a file1.b file2.c file2.d', '.a .b .c .d', ['.a .b', '.c .d'], 'file2.c', 'file2.c file2.d'),
('file1.a file1.b file2.c file2.d', '.a .b .c .d', ['.a .b', '.c .d'], 'file2.d', 'file2.c file2.d'),
# incomplete group should be ok when
# incomplete group should be ok when
# unambiguous = False (the default)
('file.a', '.a .b', ['.a .b'], 'file', 'file.a'),
('file.a', '.a .b', ['.a .b'], 'file.a', 'file.a'),
# Unambiguous/complete group should
# Unambiguous/complete group should
# be ok when unambiguous = True
('file.a file.b file.c', '.a .b .c', ['.a .b'], 'file.a', 'file.a file.b', True),
('file.a file.b file.c', '.a .b .c', ['.a .b'], 'file.b', 'file.a file.b', True),
......@@ -809,7 +804,7 @@ def test_getFileGroup_otherFiles_shouldPass():
if len(test) == 6: unambiguous = test[5]
else: unambiguous = False
files_to_create = files_to_create.split()
allowedExts = allowedExts.split()
......@@ -864,13 +859,13 @@ def test_getFileGroup_shouldFail():
# Unsupported extension
('file.a', 'file.a', '.b', []),
# Incomplete path, and allowedExts is None
('file.a', 'file', '', []),
# non existent path
('file.a', 'file.b', '.a', []),
# ambigiuous
('file.a file.b file.c file.d', 'file', '.a .b .c .d', ['.a .b', '.c .d']),
......@@ -886,7 +881,7 @@ def test_getFileGroup_shouldFail():
# Part of more than one group, when unambiguous is True
('file.a file.b file.c', 'file.a', '.a .b', ['.a .b', '.a .c'], True),
]
workdir = tempfile.mkdtemp()
try:
......@@ -934,7 +929,7 @@ def test_getFileGroup_shouldFail():
fileGroups=fileGroups,
fullPaths=False,
unambiguous=unambiguous)
print('exts: ', exts)
cleardir(workdir)
......@@ -947,7 +942,7 @@ def test_getFileGroup_shouldFail():
def test_removeDuplicates_imageFiles_shouldPass():
allowedExts = fslimage.ALLOWED_EXTENSIONS
groups = fslimage.FILE_GROUPS
groups = fslimage.FILE_GROUPS
# [(files_to_create,
# [(paths, expected),
......@@ -957,52 +952,52 @@ def test_removeDuplicates_imageFiles_shouldPass():
# ]
allTests = [
('file.hdr file.img', [
('file', 'file.img'),
('file file', 'file.img'),
('file file.hdr', 'file.img'),
('file file.img', 'file.img'),
('file.hdr file', 'file.img'),
('file.hdr file.hdr', 'file.img'),
('file.hdr file.img', 'file.img'),
('file.img file', 'file.img'),
('file.img file.hdr', 'file.img'),
('file.img file.img', 'file.img'),
('file.hdr', 'file.img'),
('file.img', 'file.img'),
('file.hdr file.img', 'file.img'),
('file.img file.hdr', 'file.img'),
('file', 'file.hdr'),
('file file', 'file.hdr'),
('file file.hdr', 'file.hdr'),
('file file.img', 'file.hdr'),
('file.hdr file', 'file.hdr'),
('file.hdr file.hdr', 'file.hdr'),
('file.hdr file.img', 'file.hdr'),
('file.img file', 'file.hdr'),
('file.img file.hdr', 'file.hdr'),
('file.img file.img', 'file.hdr'),
('file.hdr', 'file.hdr'),
('file.img', 'file.hdr'),
('file.hdr file.img', 'file.hdr'),
('file.img file.hdr', 'file.hdr'),
]),
('file.hdr file.img file.blob', [
('file', 'file.img'),
('file.hdr', 'file.img'),
('file.img', 'file.img'),
('file.hdr file.img', 'file.img'),
('file.img file.hdr', 'file.img'),
('file', 'file.hdr'),
('file.hdr', 'file.hdr'),
('file.img', 'file.hdr'),
('file.hdr file.img', 'file.hdr'),
('file.img file.hdr', 'file.hdr'),
]),
('file.hdr file.img file.nii', [
('file.hdr', 'file.img'),
('file.img', 'file.img'),
('file.hdr file.nii', 'file.img file.nii'),
('file.img file.nii', 'file.img file.nii'),
('file.hdr file.img', 'file.img'),
('file.img file.hdr', 'file.img'),
('file.img file.hdr', 'file.img'),
('file.hdr file.img file.nii', 'file.img file.nii'),
('file.img file.hdr file.nii', 'file.img file.nii'),
('file.img file.hdr file.nii', 'file.img file.nii'),
]),
('file.hdr', 'file.hdr'),
('file.img', 'file.hdr'),
('file.hdr file.nii', 'file.hdr file.nii'),
('file.img file.nii', 'file.hdr file.nii'),
('file.hdr file.img', 'file.hdr'),
('file.img file.hdr', 'file.hdr'),
('file.img file.hdr', 'file.hdr'),
('file.hdr file.img file.nii', 'file.hdr file.nii'),
('file.img file.hdr file.nii', 'file.hdr file.nii'),
('file.img file.hdr file.nii', 'file.hdr file.nii'),
]),
('001.hdr 001.img 002.hdr 002.img 003.hdr 003.img', [
('001 002 003', '001.img 002.img 003.img'),
('001.hdr 002.hdr 003.hdr', '001.img 002.img 003.img'),
('001.img 002.img 003.img', '001.img 002.img 003.img'),
('001.hdr 001.img 002.hdr 002.img 003.img', '001.img 002.img 003.img'),
('001.hdr 001.img 002.hdr 002.img 003.hdr 003.img', '001.img 002.img 003.img'),
('001.img 001.hdr 002.img 002.hdr 003.img 003.hdr', '001.img 002.img 003.img'),
('001 002 003', '001.hdr 002.hdr 003.hdr'),
('001.hdr 002.hdr 003.hdr', '001.hdr 002.hdr 003.hdr'),
('001.img 002.img 003.img', '001.hdr 002.hdr 003.hdr'),
('001.hdr 001.img 002.hdr 002.img 003.img', '001.hdr 002.hdr 003.hdr'),
('001.hdr 001.img 002.hdr 002.img 003.hdr 003.img', '001.hdr 002.hdr 003.hdr'),
('001.img 001.hdr 002.img 002.hdr 003.img 003.hdr', '001.hdr 002.hdr 003.hdr'),
])
]
......@@ -1012,7 +1007,7 @@ def test_removeDuplicates_imageFiles_shouldPass():
for files_to_create, tests in allTests:
files_to_create = files_to_create.split()
for fn in files_to_create:
with open(op.join(workdir, fn), 'wt') as f:
f.write('{}\n'.format(fn))
......@@ -1021,12 +1016,12 @@ def test_removeDuplicates_imageFiles_shouldPass():
paths = paths.split()
expected = expected.split()
print()
print('files_to_create: ', files_to_create)
print('paths: ', paths)
print('expected: ', expected)
paths = [op.join(workdir, p) for p in paths]
result = fslpath.removeDuplicates(paths, allowedExts, groups)
......@@ -1035,38 +1030,38 @@ def test_removeDuplicates_imageFiles_shouldPass():
assert result == [op.join(workdir, e) for e in expected]
cleardir(workdir)
finally:
shutil.rmtree(workdir)
def test_removeDuplicates_otherFiles_shouldPass():
# files_to_create, paths, allowedExts, fileGroups, expected
tests = [
# allowedExts is None, but paths are unambiguouos
('file.a file.b', 'file.a file.b', '', [], 'file.a file.b'),
# Retured path should be the first in the group
('file.a file.b', 'file.a file.b', '', ['.a .b'], 'file.a'),
('file.a file.b', 'file.a file.b', '', ['.b .a'], 'file.b'),
('file.a file.b file.c', 'file.a file.b file.c', '', ['.a .b'], 'file.a file.c'),
('file.a file.b file.c', 'file.a file.b file.c', '', ['.b .a'], 'file.b file.c'),
('file.a file.b file.c', 'file.a file.b file.c', '', ['.a .b .c'], 'file.a'),
('file.a file.b file.c', 'file.a file.b file.c', '', ['.a .b .c'], 'file.a'),
('file.a file.b file.c', 'file.a file.b file.c', '', ['.a .b .c'], 'file.a'),
('file.a file.b file.c file.d', 'file.a file.b file.c file.d', '', ['.a .b', '.c .d'], 'file.a file.c'),
('file1.a file1.b file2.a file2.b', 'file1.a file1.b file2.a file2.b', '', ['.a .b'], 'file1.a file2.a'),
# Incomplete paths (but are unambiguouos because of allowedExts)
('file.a' , 'file', '.a', [], 'file.a'),
('file.a' , 'file', '.a', [], 'file.a'),
('file.a' , 'file.a', '.a', [], 'file.a'),
('file.a file.b', 'file.a', '.a', [], 'file.a'),
('file.a file.b', 'file.a file.b', '.a .b', [], 'file.a file.b'),
('file.a file.b', 'file', '.a .b', ['.a .b'], 'file.a'),
......@@ -1103,7 +1098,7 @@ def test_removeDuplicates_otherFiles_shouldPass():
print('fileGroups: {}'.format(fileGroups))
print('workdir: {}'.format(os.listdir(workdir)))
print('expected: {}'.format(expected))
result = fslpath.removeDuplicates([op.join(workdir, p) for p in paths],
allowedExts=allowedExts,
fileGroups=fileGroups)
......@@ -1166,8 +1161,8 @@ def test_removeDuplicates_shouldFail():
result = fslpath.removeDuplicates(path,
allowedExts=allowedExts,
fileGroups=fileGroups)
print('result: ', result)
print('result: ', result)
finally:
shutil.rmtree(workdir)
......@@ -1230,7 +1225,7 @@ def test_uniquePrefix():
100307.corrThickness.32k_fs_LR.dscalar.nii
100307.curvature.32k_fs_LR.dscalar.nii
100307.sulc.32k_fs_LR.dscalar.nii
100307.thickness.32k_fs_LR.dscalar.nii
100307.thickness.32k_fs_LR.dscalar.nii
""".split()
# (filename, expected_result)
......@@ -1244,7 +1239,7 @@ def test_uniquePrefix():
('100307.SmoothedMyelinMap.32k_fs_LR.dscalar.nii', '100307.SmoothedMyelinMap.'),
('100307.sulc.32k_fs_LR.dscalar.nii', '100307.s'),
]
workdir = tempfile.mkdtemp()
try:
......
tests/test_immv_imcp.py
+ 2
− 6
View file @ a3c38e7f
......@@ -440,12 +440,8 @@ def test_imcp_script_shouldFail(move=False):
cmd = cmd.replace('indir', indir).replace('outdir', outdir)
sp.call(cmd.split())
try:
if move: immv_script.main(imcp_args)
else: imcp_script.main(imcp_args)
assert False
except (RuntimeError, IOError, fslpath.PathError, ImageFileError):
pass
if move: assert immv_script.main(imcp_args) != 0
else: assert imcp_script.main(imcp_args) != 0
sp.call('chmod u+rwx {}'.format(indir) .split())
sp.call('chmod u+rwx {}'.format(outdir).split())
......
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