def test_get_similar_pkg_installed_by_conda():
"""
Test the get_similar_pkg_installed_by_conda function
"""
pytest_enable_socket()
## Test a non similar package name
not_installed = "Not_an_installed_package"
assert uninstall.get_similar_pkg_installed_by_conda(not_installed) == ""
installed_requirement = "request"
output = uninstall.get_similar_pkg_installed_by_conda(installed_requirement)
assert "requests" in output
assert "pyyaml" not in output
installed_requirement = "yaml"
output = uninstall.get_similar_pkg_installed_by_conda(installed_requirement)
assert "pyyaml" in output
assert "oyaml" in output
assert "requests" not in output
## Make sure hg19-gaps-v1 is installed
ggd_recipe = "hg19-gaps-ucsc-v1"
list_files_args = Namespace(channel='genomics', command='list-files', genome_build=None, name=ggd_recipe, pattern=None, prefix=None, species=None, version=None)
try:
list_files.list_files((),list_files_args)
except SystemExit as e:
if str(e) == "1": ## If exit code is 1, implying that there were not files found
install_hg19_gaps_ucsc_v1()
ggd_recipe = "hg19-gaps"
output = uninstall.get_similar_pkg_installed_by_conda(ggd_recipe)
assert "hg19-gaps-ucsc-v1" in output
def test_list_files_internet_free():
"""
test the list_files function in list-files in an internet free context
(list-files)
"""
## Install hg19-gaps
try:
pytest_enable_socket()
install_hg19_gaps_ucsc_v1()
except:
pass
## Check show-env in an internet free context
pytest_disable_socket()
### Check that there is no interent
assert utils.check_for_internet_connection() == False
## Test list-files
ggd_package = "hg19-gaps-ucsc-v1"
file1 = "{}.bed.gz".format(ggd_package)
file2 = "{}.bed.gz.tbi".format(ggd_package)
##Test that the correct file paths are returned
args = Namespace(channel='genomics',
command='list-files',
genome_build=None,
name=ggd_package,
pattern=None,
prefix=None,
species=None,
version=None)
temp_stdout = StringIO()
with redirect_stdout(temp_stdout):
list_files.list_files((), args)
output = str(temp_stdout.getvalue().strip())
assert re.search(file1 + "$", sorted(output.split("\n"))[0])
assert re.search(file2 + "$", sorted(output.split("\n"))[1])
assert len(output.split("\n")) == 2
##Test that the correct file paths are returned with the genome_build key set
args = Namespace(channel='genomics',
command='list-files',
genome_build="hg19",
name=ggd_package,
pattern=None,
prefix=None,
species=None,
version=None)
temp_stdout = StringIO()
with redirect_stdout(temp_stdout):
list_files.list_files((), args)
output = str(temp_stdout.getvalue().strip())
assert re.search(file1 + "$", sorted(output.split("\n"))[0])
assert re.search(file2 + "$", sorted(output.split("\n"))[1])
assert len(output.split("\n")) == 2
##Test that the correct file paths are returned with the species key set
args = Namespace(channel='genomics',
command='list-files',
genome_build=None,
name=ggd_package,
pattern=None,
prefix=None,
species="Homo_sapiens",
version=None)
temp_stdout = StringIO()
with redirect_stdout(temp_stdout):
list_files.list_files((), args)
output = str(temp_stdout.getvalue().strip())
assert re.search(file1 + "$", sorted(output.split("\n"))[0])
assert re.search(file2 + "$", sorted(output.split("\n"))[1])
assert len(output.split("\n")) == 2
##Test that the correct file paths are returned with version key set
args = Namespace(channel='genomics',
command='list-files',
genome_build=None,
name=ggd_package,
pattern=None,
prefix=None,
species=None,
version="1")
temp_stdout = StringIO()
with redirect_stdout(temp_stdout):
list_files.list_files((), args)
output = str(temp_stdout.getvalue().strip())
assert re.search(file1 + "$", sorted(output.split("\n"))[0])
assert re.search(file2 + "$", sorted(output.split("\n"))[1])
assert len(output.split("\n")) == 2
## Test that nothing is returned when a bad ggd package name is given
args = Namespace(channel='genomics',
command='list-files',
genome_build=None,
name="NOT_a_real_package_name",
pattern=None,
prefix=None,
species=None,
version=None)
with pytest.raises(SystemExit) as pytest_wrapped_e:
list_files.list_files((), args)
assert "SystemExit" in str(pytest_wrapped_e.exconly(
)) ## test that systemexit was raised by sys.exit()
assert pytest_wrapped_e.match("2") ## check that the exit code is 1
##Test that the function exits if a bad genome build is given
args = Namespace(channel='genomics',
command='list-files',
genome_build="Bad_Build",
name=ggd_package,
pattern=None,
species=None,
prefix=None,
version=None)
with pytest.raises(SystemExit) as pytest_wrapped_e:
list_files.list_files((), args)
assert "SystemExit" in str(pytest_wrapped_e.exconly(
)) ## test that systemexit was raised by sys.exit()
assert pytest_wrapped_e.match("3") ## check that the exit code is 1
##Test that the function exits if a bad species is given
args = Namespace(channel='genomics',
command='list-files',
genome_build=None,
name=ggd_package,
pattern=None,
prefix=None,
species="Mus_musculus",
version=None)
with pytest.raises(SystemExit) as pytest_wrapped_e:
list_files.list_files((), args)
assert "SystemExit" in str(pytest_wrapped_e.exconly(
)) ## test that systemexit was raised by sys.exit()
assert pytest_wrapped_e.match("3") ## check that the exit code is 1
##Test that the function exits if a bad version is given
args = Namespace(channel='genomics',
command='list-files',
genome_build=None,
name=ggd_package,
pattern=None,
prefix=None,
species=None,
version="99999")
with pytest.raises(SystemExit) as pytest_wrapped_e:
list_files.list_files((), args)
assert "SystemExit" in str(pytest_wrapped_e.exconly(
)) ## test that systemexit was raised by sys.exit()
assert pytest_wrapped_e.match("1") ## check that the exit code is 1
##Test that the function exits if a bad pattern is given
args = Namespace(channel='genomics',
command='list-files',
genome_build=None,
name=ggd_package,
pattern="BAD_PATTERN",
prefix=None,
species=None,
version=None)
with pytest.raises(SystemExit) as pytest_wrapped_e:
list_files.list_files((), args)
assert "SystemExit" in str(pytest_wrapped_e.exconly(
)) ## test that systemexit was raised by sys.exit()
assert pytest_wrapped_e.match("1") ## check that the exit code is 1
##Test that the function exits if a bad channel is given
args = Namespace(channel='bad-channel',
command='list-files',
genome_build=None,
name=ggd_package,
pattern=None,
prefix=None,
species=None,
version=None)
with pytest.raises(SystemExit) as pytest_wrapped_e:
list_files.list_files((), args)
assert "SystemExit" in str(pytest_wrapped_e.exconly(
)) ## test that systemexit was raised by sys.exit()
assert pytest_wrapped_e.match("2") ## check that the exit code is 1
def test_list_file_with_prefix_internet_free():
"""
test the --prefix flag of list-files in a internet free context
(list-files --prefix)
"""
## enable socket
pytest_enable_socket()
## Temp conda environment
temp_env = os.path.join(utils.conda_root(), "envs",
"temp_env_internet_free")
### Remove temp env if it already exists
sp.check_output(
["conda", "env", "remove", "--name", "temp_env_internet_free"])
try:
shutil.rmtree(temp_env)
except Exception:
pass
## Create conda environmnet
sp.check_output(["conda", "create", "--name", "temp_env_internet_free"])
## Install ggd recipe using conda into temp_env
ggd_package = "hg19-pfam-domains-ucsc-v1"
install_args = Namespace(channel='genomics',
command='install',
debug=False,
name=[ggd_package],
file=[],
prefix=temp_env,
id=None)
assert install.install((), install_args) == True
## Check show-env in an internet free context
pytest_disable_socket()
### Check that there is no interent
assert utils.check_for_internet_connection() == False
## Test the list-files method can access info from the files in a different prefix
args = Namespace(channel='genomics',
command='list-files',
genome_build=None,
name=ggd_package,
pattern=None,
prefix=temp_env,
species=None,
version=None)
file1 = "{}.bed12.bed.gz".format(ggd_package)
file2 = "{}.bed12.bed.gz.tbi".format(ggd_package)
temp_stdout = StringIO()
with redirect_stdout(temp_stdout):
list_files.list_files((), args)
output = str(temp_stdout.getvalue().strip())
assert file1 in output
assert file2 in output
assert temp_env in output
assert len(output.split("\n")) == 2
## Check output has correct file path
### Enable socket
pytest_enable_socket()
jdict = install.check_ggd_recipe(ggd_package, "genomics")
species = jdict["packages"][ggd_package]["identifiers"]["species"]
build = jdict["packages"][ggd_package]["identifiers"]["genome-build"]
version = jdict["packages"][ggd_package]["version"]
assert os.path.join(temp_env, "share", "ggd", species, build, ggd_package,
version, file1) in output
assert os.path.join(temp_env, "share", "ggd", species, build, ggd_package,
version, file2) in output
assert os.path.exists(
os.path.join(temp_env, "share", "ggd", species, build, ggd_package,
version, file1))
assert os.path.exists(
os.path.join(temp_env, "share", "ggd", species, build, ggd_package,
version, file2))
## Remove temp env
sp.check_output(
["conda", "env", "remove", "--name", "temp_env_internet_free"])
try:
shutil.rmtree(temp_env)
except Exception:
pass
assert os.path.exists(temp_env) == False
def test_list_files():
"""
Test the main method of list-files
"""
ggd_package = "hg19-gaps-v1"
file1 = "{}.bed.gz".format(ggd_package)
file2 = "{}.bed.gz.tbi".format(ggd_package)
##Test that the correct file paths are returned
args = Namespace(channel='genomics', command='list-files', genome_build=None, name=ggd_package, pattern=None, species=None, version=None)
temp_stdout = StringIO()
with redirect_stdout(temp_stdout):
list_files.list_files((),args)
output = str(temp_stdout.getvalue().strip())
assert re.search(file1+"$", sorted(output.split("\n"))[0])
assert re.search(file2+"$", sorted(output.split("\n"))[1])
assert len(output.split("\n")) == 2
##Test that the correct file paths are returned with the genome_build key set
args = Namespace(channel='genomics', command='list-files', genome_build="hg19", name=ggd_package, pattern=None, species=None, version=None)
temp_stdout = StringIO()
with redirect_stdout(temp_stdout):
list_files.list_files((),args)
output = str(temp_stdout.getvalue().strip())
assert re.search(file1+"$", sorted(output.split("\n"))[0])
assert re.search(file2+"$", sorted(output.split("\n"))[1])
assert len(output.split("\n")) == 2
##Test that the correct file paths are returned with the species key set
args = Namespace(channel='genomics', command='list-files', genome_build=None, name=ggd_package, pattern=None, species="Homo_sapiens", version=None)
temp_stdout = StringIO()
with redirect_stdout(temp_stdout):
list_files.list_files((),args)
output = str(temp_stdout.getvalue().strip())
assert re.search(file1+"$", sorted(output.split("\n"))[0])
assert re.search(file2+"$", sorted(output.split("\n"))[1])
assert len(output.split("\n")) == 2
##Test that the correct file paths are returned with version key set
args = Namespace(channel='genomics', command='list-files', genome_build=None, name=ggd_package, pattern=None, species=None, version="1")
temp_stdout = StringIO()
with redirect_stdout(temp_stdout):
list_files.list_files((),args)
output = str(temp_stdout.getvalue().strip())
assert re.search(file1+"$", sorted(output.split("\n"))[0])
assert re.search(file2+"$", sorted(output.split("\n"))[1])
assert len(output.split("\n")) == 2
##Test that the correct file paths are returned with the patterns key set key set
args = Namespace(channel='genomics', command='list-files', genome_build=None, name=ggd_package, pattern=file1, species=None, version=None)
temp_stdout = StringIO()
with redirect_stdout(temp_stdout):
list_files.list_files((),args)
output = str(temp_stdout.getvalue().strip())
assert re.search(file1+"$", output)
assert re.search(file2+"$", output) == None
assert len(output.split("\n")) == 1
args = Namespace(channel='genomics', command='list-files', genome_build=None, name=ggd_package, pattern=file2, species=None, version=None)
temp_stdout = StringIO()
with redirect_stdout(temp_stdout):
list_files.list_files((),args)
output = str(temp_stdout.getvalue().strip())
assert re.search(file1+"$", output) == None
assert re.search(file2+"$", output)
assert len(output.split("\n")) == 1
## Test that nothing is returned when a bad ggd package name is given
args = Namespace(channel='genomics', command='list-files', genome_build=None, name="NOT_a_real_package_name", pattern=None, species=None, version=None)
with pytest.raises(SystemExit) as pytest_wrapped_e:
list_files.list_files((), args)
assert "SystemExit" in str(pytest_wrapped_e.exconly()) ## test that systemexit was raised by sys.exit()
assert pytest_wrapped_e.match("1") ## check that the exit code is 1
##Test that the function exits if a bad genome build is given
args = Namespace(channel='genomics', command='list-files', genome_build="Bad_Build", name=ggd_package, pattern=None, species=None, version=None)
with pytest.raises(SystemExit) as pytest_wrapped_e:
list_files.list_files((), args)
assert "SystemExit" in str(pytest_wrapped_e.exconly()) ## test that systemexit was raised by sys.exit()
assert pytest_wrapped_e.match("1") ## check that the exit code is 1
##Test that the function exits if a bad species is given
args = Namespace(channel='genomics', command='list-files', genome_build=None, name=ggd_package, pattern=None, species="Mus_musculus", version=None)
with pytest.raises(SystemExit) as pytest_wrapped_e:
list_files.list_files((), args)
assert "SystemExit" in str(pytest_wrapped_e.exconly()) ## test that systemexit was raised by sys.exit()
assert pytest_wrapped_e.match("1") ## check that the exit code is 1
##Test that the function exits if a bad version is given
args = Namespace(channel='genomics', command='list-files', genome_build=None, name=ggd_package, pattern=None, species=None, version="99999")
with pytest.raises(SystemExit) as pytest_wrapped_e:
list_files.list_files((), args)
assert "SystemExit" in str(pytest_wrapped_e.exconly()) ## test that systemexit was raised by sys.exit()
assert pytest_wrapped_e.match("1") ## check that the exit code is 1
##Test that the function exits if a bad pattern is given
args = Namespace(channel='genomics', command='list-files', genome_build=None, name=ggd_package, pattern="BAD_PATTERN", species=None, version=None)
with pytest.raises(SystemExit) as pytest_wrapped_e:
list_files.list_files((), args)
assert "SystemExit" in str(pytest_wrapped_e.exconly()) ## test that systemexit was raised by sys.exit()
assert pytest_wrapped_e.match("1") ## check that the exit code is 1