def test_main():
args = [
'generate', '-b', 'ubuntu:17.04', '-p', 'apt', '--ants',
'version=2.1.0', '--fsl', 'version=5.0.10', '--miniconda',
'env_name=default', 'python_version=3.5.1', '--mrtrix3',
'--neurodebian', 'os_codename=zesty', 'download_server=usa-nh',
'--spm', 'version=12', 'matlab_version=R2017a', '--no-check-urls'
]
main(args)
args = ['generate', '-b', 'ubuntu:17.04', '-p', 'apt', '--no-check-urls']
main(args)
with pytest.raises(SystemExit):
args = ['-b', 'ubuntu:17.04']
main(args)
with pytest.raises(SystemExit):
main()
args = [
'generate', '-b', 'ubuntu:17.04', '-p', 'apt', '--ants', 'option=value'
]
with pytest.raises(ValueError):
main(args)
def test_generate_from_json(capsys, tmpdir):
cmd = "generate docker -b debian:stretch -p apt --convert3d version=1.0.0"
main(cmd.split())
true, _ = capsys.readouterr()
specs = {
'instructions': [['base', 'debian:stretch'],
['convert3d', {
'version': '1.0.0'
}]],
'pkg_manager':
'apt'
}
str_specs = json.dumps(specs)
filepath = tmpdir.join("specs.json")
filepath.write(str_specs)
gen_cmd = "generate docker {}".format(filepath)
main(gen_cmd.split())
test, _ = capsys.readouterr()
# Remove last RUN instruction (it contains saving to JSON and order is not guaranteed).
true = "RUN".join(true.split("RUN")[:-1])
test = "RUN".join(test.split("RUN")[:-1])
# Remove comments.
true = [t for t in true.splitlines() if not t.startswith('#')]
test = [t for t in test.splitlines() if not t.startswith('#')]
assert true == test
def test_generate_from_json(capsys, tmpdir):
cmd = "generate docker -b debian:stretch -p apt --convert3d version=1.0.0"
main(cmd.split())
true, _ = capsys.readouterr()
specs = {
"instructions": [
["base", "debian:stretch"],
["convert3d", {
"version": "1.0.0"
}],
],
"pkg_manager":
"apt",
}
str_specs = json.dumps(specs)
filepath = tmpdir.join("specs.json")
filepath.write(str_specs)
gen_cmd = "generate docker {}".format(filepath)
main(gen_cmd.split())
test, _ = capsys.readouterr()
# Remove last RUN instruction (it contains saving to JSON and order is not guaranteed).
true = "RUN".join(true.split("RUN")[:-1])
test = "RUN".join(test.split("RUN")[:-1])
# Remove comments.
true = [t for t in true.splitlines() if not t.startswith("#")]
test = [t for t in test.splitlines() if not t.startswith("#")]
assert true == test
def test_generate_from_json(capsys, tmpdir):
import json
cmd = "generate -b debian:stretch -p apt --c3d version=1.0.0"
main(cmd.split())
true, _ = capsys.readouterr()
specs = {
'check_urls': True,
'generation_timestamp': '2017-08-31 21:49:04',
'instructions': [['base', 'debian:stretch'],
['c3d', {
'version': '1.0.0'
}]],
'neurodocker_version': '0.2.0-18-g9227b17',
'pkg_manager': 'apt'
}
str_specs = json.dumps(specs)
filepath = tmpdir.join("specs.json")
filepath.write(str_specs)
gen_cmd = "generate --file {}".format(filepath)
main(gen_cmd.split())
test, _ = capsys.readouterr()
# These indices chop off the header (with timestamp) and the layer that
# saves to JSON (with timestamp).
sl = slice(8, -19)
assert true.split('\n')[sl] == test.split('\n')[sl]
def test_generate():
args = ("generate -b ubuntu:17.04 -p apt"
" --afni version=latest"
" --ants version=2.2.0"
" --freesurfer version=6.0.0"
" --fsl version=5.0.10"
" --user=neuro"
" --miniconda env_name=neuro python_version=3.6"
" --user=root"
" --mrtrix3"
" --neurodebian os_codename=zesty download_server=usa-nh"
" --spm version=12 matlab_version=R2017a"
" --no-check-urls"
" --expose 1234 9000"
" --copy relpath/to/file.txt /tmp/file.txt"
" --add relpath/to/file2.txt /tmp/file2.txt"
" --workdir /home"
" --install git"
" --user=neuro")
main(args.split())
with pytest.raises(SystemExit):
args = "-b ubuntu"
main(args.split())
with pytest.raises(SystemExit):
args = "-p apt"
main(args.split())
with pytest.raises(SystemExit):
main()
args = "generate -b ubuntu -p apt --ants option=value"
with pytest.raises(ValueError):
main(args.split())
def test_generate_save(tmpdir):
outfile = tmpdir.join("test.txt")
args = ['generate', '-b', 'ubuntu:17.04', '-p', 'apt', '--mrtrix3',
'use_binaries=false', '--no-print-df', '-o', outfile.strpath,
'--no-check-urls']
main(args)
assert outfile.read(), "saved Dockerfile is empty"
assert "git clone https://github.com/MRtrix3/mrtrix3.git" in outfile.read()
def test_generate_no_print(capsys):
args = ['generate', '-b', 'ubuntu:17.04', '-p', 'apt', '--no-check-urls']
main(args)
out, _ = capsys.readouterr()
assert "FROM" in out and "RUN" in out
args.append('--no-print-df')
main(args)
out, _ = capsys.readouterr()
assert not out
def test_generate():
args = ("generate docker -b ubuntu:17.04 -p apt"
" --arg FOO=BAR BAZ"
" --ndfreeze date=20180312"
" --afni version=latest method=source"
" --ants version=2.2.0 method=source"
" --freesurfer version=6.0.0"
" --fsl version=5.0.10"
" --user=neuro"
" --miniconda create_env=neuro conda_install=python=3.6.2"
" --user=root"
" --mrtrix3 version=3.0_RC3"
" --neurodebian os_codename=zesty server=usa-nh"
" --spm12 version=r7219 matlab_version=R2017a"
" --expose 1234 9000"
" --volume /var /usr/bin"
" --label FOO=BAR BAZ=CAT"
" --copy relpath/to/file.txt /tmp/file.txt"
" --add relpath/to/file2.txt /tmp/file2.txt"
" --cmd '--arg1' '--arg2'"
" --workdir /home"
" --install git"
" --user=neuro")
main(args.split())
with pytest.raises(SystemExit):
args = "-b ubuntu"
main(args.split())
with pytest.raises(SystemExit):
args = "-p apt"
main(args.split())
with pytest.raises(SystemExit):
main()
def test_generate_from_json_stdin(capsys, monkeypatch):
specs = {
"instructions": [["base", "debian:stretch"], ["install", ["git", "vim"]]],
"pkg_manager": "apt",
}
monkeypatch.setattr("sys.stdin", io.StringIO(json.dumps(specs)))
main("generate docker -".split())
test, _ = capsys.readouterr()
true_cmd = "generate docker -b debian:stretch -p apt --install git vim"
main(true_cmd.split())
true, _ = capsys.readouterr()
# Remove last RUN instruction (it contains saving to JSON and order is not guaranteed).
true = "RUN".join(true.split("RUN")[:-1])
test = "RUN".join(test.split("RUN")[:-1])
# Remove comments.
true = [t for t in true.splitlines() if not t.startswith("#")]
test = [t for t in test.splitlines() if not t.startswith("#")]
assert true == test
def test_generate_from_json_stdin(capsys, monkeypatch):
specs = {
'instructions': [['base', 'debian:stretch'],
['install', ['git', 'vim']]],
'pkg_manager': 'apt',
}
monkeypatch.setattr('sys.stdin', io.StringIO(json.dumps(specs)))
main("generate docker -".split())
test, _ = capsys.readouterr()
true_cmd = "generate docker -b debian:stretch -p apt --install git vim"
main(true_cmd.split())
true, _ = capsys.readouterr()
# Remove last RUN instruction (it contains saving to JSON and order is not guaranteed).
true = "RUN".join(true.split("RUN")[:-1])
test = "RUN".join(test.split("RUN")[:-1])
# Remove comments.
true = [t for t in true.splitlines() if not t.startswith('#')]
test = [t for t in test.splitlines() if not t.startswith('#')]
assert true == test
def test_dockerfile_opts(capsys):
args = "generate -b ubuntu:17.04 -p apt --no-check-urls {}"
main(args.format('--user=neuro').split())
out, _ = capsys.readouterr()
assert "USER neuro" in out
main(args.format('--env KEY=VAL KEY2=VAL').split())
out, _ = capsys.readouterr()
assert 'ENV KEY="VAL" \\' in out
assert ' KEY2="VAL"' in out
main(args.format('--expose 1230 1231').split())
out, _ = capsys.readouterr()
assert "EXPOSE 1230 1231" in out
def test_generate_opts(capsys):
args = "generate docker -b ubuntu:17.04 -p apt {}"
main(args.format('--user=neuro').split())
out, _ = capsys.readouterr()
assert "USER neuro" in out
main(args.format('--add path/to/file.txt /tmp/file.txt').split())
out, _ = capsys.readouterr()
assert 'ADD ["path/to/file.txt", "/tmp/file.txt"]' in out
main(args.format('--copy path/to/file.txt /tmp/file.txt').split())
out, _ = capsys.readouterr()
assert 'COPY ["path/to/file.txt", "/tmp/file.txt"]' in out
main(args.format('--env KEY=VAL KEY2=VAL').split())
out, _ = capsys.readouterr()
assert (('ENV KEY="VAL" \\' in out and 'KEY="VAL"' in out)
or ('ENV KEY2="VAL" \\' in out and 'KEY="VAL"'))
main(args.format('--expose 1230 1231').split())
out, _ = capsys.readouterr()
assert "EXPOSE 1230 1231" in out
main(args.format('--workdir /home').split())
out, _ = capsys.readouterr()
assert "WORKDIR /home" in out
main(args.format('--install vi').split())
out, _ = capsys.readouterr()
assert "vi" in out
# Test that nd_freeze comes before the header.
main(args.format('--ndfreeze date=20180312').split())
out, _ = capsys.readouterr()
assert out.find("nd_freeze") < out.find("ND_ENTRYPOINT")
def test_generate_opts(capsys):
args = "generate docker -b ubuntu:17.04 -p apt {}"
main(args.format("--user=neuro").split())
out, _ = capsys.readouterr()
assert "USER neuro" in out
main(args.format("--add path/to/file.txt /tmp/file.txt").split())
out, _ = capsys.readouterr()
assert 'ADD ["path/to/file.txt", "/tmp/file.txt"]' in out
main(args.format("--copy path/to/file.txt /tmp/file.txt").split())
out, _ = capsys.readouterr()
assert 'COPY ["path/to/file.txt", "/tmp/file.txt"]' in out
main(args.format("--env KEY=VAL KEY2=VAL").split())
out, _ = capsys.readouterr()
assert ('ENV KEY="VAL" \\' in out
and 'KEY="VAL"' in out) or ('ENV KEY2="VAL" \\' in out
and 'KEY="VAL"')
main(args.format("--expose 1230 1231").split())
out, _ = capsys.readouterr()
assert "EXPOSE 1230 1231" in out
main(args.format("--workdir /home").split())
out, _ = capsys.readouterr()
assert "WORKDIR /home" in out
main(args.format("--install vi").split())
out, _ = capsys.readouterr()
assert "vi" in out
# Test that nd_freeze comes before the header.
main(args.format("--ndfreeze date=20180312").split())
out, _ = capsys.readouterr()
assert out.find("nd_freeze") < out.find("ND_ENTRYPOINT")
with mock.patch("neurodocker.interfaces.Miniconda._installed", False):
main(
args.format("--miniconda create_env=newenv version=4.7.10 "
"conda_install=python=3.7").split())
out, _ = capsys.readouterr()
assert (
"https://repo.continuum.io/miniconda/Miniconda3-4.7.10-Linux-x86_64.sh"
in out)
def test_generate_opts(capsys):
args = "generate -b ubuntu:17.04 -p apt --no-check-urls {}"
main(args.format('--user=neuro').split())
out, _ = capsys.readouterr()
assert "USER neuro" in out
main(args.format('--add path/to/file.txt /tmp/file.txt').split())
out, _ = capsys.readouterr()
assert 'ADD ["path/to/file.txt", "/tmp/file.txt"]' in out
main(args.format('--copy path/to/file.txt /tmp/file.txt').split())
out, _ = capsys.readouterr()
assert 'COPY ["path/to/file.txt", "/tmp/file.txt"]' in out
main(args.format('--env KEY=VAL KEY2=VAL').split())
out, _ = capsys.readouterr()
assert 'ENV KEY="VAL" \\' in out
assert ' KEY2="VAL"' in out
main(args.format('--expose 1230 1231').split())
out, _ = capsys.readouterr()
assert "EXPOSE 1230 1231" in out
main(args.format('--workdir /home').split())
out, _ = capsys.readouterr()
assert "WORKDIR /home" in out
main(args.format('--install vi').split())
out, _ = capsys.readouterr()
assert "vi" in out
main(args.format('--instruction RUNecho').split())
out, _ = capsys.readouterr()
assert "RUNecho" in out
def _get_dockerfile_from_stdout(args):
f = io.StringIO()
with redirect_stdout(f):
main(args)
return f.getvalue()
