diff --git a/tests/test_fsl_utils_path.py b/tests/test_fsl_utils_path.py
index 29ed7e3704fb97b50fc1de64a31e8f2243de2c63..d577739df5d44218190bae9788a5019600e330e3 100644
--- a/tests/test_fsl_utils_path.py
+++ b/tests/test_fsl_utils_path.py
@@ -629,7 +629,7 @@ def test_getFileGroup_imageFiles_shouldPass():
allowedExts = fslimage.ALLOWED_EXTENSIONS
groups = fslimage.FILE_GROUPS
- # [(files_to_create, path, files_to_expect),
+ # [(files_to_create, path, files_to_expect [, unambiguous]),
# ...
# ]
#
@@ -666,13 +666,30 @@ def test_getFileGroup_imageFiles_shouldPass():
# file groups should still work.
('file.hdr', 'file', 'file.hdr'),
('file.hdr', 'file.hdr', 'file.hdr'),
+
+ # Unambigiuous paths, when
+ # unambiguous = True,
+ # should be ok.
+ ('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:
- for files_to_create, path, files_to_expect in tests:
+ for test in tests:
+
+ files_to_create = test[0]
+ path = test[1]
+ files_to_expect = test[2]
+
+ if len(test) == 4: unambiguous = test[3]
+ else: unambiguous = False
files_to_create = files_to_create.split()
files_to_expect = files_to_expect.split()
@@ -690,12 +707,14 @@ def test_getFileGroup_imageFiles_shouldPass():
op.join(workdir, path),
allowedExts=allowedExts,
fileGroups=groups,
- fullPaths=True)
+ fullPaths=True,
+ unambiguous=unambiguous)
exts = fslpath.getFileGroup(
op.join(workdir, path),
allowedExts=allowedExts,
fileGroups=groups,
- fullPaths=False)
+ fullPaths=False,
+ unambiguous=unambiguous)
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])
@@ -708,7 +727,7 @@ def test_getFileGroup_imageFiles_shouldPass():
def test_getFileGroup_otherFiles_shouldPass():
- # (files_to_create, allowedExts, fileGroups, path, files_to_expect)
+ # (files_to_create, allowedExts, fileGroups, path, files_to_expect [, unambiguous])
tests = [
# allowedExts is None - incomplete paths are not allowed
@@ -758,16 +777,34 @@ 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
+ # 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
+ # 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),
+ ('file.a file.b file.c', '.a .b .c', ['.a .b'], 'file.c', 'file.c', True),
]
workdir = tempfile.mkdtemp()
try:
- for files_to_create, allowedExts, fileGroups, path, files_to_expect in tests:
+ for test in tests:
+
+ files_to_create = test[0]
+ allowedExts = test[1]
+ fileGroups = test[2]
+ path = test[3]
+ files_to_expect = test[4]
+
+ if len(test) == 6: unambiguous = test[5]
+ else: unambiguous = False
+
files_to_create = files_to_create.split()
allowedExts = allowedExts.split()
@@ -792,12 +829,14 @@ def test_getFileGroup_otherFiles_shouldPass():
op.join(workdir, path),
allowedExts=allowedExts,
fileGroups=fileGroups,
- fullPaths=True)
+ fullPaths=True,
+ unambiguous=unambiguous)
exts = fslpath.getFileGroup(
op.join(workdir, path),
allowedExts=allowedExts,
fileGroups=fileGroups,
- fullPaths=False)
+ fullPaths=False,
+ unambiguous=unambiguous)
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])
@@ -837,7 +876,10 @@ def test_getFileGroup_shouldFail():
('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),
+ ('file.img', 'file.img', allowedExts, fileGroups, True),
+
+ # 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()
diff --git a/tests/test_immv_imcp.py b/tests/test_immv_imcp.py
index eb01fa7596de1bd052cd8f30171f034183c55d45..73e6fb29fef2e76d1d085dfe8097d1ea7ff64d92 100644
--- a/tests/test_immv_imcp.py
+++ b/tests/test_immv_imcp.py
@@ -5,14 +5,19 @@
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
-import os
-import os.path as op
-import shutil
-import tempfile
+from __future__ import print_function
+
+import os
+import os.path as op
+import shutil
+import subprocess as sp
+import tempfile
import numpy as np
import nibabel as nib
+import pytest
+
import fsl.utils.path as fslpath
import fsl.utils.imcp as imcp
import fsl.scripts.imcp as imcp_script
@@ -23,11 +28,22 @@ import fsl.data.image as fslimage
def createImageFile(filename):
data = np.random.random((10, 10, 10))
- img = nib.Nifti1Image(data, np.eye(4))
- nib.save(img, filename)
+ # Image file
+ try:
+ img = nib.Nifti1Image(data, np.eye(4))
+
+ nib.save(img, filename)
+
+ return hash(data.tobytes())
- return hash(data.tobytes())
+ # Non-image file
+ except:
+ contents = '{}\n'.format(op.basename(filename))
+ with open(filename, 'wt') as f:
+ f.write(contents)
+
+ return hash(contents)
def checkImageFile(filename, datahash):
@@ -42,19 +58,35 @@ def checkFilesToExpect(files, outdir, outputType, datahashes):
'NIFTI' : ['.nii'],
'NIFTI_PAIR' : ['.hdr', '.img'],
'NIFTI_GZ' : ['.nii.gz'],
- }.get(outputType, ['.nii.gz'])
-
+ '' : ['.nii.gz'],
+ }.get(outputType, None)
allFiles = []
- for f, h in zip(files.split(), datahashes):
+ if isinstance(files, str):
+ files = files.split()
+
+ for f in files:
+
+ f, fe = fslimage.splitExt(f)
+ fexts = exts
- for e in exts:
+ if fexts is None:
+ fexts = {
+ '.img' : ['.hdr', '.img'],
+ '.hdr' : ['.hdr', '.img'],
+ '.nii' : ['.nii'],
+ '.nii.gz' : ['.nii.gz']
+ }.get(fe, [])
+
+ for e in fexts:
expected = op.join(outdir, f + e)
allFiles.append(expected)
+ print(' ', expected)
+
assert op.exists(expected)
allThatExist = os.listdir(outdir)
@@ -62,19 +94,37 @@ def checkFilesToExpect(files, outdir, outputType, datahashes):
assert len(allThatExist) == len(allFiles)
- for f, h in zip(files.split(), datahashes):
+ for i, f in enumerate(files):
f = fslimage.addExt(op.join(outdir, f), mustExist=True)
+ if isinstance(datahashes, list):
+ if len(datahashes) > len(files):
+ diff = len(datahashes) - len(files)
+ h = datahashes[i + diff]
+
+ else:
+ h = datahashes[i]
+ else:
+ h = datahashes[op.basename(f)]
+
checkImageFile(f, h)
+def cleardir(dir):
+
+ for f in os.listdir(dir):
+ f = op.join(dir, f)
+ if op.isfile(f): os.remove(f)
+ elif op.isdir(f): shutil.rmtree(f)
+
def test_imcp_script_shouldPass(move=False):
# The imcp/immv scripts should honour the
# FSLOUTPUTTYPE env var. If it is unset
- # or invalid), they should produce .nii.gz
- outputTypes = ['NIFTI', 'NIFTI_PAIR', 'NIFTI_GZ', 'BLAH_DI_BLAH']
+ # or invalid - '' in this case), they
+ # should produce .nii.gz
+ outputTypes = ['NIFTI', 'NIFTI_PAIR', 'NIFTI_GZ', '']
# Test tuples have the following structure (each
@@ -242,7 +292,24 @@ def test_imcp_script_shouldPass(move=False):
('a.img b.img', 'a.hdr a.hdr b b.hdr .', 'a b'),
('a.img b.img', 'a.hdr a.hdr b.img b .', 'a b'),
('a.img b.img', 'a.hdr a.hdr b.img b.img .', 'a b'),
- ('a.img b.img', 'a.hdr a.hdr b.img b.hdr .', 'a b'),
+ ('a.img b.img', 'a.hdr a.hdr b.img b.hdr .', 'a b'),
+
+ # Inputs which cause the destination
+ # to be overwritten - this should be
+ # ok, the destination should be the
+ # last specified input. The order of
+ # files_to_create has to match the
+ # imcp_args order, otherwise my bodgy
+ # checkFilesToExpect function will
+ # break.
+ ('a.nii a.img', 'a.nii a.img .', 'a'),
+ ('a.img a.nii', 'a.img a.nii .', 'a'),
+ ('a.nii a.img a.nii.gz', 'a.nii a.img a.nii.gz .', 'a'),
+ ('a.nii a.nii.gz a.img ', 'a.nii a.nii.gz a.img .', 'a'),
+ ('a.img a.nii.gz a.nii ', 'a.img a.nii.gz a.nii .', 'a'),
+ ('a.img a.nii a.nii.gz', 'a.img a.nii a.nii.gz .', 'a'),
+ ('a.nii.gz a.img a.nii ', 'a.nii.gz a.img a.nii .', 'a'),
+ ('a.nii.gz a.nii a.img ', 'a.nii.gz a.nii a.img .', 'a'),
]
indir = tempfile.mkdtemp()
@@ -258,12 +325,12 @@ def test_imcp_script_shouldPass(move=False):
imageHashes = []
- print
- print 'files_to_create: ', files_to_create
- print 'imcp_args: ', imcp_args
- print 'files_to_expect: ', files_to_expect
+ print()
+ print('files_to_create: ', files_to_create)
+ print('imcp_args: ', imcp_args)
+ print('files_to_expect: ', files_to_expect)
- for fname in files_to_create.split():
+ for i, fname in enumerate(files_to_create.split()):
imageHashes.append(createImageFile(op.join(indir, fname)))
imcp_args = imcp_args.split()
@@ -271,26 +338,26 @@ def test_imcp_script_shouldPass(move=False):
imcp_args[:-1] = [op.join(indir, a) for a in imcp_args[:-1]]
imcp_args[ -1] = op.join(outdir, imcp_args[-1])
+ print('indir before: ', os.listdir(indir))
+ print('outdir before: ', os.listdir(outdir))
if move: immv_script.main(imcp_args)
else: imcp_script.main(imcp_args)
- checkFilesToExpect(files_to_expect, outdir, outputType, imageHashes)
+ print('indir after: ', os.listdir(indir))
+ print('outdir after: ', os.listdir(outdir))
+
+ checkFilesToExpect(
+ files_to_expect, outdir, outputType, imageHashes)
if move:
infiles = os.listdir(indir)
infiles = [f for f in infiles if op.isfile(f)]
assert len(infiles) == 0
- for f in os.listdir(outdir):
- f = op.join(outdir, f)
- if op.isfile(f):
- os.remove(f)
+ cleardir(indir)
+ cleardir(outdir)
- for f in os.listdir(indir):
- f = op.join(indir, f)
- if op.isfile(f):
- os.remove(f)
finally:
shutil.rmtree(indir)
@@ -300,149 +367,248 @@ def test_imcp_script_shouldPass(move=False):
def test_imcp_script_shouldFail(move=False):
- # - non-existent input
- # - destination exists
+ # - len(srcs) > 1 and dest is not dir
# - input not readable
# - move=True and input not deleteable
- # - destination not writeable
- pass
+ # - ambiguous inputs
+ # - input is incomplete pair (e.g. .hdr
+ # without corresponding .img)
+
+ # a.img
+ # a.hdr
+ # a.nii
+ #
+ # FAIL: imcp a dest
+
+ # (files_to_create, imcp_args[, preproc])
+ tests = [
+
+ # non-existent input
+ ('', 'a b'),
+ ('a.img', 'b.img a'),
+
+ # dest is non-existent dir
+ ('a.img', 'a.img non_existent_dir/'),
+
+ # len(srcs) > 1, but dest is not dir
+ ('a.img b.img', 'a b c.img'),
+
+ # destination not writeable
+ ('a.img b.img', 'a b ./readonly_dir', 'mkdir outdir/readonly_dir; chmod a-wx outdir/readonly_dir'),
+ ('a.img', 'a b', 'mkdir outdir/b.nii.gz; chmod a-wx outdir/b.nii.gz'),
+
+ # input not readable
+ ('a.img', 'a b', 'chmod a-rwx indir/a.img'),
+
+ # ambiguous input
+ ('a.img a.nii', 'a b'),
+
+ # input is part of incomplete pair
+ ('a.img', 'a b', 'rm indir/a.hdr'),
+ ('a.img', 'a.img b', 'rm indir/a.hdr'),
+ ('a.img', 'a.hdr b', 'rm indir/a.hdr'),
+ ('a.img', 'a b', 'rm indir/a.img'),
+ ('a.img', 'a.img b', 'rm indir/a.img'),
+ ('a.img', 'a.hdr b', 'rm indir/a.img'),
+ ]
+
+ if move:
+ tests = tests + [
+ # Input not deletable
+ ('a.img', 'a b', 'chmod a-wx indir'),
+ ('a.img', 'a b', 'chmod a-wx indir'),
+ ('a.nii', 'a b', 'chmod a-wx indir')
+ ]
+
+ indir = tempfile.mkdtemp()
+ outdir = tempfile.mkdtemp()
+
+ try:
+ for test in tests:
+
+ files_to_create = test[0]
+ imcp_args = test[1]
+
+ if len(test) == 3: preproc = test[2]
+ else: preproc = None
+
+ files_to_create = files_to_create.split()
+ imcp_args = imcp_args .split()
+
+ for fname in files_to_create:
+ createImageFile(op.join(indir, fname))
+
+ imcp_args[:-1] = [op.join(indir, a) for a in imcp_args[:-1]]
+ imcp_args[ -1] = op.join(outdir, imcp_args[-1])
+
+ if preproc is not None:
+ for cmd in preproc.split(';'):
+ 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):
+ pass
+
+ sp.call('chmod u+rwx {}'.format(indir) .split())
+ sp.call('chmod u+rwx {}'.format(outdir).split())
+
+ cleardir(indir)
+ cleardir(outdir)
+
+ finally:
+ shutil.rmtree(indir)
+ shutil.rmtree(outdir)
+
def test_immv_script_shouldPass():
test_imcp_script_shouldPass(move=True)
+
+def test_immv_script_shouldFail():
+ test_imcp_script_shouldFail(move=True)
+
def test_imcp_shouldPass(move=False):
+
+ #
+ # if not useDefaultExt:
+ #
+ # imcp src.img dest -> dest.img
+ # imcp src.img dest.nii -> dest.nii
+ #
+ # if defaultExt:
+ # imgp src.img dest -> dest.nii.gz
+ # imgp src.img dest.nii -> dest.nii.gz
+
#
# (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]),
+ # [( imcp_args, 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.img', [
+ ('file file', 'file.img'),
+ ('file file.img', 'file.img'),
+ ('file file.hdr', 'file.img'),
+ ('file .', 'file.img'),
+ ('file.img file', 'file.img'),
+ ('file.img file.img', 'file.img'),
+ ('file.img file.hdr', 'file.img'),
+ ('file.img .', 'file.img'),
+ ('file.hdr file', 'file.img'),
+ ('file.hdr file.img', 'file.img'),
+ ('file.hdr file.hdr', 'file.img'),
+ ('file.hdr .', 'file.img'),
]),
- (['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.img file.blob', [
+ ('file file', 'file.img'),
+ ('file file.img', 'file.img'),
+ ('file file.hdr', 'file.img'),
+ ('file .', 'file.img'),
+ ('file.img file', 'file.img'),
+ ('file.img file.img', 'file.img'),
+ ('file.img file.hdr', 'file.img'),
+ ('file.img .', 'file.img'),
+ ('file.hdr file', 'file.img'),
+ ('file.hdr file.img', 'file.img'),
+ ('file.hdr file.hdr', 'file.img'),
+ ('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.img file.nii', [
+ ('file.img file', 'file.img'),
+ ('file.img file.img', 'file.img'),
+ ('file.img file.hdr', 'file.img'),
+ ('file.img .', 'file.img'),
+ ('file.hdr file', 'file.img'),
+ ('file.hdr file.img', 'file.img'),
+ ('file.hdr file.hdr', 'file.img'),
+ ('file.hdr .', 'file.img'),
+ ('file.nii file', 'file.nii'),
+ ('file.nii file.nii', 'file.nii'),
+
+ # TODO both img/nii files
]),
- (['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', [
+ ('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.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.gz', [
+ ('file file', 'file.nii.gz'),
+ ('file file.nii.gz', 'file.nii.gz'),
+ ('file .', 'file.nii.gz'),
+ ('file.nii.gz file', 'file.nii.gz'),
+ ('file.nii.gz file.nii.gz', 'file.nii.gz'),
+ ('file.nii.gz .', 'file.nii.gz'),
]),
- (['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.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.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']),
+ # TODO both
+ ]),
- ('file.nii', '', 'file.nii'),
- (['file.nii', 'file.nii.gz'], '', ['file.nii', 'file.nii.gz']),
+ ('file.img file.nii file.nii.gz', [
+ ('file.img file.nii file.nii.gz .', 'file.img file.nii file.nii.gz'),
+ ('file.img .', 'file.img'),
+ ('file.img .', '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.img 002.img 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'),
+ ('001 002 003 .', '001.img 002.img 003.img'),
+ ('001.img 002.img 003.img .', '001.img 002.img 003.img'),
+ ('001.hdr 002.hdr 003.hdr .', '001.img 002.img 003.img'),
+
+ ('001.img 002 003 .', '001.img 002.img 003.img'),
+ ('001.hdr 002 003 .', '001.img 002.img 003.img'),
+
+ ('001.img 002.hdr 003.img .', '001.img 002.img 003.img'),
+ ('001.hdr 002.img 003.hdr .', '001.img 002.img 003.img'),
+
+ ('001 003 .', '001.img 003.img'),
+ ('001.img 003.img .', '001.img 003.img'),
+ ('001.hdr 003.hdr .', '001.img 003.img'),
+
+ ('001.img 003 .', '001.img 003.img'),
+ ('001.hdr 003 .', '001.img 003.img'),
+
+ ('001.img 003.img .', '001.img 003.img'),
+ ('001.hdr 003.hdr .', '001.img 003.img'),
]),
]
@@ -453,51 +619,45 @@ def test_imcp_shouldPass(move=False):
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]
+ files_to_create = files_to_create.split()
+
+ for imcp_args, should_exist in tests:
- imcp_dest = op.join(outdir, imcp_dest)
+ should_exist = should_exist.split()
+ imcp_args = imcp_args.split()
+ imcp_srcs = imcp_args[:-1]
+ imcp_dest = imcp_args[ -1]
- # Each input file contains
- # its name in plain text,
- # so we can verify that the
- # files were correctly copied
- hashes = []
+ hashes = {}
for fn in files_to_create:
- hashes.append(createImageFile(op.join(indir, fn)))
+ hashes[fn] = createImageFile(op.join(indir, fn))
print()
print('files_to_create: ', files_to_create)
- print('imcp_src: ', imcp_src)
+ print('imcp_srcs: ', imcp_srcs)
print('imcp_dest: ', imcp_dest)
print('should_exist: ', should_exist)
+ print('indir: ', os.listdir(indir))
- for src in imcp_src:
+ for src in imcp_srcs:
print(' src: {}'.format(src))
src = op.join(indir, src)
- if move: imcp.immv(src, imcp_dest, overwrite=True)
- else: imcp.imcp(src, imcp_dest, overwrite=True)
-
- copied = os.listdir(outdir)
- copied = [f for f in copied if op.isfile(op.join(outdir, f))]
+ if move: imcp.immv(src, op.join(outdir, imcp_dest), overwrite=True)
+ else: imcp.imcp(src, op.join(outdir, imcp_dest), overwrite=True)
- assert sorted(copied) == sorted(should_exist)
+ print('indir after: ', os.listdir(indir))
+ print('outdir after: ', os.listdir(outdir))
- # check file contents
- for fn in should_exist:
- with open(op.join(outdir, fn), 'rt') as f:
- assert f.read() == '{}\n'.format(fn)
+ # check file contents
+ checkFilesToExpect(should_exist,
+ outdir,
+ None,
+ hashes)
# If move, check that
# input files are gone
@@ -505,11 +665,11 @@ def test_imcp_shouldPass(move=False):
for f in should_exist:
assert not op.exists(op.join(indir, f))
- for f in files_to_create:
+ for f in os.listdir(indir):
try: os.remove(op.join(indir, f))
except: pass
- for f in should_exist:
+ for f in os.listdir(outdir):
os.remove(op.join(outdir, f))