def do_generate(args):
# Make sure the requested configuration file exists
for conf in args.config:
if not conf.exists():
exit(msg="No such configuration file: %s" % conf, status=1)
# Build but DON'T PROCESS the Config object
# This is fast, and gives us enough information to check whether or not
try:
config = Configuration(configfile=args.config,
stdin_data=args.stdin,
prior=args.prior,
force_glottolog_load=args.report)
except wrap_errors as e: # PRAGMA: NO COVER
exit(msg="Error encountered while parsing configuration file:",
status=2,
exception=True)
# Make sure we can write to the appropriate output filename
output_filename = pathlib.Path(
args.output) if args.output else config.admin.path(".xml")
if output_filename.exists() and not args.overwrite:
exit(
msg=
"File %s already exists! Run beastling with the --overwrite option if you wish "
"to overwrite it." % output_filename,
status=4)
# Now that we know we will be able to save the resulting XML, we can take
# the time to process the config object
try:
config.process()
except wrap_errors as e: # pragma: no cover
exit(msg="Error encountered while parsing configuration file:",
status=2,
exception=True)
# Build XML file
try:
xml = BeastXml(config)
except wrap_errors as e: # pragma: no cover
exit(msg="Error encountered while building BeastXML object:",
status=3,
exception=True)
# Write XML file
xml.write_file(output_filename)
# Build and write report
if args.report:
report = BeastlingReport(config)
report.write_file(output_filename.parent / config.admin.path(".md"))
geojson = BeastlingGeoJSON(config)
geojson.write_file(output_filename.parent /
config.admin.path(".geojson"))
# Build and write language list
if args.language_list:
write_language_list(config)
def test_calibration(config_factory):
config = _processed_config(config_factory, 'basic', 'calibration')
assert {'Cushitic'} == set(config.calibrations)
v = config.calibrations['Cushitic']
assert 'DistributionForCushiticMRCA' in BeastXml(config).tostring().decode('utf8')
# Now remove one calibration point ...
del config.calibrations['Cushitic']
assert 'DistributionForCushiticMRCA' not in BeastXml(config).tostring().decode('utf8')
# ... and add it back in with using the glottocode:
config.calibrations['cush1243'] = v
assert 'DistributionForcush1243MRCA' in BeastXml(config).tostring().decode('utf8')
def test_file_embedding(self):
config = self._make_cfg('glottolog_families_from_file', 'embed_data')
xml = BeastXml(config).tostring().decode('utf8')
# Check for evidence of data
self.assertTrue("aari1239,1,1,1,1,1,1,?,1,?,1" in xml)
# Check for evidence of families
self.assertTrue("Malayo-Polynesian" in xml)
def test_binarisation_ascertainment(self):
# Even with ascertainment = False, ascertainment should still
# be done for recoded data
config = self._make_cfg('covarion_binarised', 'ascertainment_false')
config.process()
xml = BeastXml(config).tostring().decode('utf8')
self.assertTrue("ascertained=\"true\"" in xml)
self.assertTrue("excludeto=\"1\"" in xml)
def test_calibration(self):
config = self._make_cfg('basic', 'calibration')
config.process()
self.assertIn('Austronesian', config.calibrations)
v = config.calibrations['Austronesian']
xml1 = BeastXml(config).tostring().decode('utf8')
# Now remove one calibration point ...
del config.calibrations['Austronesian']
xml2 = BeastXml(config).tostring().decode('utf8')
self.assertNotEqual(len(xml1.split('CalibrationDistribution.')),
len(xml2.split('CalibrationDistribution.')))
# ... and add it back in with using the glottocode:
config.calibrations['aust1307'] = v
xml2 = BeastXml(config).tostring().decode('utf8')
self.assertEqual(len(xml1.split('CalibrationDistribution.')),
len(xml2.split('CalibrationDistribution.')))
def do_generate(args):
# Build config object
for conf in args.config:
if not os.path.exists(conf):
errmsg("No such configuration file: %s\n" % conf)
sys.exit(1)
try:
config = beastling.configuration.Configuration(
configfile=args.config, stdin_data=args.stdin, prior=args.prior)
config.process()
except Exception as e:
errmsg("Error encountered while parsing configuration file:\n")
traceback.print_exc()
sys.exit(2)
# If verbose mode is on, print any messages which were generated while
# processing the configuration
if args.verbose:
for msg in config.messages:
errmsg(msg + "\n")
# Build XML file
try:
xml = BeastXml(config)
except Exception as e:
errmsg("Error encountered while building BeastXML object:\n")
traceback.print_exc()
sys.exit(3)
# Write XML file
filename = args.output if args.output else config.basename+".xml"
if os.path.exists(filename) and not args.overwrite:
errmsg("File %s already exists! Run beastling with the --overwrite option if you wish to overwrite it.\n" % filename)
sys.exit(4)
xml.write_file(filename)
# Build and write report
if args.report:
report = BeastlingReport(config)
report.write_file(config.basename+".md")
geojson = BeastlingGeoJSON(config)
geojson.write_file(config.basename+".geojson")
def test_validate_ids(config_factory):
config = config_factory('basic')
bml = BeastXml(config)
xml.data(bml.beast, id='theid')
xml.data(bml.beast, id='theid')
with pytest.raises(ValueError, match='Duplicate'):
bml.validate_ids()
bml = BeastXml(config)
xml.data(bml.beast, idref='theid')
with pytest.raises(ValueError, match='missing'):
bml.validate_ids()
def test_calibration(self):
config = self._make_cfg('basic', 'calibration')
config.process()
self.assertEqual({'Cushitic'}, set(config.calibrations))
v = config.calibrations['Cushitic']
self.assert_in_xml('DistributionForCushiticMRCA', config)
# Now remove one calibration point ...
del config.calibrations['Cushitic']
xml2 = BeastXml(config).tostring().decode('utf8')
self.assertNotIn('DistributionForCushiticMRCA', xml2)
# ... and add it back in with using the glottocode:
config.calibrations['cush1243'] = v
self.assert_in_xml('DistributionForcush1243MRCA', config)
def test_calibration(self):
config = self._make_cfg('basic', 'calibration')
config.process()
self.assertIn('austronesian', config.calibrations)
v = config.calibrations['austronesian']
xml1 = BeastXml(config).tostring().decode('utf8')
# Now remove one calibration point ...
del config.calibrations['austronesian']
xml2 = BeastXml(config).tostring().decode('utf8')
self.assertNotEqual(
len(xml1.split('CalibrationDistribution.')), len(xml2.split('CalibrationDistribution.')))
# ... and add it back in with using the glottocode:
config.calibrations['aust1307'] = v
xml2 = BeastXml(config).tostring().decode('utf8')
self.assertEqual(
len(xml1.split('CalibrationDistribution.')), len(xml2.split('CalibrationDistribution.')))
def test_random_tree(config_factory):
"""Load a very basic config file and test that RandomTree
from the BEAST core is used."""
config = config_factory('basic')
xml = BeastXml(config).tostring().decode('utf8')
assert "beast.evolution.tree.RandomTree" in xml
def test_bad_frequencies(config_factory):
cfg = _processed_config(config_factory, "bad_frequencies")
with pytest.raises(ValueError):
# This is an error in a model section, which is only raised
# when the model is constructed as XML.
BeastXml(cfg)
def test_simple_random_tree(config_factory):
"""Load a config file with a Uniform calibration and test that
SimpleRandomTree from BEASTLabs is used."""
config = config_factory('basic', 'calibration_uniform_range')
xml = BeastXml(config).tostring().decode('utf8')
assert "beast.evolution.tree.SimpleRandomTree" in xml
def test_constrained_random_tree(config_factory):
"""Load a config file with monophyly constraints and test that
ConstraintedRandomTree from BEASTLabs is used."""
config = config_factory('basic', 'monophyletic')
xml = BeastXml(config).tostring().decode('utf8')
assert "beast.evolution.tree.ConstrainedRandomTree" in xml
def test_constrained_random_tree(self):
"""Load a config file with monophyly constraints and test that
ConstraintedRandomTree from BEASTLabs is used."""
config = self._make_cfg('basic', 'monophyletic')
xml = BeastXml(config).tostring().decode('utf8')
self.assertTrue("beast.evolution.tree.ConstrainedRandomTree" in xml)
def test_random_tree(self):
"""Load a very basic config file and test that RandomTree
from the BEAST core is used."""
config = self._make_cfg('basic')
xml = BeastXml(config).tostring().decode('utf8')
self.assertTrue("beast.evolution.tree.RandomTree" in xml)
def test_simple_random_tree(self):
"""Load a config file with a Uniform calibration and test that
SimpleRandomTree from BEASTLabs is used."""
config = self._make_cfg('basic', 'calibration_uniform_range')
xml = BeastXml(config).tostring().decode('utf8')
self.assertTrue("beast.evolution.tree.SimpleRandomTree" in xml)
def test_xml(config_factory, cfgs, in_xml):
config = _processed_config(config_factory, *cfgs)
xml = BeastXml(config).tostring().decode('utf8')
for s in in_xml:
assert s in xml, s
def test_path_sampling(config_factory):
config = config_factory('basic')
config.mcmc.path_sampling = True
bml = BeastXml(config)
bml.validate_ids()
def test_bad_frequencies(self):
cfg = self._make_bad_cfg("bad_frequencies")
cfg.process()
# This is an error in a model section, which is only raised
# when the model is constructed as XML.
BeastXml(cfg)
def assert_in_xml(self, string, config):
xml = BeastXml(config).tostring().decode('utf8')
self.assertIn(string, xml)
