hansel.tests.test_has_files() - Code Metrics - Inspection of "Update .scrutinizer.yml" - alexsavio/hansel - Measure and Improve Code Quality continuously with Scrutinizer

Completed

Push — master ( 6ce243...b034e1 )

by Alexandre M.

created 2015-12-29 21:26 UTC

hansel.tests.test_has_files() F

↳ Parent: Project

Complexity

Conditions

Size

Total Lines

Duplication

Lines	0
Ratio	0 %

Metric	Value
cc	10
dl	0
loc	24
rs	3.5556

How to fix Complexity

# -*- coding: utf-8 -*-
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:


import pytest

import os
import os.path  as op
import shutil
from   copy     import copy
from   pathlib  import Path
from   tempfile import TemporaryDirectory

from   six      import string_types
from   hansel   import Crumb, mktree
from   hansel.utils import ParameterGrid


BASE_DIR = op.expanduser('~/data/cobre')


@pytest.fixture
def crumb(request):

    crumb = Crumb("{base_dir}/raw/{subject_id}/{session_id}/{modality}/{image}")

    def fin():
        print("teardown crumb")

    request.addfinalizer(fin)
    return crumb  # provide the fixture value


@pytest.fixture
def tmp_crumb(request):
    from tempfile import TemporaryDirectory

    crumb = Crumb("{base_dir}/raw/{subject_id}/{session_id}/{modality}/{image}")
    base_dir = TemporaryDirectory(prefix='crumbtest_')
    crumb2 = crumb.replace(base_dir=base_dir.name)

    def fin():
        print("teardown tmp_crumb")
    #    shutil.rmtree(base_dir.name)
    #    #os.removedirs(base_dir.name)

    request.addfinalizer(fin)
    return crumb2  # provide the fixture value


def test__get_path(tmp_crumb):
    pytest.raises(TypeError, tmp_crumb._get_path, {})
    pytest.raises(TypeError, tmp_crumb._get_path, [])

    assert tmp_crumb._get_path(tmp_crumb) == tmp_crumb._path


def test_path_property(crumb):

    assert crumb.path == crumb._path

    base_dir = BASE_DIR
    crumb2 = crumb.replace(base_dir=base_dir)

    assert crumb2.path == crumb2._path
    assert crumb.path != crumb2._path
    assert crumb._argidx != crumb2._argidx

    crumb.path = crumb2.path

    assert crumb.path == crumb.path
    assert crumb._argidx == crumb2._argidx


def test_replace_and_setitem(crumb):
    base_dir = BASE_DIR
    crumb.path = op.join(crumb.path, '{hansel}', '{gretel}')

    # use replace
    crumb2 = crumb.replace(base_dir=base_dir)

    assert crumb2._path == op.join(base_dir, crumb._path.replace('{base_dir}/', ''))
    assert 'base_dir' not in crumb2._argidx

    # use setitem
    crumb3 = crumb.copy(crumb)
    crumb3['base_dir'] = base_dir

    assert crumb3._replace1(**dict()) == crumb3._path
    assert crumb3._replace2(**dict()) == crumb3._path

    assert crumb3 is not crumb2
    assert crumb3 == crumb2
    assert crumb3._path == crumb2._path
    assert 'base_dir' not in crumb3._argidx

    assert crumb3.replace(**{})._path == crumb3._path

    pytest.raises(KeyError, crumb2.replace,     grimm='brothers')
    pytest.raises(KeyError, crumb2._replace1,   grimm='brothers')
    pytest.raises(KeyError, crumb2._replace2,   grimm='brothers')
    pytest.raises(KeyError, crumb2.__setitem__, 'grimm', 'brothers')


def test_firstarg(crumb):
    an, ai = crumb._firstarg()
    assert an == 'base_dir'
    assert ai == 0

    base_dir = BASE_DIR
    crumb2 = crumb.replace(base_dir=base_dir)

    an, ai = crumb2._firstarg()
    assert an == 'subject_id'
    assert ai == len(base_dir.split(op.sep)) + 1


def test_lastarg(crumb):
    an, ai = crumb._lastarg()
    assert an == 'image'
    assert ai == len(crumb._path_split()) - 1

    base_dir = BASE_DIR
    crumb2 = crumb.replace(base_dir=base_dir)

    an, ai = crumb2._lastarg()
    assert an == 'image'
    assert ai == len(crumb2._path_split()) - 1


def test_isabs(crumb):
    base_dir = BASE_DIR
    crumb2 = crumb.replace(base_dir=base_dir)

    assert not crumb.isabs()
    assert crumb2.isabs()


def test_argidx_order(crumb):
    base_dir = BASE_DIR
    crumb2 = crumb.replace(base_dir=base_dir)

    assert sorted(list(crumb._argidx.values()))  == list(crumb._argidx.values())
    assert sorted(list(crumb2._argidx.values())) == list(crumb2._argidx.values())


def test_abspath(crumb):
    crumb2 = crumb.abspath(first_is_basedir=False)
    assert crumb2._path == op.join(op.abspath(op.curdir), crumb._path)
    assert crumb is not crumb2
    assert crumb2.isabs()
    assert crumb != crumb2
    assert 'base_dir' in crumb2._argidx

    crumb3 = crumb.abspath(first_is_basedir=True)
    assert crumb3._path == op.join(op.abspath(op.curdir), crumb._path.replace('{base_dir}/', ''))
    assert crumb is not crumb3
    assert crumb3.isabs()

    assert crumb3 != crumb2

    assert Crumb(op.expanduser('~'))._abspath() == op.expanduser('~')

    base_dir = BASE_DIR
    crumb2 = crumb.replace(base_dir=base_dir)
    crumbc = crumb2.abspath(first_is_basedir=False)
    assert crumbc == crumb2
    assert crumbc is not crumb2


def test_copy(crumb):
    copy = Crumb.copy(crumb)
    assert crumb is not copy
    assert crumb == copy

    pytest.raises(TypeError, crumb.copy, {})


def test_equal_no_copy(crumb):
    crumb2 = crumb
    assert crumb2 == crumb

    crumb2._path += '/'
    assert crumb2 == crumb

    crumb2.path == op.join(crumb._path, '{test}')
    assert crumb2 == crumb

    crumb2._argidx['hansel'] = []
    assert crumb2 == crumb


def test_equal_copy(crumb):
    crumb2 = Crumb.copy(crumb)
    assert crumb2 == crumb

    crumb2._path += '/'
    assert crumb2 != crumb

    crumb2._path == op.join(crumb._path, '{test}')
    assert crumb2 != crumb

    crumb2._argidx['hansel'] = []
    assert crumb2 != crumb


def test_split(crumb):
    splt = crumb.split()
    for s in splt:
        if op.isdir(s):
            assert op.exists(s)
        else:
            assert Crumb._is_crumb_arg(s) or isinstance(s, string_types)


def test_is_valid_a_bit(crumb):
    assert Crumb.is_valid(crumb)

    crumb_path = crumb._path
    crumb_path = crumb_path[:3] + Crumb._arg_start_sym + crumb_path[3:-1]

    assert isinstance(Crumb.from_path(Path(crumb_path)), Path)
    pytest.raises(ValueError, Crumb.from_path, crumb_path)
    pytest.raises(TypeError, crumb.from_path, {})

    assert not Crumb.is_valid(crumb_path)
    assert Crumb.is_valid(op.expanduser('~'))

    crumb._path = crumb_path
    pytest.raises(ValueError, crumb._check)
    pytest.raises(ValueError, crumb.isabs)
    pytest.raises(ValueError, crumb.abspath)


def test_arg_name(crumb):
    pytest.raises(ValueError, crumb._arg_name, 'hansel')
    assert not crumb._is_crumb_arg(Path(op.expanduser('~')))


def test_has_crumbs(crumb):
    assert Crumb.has_crumbs(crumb)

    assert not Crumb.has_crumbs('')
    assert not Crumb.has_crumbs('/home/hansel/.config')


def test_str(crumb):
    assert crumb._path == str(crumb)


def test_ls_raises():
    crumb = Crumb(op.join('{home}', '{user_folder}'))

    pytest.raises(ValueError, crumb.ls, 'hansel')

    pytest.raises(NotImplementedError, crumb.ls, 'home')

    pytest.raises(ValueError, crumb.ls, 'user',
                  make_crumbs=True, fullpath=False)


def test_ls_and_getitem():
    base_dir = op.expanduser('~')
    crumb = Crumb(op.join(base_dir, '{user_folder}'))

    lst = crumb.ls('user_folder',
                   fullpath     = False,
                   duplicates   = True,
                   make_crumbs  = False,
                   check_exists = False)
    assert set(lst) == set(os.listdir(base_dir))

    crumb = Crumb(op.join(base_dir, '{user_folder}', '{files}'))
    lst = crumb.ls('user_folder',
                   fullpath     = False,
                   duplicates   = True,
                   make_crumbs  = False,
                   check_exists = False)
    assert set(lst) == set([d for d in os.listdir(base_dir) if op.isdir(op.join(base_dir, d))])

    flst = crumb.ls('user_folder',
                    fullpath     = True,
                    duplicates   = True,
                    make_crumbs  = False,
                    check_exists = False)
    assert all([isinstance(f, string_types) for f in flst])
    assert all([not op.exists(f) for f in flst])

    flst = crumb.ls('files',
                    fullpath     = True,
                    duplicates   = True,
                    make_crumbs  = False,
                    check_exists = False)
    assert all([isinstance(f, string_types) for f in flst])
    assert all([op.exists(f) or op.islink(f) for f in flst])

    flst = crumb.ls('files',
                    fullpath     = True,
                    duplicates   = True,
                    make_crumbs  = True,
                    check_exists = False)
    assert all([isinstance(f, Path) for f in flst])
    assert all([f.exists() or f.is_symlink() for f in flst])

    flst1 = crumb.ls('files',
                     fullpath     = False,
                     duplicates   = False,
                     make_crumbs  = False,
                     check_exists = True)
    flst2 = crumb['files']
    assert all([isinstance(f, str) for f in flst1])
    assert flst1 == flst2

    flst = crumb.ls('user_folder',
                     fullpath     = True,
                     duplicates   = True,
                     make_crumbs  = True,
                     check_exists = False)
    assert all([isinstance(f, Crumb) for f in flst])
    # check if all crumbs exist
    assert all([c.exists() for c in flst])

    #TODO: missing test ls with duplicates=False


def test_ls3():
    from glob import glob
    base_dir = op.expanduser('~')
    files = [d for d in glob(op.join(base_dir, '*')) if op.isfile(d)]
    crumb = Crumb(op.join(files[0], '{user_folder}', '{files}'))
    lst = crumb.ls('user_folder')
    assert not lst

    lst = crumb.ls('files')
    assert not lst


def test_rem_deps(crumb):

    values = copy(crumb._argidx)
    assert not crumb._remaining_deps(values)

    del values['base_dir']
    assert crumb._remaining_deps(values) == ['base_dir']

    del values['subject_id']
    assert crumb._remaining_deps(values) == ['subject_id', 'base_dir']

    values = copy(crumb._argidx)
    del values['base_dir']
    del values['modality']
    assert crumb._remaining_deps(values) == ['modality', 'base_dir']

    values = copy(crumb._argidx)
    del values['image']
    del values['modality']
    assert not crumb._remaining_deps(values)


# def test_remdeps2(tmp_crumb):
#     values_dict = {'session_id': ['session_' + str(i) for i in range(2)],
#                    'subject_id': ['subj_' + str(i) for i in range(3)],
#                    'modality':   ['anat', 'rest', 'pet'],
#                    'image':      ['mprage.nii', 'rest.nii', 'pet.nii'],
#                    }
#
#     del values_dict['subject_id']
#     del values_dict['image']
#     values_map = list(ParameterGrid(values_dict))
#
#     assert tmp_crumb._remaining_deps(['image']) == ['modality', 'base_dir']


def test_touch(tmp_crumb):
    assert not op.exists(tmp_crumb.split()[0])
    path = tmp_crumb.touch()
    assert path == tmp_crumb.split()[0]
    assert op.exists(path)


def test__touch():
    base_dir = TemporaryDirectory()
    path = op.join(base_dir.name, 'hansel')

    assert not op.exists(path)

    nupath = Crumb._touch(path)
    assert nupath == path
    assert op.exists(nupath)

    pytest.raises(IOError, Crumb._touch, nupath, exist_ok=False)

    #pytest.raises(IOError, Crumb._touch, path + '\\', exist_ok=False)


def test_arg_values(tmp_crumb):
    # the most of _arg_values is being tested in test_ls
    pytest.raises(ValueError, tmp_crumb._arg_values, 'session_id')


def test_exists(tmp_crumb):
    assert not op.exists(tmp_crumb.split()[0])

    values_map = {'session_id': ['session_' + str(i) for i in range(2)],
                  'subject_id': ['subj_' + str(i) for i in range(3)]}

    pytest.raises(IOError, tmp_crumb._arg_values, 'subject_id')
    assert not tmp_crumb.exists()

    _ = mktree(tmp_crumb, list(ParameterGrid(values_map)))

    assert tmp_crumb.exists()

    assert not Crumb._split_exists('/_/asdfasdfasdf?/{hansel}')


def test_contains(tmp_crumb):
    assert 'modality'   in tmp_crumb
    assert 'subject_id' in tmp_crumb
    assert 'image'      in tmp_crumb
    assert 'raw'    not in tmp_crumb

    tmp_crumb['image'] = 'image'

    assert 'image' not in tmp_crumb


def test_ls_with_check(tmp_crumb):
    assert not op.exists(tmp_crumb._path)

    values_dict = {'session_id': ['session_' + str(i) for i in range(2)],
                   'subject_id': ['subj_' + str(i) for i in range(3)],
                   'modality':   ['anat'],
                   'image':      ['mprage1.nii', 'mprage2.nii', 'mprage3.nii'],
                   }

    paths = mktree(tmp_crumb, list(ParameterGrid(values_dict)))

    assert op.exists(tmp_crumb.split()[0])

    assert all([op.exists(p) for p in paths])

    images = tmp_crumb.ls('image',
                          fullpath     = True,
                          make_crumbs  = True,
                          duplicates   = False,
                          check_exists = True)

    modalities = tmp_crumb.ls('modality',
                              fullpath     = True,
                              make_crumbs  = True,
                              duplicates   = False,
                              check_exists = True)

    assert all([img.exists() for img in images])
    assert all([mod.exists() for mod in modalities])

    images[0].rmdir()

    images2 = tmp_crumb.ls('image',
                           fullpath     = True,
                           make_crumbs  = True,
                           duplicates   = False,
                           check_exists = True)

    assert images != images2
    assert len(images) == len(images2) + 1
    assert not all([img.exists() for img in images])
    assert     all([img.exists() for img in images2])

    images[1].rmdir()
    images[2].rmdir()

    images2 = tmp_crumb.ls('image',
                           fullpath     = True,
                           make_crumbs  = True,
                           duplicates   = False,
                           check_exists = True)

    assert not all([img.exists() for img in images])
    assert     all([img.exists() for img in images2])

    modalities2 = tmp_crumb.ls('modality',
                               fullpath     = True,
                               make_crumbs  = True,
                               duplicates   = False,
                               check_exists = True)

    str_modalities2 = tmp_crumb.ls('modality',
                                   fullpath     = True,
                                   make_crumbs  = False,
                                   duplicates   = False,
                                   check_exists = True)

    assert images != images2
    assert len(images) == len(images2) + 3

    assert modalities == modalities2
    assert all([mod.exists() for mod in modalities])
    assert all([mod.exists() for mod in modalities2])
    assert all([mod._path == smod for mod, smod in zip(modalities2, str_modalities2)])

    os.removedirs(modalities2[0].split()[0])

    modalities3 = tmp_crumb.ls('modality',
                               fullpath     = True,
                               make_crumbs  = True,
                               duplicates   = False,
                               check_exists = True)

    assert modalities2 != modalities3
    assert not all([mod.exists() for mod in modalities2])
    assert     all([mod.exists() for mod in modalities3])

    pytest.raises(IOError, modalities2[0].__getitem__, 'image')

    img_crumb = tmp_crumb.replace(image='mprage1.nii')
    img_crumb['modality'] = 'anat'

    assert img_crumb['session_id'].count('session_1') > img_crumb['session_id'].count('session_0')

    img_crumb['session_id'] = 'session_0'

    assert 'subj_0' not in img_crumb['subject_id']


def test_has_files(tmp_crumb):
    assert not op.exists(tmp_crumb._path)

    assert not tmp_crumb.has_files()

    values_dict = {'session_id': ['session_' + str(i) for i in range(2)],
                   'subject_id': ['subj_' + str(i) for i in range(3)],
                   'modality':   ['anat'],
                   'image':      ['mprage1.nii', 'mprage2.nii', 'mprage3.nii'],
                   }

    paths = mktree(tmp_crumb, list(ParameterGrid(values_dict)))

    assert op.exists(tmp_crumb.split()[0])

    assert not tmp_crumb.has_files()

    pa = Path(paths[0])
    pa.rmdir()
    pa.touch()

    assert pa.exists()
    assert pa.is_file()
    assert tmp_crumb.has_files()


def test_repr(crumb):
    assert crumb.__repr__() == 'Crumb("{base_dir}/raw/{subject_id}/{session_id}/{modality}/{image}")'


if __name__ == '__main__':
    import os.path as op
    from tempfile import TemporaryDirectory
    from hansel import Crumb
    from hansel.utils import ParameterGrid

    # crumb = Crumb("{base_dir}/raw/{subject_id}/{session_id}/{modality}/{image}")
    # base_dir = TemporaryDirectory()
    # crumb2 = crumb.replace(base_dir=base_dir.name)
    #
    # values_map = {'session_id': ['session_' + str(i) for i in range(2)],
    #               'subject_id': ['subj_' + str(i) for i in range(3)],
    #               'modality':   ['anat', 'rest', 'pet'],
    #               }
    #
    # nupaths = crumb2.mktree(list(ParameterGrid(values_map)))
    #
    # assert all([op.exists(npath) for npath in nupaths])
    #
    # anat_crumb = crumb2.replace(modality='anat')
    #
    # anat_crumb.ls('subject_id')


    base_dir = op.expanduser('~/data/cobre')
    crumb = Crumb("{base_dir}/raw/{subject_id}/{session_id}/{modality}/{image}")

    crumb['base_dir'] = base_dir
    crumb['session_id'] = 'session_1'

    rest_crumb = Crumb.copy(crumb)
    anat_crumb = Crumb.copy(crumb)

    rest_crumb['modality'] = 'rest_1'
    rest_crumb['image'] = 'rest.nii.gz'

    anat_crumb['modality'] = 'anat_1'
    anat_crumb['image'] = 'mprage.nii.gz'


1			# -- coding: utf-8 --
2			# emacs: -- mode: python; py-indent-offset: 4; indent-tabs-mode: nil --
3			# vi: set ft=python sts=4 ts=4 sw=4 et:
4
5
6			import pytest
7
8			import os
9			import os.path as op
10			import shutil
11			from copy import copy
12			from pathlib import Path
13			from tempfile import TemporaryDirectory
14
15			from six import string_types
16			from hansel import Crumb, mktree
17			from hansel.utils import ParameterGrid
18
19
20			BASE_DIR = op.expanduser('~/data/cobre')
21
22
23			@pytest.fixture
24			def crumb(request):
25
26			crumb = Crumb("{base_dir}/raw/{subject_id}/{session_id}/{modality}/{image}")
27
28			def fin():
29			print("teardown crumb")
30
31			request.addfinalizer(fin)
32			return crumb # provide the fixture value
33
34
35			@pytest.fixture
36			def tmp_crumb(request):
37			from tempfile import TemporaryDirectory
38
39			crumb = Crumb("{base_dir}/raw/{subject_id}/{session_id}/{modality}/{image}")
40			base_dir = TemporaryDirectory(prefix='crumbtest_')
41			crumb2 = crumb.replace(base_dir=base_dir.name)
42
43			def fin():
44			print("teardown tmp_crumb")
45			# shutil.rmtree(base_dir.name)
46			# #os.removedirs(base_dir.name)
47
48			request.addfinalizer(fin)
49			return crumb2 # provide the fixture value
50
51
52			def test__get_path(tmp_crumb):
53			pytest.raises(TypeError, tmp_crumb._get_path, {})
54			pytest.raises(TypeError, tmp_crumb._get_path, [])
55
56			assert tmp_crumb._get_path(tmp_crumb) == tmp_crumb._path
57
58
59			def test_path_property(crumb):
60
61			assert crumb.path == crumb._path
62
63			base_dir = BASE_DIR
64			crumb2 = crumb.replace(base_dir=base_dir)
65
66			assert crumb2.path == crumb2._path
67			assert crumb.path != crumb2._path
68			assert crumb._argidx != crumb2._argidx
69
70			crumb.path = crumb2.path
71
72			assert crumb.path == crumb.path
73			assert crumb._argidx == crumb2._argidx
74
75
76			def test_replace_and_setitem(crumb):
77			base_dir = BASE_DIR
78			crumb.path = op.join(crumb.path, '{hansel}', '{gretel}')
79
80			# use replace
81			crumb2 = crumb.replace(base_dir=base_dir)
82
83			assert crumb2._path == op.join(base_dir, crumb._path.replace('{base_dir}/', ''))
84			assert 'base_dir' not in crumb2._argidx
85
86			# use setitem
87			crumb3 = crumb.copy(crumb)
88			crumb3['base_dir'] = base_dir
89
90			assert crumb3._replace1(**dict()) == crumb3._path
91			assert crumb3._replace2(**dict()) == crumb3._path
92
93			assert crumb3 is not crumb2
94			assert crumb3 == crumb2
95			assert crumb3._path == crumb2._path
96			assert 'base_dir' not in crumb3._argidx
97
98			assert crumb3.replace(**{})._path == crumb3._path
99
100			pytest.raises(KeyError, crumb2.replace, grimm='brothers')
101			pytest.raises(KeyError, crumb2._replace1, grimm='brothers')
102			pytest.raises(KeyError, crumb2._replace2, grimm='brothers')
103			pytest.raises(KeyError, crumb2.__setitem__, 'grimm', 'brothers')
104
105
106			def test_firstarg(crumb):
107			an, ai = crumb._firstarg()
108			assert an == 'base_dir'
109			assert ai == 0
110
111			base_dir = BASE_DIR
112			crumb2 = crumb.replace(base_dir=base_dir)
113
114			an, ai = crumb2._firstarg()
115			assert an == 'subject_id'
116			assert ai == len(base_dir.split(op.sep)) + 1
117
118
119			def test_lastarg(crumb):
120			an, ai = crumb._lastarg()
121			assert an == 'image'
122			assert ai == len(crumb._path_split()) - 1
123
124			base_dir = BASE_DIR
125			crumb2 = crumb.replace(base_dir=base_dir)
126
127			an, ai = crumb2._lastarg()
128			assert an == 'image'
129			assert ai == len(crumb2._path_split()) - 1
130
131
132			def test_isabs(crumb):
133			base_dir = BASE_DIR
134			crumb2 = crumb.replace(base_dir=base_dir)
135
136			assert not crumb.isabs()
137			assert crumb2.isabs()
138
139
140			def test_argidx_order(crumb):
141			base_dir = BASE_DIR
142			crumb2 = crumb.replace(base_dir=base_dir)
143
144			assert sorted(list(crumb._argidx.values())) == list(crumb._argidx.values())
145			assert sorted(list(crumb2._argidx.values())) == list(crumb2._argidx.values())
146
147
148			def test_abspath(crumb):
149			crumb2 = crumb.abspath(first_is_basedir=False)
150			assert crumb2._path == op.join(op.abspath(op.curdir), crumb._path)
151			assert crumb is not crumb2
152			assert crumb2.isabs()
153			assert crumb != crumb2
154			assert 'base_dir' in crumb2._argidx
155
156			crumb3 = crumb.abspath(first_is_basedir=True)
157			assert crumb3._path == op.join(op.abspath(op.curdir), crumb._path.replace('{base_dir}/', ''))
158			assert crumb is not crumb3
159			assert crumb3.isabs()
160
161			assert crumb3 != crumb2
162
163			assert Crumb(op.expanduser('~'))._abspath() == op.expanduser('~')
164
165			base_dir = BASE_DIR
166			crumb2 = crumb.replace(base_dir=base_dir)
167			crumbc = crumb2.abspath(first_is_basedir=False)
168			assert crumbc == crumb2
169			assert crumbc is not crumb2
170
171
172			def test_copy(crumb):
173			copy = Crumb.copy(crumb)
174			assert crumb is not copy
175			assert crumb == copy
176
177			pytest.raises(TypeError, crumb.copy, {})
178
179
180			def test_equal_no_copy(crumb):
181			crumb2 = crumb
182			assert crumb2 == crumb
183
184			crumb2._path += '/'
185			assert crumb2 == crumb
186
187			crumb2.path == op.join(crumb._path, '{test}')
188			assert crumb2 == crumb
189
190			crumb2._argidx['hansel'] = []
191			assert crumb2 == crumb
192
193
194			def test_equal_copy(crumb):
195			crumb2 = Crumb.copy(crumb)
196			assert crumb2 == crumb
197
198			crumb2._path += '/'
199			assert crumb2 != crumb
200
201			crumb2._path == op.join(crumb._path, '{test}')
202			assert crumb2 != crumb
203
204			crumb2._argidx['hansel'] = []
205			assert crumb2 != crumb
206
207
208			def test_split(crumb):
209			splt = crumb.split()
210			for s in splt:
211			if op.isdir(s):
212			assert op.exists(s)
213			else:
214			assert Crumb._is_crumb_arg(s) or isinstance(s, string_types)
215
216
217			def test_is_valid_a_bit(crumb):
218			assert Crumb.is_valid(crumb)
219
220			crumb_path = crumb._path
221			crumb_path = crumb_path[:3] + Crumb._arg_start_sym + crumb_path[3:-1]
222
223			assert isinstance(Crumb.from_path(Path(crumb_path)), Path)
224			pytest.raises(ValueError, Crumb.from_path, crumb_path)
225			pytest.raises(TypeError, crumb.from_path, {})
226
227			assert not Crumb.is_valid(crumb_path)
228			assert Crumb.is_valid(op.expanduser('~'))
229
230			crumb._path = crumb_path
231			pytest.raises(ValueError, crumb._check)
232			pytest.raises(ValueError, crumb.isabs)
233			pytest.raises(ValueError, crumb.abspath)
234
235
236			def test_arg_name(crumb):
237			pytest.raises(ValueError, crumb._arg_name, 'hansel')
238			assert not crumb._is_crumb_arg(Path(op.expanduser('~')))
239
240
241			def test_has_crumbs(crumb):
242			assert Crumb.has_crumbs(crumb)
243
244			assert not Crumb.has_crumbs('')
245			assert not Crumb.has_crumbs('/home/hansel/.config')
246
247
248			def test_str(crumb):
249			assert crumb._path == str(crumb)
250
251
252			def test_ls_raises():
253			crumb = Crumb(op.join('{home}', '{user_folder}'))
254
255			pytest.raises(ValueError, crumb.ls, 'hansel')
256
257			pytest.raises(NotImplementedError, crumb.ls, 'home')
258
259			pytest.raises(ValueError, crumb.ls, 'user',
260			make_crumbs=True, fullpath=False)
261
262
263			def test_ls_and_getitem():
264			base_dir = op.expanduser('~')
265			crumb = Crumb(op.join(base_dir, '{user_folder}'))
266
267			lst = crumb.ls('user_folder',
268			fullpath = False,
269			duplicates = True,
270			make_crumbs = False,
271			check_exists = False)
272			assert set(lst) == set(os.listdir(base_dir))
273
274			crumb = Crumb(op.join(base_dir, '{user_folder}', '{files}'))
275			lst = crumb.ls('user_folder',
276			fullpath = False,
277			duplicates = True,
278			make_crumbs = False,
279			check_exists = False)
280			assert set(lst) == set([d for d in os.listdir(base_dir) if op.isdir(op.join(base_dir, d))])
281
282			flst = crumb.ls('user_folder',
283			fullpath = True,
284			duplicates = True,
285			make_crumbs = False,
286			check_exists = False)
287			assert all([isinstance(f, string_types) for f in flst])
288			assert all([not op.exists(f) for f in flst])
289
290			flst = crumb.ls('files',
291			fullpath = True,
292			duplicates = True,
293			make_crumbs = False,
294			check_exists = False)
295			assert all([isinstance(f, string_types) for f in flst])
296			assert all([op.exists(f) or op.islink(f) for f in flst])
297
298			flst = crumb.ls('files',
299			fullpath = True,
300			duplicates = True,
301			make_crumbs = True,
302			check_exists = False)
303			assert all([isinstance(f, Path) for f in flst])
304			assert all([f.exists() or f.is_symlink() for f in flst])
305
306			flst1 = crumb.ls('files',
307			fullpath = False,
308			duplicates = False,
309			make_crumbs = False,
310			check_exists = True)
311			flst2 = crumb['files']
312			assert all([isinstance(f, str) for f in flst1])
313			assert flst1 == flst2
314
315			flst = crumb.ls('user_folder',
316			fullpath = True,
317			duplicates = True,
318			make_crumbs = True,
319			check_exists = False)
320			assert all([isinstance(f, Crumb) for f in flst])
321			# check if all crumbs exist
322			assert all([c.exists() for c in flst])
323
324			#TODO: missing test ls with duplicates=False
325
326
327			def test_ls3():
328			from glob import glob
329			base_dir = op.expanduser('~')
330			files = [d for d in glob(op.join(base_dir, '*')) if op.isfile(d)]
331			crumb = Crumb(op.join(files[0], '{user_folder}', '{files}'))
332			lst = crumb.ls('user_folder')
333			assert not lst
334
335			lst = crumb.ls('files')
336			assert not lst
337
338
339			def test_rem_deps(crumb):
340
341			values = copy(crumb._argidx)
342			assert not crumb._remaining_deps(values)
343
344			del values['base_dir']
345			assert crumb._remaining_deps(values) == ['base_dir']
346
347			del values['subject_id']
348			assert crumb._remaining_deps(values) == ['subject_id', 'base_dir']
349
350			values = copy(crumb._argidx)
351			del values['base_dir']
352			del values['modality']
353			assert crumb._remaining_deps(values) == ['modality', 'base_dir']
354
355			values = copy(crumb._argidx)
356			del values['image']
357			del values['modality']
358			assert not crumb._remaining_deps(values)
359
360
361			# def test_remdeps2(tmp_crumb):
362			# values_dict = {'session_id': ['session_' + str(i) for i in range(2)],
363			# 'subject_id': ['subj_' + str(i) for i in range(3)],
364			# 'modality': ['anat', 'rest', 'pet'],
365			# 'image': ['mprage.nii', 'rest.nii', 'pet.nii'],
366			# }
367			#
368			# del values_dict['subject_id']
369			# del values_dict['image']
370			# values_map = list(ParameterGrid(values_dict))
371			#
372			# assert tmp_crumb._remaining_deps(['image']) == ['modality', 'base_dir']
373
374
375			def test_touch(tmp_crumb):
376			assert not op.exists(tmp_crumb.split()[0])
377			path = tmp_crumb.touch()
378			assert path == tmp_crumb.split()[0]
379			assert op.exists(path)
380
381
382			def test__touch():
383			base_dir = TemporaryDirectory()
384			path = op.join(base_dir.name, 'hansel')
385
386			assert not op.exists(path)
387
388			nupath = Crumb._touch(path)
389			assert nupath == path
390			assert op.exists(nupath)
391
392			pytest.raises(IOError, Crumb._touch, nupath, exist_ok=False)
393
394			#pytest.raises(IOError, Crumb._touch, path + '\\', exist_ok=False)
395
396
397			def test_arg_values(tmp_crumb):
398			# the most of _arg_values is being tested in test_ls
399			pytest.raises(ValueError, tmp_crumb._arg_values, 'session_id')
400
401
402			def test_exists(tmp_crumb):
403			assert not op.exists(tmp_crumb.split()[0])
404
405			values_map = {'session_id': ['session_' + str(i) for i in range(2)],
406			'subject_id': ['subj_' + str(i) for i in range(3)]}
407
408			pytest.raises(IOError, tmp_crumb._arg_values, 'subject_id')
409			assert not tmp_crumb.exists()
410
411			_ = mktree(tmp_crumb, list(ParameterGrid(values_map)))
412
413			assert tmp_crumb.exists()
414
415			assert not Crumb._split_exists('/_/asdfasdfasdf?/{hansel}')
416
417
418			def test_contains(tmp_crumb):
419			assert 'modality' in tmp_crumb
420			assert 'subject_id' in tmp_crumb
421			assert 'image' in tmp_crumb
422			assert 'raw' not in tmp_crumb
423
424			tmp_crumb['image'] = 'image'
425
426			assert 'image' not in tmp_crumb
427
428
429			def test_ls_with_check(tmp_crumb):
430			assert not op.exists(tmp_crumb._path)
431
432			values_dict = {'session_id': ['session_' + str(i) for i in range(2)],
433			'subject_id': ['subj_' + str(i) for i in range(3)],
434			'modality': ['anat'],
435			'image': ['mprage1.nii', 'mprage2.nii', 'mprage3.nii'],
436			}
437
438			paths = mktree(tmp_crumb, list(ParameterGrid(values_dict)))
439
440			assert op.exists(tmp_crumb.split()[0])
441
442			assert all([op.exists(p) for p in paths])
443
444			images = tmp_crumb.ls('image',
445			fullpath = True,
446			make_crumbs = True,
447			duplicates = False,
448			check_exists = True)
449
450			modalities = tmp_crumb.ls('modality',
451			fullpath = True,
452			make_crumbs = True,
453			duplicates = False,
454			check_exists = True)
455
456			assert all([img.exists() for img in images])
457			assert all([mod.exists() for mod in modalities])
458
459			images[0].rmdir()
460
461			images2 = tmp_crumb.ls('image',
462			fullpath = True,
463			make_crumbs = True,
464			duplicates = False,
465			check_exists = True)
466
467			assert images != images2
468			assert len(images) == len(images2) + 1
469			assert not all([img.exists() for img in images])
470			assert all([img.exists() for img in images2])
471
472			images[1].rmdir()
473			images[2].rmdir()
474
475			images2 = tmp_crumb.ls('image',
476			fullpath = True,
477			make_crumbs = True,
478			duplicates = False,
479			check_exists = True)
480
481			assert not all([img.exists() for img in images])
482			assert all([img.exists() for img in images2])
483
484			modalities2 = tmp_crumb.ls('modality',
485			fullpath = True,
486			make_crumbs = True,
487			duplicates = False,
488			check_exists = True)
489
490			str_modalities2 = tmp_crumb.ls('modality',
491			fullpath = True,
492			make_crumbs = False,
493			duplicates = False,
494			check_exists = True)
495
496			assert images != images2
497			assert len(images) == len(images2) + 3
498
499			assert modalities == modalities2
500			assert all([mod.exists() for mod in modalities])
501			assert all([mod.exists() for mod in modalities2])
502			assert all([mod._path == smod for mod, smod in zip(modalities2, str_modalities2)])
503
504			os.removedirs(modalities2[0].split()[0])
505
506			modalities3 = tmp_crumb.ls('modality',
507			fullpath = True,
508			make_crumbs = True,
509			duplicates = False,
510			check_exists = True)
511
512			assert modalities2 != modalities3
513			assert not all([mod.exists() for mod in modalities2])
514			assert all([mod.exists() for mod in modalities3])
515
516			pytest.raises(IOError, modalities2[0].__getitem__, 'image')
517
518			img_crumb = tmp_crumb.replace(image='mprage1.nii')
519			img_crumb['modality'] = 'anat'
520
521			assert img_crumb['session_id'].count('session_1') > img_crumb['session_id'].count('session_0')
522
523			img_crumb['session_id'] = 'session_0'
524
525			assert 'subj_0' not in img_crumb['subject_id']
526
527
528			def test_has_files(tmp_crumb):
529			assert not op.exists(tmp_crumb._path)
530
531			assert not tmp_crumb.has_files()
532
533			values_dict = {'session_id': ['session_' + str(i) for i in range(2)],
534			'subject_id': ['subj_' + str(i) for i in range(3)],
535			'modality': ['anat'],
536			'image': ['mprage1.nii', 'mprage2.nii', 'mprage3.nii'],
537			}
538
539			paths = mktree(tmp_crumb, list(ParameterGrid(values_dict)))
540
541			assert op.exists(tmp_crumb.split()[0])
542
543			assert not tmp_crumb.has_files()
544
545			pa = Path(paths[0])
546			pa.rmdir()
547			pa.touch()
548
549			assert pa.exists()
550			assert pa.is_file()
551			assert tmp_crumb.has_files()
552
553
554			def test_repr(crumb):
555			assert crumb.__repr__() == 'Crumb("{base_dir}/raw/{subject_id}/{session_id}/{modality}/{image}")'
556
557
558			if __name__ == '__main__':
559			import os.path as op
560			from tempfile import TemporaryDirectory
561			from hansel import Crumb
562			from hansel.utils import ParameterGrid
563
564			# crumb = Crumb("{base_dir}/raw/{subject_id}/{session_id}/{modality}/{image}")
565			# base_dir = TemporaryDirectory()
566			# crumb2 = crumb.replace(base_dir=base_dir.name)
567			#
568			# values_map = {'session_id': ['session_' + str(i) for i in range(2)],
569			# 'subject_id': ['subj_' + str(i) for i in range(3)],
570			# 'modality': ['anat', 'rest', 'pet'],
571			# }
572			#
573			# nupaths = crumb2.mktree(list(ParameterGrid(values_map)))
574			#
575			# assert all([op.exists(npath) for npath in nupaths])
576			#
577			# anat_crumb = crumb2.replace(modality='anat')
578			#
579			# anat_crumb.ls('subject_id')
580
581
582			base_dir = op.expanduser('~/data/cobre')
583			crumb = Crumb("{base_dir}/raw/{subject_id}/{session_id}/{modality}/{image}")
584
585			crumb['base_dir'] = base_dir
586			crumb['session_id'] = 'session_1'
587
588			rest_crumb = Crumb.copy(crumb)
589			anat_crumb = Crumb.copy(crumb)
590
591			rest_crumb['modality'] = 'rest_1'
592			rest_crumb['image'] = 'rest.nii.gz'
593
594			anat_crumb['modality'] = 'anat_1'
595			anat_crumb['image'] = 'mprage.nii.gz'
596

alexsavio / hansel

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hansel.tests.test_has_files() F

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