def run_local_topology(name=None, env_name=None, time=0, options=None):
"""Run a topology locally using Flux and `storm jar`."""
name, topology_file = get_topology_definition(name)
env_name, env_config = get_env_config(env_name)
topology_class = get_topology_from_file(topology_file)
storm_options = resolve_options(options, env_config, topology_class, name)
if storm_options['topology.acker.executors'] != 0:
storm_options['topology.acker.executors'] = 1
storm_options['topology.workers'] = 1
# Check Storm version is the same
local_version = local_storm_version()
project_version = storm_lib_version()
if local_version != project_version:
raise ValueError('Local Storm version, {}, is not the same as the '
'version in your project.clj, {}. The versions must '
'match.'.format(local_version, project_version))
# Prepare a JAR that has Storm dependencies packaged
topology_jar = jar_for_deploy(simple_jar=False)
if time <= 0:
time = 9223372036854775807 # Max long value in Java
# Write YAML file
with NamedTemporaryFile(mode='w', suffix='.yaml', delete=False) as yaml_file:
topology_flux_dict = topology_class.to_flux_dict(name)
topology_flux_dict['config'] = storm_options
yaml.safe_dump(topology_flux_dict, yaml_file)
cmd = ('storm jar {jar} org.apache.storm.flux.Flux --local --no-splash '
'--sleep {time} {yaml}'.format(jar=topology_jar,
time=time,
yaml=yaml_file.name))
local(cmd)
def do_run(problem,
hparam_set: str = None,
extra_hparams: dict = None,
progress: bool = False,
cuda: bool = False,
device: str = None,
log_dir: str = None,
resume: bool = False,
start_epoch: int = None,
checkpoint_prefix: str = 'checkpoint',
**kwargs):
problem_cls = registry.get_problem(problem)
if not hparam_set:
hparam_set_list = registry.get_problem_hparam(problem)
assert hparam_set_list
hparam_set = hparam_set_list[0]
hparams = registry.get_hparam(hparam_set)()
if extra_hparams:
hparams.update(extra_hparams)
cuda = cuda and torch.cuda.is_available()
if not cuda:
device = 'cpu'
if log_dir:
os.makedirs(log_dir, exist_ok=True)
if os.listdir(log_dir):
warnings.warn('Directory "{}" not empty!'.format(log_dir))
hparams_file_path = os.path.join(log_dir, 'hparams.yaml')
args_file_path = os.path.join(log_dir, 'args.yaml')
args = {
'problem': problem,
'seed': kwargs.get('seed', None),
'checkpoint_prefix': checkpoint_prefix,
}
with open(hparams_file_path, 'w') as hparams_file, \
open(args_file_path, 'w') as args_file:
yaml.safe_dump(hparams.__dict__,
stream=hparams_file,
default_flow_style=False)
yaml.safe_dump(args, stream=args_file, default_flow_style=False)
problem = problem_cls(hparams,
argparse.Namespace(**kwargs),
log_dir,
device=device,
show_progress=progress,
checkpoint_prefix=checkpoint_prefix)
if resume:
problem.load_checkpoint(log_dir, epoch=start_epoch)
problem.run()
def run_local_topology(
name=None, env_name=None, time=0, options=None, config_file=None
):
"""Run a topology locally using Flux and `storm jar`."""
name, topology_file = get_topology_definition(name, config_file=config_file)
config = get_config(config_file=config_file)
env_name, env_config = get_env_config(env_name, config_file=config_file)
topology_class = get_topology_from_file(topology_file)
set_topology_serializer(env_config, config, topology_class)
storm_options = resolve_options(
options, env_config, topology_class, name, local_only=True
)
if storm_options["topology.acker.executors"] != 0:
storm_options["topology.acker.executors"] = 1
storm_options["topology.workers"] = 1
# Set parallelism based on env_name if necessary
for spec in topology_class.specs:
if isinstance(spec.par, dict):
spec.par = spec.par.get(env_name)
# Check Storm version is the same
local_version = local_storm_version()
project_version = storm_lib_version()
if local_version != project_version:
raise ValueError(
"Local Storm version, {}, is not the same as the "
"version in your project.clj, {}. The versions must "
"match.".format(local_version, project_version)
)
# Prepare a JAR that has Storm dependencies packaged
topology_jar = jar_for_deploy(simple_jar=False)
if time <= 0:
time = 9223372036854775807 # Max long value in Java
# Write YAML file
with show("output"):
with NamedTemporaryFile(mode="w", suffix=".yaml", delete=False) as yaml_file:
topology_flux_dict = topology_class.to_flux_dict(name)
topology_flux_dict["config"] = storm_options
if yaml.version_info < (0, 15):
yaml.safe_dump(topology_flux_dict, yaml_file, default_flow_style=False)
else:
yml = yaml.YAML(typ="safe", pure=True)
yml.default_flow_style = False
yml.dump(topology_flux_dict, yaml_file)
cmd = (
"storm jar {jar} org.apache.storm.flux.Flux --local --no-splash "
"--sleep {time} {yaml}".format(
jar=topology_jar, time=time, yaml=yaml_file.name
)
)
local(cmd)
def __init__(self, parameters, target_file_path):
export = {"parameters": {"hexaa_service_entityids": parameters}}
with open(target_file_path, 'w') as yaml_file:
ryaml.safe_dump(export,
yaml_file,
default_flow_style=False,
allow_unicode=True,
indent=4,
width=float('inf'))
def save(self, filename):
filename = pathlib.Path(filename)
if filename.suffix == '.json':
filename.write_text(json.dumps(dict(self)))
elif filename.suffix in ('.yml', '.yaml'):
import ruamel.yaml as yaml
with filename.open('w') as f:
yaml.safe_dump(dict(self), f)
else:
raise NotImplementedError(filename.suffix)
def dump_yaml(yaml_name, data: dict):
"""
将字典格式数据写入到yaml文件
:param yaml_name:将被创建的yaml文件名
:param data:字典格式数据
:return:没有返回值
"""
# 创建env.yaml文件，给可写权限，将env中数据写入env.yaml
with open(yaml_name, "w") as f:
yaml.safe_dump(data=data, stream=f)
def migrate(self, recipe_dir: str, attrs: "AttrsTypedDict",
**kwargs: Any) -> "MigrationUidTypedDict":
with indir(recipe_dir + "/.."):
self.set_build_number("recipe/meta.yaml")
with open("conda-forge.yml", "r") as f:
y = safe_load(f)
y.update(self.additional_keys)
with open("conda-forge.yml", "w") as f:
safe_dump(y, f)
return super().migrate(recipe_dir, attrs, **kwargs)
def set_definitions_version(new_version, version_file='./VERSION'):
'''Update the version information stored in 'version_file'.
The new version must be a whole number. If 'version_file' doesn't exist,
it will be created.
'''
version_info = {'version': new_version}
with open(version_file, 'w') as f:
# If 'default_flow_style' is True (the default) then the output here
# will look like "{version: 0}" instead of "version: 0".
yaml.safe_dump(version_info, f, default_flow_style=False)
def to_speaker():
data = yaml.safe_load(read_text('ttslib.data', 'supported.yaml'))
d0 = dict()
for platform, d in data.items():
for lang, speakers in d.items():
if speakers:
d0.setdefault(lang,
dict.fromkeys(data.keys()))[platform] = speakers
with open('../ttslib/data/to_speaker.yaml', 'w') as f:
yaml.safe_dump(d0, f)
def set_definitions_version(new_version, version_file='./VERSION'):
'''Update the version information stored in 'version_file'.
The new version must be a whole number. If 'version_file' doesn't exist,
it will be created.
'''
version_info = {'version': new_version}
with open(version_file, 'w') as f:
# If 'default_flow_style' is True (the default) then the output here
# will look like "{version: 0}" instead of "version: 0".
yaml.safe_dump(version_info, f, default_flow_style=False)
def _set_data(self, code: str) -> NoReturn:
if len(code.split()) > 0:
cwd = Path(self._cwl_executor.file_manager.get_files_uri().path)
data = self._preprocess_data(yaml.load(code, Loader=yaml.Loader))
self._cwl_executor.validate_input_files(data, cwd)
code_stream = StringIO()
yaml.safe_dump(data, code_stream)
self._yaml_input_data = code_stream.getvalue()
self.send_response(self.iopub_socket, 'stream', {
'name': 'stdout',
'text': 'Add data in memory'
})
def run_project_config(self, *, project_config=None, **kwargs):
# First load the project.conf and substitute {project_dir}
#
# Save the original project.conf, because we will run more than
# once in the same temp directory
#
project_directory = kwargs["project"]
project_filename = os.path.join(project_directory, "project.conf")
project_backup = os.path.join(project_directory, "project.conf.backup")
project_load_filename = project_filename
if not os.path.exists(project_backup):
shutil.copy(project_filename, project_backup)
else:
project_load_filename = project_backup
with open(project_load_filename) as f:
config = f.read()
config = config.format(project_dir=project_directory)
if project_config is not None:
# If a custom project configuration dictionary was
# specified, composite it on top of the already
# substituted base project configuration
#
base_config = _yaml.load_data(config)
# In order to leverage _yaml.composite_dict(), both
# dictionaries need to be loaded via _yaml.load_data() first
#
with tempfile.TemporaryDirectory(
dir=project_directory) as scratchdir:
temp_project = os.path.join(scratchdir, "project.conf")
with open(temp_project, "w") as f:
yaml.safe_dump(project_config, f)
project_config = _yaml.load(temp_project,
shortname="project.conf")
project_config._composite(base_config)
_yaml.roundtrip_dump(base_config, project_filename)
else:
# Otherwise, just dump it as is
with open(project_filename, "w") as f:
f.write(config)
return super().run(**kwargs)
def save_server(self, server_id, data=None):
if not data:
data = self.data[server_id]
try:
if not os.path.exists("data/{}".format(server_id)):
self.add_server(server_id)
with open("data/{}/config.yml".format(server_id), "w") as config_fh:
yaml.safe_dump(data["config"], config_fh)
except Exception:
log.exception("Error saving server '{}'".format(server_id))
def save_context(context, **kwargs):
project_dir = yield
with open(os.path.join(project_dir, '.cookiecutterrc'),
'w',
encoding='utf8') as fh:
fh.write(
"# Generated by cookiepatcher, a small shim around cookiecutter (pip install cookiepatcher)\n\n"
)
yaml.safe_dump(context,
fh,
indent=4,
default_flow_style=False,
allow_unicode=True)
def save_trials(self, trials_dir, num=1):
trials_dir = os.path.abspath(trials_dir)
os.makedirs(trials_dir, exist_ok=True)
for trial in self.trials(num=num):
name = '{}-{}-{}'.format(self.exp_class.__name__, trial['name'],
time.time())
t_dir = os.path.join(trials_dir, name)
os.makedirs(t_dir, exist_ok=True)
with open(os.path.join(t_dir, 'trial.yaml'), 'w') as f:
trial['name'] = name
trial['log_dir'] = t_dir
yaml.safe_dump(trial, stream=f, default_flow_style=False)
def renameElements(filename, suffix, debug):
print("Renaming elemnts in filename: \"{}\"".format(filename))
elementNamesMap = {}
with root_open(filename, "UPDATE") as f:
if debug:
print("f.ls() pre:")
f.ls()
# Cannot just iterate over GetListOfKeys because the hash list is updated when an element is added to a file...
# Instead, we copy the keys so the iterable is not updated (this should really be treated as a ROOT bug...)
keys = f.GetListOfKeys()
simpleListOfKeys = []
for key in keys:
simpleListOfKeys.append(key.GetName())
# Loop over the available keys. If it is the correction task, then unpack the component lists
for key in simpleListOfKeys:
if key.endswith("_" + suffix):
print(
"Skipping the processing of element {} since it has already been processed!"
.format(key))
# Same the name in the proper formatt to be used in the YAML map
elementNamesMap[key.replace("_" + suffix, "")] = [key]
# Don't apply the suffix twice
continue
element = f.Get(key)
print("Processing element: {}".format(element.GetName()))
# Remove the existing element from the file
f.Delete(element.GetName() + ";*")
# Rewrite the name
if "AliEmcalCorrectionTask" in element.GetName():
for component in element:
elementNamesMap = rewriteWithDifferentName(
component, suffix, elementNamesMap)
else:
elementNamesMap = rewriteWithDifferentName(
element, suffix, elementNamesMap)
if debug:
print("keys: {}".format(keys.GetEntries()))
print("f.ls() post:")
f.ls()
# Save the map for user with the comparison script
# Write the reference map to the same directory as the reference file
yamlReferenceMapLocation = os.path.join(os.path.dirname(filename),
"referenceMap.yaml")
print("Writing yaml reference map to \"{}\"".format(
yamlReferenceMapLocation))
with open(yamlReferenceMapLocation, "w+b") as f:
yaml.safe_dump(elementNamesMap, f, default_flow_style=False)
def get_alias():
data = yaml.safe_load(read_text('ttslib.data', 'to_speaker.yaml'))
d = dict()
for k in data.keys():
match_obj = re.fullmatch(r'(..)_(..)', k)
if match_obj:
for k1 in match_obj.groups():
d.setdefault(k1, []).append(k)
else:
d.setdefault(k[:2], []).append(k)
with open('../ttslib/data/alias.yaml', 'w') as f:
yaml.safe_dump(d, f)
def yaml_dump(filepath, conf):
"""Write a configuration to a YAML configuration file
Arguments:
filepath {Path} -- Configuration file's path to write to
conf {dict} -- Configuration values
"""
with filepath.open('w') as f:
f.write("""#
# This file was generated using mkctf utility. Do not edit it manually unless
# you know exactly what you're doing. #PEBCAK
#
""")
yaml.safe_dump(conf, f, default_flow_style=False)
def dump_yaml(data, *path):
def convert(obj):
if isinstance(obj, dict):
obj = {k: v for k, v in obj.items() if not k.startswith('_')}
return {convert(k): convert(v) for k, v in obj.items()}
if isinstance(obj, list):
return [convert(x) for x in obj]
if isinstance(obj, type):
return obj.__name__
return obj
filename = os.path.join(*path)
ensure_directory(os.path.dirname(filename))
with open(filename, 'w') as file_:
yaml.safe_dump(convert(data), file_, default_flow_style=False)
def write_dois_debian(dois, file):
parsed_yaml = parse_yaml(file)
identifiers = parsed_yaml['identifiers']
# if doi doesn't exist
if 'doi' not in identifiers:
identifiers['doi'] = [dois.pop()]
for doi in dois:
identifiers['doi'].append(doi)
parsed_yaml['identifiers'] = identifiers
with open(file, 'w') as outfile:
# do something fancy like indentation/mapping/sequence/offset
yaml.safe_dump(parsed_yaml, outfile, default_flow_style=False)
def test_no_change(self, tmpdir, spec, config_file, new_config):
with open(config_file, "w") as f:
yaml.safe_dump(new_config,
stream=f,
default_flow_style=False,
encoding="utf-8")
beer_garden.config.load(["-c", str(config_file)], force=True)
assert beer_garden.config.get("log.level") == "INFO"
with open(config_file) as f:
new_config_value = yaml.safe_load(f)
assert new_config_value == new_config
assert len(os.listdir(tmpdir)) == 1
def run_local_topology(name=None, env_name=None, time=0, options=None):
"""Run a topology locally using Flux and `storm jar`."""
name, topology_file = get_topology_definition(name)
config = get_config()
env_name, env_config = get_env_config(env_name)
topology_class = get_topology_from_file(topology_file)
set_topology_serializer(env_config, config, topology_class)
storm_options = resolve_options(options, env_config, topology_class, name)
if storm_options['topology.acker.executors'] != 0:
storm_options['topology.acker.executors'] = 1
storm_options['topology.workers'] = 1
# Check Storm version is the same
local_version = local_storm_version()
project_version = storm_lib_version()
if local_version != project_version:
raise ValueError('Local Storm version, {}, is not the same as the '
'version in your project.clj, {}. The versions must '
'match.'.format(local_version, project_version))
# Prepare a JAR that has Storm dependencies packaged
topology_jar = jar_for_deploy(simple_jar=False)
if time <= 0:
time = 9223372036854775807 # Max long value in Java
# Write YAML file
with show('output'):
with NamedTemporaryFile(mode='w', suffix='.yaml',
delete=False) as yaml_file:
topology_flux_dict = topology_class.to_flux_dict(name)
topology_flux_dict['config'] = storm_options
if yaml.version_info < (0, 15):
yaml.safe_dump(topology_flux_dict,
yaml_file,
default_flow_style=False)
else:
yml = yaml.YAML(typ='safe', pure=True)
yml.default_flow_style = False
yml.dump(topology_flux_dict, yaml_file)
cmd = (
'storm jar {jar} org.apache.storm.flux.Flux --local --no-splash '
'--sleep {time} {yaml}'.format(jar=topology_jar,
time=time,
yaml=yaml_file.name))
local(cmd)
def test_model_hot_reloading(app, rasa_default_train_data):
query = "http://dummy-uri/parse?q=hello&project=my_keyword_model"
response = yield app.get(query)
assert response.code == 404, "Project should not exist yet"
train_u = "http://dummy-uri/train?project=my_keyword_model"
model_config = {"pipeline": "keyword", "data": rasa_default_train_data}
model_str = yaml.safe_dump(model_config, default_flow_style=False,
allow_unicode=True)
response = app.post(train_u,
headers={b"Content-Type": b"application/x-yml"},
data=model_str)
time.sleep(3)
app.flush()
response = yield response
assert response.code == 200, "Training should end successfully"
response = app.post(train_u,
headers={b"Content-Type": b"application/json"},
data=json.dumps(model_config))
time.sleep(3)
app.flush()
response = yield response
assert response.code == 200, "Training should end successfully"
response = yield app.get(query)
assert response.code == 200, "Project should now exist after it got trained"
def _write(f, data):
try:
_f = open(f, "w")
except IOError:
raise KeyError
else:
return yaml.safe_dump(data, _f, default_flow_style=False)
def write(self):
''' write to file '''
if not self.filename:
raise YeditException('Please specify a filename.')
if self.backup and self.file_exists():
shutil.copy(self.filename, '{}{}'.format(self.filename, self.backup_ext))
# Try to set format attributes if supported
try:
self.yaml_dict.fa.set_block_style()
except AttributeError:
pass
# Try to use RoundTripDumper if supported.
if self.content_type == 'yaml':
try:
Yedit._write(self.filename, yaml.dump(self.yaml_dict, Dumper=yaml.RoundTripDumper))
except AttributeError:
Yedit._write(self.filename, yaml.safe_dump(self.yaml_dict, default_flow_style=False))
elif self.content_type == 'json':
Yedit._write(self.filename, json.dumps(self.yaml_dict, indent=4, sort_keys=True))
else:
raise YeditException('Unsupported content_type: {}.'.format(self.content_type) +
'Please specify a content_type of yaml or json.')
return (True, self.yaml_dict)
def write(self):
''' write to file '''
if not self.filename:
raise YeditException('Please specify a filename.')
if self.backup and self.file_exists():
shutil.copy(self.filename, self.filename + '.orig')
# Try to set format attributes if supported
try:
self.yaml_dict.fa.set_block_style()
except AttributeError:
pass
# Try to use RoundTripDumper if supported.
if self.content_type == 'yaml':
try:
Yedit._write(self.filename, yaml.dump(self.yaml_dict, Dumper=yaml.RoundTripDumper))
except AttributeError:
Yedit._write(self.filename, yaml.safe_dump(self.yaml_dict, default_flow_style=False))
elif self.content_type == 'json':
Yedit._write(self.filename, json.dumps(self.yaml_dict, indent=4, sort_keys=True))
else:
raise YeditException('Unsupported content_type: {}.'.format(self.content_type) +
'Please specify a content_type of yaml or json.')
return (True, self.yaml_dict)
def test_catastrophe(self, capsys, tmpdir, spec, config_file, old_config):
with open(config_file, "w") as f:
yaml.safe_dump(old_config,
stream=f,
default_flow_style=False,
encoding="utf-8")
with patch("os.rename", Mock(side_effect=[Mock(), ValueError])):
with pytest.raises(ValueError):
beer_garden.config.load(["-c", str(config_file)], force=True)
# Make sure we printed something
assert capsys.readouterr().err
# Both the tmp file and the old JSON should still be there.
assert len(os.listdir(tmpdir)) == 2
def test_model_hot_reloading(app, rasa_default_train_data):
query = "http://dummy-uri/parse?q=hello&project=my_keyword_model"
response = yield app.get(query)
assert response.code == 404, "Project should not exist yet"
train_u = "http://dummy-uri/train?project=my_keyword_model"
model_config = {"pipeline": "keyword", "data": rasa_default_train_data}
model_str = yaml.safe_dump(model_config,
default_flow_style=False,
allow_unicode=True)
response = app.post(train_u,
headers={b"Content-Type": b"application/x-yml"},
data=model_str)
time.sleep(3)
app.flush()
response = yield response
assert response.code == 200, "Training should end successfully"
response = app.post(train_u,
headers={b"Content-Type": b"application/json"},
data=json.dumps(model_config))
time.sleep(3)
app.flush()
response = yield response
assert response.code == 200, "Training should end successfully"
response = yield app.get(query)
assert response.code == 200, "Project should now exist after it got trained"
def format_base64_as_yaml(source: str) -> str:
s = yaml.safe_dump(yaml.safe_load(base64.b64decode(source)),
default_flow_style=False)
if not isinstance(s, str):
raise AssertionError("cannot format base64 string to yaml")
return s
def write(self):
''' write to file '''
if not self.filename:
raise YeditException('Please specify a filename.')
if self.backup and self.file_exists():
shutil.copy(self.filename, self.filename + '.orig')
# Try to set format attributes if supported
try:
self.yaml_dict.fa.set_block_style()
except AttributeError:
pass
# Try to use RoundTripDumper if supported.
try:
Yedit._write(
self.filename,
yaml.dump(self.yaml_dict, Dumper=yaml.RoundTripDumper))
except AttributeError:
Yedit._write(
self.filename,
yaml.safe_dump(self.yaml_dict, default_flow_style=False))
return (True, self.yaml_dict)
def inner(self, req, resp, *args, **kwargs):
try:
data = func(self, req, resp, *args, **kwargs)
except Exception as e:
log.exception("Error in API call")
resp.status = "500 Internal Server Error"
resp.content_type = "text"
resp.body = str(e)
return
if not data:
return
accepts = req.get_header("Accepts")
if not accepts:
accepts = "application/json"
accepts = accepts.lower()
if accepts == "application/x-yaml":
resp.content_type = accepts
resp.body = yaml.safe_dump(data)
elif accepts == "application/json":
resp.content_type = accepts
resp.body = json.dumps(data)
elif accepts == "application/xml":
resp.content_type = accepts
resp.body = dicttoxml(data)
else:
resp.status = "400 Bad Request"
resp.content_type = "text"
resp.body = "Unknown or unsupported content type: {}\n\n" \
"We support application/json, application/xml or application/x-yaml".format(accepts)
def get_styles(self, out_file=None, skip_cell_formatting=True):
formatting = self._to_styles(self.wb, skip_cell_formatting)
if out_file is not None:
return Path(out_file).write_text(yaml.safe_dump(formatting))
else:
return formatting
def write_file_config(file_config):
with tempfile.NamedTemporaryFile("w+",
suffix="_tmp_config_file.yml",
delete=False) as f:
f.write(yaml.safe_dump(file_config))
f.flush()
return f
def migrate(self, recipe_dir: str, attrs: "AttrsTypedDict",
**kwargs: Any) -> "MigrationUidTypedDict":
with indir(recipe_dir + "/.."):
self.set_build_number("recipe/meta.yaml")
with open("conda-forge.yml", "r") as f:
y = safe_load(f)
if "provider" not in y:
y["provider"] = {}
for k, v in self.arches.items():
if k not in y["provider"]:
y["provider"][k] = v
with open("conda-forge.yml", "w") as f:
safe_dump(y, f)
return super().migrate(recipe_dir, attrs, **kwargs)
def write_file_config(file_config):
with tempfile.NamedTemporaryFile("w+",
suffix="_tmp_config_file.yml",
delete=False) as f:
f.write(yaml.safe_dump(file_config))
f.flush()
return f
def parse_shannon_radii():
with open('periodic_table.yaml', 'r') as f:
data = yaml.load(f)
from openpyxl import load_workbook
import collections
wb = load_workbook('Shannon Radii.xlsx')
print(wb.get_sheet_names())
sheet = wb["Sheet1"]
i = 2
radii = collections.defaultdict(dict)
while sheet["E%d" % i].value:
if sheet["A%d" % i].value:
el = sheet["A%d" % i].value
if sheet["B%d" % i].value:
charge = int(sheet["B%d" % i].value)
radii[el][charge] = dict()
if sheet["C%d" % i].value:
cn = sheet["C%d" % i].value
if cn not in radii[el][charge]:
radii[el][charge][cn] = dict()
if sheet["D%d" % i].value is not None:
spin = sheet["D%d" % i].value
else:
spin = ""
# print("%s - %d - %s" % (el, charge, cn))
radii[el][charge][cn][spin] = {
"crystal_radius": float(sheet["E%d" % i].value),
"ionic_radius": float(sheet["F%d" % i].value),
}
i += 1
for el in radii.keys():
if el in data:
data[el]["Shannon radii"] = dict(radii[el])
with open('periodic_table.yaml', 'w') as f:
yaml.safe_dump(data, f)
with open('periodic_table.json', 'w') as f:
json.dump(data, f)
def dump(data, stream=None, **kwargs):
# type: (Any, Optional[IO[AnyStr]], Any) -> str
"""Dumps the given YAML data to the stream.
Args:
data: The YAML serializable Python object to dump.
stream: The stream to write the data to or None to return it as a string.
**kwargs: Other arguments to the dump method.
Returns:
The string representation of the YAML data if stream is None.
"""
return yaml.safe_dump(
data, stream=stream, default_flow_style=False, indent=2, **kwargs)
def to_format(self, f_format='json', **kwargs):
"""
returns a String representation in the given format
Args:
f_format (str): the format to output to (default json)
"""
if f_format == 'json':
return json.dumps(self.to_dict(), default=DATETIME_HANDLER, **kwargs)
elif f_format == 'yaml':
# start with the JSON format, and convert to YAML
return yaml.safe_dump(self.to_dict(), default_flow_style=YAML_STYLE,
allow_unicode=True)
else:
raise ValueError('Unsupported format {}'.format(f_format))
def write(self):
''' write to file '''
if not self.filename:
raise YeditException('Please specify a filename.')
if self.backup and self.file_exists():
shutil.copy(self.filename, self.filename + '.orig')
# Try to set format attributes if supported
try:
self.yaml_dict.fa.set_block_style()
except AttributeError:
pass
# Try to use RoundTripDumper if supported.
try:
Yedit._write(self.filename, yaml.dump(self.yaml_dict, Dumper=yaml.RoundTripDumper))
except AttributeError:
Yedit._write(self.filename, yaml.safe_dump(self.yaml_dict, default_flow_style=False))
return (True, self.yaml_dict)
def create_tmp_file_from_contents(rname, data, ftype='yaml'):
''' create a file in tmp with name and contents'''
tmp = Utils.create_tmpfile(prefix=rname)
if ftype == 'yaml':
# AUDIT:no-member makes sense here due to ruamel.YAML/PyYAML usage
# pylint: disable=no-member
if hasattr(yaml, 'RoundTripDumper'):
Utils._write(tmp, yaml.dump(data, Dumper=yaml.RoundTripDumper))
else:
Utils._write(tmp, yaml.safe_dump(data, default_flow_style=False))
elif ftype == 'json':
Utils._write(tmp, json.dumps(data))
else:
Utils._write(tmp, data)
# Register cleanup when module is done
atexit.register(Utils.cleanup, [tmp])
return tmp
def generate_biobox_file_content(args):
output = {"version" : "0.9.0", "arguments" : args}
return yaml.safe_dump(output, default_flow_style = False)
def save_context(context, **kwargs):
project_dir = yield
with io.open(os.path.join(project_dir, '.cookiecutterrc'), 'w', encoding='utf8') as fh:
fh.write(u"# Generated by cookiepatcher, a small shim around cookiecutter (pip install cookiepatcher)\n\n")
yaml.safe_dump(context, fh, indent=4, default_flow_style=False, allow_unicode=True)
def main(argsl=None, # type: List[str]
args=None, # type: argparse.Namespace
job_order_object=None, # type: MutableMapping[Text, Any]
stdin=sys.stdin, # type: IO[Any]
stdout=None, # type: Union[TextIO, codecs.StreamWriter]
stderr=sys.stderr, # type: IO[Any]
versionfunc=versionstring, # type: Callable[[], Text]
logger_handler=None, #
custom_schema_callback=None, # type: Callable[[], None]
executor=None, # type: Callable[..., Tuple[Dict[Text, Any], Text]]
loadingContext=None, # type: LoadingContext
runtimeContext=None # type: RuntimeContext
): # type: (...) -> int
if not stdout: # force UTF-8 even if the console is configured differently
if (hasattr(sys.stdout, "encoding") # type: ignore
and sys.stdout.encoding != 'UTF-8'): # type: ignore
if six.PY3 and hasattr(sys.stdout, "detach"):
stdout = io.TextIOWrapper(sys.stdout.buffer, encoding='utf-8')
else:
stdout = codecs.getwriter('utf-8')(sys.stdout) # type: ignore
else:
stdout = cast(TextIO, sys.stdout) # type: ignore
_logger.removeHandler(defaultStreamHandler)
if logger_handler:
stderr_handler = logger_handler
else:
stderr_handler = logging.StreamHandler(stderr)
_logger.addHandler(stderr_handler)
# pre-declared for finally block
workflowobj = None
try:
if args is None:
if argsl is None:
argsl = sys.argv[1:]
args = arg_parser().parse_args(argsl)
if runtimeContext is None:
runtimeContext = RuntimeContext(vars(args))
else:
runtimeContext = runtimeContext.copy()
# If on Windows platform, a default Docker Container is used if not
# explicitely provided by user
if onWindows() and not runtimeContext.default_container:
# This docker image is a minimal alpine image with bash installed
# (size 6 mb). source: https://github.com/frol/docker-alpine-bash
runtimeContext.default_container = windows_default_container_id
# If caller parsed its own arguments, it may not include every
# cwltool option, so fill in defaults to avoid crashing when
# dereferencing them in args.
for key, val in six.iteritems(get_default_args()):
if not hasattr(args, key):
setattr(args, key, val)
rdflib_logger = logging.getLogger("rdflib.term")
rdflib_logger.addHandler(stderr_handler)
rdflib_logger.setLevel(logging.ERROR)
if args.quiet:
_logger.setLevel(logging.WARN)
if runtimeContext.debug:
_logger.setLevel(logging.DEBUG)
rdflib_logger.setLevel(logging.DEBUG)
if args.timestamps:
formatter = logging.Formatter("[%(asctime)s] %(message)s",
"%Y-%m-%d %H:%M:%S")
stderr_handler.setFormatter(formatter)
if args.version:
print(versionfunc())
return 0
_logger.info(versionfunc())
if args.print_supported_versions:
print("\n".join(supported_cwl_versions(args.enable_dev)))
return 0
if not args.workflow:
if os.path.isfile("CWLFile"):
setattr(args, "workflow", "CWLFile")
else:
_logger.error("")
_logger.error("CWL document required, no input file was provided")
arg_parser().print_help()
return 1
if args.relax_path_checks:
command_line_tool.ACCEPTLIST_RE = command_line_tool.ACCEPTLIST_EN_RELAXED_RE
if args.ga4gh_tool_registries:
ga4gh_tool_registries[:] = args.ga4gh_tool_registries
if not args.enable_ga4gh_tool_registry:
del ga4gh_tool_registries[:]
if custom_schema_callback:
custom_schema_callback()
elif args.enable_ext:
res = pkg_resources.resource_stream(__name__, 'extensions.yml')
use_custom_schema("v1.0", "http://commonwl.org/cwltool", res.read())
res.close()
else:
use_standard_schema("v1.0")
#call function from provenance.py if the provenance flag is enabled.
if args.provenance:
if not args.compute_checksum:
_logger.error("--provenance incompatible with --no-compute-checksum")
return 1
runtimeContext.research_obj = ResearchObject(
temp_prefix_ro=args.tmpdir_prefix,
# Optionals, might be None
orcid=args.orcid,
full_name=args.cwl_full_name)
if loadingContext is None:
loadingContext = LoadingContext(vars(args))
else:
loadingContext = loadingContext.copy()
loadingContext.research_obj = runtimeContext.research_obj
loadingContext.disable_js_validation = \
args.disable_js_validation or (not args.do_validate)
loadingContext.construct_tool_object = getdefault(
loadingContext.construct_tool_object, workflow.default_make_tool)
loadingContext.resolver = getdefault(loadingContext.resolver, tool_resolver)
uri, tool_file_uri = resolve_tool_uri(
args.workflow, resolver=loadingContext.resolver,
fetcher_constructor=loadingContext.fetcher_constructor)
try_again_msg = "" if args.debug else ", try again with --debug for more information"
try:
job_order_object, input_basedir, jobloader = load_job_order(
args, stdin, loadingContext.fetcher_constructor,
loadingContext.overrides_list, tool_file_uri)
if args.overrides:
loadingContext.overrides_list.extend(load_overrides(
file_uri(os.path.abspath(args.overrides)), tool_file_uri))
document_loader, workflowobj, uri = fetch_document(
uri, resolver=loadingContext.resolver,
fetcher_constructor=loadingContext.fetcher_constructor)
if args.print_deps:
printdeps(workflowobj, document_loader, stdout, args.relative_deps, uri)
return 0
document_loader, avsc_names, processobj, metadata, uri \
= validate_document(document_loader, workflowobj, uri,
enable_dev=loadingContext.enable_dev,
strict=loadingContext.strict,
preprocess_only=(args.print_pre or args.pack),
fetcher_constructor=loadingContext.fetcher_constructor,
skip_schemas=args.skip_schemas,
overrides=loadingContext.overrides_list,
do_validate=loadingContext.do_validate)
if args.pack:
stdout.write(print_pack(document_loader, processobj, uri, metadata))
return 0
if args.provenance and runtimeContext.research_obj:
# Can't really be combined with args.pack at same time
runtimeContext.research_obj.packed_workflow(
print_pack(document_loader, processobj, uri, metadata))
if args.print_pre:
stdout.write(json_dumps(processobj, indent=4))
return 0
loadingContext.overrides_list.extend(metadata.get("cwltool:overrides", []))
tool = make_tool(document_loader, avsc_names,
metadata, uri, loadingContext)
if args.make_template:
yaml.safe_dump(generate_input_template(tool), sys.stdout,
default_flow_style=False, indent=4,
block_seq_indent=2)
return 0
if args.validate:
_logger.info("Tool definition is valid")
return 0
if args.print_rdf:
stdout.write(printrdf(tool, document_loader.ctx, args.rdf_serializer))
return 0
if args.print_dot:
printdot(tool, document_loader.ctx, stdout)
return 0
except (validate.ValidationException) as exc:
_logger.error(u"Tool definition failed validation:\n%s", exc,
exc_info=args.debug)
return 1
except (RuntimeError, WorkflowException) as exc:
_logger.error(u"Tool definition failed initialization:\n%s", exc,
exc_info=args.debug)
return 1
except Exception as exc:
_logger.error(
u"I'm sorry, I couldn't load this CWL file%s.\nThe error was: %s",
try_again_msg,
exc if not args.debug else "",
exc_info=args.debug)
return 1
if isinstance(tool, int):
return tool
# If on MacOS platform, TMPDIR must be set to be under one of the
# shared volumes in Docker for Mac
# More info: https://dockstore.org/docs/faq
if sys.platform == "darwin":
default_mac_path = "/private/tmp/docker_tmp"
if runtimeContext.tmp_outdir_prefix == DEFAULT_TMP_PREFIX:
runtimeContext.tmp_outdir_prefix = default_mac_path
for dirprefix in ("tmpdir_prefix", "tmp_outdir_prefix", "cachedir"):
if getattr(runtimeContext, dirprefix) and getattr(runtimeContext, dirprefix) != DEFAULT_TMP_PREFIX:
sl = "/" if getattr(runtimeContext, dirprefix).endswith("/") or dirprefix == "cachedir" \
else ""
setattr(runtimeContext, dirprefix,
os.path.abspath(getattr(runtimeContext, dirprefix)) + sl)
if not os.path.exists(os.path.dirname(getattr(runtimeContext, dirprefix))):
try:
os.makedirs(os.path.dirname(getattr(runtimeContext, dirprefix)))
except Exception as e:
_logger.error("Failed to create directory: %s", e)
return 1
if args.cachedir:
if args.move_outputs == "move":
runtimeContext.move_outputs = "copy"
runtimeContext.tmp_outdir_prefix = args.cachedir
runtimeContext.secret_store = getdefault(runtimeContext.secret_store, SecretStore())
runtimeContext.make_fs_access = getdefault(runtimeContext.make_fs_access, StdFsAccess)
try:
initialized_job_order_object = init_job_order(
job_order_object, args, tool, jobloader, stdout,
print_input_deps=args.print_input_deps,
relative_deps=args.relative_deps,
make_fs_access=runtimeContext.make_fs_access,
input_basedir=input_basedir,
secret_store=runtimeContext.secret_store)
except SystemExit as err:
return err.code
if not executor:
if args.parallel:
executor = MultithreadedJobExecutor()
runtimeContext.select_resources = executor.select_resources
else:
executor = SingleJobExecutor()
assert executor is not None
try:
runtimeContext.basedir = input_basedir
del args.workflow
del args.job_order
conf_file = getattr(args, "beta_dependency_resolvers_configuration", None) # Text
use_conda_dependencies = getattr(args, "beta_conda_dependencies", None) # Text
if conf_file or use_conda_dependencies:
runtimeContext.job_script_provider = DependenciesConfiguration(args)
runtimeContext.find_default_container = functools.partial(
find_default_container,
default_container=runtimeContext.default_container,
use_biocontainers=args.beta_use_biocontainers)
(out, status) = executor(tool,
initialized_job_order_object,
runtimeContext,
logger=_logger)
if out is not None:
def loc_to_path(obj):
for field in ("path", "nameext", "nameroot", "dirname"):
if field in obj:
del obj[field]
if obj["location"].startswith("file://"):
obj["path"] = uri_file_path(obj["location"])
visit_class(out, ("File", "Directory"), loc_to_path)
# Unsetting the Generation from final output object
visit_class(out, ("File", ), MutationManager().unset_generation)
if isinstance(out, string_types):
stdout.write(out)
else:
stdout.write(json_dumps(out, indent=4, # type: ignore
ensure_ascii=False))
stdout.write("\n")
if hasattr(stdout, "flush"):
stdout.flush() # type: ignore
if status != "success":
_logger.warning(u"Final process status is %s", status)
return 1
_logger.info(u"Final process status is %s", status)
return 0
except (validate.ValidationException) as exc:
_logger.error(u"Input object failed validation:\n%s", exc,
exc_info=args.debug)
return 1
except UnsupportedRequirement as exc:
_logger.error(
u"Workflow or tool uses unsupported feature:\n%s", exc,
exc_info=args.debug)
return 33
except WorkflowException as exc:
_logger.error(
u"Workflow error%s:\n%s", try_again_msg, strip_dup_lineno(six.text_type(exc)),
exc_info=args.debug)
return 1
except Exception as exc:
_logger.error(
u"Unhandled error%s:\n %s", try_again_msg, exc, exc_info=args.debug)
return 1
finally:
if args and runtimeContext and runtimeContext.research_obj \
and args.rm_tmpdir and workflowobj:
#adding all related cwl files to RO
prov_dependencies = printdeps(
workflowobj, document_loader, stdout, args.relative_deps, uri,
runtimeContext.research_obj)
prov_dep = prov_dependencies[1]
assert prov_dep
runtimeContext.research_obj.generate_snapshot(prov_dep)
runtimeContext.research_obj.close(args.provenance)
_logger.removeHandler(stderr_handler)
_logger.addHandler(defaultStreamHandler)
def _write_yaml(self, config_dict, dest):
with io.open(dest, 'w', encoding='UTF-8') as f:
yaml.safe_dump(config_dict, f, default_flow_style=False)
def _write_yaml(self, config_dict, dest):
with open(dest, 'w') as f:
yaml.safe_dump(config_dict, f, default_flow_style=False)
def run(self, cmd, args, options):
if args['--example']:
s = '''
# Example client specification file
# Specification files are in YAML format (a superset of JSON
# with more readable syntax and support for comments) and
# look like this. They may contain comments that begin
# with a # sign.
# Device client model information
device:
model: "myModel"
vendor: "myVendor"
# list of dataports that must exist
dataports:
# this the absolute minimum needed to specify a
# dataport.
- alias: mystring
# names are created, but not compared
- name: Temperature
# aliases, type, and format are created
# and compared
alias: temp
format: float
unit: °F
- name: LED Control
alias: led6
format: integer
- alias: config
# format should be string, and parseable JSON
format: string/json
# initial value (if no other value is read back)
initial: '{"text": "555-555-1234", "email": "*****@*****.**"}'
- alias: person
format: string/json
# JSON schema specified inline (http://json-schema.org/)
# format must be string/json to do validate
# you may also specify a string to reference schema in an
# external file. E.g. jsonschema: personschema.json
jsonschema: {"title": "Person Schema",
"type": "object",
"properties": {"name": {"type": "string"}},
"required": ["name"]}
initial: '{"name":"John Doe"}'
- alias: place
# An description of the dataport.
description: 'This is a place I have been'
# Dataports are not public by default,
# but if you want to share one with the world
public: true
# any dataports not listed but found in the client
# are ignored. The spec command does not delete things.
# list of script datarules that must exist
scripts:
# by default, scripts are datarules with
# names and aliases set to the file name
- file: test/files/helloworld.lua
# you can also set them explicitly
- file: test/files/helloworld.lua
alias: greeting
# you can also place lua code inline
- alias: singleLineScript
code: debug('hello from inside lua!')
# multiline lua scripts should start with | and
# be indented inside the "code:" key.
- alias: multilineScript
code: |
for x=1,10 do
debug('hello from for loop ' .. x)
end
# simple templating for script aliases and
# content is also supported.
- file: test/files/convert.lua
# if <% id %> is embedded in aliases
# or script content, the --ids parameter must
# be passed in. The spec command then expects
# a script or dataport resource per id passed, substituting
# each ID for <% id %>. In this example, if the command was:
#
# $ exo spec mysensor sensorspec.yaml --ids=A,B
#
# ...then the spec command looks for *two* script datarules
# in mysensor, with aliases convertA.lua and convertB.lua.
# Additionally, any instances of <% id %> in the content of
# convert.lua are substituted with A and B before being
# written to each script datarule.
#
alias: convert<% id %>.lua
# list of dispatches that must exist
dispatches:
- alias: myDispatch
# email | http_get | http_post | http_put | sms | xmpp
method: email
recipient: [email protected]
message: hello from Exoline spec example!
subject: hello!
# may be an RID or alias
subscribe: mystring
# list of simple datarules that must exist.
# scripts may go here too, but it's better to
# to put them under scripts (above)
datarules:
- alias: highTemp
format: float
subscribe: temp
rule: {
"simple": {
"comparison": "gt",
"constant": 80,
"repeat": true
}
}
'''
if not six.PY3:
s = s.encode('utf-8')
print(s)
return
ExoException = options['exception']
def load_file(path, base_url=None):
'''load a file based on a path that may be a filesystem path
or a URL. Consider it a URL if it starts with two or more
alphabetic characters followed by a colon'''
def load_from_url(url):
# URL. use requests
r = requests.get(url)
if r.status_code >= 300:
raise ExoException('Failed to read file at URL ' + url)
return r.text, '/'.join(r.url.split('/')[:-1])
if re.match('[a-z]{2}[a-z]*:', path):
return load_from_url(path)
elif base_url is not None:
# non-url paths when spec is loaded from URLs
# are considered relative to that URL
return load_from_url(base_url + '/' + path)
else:
with open(path, 'rb') as f:
return f.read(), None
def load_spec(args):
# returns loaded spec and path for script files
try:
content, base_url = load_file(args['<spec-yaml>'])
spec = yaml.safe_load(content)
return spec, base_url
except yaml.scanner.ScannerError as ex:
raise ExoException('Error parsing YAML in {0}\n{1}'.format(args['<spec-yaml>'],ex))
def check_spec(spec, args):
msgs = []
for typ in TYPES:
if typ in spec and plural(typ) not in spec:
msgs.append('found "{0}"... did you mean "{1}"?'.format(typ, typ + 's'))
for dp in spec.get('dataports', []):
if 'alias' not in dp:
msgs.append('dataport is missing alias: {0}'.format(dp))
continue
alias = dp['alias']
if 'jsonschema' in dp:
schema = dp['jsonschema']
if isinstance(schema, six.string_types):
schema = json.loads(open(schema).read())
try:
jsonschema.Draft4Validator.check_schema(schema)
except Exception as ex:
msgs.append('{0} failed jsonschema validation.\n{1}'.format(alias, str(ex)))
if len(msgs) > 0:
raise ExoException('Found some problems in spec:\n' + '\n'.join(msgs))
if args['--check']:
# Validate all the jsonschema
spec, base_url = load_spec(args)
check_spec(spec, args)
return
reid = re.compile('<% *id *%>')
def infoval(input_cik, alias):
'''Get info and latest value for a resource'''
return rpc._exomult(
input_cik,
[['info', {'alias': alias}, {'description': True, 'basic': True}],
['read', {'alias': alias}, {'limit': 1}]])
def check_or_create_description(auth, info, args):
if 'device' in spec and 'limits' in spec['device']:
speclimits = spec['device']['limits']
infolimits = info['description']['limits']
limits_mismatched = False
for limit in speclimits:
if limit not in infolimits:
raise ExoException('spec file includes invalid limit {0}'.format(limit))
if speclimits[limit] != infolimits[limit]:
limits_mismatched = True
if limits_mismatched:
if create:
if 'client_id' not in auth:
raise ExoException('limits update for client requires --portal or --domain')
rpc.update(auth['cik'], auth['client_id'], {'limits': speclimits})
sys.stdout.write('updated limits for client' +
' RID {0}'.format(auth['client_id']))
else:
sys.stdout.write(
'limits for client {0} do not match spec:\nspec: {1}\nclient: {2}'.format(
auth,
json.dumps(speclimits, sort_keys=True),
json.dumps(infolimits, sort_keys=True)))
def check_or_create_common(auth, res, info, alias, aliases):
if info['basic']['type'] != typ:
raise ExoException('{0} is a {1} but should be a {2}.'.format(alias, info['basic']['type'], typ))
new_desc = info['description'].copy()
need_update = False
if 'public' in res:
res_pub = res['public']
desc = info['description']
if desc['public'] != res_pub:
if create:
new_desc['public'] = res_pub
need_update = True
else:
sys.stdout.write('spec expects public for {0} to be {1}, but it is not.\n'.format(alias, res_pub))
print(json.dumps(res))
if 'subscribe' in res:
# Alias *must* be local to this client
resSub = res['subscribe']
# Lookup alias/name if need be
if resSub in aliases:
resSub = aliases[resSub]
desc = info['description']
if desc['subscribe'] != resSub:
if create:
new_desc['subscribe'] = resSub
need_update = True
else:
sys.stdout.write('spec expects subscribe for {0} to be {1}, but they are not.\n'.format(alias, resSub))
if 'preprocess' in res:
def fromAliases(pair):
if pair[1] in aliases:
return [pair[0], aliases[pair[1]]]
else:
return pair
resPrep = [fromAliases(x) for x in res['preprocess']]
preprocess = info['description']['preprocess']
if create:
new_desc['preprocess'] = resPrep
need_update = True
else:
if preprocess is None or len(preprocess) == 0:
sys.stdout.write('spec expects preprocess for {0} to be {1}, but they are missing.\n'.format(alias, resPrep))
elif preprocess != resPrep:
sys.stdout.write('spec expects preprocess for {0} to be {1}, but they are {2}.\n'.format(alias, resPrep, preprocess))
if 'retention' in res:
resRet = {}
if 'count' in res['retention']:
resRet['count'] = res['retention']['count']
if 'duration' in res['retention']:
resRet['duration'] = res['retention']['duration']
retention = info['description']['retention']
if create:
new_desc['retention'] = resRet
need_update = True
elif retention != resRet:
sys.stdout.write('spec expects retention for {0} to be {1}, but they are {2}.\n'.format(alias, resRet, retention))
if need_update:
rpc.update(auth, {'alias': alias}, new_desc)
def get_format(res, default='string'):
format = res['format'] if 'format' in res else default
pieces = format.split('/')
if len(pieces) > 1:
format = pieces[0]
format_content = pieces[1]
else:
format_content = None
return format, format_content
def add_desc(key, res, desc, required=False):
'''add key from spec resource to a 1P resource description'''
if key in res:
desc[key] = res[key]
else:
if required:
raise ExoException('{0} in spec is missing required property {1}.'.format(alias, key))
def create_resource(auth, typ, desc, alias, msg=''):
name = res['name'] if 'name' in res else alias
print('Creating {0} with name: {1}, alias: {2}{3}'.format(
typ, name, alias, msg))
rid = rpc.create(auth, typ, desc, name=name)
rpc.map(auth, rid, alias)
info, val = infoval(auth, alias)
aliases[alias] = rid
return info, val
def check_or_create_datarule(auth, res, info, val, alias, aliases):
format, format_content = get_format(res, 'float')
if not exists and create:
desc = {'format': format}
desc['retention'] = {'count': 'infinity', 'duration': 'infinity'}
add_desc('rule', res, desc, required=True)
info, val = create_resource(
auth,
'datarule',
desc,
alias,
msg=', format: {0}, rule: {1}'.format(desc['format'], desc['rule']))
# check format
if format != info['description']['format']:
raise ExoException(
'{0} is a {1} but should be a {2}.'.format(
alias, info['description']['format'], format))
# check rule
infoRule = json.dumps(info['description']['rule'], sort_keys=True)
specRule = json.dumps(res['rule'], sort_keys=True)
if infoRule != specRule:
if create:
info['description']['rule'] = res['rule']
rpc.update(auth, {'alias': alias}, info['description'])
sys.stdout.write('updated rule for {0}\n'.format(alias))
else:
sys.stdout.write(
'spec expects rule for {0} to be:\n{1}\n...but it is:\n{2}\n'.format(
alias, specRule, infoRule))
check_or_create_common(auth, res, info, alias, aliases)
def check_or_create_dataport(auth, res, info, val, alias, aliases):
format, format_content = get_format(res, 'string')
if not exists and create:
desc = {'format': format}
desc['retention'] = {'count': 'infinity', 'duration': 'infinity'}
info, val = create_resource(
auth,
'dataport',
desc,
alias,
msg=', format: {0}'.format(format))
# check format
if format != info['description']['format']:
raise ExoException(
'{0} is a {1} but should be a {2}.'.format(
alias, info['description']['format'], format))
# check initial value
if 'initial' in res and len(val) == 0:
if create:
initialValue = template(res['initial'])
print('Writing initial value {0}'.format(initialValue))
rpc.write(auth, {'alias': alias}, initialValue)
# update values being validated
info, val = infoval(auth, alias)
else:
print('Required initial value not found in {0}. Pass --create to write initial value.'.format(alias))
# check format content (e.g. json)
if format_content == 'json':
if format != 'string':
raise ExoException(
'Invalid spec for {0}. json content type only applies to string, not {1}.'.format(alias, format));
if len(val) == 0:
print('Spec requires {0} be in JSON format, but it is empty.'.format(alias))
else:
obj = None
try:
obj = json.loads(val[0][1])
except:
print('Spec requires {0} be in JSON format, but it does not parse as JSON. Value: {1}'.format(
alias,
val[0][1]))
if obj is not None and 'jsonschema' in res:
schema = res['jsonschema']
if isinstance(schema, six.string_types):
schema = json.loads(open(schema).read())
try:
jsonschema.validate(obj, schema)
except Exception as ex:
print("{0} failed jsonschema validation.".format(alias))
print(ex)
elif format_content is not None:
raise ExoException(
'Invalid spec for {0}. Unrecognized format content {1}'.format(alias, format_content))
# check unit
if 'unit' in res or 'description' in res:
meta_string = info['description']['meta']
try:
meta = json.loads(meta_string)
except:
meta = None
def bad_desc_msg(s):
desc='""'
if 'description' in res:
desc = res['description']
sys.stdout.write('spec expects description for {0} to be {1}{2}\n'.format(alias, desc, s))
def bad_unit_msg(s):
unit=''
if 'unit' in res:
unit = res['unit']
sys.stdout.write('spec expects unit for {0} to be {1}{2}\n'.format(alias, unit, s))
if create:
if meta is None:
meta = {'datasource':{'description':'','unit':''}}
if 'datasource' not in meta:
meta['datasource'] = {'description':'','unit':''}
if 'unit' in res:
meta['datasource']['unit'] = res['unit']
if 'description:' in res:
meta['datasource']['description'] = res['description']
info['description']['meta'] = json.dumps(meta)
rpc.update(auth, {'alias': alias}, info['description'])
else:
if meta is None:
sys.stdout.write('spec expects metadata but found has no metadata at all. Pass --create to write metadata.\n')
elif 'datasource' not in meta:
sys.stdout.write('spec expects datasource in metadata but found its not there. Pass --create to write metadata.\n')
elif 'unit' not in meta['datasource'] and 'unit' in res:
bad_unit_msg(', but no unit is specified in metadata. Pass --create to set unit.\n')
elif 'description' not in meta['datasource'] and 'description' in res:
bad_desc_msg(', but no description is specified in metadata. Pass --create to set description.\n')
elif 'unit' in res and meta['datasource']['unit'] != res['unit']:
bad_unit_msg(', but metadata specifies unit of {0}. Pass --create to update unit.\n'.format(meta['datasource']['unit']))
elif 'description' in res and meta['datasource']['description'] != res['description']:
bad_desc_msg(', but metadata specifies description of {0}. Pass --create to update description.\n'.format(meta['datasource']['description']))
check_or_create_common(auth, res, info, alias, aliases)
def check_or_create_dispatch(auth, res, info, alias, aliases):
if not exists and create:
desc = {}
add_desc('method', res, desc, required=True)
add_desc('recipient', res, desc, required=True)
add_desc('subject', res, desc)
add_desc('message', res, desc)
desc['retention'] = {'count': 'infinity', 'duration': 'infinity'}
info, val = create_resource(
auth,
'dispatch',
desc,
alias,
msg=', method: {0}, recipient: {1}'.format(desc['method'], desc['recipient']))
# check dispatch-specific things
def check_desc(key, res, desc):
'''check a specific key and return whether an update is required'''
if key in res and desc[key] != res[key]:
if create:
desc[key] = res[key]
return True
else:
sys.stdout.write(
'spec expects {0} for {1} to be {2} but it is {3}\n'.format(
key, alias, res[key], desc[key]))
return False
desc = info['description']
need_update = False
need_update = check_desc('method', res, desc) or need_update
need_update = check_desc('recipient', res, desc) or need_update
need_update = check_desc('subject', res, desc) or need_update
need_update = check_desc('message', res, desc) or need_update
if need_update:
rpc.update(auth, {'alias': alias}, desc)
sys.stdout.write('updated {0} to {1}\n'.format(alias, json.dumps(desc, sort_keys=True)))
check_or_create_common(auth, res, info, alias, aliases)
input_cik = options['cik']
rpc = options['rpc']
asrid = args['--asrid']
if cmd == 'spec':
if args['--generate'] is not None:
spec_file = args['--generate']
if args['--scripts'] is not None:
script_dir = args['--scripts']
else:
script_dir = 'scripts'
print('Generating spec for {0}.'.format(input_cik))
print('spec file: {0}, scripts directory: {1}'.format(spec_file, script_dir))
# generate spec file, download scripts
spec = {}
info, listing = rpc._exomult(input_cik,
[['info', {'alias': ''}, {'basic': True,
'description': True,
'aliases': True}],
['listing', ['dataport', 'datarule', 'dispatch'], {}, {'alias': ''}]])
rids = listing['dataport'] + listing['datarule'] + listing['dispatch']
if len(rids) > 0:
child_info = rpc._exomult(input_cik, [['info', rid, {'basic': True, 'description': True}] for rid in rids])
for idx, rid in enumerate(rids):
myinfo = child_info[idx]
name = myinfo['description']['name']
def skip_msg(msg):
print('Skipping {0} (name: {1}). {2}'.format(rid, name, msg))
if rid not in info['aliases']:
skip_msg('It needs an alias.')
continue
# adds properties common to dataports and dispatches:
# preprocess, subscribe, retention, meta, public
def add_common_things(res):
res['name'] = myinfo['description']['name']
res['alias'] = info['aliases'][rid][0]
preprocess = myinfo['description']['preprocess']
if preprocess is not None and len(preprocess) > 0:
def toAlias(pair):
if not asrid and pair[1] in info['aliases']:
return [pair[0], info['aliases'][pair[1]][0]]
else:
return pair
res['preprocess'] = [toAlias(x) for x in preprocess]
subscribe = myinfo['description']['subscribe']
if subscribe is not None and subscribe is not "":
if not asrid and subscribe in info['aliases']:
res['subscribe'] = info['aliases'][subscribe][0]
else:
res['subscribe'] = subscribe
retention = myinfo['description']['retention']
if retention is not None:
count = retention['count']
duration = retention['duration']
if count is not None and duration is not None:
if count == 'infinity':
del retention['count']
if duration == 'infinity':
del retention['duration']
if len(retention) > 0:
res['retention'] = retention
meta_string = myinfo['description']['meta']
try:
meta = json.loads(meta_string)
unit = meta['datasource']['unit']
if len(unit) > 0:
res['unit'] = unit
desc = meta['datasource']['description']
if len(desc) > 0:
res['description'] = desc
except:
# assume unit is not present in metadata
pass
public = myinfo['description']['public']
if public is not None and public:
res['public'] = public
typ = myinfo['basic']['type']
if typ == 'dataport':
res = {
'format': myinfo['description']['format']
}
add_common_things(res)
spec.setdefault('dataports', []).append(res)
elif typ == 'datarule':
desc = myinfo['description']
is_script = desc['format'] == 'string' and 'rule' in desc and 'script' in desc['rule']
if is_script:
filename = os.path.join(script_dir, info['aliases'][rid][0])
spec.setdefault('scripts', []).append({'file': filename})
with open(filename, 'w') as f:
print('Writing {0}...'.format(filename))
f.write(desc['rule']['script'])
else:
res = {
'rule': desc['rule']
}
add_common_things(res)
spec.setdefault('datarules', []).append(res)
elif typ == 'dispatch':
desc = myinfo['description']
res = {
'method': desc['method'],
'message': desc['message'],
'recipient': desc['recipient'],
'subject': desc['subject']
}
add_common_things(res)
spec.setdefault('dispatches', []).append(res)
with open(spec_file, 'w') as f:
print('Writing {0}...'.format(spec_file))
yaml.safe_dump(spec, f, encoding='utf-8', indent=4, default_flow_style=False, allow_unicode=True)
return
updatescripts = args['--update-scripts']
create = args['--create']
def query_yes_no(question, default="yes"):
"""Ask a yes/no question via raw_input() and return their answer.
"question" is a string that is presented to the user.
"default" is the presumed answer if the user just hits <Enter>.
It must be "yes" (the default), "no" or None (meaning
an answer is required of the user).
The "answer" return value is one of "yes" or "no".
"""
valid = {"yes":True, "y":True, "ye":True,
"no":False, "n":False}
if default == None:
prompt = " [y/n] "
elif default == "yes":
prompt = " [Y/n] "
elif default == "no":
prompt = " [y/N] "
else:
raise ValueError("invalid default answer: '%s'" % default)
while True:
sys.stdout.write(question + prompt)
choice = raw_input().lower()
if default is not None and choice == '':
return valid[default]
elif choice in valid:
return valid[choice]
else:
sys.stdout.write("Please respond with 'yes' or 'no' "\
"(or 'y' or 'n').\n")
def generate_aliases_and_data(res, args):
ids = args['--ids']
if 'alias' in res:
alias = res['alias']
else:
if 'file' in res:
alias = os.path.basename(res['file'])
else:
raise ExoException('Resources in spec must have an alias. (For scripts, "file" will substitute.)')
if reid.search(alias) is None:
yield alias, None
else:
alias_template = alias
if ids is None:
raise ExoException('This spec requires --ids')
ids = ids.split(',')
for id, alias in [(id, reid.sub(id, alias_template)) for id in ids]:
yield alias, {'id': id}
spec, base_url = load_spec(args)
check_spec(spec, args)
device_auths = []
portal_ciks = []
iterate_portals = False
def auth_string(auth):
if isinstance(auth, dict):
return json.dumps(auth)
else:
return auth
if args['--portal'] == True:
portal_ciks.append((input_cik,''))
iterate_portals = True
if args['--domain'] == True:
#set iterate_portals flag to true so we can interate over each portal
iterate_portals = True
# Get list of users under a domain
user_keys = []
clients = rpc._listing_with_info(input_cik,['client'])
email_regex = re.compile(r'[^@]+@[^@]+\.[^@]+')
for k,v in clients['client'].items():
name = v['description']['name']
# if name is an email address
if email_regex.match(name):
user_keys.append(v['key'])
# Get list of each portal
for key in user_keys:
userlisting = rpc._listing_with_info(key,['client'])
for k,v in userlisting['client'].items():
portal_ciks.append((v['key'],v['description']['name']))
#print(x)
if iterate_portals == True:
for portal_cik, portal_name in portal_ciks:
# If user passed in the portal flag, but the spec doesn't have
# a vendor/model, exit
if (not 'device' in spec) or (not 'model' in spec['device']) or (not 'vendor' in spec['device']):
print("With --portal (or --domain) option, spec file requires a\r\n"
"device model and vendor field:\r\n"
"e.g.\r\n"
"device:\r\n"
" model: modelName\r\n"
" vendor: vendorName\r\n")
raise ExoException('--portal flag requires a device model/vendor in spec file')
else:
# get device vendor and model
modelName = spec['device']['model']
vendorName = spec['device']['vendor']
# If the portal has no name, use the cik as the name
if portal_name == '':
portal_name = portal_cik
print('Looking in ' + portal_name + ' for ' + modelName + '/' + vendorName)
# Get all clients in the portal
clients = rpc._listing_with_info(portal_cik, ['client'])
#print(modelName)
# for each client
for rid, v in iteritems(list(iteritems(clients))[0][1]):
# Get meta field
validJson = False
meta = None
try:
meta = json.loads(v['description']['meta'])
validJson = True
except ValueError as e:
# no json in this meat field
validJson = False
if validJson == True:
# get device type (only vendor types have a model and vendor
typ = meta['device']['type']
# if the device type is 'vendor'
if typ == 'vendor':
# and it matches our vendor/model in the spec file
if meta['device']['vendor'] == vendorName:
if meta['device']['model'] == modelName:
# Append an auth for this device to our list
auth = {
'cik': portal_cik, # v['key'],
'client_id': rid
}
device_auths.append(auth)
print(' found: {0} {1}'.format(v['description']['name'], auth_string(auth)))
else:
# only for single client
device_auths.append(input_cik)
# Make sure user knows they are about to update multiple devices
# unless the `-f` flag is passed
if ((args['--portal'] or args['--domain']) and args['--create']) and not args['-f']:
res = query_yes_no("You are about to update " + str(len(device_auths)) + " devices, are you sure?")
if res == False:
print('exiting')
return
# for each device in our list of device_auths
for auth in device_auths:
try:
aliases = {}
print("Running spec on: {0}".format(auth_string(auth)))
# apply spec [--create]
# Get map of aliases and description
info = rpc.info(auth, {'alias': ''}, {'aliases': True, 'description': True})
try:
for rid, alist in info['aliases'].items():
for alias in alist:
aliases[alias] = rid
except:
pass
# Check limits
check_or_create_description(auth, info, args)
for typ in TYPES:
for res in spec.get(plural(typ), []):
for alias, resource_data in generate_aliases_and_data(res, args):
# TODO: handle nonexistence
exists = True
try:
info, val = infoval(auth, alias)
except rpc.RPCException as e:
info = None
val = None
exists = False
print('{0} not found.'.format(alias))
if not create:
print('Pass --create to create it')
continue
except pyonep.exceptions.OnePlatformException as ex:
exc = ast.literal_eval(ex.message)
if exc['code'] == 401:
raise Spec401Exception()
else:
raise ex
def template(script):
if resource_data is None:
return script
else:
return reid.sub(resource_data['id'], script)
if typ == 'client':
if not exists:
if create:
print('Client creation is not yet supported')
continue
elif typ == 'dataport':
check_or_create_dataport(auth, res, info, val, alias, aliases)
elif typ == 'dispatch':
check_or_create_dispatch(auth, res, info, alias, aliases)
elif typ == 'datarule':
check_or_create_datarule(auth, res, info, val, alias, aliases)
elif typ == 'script':
if 'file' not in res and 'code' not in res:
raise ExoException('{0} is a script, so it needs a "file" or "code" key'.format(alias))
if 'file' in res and 'code' in res:
raise ExoException('{0} specifies both "file" and "code" keys, but they\'re mutually exclusive.')
name = res['name'] if 'name' in res else alias
if 'file' in res:
content, _ = load_file(res['file'], base_url=base_url)
if not six.PY3 or type(content) is bytes:
content = content.decode('utf8')
else:
content = res['code']
if not exists and create:
rpc.upload_script_content([auth], content, name=alias, create=True, filterfn=template)
continue
script_spec = template(content)
script_svr = info['description']['rule']['script']
script_friendly = 'file {0}'.format(res['file']) if 'file' in res else '"code" value in spec'
if script_svr != script_spec:
print('Script for {0} does not match {1}.'.format(alias, script_friendly))
if updatescripts:
print('Uploading script to {0}...'.format(alias))
rpc.upload_script_content([auth], script_spec, name=name, create=False, filterfn=template)
elif not args['--no-diff']:
# show diff
import difflib
differences = '\n'.join(
difflib.unified_diff(
script_spec.splitlines(),
script_svr.splitlines(),
fromfile=script_friendly,
tofile='info["description"]["rule"]["script"]'))
print(differences)
else:
raise ExoException('Found unsupported type {0} in spec.'.format(typ))
except Spec401Exception as ex:
print("******WARNING******* 401 received in spec, is the device expired?")
pass
formatter = Terminal256Formatter
else:
formatter = NullFormatter
if sys.version_info < (3, 0):
sys.stdout.write("Sorry, Python 3 og higher required\n")
sys.exit(1)
try: # ... to read json
i = args.infile.read()
d = json.loads( i )
if args.alwaysjson:
if pygments:
i = highlight( out, JsonLexer(), formatter() )
print( i )
else:
out = yaml.safe_dump(d, indent=args.indent, allow_unicode=True )
if pygments:
out = highlight( out, YamlLexer(), formatter() )
print( out )
except:
try: # ... to read yaml
d = yaml.load( i )
out = json.dumps(d, indent=args.indent)
if pygments:
out = highlight(out, JsonLexer(), formatter() )
print(out)
except:
print("input error: invalid json or yaml format")
def main(argsl=None, # type: List[str]
args=None, # type: argparse.Namespace
executor=single_job_executor, # type: Callable[..., Tuple[Dict[Text, Any], Text]]
makeTool=workflow.defaultMakeTool, # type: Callable[..., Process]
selectResources=None, # type: Callable[[Dict[Text, int]], Dict[Text, int]]
stdin=sys.stdin, # type: IO[Any]
stdout=sys.stdout, # type: IO[Any]
stderr=sys.stderr, # type: IO[Any]
versionfunc=versionstring, # type: Callable[[], Text]
job_order_object=None, # type: MutableMapping[Text, Any]
make_fs_access=StdFsAccess, # type: Callable[[Text], StdFsAccess]
fetcher_constructor=None, # type: FetcherConstructorType
resolver=tool_resolver,
logger_handler=None,
custom_schema_callback=None # type: Callable[[], None]
):
# type: (...) -> int
_logger.removeHandler(defaultStreamHandler)
if logger_handler:
stderr_handler = logger_handler
else:
stderr_handler = logging.StreamHandler(stderr)
_logger.addHandler(stderr_handler)
try:
if args is None:
if argsl is None:
argsl = sys.argv[1:]
args = arg_parser().parse_args(argsl)
# If On windows platform, A default Docker Container is Used if not explicitely provided by user
if onWindows() and not args.default_container:
# This docker image is a minimal alpine image with bash installed(size 6 mb). source: https://github.com/frol/docker-alpine-bash
args.default_container = windows_default_container_id
# If caller provided custom arguments, it may be not every expected
# option is set, so fill in no-op defaults to avoid crashing when
# dereferencing them in args.
for k, v in six.iteritems({'print_deps': False,
'print_pre': False,
'print_rdf': False,
'print_dot': False,
'relative_deps': False,
'tmp_outdir_prefix': 'tmp',
'tmpdir_prefix': 'tmp',
'print_input_deps': False,
'cachedir': None,
'quiet': False,
'debug': False,
'js_console': False,
'version': False,
'enable_dev': False,
'enable_ext': False,
'strict': True,
'skip_schemas': False,
'rdf_serializer': None,
'basedir': None,
'tool_help': False,
'workflow': None,
'job_order': None,
'pack': False,
'on_error': 'continue',
'relax_path_checks': False,
'validate': False,
'enable_ga4gh_tool_registry': False,
'ga4gh_tool_registries': [],
'find_default_container': None,
'make_template': False,
'overrides': None
}):
if not hasattr(args, k):
setattr(args, k, v)
if args.quiet:
_logger.setLevel(logging.WARN)
if args.debug:
_logger.setLevel(logging.DEBUG)
if args.version:
print(versionfunc())
return 0
else:
_logger.info(versionfunc())
if args.print_supported_versions:
print("\n".join(supportedCWLversions(args.enable_dev)))
return 0
if not args.workflow:
if os.path.isfile("CWLFile"):
setattr(args, "workflow", "CWLFile")
else:
_logger.error("")
_logger.error("CWL document required, no input file was provided")
arg_parser().print_help()
return 1
if args.relax_path_checks:
draft2tool.ACCEPTLIST_RE = draft2tool.ACCEPTLIST_EN_RELAXED_RE
if args.ga4gh_tool_registries:
ga4gh_tool_registries[:] = args.ga4gh_tool_registries
if not args.enable_ga4gh_tool_registry:
del ga4gh_tool_registries[:]
if custom_schema_callback:
custom_schema_callback()
elif args.enable_ext:
res = pkg_resources.resource_stream(__name__, 'extensions.yml')
use_custom_schema("v1.0", "http://commonwl.org/cwltool", res.read())
res.close()
else:
use_standard_schema("v1.0")
uri, tool_file_uri = resolve_tool_uri(args.workflow,
resolver=resolver,
fetcher_constructor=fetcher_constructor)
overrides = [] # type: List[Dict[Text, Any]]
try:
job_order_object, input_basedir, jobloader = load_job_order(args,
stdin,
fetcher_constructor,
overrides,
tool_file_uri)
except Exception as e:
_logger.error(Text(e), exc_info=args.debug)
if args.overrides:
overrides.extend(load_overrides(file_uri(os.path.abspath(args.overrides)), tool_file_uri))
try:
document_loader, workflowobj, uri = fetch_document(uri, resolver=resolver,
fetcher_constructor=fetcher_constructor)
if args.print_deps:
printdeps(workflowobj, document_loader, stdout, args.relative_deps, uri)
return 0
document_loader, avsc_names, processobj, metadata, uri \
= validate_document(document_loader, workflowobj, uri,
enable_dev=args.enable_dev, strict=args.strict,
preprocess_only=args.print_pre or args.pack,
fetcher_constructor=fetcher_constructor,
skip_schemas=args.skip_schemas,
overrides=overrides)
if args.print_pre:
stdout.write(json.dumps(processobj, indent=4))
return 0
overrides.extend(metadata.get("cwltool:overrides", []))
conf_file = getattr(args, "beta_dependency_resolvers_configuration", None) # Text
use_conda_dependencies = getattr(args, "beta_conda_dependencies", None) # Text
make_tool_kwds = vars(args)
job_script_provider = None # type: Callable[[Any, List[str]], Text]
if conf_file or use_conda_dependencies:
dependencies_configuration = DependenciesConfiguration(args) # type: DependenciesConfiguration
make_tool_kwds["job_script_provider"] = dependencies_configuration
make_tool_kwds["find_default_container"] = functools.partial(find_default_container, args)
make_tool_kwds["overrides"] = overrides
tool = make_tool(document_loader, avsc_names, metadata, uri,
makeTool, make_tool_kwds)
if args.make_template:
yaml.safe_dump(generate_input_template(tool), sys.stdout,
default_flow_style=False, indent=4,
block_seq_indent=2)
return 0
if args.validate:
_logger.info("Tool definition is valid")
return 0
if args.pack:
stdout.write(print_pack(document_loader, processobj, uri, metadata))
return 0
if args.print_rdf:
stdout.write(printrdf(tool, document_loader.ctx, args.rdf_serializer))
return 0
if args.print_dot:
printdot(tool, document_loader.ctx, stdout)
return 0
except (validate.ValidationException) as exc:
_logger.error(u"Tool definition failed validation:\n%s", exc,
exc_info=args.debug)
return 1
except (RuntimeError, WorkflowException) as exc:
_logger.error(u"Tool definition failed initialization:\n%s", exc,
exc_info=args.debug)
return 1
except Exception as exc:
_logger.error(
u"I'm sorry, I couldn't load this CWL file%s",
", try again with --debug for more information.\nThe error was: "
"%s" % exc if not args.debug else ". The error was:",
exc_info=args.debug)
return 1
if isinstance(tool, int):
return tool
for dirprefix in ("tmpdir_prefix", "tmp_outdir_prefix", "cachedir"):
if getattr(args, dirprefix) and getattr(args, dirprefix) != 'tmp':
sl = "/" if getattr(args, dirprefix).endswith("/") or dirprefix == "cachedir" else ""
setattr(args, dirprefix,
os.path.abspath(getattr(args, dirprefix)) + sl)
if not os.path.exists(os.path.dirname(getattr(args, dirprefix))):
try:
os.makedirs(os.path.dirname(getattr(args, dirprefix)))
except Exception as e:
_logger.error("Failed to create directory: %s", e)
return 1
if args.cachedir:
if args.move_outputs == "move":
setattr(args, 'move_outputs', "copy")
setattr(args, "tmp_outdir_prefix", args.cachedir)
try:
job_order_object = init_job_order(job_order_object, args, tool,
print_input_deps=args.print_input_deps,
relative_deps=args.relative_deps,
stdout=stdout,
make_fs_access=make_fs_access,
loader=jobloader,
input_basedir=input_basedir)
except SystemExit as e:
return e.code
if isinstance(job_order_object, int):
return job_order_object
try:
setattr(args, 'basedir', input_basedir)
del args.workflow
del args.job_order
(out, status) = executor(tool, job_order_object,
makeTool=makeTool,
select_resources=selectResources,
make_fs_access=make_fs_access,
**vars(args))
# This is the workflow output, it needs to be written
if out is not None:
def locToPath(p):
for field in ("path", "nameext", "nameroot", "dirname"):
if field in p:
del p[field]
if p["location"].startswith("file://"):
p["path"] = uri_file_path(p["location"])
visit_class(out, ("File", "Directory"), locToPath)
# Unsetting the Generation fron final output object
visit_class(out,("File",), MutationManager().unset_generation)
if isinstance(out, six.string_types):
stdout.write(out)
else:
stdout.write(json.dumps(out, indent=4))
stdout.write("\n")
stdout.flush()
if status != "success":
_logger.warning(u"Final process status is %s", status)
return 1
else:
_logger.info(u"Final process status is %s", status)
return 0
except (validate.ValidationException) as exc:
_logger.error(u"Input object failed validation:\n%s", exc,
exc_info=args.debug)
return 1
except UnsupportedRequirement as exc:
_logger.error(
u"Workflow or tool uses unsupported feature:\n%s", exc,
exc_info=args.debug)
return 33
except WorkflowException as exc:
_logger.error(
u"Workflow error, try again with --debug for more "
"information:\n%s", strip_dup_lineno(six.text_type(exc)), exc_info=args.debug)
return 1
except Exception as exc:
_logger.error(
u"Unhandled error, try again with --debug for more information:\n"
" %s", exc, exc_info=args.debug)
return 1
finally:
_logger.removeHandler(stderr_handler)
_logger.addHandler(defaultStreamHandler)
