def test_show_env_internet_free():
"""
test the show-env ggd call can run an internet free context
(show-env)
"""
## 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
args = Namespace(command='show-env', pattern=None)
dir_env_var_name = "$ggd_hg19_gaps_ucsc_v1_dir"
file_env_var_name = "$ggd_hg19_gaps_ucsc_v1_file"
## Test show_env
temp_stdout = StringIO()
with redirect_stdout(temp_stdout):
show_env.show_env((), args)
output = temp_stdout.getvalue().strip()
assert (dir_env_var_name in output)
assert (file_env_var_name in output)
def test_show_env_no_envvars():
## uninstalled hg19_gaps() testing
uninstall_hg19_gaps_v1()
parser = ()
args = Namespace(command='show-env', pattern=None)
env_var_name = "$ggd_hg19_gaps_v1"
## Test a normal run
temp_stdout = StringIO()
with redirect_stdout(temp_stdout):
show_env.show_env(parser,args)
output = temp_stdout.getvalue().strip()
assert (env_var_name not in output)
def test_show_env_with_pattern():
"""
Test that adding the pattern parameter to show-env properly filters the results
"""
env_var_name = "$ggd_hg19_gaps_v1"
parser = ()
## Good pattern should have "ggd_hg19_gaps" in the results
args = Namespace(command='show-env', pattern="gaps")
temp_stdout = StringIO()
with redirect_stdout(temp_stdout):
show_env.show_env(parser,args)
output = temp_stdout.getvalue().strip()
assert (env_var_name in output)
## Bad pattern should return "No matching recipe variables found for this environment"
args = Namespace(command='show-env', pattern="NONE")
temp_stdout = StringIO()
with redirect_stdout(temp_stdout):
show_env.show_env(parser,args)
output = temp_stdout.getvalue().strip()
assert (env_var_name not in output)
assert ("No matching recipe variables found for this environment" in output)
## invalid pattern should exit
args = Namespace(command='show-env', pattern=")()(")
with pytest.raises(SystemExit) as pytest_wrapped_e:
show_env.show_env(parser,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
def test_show_env_goodrun():
"""
Test that show_env functoin properly provides the environment variable for an installed package
"""
## Install hg19_gaps()
try:
install_hg19_gaps_v1()
except:
pass
parser = ()
args = Namespace(command='show-env', pattern=None)
env_var_name = "$ggd_hg19_gaps_v1"
## Test a normal run
temp_stdout = StringIO()
with redirect_stdout(temp_stdout):
show_env.show_env(parser,args)
output = temp_stdout.getvalue().strip()
assert (env_var_name in output)
## Test active environment variables
sp.check_call(["activate", "base"])
temp_stdout = StringIO()
with redirect_stdout(temp_stdout):
show_env.show_env(parser,args)
output = temp_stdout.getvalue().strip()
newout = ""
active = False
for line in output.strip().split("\n"):
if "Active environment variables:" in line:
active = True
if "Inactive or out-of-date environment variables:" in line:
active = False
if active:
newout += line
assert (env_var_name in output)
def test_check_for_installation():
"""
Test the check_for_installation function to check if the ggd package is installed using the ggd file handling information
"""
pytest_enable_socket()
## Test a not installed ggd recipe
ggd_recipe = "grch37-reference-genome-1000g-v1"
ggd_channel = "genomics"
jdict = uninstall.get_channeldata(ggd_recipe,ggd_channel)
temp_stdout = StringIO()
with redirect_stdout(temp_stdout):
uninstall.check_for_installation([ggd_recipe],jdict)
output = temp_stdout.getvalue().strip()
assert "{} is not in the ggd recipe storage".format(ggd_recipe) in output
## Test installed package
ggd_recipe = "hg19-gaps-ucsc-v1"
ggd_channel = "genomics"
jdict = uninstall.get_channeldata(ggd_recipe,ggd_channel)
temp_stdout = StringIO()
with redirect_stdout(temp_stdout):
uninstall.check_for_installation([ggd_recipe],jdict)
output = temp_stdout.getvalue().strip()
assert "Removing {} version {} file(s) from ggd recipe storage".format(ggd_recipe,jdict["packages"][ggd_recipe]["version"]) in output
## Update local metadata
utils.update_installed_pkg_metadata(prefix=conda_root())
args = Namespace(command="show-env", pattern=None)
temp_stdout = StringIO()
with redirect_stdout(temp_stdout):
show_env.show_env((),args)
output = temp_stdout.getvalue().strip()
assert "$ggd_hg19_gaps_v1_file" not in output
assert "$ggd_hg19_gaps_v1_dir" not in output
def test_check_for_installation_different_prefix():
"""
Test that check_for_installation when a prefix is provided
"""
## Test installed package
ggd_recipe = "hg19-pfam-domains-ucsc-v1"
ggd_channel = "genomics"
### Uninstall ggd recipe
uninstall_args = Namespace(channel='genomics', command='uninstall', name=ggd_recipe)
try:
uninstall.uninstall((),uninstall_args)
except:
pass
### Install ggd recipe
install_args = Namespace(channel='genomics', command='install', debug=False, name=[ggd_recipe], file=[], prefix = conda_root())
try:
install.install((), install_args)
except:
pass
## jdict and info
jdict = uninstall.get_channeldata(ggd_recipe,ggd_channel)
species = jdict["packages"][ggd_recipe]["identifiers"]["species"]
build = jdict["packages"][ggd_recipe]["identifiers"]["genome-build"]
version = jdict["packages"][ggd_recipe]["version"]
## Test the package in "conda_root" exists
args = Namespace(command='list', pattern=None, prefix=conda_root())
temp_stdout = StringIO()
with redirect_stdout(temp_stdout):
list_installed_pkgs.list_installed_packages((), args)
output = temp_stdout.getvalue().strip()
assert ggd_recipe in output
path = os.path.join(conda_root(),"share","ggd",species,build,ggd_recipe,version,"*")
files = glob.glob(path)
assert len(files) == 2
## Create temp envi
temp_env = os.path.join(utils.conda_root(), "envs", "temp_env10")
### Remove temp env if it already exists
sp.check_output(["conda", "env", "remove", "--name", "temp_env10"])
try:
shutil.rmtree(temp_env)
except Exception:
pass
### Create conda environmnet
sp.check_output(["conda", "create", "--name", "temp_env10"])
## Test prefix
### Install ggd recipe using conda into temp_env
install_args = Namespace(channel='genomics', command='install', debug=False, name=[ggd_recipe],file=[], prefix = temp_env)
assert install.install((), install_args) == True
## Test that the files are removed
temp_stdout = StringIO()
with redirect_stdout(temp_stdout):
uninstall.check_for_installation([ggd_recipe],jdict,prefix=temp_env)
output = temp_stdout.getvalue().strip()
assert "Removing {} version {} file(s) from ggd recipe storage".format(ggd_recipe,jdict["packages"][ggd_recipe]["version"]) in output
## Update local metadata
utils.update_installed_pkg_metadata(prefix=temp_env)
## Test the package was removed from the ggd info list
args = Namespace(command='list', pattern=None, prefix=temp_env)
temp_stdout = StringIO()
with redirect_stdout(temp_stdout):
list_installed_pkgs.list_installed_packages((), args)
output = temp_stdout.getvalue().strip()
assert ggd_recipe not in output
path = os.path.join(temp_env,"share","ggd",species,build,ggd_recipe,version,"*")
files = glob.glob(path)
assert len(files) == 0
## Test the package in "conda_root" was not removed
args = Namespace(command='list', pattern=None, prefix=conda_root())
temp_stdout = StringIO()
with redirect_stdout(temp_stdout):
list_installed_pkgs.list_installed_packages((), args)
output = temp_stdout.getvalue().strip()
assert ggd_recipe in output
path = os.path.join(conda_root(),"share","ggd",species,build,ggd_recipe,version,"*")
files = glob.glob(path)
assert len(files) == 2
## Remove prefix
sp.check_output(["conda", "env", "remove", "--name", "temp_env10"])
try:
shutil.rmtree(temp_env)
except Exception:
pass
assert os.path.exists(temp_env) == False
## Test the current environment (conda_root)
temp_stdout = StringIO()
with redirect_stdout(temp_stdout):
uninstall.check_for_installation([ggd_recipe],jdict,prefix=utils.conda_root())
output = temp_stdout.getvalue().strip()
assert "Removing {} version {} file(s) from ggd recipe storage".format(ggd_recipe,jdict["packages"][ggd_recipe]["version"]) in output
## Update local metadata
utils.update_installed_pkg_metadata(prefix=conda_root())
## Test environment variables removed
args = Namespace(command="show-env", pattern=None)
temp_stdout = StringIO()
with redirect_stdout(temp_stdout):
show_env.show_env((),args)
output = temp_stdout.getvalue().strip()
assert "hg19_pfam_domains_ucsc_v1_file" not in output
assert "hg19_pfam_domains_ucsc_v1_dir" not in output
args = Namespace(command='list', pattern=None, prefix=conda_root())
temp_stdout = StringIO()
with redirect_stdout(temp_stdout):
list_installed_pkgs.list_installed_packages((), args)
output = temp_stdout.getvalue().strip()
assert ggd_recipe not in output
path = os.path.join(conda_root(),"share","ggd",species,build,ggd_recipe,version,"*")
files = glob.glob(path)
assert len(files) == 0