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Commit ce2d5b52 authored by Paul McCarthy's avatar Paul McCarthy
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fsl.utils.path test suite updated.

parent 5d644d61
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tests/test_fsl_utils_path.py
View file @ ce2d5b52
......@@ -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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