def test_get_pkg_info_internet_free():
"""
Test that get_pkg_info in pkg-info in a internet free context
(pkg-info)
"""
## 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 a normal run that should pass
ggd_package = "hg19-gaps-ucsc-v1"
ggd_channel = "genomics"
assert list_pkg_info.get_pkg_info(ggd_package, ggd_channel, False) == True
## Test that a uninstalled package is handled correctly
ggd_package = "Bad_package"
ggd_channel = "genomics"
temp_stdout = StringIO()
with redirect_stdout(temp_stdout):
list_pkg_info.get_pkg_info(ggd_package, ggd_channel, False)
output = temp_stdout.getvalue().strip()
assert ggd_package + " is not downloaded on your system, or was downloaded incorrectly" in output
assert list_pkg_info.get_pkg_info(ggd_package, ggd_channel, False) == False
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_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_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_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_info_main_internet_free():
"""
test the pkg-info main funtion in an internet free context
(pkg-info)
"""
## 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
## Normal run
ggd_package = "hg19-gaps-ucsc-v1"
ggd_channel = "genomics"
args = Namespace(all_versions=False,
channel=ggd_channel,
command='pkg-info',
name=ggd_package,
show_recipe=False,
prefix=None)
assert list_pkg_info.info((), args) == True
temp_stdout = StringIO()
with redirect_stdout(temp_stdout):
list_pkg_info.info((), args)
output = temp_stdout.getvalue().strip()
lines = output.strip().split("\n")
assert lines[2] == "\t\x1b[1mGGD-Package:\x1b[0m {}".format(ggd_package)
assert lines[4] == "\t\x1b[1mGGD-Channel:\x1b[0m ggd-{}".format(
ggd_channel)
assert lines[6] == "\t\x1b[1mGGD Pkg Version:\x1b[0m 1"
assert lines[
8] == "\t\x1b[1mSummary:\x1b[0m Assembly gaps from UCSC in bed fromat. Scaffoldings that are not contained in the hg19.genome file are removed"
assert lines[10] == "\t\x1b[1mSpecies:\x1b[0m Homo_sapiens"
assert lines[12] == "\t\x1b[1mGenome Build:\x1b[0m hg19"
assert lines[
14] == "\t\x1b[1mKeywords:\x1b[0m gaps, regions, gap-locations, Assembly-Gaps, clone-gaps, contig-gaps, centromere-gaps, telomere-gaps, heterochromatin-gaps, short-arm-gaps"
assert lines[16] == "\t\x1b[1mCached:\x1b[0m uploaded_to_aws"
def test_in_ggd_channel_internet_free():
"""
Test the in_ggd_channel 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 that in_ggd_channel properly returns the species, genome-build, and versoin if it is in the channel
ggd_package = "hg19-gaps-ucsc-v1"
channel = "genomics"
species, build, version = list_files.in_ggd_channel([ggd_package], channel,
utils.conda_root())
assert species == "Homo_sapiens"
assert build == "hg19"
assert version == "1"
## test that in_ggd_channel properly handels bad channels
ggd_package = "hg19-gaps-ucsc-v1"
channel = "not_a_real_channel"
with pytest.raises(SystemExit) as pytest_wrapped_e:
list_files.in_ggd_channel([ggd_package], channel, utils.conda_root())
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 in_ggd_channel properly handels bad recipe name
ggd_package = "NOT_A_REAL_PACKAGE_NAME"
channel = "genomics"
with pytest.raises(SystemExit) as pytest_wrapped_e:
list_files.in_ggd_channel([ggd_package], channel, utils.conda_root())
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_installed_packages_internet_free():
"""
Test the main function of ggd list in an internet free context
"""
## 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='list', pattern=None, prefix=None, reset=False)
temp_stdout = StringIO()
with redirect_stdout(temp_stdout):
list_installed_pkgs.list_installed_packages((), args)
output = temp_stdout.getvalue().strip()
assert "hg19-gaps-ucsc-v1" in output
assert "Name" in output and "Pkg-Version" in output and "Pkg-Build" in output and "Channel" in output and "Environment-Variables" in output
assert "To use the environment variables run `source activate base" in output
assert "You can see the available ggd data package environment variables by running `ggd show-env" in output
args = Namespace(command='list',
pattern=None,
prefix=utils.conda_root(),
reset=False)
temp_stdout = StringIO()
with redirect_stdout(temp_stdout):
list_installed_pkgs.list_installed_packages((), args)
output = temp_stdout.getvalue().strip()
assert "hg19-gaps-ucsc-v1" in output
assert "Name" in output and "Pkg-Version" in output and "Pkg-Build" in output and "Channel" in output and "Environment-Variables" in output
assert "The environment variables are only available when you are using the '{}' conda environment".format(
utils.conda_root()) 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_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_update_installed_pkg_metadata():
"""
Test that the update_installed_pkg_metadata method correctly updates the ggd info metadata with installed packages
"""
## enable socket
pytest_enable_socket()
ggd_package = "hg19-gaps-ucsc-v1"
## Try to install ggd_package. If fails, most likely due to the fact that it is already installed
try:
install_hg19_gaps_ucsc_v1()
except Exception:
pass
ggd_info_dir = os.path.join(utils.conda_root(),"share","ggd_info")
## Test normal run
if os.path.isdir(ggd_info_dir):
shutil.rmtree(ggd_info_dir)
assert os.path.exists(ggd_info_dir) == False
assert utils.update_installed_pkg_metadata() == True
matches = [re.search(ggd_package+".+",x).group() for x in os.listdir(os.path.join(ggd_info_dir,"noarch")) if re.search(ggd_package,x) != None]
assert len(matches) > 0
with open(os.path.join(ggd_info_dir,"channeldata.json")) as jsonFile:
jdict = json.load(jsonFile)
assert ggd_package in jdict["packages"]
assert os.path.exists(ggd_info_dir) == True
## Test add_package != None and remove_old == True
### add_package != None and remove_old == True should never happen. This would result in only 1 package in the metadata
temp_stdout = StringIO()
with redirect_stdout(temp_stdout):
utils.update_installed_pkg_metadata(add_packages=["hg19-gaps-ucsc-v1"],remove_old=True)
output = temp_stdout.getvalue().strip()
assert ("Warning: You indicated to add a single package to ggd info metadata but also indicated to re-build the metadata. This would result in the single indicated package being the only package in the metadata" in output)
assert ("The ggd info metadata will be re-built and all ggd packages will be added" in output)
## Test prefix not set:
### Temp conda environment
temp_env = os.path.join(utils.conda_root(), "envs", "temp_env9")
### Remove temp env if it already exists
sp.check_output(["conda", "env", "remove", "--name", "temp_env9"])
try:
shutil.rmtree(temp_env)
except Exception:
pass
### Create conda environmnet
sp.check_output(["conda", "create", "--name", "temp_env9"])
### Install ggd recipe using conda into temp_env
ggd_package2 = "hg19-pfam-domains-ucsc-v1"
install_args = Namespace(channel='genomics', command='install', debug=False, name=[ggd_package2], file=[], prefix = temp_env)
assert install.install((), install_args) == True
ggd_info_dir2 = os.path.join(temp_env,"share","ggd_info")
## Test the installed created the ggd info metadata
matches = [re.search(ggd_package2+".+",x).group() for x in os.listdir(os.path.join(ggd_info_dir2,"noarch")) if re.search(ggd_package2,x) != None]
assert len(matches) > 0
with open(os.path.join(ggd_info_dir2,"channeldata.json")) as jsonFile:
jdict = json.load(jsonFile)
assert ggd_package2 in jdict["packages"]
assert os.path.exists(ggd_info_dir2) == True
## remove ggd info metadata
if os.path.isdir(ggd_info_dir2):
shutil.rmtree(ggd_info_dir2)
assert os.path.exists(ggd_info_dir2) == False
## Run the update with prefix set and check the prefix
assert utils.update_installed_pkg_metadata(prefix=temp_env) == True
matches = [re.search(ggd_package2+".+",x).group() for x in os.listdir(os.path.join(ggd_info_dir2,"noarch")) if re.search(ggd_package2,x) != None]
assert len(matches) > 0
with open(os.path.join(ggd_info_dir2,"channeldata.json")) as jsonFile:
jdict = json.load(jsonFile)
assert ggd_package2 in jdict["packages"]
assert os.path.exists(ggd_info_dir2) == True
### Remove temp env
sp.check_output(["conda", "env", "remove", "--name", "temp_env9"])
try:
shutil.rmtree(temp_env)
except Exception:
pass
assert os.path.exists(temp_env) == False