From ce2d5b521327002af629bbd1c0b002a50bcc4a90 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Mon, 14 Nov 2016 18:27:23 +0000
Subject: [PATCH] fsl.utils.path test suite updated.
---
tests/test_fsl_utils_path.py | 365 +++++++++++++++++++++++++++++++++--
1 file changed, 344 insertions(+), 21 deletions(-)
diff --git a/tests/test_fsl_utils_path.py b/tests/test_fsl_utils_path.py
index 25f945620..e733fd8fb 100644
--- a/tests/test_fsl_utils_path.py
+++ b/tests/test_fsl_utils_path.py
@@ -5,7 +5,12 @@
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
+from __future__ import print_function
+
+import os
import os.path as op
+import shutil
+import tempfile
import pytest
@@ -18,7 +23,7 @@ def test_addExt_exists_shouldPass(testdir):
are valid.
"""
- replacements = fslimage.REPLACEMENTS
+ groups = fslimage.FILE_GROUPS
allowedExts = fslimage.ALLOWED_EXTENSIONS
tests = [
@@ -41,7 +46,7 @@ def test_addExt_exists_shouldPass(testdir):
assert fslpath.addExt(prefix,
allowedExts,
mustExist=True,
- replace=replacements) == output
+ fileGroups=groups) == output
def test_addExt_exists_shouldFail(testdir):
@@ -49,8 +54,8 @@ def test_addExt_exists_shouldFail(testdir):
error.
"""
- replacements = fslimage.REPLACEMENTS
- allowedExts = fslimage.ALLOWED_EXTENSIONS
+ groups = fslimage.FILE_GROUPS
+ allowedExts = fslimage.ALLOWED_EXTENSIONS
shouldFail = [
@@ -83,7 +88,7 @@ def test_addExt_exists_shouldFail(testdir):
for test in shouldFail:
prefix = op.join(testdir, 'nifti_formats', test[0])
allowed = allowedExts
- replace = replacements
+ group = groups
if len(test) >= 2:
if not (test[1] == False):
@@ -91,14 +96,14 @@ def test_addExt_exists_shouldFail(testdir):
if len(test) == 3:
if not (test[2] == False):
- replace = test[2]
+ group = test[2]
with pytest.raises(fslpath.PathError):
fslpath.addExt(prefix,
allowed,
mustExist=True,
- replace=replace)
+ fileGroups=group)
def test_addExt_noExist(testdir):
@@ -136,7 +141,7 @@ def test_addExt_noExist(testdir):
-def test_removeExt(testdir):
+def test_removeExt():
allowedExts = fslimage.ALLOWED_EXTENSIONS
@@ -170,13 +175,13 @@ def test_removeExt(testdir):
assert fslpath.removeExt(path, allowed) == output
-def test_getExt(testdir):
+def test_getExt():
allowedExts = fslimage.ALLOWED_EXTENSIONS
# len(test) == 2 -> allowedExts set from above
# Otherwise, allowedExts set from test tuple
- shouldPass = [
+ tests = [
('blah.blah', '.blah', None),
('blah.blah', '.blah', ['.blah']),
('blah.blah', 'blah', ['blah']),
@@ -189,36 +194,74 @@ def test_getExt(testdir):
('blah.hdr', '.hdr'),
('blah.img', '.img'),
('blah.img.gz', '.img.gz'),
- ]
- shouldRaise = [
('blah', ''),
('blah.blah', ''),
('blah.blah', '', ['bla']),
('blah.nii.gz', '', ['.nii']),
]
- for test in shouldPass:
+ for test in tests:
filename = test[0]
output = test[1]
if len(test) == 2: allowed = allowedExts
else: allowed = test[2]
- print filename, '==', output
+ print(filename, '==', output)
assert fslpath.getExt(filename, allowed) == output
+
+def test_splitExt():
+
+ allowedExts = fslimage.ALLOWED_EXTENSIONS
- for test in shouldRaise:
- filename = test[0]
- output = test[1]
+ # len(test) == 2 -> allowedExts set from above
+ # Otherwise, allowedExts set from test tuple
+ tests = [
+ ('blah', ('blah', '')),
+ ('blah.blah', ('blah.blah', '')),
+ ('blah.blah', ('blah', '.blah'), ['.blah']),
+ ('blah.blah', ('blah.', 'blah'), ['blah']),
+ ('blah.nii', ('blah', '.nii')),
+ ('blah.nii.gz', ('blah', '.nii.gz')),
+ ('blah.img', ('blah', '.img')),
+ ('blah.hdr', ('blah', '.hdr')),
+ ('blah.img.gz', ('blah', '.img.gz')),
+ ('blah.nii.gz', ('blah.nii.gz', ''), []),
+ ('blah.nii.gz', ('blah.nii', '.gz'), ['.gz']),
+ ('blah.nii.gz', ('blah.nii.gz', ''), ['.nii']),
+ ('blah.nii.gz', ('blah', '.nii.gz'), ['.nii.gz']),
+ ('blah.nii.gz', ('blah.', 'nii.gz'), ['nii.gz']),
+ ('blah.blah', ('blah', '.blah'), None),
+ ('blah.blah', ('blah', '.blah'), ['.blah']),
+ ('blah.blah', ('blah.', 'blah'), ['blah']),
+ ('blah', ('blah', ''), None),
+ ('blah.nii', ('blah', '.nii'), None),
+ ('blah.nii.gz', ('blah.nii', '.gz'), None),
+
+ ('blah.nii', ('blah', '.nii')),
+ ('blah.nii.gz', ('blah', '.nii.gz')),
+ ('blah.hdr', ('blah', '.hdr')),
+ ('blah.img', ('blah', '.img')),
+ ('blah.img.gz', ('blah', '.img.gz')),
+
+ ('blah', ('blah', '')),
+ ('blah.blah', ('blah.blah', '')),
+ ('blah.blah', ('blah.blah', ''), ['bla']),
+ ('blah.nii.gz', ('blah.nii.gz', ''), ['.nii']),
+ ]
+
+ for test in tests:
+ filename = test[0]
+ outbase, outext = test[1]
if len(test) == 2: allowed = allowedExts
else: allowed = test[2]
-
- with pytest.raises(fslpath.PathError):
- fslpath.getExt(filename, allowed)
+ print(filename, '==', (outbase, outext))
+ assert fslpath.splitExt(filename, allowed) == (outbase, outext)
+
def test_deepest():
@@ -281,4 +324,284 @@ def test_shallowest():
]
for path, suffixes, output in tests:
- assert fslpath.shallowest(path, suffixes) == output
+ assert fslpath.shallowest(path, suffixes) == output
+
+
+def test_getFileGroup():
+
+ allowedExts = fslimage.ALLOWED_EXTENSIONS
+ groups = fslimage.FILE_GROUPS
+
+ # (files_to_create,
+ # [(path, expected),
+ # ...
+ # ]
+ # )
+ #
+ # expected == 'all' is equivalent to expected == files_to_create
+ allTests = [
+ (['file.hdr', 'file.img'], [
+ ('file.hdr', 'all'),
+ ('file.img', 'all')]),
+
+ (['file.hdr.gz', 'file.img.gz'], [
+ ('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'])]),
+
+
+ (['file.hdr'], [
+ ('file.hdr', ['file.hdr']),
+ ('file.img', ['file.img'])]),
+
+ (['file.img'], [
+ ('file.hdr', ['file.hdr']),
+ ('file.img', ['file.img'])]),
+ ]
+
+ workdir = tempfile.mkdtemp()
+
+ try:
+
+ for files_to_create, tests in allTests:
+
+ for fn in files_to_create:
+ with open(op.join(workdir, fn), 'wt') as f:
+ f.write('{}\n'.format(fn))
+
+ for path, expected in tests:
+ if expected == 'all':
+ expected = list(files_to_create)
+
+
+ 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])
+
+ for f in files_to_create:
+ try: os.remove(op.join(workdir, f))
+ except: pass
+
+ finally:
+ shutil.rmtree(workdir)
+
+
+def test_imcp_shouldPass(move=False):
+
+ allowedExts = fslimage.ALLOWED_EXTENSIONS
+ groups = fslimage.FILE_GROUPS
+ #
+ # (files_to_create,
+ # [( imcp_src, imcp_dest, files_which_should_exist),
+ # ( imcp_src, imcp_dest, [files_which_should_exist]),
+ # ([imcp_srcs], imcp_dest, files_which_should_exist),
+ # ([imcp_srcs], imcp_dest, [files_which_should_exist]),
+ # ...
+ # ]
+ # )
+ #
+ # if icmp_dest == '', it means to copy to the directory
+ # files_which_should_exist == 'all' is equivalent to files_which_should_exist == files_to_create
+ shouldPass = [
+ (['file.hdr', 'file.img'], [
+ ('file', 'file', 'all'),
+ ('file', 'file.img', 'all'),
+ ('file', 'file.hdr', 'all'),
+ ('file', '', 'all'),
+ ('file.img', 'file', 'all'),
+ ('file.img', 'file.img', 'all'),
+ ('file.img', 'file.hdr', 'all'),
+ ('file.img', '', 'all'),
+ ('file.hdr', 'file', 'all'),
+ ('file.hdr', 'file.img', 'all'),
+ ('file.hdr', 'file.hdr', 'all'),
+ ('file.hdr', '', 'all'),
+ ]),
+
+ (['file.hdr', 'file.img', 'file.blob'], [
+ ('file', 'file', ['file.hdr', 'file.img']),
+ ('file', 'file.img', ['file.hdr', 'file.img']),
+ ('file', 'file.hdr', ['file.hdr', 'file.img']),
+ ('file', '', ['file.hdr', 'file.img']),
+ ('file.img', 'file', ['file.hdr', 'file.img']),
+ ('file.img', 'file.img', ['file.hdr', 'file.img']),
+ ('file.img', 'file.hdr', ['file.hdr', 'file.img']),
+ ('file.img', '', ['file.hdr', 'file.img']),
+ ('file.hdr', 'file', ['file.hdr', 'file.img']),
+ ('file.hdr', 'file.img', ['file.hdr', 'file.img']),
+ ('file.hdr', 'file.hdr', ['file.hdr', 'file.img']),
+ ('file.hdr', '', ['file.hdr', 'file.img']),
+ ]),
+
+
+ (['file.hdr', 'file.img', 'file.nii'], [
+ ('file.img', 'file', ['file.hdr', 'file.img']),
+ ('file.img', 'file.img', ['file.hdr', 'file.img']),
+ ('file.img', 'file.hdr', ['file.hdr', 'file.img']),
+ ('file.img', '', ['file.hdr', 'file.img']),
+ ('file.hdr', 'file', ['file.hdr', 'file.img']),
+ ('file.hdr', 'file.img', ['file.hdr', 'file.img']),
+ ('file.hdr', 'file.hdr', ['file.hdr', 'file.img']),
+ ('file.hdr', '', ['file.hdr', 'file.img']),
+ ('file.nii', 'file', 'file.nii'),
+ ('file.nii', 'file.nii', 'file.nii'),
+ ('file.nii', '', 'file.nii'),
+ ]),
+
+
+ (['file.nii'], [
+ ('file', 'file', 'all'),
+ ('file', 'file.nii', 'all'),
+ ('file', '', 'all'),
+ ('file.nii', 'file', 'all'),
+ ('file.nii', 'file.nii', 'all'),
+ ('file.nii', '', 'all'),
+ ]),
+
+ (['file.nii.gz'], [
+ ('file', 'file', 'all'),
+ ('file', 'file.nii.gz', 'all'),
+ ('file', '', 'all'),
+ ('file.nii.gz', 'file', 'all'),
+ ('file.nii.gz', 'file.nii.gz', 'all'),
+ ('file.nii.gz', '', 'all'),
+ ]),
+
+
+ (['file.nii', 'file.blob'], [
+ ('file', 'file', 'file.nii'),
+ ('file', 'file.nii', 'file.nii'),
+ ('file', '', 'file.nii'),
+ ('file.nii', 'file', 'file.nii'),
+ ('file.nii', 'file.nii', 'file.nii'),
+ ('file.nii', '', 'file.nii'),
+ ]),
+
+
+ (['file.nii', 'file.nii.gz'], [
+ ('file.nii', 'file', '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.nii.gz', '', 'file.nii.gz'),
+ ]),
+
+ (['file.hdr', 'file.img', 'file.nii', 'file.nii.gz'], [
+ (['file.img', 'file.nii', 'file.nii.gz'], '', 'all'),
+ ('file.img', '', ['file.hdr', 'file.img']),
+ (['file.hdr', 'file.img'], '', ['file.hdr', 'file.img']),
+
+ ('file.nii', '', 'file.nii'),
+ (['file.nii', 'file.nii.gz'], '', ['file.nii', 'file.nii.gz']),
+ ]),
+
+
+ (['001.hdr', '001.img', '002.hdr', '002.img', '003.hdr', '003.img'], [
+
+ (['001', '002', '003'], '', 'all'),
+ (['001.img', '002.img', '003.img'], '', 'all'),
+ (['001.hdr', '002.hdr', '003.hdr'], '', 'all'),
+
+ (['001.img', '002', '003'], '', 'all'),
+ (['001.hdr', '002', '003'], '', 'all'),
+
+ (['001.img', '002.hdr', '003.img'], '', 'all'),
+ (['001.hdr', '002.img', '003.hdr'], '', 'all'),
+
+ (['001', '003'], '', ['001.hdr', '001.img', '003.hdr', '003.img']),
+ (['001.img', '003.img'], '', ['001.hdr', '001.img', '003.hdr', '003.img']),
+ (['001.hdr', '003.hdr'], '', ['001.hdr', '001.img', '003.hdr', '003.img']),
+
+ (['001.img', '003'], '', ['001.hdr', '001.img', '003.hdr', '003.img']),
+ (['001.hdr', '003'], '', ['001.hdr', '001.img', '003.hdr', '003.img']),
+
+ (['001.img', '003.img'], '', ['001.hdr', '001.img', '003.hdr', '003.img']),
+ (['001.hdr', '003.hdr'], '', ['001.hdr', '001.img', '003.hdr', '003.img']),
+
+ (['001.img', '001.hdr', '002.img', '002.hdr', '003.img', '003.hdr'], '', 'all'),
+ ]),
+ ]
+
+
+ indir = tempfile.mkdtemp()
+ outdir = tempfile.mkdtemp()
+
+ try:
+
+ for files_to_create, tests in shouldPass:
+
+ if not isinstance(files_to_create, list):
+ files_to_create = [files_to_create]
+
+ for imcp_src, imcp_dest, should_exist in tests:
+
+ if not isinstance(imcp_src, list): imcp_src = [imcp_src]
+ if should_exist == 'all': should_exist = list(files_to_create)
+ elif not isinstance(should_exist, list): should_exist = [should_exist]
+
+ imcp_dest = op.join(outdir, imcp_dest)
+
+ # Each input file contains
+ # its name in plain text,
+ # so we can verify that the
+ # files were correctly copied
+ for fn in files_to_create:
+ with open(op.join(indir, fn), 'wt') as f:
+ f.write('{}\n'.format(fn))
+
+ for src in imcp_src:
+
+ src = op.join(indir, src)
+
+ if move: fslpath.immv(src, imcp_dest, allowedExts=allowedExts, fileGroups=groups)
+ else: fslpath.imcp(src, imcp_dest, allowedExts=allowedExts, fileGroups=groups)
+
+ copied = os.listdir(outdir)
+ copied = [f for f in copied if op.isfile(op.join(outdir, f))]
+
+ assert sorted(copied) == sorted(should_exist)
+
+ # check file contents
+ for fn in should_exist:
+ with open(op.join(outdir, fn), 'rt') as f:
+ assert f.read() == '{}\n'.format(fn)
+
+ # If move, check that
+ # input files are gone
+ if move:
+ for f in should_exist:
+ assert not op.exists(op.join(indir, f))
+
+ for f in files_to_create:
+ try: os.remove(op.join(indir, f))
+ except: pass
+
+ for f in should_exist:
+ os.remove(op.join(outdir, f))
+
+
+ finally:
+ shutil.rmtree(indir)
+ shutil.rmtree(outdir)
+
+
+def test_immv_shouldPass():
+ test_imcp_shouldPass(move=True)
--
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