async def test_lovelace_update_view(hass, hass_ws_client):
"""Test update_view command."""
await async_setup_component(hass, 'lovelace')
client = await hass_ws_client(hass)
yaml = YAML(typ='rt')
origyaml = yaml.load(TEST_YAML_A)
with patch('homeassistant.util.ruamel_yaml.load_yaml',
return_value=origyaml), \
patch('homeassistant.util.ruamel_yaml.save_yaml') \
as save_yaml_mock:
await client.send_json({
'id': 5,
'type': 'lovelace/config/view/update',
'view_id': 'example',
'view_config': 'id: example2\ntitle: New title\n',
})
msg = await client.receive_json()
result = save_yaml_mock.call_args_list[0][0][1]
orig_view = origyaml.mlget(['views', 0], list_ok=True)
new_view = result.mlget(['views', 0], list_ok=True)
assert new_view['title'] == 'New title'
assert new_view['cards'] == orig_view['cards']
assert 'theme' not in new_view
assert msg['id'] == 5
assert msg['type'] == TYPE_RESULT
assert msg['success']
async def test_lovelace_move_card_view_position(hass, hass_ws_client):
"""Test move_card to view with position command."""
await async_setup_component(hass, 'lovelace')
client = await hass_ws_client(hass)
yaml = YAML(typ='rt')
with patch('homeassistant.util.ruamel_yaml.load_yaml',
return_value=yaml.load(TEST_YAML_A)), \
patch('homeassistant.util.ruamel_yaml.save_yaml') \
as save_yaml_mock:
await client.send_json({
'id': 5,
'type': 'lovelace/config/card/move',
'card_id': 'test',
'new_view_id': 'example',
'new_position': 1,
})
msg = await client.receive_json()
result = save_yaml_mock.call_args_list[0][0][1]
assert result.mlget(['views', 0, 'cards', 1, 'title'],
list_ok=True) == 'Test card'
assert msg['id'] == 5
assert msg['type'] == TYPE_RESULT
assert msg['success']
def parse(self, input):
"""parse the given file or file source string"""
if hasattr(input, 'name'):
self.filename = input.name
elif not getattr(self, 'filename', ''):
self.filename = ''
if hasattr(input, "read"):
src = input.read()
input.close()
input = src
if isinstance(input, bytes):
input = input.decode('utf-8')
yaml = YAML()
try:
self._file = yaml.load(input)
except YAMLError as e:
message = e.problem if hasattr(e, 'problem') else e.message
if hasattr(e, 'problem_mark'):
message += ' {0}'.format(e.problem_mark)
raise base.ParseError(message)
self._file = self.preprocess(self._file)
for k, data in self._flatten(self._file):
unit = self.UnitClass(data)
unit.setid(k)
self.addunit(unit)
def handle(self, *args, **options):
def flatten(l):
return [item for sublist in l for item in sublist]
yaml = YAML()
with open(options['yaml']) as yamlfile:
data = yaml.load(yamlfile)
for attribute in flatten(data['attributes'].values()):
SuomiFiUserAttribute.objects.update_or_create(
friendly_name=attribute['friendly_name'],
uri=attribute['uri'],
name=attribute['name'],
description=attribute['description']
)
for level, details in data['access_levels'].items():
access_level, created = SuomiFiAccessLevel.objects.update_or_create(shorthand=level)
for language, name in details['name'].items():
access_level.set_current_language(language)
access_level.name = name
for language, description in details['description'].items():
access_level.set_current_language(language)
access_level.description = description
for attribute in flatten(details['fields']):
access_level.attributes.add(SuomiFiUserAttribute.objects.get(friendly_name=attribute['friendly_name']))
access_level.save()
def mocked_config_file_path(
fake_temp_data_pocketsphinx_dic, fake_temp_data_pocketsphinx_lm, tmpdir_factory
):
path_to_pocketsphix_dic = os.path.join(
str(fake_temp_data_pocketsphinx_dic), "fake.dic"
)
path_to_pocketsphix_lm = os.path.join(
str(fake_temp_data_pocketsphinx_lm), "fake.lm"
)
# config part
base = tempfile.mkdtemp()
config_file = os.path.join(base, "config.yaml")
yaml = YAML()
m_cfg = yaml.load(COMMON_MOCKED_CONFIG)
m_cfg["pocketsphinx"]["dic"] = path_to_pocketsphix_dic
m_cfg["pocketsphinx"]["lm"] = path_to_pocketsphix_lm
with open(config_file, "w", encoding="utf-8") as fp:
yaml.dump(m_cfg, fp)
yield config_file
shutil.rmtree(base)
def obj_from_file(filename='annotation.yaml', filetype='auto'):
''' Read object from file '''
if filetype == 'auto':
_, ext = os.path.splitext(filename)
filetype = ext[1:]
if filetype in ('yaml', 'yml'):
from ruamel.yaml import YAML
yaml = YAML(typ="unsafe")
with open(filename, encoding="utf-8") as f:
obj = yaml.load(f)
if obj is None:
obj = {}
# import yaml
# with open(filename, encoding="utf-8") as f:
# intext = f.read()
# obj = yaml.load(intext)
elif filetype in ('pickle', 'pkl', 'pklz', 'picklezip'):
fcontent = read_pkl_and_pklz(filename)
# import pickle
if sys.version_info[0] < 3:
import cPickle as pickle
else:
import _pickle as pickle
# import sPickle as pickle
if sys.version_info.major == 2:
obj = pickle.loads(fcontent)
else:
obj = pickle.loads(fcontent, encoding="latin1")
else:
logger.error('Unknown filetype ' + filetype)
return obj
async def test_lovelace_get_view(hass, hass_ws_client):
"""Test get_view command."""
await async_setup_component(hass, 'lovelace')
client = await hass_ws_client(hass)
yaml = YAML(typ='rt')
with patch('homeassistant.util.ruamel_yaml.load_yaml',
return_value=yaml.load(TEST_YAML_A)):
await client.send_json({
'id': 5,
'type': 'lovelace/config/view/get',
'view_id': 'example',
})
msg = await client.receive_json()
assert msg['id'] == 5
assert msg['type'] == TYPE_RESULT
assert msg['success']
assert "".join(msg['result'].split()) == "".join('title: Example\n # \
Optional unique id for direct\
access /lovelace/${id}\nid: example\n # Optional\
background (overwrites the global background).\n\
background: radial-gradient(crimson, skyblue)\n\
# Each view can have a different theme applied.\n\
theme: dark-mode\n'.split())
def test_to_file(self):
filename = "ff_test.yaml"
b = self.benzene
b.to_file(filename=filename)
yaml = YAML(typ="safe")
with open(filename, "r") as f:
d = yaml.load(f)
self.assertListEqual(d["mass_info"], [list(m) for m in b.mass_info])
self.assertListEqual(d["pair_coeffs"], b.pair_coeffs)
def test_to_file(self):
filename = "ff_test.yaml"
v = self.virus
v.to_file(filename=filename)
yaml = YAML(typ="safe")
with open(filename, "r") as f:
d = yaml.load(f)
self.assertListEqual(d["mass_info"], [list(m) for m in v.mass_info])
self.assertListEqual(d["nonbond_coeffs"], v.nonbond_coeffs)
def test_id_not_changed():
"""Test if id is not changed if already exists."""
yaml = YAML(typ='rt')
fname = "dummy.yaml"
with patch('homeassistant.util.ruamel_yaml.load_yaml',
return_value=yaml.load(TEST_YAML_B)), \
patch('homeassistant.util.ruamel_yaml.save_yaml') \
as save_yaml_mock:
migrate_config(fname)
assert save_yaml_mock.call_count == 0
class TestYAML(unittest.TestCase):
"""Test lovelace.yaml save and load."""
def setUp(self):
"""Set up for tests."""
self.tmp_dir = mkdtemp()
self.yaml = YAML(typ='rt')
def tearDown(self):
"""Clean up after tests."""
for fname in os.listdir(self.tmp_dir):
os.remove(os.path.join(self.tmp_dir, fname))
os.rmdir(self.tmp_dir)
def _path_for(self, leaf_name):
return os.path.join(self.tmp_dir, leaf_name+".yaml")
def test_save_and_load(self):
"""Test saving and loading back."""
fname = self._path_for("test1")
open(fname, "w+")
util_yaml.save_yaml(fname, self.yaml.load(TEST_YAML_A))
data = util_yaml.load_yaml(fname, True)
assert data == self.yaml.load(TEST_YAML_A)
def test_overwrite_and_reload(self):
"""Test that we can overwrite an existing file and read back."""
fname = self._path_for("test2")
open(fname, "w+")
util_yaml.save_yaml(fname, self.yaml.load(TEST_YAML_A))
util_yaml.save_yaml(fname, self.yaml.load(TEST_YAML_B))
data = util_yaml.load_yaml(fname, True)
assert data == self.yaml.load(TEST_YAML_B)
def test_load_bad_data(self):
"""Test error from trying to load unserialisable data."""
fname = self._path_for("test3")
with open(fname, "w") as fh:
fh.write(TEST_BAD_YAML)
with pytest.raises(HomeAssistantError):
util_yaml.load_yaml(fname, True)
def test_save_yaml_model(tmpdir, mini_model):
jsonschema = pytest.importorskip("jsonschema")
"""Test the writing of YAML model."""
output_file = tmpdir.join("mini.yml")
cio.save_yaml_model(mini_model, output_file.strpath, sort=True)
# validate against schema
yaml = YAML(typ="unsafe")
with open(output_file.strpath, "r") as infile:
yaml_to_dict = yaml.load(infile)
dict_to_json = json.dumps(yaml_to_dict)
loaded = json.loads(dict_to_json)
assert jsonschema.validate(loaded, cio.json.json_schema)
def from_file(cls, filename):
"""
Constructor that reads in a file in YAML format.
Args:
filename (str): Filename.
"""
yaml = YAML(typ="safe")
with open(filename, "r") as f:
d = yaml.load(f)
return cls.from_dict(d)
def edit_tmpvault(filename):
'''Update yaml config and by changing any key with the value CHANGE_AND_REKEY
requests a master password and uses pbkdf2 to get a master key to base all
of the new keys off of
'''
yaml = YAML()
with open(filename) as fobj:
vault_dict = yaml.load(fobj)
master_pass = getpass.getpass("Enter master key to generate values: ").encode('utf-8')
master_key = hashlib.pbkdf2_hmac('sha256', master_pass, os.urandom(16), 100000)
change_values(vault_dict, 'CHANGE_AND_REKEY', master_key)
with open(filename, 'w') as fobj:
yaml.dump(vault_dict, fobj)
def vt2esofspy(vesseltree, outputfilename="tracer.txt", axisorder=[0, 1, 2]):
"""
exports vesseltree to esofspy format
:param vesseltree: filename or vesseltree dictionary structure
:param outputfilename: output file name
:param axisorder: order of axis can be specified with this option
:return:
"""
if (type(vesseltree) == str) and os.path.isfile(vesseltree):
from ruamel.yaml import YAML
yaml = YAML(typ="unsafe")
with open(vesseltree, encoding="utf-8") as f:
vt = yaml.load(f)
else:
vt = vesseltree
logger.debug(str(vt['general']))
logger.debug(str(vt.keys()))
vtgm = vt['graph']['microstructure']
lines = []
vs = vt['general']['voxel_size_mm']
sh = vt['general']['shape_px']
# switch axis
ax = axisorder
lines.append("#Tracer+\n")
lines.append("#voxelsize mm %f %f %f\n" % (vs[ax[0]], vs[ax[1]], vs[ax[2]]))
lines.append("#shape %i %i %i\n" % (sh[ax[0]], sh[ax[1]], sh[ax[2]]))
lines.append(str(len(vtgm) * 2)+"\n")
i = 1
for id in vtgm:
try:
nda = vtgm[id]['nodeA_ZYX']
ndb = vtgm[id]['nodeB_ZYX']
lines.append("%i\t%i\t%i\t%i\n" % (nda[ax[0]], nda[ax[1]], nda[ax[2]], i))
lines.append("%i\t%i\t%i\t%i\n" % (ndb[ax[0]], ndb[ax[1]], ndb[ax[2]], i))
i += 1
except:
pass
lines.append("%i\t%i\t%i\t%i" % (0, 0, 0, 0))
lines[3] = str(i - 1) + "\n"
from builtins import str as text
with open(outputfilename, 'wt') as f:
for line in lines:
f.write(text(line))
def test_add_id():
"""Test if id is added."""
yaml = YAML(typ='rt')
fname = "dummy.yaml"
with patch('homeassistant.util.ruamel_yaml.load_yaml',
return_value=yaml.load(TEST_YAML_A)), \
patch('homeassistant.util.ruamel_yaml.save_yaml') \
as save_yaml_mock:
migrate_config(fname)
result = save_yaml_mock.call_args_list[0][0][1]
assert 'id' in result['views'][0]['cards'][0]
assert 'id' in result['views'][1]
def loadtestDictsFromFilePaths(self, testFilePaths):
"""Parses yaml files from given filepaths
:param testFilePaths: file names to parse
:type testFilePaths: list of strings
:return: list of dict parsed from the yaml
:rtype: list of dicts
"""
testDicts = []
yaml = YAML()
for testFile in testFilePaths:
with open(testFile) as f:
testDict = yaml.load(f)
testDicts.append(dict(testDict))
return testDicts
def get_default_opttask_kwargs():
"""
Get the default configuration kwargs for OptTask.
Args:
None
Returns:
conf_dict (dict): The default kwargs for OptTask
"""
cwd = os.path.dirname(os.path.realpath(__file__))
fname = os.path.join(cwd, "defaults.yaml")
with open(fname, 'r') as config_raw:
yaml = YAML()
conf_dict = dict(yaml.load(config_raw))
return conf_dict
async def test_lovelace_get_card(hass, hass_ws_client):
"""Test get_card command."""
await async_setup_component(hass, 'lovelace')
client = await hass_ws_client(hass)
yaml = YAML(typ='rt')
with patch('homeassistant.util.ruamel_yaml.load_yaml',
return_value=yaml.load(TEST_YAML_A)):
await client.send_json({
'id': 5,
'type': 'lovelace/config/card/get',
'card_id': 'test',
})
msg = await client.receive_json()
assert msg['id'] == 5
assert msg['type'] == TYPE_RESULT
assert msg['success']
assert msg['result'] == 'id: test\ntype: entities\ntitle: Test card\n'
async def test_lovelace_get_view_not_found(hass, hass_ws_client):
"""Test get_card command cannot find card."""
await async_setup_component(hass, 'lovelace')
client = await hass_ws_client(hass)
yaml = YAML(typ='rt')
with patch('homeassistant.util.ruamel_yaml.load_yaml',
return_value=yaml.load(TEST_YAML_A)):
await client.send_json({
'id': 5,
'type': 'lovelace/config/view/get',
'view_id': 'not_found',
})
msg = await client.receive_json()
assert msg['id'] == 5
assert msg['type'] == TYPE_RESULT
assert msg['success'] is False
assert msg['error']['code'] == 'view_not_found'
def _readConfig(self, fileName):
try:
with open(fileName, "r") as config:
yaml = YAML()
configData = yaml.load(config)
if not configData:
configData = {}
except Exception as e:
raise ConfigError(fileName, e)
if "include" in configData:
for fileName in configData["include"]:
includeConfig = self._readConfig(fileName)
for key, val in includeConfig.iteritems():
if key not in configData:
configData[key] = val
elif not isinstance(configData[key], basestring): # Let's try to merge them if they're collections
if isinstance(val, basestring):
raise ConfigError(fileName, "The included configuration file tried to merge a non-string "
"with a string.")
try: # Make sure both things we're merging are still iterable types (not numbers or whatever)
iter(configData[key])
iter(val)
except TypeError:
pass # Just don't merge them if they're not
else:
try:
configData[key] += val # Merge with the + operator
except TypeError: # Except that some collections (dicts) can't
try:
for subkey, subval in val.iteritems(): # So merge them manually
if subkey not in configData[key]:
configData[key][subkey] = subval
except (AttributeError, TypeError):
# If either of these, they weren't both dicts (but were still iterable);
# requires user to resolve
raise ConfigError(fileName, "The variable {} could not be successfully merged "
"across files.".format(key))
del configData["include"]
return configData
async def test_lovelace_update_card_bad_yaml(hass, hass_ws_client):
"""Test update_card command bad yaml."""
await async_setup_component(hass, 'lovelace')
client = await hass_ws_client(hass)
yaml = YAML(typ='rt')
with patch('homeassistant.util.ruamel_yaml.load_yaml',
return_value=yaml.load(TEST_YAML_A)), \
patch('homeassistant.util.ruamel_yaml.yaml_to_object',
side_effect=HomeAssistantError):
await client.send_json({
'id': 5,
'type': 'lovelace/config/card/update',
'card_id': 'test',
'card_config': 'id: test\ntype: glance\n',
})
msg = await client.receive_json()
assert msg['id'] == 5
assert msg['type'] == TYPE_RESULT
assert msg['success'] is False
assert msg['error']['code'] == 'error'
async def test_lovelace_add_view(hass, hass_ws_client):
"""Test add_view command."""
await async_setup_component(hass, 'lovelace')
client = await hass_ws_client(hass)
yaml = YAML(typ='rt')
with patch('homeassistant.util.ruamel_yaml.load_yaml',
return_value=yaml.load(TEST_YAML_A)), \
patch('homeassistant.util.ruamel_yaml.save_yaml') \
as save_yaml_mock:
await client.send_json({
'id': 5,
'type': 'lovelace/config/view/add',
'view_config': 'id: test\ntitle: added\n',
})
msg = await client.receive_json()
result = save_yaml_mock.call_args_list[0][0][1]
assert result.mlget(['views', 2, 'title'],
list_ok=True) == 'added'
assert msg['id'] == 5
assert msg['type'] == TYPE_RESULT
assert msg['success']
async def test_lovelace_update_card(hass, hass_ws_client):
"""Test update_card command."""
await async_setup_component(hass, 'lovelace')
client = await hass_ws_client(hass)
yaml = YAML(typ='rt')
with patch('homeassistant.util.ruamel_yaml.load_yaml',
return_value=yaml.load(TEST_YAML_A)), \
patch('homeassistant.util.ruamel_yaml.save_yaml') \
as save_yaml_mock:
await client.send_json({
'id': 5,
'type': 'lovelace/config/card/update',
'card_id': 'test',
'card_config': 'id: test\ntype: glance\n',
})
msg = await client.receive_json()
result = save_yaml_mock.call_args_list[0][0][1]
assert result.mlget(['views', 1, 'cards', 0, 'type'],
list_ok=True) == 'glance'
assert msg['id'] == 5
assert msg['type'] == TYPE_RESULT
assert msg['success']
async def test_lovelace_delete_view(hass, hass_ws_client):
"""Test delete_card command."""
await async_setup_component(hass, 'lovelace')
client = await hass_ws_client(hass)
yaml = YAML(typ='rt')
with patch('homeassistant.util.ruamel_yaml.load_yaml',
return_value=yaml.load(TEST_YAML_A)), \
patch('homeassistant.util.ruamel_yaml.save_yaml') \
as save_yaml_mock:
await client.send_json({
'id': 5,
'type': 'lovelace/config/view/delete',
'view_id': 'example',
})
msg = await client.receive_json()
result = save_yaml_mock.call_args_list[0][0][1]
views = result.get('views', [])
assert len(views) == 1
assert views[0]['title'] == 'Second view'
assert msg['id'] == 5
assert msg['type'] == TYPE_RESULT
assert msg['success']
def parser_from_buffer(cls, fp):
"""Construct YamlParser from a file pointer."""
yaml = YAML(typ="safe")
return cls(yaml.load(fp))
mask = connected_components == largest_component_label
return mask.astype(float)
if __name__ == '__main__':
parser = argparse.ArgumentParser(description='Data processing')
parser.add_argument('-c',
'--config',
default='config.json',
type=str,
help='Path to the config file (default: config.json)')
args = parser.parse_args()
yaml = YAML(typ='safe')
with open('config.yaml', encoding='utf-8') as file:
config = yaml.load(file) # 为列表类型
save_pickle(
config["path"] + "/DRIVE/training",
*data_process(config["path"],
name="DRIVE",
mode="training",
**config["data_process"]))
save_pickle(
config["path"] + "/DRIVE/test",
*data_process(config["path"],
name="DRIVE",
mode="test",
**config["data_process"]))
save_pickle(
config["path"] + "/CHASEDB1",
*data_process(config["path"],
from ipam.models import VLAN, VLANGroup, Role
from ipam.constants import VLAN_STATUS_CHOICES
from tenancy.models import Tenant, TenantGroup
from extras.models import CustomField, CustomFieldValue
from ruamel.yaml import YAML
from pathlib import Path
import sys
file = Path('/opt/netbox/initializers/vlans.yml')
if not file.is_file():
sys.exit()
with file.open('r') as stream:
yaml = YAML(typ='safe')
vlans = yaml.load(stream)
optional_assocs = {
'site': (Site, 'name'),
'tenant': (Tenant, 'name'),
'tenant_group': (TenantGroup, 'name'),
'group': (VLANGroup, 'name'),
'role': (Role, 'name')
}
if vlans is not None:
for params in vlans:
custom_fields = params.pop('custom_fields', None)
for assoc, details in optional_assocs.items():
if assoc in params:
def getconfig():
dados = open('config.yaml', 'r').read()
yaml = YAML()
data = yaml.load(dados)
cdata = json.loads(json.dumps(data))
return cdata
"%s has values (%s) not found in owl entity dictionaries t (%s): "
% (field.full_path, str(
quoted.difference(owl_entities)), str(owl_entities)))
stat = False
else:
warnings.warn("Pattern has no text fields")
return stat
schema_url = 'https://raw.githubusercontent.com/dosumis/dead_simple_owl_design_patterns/master/spec/DOSDP_schema_full.yaml'
dosdp_full_text = requests.get(schema_url)
ryaml = YAML(typ='safe')
dosdp = ryaml.load(dosdp_full_text.text)
# TODO - Add better parsing for ryaml execptions.
v = Draft7Validator(dosdp)
pattern_docs = glob.glob(sys.argv[1] + "*.yaml")
pattern_docs.extend(glob.glob(sys.argv[1] + "*.yml"))
stat = True
for pattern_doc in pattern_docs:
warnings.warn("Checking %s" % pattern_doc)
file = open(pattern_doc, "r")
pattern = ryaml.load(file.read())
if not test_jschema(v, pattern): stat = False
if not test_vars(pattern): stat = False
if not test_text_fields(pattern): stat = False
# Get the path to the definition file.
path_to_file = os.path.join(dirpath, def_file)
# Get the type of HTTP method from the file name by removing the ".yaml" file
# extension from the string.
http_method = def_file[:-len(".yaml")]
# File names for our resource definitions should be in the form of:
# "get.yaml"
# "post.yaml"
# or some other RESTful HTTP method that we support in our API. If the current
# file being processed isn't like that, then we skip over that file since it's
# not a resource definition.
if http_method not in ALLOWED_HTTP_METHODS:
continue
# Load the yaml data from the current file being processed
with open(path_to_file, "r") as yaml_file:
definition = yaml.load(yaml_file)
resource_url_path = RESOURCE_PATH_LOOKUP[resource_name]
# Set the value of the resource path in the base dictionary to the
# definition we loaded from the yaml file. It will look something like this
# in the paths dictionary:
#
# paths:
# /:
# get:
# ...
openapi_definition['paths'][resource_url_path][
http_method] = definition
# Get the date and time that the script was run, then generate a name for the definition
# file.
# We generate the file name with the date and time so that we can keep different versions
class SavedBundleConfig(object):
def __init__(self, bento_service=None, kind="BentoService"):
self.kind = kind
self._yaml = YAML()
self._yaml.default_flow_style = False
self.config = self._yaml.load(
BENTOML_CONFIG_YAML_TEPMLATE.format(
kind=self.kind,
bentoml_version=get_bentoml_deploy_version(),
created_at=str(datetime.utcnow()),
)
)
if bento_service is not None:
self.config["metadata"].update(
{
"service_name": bento_service.name,
"service_version": bento_service.version,
}
)
self.config["env"] = bento_service.env.to_dict()
self.config['apis'] = _get_apis_list(bento_service)
self.config['artifacts'] = _get_artifacts_list(bento_service)
def write_to_path(self, path, filename="bentoml.yml"):
return self._yaml.dump(self.config, Path(os.path.join(path, filename)))
@classmethod
def load(cls, filepath):
conf = cls()
with open(filepath, "rb") as config_file:
yml_content = config_file.read()
conf.config = conf._yaml.load(yml_content)
ver = str(conf["version"])
if ver != BENTOML_VERSION:
msg = (
"Saved BentoService bundle version mismatch: loading BentoService "
"bundle create with BentoML version {}, but loading from BentoML "
"version {}".format(conf["version"], BENTOML_VERSION)
)
# If major version is different, then there could be incompatible API
# changes. Raise error in this case.
if ver.split(".")[0] != BENTOML_VERSION.split(".")[0]:
if not BENTOML_VERSION.startswith('0+untagged'):
raise BentoMLConfigException(msg)
else:
logger.warning(msg)
else: # Otherwise just show a warning.
logger.warning(msg)
return conf
def get_bento_service_metadata_pb(self):
bento_service_metadata = BentoServiceMetadata()
bento_service_metadata.name = self.config["metadata"]["service_name"]
bento_service_metadata.version = self.config["metadata"]["service_version"]
bento_service_metadata.created_at.FromDatetime(
self.config["metadata"]["created_at"]
)
if "env" in self.config:
if "setup_sh" in self.config["env"]:
bento_service_metadata.env.setup_sh = self.config["env"]["setup_sh"]
if "conda_env" in self.config["env"]:
bento_service_metadata.env.conda_env = dump_to_yaml_str(
self.config["env"]["conda_env"]
)
if "pip_dependencies" in self.config["env"]:
bento_service_metadata.env.pip_dependencies = "\n".join(
self.config["env"]["pip_dependencies"]
)
if "python_version" in self.config["env"]:
bento_service_metadata.env.python_version = self.config["env"][
"python_version"
]
if "docker_base_image" in self.config["env"]:
bento_service_metadata.env.docker_base_image = self.config["env"][
"docker_base_image"
]
if "apis" in self.config:
for api_config in self.config["apis"]:
if 'handler_type' in api_config:
# Convert handler type to input type for saved bundle created
# before version 0.8.0
input_type = api_config.get('handler_type')
elif 'input_type' in api_config:
input_type = api_config.get('input_type')
else:
input_type = "unknown"
if 'output_type' in api_config:
output_type = api_config.get('output_type')
else:
output_type = "DefaultOutput"
api_metadata = BentoServiceMetadata.BentoServiceApi(
name=api_config["name"],
docs=api_config["docs"],
input_type=input_type,
output_type=output_type,
)
if "handler_config" in api_config:
# Supports viewing API input config info for saved bundle created
# before version 0.8.0
for k, v in api_config["handler_config"].items():
if k in {'mb_max_latency', 'mb_max_batch_size'}:
setattr(api_metadata, k, v)
else:
api_metadata.input_config[k] = v
else:
if 'mb_max_latency' in api_config:
api_metadata.mb_max_latency = api_config["mb_max_latency"]
else:
api_metadata.mb_max_latency = DEFAULT_MAX_LATENCY
if 'mb_max_batch_size' in api_config:
api_metadata.mb_max_batch_size = api_config["mb_max_batch_size"]
else:
api_metadata.mb_max_batch_size = DEFAULT_MAX_BATCH_SIZE
if "input_config" in api_config:
for k, v in api_config["input_config"].items():
api_metadata.input_config[k] = v
if "output_config" in api_config:
for k, v in api_config["output_config"].items():
api_metadata.output_config[k] = v
bento_service_metadata.apis.extend([api_metadata])
if "artifacts" in self.config:
for artifact_config in self.config["artifacts"]:
artifact_metadata = BentoServiceMetadata.BentoArtifact()
if "name" in artifact_config:
artifact_metadata.name = artifact_config["name"]
if "artifact_type" in artifact_config:
artifact_metadata.artifact_type = artifact_config["artifact_type"]
bento_service_metadata.artifacts.extend([artifact_metadata])
return bento_service_metadata
def __getitem__(self, item):
return self.config[item]
def __setitem__(self, key, value):
self.config[key] = value
def __contains__(self, item):
return item in self.config
def offline_inference(config, encoder, decoder, audio_file):
MODEL_YAML = config
CHECKPOINT_ENCODER = encoder
CHECKPOINT_DECODER = decoder
sample_rate, signal = wave.read(audio_file)
# get labels (vocab)
yaml = YAML(typ="safe")
with open(MODEL_YAML) as f:
jasper_model_definition = yaml.load(f)
labels = jasper_model_definition['labels']
# build neural factory and neural modules
neural_factory = nemo.core.NeuralModuleFactory(
placement=nemo.core.DeviceType.GPU,
backend=nemo.core.Backend.PyTorch)
data_preprocessor = nemo_asr.AudioToMelSpectrogramPreprocessor(
factory=neural_factory,
**jasper_model_definition["AudioToMelSpectrogramPreprocessor"])
jasper_encoder = nemo_asr.JasperEncoder(
feat_in=jasper_model_definition["AudioToMelSpectrogramPreprocessor"]["features"],
**jasper_model_definition["JasperEncoder"])
jasper_decoder = nemo_asr.JasperDecoderForCTC(
feat_in=jasper_model_definition["JasperEncoder"]["jasper"][-1]["filters"],
num_classes=len(labels))
greedy_decoder = nemo_asr.GreedyCTCDecoder()
# load model
jasper_encoder.restore_from(CHECKPOINT_ENCODER)
jasper_decoder.restore_from(CHECKPOINT_DECODER)
# AudioDataLayer
class AudioDataLayer(DataLayerNM):
@staticmethod
def create_ports():
input_ports = {}
output_ports = {
"audio_signal": NeuralType({0: AxisType(BatchTag),
1: AxisType(TimeTag)}),
"a_sig_length": NeuralType({0: AxisType(BatchTag)}),
}
return input_ports, output_ports
def __init__(self, **kwargs):
DataLayerNM.__init__(self, **kwargs)
self.output_enable = False
def __iter__(self):
return self
def __next__(self):
if not self.output_enable:
raise StopIteration
self.output_enable = False
return torch.as_tensor(self.signal, dtype=torch.float32), \
torch.as_tensor(self.signal_shape, dtype=torch.int64)
def set_signal(self, signal):
self.signal = np.reshape(signal.astype(np.float32)/32768., [1, -1])
self.signal_shape = np.expand_dims(self.signal.size, 0).astype(np.int64)
self.output_enable = True
def __len__(self):
return 1
@property
def dataset(self):
return None
@property
def data_iterator(self):
return self
# Instantiate necessary neural modules
data_layer = AudioDataLayer()
# Define inference DAG
audio_signal, audio_signal_len = data_layer()
processed_signal, processed_signal_len = data_preprocessor(
input_signal=audio_signal,
length=audio_signal_len)
encoded, encoded_len = jasper_encoder(audio_signal=processed_signal,
length=processed_signal_len)
log_probs = jasper_decoder(encoder_output=encoded)
predictions = greedy_decoder(log_probs=log_probs)
# audio inference
data_layer.set_signal(signal)
tensors = neural_factory.infer([
audio_signal,
processed_signal,
encoded,
log_probs,
predictions], verbose=False)
# results
audio = tensors[0][0][0].cpu().numpy()
features = tensors[1][0][0].cpu().numpy()
encoded_features = tensors[2][0][0].cpu().numpy(),
probs = tensors[3][0][0].cpu().numpy()
preds = tensors[4][0]
transcript = post_process_predictions([preds], labels)
return transcript, audio, features, encoded_features, probs, preds
def callback(data):
yaml = YAML()
return yaml.load(data)
def main(config=None):
print(banner)
parser = argparse.ArgumentParser(
description='Boa, the fast build tool for conda packages.')
subparsers = parser.add_subparsers(help='sub-command help', dest='command')
parent_parser = argparse.ArgumentParser(add_help=False)
parent_parser.add_argument('recipe_dir', type=str)
render_parser = subparsers.add_parser('render',
parents=[parent_parser],
help='render a recipe')
build_parser = subparsers.add_parser('build',
parents=[parent_parser],
help='build a recipe')
args = parser.parse_args()
command = args.command
folder = args.recipe_dir
config = get_or_merge_config(None, {})
config_files = find_config_files(folder)
parsed_cfg = collections.OrderedDict()
for f in config_files:
parsed_cfg[f] = parse_config_file(f, config)
normalized = {}
for k in parsed_cfg[f].keys():
if "_" in k:
n = k.replace("_", "-")
normalized[n] = parsed_cfg[f][k]
parsed_cfg[f].update(normalized)
# TODO just using latest config here, should merge!
if len(config_files):
cbc = parsed_cfg[config_files[-1]]
else:
cbc = {}
update_index(os.path.dirname(config.output_folder),
verbose=config.debug,
threads=1)
recipe_path = os.path.join(folder, "recipe.yaml")
# step 1: parse YAML
with open(recipe_path) as fi:
loader = YAML(typ="safe")
ydoc = loader.load(fi)
# step 2: fill out context dict
context_dict = ydoc.get("context") or {}
jenv = jinja2.Environment()
for key, value in context_dict.items():
if isinstance(value, str):
tmpl = jenv.from_string(value)
context_dict[key] = tmpl.render(context_dict)
if ydoc.get("context"):
del ydoc["context"]
# step 3: recursively loop over the entire recipe and render jinja with context
jenv.globals.update(jinja_functions(config, context_dict))
for key in ydoc:
render_recursive(ydoc[key], context_dict, jenv)
flatten_selectors(ydoc, ns_cfg(config))
# We need to assemble the variants for each output
variants = {}
# if we have a outputs section, use that order the outputs
if ydoc.get("outputs"):
# if ydoc.get("build"):
# raise InvalidRecipeError("You can either declare outputs, or build?")
for o in ydoc["outputs"]:
# inherit from global package
pkg_meta = {}
pkg_meta.update(ydoc["package"])
pkg_meta.update(o["package"])
o["package"] = pkg_meta
build_meta = {}
build_meta.update(ydoc.get("build"))
build_meta.update(o.get("build") or {})
o["build"] = build_meta
variants[o["package"]["name"]] = get_dependency_variants(
o["requirements"], cbc, config)
else:
# we only have one output
variants[ydoc["package"]["name"]] = get_dependency_variants(
ydoc["requirements"], cbc, config)
# this takes in all variants and outputs, builds a dependency tree and returns
# the final metadata
sorted_outputs = to_build_tree(ydoc, variants, config)
# then we need to solve and build from the bottom up
# we can't first solve all packages without finalizing everything
# - solve the package
# - solv build, add weak run exports to
# - add run exports from deps!
if command == 'render':
for o in sorted_outputs:
print(o)
exit()
solver = MambaSolver(["conda-forge"], "linux-64")
for o in sorted_outputs:
solver.replace_channels()
o.finalize_solve(sorted_outputs, solver)
print(o)
o.config.compute_build_id(o.name)
print(o.config.host_prefix)
if 'build' in o.transactions:
mkdir_p(o.config.build_prefix)
print(o.transactions)
o.transactions['build'].execute(
PrefixData(o.config.build_prefix),
PackageCacheData.first_writable().pkgs_dir)
if 'host' in o.transactions:
mkdir_p(o.config.host_prefix)
print(o.transactions)
o.transactions['host'].execute(
PrefixData(o.config.host_prefix),
PackageCacheData.first_writable().pkgs_dir)
print(o.sections)
stats = {}
print("Final variant config")
print(config.variant)
print(o.variant)
build(MetaData(recipe_path, o), None)
# sorted_outputs
# print(sorted_outputs[0].config.host_prefix)
exit()
for o in sorted_outputs:
print("\n")
print(o)
"""
Enables recursive dot notation for ``dict``.
"""
return json.loads(json.dumps(inpt),
object_hook=lambda x: Bunch(**{
**Bunch(),
**x
}))
# Read the BIDS schema data
with (BIDSCOIN_SCHEMA_DIR.joinpath('objects/datatypes.yaml')
).open('r') as _stream:
bidsdatatypesdef = yaml.load(
_stream
) # The valid BIDS datatypes, along with their full names and descriptions
bidsdatatypes = {}
for _datatype in bidsdatatypesdef: # The entities that can/should be present for each BIDS datatype
with (BIDSCOIN_SCHEMA_DIR.joinpath(f'rules/datatypes/{_datatype}')
).with_suffix('.yaml').open('r') as _stream:
bidsdatatypes[_datatype] = yaml.load(_stream)
with (BIDSCOIN_SCHEMA_DIR.joinpath('objects/suffixes.yaml')
).open('r') as _stream:
suffixes = yaml.load(
_stream) # The descriptions of the valid BIDS file suffixes
with (BIDSCOIN_SCHEMA_DIR.joinpath('objects/entities.yaml')
).open('r') as _stream:
entities = yaml.load(
_stream) # The descriptions of the entities present in BIDS filenames
with (BIDSCOIN_SCHEMA_DIR.joinpath('rules/entities.yaml')
'conda', 'smithy', 'register-feedstock-token',
'--feedstock_directory', feedstock_dir
] + owner_info)
write_token('anaconda', os.environ['STAGING_BINSTAR_TOKEN'])
subprocess.check_call([
'conda', 'smithy', 'rotate-binstar-token',
'--without-appveyor', '--token_name',
'STAGING_BINSTAR_TOKEN'
],
cwd=feedstock_dir)
yaml = YAML()
with open(os.path.join(feedstock_dir, "conda-forge.yml"),
"r") as fp:
_cfg = yaml.load(fp.read())
_cfg["conda_forge_output_validation"] = True
with open(os.path.join(feedstock_dir, "conda-forge.yml"),
"w") as fp:
yaml.dump(_cfg, fp)
subprocess.check_call(["git", "add", "conda-forge.yml"],
cwd=feedstock_dir)
subprocess.check_call(['conda', 'smithy', 'rerender'],
cwd=feedstock_dir)
except subprocess.CalledProcessError:
exit_code = 0
traceback.print_exception(*sys.exc_info())
continue
print("making a commit and pushing...")
subprocess.check_call([
from ruamel.yaml import YAML
import requests
"""
This script print all the tools that do not have a corresponding biotools accession or doi.
"""
yaml = YAML()
yaml_recipe = YAML(typ="rt") # pylint: disable=invalid-name
with open('../annotations.yaml', 'r') as read_file:
file_annotations = yaml.load(read_file)
tools = {}
not_biotools = []
def search_tool(key):
count = 0
url = 'https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=' + key + '&format=json&pageSize=1000'
try:
page = requests.get(url).json()
if 'resultList' in page:
for publication in page['resultList']['result']:
common_name = key + ":"
# if common_name in publication['title'].lower() and (
# 'nmeth.' in publication['doi'] or 'bioinformatics' in publication['doi'] or 'nar\/' in publication['doi'] or 'gigascience' in publication['doi'] or 'nbt.' in publication['doi']):
# print(key + ' ---- ' + publication['title'] + ' --- ' + publication['doi'])
if common_name in publication['title'].lower():
print(key + ' ---- ' + publication['title'] + ' --- ' +
' -' + ' doi:' + publication['doi'])
#!/usr/bin/python3 # Changes namespace, name, and version in Galaxy metadata. # Useful for releasing to Automation Hub, where Collections live # in namespaces separated from Ansible Galaxy. import sys from ruamel.yaml import YAML filepath = "galaxy.yml" buf = open(filepath).read() yaml = YAML(typ="rt") yaml.default_flow_style = False yaml.preserve_quotes = True yaml.indent(mapping=2, sequence=4, offset=2) code = yaml.load(buf) code["namespace"] = sys.argv[1] code["name"] = sys.argv[2] code["version"] = sys.argv[3] yaml.dump(code, sys.stdout)
class Unifier:
def __init__(self,
indir: str,
dir_name=INTEGRATIONS_DIR,
outdir='',
image_prefix=DEFAULT_IMAGE_PREFIX):
directory_name = ""
for optional_dir_name in DIR_TO_PREFIX:
if optional_dir_name in indir:
directory_name = optional_dir_name
if not directory_name:
print_error(
'You have failed to provide a legal file path, a legal file path '
'should contain either Integrations or Scripts directories')
self.image_prefix = image_prefix
self.package_path = indir
if self.package_path.endswith(os.sep):
self.package_path = self.package_path.rstrip(os.sep)
self.dest_path = outdir
yml_paths, self.yml_path = get_yml_paths_in_dir(
self.package_path, Errors.no_yml_file(self.package_path))
for path in yml_paths:
# The plugin creates a unified YML file for the package.
# In case this script runs locally and there is a unified YML file in the package we need to ignore it.
# Also,
# we don't take the unified file by default because
# there might be packages that were not created by the plugin.
if 'unified' not in path:
self.yml_path = path
break
self.ryaml = YAML()
self.ryaml.preserve_quotes = True
self.ryaml.width = 400 # make sure long lines will not break (relevant for code section)
if self.yml_path:
with open(self.yml_path, 'r') as yml_file:
self.yml_data = self.ryaml.load(yml_file)
else:
self.yml_data = {}
print_error(f'No yml found in path: {self.package_path}')
# script key for scripts is a string.
# script key for integrations is a dictionary.
self.is_script_package = isinstance(self.yml_data.get('script'), str)
self.dir_name = SCRIPTS_DIR if self.is_script_package else dir_name
def write_yaml_with_docker(self, yml_unified, yml_data, script_obj):
"""Write out the yaml file taking into account the dockerimage45 tag.
If it is present will create 2 integration files
One for 4.5 and below and one for 5.0.
Arguments:
output_path {str} -- output path
yml_unified {dict} -- unified yml dict
yml_data {dict} -- yml object
script_obj {dict} -- script object
Returns:
dict -- dictionary mapping output path to unified data
"""
output_map = {self.dest_path: yml_unified}
if 'dockerimage45' in script_obj:
# we need to split into two files 45 and 50. Current one will be from version 5.0
if self.is_script_package: # scripts
del yml_unified['dockerimage45']
else: # integrations
del yml_unified['script']['dockerimage45']
yml_unified45 = copy.deepcopy(yml_unified)
# validate that this is a script/integration which targets both 4.5 and 5.0+.
if server_version_compare(yml_data.get('fromversion', '0.0.0'),
'5.0.0') >= 0:
raise ValueError(
f'Failed: {self.dest_path}. dockerimage45 set for 5.0 and later only'
)
yml_unified['fromversion'] = '5.0.0'
# validate that this is a script/integration which targets both 4.5 and 5.0+.
if server_version_compare(yml_data.get('toversion', '99.99.99'),
'5.0.0') < 0:
raise ValueError(
f'Failed: {self.dest_path}. dockerimage45 set for 4.5 and earlier only'
)
yml_unified45['toversion'] = '4.5.9'
if script_obj.get(
'dockerimage45'
): # we have a value for dockerimage45 set it as dockerimage
if self.is_script_package: # scripts
yml_unified45['dockerimage'] = script_obj.get(
'dockerimage45')
else: # integrations
yml_unified45['script']['dockerimage'] = script_obj.get(
'dockerimage45')
else: # no value for dockerimage45 remove the dockerimage entry
del yml_unified45['dockerimage']
output_path45 = re.sub(r'\.yml$', '_45.yml', self.dest_path)
output_map = {
self.dest_path: yml_unified,
output_path45: yml_unified45,
}
for file_path, file_data in output_map.items():
if os.path.isfile(file_path):
raise ValueError(
f'Output file already exists: {self.dest_path}.'
' Make sure to remove this file from source control'
' or rename this package (for example if it is a v2).')
with io.open(file_path, mode='w', encoding='utf-8') as file_:
self.ryaml.dump(file_data, file_)
return output_map
def merge_script_package_to_yml(self):
"""Merge the various components to create an output yml file
"""
print("Merging package: {}".format(self.package_path))
package_dir_name = os.path.basename(self.package_path)
output_filename = '{}-{}.yml'.format(DIR_TO_PREFIX[self.dir_name],
package_dir_name)
if self.dest_path:
self.dest_path = os.path.join(self.dest_path, output_filename)
else:
self.dest_path = os.path.join(self.dir_name, output_filename)
script_obj = self.yml_data
if not self.is_script_package:
script_obj = self.yml_data['script']
script_type = TYPE_TO_EXTENSION[script_obj['type']]
yml_unified = copy.deepcopy(self.yml_data)
yml_unified, script_path = self.insert_script_to_yml(
script_type, yml_unified, self.yml_data)
image_path = None
desc_path = None
if not self.is_script_package:
yml_unified, image_path = self.insert_image_to_yml(
self.yml_data, yml_unified)
yml_unified, desc_path = self.insert_description_to_yml(
self.yml_data, yml_unified)
output_map = self.write_yaml_with_docker(yml_unified, self.yml_data,
script_obj)
unifier_outputs = list(output_map.keys(
)), self.yml_path, script_path, image_path, desc_path
print_color(f'Created unified yml: {list(output_map.keys())}',
LOG_COLORS.GREEN)
return unifier_outputs[0]
def insert_image_to_yml(self, yml_data, yml_unified):
image_data, found_img_path = self.get_data("*png")
image_data = self.image_prefix + base64.b64encode(image_data).decode(
'utf-8')
if yml_data.get('image'):
raise ValueError(
'Please move the image from the yml to an image file (.png)'
f' in the package: {self.package_path}')
yml_unified['image'] = image_data
return yml_unified, found_img_path
def insert_description_to_yml(self, yml_data, yml_unified):
desc_data, found_desc_path = self.get_data('*_description.md')
if yml_data.get('detaileddescription'):
raise ValueError(
'Please move the detailed description from the yml to a description file (.md)'
f' in the package: {self.package_path}')
if desc_data:
yml_unified['detaileddescription'] = FoldedScalarString(
desc_data.decode('utf-8'))
return yml_unified, found_desc_path
def get_data(self, extension):
data_path = glob.glob(os.path.join(self.package_path, extension))
data = None
found_data_path = None
if not self.is_script_package and data_path:
found_data_path = data_path[0]
with open(found_data_path, 'rb') as data_file:
data = data_file.read()
return data, found_data_path
def get_code_file(self, script_type):
"""Return the first code file in the specified directory path
:param script_type: script type: .py or .js
:type script_type: str
:return: path to found code file
:rtype: str
"""
ignore_regex = (
r'CommonServerPython\.py|CommonServerUserPython\.py|demistomock\.py|_test\.py'
r'|conftest\.py|__init__\.py|ApiModule\.py')
if self.package_path.endswith('Scripts/CommonServerPython'):
return os.path.join(self.package_path, 'CommonServerPython.py')
if self.package_path.endswith('ApiModule'):
return os.path.join(
self.package_path,
os.path.basename(os.path.normpath(self.package_path)) + '.py')
script_path = list(
filter(
lambda x: not re.search(ignore_regex, x),
glob.glob(os.path.join(self.package_path,
'*' + script_type))))[0]
return script_path
def insert_script_to_yml(self, script_type, yml_unified, yml_data):
script_path = self.get_code_file(script_type)
with io.open(script_path, mode='r', encoding='utf-8') as script_file:
script_code = script_file.read()
# Check if the script imports an API module. If it does,
# the API module code will be pasted in place of the import.
module_import, module_name = self.check_api_module_imports(script_code)
if module_import:
script_code = self.insert_module_code(script_code, module_import,
module_name)
clean_code = self.clean_python_code(script_code)
if self.is_script_package:
if yml_data.get('script', '') not in ('', '-'):
print_warning(
f'Script section is not empty in package {self.package_path}.'
f'It should be blank or a dash(-).')
yml_unified['script'] = FoldedScalarString(clean_code)
else:
if yml_data['script'].get('script', '') not in ('', '-'):
print_warning(
f'Script section is not empty in package {self.package_path}.'
f'It should be blank or a dash(-).')
yml_unified['script']['script'] = FoldedScalarString(clean_code)
return yml_unified, script_path
def get_script_package_data(self):
# should be static method
_, yml_path = get_yml_paths_in_dir(self.package_path, error_msg='')
if not yml_path:
raise Exception(
f'No yml files found in package path: {self.package_path}. '
'Is this really a package dir?')
code_type = get_yaml(yml_path).get('type')
unifier = Unifier(self.package_path)
code_path = unifier.get_code_file(TYPE_TO_EXTENSION[code_type])
with open(code_path, 'r') as code_file:
code = code_file.read()
return yml_path, code
@staticmethod
def check_api_module_imports(script_code: str) -> Tuple[str, str]:
"""
Checks integration code for API module imports
:param script_code: The integration code
:return: The import string and the imported module name
"""
# General regex to find API module imports, for example: "from MicrosoftApiModule import * # noqa: E402"
module_regex = r'from ([\w\d]+ApiModule) import \*(?: # noqa: E402)?'
module_match = re.search(module_regex, script_code)
if module_match:
return module_match.group(), module_match.group(1)
return '', ''
@staticmethod
def insert_module_code(script_code: str, module_import: str,
module_name: str) -> str:
"""
Inserts API module in place of an import to the module according to the module name
:param script_code: The integration code
:param module_import: The module import string to replace
:param module_name: The module name
:return: The integration script with the module code appended in place of the import
"""
module_path = os.path.join('./Packs', 'ApiModules', 'Scripts',
module_name, module_name + '.py')
module_code = Unifier._get_api_module_code(module_name, module_path)
module_code = '\n### GENERATED CODE ###\n# This code was inserted in place of an API module.{}\n' \
.format(module_code)
return script_code.replace(module_import, module_code)
@staticmethod
def _get_api_module_code(module_name, module_path):
"""
Attempts to get the API module code from the ApiModules pack.
:param module_name: The API module name
:param module_path: The API module code file path
:return: The API module code
"""
try:
with io.open(module_path, mode='r',
encoding='utf-8') as script_file:
module_code = script_file.read()
except Exception as exc:
raise ValueError(
'Could not retrieve the module [{}] code: {}'.format(
module_name, str(exc)))
return module_code
@staticmethod
def clean_python_code(script_code, remove_print_future=True):
script_code = script_code.replace("import demistomock as demisto", "")
script_code = script_code.replace("from CommonServerPython import *",
"")
script_code = script_code.replace(
"from CommonServerUserPython import *", "")
# print function is imported in python loop
if remove_print_future: # docs generation requires to leave this
script_code = script_code.replace(
"from __future__ import print_function", "")
return script_code
def __init__(self, meta_yaml):
_yml = YAML(typ='jinja2')
_yml.indent(mapping=2, sequence=4, offset=2)
_yml.width = 160
_yml.allow_duplicate_keys = True
self.meta = _yml.load(meta_yaml)
def main():
parser = argparse.ArgumentParser(description='Jasper')
parser.add_argument("--local_rank", default=None, type=int)
parser.add_argument("--batch_size", default=32, type=int)
parser.add_argument("--model_config", type=str, required=True)
parser.add_argument("--eval_datasets", type=str, required=True)
parser.add_argument("--load_dir", type=str, required=True)
parser.add_argument("--vocab_file", type=str, required=True)
parser.add_argument("--save_logprob", default=None, type=str)
parser.add_argument("--lm_path", default=None, type=str)
parser.add_argument("--beam_width", default=50, type=int)
parser.add_argument("--alpha", default=2.0, type=float)
parser.add_argument("--beta", default=1.0, type=float)
parser.add_argument("--cutoff_prob", default=0.99, type=float)
parser.add_argument("--cutoff_top_n", default=40, type=int)
args = parser.parse_args()
batch_size = args.batch_size
load_dir = args.load_dir
if args.local_rank is not None:
if args.lm_path:
raise NotImplementedError(
"Beam search decoder with LM does not currently support evaluation on multi-gpu."
)
device = nemo.core.DeviceType.AllGpu
else:
device = nemo.core.DeviceType.GPU
# Instantiate Neural Factory with supported backend
neural_factory = nemo.core.NeuralModuleFactory(
backend=nemo.core.Backend.PyTorch,
local_rank=args.local_rank,
optimization_level=nemo.core.Optimization.mxprO1,
placement=device,
)
if args.local_rank is not None:
logging.info('Doing ALL GPU')
yaml = YAML(typ="safe")
with open(args.model_config) as f:
jasper_params = yaml.load(f)
vocab = load_vocab(args.vocab_file)
sample_rate = jasper_params['sample_rate']
eval_datasets = args.eval_datasets
eval_dl_params = copy.deepcopy(jasper_params["AudioToTextDataLayer"])
eval_dl_params.update(jasper_params["AudioToTextDataLayer"]["eval"])
eval_dl_params["normalize_transcripts"] = False
del eval_dl_params["train"]
del eval_dl_params["eval"]
data_layer = nemo_asr.AudioToTextDataLayer(
manifest_filepath=eval_datasets,
sample_rate=sample_rate,
labels=vocab,
batch_size=batch_size,
**eval_dl_params,
)
n = len(data_layer)
logging.info('Evaluating {0} examples'.format(n))
data_preprocessor = nemo_asr.AudioToMelSpectrogramPreprocessor(
sample_rate=sample_rate, **jasper_params["AudioToMelSpectrogramPreprocessor"],
)
jasper_encoder = nemo_asr.JasperEncoder(
feat_in=jasper_params["AudioToMelSpectrogramPreprocessor"]["features"], **jasper_params["JasperEncoder"],
)
jasper_decoder = nemo_asr.JasperDecoderForCTC(
feat_in=jasper_params["JasperEncoder"]["jasper"][-1]["filters"], num_classes=len(vocab),
)
greedy_decoder = nemo_asr.GreedyCTCDecoder()
if args.lm_path:
beam_width = args.beam_width
alpha = args.alpha
beta = args.beta
cutoff_prob = args.cutoff_prob
cutoff_top_n = args.cutoff_top_n
beam_search_with_lm = nemo_asr.BeamSearchDecoderWithLM(
vocab=vocab,
beam_width=beam_width,
alpha=alpha,
beta=beta,
cutoff_prob=cutoff_prob,
cutoff_top_n=cutoff_top_n,
lm_path=args.lm_path,
num_cpus=max(os.cpu_count(), 1),
)
logging.info('================================')
logging.info(f"Number of parameters in encoder: {jasper_encoder.num_weights}")
logging.info(f"Number of parameters in decoder: {jasper_decoder.num_weights}")
logging.info(f"Total number of parameters in model: " f"{jasper_decoder.num_weights + jasper_encoder.num_weights}")
logging.info('================================')
(audio_signal_e1, a_sig_length_e1, transcript_e1, transcript_len_e1,) = data_layer()
processed_signal_e1, p_length_e1 = data_preprocessor(input_signal=audio_signal_e1, length=a_sig_length_e1)
encoded_e1, encoded_len_e1 = jasper_encoder(audio_signal=processed_signal_e1, length=p_length_e1)
log_probs_e1 = jasper_decoder(encoder_output=encoded_e1)
predictions_e1 = greedy_decoder(log_probs=log_probs_e1)
eval_tensors = [
log_probs_e1,
predictions_e1,
transcript_e1,
transcript_len_e1,
encoded_len_e1,
]
if args.lm_path:
beam_predictions_e1 = beam_search_with_lm(log_probs=log_probs_e1, log_probs_length=encoded_len_e1)
eval_tensors.append(beam_predictions_e1)
evaluated_tensors = neural_factory.infer(tensors=eval_tensors, checkpoint_dir=load_dir,)
greedy_hypotheses = post_process_predictions(evaluated_tensors[1], vocab)
references = post_process_transcripts(evaluated_tensors[2], evaluated_tensors[3], vocab)
cer = word_error_rate(hypotheses=greedy_hypotheses, references=references, use_cer=True)
logging.info("Greedy CER {:.2f}%".format(cer * 100))
if args.lm_path:
beam_hypotheses = []
# Over mini-batch
for i in evaluated_tensors[-1]:
# Over samples
for j in i:
beam_hypotheses.append(j[0][1])
cer = word_error_rate(hypotheses=beam_hypotheses, references=references, use_cer=True)
logging.info("Beam CER {:.2f}".format(cer * 100))
if args.save_logprob:
# Convert logits to list of numpy arrays
logprob = []
for i, batch in enumerate(evaluated_tensors[0]):
for j in range(batch.shape[0]):
logprob.append(batch[j][: evaluated_tensors[4][i][j], :].cpu().numpy())
with open(args.save_logprob, 'wb') as f:
pickle.dump(logprob, f, protocol=pickle.HIGHEST_PROTOCOL)
def startup():
if not os.path.exists(CONFIG_PATH):
info("Foxify Directory Missing! Creating One For You...")
os.makedirs(CONFIG_PATH)
if not os.path.exists(DEFAULT_THEME_PATH):
os.makedirs(DEFAULT_THEME_PATH)
if not os.path.exists(DEFAULT_TWEAK_PATH):
os.makedirs(DEFAULT_TWEAK_PATH)
if not os.path.exists(DEFAULT_CONFIG):
while True:
info("If you have not yet setup userChrome CSS Cusotmization\nPlease Open Up Your Firefox Browser and Follow These Steps:")
print("""\
1. Go to "about:support" by typing it into your Address Bar
2. Copy the File Path for your Profile Folder
3. Enter it below""")
filepath = input("> ")
print("You Entered:", filepath.strip())
print("Is this correct? Y\\n")
ans = input("> ")
if ans.lower() == "y":
DCONF['active_profile'] = os.path.realpath(filepath.strip())
info("Writing Default Configuration...")
with open(DEFAULT_CONFIG, 'w') as f:
yaml = YAML()
yaml.default_flow_style = False
yaml.dump(DCONF, f)
info("Checking If userChrome CSS Customization is Enabled")
with open(DCONF['active_profile'] + '/prefs.js', 'r') as f:
match = False
deact_match = False
for line in f.readlines():
if line == '"user_pref("toolkit.legacyUserProfileCustomizations.stylesheets", true);"':
match = True
if line == '"user_pref("toolkit.legacyUserProfileCustomizations.stylesheets", false);"':
deact_match = True
if not match:
info('Enabling userChrome CSS Customization')
with open(DCONF['active_profile'] + '/prefs.js', 'a') as f:
f.write('user_pref("toolkit.legacyUserProfileCustomizations.stylesheets", false);')
if not match and deact_match:
info('Enabling userChrome CSS Customization')
with open(DCONF['active_profile'] + '/prefs.js', 'w') as f:
content = f.read()
content = content.replace('user_pref("toolkit.legacyUserProfileCustomizations.stylesheets", false);', 'user_pref("toolkit.legacyUserProfileCustomizations.stylesheets", true);')
f.write()
info('Checking For Chrome and Backup Directory')
if not os.path.exists(DCONF['active_profile'] + '/chrome'):
os.makedirs(DCONF['active_profile'] + '/chrome')
if not os.path.exists(DCONF['active_profile'] + '/chrome_backup'):
os.makedirs(DCONF['active_profile'] + '/chrome_backup')
info('Chrome Directory and Backup Directory Created')
break
else:
pass
else:
with open(DEFAULT_CONFIG, 'r') as f:
yaml = YAML(typ='safe')
config = yaml.load(f)
if not config.get('config_version'):
for k, v in DCONF.items():
if not config.get(k):
config[k] = v
with open(DEFAULT_CONFIG, 'w') as f:
yaml = YAML()
yaml.default_flow_style = False
yaml.dump(config, f)
if config['config_version'] != CONFIG_VERSION:
for k, v in DCONF.items():
if not config.get(k):
config[k] = v
with open(DEFAULT_CONFIG, 'w') as f:
yaml = YAML()
yaml.default_flow_style = False
yaml.dump(config, f)
if config['check_for_updates']:
res = requests.get('https://raw.githubusercontent.com/M4cs/foxify-cli/master/version').text
if res == version:
config['version'] = version
with open(DEFAULT_CONFIG, 'w') as f:
yaml = YAML()
yaml.default_flow_style = False
yaml.dump(config, f)
else:
info("Update Available! Run 'pip3 install --upgrade foxify-cli' to Update to Version: " + res)
key = newkey
newkey = ''
lineNum += 1
return ret_val
with open('index.md', 'r') as f:
endReached = False
data = f.read().split('\n')
for d in data:
print d
if "<!-- AUTO-GENERATED-START -->" in d:
print '| Key | Default Value | Description |'
print '| --- | --- | --- |'
break
with open('values.yaml', 'r') as f_v:
d_v = f_v.read()
yaml = YAML()
code = yaml.load(d_v)
yaml.explicit_start = True
yaml.dump(code, sys.stdout, transform=decode_helm_yaml)
for d in data:
if "<!-- AUTO-GENERATED-END -->" in d:
endReached = True
if endReached:
print d
def create_all_dags(args, neural_factory):
'''
creates train and eval dags as well as their callbacks
returns train loss tensor and callbacks'''
# parse the config files
yaml = YAML(typ="safe")
with open(args.model_config) as f:
contextnet_params = yaml.load(f)
vocab = contextnet_params['labels']
sample_rate = contextnet_params['sample_rate']
# Calculate num_workers for dataloader
total_cpus = os.cpu_count()
cpu_per_traindl = max(int(total_cpus / neural_factory.world_size), 1)
# create data layer for training
train_dl_params = copy.deepcopy(contextnet_params["AudioToTextDataLayer"])
train_dl_params.update(contextnet_params["AudioToTextDataLayer"]["train"])
del train_dl_params["train"]
del train_dl_params["eval"]
# del train_dl_params["normalize_transcripts"]
data_layer_train = nemo_asr.AudioToTextDataLayer(
manifest_filepath=args.train_dataset,
sample_rate=sample_rate,
labels=vocab,
batch_size=args.batch_size,
num_workers=cpu_per_traindl,
**train_dl_params,
)
N = len(data_layer_train)
steps_per_epoch = int(
N / (args.batch_size * args.iter_per_step * args.num_gpus))
# create separate data layers for eval
# we need separate eval dags for separate eval datasets
# but all other modules in these dags will be shared
eval_dl_params = copy.deepcopy(contextnet_params["AudioToTextDataLayer"])
eval_dl_params.update(contextnet_params["AudioToTextDataLayer"]["eval"])
del eval_dl_params["train"]
del eval_dl_params["eval"]
data_layers_eval = []
if args.eval_datasets:
for eval_dataset in args.eval_datasets:
data_layer_eval = nemo_asr.AudioToTextDataLayer(
manifest_filepath=eval_dataset,
sample_rate=sample_rate,
labels=vocab,
batch_size=args.eval_batch_size,
num_workers=cpu_per_traindl,
**eval_dl_params,
)
data_layers_eval.append(data_layer_eval)
else:
logging.warning("There were no val datasets passed")
# create shared modules
data_preprocessor = nemo_asr.AudioToMelSpectrogramPreprocessor(
sample_rate=sample_rate,
**contextnet_params["AudioToMelSpectrogramPreprocessor"],
)
# Inject the `kernel_size_factor` kwarg to the ContextNet config
# Skip the last layer as that must be a pointwise kernel
for idx in range(
len(contextnet_params["ContextNetEncoder"]["jasper"]) - 1):
contextnet_params["ContextNetEncoder"]["jasper"][idx][
"kernel_size_factor"] = args.kernel_size_factor
# (ContextNet uses the Jasper baseline encoder and decoder)
encoder = nemo_asr.ContextNetEncoder(
feat_in=contextnet_params["AudioToMelSpectrogramPreprocessor"]
["features"],
**contextnet_params["ContextNetEncoder"],
)
decoder = nemo_asr.JasperDecoderForCTC(
feat_in=contextnet_params["ContextNetEncoder"]["jasper"][-1]
["filters"],
num_classes=len(vocab),
)
ctc_loss = nemo_asr.CTCLossNM(num_classes=len(vocab), zero_infinity=True)
greedy_decoder = nemo_asr.GreedyCTCDecoder()
# create augmentation modules (only used for training) if their configs
# are present
multiply_batch_config = contextnet_params.get('MultiplyBatch', None)
if multiply_batch_config:
multiply_batch = nemo_asr.MultiplyBatch(**multiply_batch_config)
spectr_augment_config = contextnet_params.get('SpectrogramAugmentation',
None)
if spectr_augment_config:
data_spectr_augmentation = nemo_asr.SpectrogramAugmentation(
**spectr_augment_config)
# assemble train DAG
(
audio_signal_t,
a_sig_length_t,
transcript_t,
transcript_len_t,
) = data_layer_train()
processed_signal_t, p_length_t = data_preprocessor(
input_signal=audio_signal_t, length=a_sig_length_t)
if multiply_batch_config:
(
processed_signal_t,
p_length_t,
transcript_t,
transcript_len_t,
) = multiply_batch(
in_x=processed_signal_t,
in_x_len=p_length_t,
in_y=transcript_t,
in_y_len=transcript_len_t,
)
if spectr_augment_config:
processed_signal_t = data_spectr_augmentation(
input_spec=processed_signal_t)
encoded_t, encoded_len_t = encoder(audio_signal=processed_signal_t,
length=p_length_t)
log_probs_t = decoder(encoder_output=encoded_t)
predictions_t = greedy_decoder(log_probs=log_probs_t)
loss_t = ctc_loss(
log_probs=log_probs_t,
targets=transcript_t,
input_length=encoded_len_t,
target_length=transcript_len_t,
)
# create train callbacks
train_callback = nemo.core.SimpleLossLoggerCallback(
tensors=[loss_t, predictions_t, transcript_t, transcript_len_t],
print_func=partial(monitor_asr_train_progress, labels=vocab),
get_tb_values=lambda x: [["loss", x[0]]],
tb_writer=neural_factory.tb_writer,
step_freq=args.update_freq,
)
callbacks = [train_callback]
if args.checkpoint_dir or args.load_dir:
chpt_callback = nemo.core.CheckpointCallback(
folder=args.checkpoint_dir,
load_from_folder=args.load_dir,
step_freq=args.checkpoint_save_freq,
)
callbacks.append(chpt_callback)
# Log training metrics to wandb
if args.project is not None:
wand_callback = nemo.core.WandbCallback(
train_tensors=[loss_t],
wandb_name=args.exp_name,
wandb_project=args.project,
update_freq=args.update_freq,
args=args,
)
callbacks.append(wand_callback)
# assemble eval DAGs
for i, eval_dl in enumerate(data_layers_eval):
(
audio_signal_e,
a_sig_length_e,
transcript_e,
transcript_len_e,
) = eval_dl()
processed_signal_e, p_length_e = data_preprocessor(
input_signal=audio_signal_e, length=a_sig_length_e)
encoded_e, encoded_len_e = encoder(audio_signal=processed_signal_e,
length=p_length_e)
log_probs_e = decoder(encoder_output=encoded_e)
predictions_e = greedy_decoder(log_probs=log_probs_e)
loss_e = ctc_loss(
log_probs=log_probs_e,
targets=transcript_e,
input_length=encoded_len_e,
target_length=transcript_len_e,
)
# create corresponding eval callback
tagname = os.path.basename(args.eval_datasets[i]).split(".")[0]
eval_callback = nemo.core.EvaluatorCallback(
eval_tensors=[
loss_e,
predictions_e,
transcript_e,
transcript_len_e,
],
user_iter_callback=partial(process_evaluation_batch, labels=vocab),
user_epochs_done_callback=partial(process_evaluation_epoch,
tag=tagname),
eval_step=args.eval_freq,
tb_writer=neural_factory.tb_writer,
)
callbacks.append(eval_callback)
return loss_t, callbacks, steps_per_epoch
from ruamel.yaml import YAML
yaml = YAML()
files = ('../remoteid/augmented.yaml', '../remoteid/canonical.yaml')
for fname in files:
try:
with open(fname, 'r') as f:
api = yaml.load(f)
with open(fname, 'w') as f:
yaml.dump(api, f)
except IOError:
pass
LOG_DIR = LOG_ROOT + TASK_NAME + '/' + time_str + '/'
os.makedirs(LOG_DIR, exist_ok=True)
LOGFILE = LOG_DIR + 'msgs.log'
TRAIN_LOG = LOG_DIR + 'training.log'
TEST_LOG = LOG_DIR + 'test.log'
MODEL_WTS = LOG_DIR + 'model_weights.hdf5'
LOG_YAML = 'logger_config.yaml'
def logfile():
return logging.FileHandler(LOGFILE)
with open(LOG_YAML, 'rt') as f:
yaml = YAML(typ='safe', pure=True)
config = yaml.load(f.read())
logging.config.dictConfig(config)
logger = logging.getLogger(TASK_NAME)
ex.logger = logger
@ex.capture
def build_train(N_train, train_batch_size, train_min_num_seq, train_max_num_seq, train_avg_len):
ntm = build_ntm(N=N_train)
data_gen = build_data_gen(ntm, train_batch_size, train_min_num_seq, train_max_num_seq, train_avg_len)
return ntm, data_gen
@ex.capture
def build_test(N_test, test_batch_size, test_min_num_seq, test_max_num_seq, test_avg_len):
def loadyaml(yamlp: YAML, source: str) -> Any:
"""Load YAML."""
return yamlp.load(source)
def load_yaml(path):
with open(path, 'r') as yfile:
yml = YAML()
return yml.load(yfile)
3. if same exit, if not, continue
4. modify bitrise.yml (update stack value)
'''
largest_semver = largest_version()
tmp_file = 'tmp.yml'
with open(BITRISE_YML, 'r') as infile:
obj_yaml = YAML()
# prevents re-formatting of yml file
obj_yaml.preserve_quotes = True
obj_yaml.width = 4096
y = obj_yaml.load(infile)
current_semver = y['workflows'][WORKFLOW]['meta']['bitrise.io'][
'stack']
# remove pattern prefix from current_semver to compare with largest
current_semver = current_semver.split(pattern)[1]
if current_semver == largest_semver:
print('Xcode version unchanged! aborting.')
else:
print('New Xcode version available: {0} ... updating bitrise.yml!'.
format(largest_semver))
# add prefix pattern back to be recognizable by bitrise
# as a valid stack value
y['workflows'][WORKFLOW]['meta']['bitrise.io'][
def read_file(self, filename):
mydoc = open(filename, "r")
yaml = YAML(typ='safe')
yaml.default_flow_style = False
return yaml, yaml.load(mydoc)
def read_yaml(file_path):
with open(file_path, 'r') as stream:
yaml = YAML()
return yaml.load(stream.read())
You are receiving this email because you indicated that you are interested in {}.
To unsubscribe, use [this link](%mailing_list_unsubscribe_url%)
""".format
MEETING_MESSAGE_FOOTER = """
---
You are receiving this email because you registered for a VSF Zoom meeting with ID {}.
""".format
if __name__ == "__main__":
yaml = YAML()
repo = common.vsf_repo()
issue = repo.get_issue(int(os.getenv("ISSUE_NUMBER")))
data = issue.body.replace('\r', '')
header, body = data.split('---', maxsplit=1)
header = yaml.load(header)
if header["to"] in ("vsf_announce", "speakers_corner"):
to = header["to"] + "@mail.virtualscienceforum.org"
body += MAILING_LIST_FOOTER(MAILING_LIST_DESCRIPTIONS[header["to"]])
response = common.api_query(requests.post,
common.MAILGUN_BASE_URL + "messages",
data={
"from": header["from"],
"to": to,
"subject": header["subject"],
"text": common.markdown_to_plain(body),
"html": common.markdown_to_email(body),
})
else:
meeting_id = int(header["to"])
# We are sending an email to zoom meeting participants
def _is_new_config(filename, tmp_filename):
with open(filename, "r") as old_file, open(tmp_filename, "r") as new_file:
yaml = YAML()
old_config = yaml.load(old_file)
new_config = yaml.load(new_file)
return old_config != new_config
from ruamel.yaml import YAML
yaml = YAML(typ='safe')
with open('config.yaml', 'r') as f:
config = yaml.load(f)
def _fix_token(config_file=None, force=False, verify=True):
from ruamel.yaml import YAML
yaml = YAML()
config_file = config_file or TRAVIS_CONFIG_FILE
with open(config_file, "r") as _file:
try:
travis_config = yaml.load(_file)
except Exception:
raise ValueError(
"Failed to parse the travis configuration. "
"Make sure the config only contains valid YAML and keys as specified by travis."
)
# Get the generated token from the top level deploy config added by the travis cli
try:
real_token = travis_config["deploy"]["api_key"]["secure"]
except (TypeError, KeyError):
raise AssertionError("Can't find any top level deployment tokens")
try:
# Find the build stage that deploys to releases
releases_stages = [
stage
for stage in travis_config["jobs"]["include"]
if stage.get("deploy", dict()).get("provider") == "releases"
]
assert (
len(releases_stages) > 0
), "Can't set the new token because there are no stages deploying to releases"
assert (
len(releases_stages) < 2
), "Can't set the new token because there are multiple stages deploying to releases"
except (TypeError, KeyError):
raise AssertionError(
"Can't set the new token because there are no deployment stages")
try:
is_mock_token = releases_stages[0]["deploy"]["token"]["secure"] == "REPLACE_ME"
is_same_token = releases_stages[0]["deploy"]["token"]["secure"] == real_token
unmodified = is_mock_token or is_same_token
except (TypeError, KeyError):
unmodified = False
# Set the new generated token as the stages deploy token
_create(releases_stages[0], "deploy", "token", "secure")
releases_stages[0]["deploy"]["token"]["secure"] = real_token
# Make sure it is fine to overwrite the config file
assert unmodified or force, (
'The secure token in the "{}" stage has already been changed. '
"Retry with --force if you are sure about replacing it.".format(
releases_stages[0].get("stage", "releases deployment")
)
)
# Remove the top level deploy config added by the travis cli
travis_config.pop("deploy")
if not unmodified and verify:
pprint.pprint(travis_config)
if (
not input("Do you want to save this configuration? (y/n) ")
.strip()
.lower()
== "y"
):
return
# Save the new travis config
assert travis_config
with open(config_file, "w") as _file:
yaml.dump(travis_config, _file)
print("Fixed!")
import tensorflow as tf
import tensorflow.contrib.slim as slim
from input_ops import create_input_ops
from model import Model
from ruamel.yaml import YAML
from util import log
try:
import better_exceptions
except ImportError:
pass
yaml_path = Path('config.yaml')
yaml = YAML(typ='safe')
config = yaml.load(yaml_path)
paths = config['paths']
h5py_dir = paths['h5py_dir']
logs_dir = paths['logs_dir']
class Trainer(object):
def __init__(self, config, dataset, dataset_test):
self.config = config
hyper_parameter_str = config.model + '-is_' + str(config.img_size) + '-bs_' + str(config.batch_size) + \
'-lr_' + "{:.2E}".format(config.learning_rate) + '-ur_' + str(config.update_rate)
self.train_dir = logs_dir + '/%s-%s/train_dir/' % (
hyper_parameter_str, time.strftime("%Y%m%d_%H%M%S"))
self.test_dir = logs_dir + '/%s-%s/test_dir/' % (
def main():
parser = argparse.ArgumentParser(description='Jasper')
# model params
parser.add_argument("--model_config", type=str, required=True)
parser.add_argument("--eval_datasets", type=str, required=True)
parser.add_argument("--load_dir", type=str, required=True)
# run params
parser.add_argument("--local_rank", default=None, type=int)
parser.add_argument("--batch_size", default=64, type=int)
parser.add_argument("--amp_opt_level", default="O1", type=str)
# store results
parser.add_argument("--save_logprob", default=None, type=str)
# lm inference parameters
parser.add_argument("--lm_path", default=None, type=str)
parser.add_argument('--alpha', default=2.0, type=float, help='value of LM weight', required=False)
parser.add_argument(
'--alpha_max',
type=float,
help='maximum value of LM weight (for a grid search in \'eval\' mode)',
required=False,
)
parser.add_argument(
'--alpha_step', type=float, help='step for LM weight\'s tuning in \'eval\' mode', required=False, default=0.1
)
parser.add_argument('--beta', default=1.5, type=float, help='value of word count weight', required=False)
parser.add_argument(
'--beta_max',
type=float,
help='maximum value of word count weight (for a grid search in \
\'eval\' mode',
required=False,
)
parser.add_argument(
'--beta_step',
type=float,
help='step for word count weight\'s tuning in \'eval\' mode',
required=False,
default=0.1,
)
parser.add_argument("--beam_width", default=128, type=int)
args = parser.parse_args()
batch_size = args.batch_size
load_dir = args.load_dir
if args.local_rank is not None:
if args.lm_path:
raise NotImplementedError(
"Beam search decoder with LM does not currently support evaluation on multi-gpu."
)
device = nemo.core.DeviceType.AllGpu
else:
device = nemo.core.DeviceType.GPU
# Instantiate Neural Factory with supported backend
neural_factory = nemo.core.NeuralModuleFactory(
local_rank=args.local_rank, optimization_level=args.amp_opt_level, placement=device,
)
if args.local_rank is not None:
logging.info('Doing ALL GPU')
yaml = YAML(typ="safe")
with open(args.model_config) as f:
jasper_params = yaml.load(f)
try:
vocab = jasper_params['labels']
sample_rate = jasper_params['sample_rate']
except KeyError:
logging.error("Please make sure you are using older config format (the ones with -old suffix)")
exit(1)
eval_datasets = args.eval_datasets
eval_dl_params = copy.deepcopy(jasper_params["AudioToTextDataLayer"])
eval_dl_params.update(jasper_params["AudioToTextDataLayer"]["eval"])
del eval_dl_params["train"]
del eval_dl_params["eval"]
data_layer = nemo_asr.AudioToTextDataLayer(
manifest_filepath=eval_datasets,
sample_rate=sample_rate,
labels=vocab,
batch_size=batch_size,
**eval_dl_params,
)
N = len(data_layer)
logging.info('Evaluating {0} examples'.format(N))
data_preprocessor = nemo_asr.AudioToMelSpectrogramPreprocessor(
sample_rate=sample_rate, **jasper_params["AudioToMelSpectrogramPreprocessor"]
)
jasper_encoder = nemo_asr.JasperEncoder(
feat_in=jasper_params["AudioToMelSpectrogramPreprocessor"]["features"], **jasper_params["JasperEncoder"]
)
jasper_decoder = nemo_asr.JasperDecoderForCTC(
feat_in=jasper_params["JasperEncoder"]["jasper"][-1]["filters"], num_classes=len(vocab)
)
greedy_decoder = nemo_asr.GreedyCTCDecoder()
logging.info('================================')
logging.info(f"Number of parameters in encoder: {jasper_encoder.num_weights}")
logging.info(f"Number of parameters in decoder: {jasper_decoder.num_weights}")
logging.info(f"Total number of parameters in model: " f"{jasper_decoder.num_weights + jasper_encoder.num_weights}")
logging.info('================================')
# Define inference DAG
audio_signal_e1, a_sig_length_e1, transcript_e1, transcript_len_e1 = data_layer()
processed_signal_e1, p_length_e1 = data_preprocessor(input_signal=audio_signal_e1, length=a_sig_length_e1)
encoded_e1, encoded_len_e1 = jasper_encoder(audio_signal=processed_signal_e1, length=p_length_e1)
log_probs_e1 = jasper_decoder(encoder_output=encoded_e1)
predictions_e1 = greedy_decoder(log_probs=log_probs_e1)
eval_tensors = [log_probs_e1, predictions_e1, transcript_e1, transcript_len_e1, encoded_len_e1]
# inference
evaluated_tensors = neural_factory.infer(tensors=eval_tensors, checkpoint_dir=load_dir)
greedy_hypotheses = post_process_predictions(evaluated_tensors[1], vocab)
references = post_process_transcripts(evaluated_tensors[2], evaluated_tensors[3], vocab)
wer = word_error_rate(hypotheses=greedy_hypotheses, references=references)
logging.info("Greedy WER {:.2f}%".format(wer * 100))
# Convert logits to list of numpy arrays
logprob = []
for i, batch in enumerate(evaluated_tensors[0]):
for j in range(batch.shape[0]):
logprob.append(batch[j][: evaluated_tensors[4][i][j], :].cpu().numpy())
if args.save_logprob:
with open(args.save_logprob, 'wb') as f:
pickle.dump(logprob, f, protocol=pickle.HIGHEST_PROTOCOL)
# language model
if args.lm_path:
if args.alpha_max is None:
args.alpha_max = args.alpha
# include alpha_max in tuning range
args.alpha_max += args.alpha_step / 10.0
if args.beta_max is None:
args.beta_max = args.beta
# include beta_max in tuning range
args.beta_max += args.beta_step / 10.0
beam_wers = []
logprobexp = [np.exp(p) for p in logprob]
for alpha in np.arange(args.alpha, args.alpha_max, args.alpha_step):
for beta in np.arange(args.beta, args.beta_max, args.beta_step):
logging.info('================================')
logging.info(f'Infering with (alpha, beta): ({alpha}, {beta})')
beam_search_with_lm = nemo_asr.BeamSearchDecoderWithLM(
vocab=vocab,
beam_width=args.beam_width,
alpha=alpha,
beta=beta,
lm_path=args.lm_path,
num_cpus=max(os.cpu_count(), 1),
input_tensor=False,
)
beam_predictions = beam_search_with_lm(log_probs=logprobexp, log_probs_length=None, force_pt=True)
beam_predictions = [b[0][1] for b in beam_predictions[0]]
lm_wer = word_error_rate(hypotheses=beam_predictions, references=references)
logging.info("Beam WER {:.2f}%".format(lm_wer * 100))
beam_wers.append(((alpha, beta), lm_wer * 100))
logging.info('Beam WER for (alpha, beta)')
logging.info('================================')
logging.info('\n' + '\n'.join([str(e) for e in beam_wers]))
logging.info('================================')
best_beam_wer = min(beam_wers, key=lambda x: x[1])
logging.info('Best (alpha, beta): ' f'{best_beam_wer[0]}, ' f'WER: {best_beam_wer[1]:.2f}%')
class Config(object):
def __init__(self, configFile: str):
self.configFile = configFile
self._configData = {}
self.yaml = YAML()
self._inBaseConfig = []
def loadConfig(self) -> None:
configData = self._readConfig(self.configFile)
self._validate(configData)
self._configData = configData
def _readConfig(self, fileName: str) -> Dict:
try:
with open(fileName, mode='r') as config:
configData = self.yaml.load(config)
if not configData:
configData = {}
# if this is the base server config, store what keys we loaded
if fileName == self.configFile:
self._inBaseConfig = list(configData.keys())
except Exception as e:
raise ConfigError(fileName, e)
if 'import' not in configData:
return configData
for fname in configData['import']:
includeConfig = self._readConfig('{}/{}.yaml'
.format(os.path.dirname(os.path.abspath(fileName)),
fname))
for key, val in includeConfig.items():
# not present in base config, just assign it
if key not in configData:
configData[key] = val
continue
# skip non-collection types that are already set
if isinstance(configData[key], (str, int)):
continue
if isinstance(val, str):
raise ConfigError(fname, 'The included config file tried '
'to merge a non-string with a '
'string')
try:
iter(configData[key])
iter(val)
except TypeError:
# not a collection, so just don't merge them
pass
else:
try:
# merge with + operator
configData[key] += val
except TypeError:
# dicts can't merge with +
try:
for subKey, subVal in val.items():
if subKey not in configData[key]:
configData[key][subKey] = subVal
except (AttributeError, TypeError):
# if either of these, they weren't both dicts.
raise ConfigError(fname, 'The variable {!r} could '
'not be successfully '
'merged'.format(key))
return configData
def writeConfig(self) -> None:
# filter the configData to only those keys
# that were present in the base server config,
# or have been modified at runtime
configData = copy.deepcopy(self._configData)
to_delete = set(configData.keys()).difference(self._inBaseConfig)
for key in to_delete:
del configData[key]
# write the filtered configData
try:
with open(self.configFile, mode='w') as config:
self.yaml.dump(configData, config)
except Exception as e:
raise ConfigError(self.configFile, e)
def getWithDefault(self, key: str, default=None) -> Any:
if key in self._configData:
return self._configData[key]
return default
def _validate(self, configData) -> None:
for key in _required:
if key not in configData:
raise ConfigError(self.configFile,
'Required item {!r} was not found in the config.'.format(key))
def __len__(self):
return len(self._configData)
def __iter__(self):
return iter(self._configData)
def __getitem__(self, key):
return self._configData[key]
def __setitem__(self, key, value):
# mark this key to be saved in the server config
if key not in self._inBaseConfig:
self._inBaseConfig.append(key)
self._configData[key] = value
def __contains__(self, key):
return key in self._configData
def create_all_dags(args, neural_factory):
"""Create Directed Acyclic Graph (DAG) for training and evaluation
"""
logger = neural_factory.logger
yaml = YAML(typ="safe")
with open(args.model_config) as f:
jasper_params = yaml.load(f)
vocab = jasper_params['labels']
sample_rate = jasper_params['sample_rate']
# Calculate num_workers for dataloader
total_cpus = os.cpu_count()
cpu_per_traindl = max(int(total_cpus / neural_factory.world_size), 1)
# train params
# perturb_config = jasper_params.get('perturb', None)
train_dl_params = copy.deepcopy(jasper_params["AudioToTextDataLayer"])
train_dl_params.update(jasper_params["AudioToTextDataLayer"]["train"])
del train_dl_params["train"]
del train_dl_params["eval"]
# del train_dl_params["normalize_transcripts"]
data_layer = nemo_asr.AudioToTextDataLayer(
manifest_filepath=args.train_dataset,
sample_rate=sample_rate,
labels=vocab,
batch_size=args.batch_size,
num_workers=cpu_per_traindl,
**train_dl_params,
# normalize_transcripts=False
)
N = len(data_layer)
steps_per_epoch = int(N / (args.batch_size * args.num_gpus))
logger.info('Have {0} examples to train on.'.format(N))
data_preprocessor = nemo_asr.AudioToMelSpectrogramPreprocessor(
sample_rate=sample_rate,
**jasper_params["AudioToMelSpectrogramPreprocessor"])
multiply_batch_config = jasper_params.get('MultiplyBatch', None)
if multiply_batch_config:
multiply_batch = nemo_asr.MultiplyBatch(**multiply_batch_config)
spectr_augment_config = jasper_params.get('SpectrogramAugmentation', None)
if spectr_augment_config:
data_spectr_augmentation = nemo_asr.SpectrogramAugmentation(
**spectr_augment_config)
eval_dl_params = copy.deepcopy(jasper_params["AudioToTextDataLayer"])
eval_dl_params.update(jasper_params["AudioToTextDataLayer"]["eval"])
del eval_dl_params["train"]
del eval_dl_params["eval"]
data_layers_eval = []
if args.eval_datasets:
for eval_datasets in args.eval_datasets:
data_layer_eval = nemo_asr.AudioToTextDataLayer(
manifest_filepath=eval_datasets,
sample_rate=sample_rate,
labels=vocab,
batch_size=args.eval_batch_size,
num_workers=cpu_per_traindl,
**eval_dl_params,
)
data_layers_eval.append(data_layer_eval)
else:
neural_factory.logger.info("There were no val datasets passed")
# set encoder and decoders
jasper_encoder = nemo_asr.JasperEncoder(
feat_in=jasper_params["AudioToMelSpectrogramPreprocessor"]["features"],
**jasper_params["JasperEncoder"])
jasper_decoder = nemo_asr.JasperDecoderForCTC(
feat_in=jasper_params["JasperEncoder"]["jasper"][-1]["filters"],
num_classes=len(vocab),
factory=neural_factory)
ctc_loss = nemo_asr.CTCLossNM(num_classes=len(vocab))
greedy_decoder = nemo_asr.GreedyCTCDecoder()
# finetuning - restore encoder and decoder
if args.finetune:
logger.info("Finetuning")
jasper_encoder.restore_from(args.load_encoder)
logger.info("Loaded encoder: {}".format(args.load_encoder))
if args.load_decoder != "":
jasper_decoder.restore_from(args.load_decoder)
logger.info("Loaded decoder: {}".format(args.load_decoder))
logger.info('================================')
logger.info(
f"Number of parameters in encoder: {jasper_encoder.num_weights}")
logger.info(
f"Number of parameters in decoder: {jasper_decoder.num_weights}")
logger.info(f"Total number of parameters: "
f"{jasper_decoder.num_weights + jasper_encoder.num_weights}")
logger.info('================================')
# Train DAG
audio_signal_t, a_sig_length_t, \
transcript_t, transcript_len_t = data_layer()
processed_signal_t, p_length_t = data_preprocessor(
input_signal=audio_signal_t, length=a_sig_length_t)
if multiply_batch_config:
processed_signal_t, p_length_t, transcript_t, transcript_len_t = \
multiply_batch(
in_x=processed_signal_t, in_x_len=p_length_t,
in_y=transcript_t,
in_y_len=transcript_len_t)
if spectr_augment_config:
processed_signal_t = data_spectr_augmentation(
input_spec=processed_signal_t)
encoded_t, encoded_len_t = jasper_encoder(audio_signal=processed_signal_t,
length=p_length_t)
log_probs_t = jasper_decoder(encoder_output=encoded_t)
predictions_t = greedy_decoder(log_probs=log_probs_t)
loss_t = ctc_loss(log_probs=log_probs_t,
targets=transcript_t,
input_length=encoded_len_t,
target_length=transcript_len_t)
# Callbacks needed to print info to console and Tensorboard
train_callback = nemo.core.SimpleLossLoggerCallback(
tensors=[loss_t, predictions_t, transcript_t, transcript_len_t],
print_func=partial(monitor_asr_train_progress,
labels=vocab,
logger=logger),
get_tb_values=lambda x: [("loss", x[0])],
tb_writer=neural_factory.tb_writer,
)
chpt_callback = nemo.core.CheckpointCallback(
folder=neural_factory.checkpoint_dir,
step_freq=args.checkpoint_save_freq)
callbacks = [train_callback, chpt_callback]
# assemble eval DAGs
for i, eval_dl in enumerate(data_layers_eval):
audio_signal_e, a_sig_length_e, transcript_e, transcript_len_e = \
eval_dl()
processed_signal_e, p_length_e = data_preprocessor(
input_signal=audio_signal_e, length=a_sig_length_e)
encoded_e, encoded_len_e = jasper_encoder(
audio_signal=processed_signal_e, length=p_length_e)
log_probs_e = jasper_decoder(encoder_output=encoded_e)
predictions_e = greedy_decoder(log_probs=log_probs_e)
loss_e = ctc_loss(log_probs=log_probs_e,
targets=transcript_e,
input_length=encoded_len_e,
target_length=transcript_len_e)
# create corresponding eval callback
tagname = os.path.basename(args.eval_datasets[i]).split(".")[0]
eval_callback = nemo.core.EvaluatorCallback(
eval_tensors=[
loss_e, predictions_e, transcript_e, transcript_len_e
],
user_iter_callback=partial(process_evaluation_batch, labels=vocab),
user_epochs_done_callback=partial(process_evaluation_epoch,
tag=tagname,
logger=logger),
eval_step=args.eval_freq,
tb_writer=neural_factory.tb_writer)
callbacks.append(eval_callback)
return loss_t, callbacks, steps_per_epoch
