From 838c016fdd85d430a2979ec1a456b216657374a8 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Fri, 18 Nov 2016 18:03:42 +0000
Subject: [PATCH] Reworked/extended path module tests
---
tests/test_fsl_utils_path.py | 1119 ++++++++++++++++++++++++++--------
1 file changed, 865 insertions(+), 254 deletions(-)
diff --git a/tests/test_fsl_utils_path.py b/tests/test_fsl_utils_path.py
index c3366d72f..29ed7e370 100644
--- a/tests/test_fsl_utils_path.py
+++ b/tests/test_fsl_utils_path.py
@@ -18,7 +18,97 @@ import fsl.utils.path as fslpath
import fsl.data.image as fslimage
-def test_addExt_exists_shouldPass(testdir):
+def make_dummy_file(path):
+ with open(path, 'wt') as f:
+ f.write('{}\n'.format(op.basename(path)))
+
+
+def make_dummy_image_file(path):
+
+ if path.endswith('.nii'): paths = [path]
+ elif path.endswith('.nii.gz'): paths = [path]
+ elif path.endswith('.img'): paths = [path, path[:-4] + '.hdr']
+ elif path.endswith('.hdr'): paths = [path, path[:-4] + '.img']
+ elif path.endswith('.img.gz'): paths = [path, path[:-7] + '.hdr.gz']
+ elif path.endswith('.hdr.gz'): paths = [path, path[:-7] + '.img.gz']
+ else: raise RuntimeError()
+
+ for path in paths:
+ make_dummy_file(path)
+
+
+def cleardir(dir):
+ for f in os.listdir(dir):
+ f = op.join(dir, f)
+ if op.isfile(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'),
+ ('/blah.feat/foo.ica/fum.gfeat/moo.ica', ['.ica'], '/blah.feat/foo.ica/fum.gfeat/moo.ica'),
+ ('/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', ['.bob'], '/blah.feat/foo.ica/fum.gfeat/moo.bob'),
+ ( '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'),
+ ( 'blah.feat/foo.ica/fum.gfeat/moo.ica', ['.ica'], 'blah.feat/foo.ica/fum.gfeat/moo.ica'),
+ ( '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),
+ ('/', ['blah'], None),
+ ('', ['blah'], None),
+ ('///', ['blah'], None),
+ ]
+
+ for path, suffixes, output in tests:
+ assert fslpath.deepest(path, suffixes) == output
+
+
+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'),
+ ('/blah.feat/foo.ica/fum.gfeat/moo.ica', ['.ica'], '/blah.feat/foo.ica'),
+ ('/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', ['.bob'], '/blah.feat/foo.ica/fum.gfeat/moo.bob'),
+ ( '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'),
+ ( 'blah.feat/foo.ica/fum.gfeat/moo.ica', ['.ica'], 'blah.feat/foo.ica'),
+ ( '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'),
+ (' blah.feat/foo.ica/fum.gfeat/moo.bob', ['.ica', '.bob'], 'blah.feat/foo.ica'),
+
+ ('/', [], None),
+ ('', [], None),
+ ('///', [], None),
+ ('/', ['blah'], None),
+ ('', ['blah'], None),
+ ('///', ['blah'], None),
+ ]
+
+ for path, suffixes, output in tests:
+ assert fslpath.shallowest(path, suffixes) == output
+
+
+def test_addExt_imageFiles_mustExist_shouldPass():
"""Tests the addExt function where the path exists, and the inputs
are valid.
"""
@@ -26,119 +116,389 @@ def test_addExt_exists_shouldPass(testdir):
groups = fslimage.FILE_GROUPS
allowedExts = fslimage.ALLOWED_EXTENSIONS
+ # (files_to_create, path, expected)
tests = [
- ('compressed', 'compressed.nii.gz'),
- ('compressed.nii.gz', 'compressed.nii.gz'),
- ('uncompressed', 'uncompressed.nii'),
- ('uncompressed.nii', 'uncompressed.nii'),
- ('img_hdr_pair', 'img_hdr_pair.img'),
- ('img_hdr_pair.hdr', 'img_hdr_pair.hdr'),
- ('img_hdr_pair.img', 'img_hdr_pair.img'),
- ('compressed_img_hdr_pair', 'compressed_img_hdr_pair.img.gz'),
- ('compressed_img_hdr_pair.hdr.gz', 'compressed_img_hdr_pair.hdr.gz'),
- ('compressed_img_hdr_pair.img.gz', 'compressed_img_hdr_pair.img.gz'),
+
+ # Single files
+ ('file.nii', 'file', '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.hdr', 'file.hdr'),
+ ('file.img', 'file.img', 'file.img'),
+ ('file.img.gz', 'file', 'file.img.gz'),
+ ('file.img.gz', 'file.hdr.gz', 'file.hdr.gz'),
+ ('file.img.gz', 'file.img.gz', 'file.img.gz'),
+
+ # Multiple suffixes should be handled
+ ('file.blob.nii', 'file.blob', 'file.blob.nii'),
+ ('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.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.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
+ # 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'),
+ ('file.img.img', 'file.img.img', 'file.img.img'),
+ ('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'),
+
+ ('file.img.gz file.img', 'file.img', 'file.img'),
+ ('file.img.gz file.img', 'file.hdr', 'file.hdr'),
+ ('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.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.img.gz', 'file1.img.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.hdr', 'file2.hdr'),
+ ('file1.nii file2.img', 'file2.img', 'file2.img'),
+
+ ('file1.img file2.img', 'file1', 'file1.img'),
+ ('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.hdr', 'file2.hdr'),
+ ('file1.img file2.img', 'file2.img', 'file2.img'),
]
- for test in tests:
- prefix = op.join(testdir, 'nifti_formats', test[0])
- output = op.join(testdir, 'nifti_formats', test[1])
+ workdir = tempfile.mkdtemp()
- assert fslpath.addExt(prefix,
- allowedExts,
- mustExist=True,
- fileGroups=groups) == output
+ try:
+
+ for files_to_create, prefix, expected in tests:
+
+ files_to_create = files_to_create.split()
+ for f in files_to_create:
+ make_dummy_image_file(op.join(workdir, f))
+
+ print('files_to_create: ', files_to_create)
+ print('workdir: ', os.listdir(workdir))
+ print('prefix: ', prefix)
+ print('expected: ', expected)
+ result = fslpath.addExt(op.join(workdir, prefix),
+ allowedExts,
+ mustExist=True,
+ fileGroups=groups)
-def test_addExt_exists_shouldFail(testdir):
+ print('result: ', result)
+
+ assert result == op.join(workdir, expected)
+
+ cleardir(workdir)
+
+ finally:
+ shutil.rmtree(workdir)
+
+
+def test_addExt_otherFiles_mustExist_shouldPass():
+
+ workdir = tempfile.mkdtemp()
+
+
+ # (files_to_create, path, allowedExts, filegroups, expected)
+ tests = [
+
+ # allowedExts is None, fileGroups is None
+ ('file.a', 'file.a', '', [], 'file.a'),
+ ('file.a file.b', 'file.a', '', [], 'file.a'),
+ ('file.a file.b', 'file.b', '', [], 'file.b'),
+
+ # fileGroups is None
+ ('file.a', 'file', '.a', [], 'file.a'),
+ ('file.a', 'file.a', '.a', [], 'file.a'),
+
+
+ ('file.a file.b', 'file', '.a', [], 'file.a'),
+ ('file.a file.b', 'file.a', '.a', [], 'file.a'),
+ ('file.a file.b', 'file.b', '.a .b', [], 'file.b'),
+
+ ('file1.a file2.b', 'file1', '.a .b', [], 'file1.a'),
+ ('file1.a file2.b', 'file1.a', '.a .b', [], 'file1.a'),
+ ('file1.a file2.b', 'file2.b', '.a .b', [], 'file2.b'),
+ ('file1.a file2.b', 'file2.b', '.a .b', [], 'file2.b'),
+
+ ('file.a file.b', 'file', '.a .b', ['.a .b'], 'file.a'),
+ ('file.a file.b', 'file', '.a .b', ['.b .a'], 'file.b'),
+ ('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.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'),
+ ('file.a file.b file.c file.d', 'file.a', '.a .b', ['.a .b'], 'file.a'),
+ ('file.a file.b file.c file.d', 'file.b', '.a .b', ['.a .b'], 'file.b'),
+
+ ('file1.a file1.b file2.a file2.b', 'file1', '.a .b', ['.a .b'], 'file1.a'),
+ ('file1.a file1.b file2.a file2.b', 'file1.a', '.a .b', ['.a .b'], 'file1.a'),
+ ('file1.a file1.b file2.a file2.b', 'file1.b', '.a .b', ['.a .b'], 'file1.b'),
+ ('file1.a file1.b file2.a file2.b', 'file2', '.a .b', ['.a .b'], 'file2.a'),
+ ('file1.a file1.b file2.a file2.b', 'file2.a', '.a .b', ['.a .b'], 'file2.a'),
+ ('file1.a file1.b file2.a file2.b', 'file2.b', '.a .b', ['.a .b'], 'file2.b'),
+
+ ('file1.a file1.b file2.c file2.d', 'file1', '.a .b .c .d', ['.a .b', '.c .d'], 'file1.a'),
+ ('file1.a file1.b file2.c file2.d', 'file1.a', '.a .b .c .d', ['.a .b', '.c .d'], 'file1.a'),
+ ('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'),
+ ]
+
+ try:
+
+ for files_to_create, prefix, allowedExts, fileGroups, expected in tests:
+
+ 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
+
+ for f in files_to_create:
+ make_dummy_file(op.join(workdir, f))
+
+ print('files_to_create: ', files_to_create)
+ print('prefix: ', prefix)
+ print('allowedExts: ', allowedExts)
+ print('fileGroups: ', fileGroups)
+ print('workdir: ', os.listdir(workdir))
+ print('expected: ', expected)
+
+ result = fslpath.addExt(op.join(workdir, prefix),
+ allowedExts=allowedExts,
+ mustExist=True,
+ fileGroups=fileGroups)
+
+ print('result: ', result)
+
+ assert result == op.join(workdir, expected)
+
+ cleardir(workdir)
+
+ finally:
+ shutil.rmtree(workdir)
+
+
+def test_addExt_imageFiles_mustExist_shouldFail():
"""Tests the addExt function with inputs that should cause it to raise an
error.
"""
-
- groups = fslimage.FILE_GROUPS
+
+ fileGroups = fslimage.FILE_GROUPS
allowedExts = fslimage.ALLOWED_EXTENSIONS
- shouldFail = [
-
- # For tests of length 1, allowedExts/replacements are set from above
- #
- # For tests of length 2, replacements is set from above, allowedExts
- # is set from the tuple (unless False)
- #
- # For tests of length 3, replacements and allowedExts are set
- # from the tuple (unless False)
- ('compressed', []),
- ('compressed', ['.badsuf']),
-
- ('img_hdr_pair'),
- ('img_hdr_pair', []),
-
- ('ambiguous'),
- ('ambiguous', []),
- ('ambiguous', False, {'.hdr' : ['.img']}),
- ('ambiguous', [], {'.hdr' : ['.img']}),
- ('ambiguous', False, {'.hdr' : ['.img.gz']}),
- ('ambiguous', [], {'.hdr' : ['.img.gz']}),
- ('ambiguous', False, {'.hdr' : ['.img', '.img.gz', '.nii']}),
- ('ambiguous', [], {'.hdr' : ['.img', '.img.gz', '.nii']}),
+ # All of these should raise an error
+
+ # (files_to_create, path)
+ tests = [
+
+ # Invalid path
+ ('', 'file.img'),
+ ('file.hdr file.img', 'blob'),
+ ('file.hdr.gz file.img.gz', 'file.img'),
+ ('file.hdr file.img', 'file1'),
+ ('file.hdr file.img', 'file1.im'),
- ('badpath'),
- ('badpath.nii.gz'),
+ ('file.hdr file.img', 'filehdr'),
+ ('file.hdr file.img', 'fileimg'),
+ ('filehdr fileimg', 'file.hdr'),
+ ('filehdr fileimg', 'file.img'),
+ ('file.hdr fileimg', 'filehdr'),
+ ('file.hdr fileimg', 'file.img'),
+ ('filehdr file.img', 'fileimg'),
+ ('filehdr file.img', 'file.hdr'),
+
+ # Unsupported type/invalid path
+ ('file.blob', 'file'),
+ ('file.blob', 'file.img'),
+ ('file.blob', 'file.nii'),
+ ('file.blob', 'file.blob'),
+
+ # Ambiguous path
+ ('file.hdr file.img file.nii', 'file'),
+ ('file.hdr file.img file.hdr.gz file.img.gz', 'file'),
+
+ # Incomplete file pairs
+ ('file.hdr', 'file.img'),
+ ('file.img', 'file.hdr'),
+ ('file1.hdr file2.img', 'file1.img'),
+ ('file1.hdr file2.img', 'file2.hdr'),
+
+ # Stupid file names
+ ('file.img.nii.gz', 'file.img'),
+ ('file.img.nii', 'file.img'),
+ ('file.img.img', 'file.img'),
+ ('file.img.img.gz', 'file.img'),
]
- for test in shouldFail:
- prefix = op.join(testdir, 'nifti_formats', test[0])
- allowed = allowedExts
- group = groups
+ workdir = tempfile.mkdtemp()
- if len(test) >= 2:
- if not (test[1] == False):
- allowed = test[1]
+ try:
- if len(test) == 3:
- if not (test[2] == False):
- group = test[2]
+ for files_to_create, prefix in tests:
- with pytest.raises(fslpath.PathError):
+ cleardir(workdir)
+
+ files_to_create = files_to_create.split()
+ for f in files_to_create:
+ make_dummy_file(op.join(workdir, f))
+
+ print('files_to_create: ', files_to_create)
+ print('prefix: ', prefix)
+ print('workdir: ', os.listdir(workdir))
- fslpath.addExt(prefix,
- allowed,
- mustExist=True,
- fileGroups=group)
+ with pytest.raises(fslpath.PathError):
+
+ result = fslpath.addExt(op.join(workdir, prefix),
+ allowedExts=allowedExts,
+ mustExist=True,
+ fileGroups=fileGroups)
+
+ print('result: ', result)
+ finally:
+ shutil.rmtree(workdir)
+
+
+def test_addExt_otherFiles_mustExist_shouldFail():
-def test_addExt_noExist(testdir):
+ workdir = tempfile.mkdtemp()
- allowedExts = fslimage.ALLOWED_EXTENSIONS
+ # Invalid path
+ # Unsupported suffix
- # Prefix, output, defaultExt, allowedExts
+ # (files_to_create, path, allowedExts, fileGroups)
tests = [
- ('blah', 'blahblah', 'blah'),
- ('blah', 'blah.blah', '.blah'),
- ('blah', None, None),
- ('blah.nii', None, None, ['blah']),
- ('blah.nii', 'blah.nii', 'blah'),
- ('blah', 'blah.nii', '.nii'),
- ('blah', 'blah.nii', '.nii', []),
- ('blah.nii.gz', 'blah.nii.gz', 'blah'),
- ('blah', 'blah.nii', '.nii'),
- ('blah', 'blah.nii', '.nii', []),
+
+ # Invalid path
+ ('', 'file.a', '', []),
+ ('file.b', 'file.a', '.a', []),
+ ('file.b', 'file.a', '.a', []),
+
+ # No supported extensions/ambiguous
+ ('file.a', 'file', '', []),
+ ('file.a file.b', 'file', '', []),
+ ('file.a file.b', 'file', '.a .b', []),
+
+ # Weird group
+ ('file.a file.b', 'file', '.a .b', ['.a']),
+
+ # 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:
- for test in tests:
+ cleardir(workdir)
+
+ 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
+
+ for f in files_to_create:
+ make_dummy_file(op.join(workdir, f))
+
+ 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),
+ allowedExts=allowedExts,
+ mustExist=True,
+ fileGroups=fileGroups)
+
+ print('result: ', result)
+
+
+ finally:
+ shutil.rmtree(workdir)
+ pass
- prefix = test[0]
- output = test[1]
+
+def test_addExt_noExist():
+
+ allowedExts = fslimage.ALLOWED_EXTENSIONS
+
+ # When mustExist=False, the addExt
+ # function does not consult fileGroups.
+ # So we are not bothering with them
+ # here.
+
+ # Prefix, defaultExt, allowedExts, expected
+ tests = [
+
+ # If the prefix already has a supported extension,
+ # it should be returned unchanged.
+ ('file.img', None, allowedExts, 'file.img'),
+ ('file.hdr', None, allowedExts, 'file.hdr'),
+ ('file.nii', None, allowedExts, 'file.nii'),
+ ('file.nii.gz', None, allowedExts, 'file.nii.gz'),
+ ('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'),
+
- if len(test) >= 3: default = test[2]
- else: default = None
- if len(test) >= 4: allowed = test[3]
- else: allowed = allowedExts
+ # 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'),
+
+ # Unrecognised prefixes should be ignored
+ ('file.blob', 'img', allowedExts, 'file.blobimg'),
+ ('file.blob', '.img', allowedExts, 'file.blob.img'),
+ ('file.blob', 'img', None, 'file.blobimg'),
+ ('file.blob', '.img', None, 'file.blob.img'),
+ ]
+ for prefix, defaultExt, allowedExts, expected in tests:
+
assert fslpath.addExt(prefix,
- allowed,
- defaultExt=default,
- mustExist=False) == output
-
+ allowedExts,
+ defaultExt=defaultExt,
+ mustExist=False) == expected
def test_removeExt():
@@ -263,137 +623,339 @@ def test_splitExt():
assert fslpath.splitExt(filename, allowed) == (outbase, outext)
-def test_deepest():
+
+def test_getFileGroup_imageFiles_shouldPass():
- # path, suffixes, output
+ allowedExts = fslimage.ALLOWED_EXTENSIONS
+ groups = fslimage.FILE_GROUPS
+
+ # [(files_to_create, path, files_to_expect),
+ # ...
+ # ]
+ #
tests = [
+ ('file.hdr file.img', 'file', 'file.hdr file.img'),
+ ('file.hdr file.img', 'file.img', 'file.hdr file.img'),
+ ('file.hdr file.img', 'file.hdr', 'file.hdr file.img'),
+
+ ('file.hdr.gz file.img.gz', 'file', 'file.hdr.gz file.img.gz'),
+ ('file.hdr.gz file.img.gz', 'file.img.gz', 'file.hdr.gz file.img.gz'),
+ ('file.hdr.gz file.img.gz', 'file.hdr.gz', 'file.hdr.gz file.img.gz'),
+
+ ('file.hdr file.img file.hdr.gz file.img.gz', 'file.hdr', 'file.hdr file.img'),
+ ('file.hdr file.img file.hdr.gz file.img.gz', 'file.img', 'file.hdr file.img'),
+ ('file.hdr file.img file.hdr.gz file.img.gz', 'file.hdr.gz', 'file.hdr.gz file.img.gz'),
+ ('file.hdr file.img file.hdr.gz file.img.gz', 'file.hdr.gz', 'file.hdr.gz file.img.gz'),
+
+ ('file.hdr file.img file.nii', 'file.img', 'file.hdr file.img'),
+ ('file.hdr file.img file.nii', 'file.hdr', 'file.hdr file.img'),
+
+ ('file.hdr file.img file.blob', 'file', 'file.hdr file.img'),
+ ('file.hdr file.img file.blob', 'file.hdr', 'file.hdr file.img'),
+ ('file.hdr file.img file.blob', 'file.img', 'file.hdr file.img'),
+
+ ('file.nii', 'file', 'file.nii'),
+ ('file.nii', 'file.nii', 'file.nii'),
+
+ ('file.nii file.hdr file.img', 'file.nii', 'file.nii'),
+ ('file.nii file.blob', 'file', 'file.nii'),
+ ('file.nii file.blob', 'file.nii', 'file.nii'),
+
+ # The unambiguous arg defaults to
+ # False, so paths to incomplete
+ # file groups should still work.
+ ('file.hdr', 'file', 'file.hdr'),
+ ('file.hdr', 'file.hdr', 'file.hdr'),
+ ]
+
+ workdir = tempfile.mkdtemp()
+
+ try:
+
+ for files_to_create, path, files_to_expect in tests:
+
+ files_to_create = files_to_create.split()
+ files_to_expect = files_to_expect.split()
+
+ for fn in files_to_create:
+ with open(op.join(workdir, fn), 'wt') as f:
+ f.write('{}\n'.format(fn))
+
+ print()
+ print('files_to_create: ', files_to_create)
+ print('path: ', path)
+ print('files_to_expect: ', files_to_expect)
+
+ fullPaths = fslpath.getFileGroup(
+ op.join(workdir, path),
+ allowedExts=allowedExts,
+ fileGroups=groups,
+ fullPaths=True)
+ exts = fslpath.getFileGroup(
+ op.join(workdir, path),
+ allowedExts=allowedExts,
+ fileGroups=groups,
+ fullPaths=False)
+
+ assert sorted(fullPaths) == sorted([op.join(workdir, e) for e in files_to_expect])
+ assert sorted(exts) == sorted([fslpath.getExt(e, allowedExts) for e in files_to_expect])
+
+ cleardir(workdir)
+
+ finally:
+ shutil.rmtree(workdir)
+
+
+def test_getFileGroup_otherFiles_shouldPass():
+
+ # (files_to_create, allowedExts, fileGroups, path, files_to_expect)
+
+ tests = [
+ # allowedExts is None - incomplete paths are not allowed
+ ('file.a', '', '', 'file.a', 'file.a'),
+ ('file.a file.b', '', '', 'file.a', 'file.a'),
+ ('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'),
- ('/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'),
- ('/blah.feat/foo.ica/fum.gfeat/moo.ica', ['.ica'], '/blah.feat/foo.ica/fum.gfeat/moo.ica'),
- ('/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', ['.bob'], '/blah.feat/foo.ica/fum.gfeat/moo.bob'),
- ( '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'),
- ( 'blah.feat/foo.ica/fum.gfeat/moo.ica', ['.ica'], 'blah.feat/foo.ica/fum.gfeat/moo.ica'),
- ( '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),
- ('/', ['blah'], None),
- ('', ['blah'], None),
- ('///', ['blah'], None),
+ ('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'),
+
+ ('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'),
+
+ # allowedExts != None - incomplete paths
+ # allowed, but must be unambiguous
+ ('file.a', '.a', '', 'file', 'file.a'),
+ ('file.a', '.a', '', 'file.a', 'file.a'),
+ ('file.a file.b', '.a .b', '', 'file.a', 'file.a'),
+ ('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'),
+
+ ('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 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'),
+ ('file.a file.b file.c', '.a .b .c', ['.a .b .c'], 'file.b', 'file.a file.b file.c'),
+ ('file.a file.b file.c', '.a .b .c', ['.a .b .c'], 'file.c', 'file.a file.b file.c'),
+
+ ('file.a file.b file.c file.d', '.a .b .c .d', ['.a .b', '.c .d'], 'file.a', 'file.a file.b'),
+ ('file.a file.b file.c file.d', '.a .b .c .d', ['.a .b', '.c .d'], 'file.b', 'file.a file.b'),
+ ('file.a file.b file.c file.d', '.a .b .c .d', ['.a .b', '.c .d'], 'file.c', 'file.c file.d'),
+ ('file.a file.b file.c file.d', '.a .b .c .d', ['.a .b', '.c .d'], 'file.d', 'file.c file.d'),
+ ('file1.a file1.b file2.c file2.d', '.a .b .c .d', ['.a .b', '.c .d'], 'file1', 'file1.a file1.b'),
+ ('file1.a file1.b file2.c file2.d', '.a .b .c .d', ['.a .b', '.c .d'], 'file1.a', 'file1.a file1.b'),
+ ('file1.a file1.b file2.c file2.d', '.a .b .c .d', ['.a .b', '.c .d'], 'file1.b', 'file1.a file1.b'),
+ ('file1.a file1.b file2.c file2.d', '.a .b .c .d', ['.a .b', '.c .d'], 'file2', 'file2.c file2.d'),
+ ('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
+ ('file.a', '.a .b', ['.a .b'], 'file', 'file.a'),
+ ('file.a', '.a .b', ['.a .b'], 'file.a', 'file.a'),
]
- for path, suffixes, output in tests:
- assert fslpath.deepest(path, suffixes) == output
+ workdir = tempfile.mkdtemp()
-def test_shallowest():
- # path, suffixes, output
+ try:
+ for files_to_create, allowedExts, fileGroups, path, files_to_expect in tests:
+
+ files_to_create = files_to_create.split()
+ allowedExts = allowedExts.split()
+ fileGroups = [g.split() for g in fileGroups]
+ files_to_expect = files_to_expect.split()
+
+ if len(allowedExts) == 0: allowedExts = None
+ if len(fileGroups) == 0: fileGroups = None
+
+ for fn in files_to_create:
+ with open(op.join(workdir, fn), 'wt') as f:
+ f.write('{}\n'.format(fn))
+
+ print()
+ print('files_to_create: ', files_to_create)
+ print('path: ', path)
+ print('allowedExts: ', allowedExts)
+ print('fileGroups: ', fileGroups)
+ print('files_to_expect: ', files_to_expect)
+
+ fullPaths = fslpath.getFileGroup(
+ op.join(workdir, path),
+ allowedExts=allowedExts,
+ fileGroups=fileGroups,
+ fullPaths=True)
+ exts = fslpath.getFileGroup(
+ op.join(workdir, path),
+ allowedExts=allowedExts,
+ fileGroups=fileGroups,
+ fullPaths=False)
+
+ assert sorted(fullPaths) == sorted([op.join(workdir, e) for e in files_to_expect])
+ assert sorted(exts) == sorted([fslpath.getExt(e, allowedExts) for e in files_to_expect])
+
+ cleardir(workdir)
+
+ finally:
+ shutil.rmtree(workdir)
+
+
+def test_getFileGroup_shouldFail():
+
+ # All of these tests should raise an error
+
+ allowedExts = ' '.join(fslimage.ALLOWED_EXTENSIONS)
+ fileGroups = [' '.join(g) for g in fslimage.FILE_GROUPS]
+
+ # (files_to_create, path, allowedExts, fileGroups[, unambiguous])
tests = [
+
+ # Unsupported extension
+ ('file.a', 'file.a', '.b', []),
- ('/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'),
- ('/blah.feat/foo.ica/fum.gfeat/moo.ica', ['.ica'], '/blah.feat/foo.ica'),
- ('/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', ['.bob'], '/blah.feat/foo.ica/fum.gfeat/moo.bob'),
- ( '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'),
- ( 'blah.feat/foo.ica/fum.gfeat/moo.ica', ['.ica'], 'blah.feat/foo.ica'),
- ( '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'),
- (' blah.feat/foo.ica/fum.gfeat/moo.bob', ['.ica', '.bob'], 'blah.feat/foo.ica'),
+ # Incomplete path, and allowedExts is None
+ ('file.a', 'file', '', []),
- ('/', [], None),
- ('', [], None),
- ('///', [], None),
- ('/', ['blah'], None),
- ('', ['blah'], None),
- ('///', ['blah'], None),
+ # 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']),
+
+ # Incomplete group, when unambiguous is set to True
+ ('file.a', 'file', '.a .b', ['.a .b'], True),
+ ('file.a', 'file.a', '.a .b', ['.a .b'], True),
+
+ ('file.hdr', 'file', allowedExts, fileGroups, True),
+ ('file.hdr', 'file.hdr', allowedExts, fileGroups, True),
+ ('file.img', 'file', allowedExts, fileGroups, True),
+ ('file.img', 'file.img', allowedExts, fileGroups, True),
]
- for path, suffixes, output in tests:
- assert fslpath.shallowest(path, suffixes) == output
+ workdir = tempfile.mkdtemp()
+
+ try:
+ for test in tests:
+
+ files_to_create = test[0]
+ path = test[1]
+ allowedExts = test[2]
+ fileGroups = test[3]
+
+ if len(test) > 4: unambiguous = test[4]
+ else: unambiguous = False
+ files_to_create = files_to_create.split()
+ allowedExts = allowedExts.split()
+ fileGroups = [g.split() for g in fileGroups]
-def test_removeDuplicates_shouldPass():
+ if len(allowedExts) == 0: allowedExts = None
+ if len(fileGroups) == 0: fileGroups = None
+
+ for fn in files_to_create:
+ with open(op.join(workdir, fn), 'wt') as f:
+ f.write('{}\n'.format(fn))
+
+ print()
+ print('files_to_create: ', files_to_create)
+ print('path: ', path)
+ print('allowedExts: ', allowedExts)
+ print('fileGroups: ', fileGroups)
+
+ with pytest.raises(fslpath.PathError):
+ fullPaths = fslpath.getFileGroup(
+ op.join(workdir, path),
+ allowedExts=allowedExts,
+ fileGroups=fileGroups,
+ fullPaths=True,
+ unambiguous=unambiguous)
+
+ print('fullPaths: ', fullPaths)
+
+ with pytest.raises(fslpath.PathError):
+ exts = fslpath.getFileGroup(
+ op.join(workdir, path),
+ allowedExts=allowedExts,
+ fileGroups=fileGroups,
+ fullPaths=False,
+ unambiguous=unambiguous)
+
+ print('exts: ', exts)
+
+ cleardir(workdir)
+
+ finally:
+ shutil.rmtree(workdir)
+
+
+
+def test_removeDuplicates_imageFiles_shouldPass():
allowedExts = fslimage.ALLOWED_EXTENSIONS
groups = fslimage.FILE_GROUPS
# [(files_to_create,
- # [([paths], [expected]),
+ # [(paths, expected),
# ...
# ]),
# ...
# ]
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.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.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.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.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.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'),
]),
- (['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.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'),
])
]
@@ -401,17 +963,23 @@ def test_removeDuplicates_shouldPass():
try:
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))
for paths, expected in tests:
+
+ 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)
@@ -419,96 +987,139 @@ def test_removeDuplicates_shouldPass():
assert result == [op.join(workdir, e) for e in expected]
- for f in files_to_create:
- os.remove(op.join(workdir, f))
+ 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'),
-def test_removeDuplicates_shouldFail():
- pass
+ # 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', '.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'),
+ ('file.a file.b', 'file file', '.a .b', ['.a .b'], 'file.a'),
+ ('file.a file.b', 'file file.a file.b', '.a .b', ['.a .b'], 'file.a'),
+
+ ('file1.a file1.b file2.a file2.b', 'file1 file1.a file2 file2.a', '.a .b', ['.a .b'], 'file1.a file2.a'),
+ ('file1.a file1.b file2.a file2.b', 'file1 file2', '.a .b', ['.a .b'], 'file1.a file2.a'),
+ ('file1.a file1.b file2.a file2.b', 'file1 file1.a file2', '.a .b', ['.a .b'], 'file1.a file2.a'),
+ ]
-def test_getFileGroup():
- allowedExts = fslimage.ALLOWED_EXTENSIONS
- groups = fslimage.FILE_GROUPS
+ workdir = tempfile.mkdtemp()
- # (files_to_create,
- # [(path, expected),
- # ...
- # ]
- # )
- #
- # expected == 'all' is equivalent to expected == files_to_create
- allTests = [
- (['file.hdr', 'file.img'], [
- ('file', 'all'),
- ('file.hdr', 'all'),
- ('file.img', 'all')]),
-
- (['file.hdr.gz', 'file.img.gz'], [
- ('file', 'all'),
- ('file.hdr.gz', 'all'),
- ('file.img.gz', 'all')]),
-
- (['file.hdr', 'file.img', 'file.nii'], [
- ('file.hdr', ['file.hdr', 'file.img']),
- ('file.img', ['file.hdr', 'file.img'])]),
-
- (['file.hdr', 'file.img', 'file.blob'], [
- ('file.hdr', ['file.hdr', 'file.img']),
- ('file.img', ['file.hdr', 'file.img'])]),
+ try:
+ for files_to_create, paths, allowedExts, fileGroups, expected in tests:
- (['file.hdr'], [
- ('file', ['file']),
- ('file.hdr', ['file.hdr']),
- ('file.img', ['file.img'])]),
+ files_to_create = files_to_create.split()
+ paths = paths.split()
+ allowedExts = allowedExts.split()
+ fileGroups = [g.split() for g in fileGroups]
+ expected = expected.split()
- (['file.img'], [
- ('file', ['file']),
- ('file.hdr', ['file.hdr']),
- ('file.img', ['file.img'])]),
- ]
+ if len(allowedExts) == 0: allowedExts = None
+ if len(fileGroups) == 0: fileGroups = None
- workdir = tempfile.mkdtemp()
+ for f in files_to_create:
+ make_dummy_file(op.join(workdir, f))
- try:
+ print('files_to_create: {}'.format(files_to_create))
+ print('paths: {}'.format(paths))
+ print('allowedExts: {}'.format(allowedExts))
+ 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)
- for files_to_create, tests in allTests:
+ print('result: {}'.format(result))
- for fn in files_to_create:
- with open(op.join(workdir, fn), 'wt') as f:
- f.write('{}\n'.format(fn))
+ assert result == [op.join(workdir, e) for e in expected]
- for path, expected in tests:
- if expected == 'all':
- expected = list(files_to_create)
+ cleardir(workdir)
- print()
- print('files_to_create: ', files_to_create)
- print('path: ', path)
- print('expected: ', expected)
+ finally:
+ shutil.rmtree(workdir)
- fullPaths = fslpath.getFileGroup(
- op.join(workdir, path),
- allowedExts=allowedExts,
- fileGroups=groups,
- fullPaths=True)
- exts = fslpath.getFileGroup(
- op.join(workdir, path),
- allowedExts=allowedExts,
- fileGroups=groups,
- fullPaths=False)
- assert sorted(fullPaths) == sorted([op.join(workdir, e) for e in expected])
- assert sorted(exts) == sorted([fslpath.getExt(e, allowedExts) for e in expected])
+def test_removeDuplicates_shouldFail():
- for f in files_to_create:
- try: os.remove(op.join(workdir, f))
- except: pass
+ # (files_to_create, paths, allowedExts, fileGroups)
+ tests = [
+ # Invalid path(s)
+ ('', 'file.a', '', []),
+ ('file.a', 'file.b', '', []),
+ ('file.a', 'file.b file.c', '', []),
+ ('file.a', 'file', '', []),
+ ('file.a', 'file.b', '.a .b', ['.a .b']),
+
+ # Unsupported extension
+ ('file.a', 'file.a', '.b', []),
+
+ # Ambiguous
+ ('file.a file.b', 'file', '.a .b', []),
+ ('file.a file.b file.c', 'file file.c', '.a .b .c', ['.a .b']),
+ ]
+
+ workdir = tempfile.mkdtemp()
+
+ try:
+ for files_to_create, path, allowedExts, fileGroups in tests:
+
+ cleardir(workdir)
+
+ 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
+
+ for fn in files_to_create:
+ with open(op.join(workdir, fn), 'wt') as f:
+ f.write('{}\n'.format(fn))
+
+ print()
+ print('files_to_create: ', files_to_create)
+ print('path: ', path)
+ print('allowedExts: ', allowedExts)
+ print('fileGroups: ', fileGroups)
+
+ with pytest.raises(fslpath.PathError):
+ result = fslpath.removeDuplicates(path,
+ allowedExts=allowedExts,
+ fileGroups=fileGroups)
+ print('result: ', result)
+
finally:
shutil.rmtree(workdir)
--
GitLab