def test_valid_config():
config = snaketools.SequanaConfig(None)
s = snaketools.Module("quality_control")
config = snaketools.SequanaConfig(s.config)
from easydev import TempFile
with TempFile() as fh:
config.save(fh.name)
def test_copy_requirements():
# We need 4 cases:
# 1- http
# 2- a sequana file (phix)
# 3- an existing file elsewhere (here just a temporary file)
# 4- an existing file in the same directory as the target dir
from easydev import TempFile
fh = tempfile.TemporaryDirectory()
targetdir = fh.name
# Case 3: a temporary file
temprequire = TempFile()
# Case 4: a local file (copy of the temp file)
# TODO
#localfile = temprequire.name.split(os.sep)[-1]
#shutil.copy(temprequire.name, targetdir)
cfg = snaketools.SequanaConfig()
cfg.config.requirements = ["phiX174.fa", temprequire.name,
#localfile,
"https://raw.githubusercontent.com/sequana/sequana/master/README.rst"]
cfg._update_yaml()
cfg.copy_requirements(target=fh.name)
# error
cfg.config.requirements = ['dummy']
try:
cfg.copy_requirements(target=fh.name)
assert False
except:
assert True
def test_sequana_config():
s = snaketools.Module("compressor")
config = snaketools.SequanaConfig(s.config)
assert config.config.get("compressor")["source"] == "fastq.gz"
assert config.config.get("kraken:dummy") == None
# --------------------------------- tests different constructors
config = snaketools.SequanaConfig()
config = snaketools.SequanaConfig({"test": 1})
assert config.config.test == 1
# with a dictionary
config = snaketools.SequanaConfig(config.config)
# with a sequanaConfig instance
config = snaketools.SequanaConfig(config)
# with a non-yaml file
try:
json = sequana_data('test_summary_fastq_stats.json')
config = snaketools.SequanaConfig(json)
assert False
except:
assert True
try:
config = snaketools.SequanaConfig("dummy_dummy")
assert False
except:
assert True
# Test an exception
s = snaketools.Module("compressor")
config = snaketools.SequanaConfig(s.config)
config._recursive_update(config._yaml_code,
{"input_directory_dummy": "test"})
#config.check_config_with_schema(s.schema_config)
# loop over all pipelines, read the config, save it and check the content is
# identical. This requires to remove the templates. We want to make sure the
# empty strings are kept and that "no value" are kept as well
#
# field1: ""
# field2:
#
# is unchanged
from easydev import TempFile
output = TempFile(suffix=".yaml")
for pipeline in snaketools.pipeline_names:
config_filename = Module(pipeline)._get_config()
cfg1 = SequanaConfig(config_filename)
cfg1.cleanup() # remove templates and strip strings
cfg1.save(output.name)
cfg2 = SequanaConfig(output.name)
assert cfg2._yaml_code == cfg1._yaml_code
cfg2._update_config()
assert cfg1.config == cfg2.config
output.delete()