def test_default_schema():
r"""Test getting default schema."""
s = schema.get_schema()
assert (s is not None)
schema.clear_schema()
assert (schema._schema is None)
s = schema.get_schema()
assert (s is not None)
for k in s.keys():
assert (isinstance(s[k].subtypes, list))
assert (isinstance(s[k].classes, list))
def prep_model(yml, iodict):
r"""Prepare yaml model entry for parsing with schema.
Args:
yml (dict): YAML entry for model that will be modified.
iodict (dict): Log of all input/outputs.
"""
class2language = get_schema().class2language
# Standardize format of input/output
for io in ['inputs', 'outputs']:
if io not in yml:
yml[io] = []
if not isinstance(yml[io], list):
yml[io] = [yml[io]]
if io[:-1] in yml:
if isinstance(yml[io[:-1]], list):
yml[io] += yml.pop(io[:-1])
else:
yml[io].append(yml.pop(io[:-1]))
for i in range(len(yml[io])):
if isinstance(yml[io][i], str):
yml[io][i] = dict(name=yml[io][i])
if 'driver' in yml[io][i]:
yml[io][i].setdefault('working_dir', yml['working_dir'])
if 'name' in yml[io][i]:
iodict[io][yml[io][i]['name']] = yml[io][i]
# Replace driver with language
if ('language' not in yml) and ('driver' in yml):
yml['language'] = class2language[yml.pop('driver')][0]
# String to list
if ('client_of' in yml) and (not isinstance(yml['client_of'], list)):
yml['client_of'] = [yml['client_of']]
def get_supported_comm():
r"""Get a list of the communication mechanisms supported by cis_interface.
Returns:
list: The names of communication mechanisms supported by cis_interface.
"""
from cis_interface import schema
s = schema.get_schema()
out = s['comm'].classes
out.remove('CommBase')
return list(set(out))
def get_supported_lang():
r"""Get a list of the model programming languages that are supported
by cis_interface.
Returns:
list: The names of programming languages supported by cis_interface.
"""
from cis_interface import schema
s = schema.get_schema()
out = s['model'].subtypes
if 'c++' in out:
out[out.index('c++')] = 'cpp'
return list(set(out))
def is_lang_installed(lang):
r"""Check to see if cis_interface can run models written in a programming
language on the current machine.
Args:
lang (str): Programming language to check.
Returns:
bool: True if models in the provided language can be run on the current
machine, False otherwise.
"""
from cis_interface import schema, drivers
s = schema.get_schema()
drv = drivers.import_driver(s.language2class[lang])
return drv.is_installed()
def test_create_schema():
r"""Test creating new schema."""
fname = 'test_schema.yml'
if os.path.isfile(fname): # pragma: debug
os.remove(fname)
# Test saving/loading schema
s0 = schema.create_schema()
s0.save(fname)
assert (os.path.isfile(fname))
s1 = schema.get_schema(fname)
nt.assert_equal(s1, s0)
os.remove(fname)
# Test getting schema
s2 = schema.load_schema(fname)
assert (os.path.isfile(fname))
nt.assert_equal(s2, s0)
os.remove(fname)
def parse_model(yml, existing):
r"""Parse a yaml entry for a model.
Args:
yml (dict): YAML dictionary for a model.
existing (dict): Dictionary of existing components.
Returns:
dict: Updated log of all entries.
"""
_lang2driver = get_schema().language2class
yml['driver'] = _lang2driver[yml.pop('language')]
# Add server driver
if yml.get('is_server', False):
srv = {
'name': yml['name'],
'driver': 'ServerDriver',
'args': yml['name'] + '_SERVER',
'working_dir': yml['working_dir']
}
yml['inputs'].append(srv)
yml['clients'] = []
# Add client driver
if yml.get('client_of', []):
srv_names = yml['client_of']
# prep_model converts to list
# if isinstance(srv_names, str):
# srv_names = [srv_names]
yml['client_of'] = srv_names
for srv in srv_names:
cli = {
'name': '%s_%s' % (srv, yml['name']),
'driver': 'ClientDriver',
'args': srv + '_SERVER',
'working_dir': yml['working_dir']
}
yml['outputs'].append(cli)
# Model index and I/O channels
yml['model_index'] = len(existing['model'])
for io in ['inputs', 'outputs']:
for x in yml[io]:
x['model_driver'] = [yml['name']]
existing = parse_component(x, io[:-1], existing=existing)
return existing
def convertSpec(self, spec):
"""Convert spec."""
cisspec = uiToCis(spec['content'])
# Write to temp file and validate
tmpfile = tempfile.NamedTemporaryFile(suffix="yml", prefix="cis",
delete=False)
yaml.safe_dump(cisspec, tmpfile, default_flow_style=False)
yml_prep = prep_yaml(tmpfile)
os.remove(tmpfile.name)
v = get_schema().validator
yml_norm = v.normalized(yml_prep)
if not v.validate(yml_norm):
print(v.errors)
raise RestException('Invalid model %s', 400, v.errors)
self.setRawResponse()
return pyaml.dump(cisspec)
def cdriver2filetype(driver):
r"""Convert a connection driver to a file type.
Args:
driver (str): The name of the connection driver.
Returns:
str: The corresponding file type for the driver.
"""
schema = get_schema()
conntypes = schema.class2conntype
filetypes = schema.class2filetype
if driver not in conntypes:
raise ValueError("%s is not a registered connection driver." % driver)
icomm, ocomm, direction = conntypes[driver][0]
if direction == 'input':
ftype = filetypes[icomm][0]
else:
ftype = filetypes[ocomm][0]
return ftype
def parse_yaml(files):
r"""Parse list of yaml files.
Args:
files (str, list): Either the path to a single yaml file or a list of
yaml files.
Raises:
ValueError: If the yml dictionary is missing a required keyword or has
an invalid value.
RuntimeError: If one of the I/O channels is not initialized with driver
information.
Returns:
dict: Dictionary of information parsed from the yamls.
"""
# Parse files using schema
yml_prep = prep_yaml(files)
v = get_schema().validator
yml_norm = v.normalized(yml_prep)
if not v.validate(yml_norm):
pprint.pprint(yml_norm)
pprint.pprint(v.errors)
raise ValueError("Invalid yaml.")
yml_all = v.document
# Parse models, then connections to ensure connections can be processed
existing = None
for k in ['models', 'connections']:
for yml in yml_all[k]:
existing = parse_component(yml, k[:-1], existing=existing)
# Make sure that I/O channels initialized
for io in ['input', 'output']:
for k, v in existing[io].items():
if 'driver' not in v:
raise RuntimeError("No driver established for %s channel %s" %
(io, k))
# Link io drivers back to models
existing = link_model_io(existing)
return existing
def parse_connection(yml, existing):
r"""Parse a yaml entry for a connection between I/O channels.
Args:
yml (dict): YAML dictionary for a connection.
existing (dict): Dictionary of existing components.
Raises:
RuntimeError: If the 'input' entry is not a model output or file.
RuntimeError: If neither the 'input' or 'output' entries correspond
to model I/O channels.
Returns:
dict: Updated log of all entries.
"""
schema = get_schema()
comm2conn = schema.conntype2class
ftyp2comm = schema.filetype2class
conn_keys_gen = ['input', 'input_file', 'output', 'output_file']
conn_keys = list(set(schema['connection'].keys()) - set(conn_keys_gen))
yml_conn = {}
if not isinstance(yml.get('input', []), list):
yml['input'] = [yml['input']]
if not isinstance(yml.get('output', []), list):
yml['output'] = [yml['output']]
# File input
if 'input_file' in yml:
fname = os.path.expanduser(yml['input_file']['name'])
if not os.path.isabs(fname):
fname = os.path.join(yml['input_file']['working_dir'], fname)
fname = os.path.normpath(fname)
if not os.path.isfile(fname):
raise RuntimeError(
("Input '%s' not found in any of the registered " +
"model outputs and is not a file.") % fname)
args = fname
name = ','.join(yml['output'])
ocomm_pair = None
icomm_pair = (ftyp2comm[yml['input_file']['filetype']], 'DefaultComm')
yml_conn.update(**yml['input_file'])
# File output
elif 'output_file' in yml:
fname = os.path.expanduser(yml['output_file']['name'])
if not yml['output_file'].get('in_temp', False):
if not os.path.isabs(fname):
fname = os.path.join(yml['output_file']['working_dir'], fname)
fname = os.path.normpath(fname)
args = fname
name = ','.join(yml['input'])
ocomm_pair = ('DefaultComm', ftyp2comm[yml['output_file']['filetype']])
icomm_pair = None
yml_conn.update(**yml['output_file'])
# Generic Input/Output
else:
iname = ','.join(yml['input'])
oname = ','.join(yml['output'])
args = '%s_to_%s' % (iname, oname)
name = args
# TODO: Use RMQ drivers when models are on different machines
# ocomm_pair = ('DefaultComm', 'rmq')
# icomm_pair = ('rmq', 'DefaultComm')
ocomm_pair = ('DefaultComm', 'DefaultComm')
icomm_pair = ('DefaultComm', 'DefaultComm')
# Output driver
xo = None
if ocomm_pair is not None:
iyml = yml['input']
iname = ','.join(iyml)
if len(iyml) == 1:
xo = existing['output'][iyml[0]]
else:
xo = {'name': iname, 'comm': [], 'model_driver': []}
for y in iyml:
xo['comm'].append(existing['output'][y])
xo['model_driver'] += existing['output'][y]['model_driver']
del existing['output'][y]
existing = parse_component(xo, 'output', existing)
xo['args'] = args
xo['driver'] = comm2conn[(ocomm_pair[0], ocomm_pair[1], 'output')]
# Input driver
xi = None
if icomm_pair is not None:
oyml = yml['output']
oname = ','.join(oyml)
if len(oyml) == 1:
xi = existing['input'][oyml[0]]
else:
xi = {'name': oname, 'comm': [], 'model_driver': []}
for y in oyml:
xi['comm'].append(existing['input'][y])
xi['model_driver'] += existing['input'][y]['model_driver']
del existing['input'][y]
existing = parse_component(xi, 'input', existing)
xi['args'] = args
xi['driver'] = comm2conn[(icomm_pair[0], icomm_pair[1], 'input')]
# Transfer connection keywords to one connection driver
yml_conn.pop('name', None)
for k in conn_keys:
if k in yml:
yml_conn[k] = yml[k]
if xi is None:
xo.update(**yml_conn)
else:
xi.update(**yml_conn)
yml['name'] = name
return existing
def bridge_io_drivers(yml, iodict):
r"""Create connection from input/output driver.
Args:
dict: YAML entry for model output that should be modified.
iodict (dict): Log of all input/outputs.
"""
s = get_schema()
conn_keys_gen = ['input', 'input_file', 'output', 'output_file']
file_keys = list(set(s['file'].keys()) - set(s['comm'].keys()))
conn_keys = list(set(s['connection'].keys()) - set(conn_keys_gen))
idrivers = []
odrivers = []
pairs = []
new_connections = []
for x in iodict['inputs'].values():
if ('driver' in x) and ('args' in x):
idrivers.append((x['args'], x['name']))
for x in iodict['outputs'].values():
if ('driver' in x) and ('args' in x):
iidx = None
for i, (iargs, iname) in enumerate(idrivers):
if x['args'] == iargs:
iidx = i
break
if iidx is not None:
pairs.append((x['name'], idrivers.pop(iidx)[1]))
else:
odrivers.append((x['args'], x['name']))
# Create direct connections from output to input
for (oname, iname) in pairs:
oyml = iodict['outputs'][oname]
iyml = iodict['inputs'][iname]
conn = dict(input=oname, output=iname)
new_connections.append((oyml, iyml, conn))
oyml.pop('working_dir', None)
iyml.pop('working_dir', None)
# File input
for k, v in idrivers:
oyml = None
iyml = iodict['inputs'][v]
fyml = dict(name=k, filetype=cdriver2filetype(iyml['driver']))
conn = dict(input_file=fyml, output=v)
new_connections.append((oyml, iyml, conn))
# File output
for k, v in odrivers:
oyml = iodict['outputs'][v]
iyml = None
fyml = dict(name=k, filetype=cdriver2filetype(oyml['driver']))
conn = dict(output_file=fyml, input=v)
new_connections.append((oyml, iyml, conn))
# Transfer keyword arguments
for oyml, iyml, conn in new_connections:
if oyml is None:
fkey = 'input_file'
fyml = iyml
ymls = [iyml]
elif iyml is None:
fkey = 'output_file'
fyml = oyml
ymls = [oyml]
else:
fkey = None
fyml = None
ymls = [oyml, iyml]
# File keywords
if fyml is not None:
for k in file_keys:
if k in fyml:
conn[fkey][k] = fyml.pop(k)
# Connection keywords
for y in ymls:
for k in conn_keys:
if k not in y:
continue
if k == 'translator':
conn.setdefault(k, [])
conn[k].append(y.pop(k))
else:
conn.setdefault(k, y.pop(k))
del y['driver'], y['args']
# Add connection
iodict['connections'].append(conn)
def prep_connection(yml, iodict):
r"""Prepare yaml connection entry for parsing with schema.
Args:
yml (dict): YAML entry for connection that will be modified.
iodict (dict): Log of all input/outputs.
"""
# Plural
if ('inputs' in yml):
yml['input'] = yml.pop('inputs')
if ('outputs' in yml):
yml['output'] = yml.pop('outputs')
# Input
if ('input' in yml):
if isinstance(yml['input'], list) and (len(yml['input']) == 1):
yml['input'] = yml['input'][0]
if ((isinstance(yml['input'], str)
and (yml['input'] not in iodict['outputs'])
and ('input_file' not in yml))):
yml['input_file'] = yml.pop('input')
elif isinstance(yml['input'], list):
for x in yml['input']:
if x not in iodict['outputs']:
raise RuntimeError(
'%s not connected and cannot be a file.' % x)
if isinstance(yml.get('input_file', None), str):
yml['input_file'] = dict(name=yml['input_file'])
if ('read_meth' in yml):
if 'input_file' not in yml:
raise ValueError("'read_meth' set, but input is not a file.")
yml['input_file'].update(**rwmeth2filetype(yml.pop('read_meth')))
# Output
if ('output' in yml):
if isinstance(yml['output'], list) and (len(yml['output']) == 1):
yml['output'] = yml['output'][0]
if ((isinstance(yml['output'], str)
and (yml['output'] not in iodict['inputs'])
and ('output_file' not in yml))):
yml['output_file'] = yml.pop('output')
elif isinstance(yml['output'], list):
for x in yml['output']:
if x not in iodict['inputs']:
raise RuntimeError(
'%s not connected and cannot be a file.' % x)
if isinstance(yml.get('output_file', None), str):
yml['output_file'] = dict(name=yml['output_file'])
if ('write_meth' in yml):
if 'output_file' not in yml:
raise ValueError("'write_meth' set, but output is not a file.")
yml['output_file'].update(**rwmeth2filetype(yml.pop('write_meth')))
# Error if neither input nor output is connected to a model
if ('input_file' in yml) and ('output_file' in yml):
raise RuntimeError(
("Input '%s' and Output '%s' are both being " +
"considered as files since neither is connected " + "to a model.")
% (yml['input_file']['name'], yml['output_file']['name']))
# Move remaining keys to input/output comm/file
working_dir = yml.pop('working_dir', None)
s = get_schema()
conn_keys = list(set(s['connection'].keys()))
def migrate_keys(from_dict, to_dict):
klist = list(from_dict.keys())
if not isinstance(to_dict, list):
to_dict = [to_dict]
for k in klist:
if k not in conn_keys:
v = from_dict.pop(k)
for d in to_dict:
d.setdefault(k, v)
if 'input_file' in yml:
if working_dir:
yml['input_file'].setdefault('working_dir', working_dir)
migrate_keys(yml, yml['input_file'])
elif 'output_file' in yml:
if working_dir:
yml['output_file'].setdefault('working_dir', working_dir)
migrate_keys(yml, yml['output_file'])
elif 'input' in yml:
if isinstance(yml['input'], list):
io_names = yml['input']
else:
io_names = [yml['input']]
allio = [iodict['outputs'][x] for x in io_names]
migrate_keys(yml, allio)