def test_get_channeldata():
"""
Test the get_channeldata method properly finds a good ggd package and handles a bad ggd package
"""
pytest_enable_socket()
## Uninstall hg19-gaps-v1
try:
uninstall_hg19_gaps_ucsc_v1()
except:
pass
## Install hg19-gaps-v1
try:
install_hg19_gaps_ucsc_v1()
except:
pass
## Test normal run
ggd_recipe = "hg19-gaps-ucsc-v1"
ggd_channel = "genomics"
jdict = uninstall.get_channeldata([ggd_recipe],ggd_channel)
assert ggd_recipe in jdict["packages"].keys()
## Similar installed package
ggd_recipe = "hg19-gaps"
ggd_channel = "genomics"
temp_stdout = StringIO()
with redirect_stdout(temp_stdout):
uninstall.get_channeldata([ggd_recipe],ggd_channel)
output = temp_stdout.getvalue().strip()
assert "Packages installed on your system that are similar include:" in output
assert "hg19-gaps-ucsc-v1" in output
assert uninstall.get_channeldata([ggd_recipe],ggd_channel) == False
## Test bad recipe
bad_recipe = "BadRecipe"
ggd_channel = "genomics"
temp_stdout = StringIO()
with redirect_stdout(temp_stdout):
uninstall.get_channeldata([bad_recipe],ggd_channel)
output = temp_stdout.getvalue().strip()
print("OUTPUT: '''", output, "''''")
assert "{} is not in the ggd-{} channel".format(bad_recipe,ggd_channel)
assert "Unable to find any package similar to the package entered. Use 'ggd search' or 'conda find' to identify the right package" in output
assert "This package may not be installed on your system" in output
assert uninstall.get_channeldata([bad_recipe],ggd_channel) == False
## Test bad channel
ggd_recipe = "hg19-gaps-ucsc-v1"
bad_channel = "BadChannel"
temp_stdout = StringIO()
with redirect_stdout(temp_stdout):
uninstall.get_channeldata([ggd_recipe],bad_channel)
output = temp_stdout.getvalue().strip()
assert "The 'BadChannel' channel is not a ggd conda channel" in output
def test_get_channeldata():
"""
Test the get_channeldata method properly finds a good ggd package and handles a bad ggd package
"""
pytest_enable_socket()
## Uninstall hg19-gaps-v1
try:
uninstall_hg19_gaps_ucsc_v1()
except:
pass
## Install hg19-gaps-v1
try:
install_hg19_gaps_ucsc_v1()
except:
pass
## Test normal run
ggd_recipe = "hg19-gaps-ucsc-v1"
ggd_channel = "genomics"
jdict = uninstall.get_channeldata(ggd_recipe,ggd_channel)
assert ggd_recipe in jdict["packages"].keys()
## Similar installed package
ggd_recipe = "hg19-gaps"
ggd_channel = "genomics"
temp_stdout = StringIO()
with redirect_stdout(temp_stdout):
uninstall.get_channeldata(ggd_recipe,ggd_channel)
output = temp_stdout.getvalue().strip()
assert "Packages installed on your system that are similar include:" in output
assert "hg19-gaps-ucsc-v1" in output
assert uninstall.get_channeldata(ggd_recipe,ggd_channel) == False
## Test bad recipe
bad_recipe = "BadRecipe"
ggd_channel = "genomics"
with redirect_stdout(temp_stdout):
uninstall.get_channeldata(bad_recipe,ggd_channel)
output = temp_stdout.getvalue().strip()
assert "Packages installed on your system that are similar include:" in output
assert "{} is not in the ggd-{} channel".format(bad_recipe,ggd_channel)
assert "Unable to find any package similar to the package entered. Use 'ggd search' or 'conda find' to identify the right package" in output
assert "This package may not be installed on your system" in output
assert uninstall.get_channeldata(bad_recipe,ggd_channel) == False
## Test bad channel
ggd_recipe = "hg19-gaps-ucsc-v1"
bad_channel = "BadChannel"
with pytest.raises(SystemExit) as pytest_wrapped_e:
uninstall.get_channeldata(ggd_recipe,bad_channel) ## Exit due to bad url from ggd.search
assert "SystemExit" in str(pytest_wrapped_e.exconly()) ## test that SystemExit was raised by sys.exit()
assert pytest_wrapped_e.match("The 'BadChannel' channel is not a ggd conda channel") ## Check that the exit code is 1
def test_remove_from_condaroot():
"""
Test that the remove_from_condaroot function properly removes installed ggd packages from the conda root
"""
## install hg19-gaps-v1
install_hg19_gaps_v1()
ggd_recipe = "hg19-gaps-v1"
ggd_channel = "genomics"
version = uninstall.get_channeldata(ggd_recipe,ggd_channel)["packages"][ggd_recipe]["version"]
## Check that the files are in the conda root
conda_root = utils.conda_root()
check_list = sp.check_output(['find', conda_root, '-name', ggd_recipe+"-"+str(version)+"*"]).decode('utf8').strip().split("\n")
for f in check_list:
if conda_root in f:
if conda_root+"/envs/" not in f:
assert ggd_recipe+"-"+str(version) in f
## remove ggd recipe files from conda root
uninstall.remove_from_condaroot(ggd_recipe,version)
## Check that the files were removed
conda_root = utils.conda_root()
check_list = sp.check_output(['find', conda_root, '-name', ggd_recipe+"-"+str(version)+"*"]).decode('utf8').strip().split("\n")
for f in check_list:
if conda_root in f:
if conda_root+"/envs/" not in f:
assert ggd_recipe+"-"+str(version) not in f
## Finish uninstalling hg19-gaps-v1
uninstall_hg19_gaps_v1()
def test_get_channeldata():
"""
Test the get_channeldata method properly finds a good ggd package and handles a bad ggd package
"""
## Uninstall hg19-gaps-v1
try:
uninstall_hg19_gaps_v1()
except:
pass
## Install hg19-gaps-v1
try:
install_hg19_gaps_v1()
except:
pass
## Test normal run
ggd_recipe = "hg19-gaps-v1"
ggd_channel = "genomics"
jdict = uninstall.get_channeldata(ggd_recipe,ggd_channel)
assert ggd_recipe in jdict["packages"].keys()
## Similar installed package
ggd_recipe = "hg19-gaps"
ggd_channel = "genomics"
temp_stdout = StringIO()
with redirect_stdout(temp_stdout):
uninstall.get_channeldata(ggd_recipe,ggd_channel)
output = temp_stdout.getvalue().strip()
assert "Packages installed on your system that are similar include:" in output
assert "hg19-gaps-v1" in output
assert uninstall.get_channeldata(ggd_recipe,ggd_channel) == False
## Test bad recipe
bad_recipe = "BadRecipe"
ggd_channel = "genomics"
with redirect_stdout(temp_stdout):
uninstall.get_channeldata(bad_recipe,ggd_channel)
output = temp_stdout.getvalue().strip()
assert "Packages installed on your system that are similar include:" in output
assert "{} is not in the ggd-{} channel".format(bad_recipe,ggd_channel)
assert "Unable to find any package similar to the package entered. Use 'ggd search' or 'conda find' to identify the right package" in output
assert "This package may not be installed on your system" in output
assert uninstall.get_channeldata(bad_recipe,ggd_channel) == False
## Test bad channel
ggd_recipe = "hg19-gaps-v1"
bad_channel = "BadChannel"
with pytest.raises(SystemExit) as pytest_wrapped_e:
uninstall.get_channeldata(ggd_recipe,bad_channel) ## Exit due to bad url from ggd.search
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_uninstall_internet_free():
"""
Test the uninstall method in an internet free context
(uninstall)
"""
## 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
## Check non-failure uninstall command
ggd_recipe = "hg19-gaps-ucsc-v1"
args = Namespace(channel='genomics',
command='uninstall',
names=[ggd_recipe])
assert uninstall.uninstall((), args) == True
#### Get jdict
ggd_channel = "genomics"
jdict = uninstall.get_channeldata([ggd_recipe], ggd_channel)
conda_root = utils.conda_root()
### Check that the files are not in the conda root
species = jdict["packages"][ggd_recipe]["identifiers"]["species"]
build = jdict["packages"][ggd_recipe]["identifiers"]["genome-build"]
version = jdict["packages"][ggd_recipe]["version"]
path = os.path.join(conda_root, "share", "ggd", species, build, ggd_recipe,
version)
check_list = sp.check_output([
"find", conda_root, "-name", ggd_recipe + "-" + str(version) + "*"
]).decode("utf8").strip().split("\n")
for f in check_list:
if conda_root in f:
if conda_root + "/envs/" not in path:
assert ggd_recipe + "-" + str(version) not in path
#### Check data files were removed
assert glob.glob(path) == []
try:
os.listdir(path)
assert False
except OSError as e:
if "No such file or directory" in str(e):
pass
else:
assert False
#### Check that the ggd package is no longer in the list of conda packages
output = sp.check_output(["conda", "list", ggd_recipe])
assert ggd_recipe not in str(output)
def test_uninstall():
"""
Test that a package is properly uninstalled using the main uninstall funciton
"""
## Test handling of a package not installed
ggd_recipe = "not-a-real-recipe"
args = Namespace(channel='genomics', command='uninstall', name=ggd_recipe)
with pytest.raises(SystemExit) as pytest_wrapped_e:
uninstall.uninstall((),args)
assert "SystemExit" in str(pytest_wrapped_e.exconly()) ## test that SystemExit was raised by sys.exit()
assert pytest_wrapped_e.match("") ## Check that the exit code is ""
## Test a good uninstall
#### Install hg19-gaps-v1
install_hg19_gaps_v1()
#### Check non-failure uninstall command
ggd_recipe = "hg19-gaps-v1"
args = Namespace(channel='genomics', command='uninstall', name=ggd_recipe)
assert uninstall.uninstall((),args) == True
#### Get jdict
ggd_channel = "genomics"
jdict = uninstall.get_channeldata(ggd_recipe,ggd_channel)
conda_root = utils.conda_root()
### Check that the files are not in the conda root
version = jdict["packages"][ggd_recipe]["version"]
check_list = sp.check_output(["find", conda_root, "-name", ggd_recipe+"-"+str(version)+"*"]).decode("utf8").strip().split("\n")
for f in check_list:
if conda_root in f:
if conda_root+"/envs/" not in path:
assert ggd_recipe+"-"+str(version) not in path
#### Check data files were removed
species = jdict["packages"][ggd_recipe]["identifiers"]["species"]
build = jdict["packages"][ggd_recipe]["identifiers"]["genome-build"]
version = jdict["packages"][ggd_recipe]["version"]
path = os.path.join(conda_root,"share","ggd",species,build,ggd_recipe,version)
assert glob.glob(path) == []
try:
os.listdir(path)
assert False
except OSError as e:
if "No such file or directory" in str(e):
pass
else:
assert False
#### Check that the ggd package is no longer in the list of conda packages
output = sp.check_output(["conda", "list", ggd_recipe])
assert ggd_recipe not in str(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
"""
## Test a not installed ggd recipe
ggd_recipe = "grch37-reference-genome-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-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
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_get_channeldata_internet_free():
"""
Test the get_channeldata function in uninstall in an internet free context
(uninstall)
"""
## 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 normal run
ggd_recipe = "hg19-gaps-ucsc-v1"
ggd_channel = "genomics"
jdict = uninstall.get_channeldata([ggd_recipe], ggd_channel)
assert ggd_recipe in jdict["packages"].keys()
def test_uninstall():
"""
Test that a package is properly uninstalled using the main uninstall funciton
"""
pytest_enable_socket()
## Test handling of a package not installed
ggd_recipe = "not-a-real-recipe"
args = Namespace(channel='genomics', command='uninstall', name=ggd_recipe)
with pytest.raises(SystemExit) as pytest_wrapped_e:
uninstall.uninstall((),args)
assert "SystemExit" in str(pytest_wrapped_e.exconly()) ## test that SystemExit was raised by sys.exit()
assert pytest_wrapped_e.match("") ## Check that the exit code is ""
## Test a good uninstall
#### Install hg19-gaps-ucsc-v1
try:
install_hg19_gaps_ucsc_v1()
except:
pass
#### Check non-failure uninstall command
ggd_recipe = "hg19-gaps-ucsc-v1"
#### Get conda list pkg info
pkg_info = get_conda_package_list(utils.conda_root(),ggd_recipe)
assert ggd_recipe in pkg_info.keys()
#### Test uninstall
args = Namespace(channel='genomics', command='uninstall', name=ggd_recipe)
assert uninstall.uninstall((),args) == True
#### Get jdict
ggd_channel = "genomics"
jdict = uninstall.get_channeldata(ggd_recipe,ggd_channel)
conda_root = utils.conda_root()
### Check that the files are not in the conda root
version = jdict["packages"][ggd_recipe]["version"]
check_list = sp.check_output(["find", conda_root, "-name", ggd_recipe+"-"+str(version)+"*"]).decode("utf8").strip().split("\n")
for f in check_list:
if conda_root in f:
if conda_root+"/envs/" not in path:
assert ggd_recipe+"-"+str(version) not in path
#### Check data files were removed
species = jdict["packages"][ggd_recipe]["identifiers"]["species"]
build = jdict["packages"][ggd_recipe]["identifiers"]["genome-build"]
version = jdict["packages"][ggd_recipe]["version"]
path = os.path.join(conda_root,"share","ggd",species,build,ggd_recipe,version)
assert glob.glob(path) == []
try:
os.listdir(path)
assert False
except OSError as e:
if "No such file or directory" in str(e):
pass
else:
assert False
#### Check that the ggd package is no longer in the list of conda packages
output = sp.check_output(["conda", "list", ggd_recipe])
assert ggd_recipe not in str(output)
### Test that the ggd_info metadata is updated with ggd pkg
version = pkg_info[ggd_recipe]["version"]
build = pkg_info[ggd_recipe]["build"]
assert os.path.exists(os.path.join(utils.conda_root(),"share","ggd_info","noarch"))
assert os.path.exists(os.path.join(utils.conda_root(),"share","ggd_info","noarch",ggd_recipe+"-{}-{}.tar.bz2".format(version,build))) == False
assert os.path.exists(os.path.join(utils.conda_root(),"share","ggd_info","channeldata.json"))
with open(os.path.join(utils.conda_root(),"share","ggd_info","channeldata.json")) as jfile:
channeldata = json.load(jfile)
assert ggd_recipe not in channeldata["packages"]
def test_remove_from_condaroot():
"""
Test that the remove_from_condaroot function properly removes installed ggd packages from the provided prefix/conda environment
"""
pytest_enable_socket()
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 hg19-pfam-domains-ucsc-v1 into current environment
sp.check_call(["ggd", "install", ggd_recipe])
## Create temp envi
temp_env = os.path.join(utils.conda_root(), "envs", "temp_env11")
### Remove temp env if it already exists
sp.check_output(["conda", "env", "remove", "--name", "temp_env11"])
try:
shutil.rmtree(temp_env)
except Exception:
pass
### Create conda environmnet
sp.check_output(["conda", "create", "--name", "temp_env11"])
## 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
## 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"]
## Check that the files are in the conda root
conda_root = utils.conda_root()
check_list = sp.check_output(['find', conda_root, '-name', ggd_recipe+"-"+str(version)+"*"]).decode('utf8').strip().split("\n")
for f in check_list:
if conda_root in f:
if conda_root+"/envs/" not in f:
assert ggd_recipe+"-"+str(version) in f
## Check that the files are in the temp_env
check_list = sp.check_output(['find', temp_env, '-name', ggd_recipe+"-"+str(version)+"*"]).decode('utf8').strip().split("\n")
for f in check_list:
if temp_env in f:
if temp_env+"/envs/" not in f:
assert ggd_recipe+"-"+str(version) in f
## Remove recipe from prefix
uninstall.remove_from_condaroot(ggd_recipe,version,temp_env)
## Check that the files were removed from prefix
check_list = sp.check_output(['find', temp_env, '-name', ggd_recipe+"-"+str(version)+"*"]).decode('utf8').strip().split("\n")
for f in check_list:
if temp_env in f:
if temp_env+"/envs/" not in f:
assert ggd_recipe+"-"+str(version) not in f
## Check that the files were NOT removed from the conda root
conda_root = utils.conda_root()
check_list = sp.check_output(['find', conda_root, '-name', ggd_recipe+"-"+str(version)+"*"]).decode('utf8').strip().split("\n")
for f in check_list:
if conda_root in f:
if conda_root+"/envs/" not in f:
assert ggd_recipe+"-"+str(version) in f
## remove ggd recipe files from conda root
uninstall.remove_from_condaroot(ggd_recipe,version,conda_root)
## Check that the files were removed
conda_root = utils.conda_root()
check_list = sp.check_output(['find', conda_root, '-name', ggd_recipe+"-"+str(version)+"*"]).decode('utf8').strip().split("\n")
for f in check_list:
if conda_root in f:
if conda_root+"/envs/" not in f:
assert ggd_recipe+"-"+str(version) not in f
## Finish uninstalling recipe
args = Namespace(channel='genomics', command='uninstall', name=ggd_recipe)
uninstall.uninstall((),args)
## Remove temp_env
sp.check_output(["conda", "env", "remove", "--name", "temp_env11"])
try:
shutil.rmtree(temp_env)
except Exception:
pass
assert os.path.exists(temp_env) == False
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
def test_uninstall_multiple_package():
"""
Test that multiple packages are uninstalled using the main uninstall function
"""
recipes = ["hg19-chrom-mapping-ensembl2ucsc-ncbi-v1","hg19-chrom-mapping-refseq2ucsc-ncbi-v1"]
## Install ggd recipe
install_args = Namespace(channel='genomics', command='install', debug=False, name=recipes, file=[], prefix = conda_root(), id = None)
try:
install.install((), install_args)
except:
pass
#### Check that the recipe are installed by conda
pkg_info = get_conda_package_list(utils.conda_root())
for recipe in recipes:
assert recipe in pkg_info.keys()
#### Get jdict
ggd_channel = "genomics"
jdict = uninstall.get_channeldata(recipes,ggd_channel)
#### Check data files exists
for ggd_recipe in recipes:
species = jdict["packages"][ggd_recipe]["identifiers"]["species"]
build = jdict["packages"][ggd_recipe]["identifiers"]["genome-build"]
version = jdict["packages"][ggd_recipe]["version"]
final_files = jdict["packages"][ggd_recipe]["tags"]["final-files"]
path = os.path.join(conda_root(),"share","ggd",species,build,ggd_recipe,version,"*")
assert sorted(glob.glob(path)) == sorted([os.path.join(path.replace("*",""),x) for x in final_files])
#### Check that the ggd metadata channeldata file contains new recipes
for ggd_recipe in recipes:
version = pkg_info[ggd_recipe]["version"]
build = pkg_info[ggd_recipe]["build"]
assert os.path.exists(os.path.join(utils.conda_root(),"share","ggd_info","noarch"))
assert os.path.exists(os.path.join(utils.conda_root(),"share","ggd_info","noarch",ggd_recipe+"-{}-{}.tar.bz2".format(version,build)))
assert os.path.exists(os.path.join(utils.conda_root(),"share","ggd_info","channeldata.json"))
with open(os.path.join(utils.conda_root(),"share","ggd_info","channeldata.json")) as jfile:
channeldata = json.load(jfile)
assert ggd_recipe in channeldata["packages"]
## Test uninstall
args = Namespace(channel='genomics', command='uninstall', names=recipes)
assert uninstall.uninstall((),args) == True
#### Check that the recipe are uninstalled by conda
pkg_info = get_conda_package_list(utils.conda_root())
for recipe in recipes:
assert recipe not in pkg_info.keys()
#### Get jdict
ggd_channel = "genomics"
jdict = uninstall.get_channeldata(recipes,ggd_channel)
#### Check data files are removed
for ggd_recipe in recipes:
species = jdict["packages"][ggd_recipe]["identifiers"]["species"]
build = jdict["packages"][ggd_recipe]["identifiers"]["genome-build"]
version = jdict["packages"][ggd_recipe]["version"]
final_files = jdict["packages"][ggd_recipe]["tags"]["final-files"]
path = os.path.join(conda_root(),"share","ggd",species,build,ggd_recipe,version)
assert glob.glob(path) == []
#### Check that the ggd metadata channeldata file does not contain the packages
for ggd_recipe in recipes:
assert os.path.exists(os.path.join(utils.conda_root(),"share","ggd_info","noarch"))
assert os.path.exists(os.path.join(utils.conda_root(),"share","ggd_info","noarch",ggd_recipe+"-{}-{}.tar.bz2".format(version,build))) == False
assert os.path.exists(os.path.join(utils.conda_root(),"share","ggd_info","channeldata.json"))
with open(os.path.join(utils.conda_root(),"share","ggd_info","channeldata.json")) as jfile:
channeldata = json.load(jfile)
assert ggd_recipe not in channeldata["packages"]