def test_module():
# a rule without README
m = snaketools.Module('mark_duplicates')
m.description
print(m)
m.path
m.snakefile
# a rule with README
m = snaketools.Module('dag')
m.description
m.overview
m.is_executable()
m.check()
# a pipeline
m = snaketools.Module('quality_control')
m.is_executable()
m.check()
m.snakefile
m.name
m
print(m)
assert m.cluster_config.endswith("cluster_config.json")
assert m.schema_config.endswith("schema.yaml")
def test_module():
# a rule without README
m = snaketools.Module('mark_duplicates_dynamic')
m.description
print(m)
m # test __repr__
m.__repr__()
m.path
m.snakefile
m.overview
# a rule with README
m = snaketools.Module('dag')
m.description
m.overview
assert m.is_executable()
m.check()
# a pipeline
m = snaketools.Module('compressor')
m.is_executable()
m.check()
m.snakefile
m.name
m
print(m)
assert m.cluster_config.endswith("cluster_config.json")
assert m.schema_config.endswith("schema.yaml")
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()
def test_yamlreader():
filename = sequana_data("test_gui_generic_config.yaml")
r = YamlDocParser(filename)
assert r.sections['N'] == '# example of docstring\n'
# check docstring is parsed with #### removed
r = YamlDocParser(snaketools.Module('quality_control').config)
docstring = r._block2docstring("fastqc")
assert docstring.startswith("FastQC")
assert r._block2docstring("dummy") is None
# check that pipelines can be parsed
for pipeline in snaketools.pipeline_names:
filename = snaketools.Module(pipeline).config
r = YamlDocParser(filename)
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_module_onweb():
m = snaketools.Module('quality_control')
m.onweb()