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 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_report(self):
config = self._make_cfg('admin', 'basic', 'calibration')
report = BeastlingReport(config)
report.tostring()
def test_report(config_factory):
config = config_factory('admin', 'basic', 'calibration')
report = BeastlingReport(config)
report.tostring()
def test_report(self):
config = self._make_cfg('admin', 'basic', 'calibration')
report = BeastlingReport(config)
report.tostring()
