def test_create():
renv = REnvironment(RHOME, LIBRARYPATH)
assert (renv.baseurl == RHOME)
assert (renv.repos == [LIBRARYPATH])
# invalid baseurl
try:
renv = REnvironment('/invalid/local/repobase', LIBRARYPATH)
pytest.fail('Constructing a REnvironment with '
'an invalid baseurl/rhome must raise an Exception!')
except Exception:
pass
# invalid repos
try:
renv = REnvironment(RHOME, 'invalid1')
pytest.fail('Constructing a REnvironment with '
'an invalid library path must raise an Exception!')
except Exception:
pass
# no R file in the bin folder
try:
renv = REnvironment(RHOME_INVALID, 'library')
pytest.fail(
'Constructing a REnvironment which '
'does not contain any R binary file must raise an Exception!')
except Exception:
pass
def test_download_single():
renv = REnvironment(RHOME, LIBRARYPATH)
destfolder = tempfile.mkdtemp()
try:
renv.download_single('energy', destfolder)
pytest.fail('The download method must raise an exception!')
except Exception:
pass
def test_ls():
renv = REnvironment(RHOME, LIBRARYPATH)
packagenames = renv.ls()
assert (len(packagenames) == 5)
assert ('energy' in packagenames)
assert ('entropy' in packagenames)
assert ('evaluate' in packagenames)
assert ('faraway' in packagenames)
assert ('fastcluster' in packagenames)
def test_find():
renv = REnvironment(RHOME, LIBRARYPATH)
# findall
findall = renv.find('*')
assert (len(findall) == 6)
assert ('energy' in findall)
assert ('entropy' in findall)
assert ('evaluate' in findall)
assert ('fake1' in findall)
assert ('faraway' in findall)
assert ('fastcluster' in findall)
# find something that does not exist
assert (len(renv.find('*.tar.gz')) == 0)
def _build_renvironment_repos(self, names):
for name in names:
logger.info('Building R environment instance \"{0}\"'.format(name))
licensecheck = False
try:
licensecheck = self._config.getboolean(name, "licensecheck")
except Exception:
licensecheck = False
provider = REnvironment(self._config.get(name, "rhome"),
self._config.get(name, "librarypath"),
licensecheck)
provider.name = name
if (provider._licensecheck):
logger.info('License checking is ON')
else:
logger.info('License checking is OFF')
self._renvironment_instances[name] = provider
def test_checkInstallationSuccess():
renv = REnvironment(RHOME, LIBRARYPATH)
# return code ok
success = renv._checkInstallationSuccess(0, "Ok", None)
assert(success)
# return code not ok
success = renv._checkInstallationSuccess(1, "Ok", None)
assert(not success)
# retrurn code ok with error message
success = renv._checkInstallationSuccess(0, "Execution halted", None)
assert(not success)
success = renv._checkInstallationSuccess(0, None, "Execution halted")
assert(not success)
success = renv._checkInstallationSuccess(0, "...", "...failed...")
assert(not success)
success = renv._checkInstallationSuccess(0, "...", "...FAILED...")
assert(not success)
success = renv._checkInstallationSuccess(0, "...", "...ERROR:...")
assert(not success)
def test_build_dependencies_graph_from_renvironment(cleanup):
RHOME = os.path.join(os.path.dirname(os.path.abspath(__file__)),
'resources/R-fake-env')
LIBRARYPATH = 'packages'
renv = REnvironment(RHOME, LIBRARYPATH)
assert (renv.baseurl == RHOME)
assert (renv.repos == [LIBRARYPATH])
print('Building dependencies graph...')
lsargs = {'packagenamesonly': True}
dt = DepTree(renv, lsargs)
dt.build()
assert (len(dt._g.nodes()) > 0)
assert (len(dt._g.edges()) > 0)
print('Generating graph...')
write_gml(dt._g, GML, stringizer=literal_stringizer)
assert (os.path.exists(GML))
def test_upload_single(mock_installpackage):
renv = REnvironment(RHOME, LIBRARYPATH)
# none existing package
status = renv.upload_single(
'/none/existent/path/to/some/none/existent/package.tar.gz')
assert (status == PackStatus.DEPLOY_FAILED)
# existing package
mock_installpackage.return_value = (0, "Ok", None)
status = renv.upload_single(RPACKAGE)
assert (status == PackStatus.DEPLOYED)
# set the unused argument
status = renv.upload_single(RPACKAGE, repo='fakerepo')
assert (status == PackStatus.DEPLOYED)
# overwrite
status = renv.upload_single(RPACKAGE, overwrite=True)
assert (status == PackStatus.DEPLOYED)
# failed installation
mock_installpackage.return_value = (1, "not Ok", "Could not install")
status = renv.upload_single(RPACKAGE)
assert (status == PackStatus.DEPLOY_FAILED)
def test_packinfo():
renv = REnvironment(RHOME, LIBRARYPATH)
# existing package
energy = renv.packinfo('energy')
print('energy: {0}'.format(energy.as_dict))
assert (energy.name == 'energy')
assert (energy.version == '1.6.2')
assert (energy.license == 'GPL (>= 2)')
assert (energy.imports == ['boot'])
# none existing package
foobar = renv.packinfo('foobar')
assert (foobar.status == PackStatus.NOT_FOUND)
# invalid package
try:
renv.packinfo('fake1')
pytest.fail('Passing a folder without any DESCRIPTION file '
'must raise an exception!')
except Exception:
pass