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swift-nav/libsbp | generator/sbpg/targets/latex.py | render_source | def render_source(output_dir, package_specs, version):
"""
Render and output
"""
destination_filename = "%s/sbp_out.tex" % output_dir
py_template = JENV.get_template(TEMPLATE_NAME)
stable_msgs = []
unstable_msgs = []
prims = []
for p in sorted(package_specs, key=attrgetter('identifier')):
pkg_name = p.identifier
stable = p.stable
# build list of required definitions (this package plus includes)
# TODO: recursively include files
definitions = p.definitions
for inc in p.includes:
inc_basename = inc.split(".")[0]
for pkg in package_specs:
if pkg.identifier.endswith(inc_basename):
definitions += pkg.definitions
if pkg_name == "swiftnav.sbp.types":
prims = p.definitions
for d in p.definitions:
if d.public and d.static and d.sbp_id:
items, size, multiplier \
= handle_fields(definitions, d.fields, "", 0, None)
adj_size = ""
if multiplier == 1:
adj_size = "N+%d" % (size - 1) if size > 1 else "N"
elif multiplier:
if multiplier == size:
adj_size = "%dN" % multiplier
else:
adj_size = "%dN+%d" % (multiplier, size - multiplier)
else:
adj_size = "%d" % size
ti = TableItem(pkg_name, d.identifier, d.sbp_id,
d.short_desc, d.desc, adj_size, items, p.stable,
p.description)
pkg_name = ""
if stable:
stable_msgs.append(ti)
else:
unstable_msgs.append(ti)
with open(destination_filename, 'w') as f:
f.write(py_template.render(msgs=stable_msgs,
umsgs=unstable_msgs,
prims=prims,
version=version))
import subprocess
import os
os.chdir(output_dir)
subprocess.call(["pdflatex", "--enable-write18",
"-shell-escape", "sbp_out.tex"])
subprocess.call(["mv", "sbp_out.pdf", "../docs/sbp.pdf"]) | python | def render_source(output_dir, package_specs, version):
"""
Render and output
"""
destination_filename = "%s/sbp_out.tex" % output_dir
py_template = JENV.get_template(TEMPLATE_NAME)
stable_msgs = []
unstable_msgs = []
prims = []
for p in sorted(package_specs, key=attrgetter('identifier')):
pkg_name = p.identifier
stable = p.stable
# build list of required definitions (this package plus includes)
# TODO: recursively include files
definitions = p.definitions
for inc in p.includes:
inc_basename = inc.split(".")[0]
for pkg in package_specs:
if pkg.identifier.endswith(inc_basename):
definitions += pkg.definitions
if pkg_name == "swiftnav.sbp.types":
prims = p.definitions
for d in p.definitions:
if d.public and d.static and d.sbp_id:
items, size, multiplier \
= handle_fields(definitions, d.fields, "", 0, None)
adj_size = ""
if multiplier == 1:
adj_size = "N+%d" % (size - 1) if size > 1 else "N"
elif multiplier:
if multiplier == size:
adj_size = "%dN" % multiplier
else:
adj_size = "%dN+%d" % (multiplier, size - multiplier)
else:
adj_size = "%d" % size
ti = TableItem(pkg_name, d.identifier, d.sbp_id,
d.short_desc, d.desc, adj_size, items, p.stable,
p.description)
pkg_name = ""
if stable:
stable_msgs.append(ti)
else:
unstable_msgs.append(ti)
with open(destination_filename, 'w') as f:
f.write(py_template.render(msgs=stable_msgs,
umsgs=unstable_msgs,
prims=prims,
version=version))
import subprocess
import os
os.chdir(output_dir)
subprocess.call(["pdflatex", "--enable-write18",
"-shell-escape", "sbp_out.tex"])
subprocess.call(["mv", "sbp_out.pdf", "../docs/sbp.pdf"]) | Render and output | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/generator/sbpg/targets/latex.py#L255-L311 |
swift-nav/libsbp | python/sbp/client/examples/udp.py | get_args | def get_args():
"""
Get and parse arguments.
"""
import argparse
parser = argparse.ArgumentParser(
description="Swift Navigation SBP Example.")
parser.add_argument(
"-s",
"--serial-port",
default=[DEFAULT_SERIAL_PORT],
nargs=1,
help="specify the serial port to use.")
parser.add_argument(
"-b",
"--baud",
default=[DEFAULT_SERIAL_BAUD],
nargs=1,
help="specify the baud rate to use.")
parser.add_argument(
"-a",
"--address",
default=[DEFAULT_UDP_ADDRESS],
nargs=1,
help="specify the serial port to use.")
parser.add_argument(
"-p",
"--udp-port",
default=[DEFAULT_UDP_PORT],
nargs=1,
help="specify the baud rate to use.")
return parser.parse_args() | python | def get_args():
"""
Get and parse arguments.
"""
import argparse
parser = argparse.ArgumentParser(
description="Swift Navigation SBP Example.")
parser.add_argument(
"-s",
"--serial-port",
default=[DEFAULT_SERIAL_PORT],
nargs=1,
help="specify the serial port to use.")
parser.add_argument(
"-b",
"--baud",
default=[DEFAULT_SERIAL_BAUD],
nargs=1,
help="specify the baud rate to use.")
parser.add_argument(
"-a",
"--address",
default=[DEFAULT_UDP_ADDRESS],
nargs=1,
help="specify the serial port to use.")
parser.add_argument(
"-p",
"--udp-port",
default=[DEFAULT_UDP_PORT],
nargs=1,
help="specify the baud rate to use.")
return parser.parse_args() | Get and parse arguments. | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/python/sbp/client/examples/udp.py#L31-L62 |
swift-nav/libsbp | generator/sbpg/targets/c.py | commentify | def commentify(value):
"""
Builds a comment.
"""
value = markdown_links(value)
if value is None:
return
if len(value.split('\n')) == 1:
return "* " + value
else:
return '\n'.join([' * ' + l for l in value.split('\n')[:-1]]) | python | def commentify(value):
"""
Builds a comment.
"""
value = markdown_links(value)
if value is None:
return
if len(value.split('\n')) == 1:
return "* " + value
else:
return '\n'.join([' * ' + l for l in value.split('\n')[:-1]]) | Builds a comment. | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/generator/sbpg/targets/c.py#L22-L32 |
swift-nav/libsbp | generator/sbpg/targets/c.py | convert | def convert(value):
"""Converts to a C language appropriate identifier format.
"""
s0 = "Sbp" + value if value in COLLISIONS else value
s1 = re.sub('(.)([A-Z][a-z]+)', r'\1_\2', s0)
return re.sub('([a-z0-9])([A-Z])', r'\1_\2', s1).lower() + "_t" | python | def convert(value):
"""Converts to a C language appropriate identifier format.
"""
s0 = "Sbp" + value if value in COLLISIONS else value
s1 = re.sub('(.)([A-Z][a-z]+)', r'\1_\2', s0)
return re.sub('([a-z0-9])([A-Z])', r'\1_\2', s1).lower() + "_t" | Converts to a C language appropriate identifier format. | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/generator/sbpg/targets/c.py#L47-L53 |
swift-nav/libsbp | generator/sbpg/targets/c.py | mk_id | def mk_id(field):
"""Builds an identifier from a field.
"""
name = field.type_id
if name == "string":
return "%s" % ("char")
elif name == "array" and field.size:
if field.options['fill'].value not in CONSTRUCT_CODE:
return "%s" % convert(field.options['fill'].value)
else:
return "%s" % field.options['fill'].value
elif name == "array":
return "%s" % convert(field.options['fill'].value)
elif name not in CONSTRUCT_CODE:
return convert(name)
else:
return name | python | def mk_id(field):
"""Builds an identifier from a field.
"""
name = field.type_id
if name == "string":
return "%s" % ("char")
elif name == "array" and field.size:
if field.options['fill'].value not in CONSTRUCT_CODE:
return "%s" % convert(field.options['fill'].value)
else:
return "%s" % field.options['fill'].value
elif name == "array":
return "%s" % convert(field.options['fill'].value)
elif name not in CONSTRUCT_CODE:
return convert(name)
else:
return name | Builds an identifier from a field. | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/generator/sbpg/targets/c.py#L55-L71 |
swift-nav/libsbp | generator/sbpg/targets/c.py | mk_size | def mk_size(field):
"""Builds an identifier for a container type.
"""
name = field.type_id
if name == "string" and field.options.get('size', None):
return "%s[%d];" % (field.identifier, field.options.get('size').value)
elif name == "string":
return "%s[0];" % field.identifier
elif name == "array" and field.options.get('size', None):
return "%s[%d];" % (field.identifier, field.options.get('size').value)
elif name == "array":
return "%s[0];" % field.identifier
else:
return '%s;' % field.identifier | python | def mk_size(field):
"""Builds an identifier for a container type.
"""
name = field.type_id
if name == "string" and field.options.get('size', None):
return "%s[%d];" % (field.identifier, field.options.get('size').value)
elif name == "string":
return "%s[0];" % field.identifier
elif name == "array" and field.options.get('size', None):
return "%s[%d];" % (field.identifier, field.options.get('size').value)
elif name == "array":
return "%s[0];" % field.identifier
else:
return '%s;' % field.identifier | Builds an identifier for a container type. | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/generator/sbpg/targets/c.py#L73-L86 |
swift-nav/libsbp | generator/sbpg/targets/c.py | render_source | def render_source(output_dir, package_spec):
"""
Render and output to a directory given a package specification.
"""
path, name = package_spec.filepath
destination_filename = "%s/%s.h" % (output_dir, name)
py_template = JENV.get_template(MESSAGES_TEMPLATE_NAME)
with open(destination_filename, 'w') as f:
f.write(py_template.render(msgs=package_spec.definitions,
pkg_name=name,
filepath="/".join(package_spec.filepath) + ".yaml",
max_msgid_len=package_spec.max_msgid_len,
description=package_spec.description,
timestamp=package_spec.creation_timestamp,
include=extensions(package_spec.includes))) | python | def render_source(output_dir, package_spec):
"""
Render and output to a directory given a package specification.
"""
path, name = package_spec.filepath
destination_filename = "%s/%s.h" % (output_dir, name)
py_template = JENV.get_template(MESSAGES_TEMPLATE_NAME)
with open(destination_filename, 'w') as f:
f.write(py_template.render(msgs=package_spec.definitions,
pkg_name=name,
filepath="/".join(package_spec.filepath) + ".yaml",
max_msgid_len=package_spec.max_msgid_len,
description=package_spec.description,
timestamp=package_spec.creation_timestamp,
include=extensions(package_spec.includes))) | Render and output to a directory given a package specification. | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/generator/sbpg/targets/c.py#L93-L107 |
swift-nav/libsbp | python/sbp/msg.py | crc16jit | def crc16jit(buf, offset, crc, length):
"""CRC16 implementation acording to CCITT standards."""
for index in range(offset, offset + length):
data = buf[index]
lookup = crc16_tab[((nb.u2(crc) >> 8) & nb.u2(0xFF)) ^ (data & nb.u2(0xFF))]
crc = ((nb.u2(crc) << nb.u2(8)) & nb.u2(0xFFFF)) ^ lookup
crc = nb.u2(crc) & nb.u2(0xFFFF)
return crc | python | def crc16jit(buf, offset, crc, length):
"""CRC16 implementation acording to CCITT standards."""
for index in range(offset, offset + length):
data = buf[index]
lookup = crc16_tab[((nb.u2(crc) >> 8) & nb.u2(0xFF)) ^ (data & nb.u2(0xFF))]
crc = ((nb.u2(crc) << nb.u2(8)) & nb.u2(0xFFFF)) ^ lookup
crc = nb.u2(crc) & nb.u2(0xFFFF)
return crc | CRC16 implementation acording to CCITT standards. | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/python/sbp/msg.py#L66-L73 |
swift-nav/libsbp | python/sbp/msg.py | crc16_nojit | def crc16_nojit(s, crc=0):
"""CRC16 implementation acording to CCITT standards."""
for ch in bytearray(s): # bytearray's elements are integers in both python 2 and 3
crc = ((crc << 8) & 0xFFFF) ^ _crc16_tab[((crc >> 8) & 0xFF) ^ (ch & 0xFF)]
crc &= 0xFFFF
return crc | python | def crc16_nojit(s, crc=0):
"""CRC16 implementation acording to CCITT standards."""
for ch in bytearray(s): # bytearray's elements are integers in both python 2 and 3
crc = ((crc << 8) & 0xFFFF) ^ _crc16_tab[((crc >> 8) & 0xFF) ^ (ch & 0xFF)]
crc &= 0xFFFF
return crc | CRC16 implementation acording to CCITT standards. | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/python/sbp/msg.py#L84-L89 |
swift-nav/libsbp | python/sbp/msg.py | SBP._get_framed | def _get_framed(self, buf, offset, insert_payload):
"""Returns the framed message and updates the CRC.
"""
header_offset = offset + self._header_len
self.length = insert_payload(buf, header_offset, self.payload)
struct.pack_into(self._header_fmt,
buf,
offset,
self.preamble,
self.msg_type,
self.sender,
self.length)
crc_offset = header_offset + self.length
preamble_bytes = 1
crc_over_len = self._header_len + self.length - preamble_bytes
self.crc = crc16jit(buf, offset+1, 0, crc_over_len)
struct.pack_into(self._crc_fmt, buf, crc_offset, self.crc)
length = preamble_bytes + crc_over_len + self._crc_len
return length | python | def _get_framed(self, buf, offset, insert_payload):
"""Returns the framed message and updates the CRC.
"""
header_offset = offset + self._header_len
self.length = insert_payload(buf, header_offset, self.payload)
struct.pack_into(self._header_fmt,
buf,
offset,
self.preamble,
self.msg_type,
self.sender,
self.length)
crc_offset = header_offset + self.length
preamble_bytes = 1
crc_over_len = self._header_len + self.length - preamble_bytes
self.crc = crc16jit(buf, offset+1, 0, crc_over_len)
struct.pack_into(self._crc_fmt, buf, crc_offset, self.crc)
length = preamble_bytes + crc_over_len + self._crc_len
return length | Returns the framed message and updates the CRC. | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/python/sbp/msg.py#L172-L191 |
swift-nav/libsbp | python/sbp/msg.py | SBP.pack | def pack(self):
"""Pack to framed binary message.
"""
buf = np.zeros(512, dtype=np.uint8)
packed_len = self._get_framed(buf, 0, self._copy_payload)
d = buf[:packed_len]
return d.tobytes() | python | def pack(self):
"""Pack to framed binary message.
"""
buf = np.zeros(512, dtype=np.uint8)
packed_len = self._get_framed(buf, 0, self._copy_payload)
d = buf[:packed_len]
return d.tobytes() | Pack to framed binary message. | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/python/sbp/msg.py#L193-L200 |
swift-nav/libsbp | python/sbp/msg.py | SBP.pack_into | def pack_into(self, buf, offset, write_payload):
"""Pack to framed binary message.
"""
return self._get_framed(buf, offset, write_payload) | python | def pack_into(self, buf, offset, write_payload):
"""Pack to framed binary message.
"""
return self._get_framed(buf, offset, write_payload) | Pack to framed binary message. | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/python/sbp/msg.py#L202-L206 |
swift-nav/libsbp | python/sbp/msg.py | SBP.unpack | def unpack(d):
"""Unpack and return a framed binary message.
"""
p = SBP._parser.parse(d)
assert p.preamble == SBP_PREAMBLE, "Invalid preamble 0x%x." % p.preamble
return SBP(p.msg_type, p.sender, p.length, p.payload, p.crc) | python | def unpack(d):
"""Unpack and return a framed binary message.
"""
p = SBP._parser.parse(d)
assert p.preamble == SBP_PREAMBLE, "Invalid preamble 0x%x." % p.preamble
return SBP(p.msg_type, p.sender, p.length, p.payload, p.crc) | Unpack and return a framed binary message. | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/python/sbp/msg.py#L209-L215 |
swift-nav/libsbp | python/sbp/msg.py | SBP.to_json | def to_json(self, sort_keys=False):
"""Produce a JSON-encoded SBP message.
"""
d = self.to_json_dict()
return json.dumps(d, sort_keys=sort_keys) | python | def to_json(self, sort_keys=False):
"""Produce a JSON-encoded SBP message.
"""
d = self.to_json_dict()
return json.dumps(d, sort_keys=sort_keys) | Produce a JSON-encoded SBP message. | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/python/sbp/msg.py#L234-L239 |
swift-nav/libsbp | python/sbp/msg.py | SBP.from_json | def from_json(s):
"""Given a JSON-encoded message, build an object.
"""
d = json.loads(s)
sbp = SBP.from_json_dict(d)
return sbp | python | def from_json(s):
"""Given a JSON-encoded message, build an object.
"""
d = json.loads(s)
sbp = SBP.from_json_dict(d)
return sbp | Given a JSON-encoded message, build an object. | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/python/sbp/msg.py#L242-L248 |
swift-nav/libsbp | python/sbp/client/drivers/pyserial_driver.py | PySerialDriver.read | def read(self, size):
"""
Read wrapper.
Parameters
----------
size : int
Number of bytes to read.
"""
try:
return self.handle.read(size)
except (OSError, serial.SerialException):
print()
print("Piksi disconnected")
print()
self.handle.close()
raise IOError | python | def read(self, size):
"""
Read wrapper.
Parameters
----------
size : int
Number of bytes to read.
"""
try:
return self.handle.read(size)
except (OSError, serial.SerialException):
print()
print("Piksi disconnected")
print()
self.handle.close()
raise IOError | Read wrapper.
Parameters
----------
size : int
Number of bytes to read. | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/python/sbp/client/drivers/pyserial_driver.py#L69-L85 |
swift-nav/libsbp | python/sbp/client/drivers/pyserial_driver.py | PySerialDriver.write | def write(self, s):
"""
Write wrapper.
Parameters
----------
s : bytes
Bytes to write
"""
try:
return self.handle.write(s)
except (OSError, serial.SerialException,
serial.writeTimeoutError) as e:
if e == serial.writeTimeoutError:
print("sbp pyserial_driver: writeTimeoutError")
return 0
else:
print()
print("Piksi disconnected")
print()
self.handle.close()
raise IOError | python | def write(self, s):
"""
Write wrapper.
Parameters
----------
s : bytes
Bytes to write
"""
try:
return self.handle.write(s)
except (OSError, serial.SerialException,
serial.writeTimeoutError) as e:
if e == serial.writeTimeoutError:
print("sbp pyserial_driver: writeTimeoutError")
return 0
else:
print()
print("Piksi disconnected")
print()
self.handle.close()
raise IOError | Write wrapper.
Parameters
----------
s : bytes
Bytes to write | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/python/sbp/client/drivers/pyserial_driver.py#L87-L108 |
swift-nav/libsbp | generator/sbpg/targets/java.py | commentify | def commentify(value):
"""
Builds a comment.
"""
value = comment_links(value)
if value is None:
return
if len(value.split('\n')) == 1:
return "* " + value
else:
return '\n'.join([' * ' + l for l in value.split('\n')[:-1]]) | python | def commentify(value):
"""
Builds a comment.
"""
value = comment_links(value)
if value is None:
return
if len(value.split('\n')) == 1:
return "* " + value
else:
return '\n'.join([' * ' + l for l in value.split('\n')[:-1]]) | Builds a comment. | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/generator/sbpg/targets/java.py#L60-L70 |
swift-nav/libsbp | generator/sbpg/targets/java.py | parse_type | def parse_type(field):
"""
Function to pull a type from the binary payload.
"""
if field.type_id == 'string':
if 'size' in field.options:
return "parser.getString(%d)" % field.options['size'].value
else:
return "parser.getString()"
elif field.type_id in JAVA_TYPE_MAP:
# Primitive java types have extractor methods in SBPMessage.Parser
return "parser.get" + field.type_id.capitalize() + "()"
if field.type_id == 'array':
# Call function to build array
t = field.options['fill'].value
if t in JAVA_TYPE_MAP:
if 'size' in field.options:
return "parser.getArrayof%s(%d)" % (t.capitalize(), field.options['size'].value)
else:
return "parser.getArrayof%s()" % t.capitalize()
else:
if 'size' in field.options:
return "parser.getArray(%s.class, %d)" % (t, field.options['size'].value)
else:
return "parser.getArray(%s.class)" % t
else:
# This is an inner class, call default constructor
return "new %s().parse(parser)" % field.type_id | python | def parse_type(field):
"""
Function to pull a type from the binary payload.
"""
if field.type_id == 'string':
if 'size' in field.options:
return "parser.getString(%d)" % field.options['size'].value
else:
return "parser.getString()"
elif field.type_id in JAVA_TYPE_MAP:
# Primitive java types have extractor methods in SBPMessage.Parser
return "parser.get" + field.type_id.capitalize() + "()"
if field.type_id == 'array':
# Call function to build array
t = field.options['fill'].value
if t in JAVA_TYPE_MAP:
if 'size' in field.options:
return "parser.getArrayof%s(%d)" % (t.capitalize(), field.options['size'].value)
else:
return "parser.getArrayof%s()" % t.capitalize()
else:
if 'size' in field.options:
return "parser.getArray(%s.class, %d)" % (t, field.options['size'].value)
else:
return "parser.getArray(%s.class)" % t
else:
# This is an inner class, call default constructor
return "new %s().parse(parser)" % field.type_id | Function to pull a type from the binary payload. | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/generator/sbpg/targets/java.py#L81-L108 |
swift-nav/libsbp | generator/sbpg/targets/java.py | build_type | def build_type(field):
"""
Function to pack a type into the binary payload.
"""
if field.type_id == 'string':
if 'size' in field.options:
return "builder.putString(%s, %d)" % (field.identifier, field.options['size'].value)
else:
return "builder.putString(%s)" % field.identifier
elif field.type_id in JAVA_TYPE_MAP:
# Primitive java types have extractor methods in SBPMessage.Builder
return "builder.put%s(%s)" % (field.type_id.capitalize(), field.identifier)
if field.type_id == 'array':
# Call function to build array
t = field.options['fill'].value
if t in JAVA_TYPE_MAP:
if 'size' in field.options:
return "builder.putArrayof%s(%s, %d)" % (t.capitalize(),
field.identifier,
field.options['size'].value)
else:
return "builder.putArrayof%s(%s)" % (t.capitalize(), field.identifier)
else:
if 'size' in field.options:
return "builder.putArray(%s, %d)" % (field.identifier, field.options['size'].value)
else:
return "builder.putArray(%s)" % field.identifier
else:
return "%s.build(builder)" % field.identifier | python | def build_type(field):
"""
Function to pack a type into the binary payload.
"""
if field.type_id == 'string':
if 'size' in field.options:
return "builder.putString(%s, %d)" % (field.identifier, field.options['size'].value)
else:
return "builder.putString(%s)" % field.identifier
elif field.type_id in JAVA_TYPE_MAP:
# Primitive java types have extractor methods in SBPMessage.Builder
return "builder.put%s(%s)" % (field.type_id.capitalize(), field.identifier)
if field.type_id == 'array':
# Call function to build array
t = field.options['fill'].value
if t in JAVA_TYPE_MAP:
if 'size' in field.options:
return "builder.putArrayof%s(%s, %d)" % (t.capitalize(),
field.identifier,
field.options['size'].value)
else:
return "builder.putArrayof%s(%s)" % (t.capitalize(), field.identifier)
else:
if 'size' in field.options:
return "builder.putArray(%s, %d)" % (field.identifier, field.options['size'].value)
else:
return "builder.putArray(%s)" % field.identifier
else:
return "%s.build(builder)" % field.identifier | Function to pack a type into the binary payload. | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/generator/sbpg/targets/java.py#L110-L138 |
swift-nav/libsbp | generator/sbpg/targets/java.py | render_source | def render_source(output_dir, package_spec, jenv=JENV):
"""
Render and output
"""
path, module_name = package_spec.filepath
java_template = jenv.get_template(TEMPLATE_NAME)
module_path = "com." + package_spec.identifier
yaml_filepath = "/".join(package_spec.filepath) + ".yaml"
includes = [".".join(i.split(".")[:-1]) for i in package_spec.includes]
includes = [i for i in includes if i != "types"]
for msg in package_spec.definitions:
msg_name = classnameify(msg.identifier) if msg.sbp_id else msg.identifier
l = "/".join(package_spec.filepath)
destination_filename = "%s/com/%s/%s.java" % (output_dir, l , msg_name)
# Create the output directory if it doesn't exist
if not os.path.exists(os.path.dirname(destination_filename)):
os.mkdir(os.path.dirname(destination_filename))
with open(destination_filename, 'w+') as f:
print(destination_filename)
f.write(java_template.render(m=msg,
filepath=yaml_filepath,
module_path=module_path,
include=includes,
description=package_spec.description)) | python | def render_source(output_dir, package_spec, jenv=JENV):
"""
Render and output
"""
path, module_name = package_spec.filepath
java_template = jenv.get_template(TEMPLATE_NAME)
module_path = "com." + package_spec.identifier
yaml_filepath = "/".join(package_spec.filepath) + ".yaml"
includes = [".".join(i.split(".")[:-1]) for i in package_spec.includes]
includes = [i for i in includes if i != "types"]
for msg in package_spec.definitions:
msg_name = classnameify(msg.identifier) if msg.sbp_id else msg.identifier
l = "/".join(package_spec.filepath)
destination_filename = "%s/com/%s/%s.java" % (output_dir, l , msg_name)
# Create the output directory if it doesn't exist
if not os.path.exists(os.path.dirname(destination_filename)):
os.mkdir(os.path.dirname(destination_filename))
with open(destination_filename, 'w+') as f:
print(destination_filename)
f.write(java_template.render(m=msg,
filepath=yaml_filepath,
module_path=module_path,
include=includes,
description=package_spec.description)) | Render and output | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/generator/sbpg/targets/java.py#L158-L183 |
swift-nav/libsbp | generator/sbpg/targets/java.py | render_table | def render_table(output_dir, packages, jenv=JENV):
"""
Render and output dispatch table
"""
destination_filename = output_dir + "/com/swiftnav/sbp/client/MessageTable.java"
with open(destination_filename, 'w+') as f:
print(destination_filename)
f.write(jenv.get_template(TEMPLATE_TABLE_NAME).render(packages=packages)) | python | def render_table(output_dir, packages, jenv=JENV):
"""
Render and output dispatch table
"""
destination_filename = output_dir + "/com/swiftnav/sbp/client/MessageTable.java"
with open(destination_filename, 'w+') as f:
print(destination_filename)
f.write(jenv.get_template(TEMPLATE_TABLE_NAME).render(packages=packages)) | Render and output dispatch table | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/generator/sbpg/targets/java.py#L185-L192 |
swift-nav/libsbp | generator/sbpg/targets/javascript.py | construct_format | def construct_format(f, type_map=CONSTRUCT_CODE):
"""
Formats for binary-parser library.
"""
formatted = ""
if type_map.get(f.type_id, None):
return "%s('%s')" % (type_map.get(f.type_id), f.identifier)
elif f.type_id == 'string' and f.options.get('size', None):
return "string('%s', { length: %d })" % (f.identifier, f.options['size'].value)
elif f.type_id == 'string':
return "string('%s', { greedy: true })" % (f.identifier)
elif f.type_id == 'array':
fill = f.options['fill'].value
f_ = copy.copy(f)
f_.type_id = fill
size = f.options.get('size', None)
size_fn = f.options.get('size_fn', None)
field_type = type_map.get(f_.type_id, None)
if field_type is None:
field_type = "%s.prototype.parser" % f_.type_id
else:
field_type = "'%s'" % field_type
if size is not None:
d = { "'uint16'" : "'uint16le'", "'uint32'" : "'uint32le'", "'uint64'" : "'uint16le'",
"'int16'" : "'int16le'", "'int32'" : "'int32le'", "'int64'" : "'int16le'" }
field_type_arr = d.get(field_type, field_type)
return "array('%s', { length: %d, type: %s })" % (f.identifier, size.value, field_type_arr)
elif f.options.get('size_fn') is not None:
return "array('%s', { type: %s, length: '%s' })" % (f_.identifier, field_type, size_fn.value)
else:
return "array('%s', { type: %s, readUntil: 'eof' })" % (f_.identifier, field_type)
else:
return "nest('%s', { type: %s.prototype.parser })" % (f.identifier, f.type_id)
return formatted | python | def construct_format(f, type_map=CONSTRUCT_CODE):
"""
Formats for binary-parser library.
"""
formatted = ""
if type_map.get(f.type_id, None):
return "%s('%s')" % (type_map.get(f.type_id), f.identifier)
elif f.type_id == 'string' and f.options.get('size', None):
return "string('%s', { length: %d })" % (f.identifier, f.options['size'].value)
elif f.type_id == 'string':
return "string('%s', { greedy: true })" % (f.identifier)
elif f.type_id == 'array':
fill = f.options['fill'].value
f_ = copy.copy(f)
f_.type_id = fill
size = f.options.get('size', None)
size_fn = f.options.get('size_fn', None)
field_type = type_map.get(f_.type_id, None)
if field_type is None:
field_type = "%s.prototype.parser" % f_.type_id
else:
field_type = "'%s'" % field_type
if size is not None:
d = { "'uint16'" : "'uint16le'", "'uint32'" : "'uint32le'", "'uint64'" : "'uint16le'",
"'int16'" : "'int16le'", "'int32'" : "'int32le'", "'int64'" : "'int16le'" }
field_type_arr = d.get(field_type, field_type)
return "array('%s', { length: %d, type: %s })" % (f.identifier, size.value, field_type_arr)
elif f.options.get('size_fn') is not None:
return "array('%s', { type: %s, length: '%s' })" % (f_.identifier, field_type, size_fn.value)
else:
return "array('%s', { type: %s, readUntil: 'eof' })" % (f_.identifier, field_type)
else:
return "nest('%s', { type: %s.prototype.parser })" % (f.identifier, f.type_id)
return formatted | Formats for binary-parser library. | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/generator/sbpg/targets/javascript.py#L120-L153 |
swift-nav/libsbp | generator/sbpg/targets/javascript.py | js_classnameify | def js_classnameify(s):
"""
Makes a classname.
"""
if not '_' in s:
return s
return ''.join(w[0].upper() + w[1:].lower() for w in s.split('_')) | python | def js_classnameify(s):
"""
Makes a classname.
"""
if not '_' in s:
return s
return ''.join(w[0].upper() + w[1:].lower() for w in s.split('_')) | Makes a classname. | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/generator/sbpg/targets/javascript.py#L156-L162 |
swift-nav/libsbp | python/sbp/observation.py | MsgEphemerisGPSDepF.from_binary | def from_binary(self, d):
"""Given a binary payload d, update the appropriate payload fields of
the message.
"""
p = MsgEphemerisGPSDepF._parser.parse(d)
for n in self.__class__.__slots__:
setattr(self, n, getattr(p, n)) | python | def from_binary(self, d):
"""Given a binary payload d, update the appropriate payload fields of
the message.
"""
p = MsgEphemerisGPSDepF._parser.parse(d)
for n in self.__class__.__slots__:
setattr(self, n, getattr(p, n)) | Given a binary payload d, update the appropriate payload fields of
the message. | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/python/sbp/observation.py#L1715-L1722 |
swift-nav/libsbp | python/sbp/observation.py | MsgEphemerisGPSDepF.to_binary | def to_binary(self):
"""Produce a framed/packed SBP message.
"""
c = containerize(exclude_fields(self))
self.payload = MsgEphemerisGPSDepF._parser.build(c)
return self.pack() | python | def to_binary(self):
"""Produce a framed/packed SBP message.
"""
c = containerize(exclude_fields(self))
self.payload = MsgEphemerisGPSDepF._parser.build(c)
return self.pack() | Produce a framed/packed SBP message. | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/python/sbp/observation.py#L1724-L1730 |
swift-nav/libsbp | python/sbp/observation.py | MsgEphemerisGPSDepF.into_buffer | def into_buffer(self, buf, offset):
"""Produce a framed/packed SBP message into the provided buffer and offset.
"""
self.payload = containerize(exclude_fields(self))
self.parser = MsgEphemerisGPSDepF._parser
self.stream_payload.reset(buf, offset)
return self.pack_into(buf, offset, self._build_payload) | python | def into_buffer(self, buf, offset):
"""Produce a framed/packed SBP message into the provided buffer and offset.
"""
self.payload = containerize(exclude_fields(self))
self.parser = MsgEphemerisGPSDepF._parser
self.stream_payload.reset(buf, offset)
return self.pack_into(buf, offset, self._build_payload) | Produce a framed/packed SBP message into the provided buffer and offset. | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/python/sbp/observation.py#L1732-L1739 |
swift-nav/libsbp | python/sbp/client/framer.py | Framer._readall | def _readall(self, size):
"""
Read until all bytes are collected.
Parameters
----------
size : int
Number of bytes to read.
"""
data = b""
while len(data) < size:
d = self._read(size - len(data))
if self._broken:
raise StopIteration
if not d:
# NOTE (Buro/jgross): Force a yield here to another thread. In
# case the stream fails midstream, the spinning here causes
# the UI thread to lock up without yielding.
time.sleep(0)
continue
data += d
return data | python | def _readall(self, size):
"""
Read until all bytes are collected.
Parameters
----------
size : int
Number of bytes to read.
"""
data = b""
while len(data) < size:
d = self._read(size - len(data))
if self._broken:
raise StopIteration
if not d:
# NOTE (Buro/jgross): Force a yield here to another thread. In
# case the stream fails midstream, the spinning here causes
# the UI thread to lock up without yielding.
time.sleep(0)
continue
data += d
return data | Read until all bytes are collected.
Parameters
----------
size : int
Number of bytes to read. | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/python/sbp/client/framer.py#L94-L115 |
swift-nav/libsbp | python/sbp/client/framer.py | Framer._receive | def _receive(self):
"""
Read and build SBP message.
"""
# preamble - not readall(1) to allow breaking before messages,
# empty input
preamble = self._read(1)
if not preamble:
return None
elif ord(preamble) != SBP_PREAMBLE:
if self._verbose:
print("Host Side Unhandled byte: 0x%02x" % ord(preamble))
return None
# hdr
hdr = self._readall(5)
msg_crc = crc16(hdr)
msg_type, sender, msg_len = struct.unpack("<HHB", hdr)
# data
data = self._readall(msg_len)
msg_crc = crc16(data, msg_crc)
# crc
crc = self._readall(2)
crc, = struct.unpack("<H", crc)
if crc != msg_crc:
if self._verbose:
print("crc mismatch: 0x%04X 0x%04X" % (msg_crc, crc))
return None
msg = SBP(msg_type, sender, msg_len, data, crc)
try:
msg = self._dispatch(msg)
except Exception as exc:
warnings.warn("SBP dispatch error: %s" % (exc,))
return msg | python | def _receive(self):
"""
Read and build SBP message.
"""
# preamble - not readall(1) to allow breaking before messages,
# empty input
preamble = self._read(1)
if not preamble:
return None
elif ord(preamble) != SBP_PREAMBLE:
if self._verbose:
print("Host Side Unhandled byte: 0x%02x" % ord(preamble))
return None
# hdr
hdr = self._readall(5)
msg_crc = crc16(hdr)
msg_type, sender, msg_len = struct.unpack("<HHB", hdr)
# data
data = self._readall(msg_len)
msg_crc = crc16(data, msg_crc)
# crc
crc = self._readall(2)
crc, = struct.unpack("<H", crc)
if crc != msg_crc:
if self._verbose:
print("crc mismatch: 0x%04X 0x%04X" % (msg_crc, crc))
return None
msg = SBP(msg_type, sender, msg_len, data, crc)
try:
msg = self._dispatch(msg)
except Exception as exc:
warnings.warn("SBP dispatch error: %s" % (exc,))
return msg | Read and build SBP message. | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/python/sbp/client/framer.py#L117-L149 |
swift-nav/libsbp | python/sbp/table.py | dispatch | def dispatch(msg, table=_SBP_TABLE):
"""
Dispatch an SBP message type based on its `msg_type` and parse its
payload.
Parameters
----------
driver : :class:`SBP`
A parsed SBP object.
table : dict
Any table mapping unique SBP message type IDs to SBP message
constructors.
Returns
----------
SBP message with a parsed payload.
"""
try:
return table[msg.msg_type](msg)
except KeyError:
warn = "No message found for msg_type id %d for msg %s." \
% (msg.msg_type, msg)
warnings.warn(warn, RuntimeWarning)
return msg
except FormatFieldError:
warnings.warn("SBP payload deserialization error! 0x%x" % msg.msg_type,
RuntimeWarning)
return msg | python | def dispatch(msg, table=_SBP_TABLE):
"""
Dispatch an SBP message type based on its `msg_type` and parse its
payload.
Parameters
----------
driver : :class:`SBP`
A parsed SBP object.
table : dict
Any table mapping unique SBP message type IDs to SBP message
constructors.
Returns
----------
SBP message with a parsed payload.
"""
try:
return table[msg.msg_type](msg)
except KeyError:
warn = "No message found for msg_type id %d for msg %s." \
% (msg.msg_type, msg)
warnings.warn(warn, RuntimeWarning)
return msg
except FormatFieldError:
warnings.warn("SBP payload deserialization error! 0x%x" % msg.msg_type,
RuntimeWarning)
return msg | Dispatch an SBP message type based on its `msg_type` and parse its
payload.
Parameters
----------
driver : :class:`SBP`
A parsed SBP object.
table : dict
Any table mapping unique SBP message type IDs to SBP message
constructors.
Returns
----------
SBP message with a parsed payload. | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/python/sbp/table.py#L70-L98 |
swift-nav/libsbp | python/sbp/client/handler.py | Handler._recv_thread | def _recv_thread(self):
"""
Internal thread to iterate over source messages and dispatch callbacks.
"""
for msg, metadata in self._source:
if msg.msg_type:
self._call(msg, **metadata)
# Break any upstream iterators
for sink in self._sinks:
i = sink()
if i is not None:
i.breakiter()
self._dead = True | python | def _recv_thread(self):
"""
Internal thread to iterate over source messages and dispatch callbacks.
"""
for msg, metadata in self._source:
if msg.msg_type:
self._call(msg, **metadata)
# Break any upstream iterators
for sink in self._sinks:
i = sink()
if i is not None:
i.breakiter()
self._dead = True | Internal thread to iterate over source messages and dispatch callbacks. | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/python/sbp/client/handler.py#L52-L64 |
swift-nav/libsbp | python/sbp/client/handler.py | Handler.filter | def filter(self, msg_type=None, maxsize=0):
"""
Get a filtered iterator of messages for synchronous, blocking use in
another thread.
"""
if self._dead:
return iter(())
iterator = Handler._SBPQueueIterator(maxsize)
# We use a weakref so that the iterator may be garbage collected if it's
# consumer no longer has a reference.
ref = weakref.ref(iterator)
self._sinks.append(ref)
def feediter(msg, **metadata):
i = ref()
if i is not None:
i(msg, **metadata)
else:
raise Handler._DeadCallbackException
self.add_callback(feediter, msg_type)
return iterator | python | def filter(self, msg_type=None, maxsize=0):
"""
Get a filtered iterator of messages for synchronous, blocking use in
another thread.
"""
if self._dead:
return iter(())
iterator = Handler._SBPQueueIterator(maxsize)
# We use a weakref so that the iterator may be garbage collected if it's
# consumer no longer has a reference.
ref = weakref.ref(iterator)
self._sinks.append(ref)
def feediter(msg, **metadata):
i = ref()
if i is not None:
i(msg, **metadata)
else:
raise Handler._DeadCallbackException
self.add_callback(feediter, msg_type)
return iterator | Get a filtered iterator of messages for synchronous, blocking use in
another thread. | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/python/sbp/client/handler.py#L79-L100 |
swift-nav/libsbp | python/sbp/client/handler.py | Handler.add_callback | def add_callback(self, callback, msg_type=None):
"""
Add per message type or global callback.
Parameters
----------
callback : fn
Callback function
msg_type : int | iterable
Message type to register callback against. Default `None` means global callback.
Iterable type adds the callback to all the message types.
"""
cb_keys = self._to_iter(msg_type)
if cb_keys is not None:
for msg_type_ in cb_keys:
self._callbacks[msg_type_].add(callback)
else:
self._callbacks[msg_type].add(callback) | python | def add_callback(self, callback, msg_type=None):
"""
Add per message type or global callback.
Parameters
----------
callback : fn
Callback function
msg_type : int | iterable
Message type to register callback against. Default `None` means global callback.
Iterable type adds the callback to all the message types.
"""
cb_keys = self._to_iter(msg_type)
if cb_keys is not None:
for msg_type_ in cb_keys:
self._callbacks[msg_type_].add(callback)
else:
self._callbacks[msg_type].add(callback) | Add per message type or global callback.
Parameters
----------
callback : fn
Callback function
msg_type : int | iterable
Message type to register callback against. Default `None` means global callback.
Iterable type adds the callback to all the message types. | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/python/sbp/client/handler.py#L115-L132 |
swift-nav/libsbp | python/sbp/client/handler.py | Handler.remove_callback | def remove_callback(self, callback, msg_type=None):
"""
Remove per message type of global callback.
Parameters
----------
callback : fn
Callback function
msg_type : int | iterable
Message type to remove callback from. Default `None` means global callback.
Iterable type removes the callback from all the message types.
"""
if msg_type is None:
msg_type = self._callbacks.keys()
cb_keys = self._to_iter(msg_type)
if cb_keys is not None:
for msg_type_ in cb_keys:
try:
self._callbacks[msg_type_].remove(callback)
except KeyError:
pass
else:
self._callbacks[msg_type].remove(callback) | python | def remove_callback(self, callback, msg_type=None):
"""
Remove per message type of global callback.
Parameters
----------
callback : fn
Callback function
msg_type : int | iterable
Message type to remove callback from. Default `None` means global callback.
Iterable type removes the callback from all the message types.
"""
if msg_type is None:
msg_type = self._callbacks.keys()
cb_keys = self._to_iter(msg_type)
if cb_keys is not None:
for msg_type_ in cb_keys:
try:
self._callbacks[msg_type_].remove(callback)
except KeyError:
pass
else:
self._callbacks[msg_type].remove(callback) | Remove per message type of global callback.
Parameters
----------
callback : fn
Callback function
msg_type : int | iterable
Message type to remove callback from. Default `None` means global callback.
Iterable type removes the callback from all the message types. | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/python/sbp/client/handler.py#L134-L156 |
swift-nav/libsbp | python/sbp/client/handler.py | Handler._gc_dead_sinks | def _gc_dead_sinks(self):
"""
Remove any dead weakrefs.
"""
deadsinks = []
for i in self._sinks:
if i() is None:
deadsinks.append(i)
for i in deadsinks:
self._sinks.remove(i) | python | def _gc_dead_sinks(self):
"""
Remove any dead weakrefs.
"""
deadsinks = []
for i in self._sinks:
if i() is None:
deadsinks.append(i)
for i in deadsinks:
self._sinks.remove(i) | Remove any dead weakrefs. | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/python/sbp/client/handler.py#L158-L167 |
swift-nav/libsbp | python/sbp/client/handler.py | Handler._call | def _call(self, msg, **metadata):
"""
Process message with all callbacks (global and per message type).
"""
if msg.msg_type:
for callback in self._get_callbacks(msg.msg_type):
try:
callback(msg, **metadata)
except Handler._DeadCallbackException:
# The callback was an upstream iterator that has been garbage
# collected. Remove it from our internal structures.
self.remove_callback(callback)
self._gc_dead_sinks()
except SystemExit:
raise
except:
import traceback
traceback.print_exc() | python | def _call(self, msg, **metadata):
"""
Process message with all callbacks (global and per message type).
"""
if msg.msg_type:
for callback in self._get_callbacks(msg.msg_type):
try:
callback(msg, **metadata)
except Handler._DeadCallbackException:
# The callback was an upstream iterator that has been garbage
# collected. Remove it from our internal structures.
self.remove_callback(callback)
self._gc_dead_sinks()
except SystemExit:
raise
except:
import traceback
traceback.print_exc() | Process message with all callbacks (global and per message type). | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/python/sbp/client/handler.py#L180-L197 |
swift-nav/libsbp | python/sbp/client/handler.py | Handler.wait | def wait(self, msg_type, timeout=1.0):
"""
Wait for a SBP message.
Parameters
----------
msg_type : int
SBP message type.
timeout : float
Waiting period
"""
event = threading.Event()
payload = {'data': None}
def cb(sbp_msg, **metadata):
payload['data'] = sbp_msg
event.set()
self.add_callback(cb, msg_type)
event.wait(timeout)
self.remove_callback(cb, msg_type)
return payload['data'] | python | def wait(self, msg_type, timeout=1.0):
"""
Wait for a SBP message.
Parameters
----------
msg_type : int
SBP message type.
timeout : float
Waiting period
"""
event = threading.Event()
payload = {'data': None}
def cb(sbp_msg, **metadata):
payload['data'] = sbp_msg
event.set()
self.add_callback(cb, msg_type)
event.wait(timeout)
self.remove_callback(cb, msg_type)
return payload['data'] | Wait for a SBP message.
Parameters
----------
msg_type : int
SBP message type.
timeout : float
Waiting period | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/python/sbp/client/handler.py#L221-L242 |
swift-nav/libsbp | python/sbp/client/handler.py | Handler.wait_callback | def wait_callback(self, callback, msg_type=None, timeout=1.0):
"""
Wait for a SBP message with a callback.
Parameters
----------
callback : fn
Callback function
msg_type : int | iterable
Message type to register callback against. Default `None` means global callback.
Iterable type adds the callback to all the message types.
timeout : float
Waiting period
"""
event = threading.Event()
def cb(msg, **metadata):
callback(msg, **metadata)
event.set()
self.add_callback(cb, msg_type)
event.wait(timeout)
self.remove_callback(cb, msg_type) | python | def wait_callback(self, callback, msg_type=None, timeout=1.0):
"""
Wait for a SBP message with a callback.
Parameters
----------
callback : fn
Callback function
msg_type : int | iterable
Message type to register callback against. Default `None` means global callback.
Iterable type adds the callback to all the message types.
timeout : float
Waiting period
"""
event = threading.Event()
def cb(msg, **metadata):
callback(msg, **metadata)
event.set()
self.add_callback(cb, msg_type)
event.wait(timeout)
self.remove_callback(cb, msg_type) | Wait for a SBP message with a callback.
Parameters
----------
callback : fn
Callback function
msg_type : int | iterable
Message type to register callback against. Default `None` means global callback.
Iterable type adds the callback to all the message types.
timeout : float
Waiting period | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/python/sbp/client/handler.py#L244-L266 |
swift-nav/libsbp | python/sbp/client/drivers/cdc_driver.py | CdcDriver.read | def read(self, size):
"""
Read wrapper.
Parameters
----------
size : int
Number of bytes to read.
"""
try:
return_val = self.handle.read(size)
if return_val == '':
print()
print("Piksi disconnected")
print()
raise IOError
return return_val
except OSError:
print()
print("Piksi disconnected")
print()
raise IOError | python | def read(self, size):
"""
Read wrapper.
Parameters
----------
size : int
Number of bytes to read.
"""
try:
return_val = self.handle.read(size)
if return_val == '':
print()
print("Piksi disconnected")
print()
raise IOError
return return_val
except OSError:
print()
print("Piksi disconnected")
print()
raise IOError | Read wrapper.
Parameters
----------
size : int
Number of bytes to read. | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/python/sbp/client/drivers/cdc_driver.py#L27-L48 |
swift-nav/libsbp | python/sbp/client/drivers/cdc_driver.py | CdcDriver.write | def write(self, s):
"""
Write wrapper.
Parameters
----------
s : bytes
Bytes to write
"""
try:
return self.handle.write(s)
except OSError:
print()
print("Piksi disconnected")
print()
raise IOError | python | def write(self, s):
"""
Write wrapper.
Parameters
----------
s : bytes
Bytes to write
"""
try:
return self.handle.write(s)
except OSError:
print()
print("Piksi disconnected")
print()
raise IOError | Write wrapper.
Parameters
----------
s : bytes
Bytes to write | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/python/sbp/client/drivers/cdc_driver.py#L50-L65 |
swift-nav/libsbp | generator/sbpg/utils.py | fmt_repr | def fmt_repr(obj):
"""
Return pretty printed string representation of an object.
"""
items = {k: v for k, v in list(obj.__dict__.items())}
return "<%s: {%s}>" % (obj.__class__.__name__, pprint.pformat(items, width=1)) | python | def fmt_repr(obj):
"""
Return pretty printed string representation of an object.
"""
items = {k: v for k, v in list(obj.__dict__.items())}
return "<%s: {%s}>" % (obj.__class__.__name__, pprint.pformat(items, width=1)) | Return pretty printed string representation of an object. | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/generator/sbpg/utils.py#L14-L20 |
swift-nav/libsbp | python/sbp/client/util/settingmonitor.py | SettingMonitor.capture_setting | def capture_setting(self, sbp_msg, **metadata):
"""Callback to extract and store setting values from
SBP_MSG_SETTINGS_READ_RESP
Messages of any type other than SBP_MSG_SETTINGS_READ_RESP are ignored
"""
if sbp_msg.msg_type == SBP_MSG_SETTINGS_READ_RESP:
section, setting, value = sbp_msg.payload.split(b'\0')[:3]
self.settings.append((section, setting, value)) | python | def capture_setting(self, sbp_msg, **metadata):
"""Callback to extract and store setting values from
SBP_MSG_SETTINGS_READ_RESP
Messages of any type other than SBP_MSG_SETTINGS_READ_RESP are ignored
"""
if sbp_msg.msg_type == SBP_MSG_SETTINGS_READ_RESP:
section, setting, value = sbp_msg.payload.split(b'\0')[:3]
self.settings.append((section, setting, value)) | Callback to extract and store setting values from
SBP_MSG_SETTINGS_READ_RESP
Messages of any type other than SBP_MSG_SETTINGS_READ_RESP are ignored | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/python/sbp/client/util/settingmonitor.py#L32-L40 |
swift-nav/libsbp | python/sbp/client/util/settingmonitor.py | SettingMonitor.wait_for_setting_value | def wait_for_setting_value(self, section, setting, value, wait_time=5.0):
"""Function to wait wait_time seconds to see a
SBP_MSG_SETTINGS_READ_RESP message with a user-specified value
"""
expire = time.time() + wait_time
ok = False
while not ok and time.time() < expire:
settings = [x for x in self.settings if (x[0], x[1]) == (section, setting)]
# Check to see if the last setting has the value we want
if len(settings) > 0:
ok = settings[-1][2] == value
time.sleep(0.1)
return ok | python | def wait_for_setting_value(self, section, setting, value, wait_time=5.0):
"""Function to wait wait_time seconds to see a
SBP_MSG_SETTINGS_READ_RESP message with a user-specified value
"""
expire = time.time() + wait_time
ok = False
while not ok and time.time() < expire:
settings = [x for x in self.settings if (x[0], x[1]) == (section, setting)]
# Check to see if the last setting has the value we want
if len(settings) > 0:
ok = settings[-1][2] == value
time.sleep(0.1)
return ok | Function to wait wait_time seconds to see a
SBP_MSG_SETTINGS_READ_RESP message with a user-specified value | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/python/sbp/client/util/settingmonitor.py#L42-L55 |
swift-nav/libsbp | python/sbp/client/util/settingmonitor.py | SettingMonitor.clear | def clear(self, section=None, setting=None, value=None):
"""Clear settings"""
match = [all((section is None or x_y_z[0] == section,
setting is None or x_y_z[1] == setting,
value is None or x_y_z[2] == value)) for x_y_z in self.settings]
keep = [setting_remove for setting_remove in zip(self.settings,match) if not setting_remove[1]]
self.settings[:] = [x[0] for x in keep] | python | def clear(self, section=None, setting=None, value=None):
"""Clear settings"""
match = [all((section is None or x_y_z[0] == section,
setting is None or x_y_z[1] == setting,
value is None or x_y_z[2] == value)) for x_y_z in self.settings]
keep = [setting_remove for setting_remove in zip(self.settings,match) if not setting_remove[1]]
self.settings[:] = [x[0] for x in keep] | Clear settings | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/python/sbp/client/util/settingmonitor.py#L57-L65 |
swift-nav/libsbp | generator/sbpg/targets/python.py | construct_format | def construct_format(f, type_map=CONSTRUCT_CODE):
"""
Formats for Construct.
"""
formatted = ""
if type_map.get(f.type_id, None):
return "'{identifier}' / {type_id}".format(type_id=type_map.get(f.type_id),
identifier=f.identifier)
elif f.type_id == 'string' and f.options.get('size', None):
return "'{id}'/ construct.Bytes({size})".format(id=f.identifier,
size=f.options['size'].value)
elif f.type_id == 'string':
return "'{id}' / construct.GreedyBytes".format(id=f.identifier)
elif f.type_id == 'array' and f.options.get('size', None):
fill = f.options['fill'].value
f_ = copy.copy(f)
f_.type_id = fill
s = f.options.get('size', None).value
return "'{id}' / construct.Array({size}, {type})".format(id=f.identifier, size=s, type=type_map.get(f_.type_id, 'construct.Byte'))
elif f.type_id == 'array':
fill = f.options['fill'].value
f_ = copy.copy(f)
f_.type_id = fill
return "construct.GreedyRange(%s)" % construct_format(f_)
else:
return "'%s' / construct.Struct(%s._parser)" % (f.identifier, f.type_id)
return formatted | python | def construct_format(f, type_map=CONSTRUCT_CODE):
"""
Formats for Construct.
"""
formatted = ""
if type_map.get(f.type_id, None):
return "'{identifier}' / {type_id}".format(type_id=type_map.get(f.type_id),
identifier=f.identifier)
elif f.type_id == 'string' and f.options.get('size', None):
return "'{id}'/ construct.Bytes({size})".format(id=f.identifier,
size=f.options['size'].value)
elif f.type_id == 'string':
return "'{id}' / construct.GreedyBytes".format(id=f.identifier)
elif f.type_id == 'array' and f.options.get('size', None):
fill = f.options['fill'].value
f_ = copy.copy(f)
f_.type_id = fill
s = f.options.get('size', None).value
return "'{id}' / construct.Array({size}, {type})".format(id=f.identifier, size=s, type=type_map.get(f_.type_id, 'construct.Byte'))
elif f.type_id == 'array':
fill = f.options['fill'].value
f_ = copy.copy(f)
f_.type_id = fill
return "construct.GreedyRange(%s)" % construct_format(f_)
else:
return "'%s' / construct.Struct(%s._parser)" % (f.identifier, f.type_id)
return formatted | Formats for Construct. | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/generator/sbpg/targets/python.py#L57-L83 |
swift-nav/libsbp | generator/sbpg/targets/python.py | render_source | def render_source(output_dir, package_spec, jenv=JENV):
"""
Render and output
"""
path, name = package_spec.filepath
directory = output_dir
destination_filename = "%s/%s.py" % (directory, name)
py_template = jenv.get_template(TEMPLATE_NAME)
module_path = ".".join(package_spec.identifier.split(".")[1:-1])
includes = [".".join(i.split(".")[:-1]) for i in package_spec.includes]
includes = [i for i in includes if i != "types"]
print(destination_filename, includes)
with open(destination_filename, 'w') as f:
f.write(py_template.render(msgs=package_spec.definitions,
filepath="/".join(package_spec.filepath) + ".yaml",
module_path=module_path,
include=includes,
timestamp=package_spec.creation_timestamp,
description=package_spec.description)) | python | def render_source(output_dir, package_spec, jenv=JENV):
"""
Render and output
"""
path, name = package_spec.filepath
directory = output_dir
destination_filename = "%s/%s.py" % (directory, name)
py_template = jenv.get_template(TEMPLATE_NAME)
module_path = ".".join(package_spec.identifier.split(".")[1:-1])
includes = [".".join(i.split(".")[:-1]) for i in package_spec.includes]
includes = [i for i in includes if i != "types"]
print(destination_filename, includes)
with open(destination_filename, 'w') as f:
f.write(py_template.render(msgs=package_spec.definitions,
filepath="/".join(package_spec.filepath) + ".yaml",
module_path=module_path,
include=includes,
timestamp=package_spec.creation_timestamp,
description=package_spec.description)) | Render and output | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/generator/sbpg/targets/python.py#L105-L123 |
swift-nav/libsbp | python/sbp/client/drivers/network_drivers.py | TCPDriver.read | def read(self, size):
"""
Read wrapper.
Parameters
----------
size : int
Number of bytes to read
"""
data = None
while True:
try:
data = self.handle.recv(size)
except socket.timeout as socket_error:
self._reconnect(socket_error)
except socket.error as socket_error:
# this is fine, just retry
if socket_error.errno == errno.EINTR:
continue
self._reconnect(IOError)
if not data:
self._reconnect(IOError)
break
return data | python | def read(self, size):
"""
Read wrapper.
Parameters
----------
size : int
Number of bytes to read
"""
data = None
while True:
try:
data = self.handle.recv(size)
except socket.timeout as socket_error:
self._reconnect(socket_error)
except socket.error as socket_error:
# this is fine, just retry
if socket_error.errno == errno.EINTR:
continue
self._reconnect(IOError)
if not data:
self._reconnect(IOError)
break
return data | Read wrapper.
Parameters
----------
size : int
Number of bytes to read | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/python/sbp/client/drivers/network_drivers.py#L81-L104 |
swift-nav/libsbp | python/sbp/client/drivers/network_drivers.py | TCPDriver.write | def write(self, s):
"""
Write wrapper.
Parameters
----------
s : bytes
Bytes to write
"""
try:
self._write_lock.acquire()
self.handle.sendall(s)
except socket.timeout:
self._connect()
except socket.error:
raise IOError
finally:
self._write_lock.release() | python | def write(self, s):
"""
Write wrapper.
Parameters
----------
s : bytes
Bytes to write
"""
try:
self._write_lock.acquire()
self.handle.sendall(s)
except socket.timeout:
self._connect()
except socket.error:
raise IOError
finally:
self._write_lock.release() | Write wrapper.
Parameters
----------
s : bytes
Bytes to write | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/python/sbp/client/drivers/network_drivers.py#L109-L126 |
swift-nav/libsbp | python/sbp/utils.py | exclude_fields | def exclude_fields(obj, exclude=EXCLUDE):
"""
Return dict of object without parent attrs.
"""
return dict([(k, getattr(obj, k)) for k in obj.__slots__ if k not in exclude]) | python | def exclude_fields(obj, exclude=EXCLUDE):
"""
Return dict of object without parent attrs.
"""
return dict([(k, getattr(obj, k)) for k in obj.__slots__ if k not in exclude]) | Return dict of object without parent attrs. | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/python/sbp/utils.py#L21-L25 |
swift-nav/libsbp | python/sbp/utils.py | walk_json_dict | def walk_json_dict(coll):
"""
Flatten a parsed SBP object into a dicts and lists, which are
compatible for JSON output.
Parameters
----------
coll : dict
"""
if isinstance(coll, dict):
return dict((k, walk_json_dict(v)) for (k, v) in iter(coll.items()))
elif isinstance(coll, bytes):
return coll.decode('ascii')
elif hasattr(coll, '__iter__') and not isinstance(coll, str):
return [walk_json_dict(seq) for seq in coll]
else:
return coll | python | def walk_json_dict(coll):
"""
Flatten a parsed SBP object into a dicts and lists, which are
compatible for JSON output.
Parameters
----------
coll : dict
"""
if isinstance(coll, dict):
return dict((k, walk_json_dict(v)) for (k, v) in iter(coll.items()))
elif isinstance(coll, bytes):
return coll.decode('ascii')
elif hasattr(coll, '__iter__') and not isinstance(coll, str):
return [walk_json_dict(seq) for seq in coll]
else:
return coll | Flatten a parsed SBP object into a dicts and lists, which are
compatible for JSON output.
Parameters
----------
coll : dict | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/python/sbp/utils.py#L28-L45 |
swift-nav/libsbp | python/sbp/utils.py | containerize | def containerize(coll):
"""Walk attribute fields passed from an SBP message and convert to
Containers where appropriate. Needed for Construct proper
serialization.
Parameters
----------
coll : dict
"""
if isinstance(coll, Container):
[setattr(coll, k, containerize(v)) for (k, v) in coll.items()]
return coll
elif isinstance(coll, dict):
return containerize(Container(**coll))
elif isinstance(coll, list):
for j, i in enumerate(coll):
if isinstance(i, dict):
coll[j] = containerize(Container(**i))
return coll
else:
return coll | python | def containerize(coll):
"""Walk attribute fields passed from an SBP message and convert to
Containers where appropriate. Needed for Construct proper
serialization.
Parameters
----------
coll : dict
"""
if isinstance(coll, Container):
[setattr(coll, k, containerize(v)) for (k, v) in coll.items()]
return coll
elif isinstance(coll, dict):
return containerize(Container(**coll))
elif isinstance(coll, list):
for j, i in enumerate(coll):
if isinstance(i, dict):
coll[j] = containerize(Container(**i))
return coll
else:
return coll | Walk attribute fields passed from an SBP message and convert to
Containers where appropriate. Needed for Construct proper
serialization.
Parameters
----------
coll : dict | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/python/sbp/utils.py#L48-L69 |
swift-nav/libsbp | python/sbp/utils.py | fmt_repr | def fmt_repr(obj):
"""Print a orphaned string representation of an object without the
clutter of its parent object.
"""
items = ["%s = %r" % (k, v) for k, v in list(exclude_fields(obj).items())]
return "<%s: {%s}>" % (obj.__class__.__name__, ', '.join(items)) | python | def fmt_repr(obj):
"""Print a orphaned string representation of an object without the
clutter of its parent object.
"""
items = ["%s = %r" % (k, v) for k, v in list(exclude_fields(obj).items())]
return "<%s: {%s}>" % (obj.__class__.__name__, ', '.join(items)) | Print a orphaned string representation of an object without the
clutter of its parent object. | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/python/sbp/utils.py#L72-L78 |
swift-nav/libsbp | generator/sbpg/specs/yaml2.py | read_spec | def read_spec(filename, verbose=False):
"""
Read an SBP specification.
Parameters
----------
filename : str
Local filename for specification.
verbose : bool
Print out some debugging info
Returns
----------
Raises
----------
Exception
On empty file.
yaml.YAMLError
On Yaml parsing error
voluptuous.Invalid
On invalid SBP schema
"""
contents = None
with open(filename, 'r') as f:
contents = yaml.load(f)
if contents is None:
raise Exception("Empty yaml file: %s." % filename)
try:
s.package_schema(contents)
except Exception as e:
sys.stderr.write("Invalid SBP YAML specification: %s.\n" % filename)
raise e
return contents | python | def read_spec(filename, verbose=False):
"""
Read an SBP specification.
Parameters
----------
filename : str
Local filename for specification.
verbose : bool
Print out some debugging info
Returns
----------
Raises
----------
Exception
On empty file.
yaml.YAMLError
On Yaml parsing error
voluptuous.Invalid
On invalid SBP schema
"""
contents = None
with open(filename, 'r') as f:
contents = yaml.load(f)
if contents is None:
raise Exception("Empty yaml file: %s." % filename)
try:
s.package_schema(contents)
except Exception as e:
sys.stderr.write("Invalid SBP YAML specification: %s.\n" % filename)
raise e
return contents | Read an SBP specification.
Parameters
----------
filename : str
Local filename for specification.
verbose : bool
Print out some debugging info
Returns
----------
Raises
----------
Exception
On empty file.
yaml.YAMLError
On Yaml parsing error
voluptuous.Invalid
On invalid SBP schema | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/generator/sbpg/specs/yaml2.py#L32-L65 |
swift-nav/libsbp | generator/sbpg/specs/yaml2.py | get_files | def get_files(input_file):
"""
Initializes an index of files to generate, returns the base
directory and index.
"""
file_index = {}
base_dir = None
if os.path.isfile(input_file):
file_index[input_file] = None
base_dir = os.path.dirname(input_file)
elif os.path.isdir(input_file):
base_dir = input_file
for inf in glob.glob(input_file + s.SBP_EXTENSION):
file_index[os.path.abspath(inf)] = None
for inf in glob.glob(input_file + '/*'):
base, index = get_files(os.path.abspath(inf))
z = file_index.copy()
z.update(index)
file_index = z
return (base_dir, file_index) | python | def get_files(input_file):
"""
Initializes an index of files to generate, returns the base
directory and index.
"""
file_index = {}
base_dir = None
if os.path.isfile(input_file):
file_index[input_file] = None
base_dir = os.path.dirname(input_file)
elif os.path.isdir(input_file):
base_dir = input_file
for inf in glob.glob(input_file + s.SBP_EXTENSION):
file_index[os.path.abspath(inf)] = None
for inf in glob.glob(input_file + '/*'):
base, index = get_files(os.path.abspath(inf))
z = file_index.copy()
z.update(index)
file_index = z
return (base_dir, file_index) | Initializes an index of files to generate, returns the base
directory and index. | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/generator/sbpg/specs/yaml2.py#L102-L122 |
swift-nav/libsbp | generator/sbpg/specs/yaml2.py | resolve_deps | def resolve_deps(base_dir, file_index):
"""
Given a base directory and an initial set of files, retrieves
dependencies and adds them to the file_index.
"""
def flatten(tree, index = {}):
for include in tree.get('include', []):
fname = base_dir + "/" + include
assert os.path.exists(fname), "File %s does not exist." % fname
if fname not in index:
index[fname] = read_spec(fname)
index.update(flatten(index[fname], file_index))
return index
for fname, contents in file_index.items():
file_index[fname] = read_spec(fname)
file_index.update(flatten(file_index[fname], file_index))
return file_index | python | def resolve_deps(base_dir, file_index):
"""
Given a base directory and an initial set of files, retrieves
dependencies and adds them to the file_index.
"""
def flatten(tree, index = {}):
for include in tree.get('include', []):
fname = base_dir + "/" + include
assert os.path.exists(fname), "File %s does not exist." % fname
if fname not in index:
index[fname] = read_spec(fname)
index.update(flatten(index[fname], file_index))
return index
for fname, contents in file_index.items():
file_index[fname] = read_spec(fname)
file_index.update(flatten(file_index[fname], file_index))
return file_index | Given a base directory and an initial set of files, retrieves
dependencies and adds them to the file_index. | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/generator/sbpg/specs/yaml2.py#L146-L163 |
swift-nav/libsbp | generator/sbpg/specs/yaml2.py | mk_package | def mk_package(contents):
"""Instantiates a package specification from a parsed "AST" of a
package.
Parameters
----------
contents : dict
Returns
----------
PackageSpecification
"""
package = contents.get('package', None)
description = contents.get('description', None)
include = contents.get('include', [])
definitions = contents.get('definitions', [])
resolved = [mk_definition(defn) for defn in definitions]
return sbp.PackageSpecification(identifier=package,
description=description,
includes=include,
definitions=resolved,
render_source=contents.get('render_source', True),
stable=contents.get('stable', False),
public=contents.get('public', True)) | python | def mk_package(contents):
"""Instantiates a package specification from a parsed "AST" of a
package.
Parameters
----------
contents : dict
Returns
----------
PackageSpecification
"""
package = contents.get('package', None)
description = contents.get('description', None)
include = contents.get('include', [])
definitions = contents.get('definitions', [])
resolved = [mk_definition(defn) for defn in definitions]
return sbp.PackageSpecification(identifier=package,
description=description,
includes=include,
definitions=resolved,
render_source=contents.get('render_source', True),
stable=contents.get('stable', False),
public=contents.get('public', True)) | Instantiates a package specification from a parsed "AST" of a
package.
Parameters
----------
contents : dict
Returns
----------
PackageSpecification | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/generator/sbpg/specs/yaml2.py#L216-L240 |
swift-nav/libsbp | generator/sbpg/specs/yaml2.py | mk_definition | def mk_definition(defn):
"""Instantiates a struct or SBP message specification from a parsed
"AST" of a struct or message.
Parameters
----------
defn : dict
Returns
----------
A Definition or a specialization of a definition, like a Struct
"""
assert len(defn) == 1
identifier, contents = next(iter(defn.items()))
fs = [mk_field(f) for f in contents.get('fields', [])]
return sbp.resolve_type(sbp.Definition(identifier=identifier,
sbp_id=contents.get('id', None),
short_desc=contents.get('short_desc', None),
desc=contents.get('desc', None),
type_id=contents.get('type'),
fields=fs,
public=contents.get('public', True))) | python | def mk_definition(defn):
"""Instantiates a struct or SBP message specification from a parsed
"AST" of a struct or message.
Parameters
----------
defn : dict
Returns
----------
A Definition or a specialization of a definition, like a Struct
"""
assert len(defn) == 1
identifier, contents = next(iter(defn.items()))
fs = [mk_field(f) for f in contents.get('fields', [])]
return sbp.resolve_type(sbp.Definition(identifier=identifier,
sbp_id=contents.get('id', None),
short_desc=contents.get('short_desc', None),
desc=contents.get('desc', None),
type_id=contents.get('type'),
fields=fs,
public=contents.get('public', True))) | Instantiates a struct or SBP message specification from a parsed
"AST" of a struct or message.
Parameters
----------
defn : dict
Returns
----------
A Definition or a specialization of a definition, like a Struct | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/generator/sbpg/specs/yaml2.py#L241-L263 |
swift-nav/libsbp | generator/sbpg/specs/yaml2.py | mk_field | def mk_field(field):
"""Instantiates a field specification from a parsed "AST" of a
field.
Parameters
----------
field : dict
Returns
----------
A Field or a specialization of a field, like a bitfield.
"""
assert len(field) == 1
identifier, contents = next(iter(field.items()))
contents = dict(list({'units': '', 'n_with_values': 0}.items()) + list(contents.items()))
return sbp.resolve_type(sbp.Field(identifier=identifier,
type_id=contents.pop('type'),
options=contents)) | python | def mk_field(field):
"""Instantiates a field specification from a parsed "AST" of a
field.
Parameters
----------
field : dict
Returns
----------
A Field or a specialization of a field, like a bitfield.
"""
assert len(field) == 1
identifier, contents = next(iter(field.items()))
contents = dict(list({'units': '', 'n_with_values': 0}.items()) + list(contents.items()))
return sbp.resolve_type(sbp.Field(identifier=identifier,
type_id=contents.pop('type'),
options=contents)) | Instantiates a field specification from a parsed "AST" of a
field.
Parameters
----------
field : dict
Returns
----------
A Field or a specialization of a field, like a bitfield. | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/generator/sbpg/specs/yaml2.py#L265-L283 |
swift-nav/libsbp | generator/sbpg/targets/haskell.py | to_global | def to_global(s):
"""
Format a global variable name.
"""
if s.startswith('GPSTime'):
s = 'Gps' + s[3:]
if '_' in s:
s = "".join([i.capitalize() for i in s.split("_")])
return s[0].lower() + s[1:] | python | def to_global(s):
"""
Format a global variable name.
"""
if s.startswith('GPSTime'):
s = 'Gps' + s[3:]
if '_' in s:
s = "".join([i.capitalize() for i in s.split("_")])
return s[0].lower() + s[1:] | Format a global variable name. | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/generator/sbpg/targets/haskell.py#L73-L82 |
swift-nav/libsbp | generator/sbpg/targets/haskell.py | to_data | def to_data(s):
"""
Format a data variable name.
"""
if s.startswith('GPSTime'):
s = 'Gps' + s[3:]
if '_' in s:
return "".join([i.capitalize() for i in s.split("_")])
return s | python | def to_data(s):
"""
Format a data variable name.
"""
if s.startswith('GPSTime'):
s = 'Gps' + s[3:]
if '_' in s:
return "".join([i.capitalize() for i in s.split("_")])
return s | Format a data variable name. | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/generator/sbpg/targets/haskell.py#L84-L93 |
swift-nav/libsbp | generator/sbpg/targets/haskell.py | to_type | def to_type(f, type_map=CONSTRUCT_CODE):
"""
Format a the proper type.
"""
name = f.type_id
if name.startswith('GPSTime'):
name = 'Gps' + name[3:]
if type_map.get(name, None):
return type_map.get(name, None)
elif name == 'array':
fill = f.options['fill'].value
f_ = copy.copy(f)
f_.type_id = fill
return "[%s]" % to_type(f_)
return name | python | def to_type(f, type_map=CONSTRUCT_CODE):
"""
Format a the proper type.
"""
name = f.type_id
if name.startswith('GPSTime'):
name = 'Gps' + name[3:]
if type_map.get(name, None):
return type_map.get(name, None)
elif name == 'array':
fill = f.options['fill'].value
f_ = copy.copy(f)
f_.type_id = fill
return "[%s]" % to_type(f_)
return name | Format a the proper type. | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/generator/sbpg/targets/haskell.py#L95-L109 |
swift-nav/libsbp | generator/sbpg/targets/haskell.py | render_source | def render_source(output_dir, package_spec):
"""
Render and output to a directory given a package specification.
"""
path, name = package_spec.filepath
module_prefix = "SwiftNav.SBP"
module_name = camel_case(name)
full_module_name = ".".join([module_prefix, module_name])
destination_filename = "%s/src/SwiftNav/SBP/%s.hs" % (output_dir, module_name)
py_template = JENV.get_template(MESSAGES_TEMPLATE_NAME)
module_includes = [".".join([module_prefix] + [camel_case(j) for j in i.split(".")[:-1]])
for i in package_spec.includes]
with open(destination_filename, 'w') as f:
f.write(py_template.render(msgs=package_spec.definitions,
description=package_spec.description,
module_name=full_module_name,
module_includes=module_includes)) | python | def render_source(output_dir, package_spec):
"""
Render and output to a directory given a package specification.
"""
path, name = package_spec.filepath
module_prefix = "SwiftNav.SBP"
module_name = camel_case(name)
full_module_name = ".".join([module_prefix, module_name])
destination_filename = "%s/src/SwiftNav/SBP/%s.hs" % (output_dir, module_name)
py_template = JENV.get_template(MESSAGES_TEMPLATE_NAME)
module_includes = [".".join([module_prefix] + [camel_case(j) for j in i.split(".")[:-1]])
for i in package_spec.includes]
with open(destination_filename, 'w') as f:
f.write(py_template.render(msgs=package_spec.definitions,
description=package_spec.description,
module_name=full_module_name,
module_includes=module_includes)) | Render and output to a directory given a package specification. | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/generator/sbpg/targets/haskell.py#L164-L181 |
swift-nav/libsbp | generator/sbpg/targets/protobuf.py | to_comment | def to_comment(value):
"""
Builds a comment.
"""
if value is None:
return
if len(value.split('\n')) == 1:
return "* " + value
else:
return '\n'.join([' * ' + l for l in value.split('\n')[:-1]]) | python | def to_comment(value):
"""
Builds a comment.
"""
if value is None:
return
if len(value.split('\n')) == 1:
return "* " + value
else:
return '\n'.join([' * ' + l for l in value.split('\n')[:-1]]) | Builds a comment. | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/generator/sbpg/targets/protobuf.py#L39-L48 |
swift-nav/libsbp | generator/sbpg/targets/protobuf.py | to_identifier | def to_identifier(s):
"""
Convert snake_case to camel_case.
"""
if s.startswith('GPS'):
s = 'Gps' + s[3:]
return ''.join([i.capitalize() for i in s.split('_')]) if '_' in s else s | python | def to_identifier(s):
"""
Convert snake_case to camel_case.
"""
if s.startswith('GPS'):
s = 'Gps' + s[3:]
return ''.join([i.capitalize() for i in s.split('_')]) if '_' in s else s | Convert snake_case to camel_case. | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/generator/sbpg/targets/protobuf.py#L50-L56 |
swift-nav/libsbp | generator/sbpg/targets/protobuf.py | render_source | def render_source(output_dir, package_spec):
"""
Render and output to a directory given a package specification.
"""
path, name = package_spec.filepath
destination_filename = '%s/%s.proto' % (output_dir, name)
pb_template = JENV.get_template(MESSAGES_TEMPLATE_NAME)
includes = [include[:-5] if include.endswith('.yaml') else include for include in package_spec.includes]
if 'types' in includes:
includes.remove('types')
with open(destination_filename, 'w') as f:
f.write(pb_template.render(
name=name,
package=package_spec.identifier,
messages=package_spec.definitions,
includes=includes,
description=package_spec.description,
)) | python | def render_source(output_dir, package_spec):
"""
Render and output to a directory given a package specification.
"""
path, name = package_spec.filepath
destination_filename = '%s/%s.proto' % (output_dir, name)
pb_template = JENV.get_template(MESSAGES_TEMPLATE_NAME)
includes = [include[:-5] if include.endswith('.yaml') else include for include in package_spec.includes]
if 'types' in includes:
includes.remove('types')
with open(destination_filename, 'w') as f:
f.write(pb_template.render(
name=name,
package=package_spec.identifier,
messages=package_spec.definitions,
includes=includes,
description=package_spec.description,
)) | Render and output to a directory given a package specification. | https://github.com/swift-nav/libsbp/blob/5a950608506b23e31b73ef7065da905b646055c1/generator/sbpg/targets/protobuf.py#L81-L98 |
dnanexus/dx-toolkit | src/python/dxpy/bindings/dxapp_container_functions.py | load_app_resource | def load_app_resource(**kwargs):
'''
:param kwargs: keyword args for :func:`~dxpy.bindings.search.find_one_data_object`, with the exception of "project"
:raises: :exc:`~dxpy.exceptions.DXError` if "project" is given, if this is called with dxpy.JOB_ID not set, or if "DX_RESOURCES_ID" or "DX_PROJECT_CONTEXT_ID" is not found in the environment variables
:returns: None if no matching object is found; otherwise returns a dxpy object handler for that class of object
Searches for a data object in the app resources container matching the given keyword arguments. If found, the
object will be cloned into the running job's workspace container, and the handler for it will be returned. If the
app resources container ID is not found in DX_RESOURCES_ID, falls back to looking in the current project.
Example::
@dxpy.entry_point('main')
def main(*args, **kwargs):
x = load_app_resource(name="Indexed genome", classname='file')
dxpy.download_dxfile(x)
'''
if 'project' in kwargs:
raise DXError('Unexpected kwarg: "project"')
if dxpy.JOB_ID is None:
raise DXError('Not called by a job')
if 'DX_RESOURCES_ID' not in os.environ and 'DX_PROJECT_CONTEXT_ID' not in os.environ:
raise DXError('App resources container ID could not be found')
kwargs['project'] = os.environ.get('DX_RESOURCES_ID', os.environ.get('DX_PROJECT_CONTEXT_ID'))
kwargs['return_handler'] = True
return find_one_data_object(**kwargs) | python | def load_app_resource(**kwargs):
'''
:param kwargs: keyword args for :func:`~dxpy.bindings.search.find_one_data_object`, with the exception of "project"
:raises: :exc:`~dxpy.exceptions.DXError` if "project" is given, if this is called with dxpy.JOB_ID not set, or if "DX_RESOURCES_ID" or "DX_PROJECT_CONTEXT_ID" is not found in the environment variables
:returns: None if no matching object is found; otherwise returns a dxpy object handler for that class of object
Searches for a data object in the app resources container matching the given keyword arguments. If found, the
object will be cloned into the running job's workspace container, and the handler for it will be returned. If the
app resources container ID is not found in DX_RESOURCES_ID, falls back to looking in the current project.
Example::
@dxpy.entry_point('main')
def main(*args, **kwargs):
x = load_app_resource(name="Indexed genome", classname='file')
dxpy.download_dxfile(x)
'''
if 'project' in kwargs:
raise DXError('Unexpected kwarg: "project"')
if dxpy.JOB_ID is None:
raise DXError('Not called by a job')
if 'DX_RESOURCES_ID' not in os.environ and 'DX_PROJECT_CONTEXT_ID' not in os.environ:
raise DXError('App resources container ID could not be found')
kwargs['project'] = os.environ.get('DX_RESOURCES_ID', os.environ.get('DX_PROJECT_CONTEXT_ID'))
kwargs['return_handler'] = True
return find_one_data_object(**kwargs) | :param kwargs: keyword args for :func:`~dxpy.bindings.search.find_one_data_object`, with the exception of "project"
:raises: :exc:`~dxpy.exceptions.DXError` if "project" is given, if this is called with dxpy.JOB_ID not set, or if "DX_RESOURCES_ID" or "DX_PROJECT_CONTEXT_ID" is not found in the environment variables
:returns: None if no matching object is found; otherwise returns a dxpy object handler for that class of object
Searches for a data object in the app resources container matching the given keyword arguments. If found, the
object will be cloned into the running job's workspace container, and the handler for it will be returned. If the
app resources container ID is not found in DX_RESOURCES_ID, falls back to looking in the current project.
Example::
@dxpy.entry_point('main')
def main(*args, **kwargs):
x = load_app_resource(name="Indexed genome", classname='file')
dxpy.download_dxfile(x) | https://github.com/dnanexus/dx-toolkit/blob/74befb53ad90fcf902d8983ae6d74580f402d619/src/python/dxpy/bindings/dxapp_container_functions.py#L34-L62 |
dnanexus/dx-toolkit | src/python/dxpy/bindings/dxapp_container_functions.py | load_from_cache | def load_from_cache(**kwargs):
'''
:param kwargs: keyword args for :func:`~dxpy.bindings.search.find_one_data_object`, with the exception of "project"
:raises: :exc:`~dxpy.exceptions.DXError` if "project" is given, if this is called with dxpy.JOB_ID not set, or if "DX_PROJECT_CACHE_ID" is not found in the environment variables
:returns: None if no matching object is found; otherwise returns a dxpy object handler for that class of object
Searches for a data object in the project cache container matching
the given keyword arguments. If found, the object will be cloned
into the running job's workspace container, and the handler for it
will be returned.
Example::
@dxpy.entry_point('main')
def main(*args, **kwargs):
x = load_from_cache(name="Indexed genome", classname='file')
if x is None:
x = compute_result(*args)
save_to_cache(x)
'''
if 'project' in kwargs:
raise DXError('Unexpected kwarg: "project"')
if dxpy.JOB_ID is None:
raise DXError('Not called by a job')
if 'DX_PROJECT_CACHE_ID' not in os.environ:
raise DXError('Project cache ID could not be found in the environment variable DX_PROJECT_CACHE_ID')
kwargs['project'] = os.environ.get('DX_PROJECT_CACHE_ID')
kwargs['return_handler'] = True
cached_object = find_one_data_object(**kwargs)
if cached_object is None:
return None
return cached_object.clone(dxpy.WORKSPACE_ID) | python | def load_from_cache(**kwargs):
'''
:param kwargs: keyword args for :func:`~dxpy.bindings.search.find_one_data_object`, with the exception of "project"
:raises: :exc:`~dxpy.exceptions.DXError` if "project" is given, if this is called with dxpy.JOB_ID not set, or if "DX_PROJECT_CACHE_ID" is not found in the environment variables
:returns: None if no matching object is found; otherwise returns a dxpy object handler for that class of object
Searches for a data object in the project cache container matching
the given keyword arguments. If found, the object will be cloned
into the running job's workspace container, and the handler for it
will be returned.
Example::
@dxpy.entry_point('main')
def main(*args, **kwargs):
x = load_from_cache(name="Indexed genome", classname='file')
if x is None:
x = compute_result(*args)
save_to_cache(x)
'''
if 'project' in kwargs:
raise DXError('Unexpected kwarg: "project"')
if dxpy.JOB_ID is None:
raise DXError('Not called by a job')
if 'DX_PROJECT_CACHE_ID' not in os.environ:
raise DXError('Project cache ID could not be found in the environment variable DX_PROJECT_CACHE_ID')
kwargs['project'] = os.environ.get('DX_PROJECT_CACHE_ID')
kwargs['return_handler'] = True
cached_object = find_one_data_object(**kwargs)
if cached_object is None:
return None
return cached_object.clone(dxpy.WORKSPACE_ID) | :param kwargs: keyword args for :func:`~dxpy.bindings.search.find_one_data_object`, with the exception of "project"
:raises: :exc:`~dxpy.exceptions.DXError` if "project" is given, if this is called with dxpy.JOB_ID not set, or if "DX_PROJECT_CACHE_ID" is not found in the environment variables
:returns: None if no matching object is found; otherwise returns a dxpy object handler for that class of object
Searches for a data object in the project cache container matching
the given keyword arguments. If found, the object will be cloned
into the running job's workspace container, and the handler for it
will be returned.
Example::
@dxpy.entry_point('main')
def main(*args, **kwargs):
x = load_from_cache(name="Indexed genome", classname='file')
if x is None:
x = compute_result(*args)
save_to_cache(x) | https://github.com/dnanexus/dx-toolkit/blob/74befb53ad90fcf902d8983ae6d74580f402d619/src/python/dxpy/bindings/dxapp_container_functions.py#L64-L100 |
dnanexus/dx-toolkit | src/python/dxpy/bindings/dxapp_container_functions.py | save_to_cache | def save_to_cache(dxobject):
'''
:param dxobject: a dxpy object handler for an object to save to the cache
:raises: :exc:`~dxpy.exceptions.DXError` if this is called with dxpy.JOB_ID not set, or if "DX_PROJECT_CACHE_ID" is not found in the environment variables
Clones the given object to the project cache.
Example::
@dxpy.entry_point('main')
def main(*args, **kwargs):
x = load_from_cache(name="Indexed genome", classname='file')
if x is None:
x = compute_result(*args)
save_to_cache(x)
'''
if dxpy.JOB_ID is None:
raise DXError('Not called by a job')
if 'DX_PROJECT_CACHE_ID' not in os.environ:
raise DXError('Project cache ID could not be found in the environment variable DX_PROJECT_CACHE_ID')
dxobject.clone(os.environ.get('DX_PROJECT_CACHE_ID')) | python | def save_to_cache(dxobject):
'''
:param dxobject: a dxpy object handler for an object to save to the cache
:raises: :exc:`~dxpy.exceptions.DXError` if this is called with dxpy.JOB_ID not set, or if "DX_PROJECT_CACHE_ID" is not found in the environment variables
Clones the given object to the project cache.
Example::
@dxpy.entry_point('main')
def main(*args, **kwargs):
x = load_from_cache(name="Indexed genome", classname='file')
if x is None:
x = compute_result(*args)
save_to_cache(x)
'''
if dxpy.JOB_ID is None:
raise DXError('Not called by a job')
if 'DX_PROJECT_CACHE_ID' not in os.environ:
raise DXError('Project cache ID could not be found in the environment variable DX_PROJECT_CACHE_ID')
dxobject.clone(os.environ.get('DX_PROJECT_CACHE_ID')) | :param dxobject: a dxpy object handler for an object to save to the cache
:raises: :exc:`~dxpy.exceptions.DXError` if this is called with dxpy.JOB_ID not set, or if "DX_PROJECT_CACHE_ID" is not found in the environment variables
Clones the given object to the project cache.
Example::
@dxpy.entry_point('main')
def main(*args, **kwargs):
x = load_from_cache(name="Indexed genome", classname='file')
if x is None:
x = compute_result(*args)
save_to_cache(x) | https://github.com/dnanexus/dx-toolkit/blob/74befb53ad90fcf902d8983ae6d74580f402d619/src/python/dxpy/bindings/dxapp_container_functions.py#L103-L125 |
dnanexus/dx-toolkit | src/python/dxpy/bindings/dxapplet.py | DXExecutable._get_run_input_common_fields | def _get_run_input_common_fields(executable_input, **kwargs):
'''
Takes the same arguments as the run method. Creates an input hash for the /executable-xxxx/run method,
translating ONLY the fields that can be handled uniformly across all executables: project, folder, name, tags,
properties, details, depends_on, allow_ssh, debug, delay_workspace_destruction, ignore_reuse, and extra_args.
'''
project = kwargs.get('project') or dxpy.WORKSPACE_ID
run_input = {"input": executable_input}
for arg in ['folder', 'name', 'tags', 'properties', 'details']:
if kwargs.get(arg) is not None:
run_input[arg] = kwargs[arg]
if kwargs.get('instance_type') is not None or kwargs.get('cluster_spec') is not None:
instance_type_srd = SystemRequirementsDict.from_instance_type(kwargs.get('instance_type'))
cluster_spec_srd = SystemRequirementsDict(kwargs.get('cluster_spec'))
run_input["systemRequirements"] = (instance_type_srd + cluster_spec_srd).as_dict()
if kwargs.get('depends_on') is not None:
run_input["dependsOn"] = []
if isinstance(kwargs['depends_on'], list):
for item in kwargs['depends_on']:
if isinstance(item, DXJob) or isinstance(item, DXDataObject):
if item.get_id() is None:
raise DXError('A dxpy handler given in depends_on does not have an ID set')
run_input["dependsOn"].append(item.get_id())
elif isinstance(item, basestring):
run_input['dependsOn'].append(item)
else:
raise DXError('Expected elements of depends_on to only be either instances of DXJob or DXDataObject, or strings')
else:
raise DXError('Expected depends_on field to be a list')
if kwargs.get('delay_workspace_destruction') is not None:
run_input["delayWorkspaceDestruction"] = kwargs['delay_workspace_destruction']
if kwargs.get('allow_ssh') is not None:
run_input["allowSSH"] = kwargs['allow_ssh']
if kwargs.get('debug') is not None:
run_input["debug"] = kwargs['debug']
if kwargs.get('priority') is not None:
run_input["priority"] = kwargs['priority']
if kwargs.get('ignore_reuse') is not None:
run_input["ignoreReuse"] = kwargs['ignore_reuse']
if dxpy.JOB_ID is None:
run_input["project"] = project
if kwargs.get('extra_args') is not None:
merge(run_input, kwargs['extra_args'])
return run_input | python | def _get_run_input_common_fields(executable_input, **kwargs):
'''
Takes the same arguments as the run method. Creates an input hash for the /executable-xxxx/run method,
translating ONLY the fields that can be handled uniformly across all executables: project, folder, name, tags,
properties, details, depends_on, allow_ssh, debug, delay_workspace_destruction, ignore_reuse, and extra_args.
'''
project = kwargs.get('project') or dxpy.WORKSPACE_ID
run_input = {"input": executable_input}
for arg in ['folder', 'name', 'tags', 'properties', 'details']:
if kwargs.get(arg) is not None:
run_input[arg] = kwargs[arg]
if kwargs.get('instance_type') is not None or kwargs.get('cluster_spec') is not None:
instance_type_srd = SystemRequirementsDict.from_instance_type(kwargs.get('instance_type'))
cluster_spec_srd = SystemRequirementsDict(kwargs.get('cluster_spec'))
run_input["systemRequirements"] = (instance_type_srd + cluster_spec_srd).as_dict()
if kwargs.get('depends_on') is not None:
run_input["dependsOn"] = []
if isinstance(kwargs['depends_on'], list):
for item in kwargs['depends_on']:
if isinstance(item, DXJob) or isinstance(item, DXDataObject):
if item.get_id() is None:
raise DXError('A dxpy handler given in depends_on does not have an ID set')
run_input["dependsOn"].append(item.get_id())
elif isinstance(item, basestring):
run_input['dependsOn'].append(item)
else:
raise DXError('Expected elements of depends_on to only be either instances of DXJob or DXDataObject, or strings')
else:
raise DXError('Expected depends_on field to be a list')
if kwargs.get('delay_workspace_destruction') is not None:
run_input["delayWorkspaceDestruction"] = kwargs['delay_workspace_destruction']
if kwargs.get('allow_ssh') is not None:
run_input["allowSSH"] = kwargs['allow_ssh']
if kwargs.get('debug') is not None:
run_input["debug"] = kwargs['debug']
if kwargs.get('priority') is not None:
run_input["priority"] = kwargs['priority']
if kwargs.get('ignore_reuse') is not None:
run_input["ignoreReuse"] = kwargs['ignore_reuse']
if dxpy.JOB_ID is None:
run_input["project"] = project
if kwargs.get('extra_args') is not None:
merge(run_input, kwargs['extra_args'])
return run_input | Takes the same arguments as the run method. Creates an input hash for the /executable-xxxx/run method,
translating ONLY the fields that can be handled uniformly across all executables: project, folder, name, tags,
properties, details, depends_on, allow_ssh, debug, delay_workspace_destruction, ignore_reuse, and extra_args. | https://github.com/dnanexus/dx-toolkit/blob/74befb53ad90fcf902d8983ae6d74580f402d619/src/python/dxpy/bindings/dxapplet.py#L46-L100 |
dnanexus/dx-toolkit | src/python/dxpy/bindings/dxapplet.py | DXExecutable._get_run_input_fields_for_applet | def _get_run_input_fields_for_applet(executable_input, **kwargs):
'''
Takes the same arguments as the run method. Creates an input
hash for the /applet-xxxx/run method.
'''
# Although it says "for_applet", this is factored out of
# DXApplet because apps currently use the same mechanism
for unsupported_arg in ['stage_instance_types', 'stage_folders', 'rerun_stages', 'ignore_reuse_stages']:
if kwargs.get(unsupported_arg):
raise DXError(unsupported_arg + ' is not supported for applets (only workflows)')
return DXExecutable._get_run_input_common_fields(executable_input, **kwargs) | python | def _get_run_input_fields_for_applet(executable_input, **kwargs):
'''
Takes the same arguments as the run method. Creates an input
hash for the /applet-xxxx/run method.
'''
# Although it says "for_applet", this is factored out of
# DXApplet because apps currently use the same mechanism
for unsupported_arg in ['stage_instance_types', 'stage_folders', 'rerun_stages', 'ignore_reuse_stages']:
if kwargs.get(unsupported_arg):
raise DXError(unsupported_arg + ' is not supported for applets (only workflows)')
return DXExecutable._get_run_input_common_fields(executable_input, **kwargs) | Takes the same arguments as the run method. Creates an input
hash for the /applet-xxxx/run method. | https://github.com/dnanexus/dx-toolkit/blob/74befb53ad90fcf902d8983ae6d74580f402d619/src/python/dxpy/bindings/dxapplet.py#L103-L114 |
dnanexus/dx-toolkit | src/python/dxpy/bindings/dxapplet.py | DXExecutable.run | def run(self, executable_input, project=None, folder=None, name=None, tags=None, properties=None, details=None,
instance_type=None, stage_instance_types=None, stage_folders=None, rerun_stages=None, cluster_spec=None,
depends_on=None, allow_ssh=None, debug=None, delay_workspace_destruction=None, priority=None,
ignore_reuse=None, ignore_reuse_stages=None, extra_args=None, **kwargs):
'''
:param executable_input: Hash of the executable's input arguments
:type executable_input: dict
:param project: Project ID of the project context
:type project: string
:param folder: Folder in which executable's outputs will be placed in *project*
:type folder: string
:param name: Name for the new job (default is "<name of the executable>")
:type name: string
:param tags: Tags to associate with the job
:type tags: list of strings
:param properties: Properties to associate with the job
:type properties: dict with string values
:param details: Details to set for the job
:type details: dict or list
:param instance_type: Instance type on which the jobs will be run, or a dict mapping function names to instance type requests
:type instance_type: string or dict
:param depends_on: List of data objects or jobs to wait that need to enter the "closed" or "done" states, respectively, before the new job will be run; each element in the list can either be a dxpy handler or a string ID
:type depends_on: list
:param allow_ssh: List of hostname or IP masks to allow SSH connections from
:type allow_ssh: list
:param debug: Configuration options for job debugging
:type debug: dict
:param delay_workspace_destruction: Whether to keep the job's temporary workspace around for debugging purposes for 3 days after it succeeds or fails
:type delay_workspace_destruction: boolean
:param priority: Priority level to request for all jobs created in the execution tree, either "normal" or "high"
:type priority: string
:param ignore_reuse: Disable job reuse for this execution
:type ignore_reuse: boolean
:param ignore_reuse_stages: Stages of a workflow (IDs, names, or indices) or "*" for which job reuse should be disabled
:type ignore_reuse_stages: list
:param extra_args: If provided, a hash of options that will be merged into the underlying JSON given for the API call
:type extra_args: dict
:returns: Object handler of the newly created job
:rtype: :class:`~dxpy.bindings.dxjob.DXJob`
Creates a new job that executes the function "main" of this executable with
the given input *executable_input*.
'''
# stage_instance_types, stage_folders, and rerun_stages are
# only supported for workflows, but we include them
# here. Applet-based executables should detect when they
# receive a truthy workflow-specific value and raise an error.
run_input = self._get_run_input(executable_input,
project=project,
folder=folder,
name=name,
tags=tags,
properties=properties,
details=details,
instance_type=instance_type,
stage_instance_types=stage_instance_types,
stage_folders=stage_folders,
rerun_stages=rerun_stages,
cluster_spec=cluster_spec,
depends_on=depends_on,
allow_ssh=allow_ssh,
ignore_reuse=ignore_reuse,
ignore_reuse_stages=ignore_reuse_stages,
debug=debug,
delay_workspace_destruction=delay_workspace_destruction,
priority=priority,
extra_args=extra_args)
return self._run_impl(run_input, **kwargs) | python | def run(self, executable_input, project=None, folder=None, name=None, tags=None, properties=None, details=None,
instance_type=None, stage_instance_types=None, stage_folders=None, rerun_stages=None, cluster_spec=None,
depends_on=None, allow_ssh=None, debug=None, delay_workspace_destruction=None, priority=None,
ignore_reuse=None, ignore_reuse_stages=None, extra_args=None, **kwargs):
'''
:param executable_input: Hash of the executable's input arguments
:type executable_input: dict
:param project: Project ID of the project context
:type project: string
:param folder: Folder in which executable's outputs will be placed in *project*
:type folder: string
:param name: Name for the new job (default is "<name of the executable>")
:type name: string
:param tags: Tags to associate with the job
:type tags: list of strings
:param properties: Properties to associate with the job
:type properties: dict with string values
:param details: Details to set for the job
:type details: dict or list
:param instance_type: Instance type on which the jobs will be run, or a dict mapping function names to instance type requests
:type instance_type: string or dict
:param depends_on: List of data objects or jobs to wait that need to enter the "closed" or "done" states, respectively, before the new job will be run; each element in the list can either be a dxpy handler or a string ID
:type depends_on: list
:param allow_ssh: List of hostname or IP masks to allow SSH connections from
:type allow_ssh: list
:param debug: Configuration options for job debugging
:type debug: dict
:param delay_workspace_destruction: Whether to keep the job's temporary workspace around for debugging purposes for 3 days after it succeeds or fails
:type delay_workspace_destruction: boolean
:param priority: Priority level to request for all jobs created in the execution tree, either "normal" or "high"
:type priority: string
:param ignore_reuse: Disable job reuse for this execution
:type ignore_reuse: boolean
:param ignore_reuse_stages: Stages of a workflow (IDs, names, or indices) or "*" for which job reuse should be disabled
:type ignore_reuse_stages: list
:param extra_args: If provided, a hash of options that will be merged into the underlying JSON given for the API call
:type extra_args: dict
:returns: Object handler of the newly created job
:rtype: :class:`~dxpy.bindings.dxjob.DXJob`
Creates a new job that executes the function "main" of this executable with
the given input *executable_input*.
'''
# stage_instance_types, stage_folders, and rerun_stages are
# only supported for workflows, but we include them
# here. Applet-based executables should detect when they
# receive a truthy workflow-specific value and raise an error.
run_input = self._get_run_input(executable_input,
project=project,
folder=folder,
name=name,
tags=tags,
properties=properties,
details=details,
instance_type=instance_type,
stage_instance_types=stage_instance_types,
stage_folders=stage_folders,
rerun_stages=rerun_stages,
cluster_spec=cluster_spec,
depends_on=depends_on,
allow_ssh=allow_ssh,
ignore_reuse=ignore_reuse,
ignore_reuse_stages=ignore_reuse_stages,
debug=debug,
delay_workspace_destruction=delay_workspace_destruction,
priority=priority,
extra_args=extra_args)
return self._run_impl(run_input, **kwargs) | :param executable_input: Hash of the executable's input arguments
:type executable_input: dict
:param project: Project ID of the project context
:type project: string
:param folder: Folder in which executable's outputs will be placed in *project*
:type folder: string
:param name: Name for the new job (default is "<name of the executable>")
:type name: string
:param tags: Tags to associate with the job
:type tags: list of strings
:param properties: Properties to associate with the job
:type properties: dict with string values
:param details: Details to set for the job
:type details: dict or list
:param instance_type: Instance type on which the jobs will be run, or a dict mapping function names to instance type requests
:type instance_type: string or dict
:param depends_on: List of data objects or jobs to wait that need to enter the "closed" or "done" states, respectively, before the new job will be run; each element in the list can either be a dxpy handler or a string ID
:type depends_on: list
:param allow_ssh: List of hostname or IP masks to allow SSH connections from
:type allow_ssh: list
:param debug: Configuration options for job debugging
:type debug: dict
:param delay_workspace_destruction: Whether to keep the job's temporary workspace around for debugging purposes for 3 days after it succeeds or fails
:type delay_workspace_destruction: boolean
:param priority: Priority level to request for all jobs created in the execution tree, either "normal" or "high"
:type priority: string
:param ignore_reuse: Disable job reuse for this execution
:type ignore_reuse: boolean
:param ignore_reuse_stages: Stages of a workflow (IDs, names, or indices) or "*" for which job reuse should be disabled
:type ignore_reuse_stages: list
:param extra_args: If provided, a hash of options that will be merged into the underlying JSON given for the API call
:type extra_args: dict
:returns: Object handler of the newly created job
:rtype: :class:`~dxpy.bindings.dxjob.DXJob`
Creates a new job that executes the function "main" of this executable with
the given input *executable_input*. | https://github.com/dnanexus/dx-toolkit/blob/74befb53ad90fcf902d8983ae6d74580f402d619/src/python/dxpy/bindings/dxapplet.py#L158-L227 |
dnanexus/dx-toolkit | src/python/dxpy/bindings/dxapplet.py | DXApplet._new | def _new(self, dx_hash, **kwargs):
'''
:param dx_hash: Standard hash populated in :func:`dxpy.bindings.DXDataObject.new()` containing attributes common to all data object classes.
:type dx_hash: dict
:param runSpec: Run specification
:type runSpec: dict
:param dxapi: API version string
:type dxapi: string
:param inputSpec: Input specification (optional)
:type inputSpec: dict
:param outputSpec: Output specification (optional)
:type outputSpec: dict
:param access: Access specification (optional)
:type access: dict
:param title: Title string (optional)
:type title: string
:param summary: Summary string (optional)
:type summary: string
:param description: Description string (optional)
:type description: string
.. note:: It is highly recommended that the higher-level module
:mod:`dxpy.app_builder` or (preferably) its frontend `dx build
<https://wiki.dnanexus.com/Command-Line-Client/Index-of-dx-Commands#build>`_
be used instead for applet creation.
Creates an applet with the given parameters. See the API
documentation for the `/applet/new
<https://wiki.dnanexus.com/API-Specification-v1.0.0/Applets-and-Entry-Points#API-method:-/applet/new>`_
method for more info. The applet is not run until :meth:`run()`
is called.
'''
for field in 'runSpec', 'dxapi':
if field not in kwargs:
raise DXError("%s: Keyword argument %s is required" % (self.__class__.__name__, field))
dx_hash[field] = kwargs[field]
del kwargs[field]
for field in 'inputSpec', 'outputSpec', 'access', 'title', 'summary', 'description':
if field in kwargs:
dx_hash[field] = kwargs[field]
del kwargs[field]
resp = dxpy.api.applet_new(dx_hash, **kwargs)
self.set_ids(resp["id"], dx_hash["project"]) | python | def _new(self, dx_hash, **kwargs):
'''
:param dx_hash: Standard hash populated in :func:`dxpy.bindings.DXDataObject.new()` containing attributes common to all data object classes.
:type dx_hash: dict
:param runSpec: Run specification
:type runSpec: dict
:param dxapi: API version string
:type dxapi: string
:param inputSpec: Input specification (optional)
:type inputSpec: dict
:param outputSpec: Output specification (optional)
:type outputSpec: dict
:param access: Access specification (optional)
:type access: dict
:param title: Title string (optional)
:type title: string
:param summary: Summary string (optional)
:type summary: string
:param description: Description string (optional)
:type description: string
.. note:: It is highly recommended that the higher-level module
:mod:`dxpy.app_builder` or (preferably) its frontend `dx build
<https://wiki.dnanexus.com/Command-Line-Client/Index-of-dx-Commands#build>`_
be used instead for applet creation.
Creates an applet with the given parameters. See the API
documentation for the `/applet/new
<https://wiki.dnanexus.com/API-Specification-v1.0.0/Applets-and-Entry-Points#API-method:-/applet/new>`_
method for more info. The applet is not run until :meth:`run()`
is called.
'''
for field in 'runSpec', 'dxapi':
if field not in kwargs:
raise DXError("%s: Keyword argument %s is required" % (self.__class__.__name__, field))
dx_hash[field] = kwargs[field]
del kwargs[field]
for field in 'inputSpec', 'outputSpec', 'access', 'title', 'summary', 'description':
if field in kwargs:
dx_hash[field] = kwargs[field]
del kwargs[field]
resp = dxpy.api.applet_new(dx_hash, **kwargs)
self.set_ids(resp["id"], dx_hash["project"]) | :param dx_hash: Standard hash populated in :func:`dxpy.bindings.DXDataObject.new()` containing attributes common to all data object classes.
:type dx_hash: dict
:param runSpec: Run specification
:type runSpec: dict
:param dxapi: API version string
:type dxapi: string
:param inputSpec: Input specification (optional)
:type inputSpec: dict
:param outputSpec: Output specification (optional)
:type outputSpec: dict
:param access: Access specification (optional)
:type access: dict
:param title: Title string (optional)
:type title: string
:param summary: Summary string (optional)
:type summary: string
:param description: Description string (optional)
:type description: string
.. note:: It is highly recommended that the higher-level module
:mod:`dxpy.app_builder` or (preferably) its frontend `dx build
<https://wiki.dnanexus.com/Command-Line-Client/Index-of-dx-Commands#build>`_
be used instead for applet creation.
Creates an applet with the given parameters. See the API
documentation for the `/applet/new
<https://wiki.dnanexus.com/API-Specification-v1.0.0/Applets-and-Entry-Points#API-method:-/applet/new>`_
method for more info. The applet is not run until :meth:`run()`
is called. | https://github.com/dnanexus/dx-toolkit/blob/74befb53ad90fcf902d8983ae6d74580f402d619/src/python/dxpy/bindings/dxapplet.py#L307-L351 |
dnanexus/dx-toolkit | src/python/dxpy/bindings/dxapplet.py | DXApplet.run | def run(self, applet_input, *args, **kwargs):
"""
Creates a new job that executes the function "main" of this applet with
the given input *applet_input*.
See :meth:`dxpy.bindings.dxapplet.DXExecutable.run` for the available
args.
"""
# Rename applet_input arg to preserve API compatibility when calling
# DXApplet.run(applet_input=...)
return super(DXApplet, self).run(applet_input, *args, **kwargs) | python | def run(self, applet_input, *args, **kwargs):
"""
Creates a new job that executes the function "main" of this applet with
the given input *applet_input*.
See :meth:`dxpy.bindings.dxapplet.DXExecutable.run` for the available
args.
"""
# Rename applet_input arg to preserve API compatibility when calling
# DXApplet.run(applet_input=...)
return super(DXApplet, self).run(applet_input, *args, **kwargs) | Creates a new job that executes the function "main" of this applet with
the given input *applet_input*.
See :meth:`dxpy.bindings.dxapplet.DXExecutable.run` for the available
args. | https://github.com/dnanexus/dx-toolkit/blob/74befb53ad90fcf902d8983ae6d74580f402d619/src/python/dxpy/bindings/dxapplet.py#L384-L394 |
dnanexus/dx-toolkit | src/python/dxpy/cli/parsers.py | set_env_from_args | def set_env_from_args(args):
''' Sets the environment variables for this process from arguments (argparse.Namespace)
and calls dxpy._initialize() to reset any values that it has already set.
'''
args = vars(args)
if args.get('apiserver_host') is not None:
config['DX_APISERVER_HOST'] = args['apiserver_host']
if args.get('apiserver_port') is not None:
config['DX_APISERVER_PORT'] = args['apiserver_port']
if args.get('apiserver_protocol') is not None:
config['DX_APISERVER_PROTOCOL'] = args['apiserver_protocol']
if args.get('project_context_id') is not None:
config['DX_PROJECT_CONTEXT_ID'] = args['project_context_id']
if args.get('workspace_id') is not None:
config['DX_WORKSPACE_ID'] = args['workspace_id']
if args.get('cli_wd') is not None:
config['DX_CLI_WD'] = args['cli_wd']
if args.get('security_context') is not None:
config['DX_SECURITY_CONTEXT'] = args['security_context']
if args.get('auth_token') is not None:
config['DX_SECURITY_CONTEXT'] = json.dumps({"auth_token": args['auth_token'],
"auth_token_type": "Bearer"}) | python | def set_env_from_args(args):
''' Sets the environment variables for this process from arguments (argparse.Namespace)
and calls dxpy._initialize() to reset any values that it has already set.
'''
args = vars(args)
if args.get('apiserver_host') is not None:
config['DX_APISERVER_HOST'] = args['apiserver_host']
if args.get('apiserver_port') is not None:
config['DX_APISERVER_PORT'] = args['apiserver_port']
if args.get('apiserver_protocol') is not None:
config['DX_APISERVER_PROTOCOL'] = args['apiserver_protocol']
if args.get('project_context_id') is not None:
config['DX_PROJECT_CONTEXT_ID'] = args['project_context_id']
if args.get('workspace_id') is not None:
config['DX_WORKSPACE_ID'] = args['workspace_id']
if args.get('cli_wd') is not None:
config['DX_CLI_WD'] = args['cli_wd']
if args.get('security_context') is not None:
config['DX_SECURITY_CONTEXT'] = args['security_context']
if args.get('auth_token') is not None:
config['DX_SECURITY_CONTEXT'] = json.dumps({"auth_token": args['auth_token'],
"auth_token_type": "Bearer"}) | Sets the environment variables for this process from arguments (argparse.Namespace)
and calls dxpy._initialize() to reset any values that it has already set. | https://github.com/dnanexus/dx-toolkit/blob/74befb53ad90fcf902d8983ae6d74580f402d619/src/python/dxpy/cli/parsers.py#L186-L208 |
dnanexus/dx-toolkit | src/python/dxpy/asset_builder.py | validate_conf | def validate_conf(asset_conf):
"""
Validates the contents of the conf file and makes sure that the required information
is provided.
{
"name": "asset_library_name",
"title": "A human readable name",
"description": " A detailed description abput the asset",
"version": "0.0.1",
"distribution": "Ubuntu",# (Optional)
"release": "12.04",
"execDepends":
[
{"name": "samtools", "package_manager": "apt"},
{"name": "bamtools"},
{"name": "bio", "package_manager": "gem", "version": "1.4.3"},
{"name": "pysam","package_manager": "pip", "version": "0.7.4"},
{"name": "Bio::SeqIO", "package_manager": "cpan", "version": "1.006924"}
]
}
"""
if 'name' not in asset_conf:
raise AssetBuilderException('The asset configuration does not contain the required field "name".')
# TODO: this default is not a good idea, and we will have to remove it once we ask customers to always provide release
if 'release' not in asset_conf:
asset_conf['release'] = "12.04"
elif asset_conf['release'] not in ['16.04', '14.04', '12.04']:
raise AssetBuilderException('The "release" field value should be either "12.04" (DEPRECATED), "14.04", "16.04".')
if 'version' not in asset_conf:
raise AssetBuilderException('The asset configuration does not contain the required field "version". ')
if 'title' not in asset_conf:
raise AssetBuilderException('The asset configuration does not contain the required field "title". ')
if 'description' not in asset_conf:
raise AssetBuilderException('The asset configuration does not contain the required field "description".')
if 'distribution' in asset_conf:
if asset_conf['distribution'] != 'Ubuntu':
raise AssetBuilderException('The distribution may only take the value "Ubuntu".')
else:
asset_conf['distribution'] = "Ubuntu" | python | def validate_conf(asset_conf):
"""
Validates the contents of the conf file and makes sure that the required information
is provided.
{
"name": "asset_library_name",
"title": "A human readable name",
"description": " A detailed description abput the asset",
"version": "0.0.1",
"distribution": "Ubuntu",# (Optional)
"release": "12.04",
"execDepends":
[
{"name": "samtools", "package_manager": "apt"},
{"name": "bamtools"},
{"name": "bio", "package_manager": "gem", "version": "1.4.3"},
{"name": "pysam","package_manager": "pip", "version": "0.7.4"},
{"name": "Bio::SeqIO", "package_manager": "cpan", "version": "1.006924"}
]
}
"""
if 'name' not in asset_conf:
raise AssetBuilderException('The asset configuration does not contain the required field "name".')
# TODO: this default is not a good idea, and we will have to remove it once we ask customers to always provide release
if 'release' not in asset_conf:
asset_conf['release'] = "12.04"
elif asset_conf['release'] not in ['16.04', '14.04', '12.04']:
raise AssetBuilderException('The "release" field value should be either "12.04" (DEPRECATED), "14.04", "16.04".')
if 'version' not in asset_conf:
raise AssetBuilderException('The asset configuration does not contain the required field "version". ')
if 'title' not in asset_conf:
raise AssetBuilderException('The asset configuration does not contain the required field "title". ')
if 'description' not in asset_conf:
raise AssetBuilderException('The asset configuration does not contain the required field "description".')
if 'distribution' in asset_conf:
if asset_conf['distribution'] != 'Ubuntu':
raise AssetBuilderException('The distribution may only take the value "Ubuntu".')
else:
asset_conf['distribution'] = "Ubuntu" | Validates the contents of the conf file and makes sure that the required information
is provided.
{
"name": "asset_library_name",
"title": "A human readable name",
"description": " A detailed description abput the asset",
"version": "0.0.1",
"distribution": "Ubuntu",# (Optional)
"release": "12.04",
"execDepends":
[
{"name": "samtools", "package_manager": "apt"},
{"name": "bamtools"},
{"name": "bio", "package_manager": "gem", "version": "1.4.3"},
{"name": "pysam","package_manager": "pip", "version": "0.7.4"},
{"name": "Bio::SeqIO", "package_manager": "cpan", "version": "1.006924"}
]
} | https://github.com/dnanexus/dx-toolkit/blob/74befb53ad90fcf902d8983ae6d74580f402d619/src/python/dxpy/asset_builder.py#L59-L97 |
dnanexus/dx-toolkit | src/python/dxpy/asset_builder.py | get_asset_tarball | def get_asset_tarball(asset_name, src_dir, dest_project, dest_folder, json_out):
"""
If the src_dir contains a "resources" directory its contents are archived and
the archived file is uploaded to the platform
"""
if os.path.isdir(os.path.join(src_dir, "resources")):
temp_dir = tempfile.mkdtemp()
try:
resource_file = os.path.join(temp_dir, asset_name + "_resources.tar.gz")
cmd = ["tar", "-czf", resource_file, "-C", os.path.join(src_dir, "resources"), "."]
subprocess.check_call(cmd)
file_id = dx_upload(resource_file, dest_project, dest_folder, json_out)
return file_id
finally:
shutil.rmtree(temp_dir) | python | def get_asset_tarball(asset_name, src_dir, dest_project, dest_folder, json_out):
"""
If the src_dir contains a "resources" directory its contents are archived and
the archived file is uploaded to the platform
"""
if os.path.isdir(os.path.join(src_dir, "resources")):
temp_dir = tempfile.mkdtemp()
try:
resource_file = os.path.join(temp_dir, asset_name + "_resources.tar.gz")
cmd = ["tar", "-czf", resource_file, "-C", os.path.join(src_dir, "resources"), "."]
subprocess.check_call(cmd)
file_id = dx_upload(resource_file, dest_project, dest_folder, json_out)
return file_id
finally:
shutil.rmtree(temp_dir) | If the src_dir contains a "resources" directory its contents are archived and
the archived file is uploaded to the platform | https://github.com/dnanexus/dx-toolkit/blob/74befb53ad90fcf902d8983ae6d74580f402d619/src/python/dxpy/asset_builder.py#L145-L159 |
dnanexus/dx-toolkit | src/python/dxpy/utils/resolver.py | pick | def pick(choices, default=None, str_choices=None, prompt=None, allow_mult=False, more_choices=False):
'''
:param choices: Strings between which the user will make a choice
:type choices: list of strings
:param default: Number the index to be used as the default
:type default: int or None
:param str_choices: Strings to be used as aliases for the choices; must be of the same length as choices and each string must be unique
:type str_choices: list of strings
:param prompt: A custom prompt to be used
:type prompt: string
:param allow_mult: Whether "*" is a valid option to select all choices
:type allow_mult: boolean
:param more_choices: Whether "m" is a valid option to ask for more options
:type more_choices: boolean
:returns: The user's choice, i.e. one of a numbered index of choices (e.g. 0 for the first item), "*" (only if allow_mult is True), or "m" (only if more_results is True)
:rtype: int or string
:raises: :exc:`EOFError` to signify quitting the process
At most one of allow_mult and more_choices should be set to True.
'''
for i in range(len(choices)):
prefix = str(i) + ') '
lines = choices[i].split("\n")
joiner = "\n" + " " * len(prefix)
print(prefix + joiner.join(lines))
if more_choices:
print('m) More options not shown...')
print('')
if prompt is None:
prompt = 'Pick a numbered choice'
if allow_mult:
prompt += ' or "*" for all'
elif more_choices:
prompt += ' or "m" for more options'
if default is not None:
prompt += ' [' + str(default) + ']'
prompt += ': '
while True:
try:
value = input(prompt)
except KeyboardInterrupt:
print('')
raise
except EOFError:
print('')
raise
if default is not None and value == '':
return default
if allow_mult and value == '*':
return value
if more_choices and value == 'm':
return value
try:
choice = str_choices.index(value)
return choice
except:
pass
try:
choice = int(value)
if choice not in range(len(choices)):
raise IndexError()
return choice
except Exception:
print('Not a valid selection') | python | def pick(choices, default=None, str_choices=None, prompt=None, allow_mult=False, more_choices=False):
'''
:param choices: Strings between which the user will make a choice
:type choices: list of strings
:param default: Number the index to be used as the default
:type default: int or None
:param str_choices: Strings to be used as aliases for the choices; must be of the same length as choices and each string must be unique
:type str_choices: list of strings
:param prompt: A custom prompt to be used
:type prompt: string
:param allow_mult: Whether "*" is a valid option to select all choices
:type allow_mult: boolean
:param more_choices: Whether "m" is a valid option to ask for more options
:type more_choices: boolean
:returns: The user's choice, i.e. one of a numbered index of choices (e.g. 0 for the first item), "*" (only if allow_mult is True), or "m" (only if more_results is True)
:rtype: int or string
:raises: :exc:`EOFError` to signify quitting the process
At most one of allow_mult and more_choices should be set to True.
'''
for i in range(len(choices)):
prefix = str(i) + ') '
lines = choices[i].split("\n")
joiner = "\n" + " " * len(prefix)
print(prefix + joiner.join(lines))
if more_choices:
print('m) More options not shown...')
print('')
if prompt is None:
prompt = 'Pick a numbered choice'
if allow_mult:
prompt += ' or "*" for all'
elif more_choices:
prompt += ' or "m" for more options'
if default is not None:
prompt += ' [' + str(default) + ']'
prompt += ': '
while True:
try:
value = input(prompt)
except KeyboardInterrupt:
print('')
raise
except EOFError:
print('')
raise
if default is not None and value == '':
return default
if allow_mult and value == '*':
return value
if more_choices and value == 'm':
return value
try:
choice = str_choices.index(value)
return choice
except:
pass
try:
choice = int(value)
if choice not in range(len(choices)):
raise IndexError()
return choice
except Exception:
print('Not a valid selection') | :param choices: Strings between which the user will make a choice
:type choices: list of strings
:param default: Number the index to be used as the default
:type default: int or None
:param str_choices: Strings to be used as aliases for the choices; must be of the same length as choices and each string must be unique
:type str_choices: list of strings
:param prompt: A custom prompt to be used
:type prompt: string
:param allow_mult: Whether "*" is a valid option to select all choices
:type allow_mult: boolean
:param more_choices: Whether "m" is a valid option to ask for more options
:type more_choices: boolean
:returns: The user's choice, i.e. one of a numbered index of choices (e.g. 0 for the first item), "*" (only if allow_mult is True), or "m" (only if more_results is True)
:rtype: int or string
:raises: :exc:`EOFError` to signify quitting the process
At most one of allow_mult and more_choices should be set to True. | https://github.com/dnanexus/dx-toolkit/blob/74befb53ad90fcf902d8983ae6d74580f402d619/src/python/dxpy/utils/resolver.py#L36-L99 |
dnanexus/dx-toolkit | src/python/dxpy/utils/resolver.py | object_exists_in_project | def object_exists_in_project(obj_id, proj_id):
'''
:param obj_id: object ID
:type obj_id: str
:param proj_id: project ID
:type proj_id: str
Returns True if the specified data object can be found in the specified
project.
'''
if obj_id is None:
raise ValueError("Expected obj_id to be a string")
if proj_id is None:
raise ValueError("Expected proj_id to be a string")
if not is_container_id(proj_id):
raise ValueError('Expected %r to be a container ID' % (proj_id,))
return try_call(dxpy.DXHTTPRequest, '/' + obj_id + '/describe', {'project': proj_id})['project'] == proj_id | python | def object_exists_in_project(obj_id, proj_id):
'''
:param obj_id: object ID
:type obj_id: str
:param proj_id: project ID
:type proj_id: str
Returns True if the specified data object can be found in the specified
project.
'''
if obj_id is None:
raise ValueError("Expected obj_id to be a string")
if proj_id is None:
raise ValueError("Expected proj_id to be a string")
if not is_container_id(proj_id):
raise ValueError('Expected %r to be a container ID' % (proj_id,))
return try_call(dxpy.DXHTTPRequest, '/' + obj_id + '/describe', {'project': proj_id})['project'] == proj_id | :param obj_id: object ID
:type obj_id: str
:param proj_id: project ID
:type proj_id: str
Returns True if the specified data object can be found in the specified
project. | https://github.com/dnanexus/dx-toolkit/blob/74befb53ad90fcf902d8983ae6d74580f402d619/src/python/dxpy/utils/resolver.py#L195-L211 |
dnanexus/dx-toolkit | src/python/dxpy/utils/resolver.py | get_last_pos_of_char | def get_last_pos_of_char(char, string):
'''
:param char: The character to find
:type char: string
:param string: The string in which to search for *char*
:type string: string
:returns: Index in *string* where *char* last appears (unescaped by a preceding "\\"), -1 if not found
:rtype: int
Finds the last occurrence of *char* in *string* in which *char* is
not present as an escaped character.
'''
pos = len(string)
while pos > 0:
pos = string[:pos].rfind(char)
if pos == -1:
return -1
num_backslashes = 0
test_index = pos - 1
while test_index >= 0 and string[test_index] == '\\':
num_backslashes += 1
test_index -= 1
if num_backslashes % 2 == 0:
return pos
return -1 | python | def get_last_pos_of_char(char, string):
'''
:param char: The character to find
:type char: string
:param string: The string in which to search for *char*
:type string: string
:returns: Index in *string* where *char* last appears (unescaped by a preceding "\\"), -1 if not found
:rtype: int
Finds the last occurrence of *char* in *string* in which *char* is
not present as an escaped character.
'''
pos = len(string)
while pos > 0:
pos = string[:pos].rfind(char)
if pos == -1:
return -1
num_backslashes = 0
test_index = pos - 1
while test_index >= 0 and string[test_index] == '\\':
num_backslashes += 1
test_index -= 1
if num_backslashes % 2 == 0:
return pos
return -1 | :param char: The character to find
:type char: string
:param string: The string in which to search for *char*
:type string: string
:returns: Index in *string* where *char* last appears (unescaped by a preceding "\\"), -1 if not found
:rtype: int
Finds the last occurrence of *char* in *string* in which *char* is
not present as an escaped character. | https://github.com/dnanexus/dx-toolkit/blob/74befb53ad90fcf902d8983ae6d74580f402d619/src/python/dxpy/utils/resolver.py#L233-L258 |
dnanexus/dx-toolkit | src/python/dxpy/utils/resolver.py | get_first_pos_of_char | def get_first_pos_of_char(char, string):
'''
:param char: The character to find
:type char: string
:param string: The string in which to search for *char*
:type string: string
:returns: Index in *string* where *char* last appears (unescaped by a preceding "\\"), -1 if not found
:rtype: int
Finds the first occurrence of *char* in *string* in which *char* is
not present as an escaped character.
'''
first_pos = -1
pos = len(string)
while pos > 0:
pos = string[:pos].rfind(char)
if pos == -1:
return first_pos
num_backslashes = 0
test_index = pos - 1
while test_index >= 0 and string[test_index] == '\\':
num_backslashes += 1
test_index -= 1
if num_backslashes % 2 == 0:
first_pos = pos
return first_pos | python | def get_first_pos_of_char(char, string):
'''
:param char: The character to find
:type char: string
:param string: The string in which to search for *char*
:type string: string
:returns: Index in *string* where *char* last appears (unescaped by a preceding "\\"), -1 if not found
:rtype: int
Finds the first occurrence of *char* in *string* in which *char* is
not present as an escaped character.
'''
first_pos = -1
pos = len(string)
while pos > 0:
pos = string[:pos].rfind(char)
if pos == -1:
return first_pos
num_backslashes = 0
test_index = pos - 1
while test_index >= 0 and string[test_index] == '\\':
num_backslashes += 1
test_index -= 1
if num_backslashes % 2 == 0:
first_pos = pos
return first_pos | :param char: The character to find
:type char: string
:param string: The string in which to search for *char*
:type string: string
:returns: Index in *string* where *char* last appears (unescaped by a preceding "\\"), -1 if not found
:rtype: int
Finds the first occurrence of *char* in *string* in which *char* is
not present as an escaped character. | https://github.com/dnanexus/dx-toolkit/blob/74befb53ad90fcf902d8983ae6d74580f402d619/src/python/dxpy/utils/resolver.py#L260-L286 |
dnanexus/dx-toolkit | src/python/dxpy/utils/resolver.py | split_unescaped | def split_unescaped(char, string, include_empty_strings=False):
'''
:param char: The character on which to split the string
:type char: string
:param string: The string to split
:type string: string
:returns: List of substrings of *string*
:rtype: list of strings
Splits *string* whenever *char* appears without an odd number of
backslashes ('\\') preceding it, discarding any empty string
elements.
'''
words = []
pos = len(string)
lastpos = pos
while pos >= 0:
pos = get_last_pos_of_char(char, string[:lastpos])
if pos >= 0:
if pos + 1 != lastpos or include_empty_strings:
words.append(string[pos + 1: lastpos])
lastpos = pos
if lastpos != 0 or include_empty_strings:
words.append(string[:lastpos])
words.reverse()
return words | python | def split_unescaped(char, string, include_empty_strings=False):
'''
:param char: The character on which to split the string
:type char: string
:param string: The string to split
:type string: string
:returns: List of substrings of *string*
:rtype: list of strings
Splits *string* whenever *char* appears without an odd number of
backslashes ('\\') preceding it, discarding any empty string
elements.
'''
words = []
pos = len(string)
lastpos = pos
while pos >= 0:
pos = get_last_pos_of_char(char, string[:lastpos])
if pos >= 0:
if pos + 1 != lastpos or include_empty_strings:
words.append(string[pos + 1: lastpos])
lastpos = pos
if lastpos != 0 or include_empty_strings:
words.append(string[:lastpos])
words.reverse()
return words | :param char: The character on which to split the string
:type char: string
:param string: The string to split
:type string: string
:returns: List of substrings of *string*
:rtype: list of strings
Splits *string* whenever *char* appears without an odd number of
backslashes ('\\') preceding it, discarding any empty string
elements. | https://github.com/dnanexus/dx-toolkit/blob/74befb53ad90fcf902d8983ae6d74580f402d619/src/python/dxpy/utils/resolver.py#L288-L314 |
dnanexus/dx-toolkit | src/python/dxpy/utils/resolver.py | clean_folder_path | def clean_folder_path(path, expected=None):
'''
:param path: A folder path to sanitize and parse
:type path: string
:param expected: Whether a folder ("folder"), a data object ("entity"), or either (None) is expected
:type expected: string or None
:returns: *folderpath*, *name*
Unescape and parse *path* as a folder path to possibly an entity
name. Consecutive unescaped forward slashes "/" are collapsed to
a single forward slash. If *expected* is "folder", *name* is
always returned as None. Otherwise, the string to the right of
the last unescaped "/" is considered a possible data object name
and returned as such.
'''
folders = split_unescaped('/', path)
if len(folders) == 0:
return '/', None
if expected == 'folder' or folders[-1] == '.' or folders[-1] == '..' or get_last_pos_of_char('/', path) == len(path) - 1:
entity_name = None
else:
entity_name = unescape_name_str(folders.pop())
sanitized_folders = []
for folder in folders:
if folder == '.':
pass
elif folder == '..':
if len(sanitized_folders) > 0:
sanitized_folders.pop()
else:
sanitized_folders.append(unescape_folder_str(folder))
return ('/' + '/'.join(sanitized_folders)), entity_name | python | def clean_folder_path(path, expected=None):
'''
:param path: A folder path to sanitize and parse
:type path: string
:param expected: Whether a folder ("folder"), a data object ("entity"), or either (None) is expected
:type expected: string or None
:returns: *folderpath*, *name*
Unescape and parse *path* as a folder path to possibly an entity
name. Consecutive unescaped forward slashes "/" are collapsed to
a single forward slash. If *expected* is "folder", *name* is
always returned as None. Otherwise, the string to the right of
the last unescaped "/" is considered a possible data object name
and returned as such.
'''
folders = split_unescaped('/', path)
if len(folders) == 0:
return '/', None
if expected == 'folder' or folders[-1] == '.' or folders[-1] == '..' or get_last_pos_of_char('/', path) == len(path) - 1:
entity_name = None
else:
entity_name = unescape_name_str(folders.pop())
sanitized_folders = []
for folder in folders:
if folder == '.':
pass
elif folder == '..':
if len(sanitized_folders) > 0:
sanitized_folders.pop()
else:
sanitized_folders.append(unescape_folder_str(folder))
return ('/' + '/'.join(sanitized_folders)), entity_name | :param path: A folder path to sanitize and parse
:type path: string
:param expected: Whether a folder ("folder"), a data object ("entity"), or either (None) is expected
:type expected: string or None
:returns: *folderpath*, *name*
Unescape and parse *path* as a folder path to possibly an entity
name. Consecutive unescaped forward slashes "/" are collapsed to
a single forward slash. If *expected* is "folder", *name* is
always returned as None. Otherwise, the string to the right of
the last unescaped "/" is considered a possible data object name
and returned as such. | https://github.com/dnanexus/dx-toolkit/blob/74befb53ad90fcf902d8983ae6d74580f402d619/src/python/dxpy/utils/resolver.py#L317-L354 |
dnanexus/dx-toolkit | src/python/dxpy/utils/resolver.py | resolve_container_id_or_name | def resolve_container_id_or_name(raw_string, is_error=False, multi=False):
'''
:param raw_string: A potential project or container ID or name
:type raw_string: string
:param is_error: Whether to raise an exception if the project or
container ID cannot be resolved
:type is_error: boolean
:returns: Project or container ID if found or else None
:rtype: string or None
:raises: :exc:`ResolutionError` if *is_error* is True and the
project or container could not be resolved
Unescapes and attempts to resolve *raw_string* to a project or
container ID.
'''
string = unescape_name_str(raw_string)
if is_container_id(string):
return ([string] if multi else string)
if string in cached_project_names:
return ([cached_project_names[string]] if multi else cached_project_names[string])
try:
results = list(dxpy.find_projects(name=string, describe=True, level='VIEW'))
except Exception as details:
raise ResolutionError(str(details))
if len(results) == 1:
cached_project_names[string] = results[0]['id']
return ([results[0]['id']] if multi else results[0]['id'])
elif len(results) == 0:
if is_error:
raise ResolutionError('Could not find a project named "' + string + '"')
return ([] if multi else None)
elif not multi:
if INTERACTIVE_CLI:
print('Found multiple projects with name "' + string + '"')
choice = pick(['{id} ({level})'.format(id=result['id'], level=result['level'])
for result in results])
return results[choice]['id']
else:
raise ResolutionError('Found multiple projects with name "' + string + '"; please use a project ID to specify the desired project')
else:
# len(results) > 1 and multi
return [result['id'] for result in results] | python | def resolve_container_id_or_name(raw_string, is_error=False, multi=False):
'''
:param raw_string: A potential project or container ID or name
:type raw_string: string
:param is_error: Whether to raise an exception if the project or
container ID cannot be resolved
:type is_error: boolean
:returns: Project or container ID if found or else None
:rtype: string or None
:raises: :exc:`ResolutionError` if *is_error* is True and the
project or container could not be resolved
Unescapes and attempts to resolve *raw_string* to a project or
container ID.
'''
string = unescape_name_str(raw_string)
if is_container_id(string):
return ([string] if multi else string)
if string in cached_project_names:
return ([cached_project_names[string]] if multi else cached_project_names[string])
try:
results = list(dxpy.find_projects(name=string, describe=True, level='VIEW'))
except Exception as details:
raise ResolutionError(str(details))
if len(results) == 1:
cached_project_names[string] = results[0]['id']
return ([results[0]['id']] if multi else results[0]['id'])
elif len(results) == 0:
if is_error:
raise ResolutionError('Could not find a project named "' + string + '"')
return ([] if multi else None)
elif not multi:
if INTERACTIVE_CLI:
print('Found multiple projects with name "' + string + '"')
choice = pick(['{id} ({level})'.format(id=result['id'], level=result['level'])
for result in results])
return results[choice]['id']
else:
raise ResolutionError('Found multiple projects with name "' + string + '"; please use a project ID to specify the desired project')
else:
# len(results) > 1 and multi
return [result['id'] for result in results] | :param raw_string: A potential project or container ID or name
:type raw_string: string
:param is_error: Whether to raise an exception if the project or
container ID cannot be resolved
:type is_error: boolean
:returns: Project or container ID if found or else None
:rtype: string or None
:raises: :exc:`ResolutionError` if *is_error* is True and the
project or container could not be resolved
Unescapes and attempts to resolve *raw_string* to a project or
container ID. | https://github.com/dnanexus/dx-toolkit/blob/74befb53ad90fcf902d8983ae6d74580f402d619/src/python/dxpy/utils/resolver.py#L357-L402 |
dnanexus/dx-toolkit | src/python/dxpy/utils/resolver.py | resolve_path | def resolve_path(path, expected=None, multi_projects=False, allow_empty_string=True):
'''
:param path: A path to a data object to attempt to resolve
:type path: string
:param expected: one of the following: "folder", "entity", or None
to indicate whether the expected path is a folder, a data
object, or either
:type expected: string or None
:returns: A tuple of 3 values: container_ID, folderpath, entity_name
:rtype: string, string, string
:raises: exc:`ResolutionError` if the project cannot be resolved by
name or the path is malformed
:param allow_empty_string: If false, a ResolutionError will be
raised if *path* is an empty string. Use this when resolving
the empty string could result in unexpected behavior.
:type allow_empty_string: boolean
Attempts to resolve *path* to a project or container ID, a folder
path, and a data object or folder name. This method will NOT
raise an exception if the specified folder or object does not
exist. This method is primarily for parsing purposes.
Returns one of the following:
(project, folder, maybe_name)
where
project is a container ID (non-null)
folder is a folder path
maybe_name is a string if the path could represent a folder or an object, or
maybe_name is None if the path could only represent a folder
OR
(maybe_project, None, object_id)
where
maybe_project is a container ID or None
object_id is a dataobject, app, or execution (specified by ID, not name)
OR
(job_id, None, output_name)
where
job_id and output_name are both non-null
'''
# TODO: callers that intend to obtain a data object probably won't be happy
# with an app or execution ID. Callers should probably have to specify
# whether they are okay with getting an execution ID or not.
# TODO: callers that are looking for a place to write data, rather than
# read it, probably won't be happy with receiving an object ID, or a
# JBOR. Callers should probably specify whether they are looking for an
# "LHS" expression or not.
if '_DX_FUSE' in os.environ:
from xattr import xattr
path = xattr(path)['project'] + ":" + xattr(path)['id']
if path == '' and not allow_empty_string:
raise ResolutionError('Cannot parse ""; expected the path to be a non-empty string')
path = _maybe_convert_stringified_dxlink(path)
# Easy case: ":"
if path == ':':
if dxpy.WORKSPACE_ID is None:
raise ResolutionError("Cannot resolve \":\": expected a project name or ID "
"to the left of the colon, or for a current project to be set")
return ([dxpy.WORKSPACE_ID] if multi_projects else dxpy.WORKSPACE_ID), '/', None
# Second easy case: empty string
if path == '':
if dxpy.WORKSPACE_ID is None:
raise ResolutionError('Expected a project name or ID to the left of a colon, '
'or for a current project to be set')
return ([dxpy.WORKSPACE_ID] if multi_projects else dxpy.WORKSPACE_ID), dxpy.config.get('DX_CLI_WD', '/'), None
# Third easy case: hash ID
if is_container_id(path):
return ([path] if multi_projects else path), '/', None
elif is_hashid(path):
return ([dxpy.WORKSPACE_ID] if multi_projects else dxpy.WORKSPACE_ID), None, path
# using a numerical sentinel value to indicate that it hasn't been
# set in case dxpy.WORKSPACE_ID is actually None
project = 0
folderpath = None
entity_name = None
wd = dxpy.config.get('DX_CLI_WD', u'/')
# Test for multiple colons
last_colon = get_last_pos_of_char(':', path)
if last_colon >= 0:
last_last_colon = get_last_pos_of_char(':', path[:last_colon])
if last_last_colon >= 0:
raise ResolutionError('Cannot parse "' + path + '" as a path; at most one unescaped colon can be present')
substrings = split_unescaped(':', path)
if len(substrings) == 2:
# One of the following:
# 1) job-id:fieldname
# 2) project-name-or-id:folderpath/to/possible/entity
if is_job_id(substrings[0]):
return ([substrings[0]] if multi_projects else substrings[0]), None, substrings[1]
if multi_projects:
project_ids = resolve_container_id_or_name(substrings[0], is_error=True, multi=True)
else:
project = resolve_container_id_or_name(substrings[0], is_error=True)
wd = '/'
elif get_last_pos_of_char(':', path) >= 0:
# :folderpath/to/possible/entity OR project-name-or-id:
# Colon is either at the beginning or at the end
wd = '/'
if path.startswith(':'):
if dxpy.WORKSPACE_ID is None:
raise ResolutionError('Cannot resolve "%s": expected a project name or ID to the left of the '
'colon, or for a current project to be set' % (path,))
project = dxpy.WORKSPACE_ID
else:
# One nonempty string to the left of a colon
project = resolve_container_id_or_name(substrings[0], is_error=True)
folderpath = '/'
else:
# One nonempty string, no colon present, do NOT interpret as
# project
project = dxpy.WORKSPACE_ID
if project is None:
raise ResolutionError('Cannot resolve "%s": expected the path to be qualified with a project name or ID, '
'and a colon; or for a current project to be set' % (path,))
# Determine folderpath and entity_name if necessary
if folderpath is None:
folderpath = substrings[-1]
folderpath, entity_name = clean_folder_path(('' if folderpath.startswith('/') else wd + '/') + folderpath, expected)
if multi_projects:
return (project_ids if project == 0 else [project]), folderpath, entity_name
else:
return project, folderpath, entity_name | python | def resolve_path(path, expected=None, multi_projects=False, allow_empty_string=True):
'''
:param path: A path to a data object to attempt to resolve
:type path: string
:param expected: one of the following: "folder", "entity", or None
to indicate whether the expected path is a folder, a data
object, or either
:type expected: string or None
:returns: A tuple of 3 values: container_ID, folderpath, entity_name
:rtype: string, string, string
:raises: exc:`ResolutionError` if the project cannot be resolved by
name or the path is malformed
:param allow_empty_string: If false, a ResolutionError will be
raised if *path* is an empty string. Use this when resolving
the empty string could result in unexpected behavior.
:type allow_empty_string: boolean
Attempts to resolve *path* to a project or container ID, a folder
path, and a data object or folder name. This method will NOT
raise an exception if the specified folder or object does not
exist. This method is primarily for parsing purposes.
Returns one of the following:
(project, folder, maybe_name)
where
project is a container ID (non-null)
folder is a folder path
maybe_name is a string if the path could represent a folder or an object, or
maybe_name is None if the path could only represent a folder
OR
(maybe_project, None, object_id)
where
maybe_project is a container ID or None
object_id is a dataobject, app, or execution (specified by ID, not name)
OR
(job_id, None, output_name)
where
job_id and output_name are both non-null
'''
# TODO: callers that intend to obtain a data object probably won't be happy
# with an app or execution ID. Callers should probably have to specify
# whether they are okay with getting an execution ID or not.
# TODO: callers that are looking for a place to write data, rather than
# read it, probably won't be happy with receiving an object ID, or a
# JBOR. Callers should probably specify whether they are looking for an
# "LHS" expression or not.
if '_DX_FUSE' in os.environ:
from xattr import xattr
path = xattr(path)['project'] + ":" + xattr(path)['id']
if path == '' and not allow_empty_string:
raise ResolutionError('Cannot parse ""; expected the path to be a non-empty string')
path = _maybe_convert_stringified_dxlink(path)
# Easy case: ":"
if path == ':':
if dxpy.WORKSPACE_ID is None:
raise ResolutionError("Cannot resolve \":\": expected a project name or ID "
"to the left of the colon, or for a current project to be set")
return ([dxpy.WORKSPACE_ID] if multi_projects else dxpy.WORKSPACE_ID), '/', None
# Second easy case: empty string
if path == '':
if dxpy.WORKSPACE_ID is None:
raise ResolutionError('Expected a project name or ID to the left of a colon, '
'or for a current project to be set')
return ([dxpy.WORKSPACE_ID] if multi_projects else dxpy.WORKSPACE_ID), dxpy.config.get('DX_CLI_WD', '/'), None
# Third easy case: hash ID
if is_container_id(path):
return ([path] if multi_projects else path), '/', None
elif is_hashid(path):
return ([dxpy.WORKSPACE_ID] if multi_projects else dxpy.WORKSPACE_ID), None, path
# using a numerical sentinel value to indicate that it hasn't been
# set in case dxpy.WORKSPACE_ID is actually None
project = 0
folderpath = None
entity_name = None
wd = dxpy.config.get('DX_CLI_WD', u'/')
# Test for multiple colons
last_colon = get_last_pos_of_char(':', path)
if last_colon >= 0:
last_last_colon = get_last_pos_of_char(':', path[:last_colon])
if last_last_colon >= 0:
raise ResolutionError('Cannot parse "' + path + '" as a path; at most one unescaped colon can be present')
substrings = split_unescaped(':', path)
if len(substrings) == 2:
# One of the following:
# 1) job-id:fieldname
# 2) project-name-or-id:folderpath/to/possible/entity
if is_job_id(substrings[0]):
return ([substrings[0]] if multi_projects else substrings[0]), None, substrings[1]
if multi_projects:
project_ids = resolve_container_id_or_name(substrings[0], is_error=True, multi=True)
else:
project = resolve_container_id_or_name(substrings[0], is_error=True)
wd = '/'
elif get_last_pos_of_char(':', path) >= 0:
# :folderpath/to/possible/entity OR project-name-or-id:
# Colon is either at the beginning or at the end
wd = '/'
if path.startswith(':'):
if dxpy.WORKSPACE_ID is None:
raise ResolutionError('Cannot resolve "%s": expected a project name or ID to the left of the '
'colon, or for a current project to be set' % (path,))
project = dxpy.WORKSPACE_ID
else:
# One nonempty string to the left of a colon
project = resolve_container_id_or_name(substrings[0], is_error=True)
folderpath = '/'
else:
# One nonempty string, no colon present, do NOT interpret as
# project
project = dxpy.WORKSPACE_ID
if project is None:
raise ResolutionError('Cannot resolve "%s": expected the path to be qualified with a project name or ID, '
'and a colon; or for a current project to be set' % (path,))
# Determine folderpath and entity_name if necessary
if folderpath is None:
folderpath = substrings[-1]
folderpath, entity_name = clean_folder_path(('' if folderpath.startswith('/') else wd + '/') + folderpath, expected)
if multi_projects:
return (project_ids if project == 0 else [project]), folderpath, entity_name
else:
return project, folderpath, entity_name | :param path: A path to a data object to attempt to resolve
:type path: string
:param expected: one of the following: "folder", "entity", or None
to indicate whether the expected path is a folder, a data
object, or either
:type expected: string or None
:returns: A tuple of 3 values: container_ID, folderpath, entity_name
:rtype: string, string, string
:raises: exc:`ResolutionError` if the project cannot be resolved by
name or the path is malformed
:param allow_empty_string: If false, a ResolutionError will be
raised if *path* is an empty string. Use this when resolving
the empty string could result in unexpected behavior.
:type allow_empty_string: boolean
Attempts to resolve *path* to a project or container ID, a folder
path, and a data object or folder name. This method will NOT
raise an exception if the specified folder or object does not
exist. This method is primarily for parsing purposes.
Returns one of the following:
(project, folder, maybe_name)
where
project is a container ID (non-null)
folder is a folder path
maybe_name is a string if the path could represent a folder or an object, or
maybe_name is None if the path could only represent a folder
OR
(maybe_project, None, object_id)
where
maybe_project is a container ID or None
object_id is a dataobject, app, or execution (specified by ID, not name)
OR
(job_id, None, output_name)
where
job_id and output_name are both non-null | https://github.com/dnanexus/dx-toolkit/blob/74befb53ad90fcf902d8983ae6d74580f402d619/src/python/dxpy/utils/resolver.py#L420-L557 |
dnanexus/dx-toolkit | src/python/dxpy/utils/resolver.py | _check_resolution_needed | def _check_resolution_needed(path, project, folderpath, entity_name, expected_classes=None, describe=True,
enclose_in_list=False):
"""
:param path: Path to the object that required resolution; propagated from
command-line
:type path: string
:param project: The potential project the entity belongs to
:type project: string
:param folderpath: Path to the entity
:type folderpath: string
:param entity_name: The name of the entity
:type entity_name: string
:param expected_classes: A list of expected classes the entity is allowed
to belong to if it is an ID (e.g. "record",
"file", "job"); if None, then entity_name may be
any data object class
:type expected_classes: list or None
:param describe: Dictionary of inputs to the describe API call; if
no describe input is provided (default value True), then
an empty mapping is passed to the describe API method
:type describe: dict or True
:param enclose_in_list: Whether the describe output is to be in the form
of a list (if False, the last return value is a
dictionary; if True, the last return value is a
list of one dictionary); it will only have an
effect if entity_name is a DX ID and is described
:type enclose_in_list: boolean
:returns: Whether or not the entity needs to be resolved with a more
general resolution method, the project, the folderpath, and the
entity name
:rtype: tuple of 4 elements
:raises: ResolutionError if the entity fails to be described
Attempts to resolve the entity to a folder or an object, and describes
the entity iff it is a DX ID of an expected class in the list
expected_classes.
Otherwise, determines whether or not more general resolution may be able
to resolve the entity.
If a more general resolution method is needed, then the return values will
look like:
(True, <project>, <folderpath>, <entity_name>)
If the entity is a DX ID, but is not one of the supplied expected
classes, then the return values will look like:
(False, None, None, None)
If the entity can be successfully described, then the return values will
look like:
<desc_output> ::= {"id": entity_name, "describe": {...}}
<desc_or_desc_list> ::= <desc_output> || [<desc_output>]
(False, <project>, <folderpath>, <desc_or_desc_list>)
If the entity may be a folder, then the return values will look like:
(False, <project>, <folderpath>, None)
TODO: Allow arbitrary flags for the describe mapping.
"""
if entity_name is None:
# Definitely a folder (or project)
# TODO: find a good way to check if folder exists and expected=folder
return False, project, folderpath, None
elif is_hashid(entity_name):
found_valid_class = True
if expected_classes is not None:
found_valid_class = False
for klass in expected_classes:
if entity_name.startswith(klass):
found_valid_class = True
if not found_valid_class:
return False, None, None, None
if describe is True:
describe = {}
# entity is an ID of a valid class, try to describe it
if 'project' not in describe:
if project != dxpy.WORKSPACE_ID:
describe['project'] = project
elif dxpy.WORKSPACE_ID is not None:
describe['project'] = dxpy.WORKSPACE_ID
try:
desc = dxpy.DXHTTPRequest('/' + entity_name + '/describe', describe)
desc = dxpy.append_underlying_workflow_describe(desc)
except Exception as details:
if 'project' in describe:
# Now try it without the hint
del describe['project']
try:
desc = dxpy.DXHTTPRequest('/' + entity_name + '/describe', describe)
except Exception as details2:
raise ResolutionError(str(details2))
else:
raise ResolutionError(str(details))
result = {"id": entity_name, "describe": desc}
if enclose_in_list:
return False, project, folderpath, [result]
else:
return False, project, folderpath, result
else:
# Need to resolve later
return True, project, folderpath, entity_name | python | def _check_resolution_needed(path, project, folderpath, entity_name, expected_classes=None, describe=True,
enclose_in_list=False):
"""
:param path: Path to the object that required resolution; propagated from
command-line
:type path: string
:param project: The potential project the entity belongs to
:type project: string
:param folderpath: Path to the entity
:type folderpath: string
:param entity_name: The name of the entity
:type entity_name: string
:param expected_classes: A list of expected classes the entity is allowed
to belong to if it is an ID (e.g. "record",
"file", "job"); if None, then entity_name may be
any data object class
:type expected_classes: list or None
:param describe: Dictionary of inputs to the describe API call; if
no describe input is provided (default value True), then
an empty mapping is passed to the describe API method
:type describe: dict or True
:param enclose_in_list: Whether the describe output is to be in the form
of a list (if False, the last return value is a
dictionary; if True, the last return value is a
list of one dictionary); it will only have an
effect if entity_name is a DX ID and is described
:type enclose_in_list: boolean
:returns: Whether or not the entity needs to be resolved with a more
general resolution method, the project, the folderpath, and the
entity name
:rtype: tuple of 4 elements
:raises: ResolutionError if the entity fails to be described
Attempts to resolve the entity to a folder or an object, and describes
the entity iff it is a DX ID of an expected class in the list
expected_classes.
Otherwise, determines whether or not more general resolution may be able
to resolve the entity.
If a more general resolution method is needed, then the return values will
look like:
(True, <project>, <folderpath>, <entity_name>)
If the entity is a DX ID, but is not one of the supplied expected
classes, then the return values will look like:
(False, None, None, None)
If the entity can be successfully described, then the return values will
look like:
<desc_output> ::= {"id": entity_name, "describe": {...}}
<desc_or_desc_list> ::= <desc_output> || [<desc_output>]
(False, <project>, <folderpath>, <desc_or_desc_list>)
If the entity may be a folder, then the return values will look like:
(False, <project>, <folderpath>, None)
TODO: Allow arbitrary flags for the describe mapping.
"""
if entity_name is None:
# Definitely a folder (or project)
# TODO: find a good way to check if folder exists and expected=folder
return False, project, folderpath, None
elif is_hashid(entity_name):
found_valid_class = True
if expected_classes is not None:
found_valid_class = False
for klass in expected_classes:
if entity_name.startswith(klass):
found_valid_class = True
if not found_valid_class:
return False, None, None, None
if describe is True:
describe = {}
# entity is an ID of a valid class, try to describe it
if 'project' not in describe:
if project != dxpy.WORKSPACE_ID:
describe['project'] = project
elif dxpy.WORKSPACE_ID is not None:
describe['project'] = dxpy.WORKSPACE_ID
try:
desc = dxpy.DXHTTPRequest('/' + entity_name + '/describe', describe)
desc = dxpy.append_underlying_workflow_describe(desc)
except Exception as details:
if 'project' in describe:
# Now try it without the hint
del describe['project']
try:
desc = dxpy.DXHTTPRequest('/' + entity_name + '/describe', describe)
except Exception as details2:
raise ResolutionError(str(details2))
else:
raise ResolutionError(str(details))
result = {"id": entity_name, "describe": desc}
if enclose_in_list:
return False, project, folderpath, [result]
else:
return False, project, folderpath, result
else:
# Need to resolve later
return True, project, folderpath, entity_name | :param path: Path to the object that required resolution; propagated from
command-line
:type path: string
:param project: The potential project the entity belongs to
:type project: string
:param folderpath: Path to the entity
:type folderpath: string
:param entity_name: The name of the entity
:type entity_name: string
:param expected_classes: A list of expected classes the entity is allowed
to belong to if it is an ID (e.g. "record",
"file", "job"); if None, then entity_name may be
any data object class
:type expected_classes: list or None
:param describe: Dictionary of inputs to the describe API call; if
no describe input is provided (default value True), then
an empty mapping is passed to the describe API method
:type describe: dict or True
:param enclose_in_list: Whether the describe output is to be in the form
of a list (if False, the last return value is a
dictionary; if True, the last return value is a
list of one dictionary); it will only have an
effect if entity_name is a DX ID and is described
:type enclose_in_list: boolean
:returns: Whether or not the entity needs to be resolved with a more
general resolution method, the project, the folderpath, and the
entity name
:rtype: tuple of 4 elements
:raises: ResolutionError if the entity fails to be described
Attempts to resolve the entity to a folder or an object, and describes
the entity iff it is a DX ID of an expected class in the list
expected_classes.
Otherwise, determines whether or not more general resolution may be able
to resolve the entity.
If a more general resolution method is needed, then the return values will
look like:
(True, <project>, <folderpath>, <entity_name>)
If the entity is a DX ID, but is not one of the supplied expected
classes, then the return values will look like:
(False, None, None, None)
If the entity can be successfully described, then the return values will
look like:
<desc_output> ::= {"id": entity_name, "describe": {...}}
<desc_or_desc_list> ::= <desc_output> || [<desc_output>]
(False, <project>, <folderpath>, <desc_or_desc_list>)
If the entity may be a folder, then the return values will look like:
(False, <project>, <folderpath>, None)
TODO: Allow arbitrary flags for the describe mapping. | https://github.com/dnanexus/dx-toolkit/blob/74befb53ad90fcf902d8983ae6d74580f402d619/src/python/dxpy/utils/resolver.py#L615-L718 |
dnanexus/dx-toolkit | src/python/dxpy/utils/resolver.py | _resolve_folder | def _resolve_folder(project, parent_folder, folder_name):
"""
:param project: The project that the folder belongs to
:type project: string
:param parent_folder: Full path to the parent folder that contains
folder_name
:type parent_folder: string
:param folder_name: Name of the folder
:type folder_name: string
:returns: The path to folder_name, if it exists, in the form of
"<parent_folder>/<folder_name>"
:rtype: string
:raises: ResolutionError if folder_name is not a folder, or if
folder_name points to a folder that does not exist
Attempts to resolve folder_name at location parent_folder in project.
"""
if '/' in folder_name:
# Then there's no way it's supposed to be a folder
raise ResolutionError('Object of name ' + str(folder_name) + ' could not be resolved in folder ' +
str(parent_folder) + ' of project ID ' + str(project))
possible_folder, _skip = clean_folder_path(parent_folder + '/' + folder_name, 'folder')
if not check_folder_exists(project, parent_folder, folder_name):
raise ResolutionError('Unable to resolve "' + folder_name +
'" to a data object or folder name in \'' + parent_folder + "'")
return possible_folder | python | def _resolve_folder(project, parent_folder, folder_name):
"""
:param project: The project that the folder belongs to
:type project: string
:param parent_folder: Full path to the parent folder that contains
folder_name
:type parent_folder: string
:param folder_name: Name of the folder
:type folder_name: string
:returns: The path to folder_name, if it exists, in the form of
"<parent_folder>/<folder_name>"
:rtype: string
:raises: ResolutionError if folder_name is not a folder, or if
folder_name points to a folder that does not exist
Attempts to resolve folder_name at location parent_folder in project.
"""
if '/' in folder_name:
# Then there's no way it's supposed to be a folder
raise ResolutionError('Object of name ' + str(folder_name) + ' could not be resolved in folder ' +
str(parent_folder) + ' of project ID ' + str(project))
possible_folder, _skip = clean_folder_path(parent_folder + '/' + folder_name, 'folder')
if not check_folder_exists(project, parent_folder, folder_name):
raise ResolutionError('Unable to resolve "' + folder_name +
'" to a data object or folder name in \'' + parent_folder + "'")
return possible_folder | :param project: The project that the folder belongs to
:type project: string
:param parent_folder: Full path to the parent folder that contains
folder_name
:type parent_folder: string
:param folder_name: Name of the folder
:type folder_name: string
:returns: The path to folder_name, if it exists, in the form of
"<parent_folder>/<folder_name>"
:rtype: string
:raises: ResolutionError if folder_name is not a folder, or if
folder_name points to a folder that does not exist
Attempts to resolve folder_name at location parent_folder in project. | https://github.com/dnanexus/dx-toolkit/blob/74befb53ad90fcf902d8983ae6d74580f402d619/src/python/dxpy/utils/resolver.py#L721-L747 |
dnanexus/dx-toolkit | src/python/dxpy/utils/resolver.py | _validate_resolution_output_length | def _validate_resolution_output_length(path, entity_name, results, allow_mult=False, all_mult=False,
ask_to_resolve=True):
"""
:param path: Path to the object that required resolution; propagated from
command-line
:type path: string
:param entity_name: Name of the object
:type entity_name: string
:param results: Result of resolution; non-empty list of object
specifications (each specification is a dictionary with
keys "project" and "id")
:type results: list of dictionaries
:param allow_mult: If True, it is okay to choose from multiple results
of a single resolved object, or return all results
found; if False, raise an error if multiple results
are found
:type allow_mult: boolean
:param all_mult: If True, return all results if multiple results are
found for a single resolved object; if False, user needs
to choose a single result if multiple are found; the value
of all_mult only has an effect if allow_mult is True)
:type all_mult: boolean
:param ask_to_resolve: Whether picking may be necessary (if True, a
list is returned; if False, only one result
is returned); if specified as True, then all
results will be returned, regardless of the
values of allow_mult and all_mult
:type ask_to_resolve: boolean
:returns: The results of resolving entity_name, expected to be of the
following form:
<resolved_object> # If only one result is present or the user
# is able to select from multiple
OR
[<resolved_object>, ...] # If multiple results are present and
# it is allowed
where <resolved_object> is of the following form:
{"project": <project_id>, "id": <object_id>}
:rtype: dict or list of dicts
:raises: ValueError if results is empty
:raises: ResolutionError if too many results are found and the user is
not in interactive mode and cannot select one
Precondition: results must be a nonempty list
Validates length of results.
If there are multiple results found and the user is in interactive mode,
then the user will be prompted to select a single result to be returned.
"""
if len(results) == 0:
raise ValueError("'results' must be nonempty.")
# Caller wants ALL results, so return the entire results list
# At this point, do not care about the values of allow_mult or all_mult
if not ask_to_resolve:
return results
if len(results) > 1:
# The other way the caller can specify it wants all results is by setting
# allow_mult to be True and allowing all_mult to be True (or if the object name is a glob pattern)
if allow_mult and (all_mult or is_glob_pattern(entity_name)):
return results
if INTERACTIVE_CLI:
print('The given path "' + path + '" resolves to the following data objects:')
if any(['describe' not in result for result in results]):
# findDataObject API call must be made to get 'describe' mappings
project, folderpath, entity_name = resolve_path(path, expected='entity')
results = _resolve_global_entity(project, folderpath, entity_name)
choice = pick([get_ls_l_desc(result['describe']) for result in results],
allow_mult=allow_mult)
if allow_mult and choice == '*':
return results
else:
return [results[choice]] if allow_mult else results[choice]
else:
raise ResolutionError('The given path "' + path + '" resolves to ' +
str(len(results)) + ' data objects')
else:
return [results[0]] if allow_mult else results[0] | python | def _validate_resolution_output_length(path, entity_name, results, allow_mult=False, all_mult=False,
ask_to_resolve=True):
"""
:param path: Path to the object that required resolution; propagated from
command-line
:type path: string
:param entity_name: Name of the object
:type entity_name: string
:param results: Result of resolution; non-empty list of object
specifications (each specification is a dictionary with
keys "project" and "id")
:type results: list of dictionaries
:param allow_mult: If True, it is okay to choose from multiple results
of a single resolved object, or return all results
found; if False, raise an error if multiple results
are found
:type allow_mult: boolean
:param all_mult: If True, return all results if multiple results are
found for a single resolved object; if False, user needs
to choose a single result if multiple are found; the value
of all_mult only has an effect if allow_mult is True)
:type all_mult: boolean
:param ask_to_resolve: Whether picking may be necessary (if True, a
list is returned; if False, only one result
is returned); if specified as True, then all
results will be returned, regardless of the
values of allow_mult and all_mult
:type ask_to_resolve: boolean
:returns: The results of resolving entity_name, expected to be of the
following form:
<resolved_object> # If only one result is present or the user
# is able to select from multiple
OR
[<resolved_object>, ...] # If multiple results are present and
# it is allowed
where <resolved_object> is of the following form:
{"project": <project_id>, "id": <object_id>}
:rtype: dict or list of dicts
:raises: ValueError if results is empty
:raises: ResolutionError if too many results are found and the user is
not in interactive mode and cannot select one
Precondition: results must be a nonempty list
Validates length of results.
If there are multiple results found and the user is in interactive mode,
then the user will be prompted to select a single result to be returned.
"""
if len(results) == 0:
raise ValueError("'results' must be nonempty.")
# Caller wants ALL results, so return the entire results list
# At this point, do not care about the values of allow_mult or all_mult
if not ask_to_resolve:
return results
if len(results) > 1:
# The other way the caller can specify it wants all results is by setting
# allow_mult to be True and allowing all_mult to be True (or if the object name is a glob pattern)
if allow_mult and (all_mult or is_glob_pattern(entity_name)):
return results
if INTERACTIVE_CLI:
print('The given path "' + path + '" resolves to the following data objects:')
if any(['describe' not in result for result in results]):
# findDataObject API call must be made to get 'describe' mappings
project, folderpath, entity_name = resolve_path(path, expected='entity')
results = _resolve_global_entity(project, folderpath, entity_name)
choice = pick([get_ls_l_desc(result['describe']) for result in results],
allow_mult=allow_mult)
if allow_mult and choice == '*':
return results
else:
return [results[choice]] if allow_mult else results[choice]
else:
raise ResolutionError('The given path "' + path + '" resolves to ' +
str(len(results)) + ' data objects')
else:
return [results[0]] if allow_mult else results[0] | :param path: Path to the object that required resolution; propagated from
command-line
:type path: string
:param entity_name: Name of the object
:type entity_name: string
:param results: Result of resolution; non-empty list of object
specifications (each specification is a dictionary with
keys "project" and "id")
:type results: list of dictionaries
:param allow_mult: If True, it is okay to choose from multiple results
of a single resolved object, or return all results
found; if False, raise an error if multiple results
are found
:type allow_mult: boolean
:param all_mult: If True, return all results if multiple results are
found for a single resolved object; if False, user needs
to choose a single result if multiple are found; the value
of all_mult only has an effect if allow_mult is True)
:type all_mult: boolean
:param ask_to_resolve: Whether picking may be necessary (if True, a
list is returned; if False, only one result
is returned); if specified as True, then all
results will be returned, regardless of the
values of allow_mult and all_mult
:type ask_to_resolve: boolean
:returns: The results of resolving entity_name, expected to be of the
following form:
<resolved_object> # If only one result is present or the user
# is able to select from multiple
OR
[<resolved_object>, ...] # If multiple results are present and
# it is allowed
where <resolved_object> is of the following form:
{"project": <project_id>, "id": <object_id>}
:rtype: dict or list of dicts
:raises: ValueError if results is empty
:raises: ResolutionError if too many results are found and the user is
not in interactive mode and cannot select one
Precondition: results must be a nonempty list
Validates length of results.
If there are multiple results found and the user is in interactive mode,
then the user will be prompted to select a single result to be returned. | https://github.com/dnanexus/dx-toolkit/blob/74befb53ad90fcf902d8983ae6d74580f402d619/src/python/dxpy/utils/resolver.py#L750-L828 |
dnanexus/dx-toolkit | src/python/dxpy/utils/resolver.py | _resolve_global_entity | def _resolve_global_entity(project_or_job_id, folderpath, entity_name, describe=True, visibility="either"):
"""
:param project_or_job_id: The project ID to which the entity belongs
(then the entity is an existing data object),
or the job ID to which the entity belongs
(then the entity is a job-based object
reference to an object that may not exist yet)
:type project_or_job_id: string
:param folderpath: Full path to the object (parsed from command line)
:type folderpath: string
:param entity_name: Name of the object
:type entity_name: string
:param describe: Input mapping used to describe the job's project if
project_or_job_id is a job ID, or True if the input
mapping is to be empty
:type describe: dict or True
:param visibility: The expected visibility of the entity ("either",
"hidden", or "visible"); to be used in resolution
:type visibility: string
:returns: The results obtained from attempting to resolve the entity;
the expected format of the return value is described below
:rtype: list
:raises: ResolutionError if dxpy.find_data_objects throws an error
If project_or_job_id is a job ID, then return value will be like:
[{"id": ..., "describe": {...}}, ...]
Otherwise, the return value will be like:
[{"id": ..., "project": ..., "describe": {...}}, ...]
Note that if the entity is successfully resolved, then the "describe"
key will be in the dictionary if and only if a nonempty describe
mapping was provided.
TODO: Inspect entity_name and conditionally treat it as a "glob" pattern.
TODO: Callers should specify exactly what fields they want, and then
hopefully we can avoid having a default set of fields that may be very
expensive
"""
if is_job_id(project_or_job_id):
if describe is True:
describe = {}
# The following function call will raise a ResolutionError if no results
# could be found.
# If the call is successful, then the project will be incorporated into the
# "describe" mapping of the returned dictionaries.
return resolve_job_ref(project_or_job_id, entity_name, describe=describe)
else:
try:
return list(dxpy.find_data_objects(project=project_or_job_id,
folder=folderpath,
name=entity_name,
name_mode='glob',
recurse=False,
describe=describe,
visibility=visibility))
except Exception as details:
raise ResolutionError(str(details)) | python | def _resolve_global_entity(project_or_job_id, folderpath, entity_name, describe=True, visibility="either"):
"""
:param project_or_job_id: The project ID to which the entity belongs
(then the entity is an existing data object),
or the job ID to which the entity belongs
(then the entity is a job-based object
reference to an object that may not exist yet)
:type project_or_job_id: string
:param folderpath: Full path to the object (parsed from command line)
:type folderpath: string
:param entity_name: Name of the object
:type entity_name: string
:param describe: Input mapping used to describe the job's project if
project_or_job_id is a job ID, or True if the input
mapping is to be empty
:type describe: dict or True
:param visibility: The expected visibility of the entity ("either",
"hidden", or "visible"); to be used in resolution
:type visibility: string
:returns: The results obtained from attempting to resolve the entity;
the expected format of the return value is described below
:rtype: list
:raises: ResolutionError if dxpy.find_data_objects throws an error
If project_or_job_id is a job ID, then return value will be like:
[{"id": ..., "describe": {...}}, ...]
Otherwise, the return value will be like:
[{"id": ..., "project": ..., "describe": {...}}, ...]
Note that if the entity is successfully resolved, then the "describe"
key will be in the dictionary if and only if a nonempty describe
mapping was provided.
TODO: Inspect entity_name and conditionally treat it as a "glob" pattern.
TODO: Callers should specify exactly what fields they want, and then
hopefully we can avoid having a default set of fields that may be very
expensive
"""
if is_job_id(project_or_job_id):
if describe is True:
describe = {}
# The following function call will raise a ResolutionError if no results
# could be found.
# If the call is successful, then the project will be incorporated into the
# "describe" mapping of the returned dictionaries.
return resolve_job_ref(project_or_job_id, entity_name, describe=describe)
else:
try:
return list(dxpy.find_data_objects(project=project_or_job_id,
folder=folderpath,
name=entity_name,
name_mode='glob',
recurse=False,
describe=describe,
visibility=visibility))
except Exception as details:
raise ResolutionError(str(details)) | :param project_or_job_id: The project ID to which the entity belongs
(then the entity is an existing data object),
or the job ID to which the entity belongs
(then the entity is a job-based object
reference to an object that may not exist yet)
:type project_or_job_id: string
:param folderpath: Full path to the object (parsed from command line)
:type folderpath: string
:param entity_name: Name of the object
:type entity_name: string
:param describe: Input mapping used to describe the job's project if
project_or_job_id is a job ID, or True if the input
mapping is to be empty
:type describe: dict or True
:param visibility: The expected visibility of the entity ("either",
"hidden", or "visible"); to be used in resolution
:type visibility: string
:returns: The results obtained from attempting to resolve the entity;
the expected format of the return value is described below
:rtype: list
:raises: ResolutionError if dxpy.find_data_objects throws an error
If project_or_job_id is a job ID, then return value will be like:
[{"id": ..., "describe": {...}}, ...]
Otherwise, the return value will be like:
[{"id": ..., "project": ..., "describe": {...}}, ...]
Note that if the entity is successfully resolved, then the "describe"
key will be in the dictionary if and only if a nonempty describe
mapping was provided.
TODO: Inspect entity_name and conditionally treat it as a "glob" pattern.
TODO: Callers should specify exactly what fields they want, and then
hopefully we can avoid having a default set of fields that may be very
expensive | https://github.com/dnanexus/dx-toolkit/blob/74befb53ad90fcf902d8983ae6d74580f402d619/src/python/dxpy/utils/resolver.py#L831-L888 |
dnanexus/dx-toolkit | src/python/dxpy/utils/resolver.py | _format_resolution_output | def _format_resolution_output(path, project, folderpath, entity_name, result):
"""
:param path: Path to the object that required resolution; propagated from
command-line
:type path: string
:param project: The potential project the entity belongs to
:type project: string
:param folderpath: Path to the entity
:type folderpath: string
:param entity_name: The name of the entity
:type entity_name: string
:param result: The result of resolving entity_name
:type result: list of dictionaries
:returns: The validated resolution output
:rtype: dictionary
Formats the output from the resolution of entity_name based on the number
of resolved entities.
If no results are found and entity_name can be resolved to a folder, then
the return value will look like:
{"project": <project>, "folder": <folder>, "name": None}
If exactly one result is found, then the return value will look like:
{"project": <project>, "folder": <folder>, "name": {"id": <id>,
"project": <project>}}
OR
{"project": None, "folder": <folder>, "name": {"id": <id>,
"project": <project>}}
Else, the return value will look like:
{"project": None, "folder": None, "name": None}
"""
try:
if len(result) == 0:
folder = _resolve_folder(project, folderpath, entity_name)
return {"project": project, "folder": folder, "name": None}
else:
validated_results = _validate_resolution_output_length(path, entity_name, result)
return {"project": None if is_job_id(project) else project,
"folder": None, "name": validated_results}
except ResolutionError:
return {"project": None, "folder": None, "name": None} | python | def _format_resolution_output(path, project, folderpath, entity_name, result):
"""
:param path: Path to the object that required resolution; propagated from
command-line
:type path: string
:param project: The potential project the entity belongs to
:type project: string
:param folderpath: Path to the entity
:type folderpath: string
:param entity_name: The name of the entity
:type entity_name: string
:param result: The result of resolving entity_name
:type result: list of dictionaries
:returns: The validated resolution output
:rtype: dictionary
Formats the output from the resolution of entity_name based on the number
of resolved entities.
If no results are found and entity_name can be resolved to a folder, then
the return value will look like:
{"project": <project>, "folder": <folder>, "name": None}
If exactly one result is found, then the return value will look like:
{"project": <project>, "folder": <folder>, "name": {"id": <id>,
"project": <project>}}
OR
{"project": None, "folder": <folder>, "name": {"id": <id>,
"project": <project>}}
Else, the return value will look like:
{"project": None, "folder": None, "name": None}
"""
try:
if len(result) == 0:
folder = _resolve_folder(project, folderpath, entity_name)
return {"project": project, "folder": folder, "name": None}
else:
validated_results = _validate_resolution_output_length(path, entity_name, result)
return {"project": None if is_job_id(project) else project,
"folder": None, "name": validated_results}
except ResolutionError:
return {"project": None, "folder": None, "name": None} | :param path: Path to the object that required resolution; propagated from
command-line
:type path: string
:param project: The potential project the entity belongs to
:type project: string
:param folderpath: Path to the entity
:type folderpath: string
:param entity_name: The name of the entity
:type entity_name: string
:param result: The result of resolving entity_name
:type result: list of dictionaries
:returns: The validated resolution output
:rtype: dictionary
Formats the output from the resolution of entity_name based on the number
of resolved entities.
If no results are found and entity_name can be resolved to a folder, then
the return value will look like:
{"project": <project>, "folder": <folder>, "name": None}
If exactly one result is found, then the return value will look like:
{"project": <project>, "folder": <folder>, "name": {"id": <id>,
"project": <project>}}
OR
{"project": None, "folder": <folder>, "name": {"id": <id>,
"project": <project>}}
Else, the return value will look like:
{"project": None, "folder": None, "name": None} | https://github.com/dnanexus/dx-toolkit/blob/74befb53ad90fcf902d8983ae6d74580f402d619/src/python/dxpy/utils/resolver.py#L891-L933 |
dnanexus/dx-toolkit | src/python/dxpy/utils/resolver.py | resolve_multiple_existing_paths | def resolve_multiple_existing_paths(paths):
"""
:param paths: A list of paths to items that need to be resolved
:type paths: list
:returns: A dictionary mapping a specified path to either its resolved
object or Nones, if the object could not be resolved
:rtype: dict
For each input given in paths, attempts to resolve the path, and returns
the resolved object in a dictionary.
The return value will look like:
{<path1>: <resolved_object1>, <path2>: <resolved_object2>,...}
If entity_id is a DX ID that can be described,
<resolved_object*> ::= {"project": None,
"folder": None,
"name": {"id": <id>,
"describe": <describe_output>}}
Else if a general resolution (or search) method will be used to resolve
the entity,
<resolved_object*> ::= {"project": <project>,
"folder": None,
"name": {"project": <project>,
"id": <resolved_id>}}
Else if <project> is a job ID,
<resolved_object*> ::= {"project": None,
"folder": None,
"name": {"project": <project>,
"id": <resolved_id>}}
Else if the path refers to a folder instead of a data object,
<resolved_object*> ::= {"project": <project>,
"folder": <folder>,
"name": None}
Else if description or resolution fails,
<resolved_object*> ::= {"project": None, "folder": None, "name": None}
"""
done_objects = {} # Return value
to_resolve_in_batch_paths = [] # Paths to resolve
to_resolve_in_batch_inputs = [] # Project, folderpath, and entity name
for path in paths:
project, folderpath, entity_name = resolve_path(path, expected='entity')
try:
must_resolve, project, folderpath, entity_name = _check_resolution_needed(
path, project, folderpath, entity_name)
except:
must_resolve = False
if must_resolve:
if is_glob_pattern(entity_name):
# TODO: Must call findDataObjects because resolveDataObjects does not support glob patterns
try:
find_results = _resolve_global_entity(project, folderpath, entity_name)
done_objects[path] = _format_resolution_output(path, project, folderpath, entity_name,
find_results)
except ResolutionError:
# Catches any ResolutionError thrown by _resolve_global_entity
done_objects[path] = {"project": None, "folder": None, "name": None}
else:
# Prepare batch call for resolveDataObjects
to_resolve_in_batch_paths.append(path)
to_resolve_in_batch_inputs.append({"project": project, "folder": folderpath, "name": entity_name})
else:
# No need to resolve
done_objects[path] = {"project": project, "folder": folderpath, "name": entity_name}
# Call resolveDataObjects
resolution_results = dxpy.resolve_data_objects(to_resolve_in_batch_inputs)
for path, inputs, result in zip(to_resolve_in_batch_paths, to_resolve_in_batch_inputs,
resolution_results):
done_objects[path] = _format_resolution_output(path, inputs["project"], inputs["folder"], inputs["name"],
result)
return done_objects | python | def resolve_multiple_existing_paths(paths):
"""
:param paths: A list of paths to items that need to be resolved
:type paths: list
:returns: A dictionary mapping a specified path to either its resolved
object or Nones, if the object could not be resolved
:rtype: dict
For each input given in paths, attempts to resolve the path, and returns
the resolved object in a dictionary.
The return value will look like:
{<path1>: <resolved_object1>, <path2>: <resolved_object2>,...}
If entity_id is a DX ID that can be described,
<resolved_object*> ::= {"project": None,
"folder": None,
"name": {"id": <id>,
"describe": <describe_output>}}
Else if a general resolution (or search) method will be used to resolve
the entity,
<resolved_object*> ::= {"project": <project>,
"folder": None,
"name": {"project": <project>,
"id": <resolved_id>}}
Else if <project> is a job ID,
<resolved_object*> ::= {"project": None,
"folder": None,
"name": {"project": <project>,
"id": <resolved_id>}}
Else if the path refers to a folder instead of a data object,
<resolved_object*> ::= {"project": <project>,
"folder": <folder>,
"name": None}
Else if description or resolution fails,
<resolved_object*> ::= {"project": None, "folder": None, "name": None}
"""
done_objects = {} # Return value
to_resolve_in_batch_paths = [] # Paths to resolve
to_resolve_in_batch_inputs = [] # Project, folderpath, and entity name
for path in paths:
project, folderpath, entity_name = resolve_path(path, expected='entity')
try:
must_resolve, project, folderpath, entity_name = _check_resolution_needed(
path, project, folderpath, entity_name)
except:
must_resolve = False
if must_resolve:
if is_glob_pattern(entity_name):
# TODO: Must call findDataObjects because resolveDataObjects does not support glob patterns
try:
find_results = _resolve_global_entity(project, folderpath, entity_name)
done_objects[path] = _format_resolution_output(path, project, folderpath, entity_name,
find_results)
except ResolutionError:
# Catches any ResolutionError thrown by _resolve_global_entity
done_objects[path] = {"project": None, "folder": None, "name": None}
else:
# Prepare batch call for resolveDataObjects
to_resolve_in_batch_paths.append(path)
to_resolve_in_batch_inputs.append({"project": project, "folder": folderpath, "name": entity_name})
else:
# No need to resolve
done_objects[path] = {"project": project, "folder": folderpath, "name": entity_name}
# Call resolveDataObjects
resolution_results = dxpy.resolve_data_objects(to_resolve_in_batch_inputs)
for path, inputs, result in zip(to_resolve_in_batch_paths, to_resolve_in_batch_inputs,
resolution_results):
done_objects[path] = _format_resolution_output(path, inputs["project"], inputs["folder"], inputs["name"],
result)
return done_objects | :param paths: A list of paths to items that need to be resolved
:type paths: list
:returns: A dictionary mapping a specified path to either its resolved
object or Nones, if the object could not be resolved
:rtype: dict
For each input given in paths, attempts to resolve the path, and returns
the resolved object in a dictionary.
The return value will look like:
{<path1>: <resolved_object1>, <path2>: <resolved_object2>,...}
If entity_id is a DX ID that can be described,
<resolved_object*> ::= {"project": None,
"folder": None,
"name": {"id": <id>,
"describe": <describe_output>}}
Else if a general resolution (or search) method will be used to resolve
the entity,
<resolved_object*> ::= {"project": <project>,
"folder": None,
"name": {"project": <project>,
"id": <resolved_id>}}
Else if <project> is a job ID,
<resolved_object*> ::= {"project": None,
"folder": None,
"name": {"project": <project>,
"id": <resolved_id>}}
Else if the path refers to a folder instead of a data object,
<resolved_object*> ::= {"project": <project>,
"folder": <folder>,
"name": None}
Else if description or resolution fails,
<resolved_object*> ::= {"project": None, "folder": None, "name": None} | https://github.com/dnanexus/dx-toolkit/blob/74befb53ad90fcf902d8983ae6d74580f402d619/src/python/dxpy/utils/resolver.py#L936-L1012 |
dnanexus/dx-toolkit | src/python/dxpy/utils/resolver.py | resolve_existing_path | def resolve_existing_path(path, expected=None, ask_to_resolve=True, expected_classes=None, allow_mult=False,
describe=True, all_mult=False, allow_empty_string=True, visibility="either"):
'''
:param expected: one of the following: "folder", "entity", or None to indicate
whether the expected path is a folder, a data object, or either
:type expected: string or None
:param ask_to_resolve: Whether picking may be necessary (if true, a list is returned; if false, only one result is returned)
:type ask_to_resolve: boolean
:param expected_classes: A list of expected classes the entity is allowed
to belong to if it is an ID (e.g. "record",
"file", "job"); if None, then entity_name may be
any data object class
:type expected_classes: list or None
:param allow_mult: Whether to allow the user to select multiple results from the same path
:type allow_mult: boolean
:param describe: Input hash to describe call for the results, or True if no describe input
is to be provided
:type describe: dict or True
:param all_mult: Whether to return all matching results without prompting (only applicable if allow_mult == True)
:type all_mult: boolean
:returns: A LIST of results when ask_to_resolve is False or allow_mult is True
:raises: :exc:`ResolutionError` if the request path was invalid, or a single result was requested and input is not a TTY
:param allow_empty_string: If false, a ResolutionError will be raised if *path* is an empty string. Use this when resolving the empty string could result in unexpected behavior.
:type allow_empty_string: boolean
:param visibility: The visibility expected ("either", "hidden", or "visible")
:type visibility: string
Returns either a list of results or a single result (depending on
how many is expected; if only one, then an interactive picking of
a choice will be initiated if input is a tty, or else throw an error).
TODO: Always treats the path as a glob pattern.
Output is of the form {"id": id, "describe": describe hash} a list
of those
TODO: Callers should specify exactly what fields they want, and then
hopefully we can avoid having a default set of fields that may be very
expensive
NOTE: if expected_classes is provided and conflicts with the class
of the hash ID, it will return None for all fields.
'''
project, folderpath, entity_name = resolve_path(path, expected=expected, allow_empty_string=allow_empty_string)
must_resolve, project, folderpath, entity_name = _check_resolution_needed(path,
project,
folderpath,
entity_name,
expected_classes=expected_classes,
describe=describe,
enclose_in_list=(not ask_to_resolve or
allow_mult))
if must_resolve:
results = _resolve_global_entity(project, folderpath, entity_name, describe=describe, visibility=visibility)
if len(results) == 0:
# Could not resolve entity, so it is probably a folder
folder = _resolve_folder(project, folderpath, entity_name)
return project, folder, None
else:
validated_results = _validate_resolution_output_length(path,
entity_name,
results,
allow_mult=allow_mult,
all_mult=all_mult,
ask_to_resolve=ask_to_resolve)
if is_job_id(project):
return None, None, validated_results
return project, None, validated_results
return project, folderpath, entity_name | python | def resolve_existing_path(path, expected=None, ask_to_resolve=True, expected_classes=None, allow_mult=False,
describe=True, all_mult=False, allow_empty_string=True, visibility="either"):
'''
:param expected: one of the following: "folder", "entity", or None to indicate
whether the expected path is a folder, a data object, or either
:type expected: string or None
:param ask_to_resolve: Whether picking may be necessary (if true, a list is returned; if false, only one result is returned)
:type ask_to_resolve: boolean
:param expected_classes: A list of expected classes the entity is allowed
to belong to if it is an ID (e.g. "record",
"file", "job"); if None, then entity_name may be
any data object class
:type expected_classes: list or None
:param allow_mult: Whether to allow the user to select multiple results from the same path
:type allow_mult: boolean
:param describe: Input hash to describe call for the results, or True if no describe input
is to be provided
:type describe: dict or True
:param all_mult: Whether to return all matching results without prompting (only applicable if allow_mult == True)
:type all_mult: boolean
:returns: A LIST of results when ask_to_resolve is False or allow_mult is True
:raises: :exc:`ResolutionError` if the request path was invalid, or a single result was requested and input is not a TTY
:param allow_empty_string: If false, a ResolutionError will be raised if *path* is an empty string. Use this when resolving the empty string could result in unexpected behavior.
:type allow_empty_string: boolean
:param visibility: The visibility expected ("either", "hidden", or "visible")
:type visibility: string
Returns either a list of results or a single result (depending on
how many is expected; if only one, then an interactive picking of
a choice will be initiated if input is a tty, or else throw an error).
TODO: Always treats the path as a glob pattern.
Output is of the form {"id": id, "describe": describe hash} a list
of those
TODO: Callers should specify exactly what fields they want, and then
hopefully we can avoid having a default set of fields that may be very
expensive
NOTE: if expected_classes is provided and conflicts with the class
of the hash ID, it will return None for all fields.
'''
project, folderpath, entity_name = resolve_path(path, expected=expected, allow_empty_string=allow_empty_string)
must_resolve, project, folderpath, entity_name = _check_resolution_needed(path,
project,
folderpath,
entity_name,
expected_classes=expected_classes,
describe=describe,
enclose_in_list=(not ask_to_resolve or
allow_mult))
if must_resolve:
results = _resolve_global_entity(project, folderpath, entity_name, describe=describe, visibility=visibility)
if len(results) == 0:
# Could not resolve entity, so it is probably a folder
folder = _resolve_folder(project, folderpath, entity_name)
return project, folder, None
else:
validated_results = _validate_resolution_output_length(path,
entity_name,
results,
allow_mult=allow_mult,
all_mult=all_mult,
ask_to_resolve=ask_to_resolve)
if is_job_id(project):
return None, None, validated_results
return project, None, validated_results
return project, folderpath, entity_name | :param expected: one of the following: "folder", "entity", or None to indicate
whether the expected path is a folder, a data object, or either
:type expected: string or None
:param ask_to_resolve: Whether picking may be necessary (if true, a list is returned; if false, only one result is returned)
:type ask_to_resolve: boolean
:param expected_classes: A list of expected classes the entity is allowed
to belong to if it is an ID (e.g. "record",
"file", "job"); if None, then entity_name may be
any data object class
:type expected_classes: list or None
:param allow_mult: Whether to allow the user to select multiple results from the same path
:type allow_mult: boolean
:param describe: Input hash to describe call for the results, or True if no describe input
is to be provided
:type describe: dict or True
:param all_mult: Whether to return all matching results without prompting (only applicable if allow_mult == True)
:type all_mult: boolean
:returns: A LIST of results when ask_to_resolve is False or allow_mult is True
:raises: :exc:`ResolutionError` if the request path was invalid, or a single result was requested and input is not a TTY
:param allow_empty_string: If false, a ResolutionError will be raised if *path* is an empty string. Use this when resolving the empty string could result in unexpected behavior.
:type allow_empty_string: boolean
:param visibility: The visibility expected ("either", "hidden", or "visible")
:type visibility: string
Returns either a list of results or a single result (depending on
how many is expected; if only one, then an interactive picking of
a choice will be initiated if input is a tty, or else throw an error).
TODO: Always treats the path as a glob pattern.
Output is of the form {"id": id, "describe": describe hash} a list
of those
TODO: Callers should specify exactly what fields they want, and then
hopefully we can avoid having a default set of fields that may be very
expensive
NOTE: if expected_classes is provided and conflicts with the class
of the hash ID, it will return None for all fields. | https://github.com/dnanexus/dx-toolkit/blob/74befb53ad90fcf902d8983ae6d74580f402d619/src/python/dxpy/utils/resolver.py#L1015-L1084 |
dnanexus/dx-toolkit | src/python/dxpy/utils/resolver.py | check_folder_exists | def check_folder_exists(project, path, folder_name):
'''
:param project: project id
:type project: string
:param path: path to where we should look for the folder in question
:type path: string
:param folder_name: name of the folder in question
:type folder_name: string
:returns: A boolean True or False whether the folder exists at the specified path
:type: boolean
:raises: :exc:'ResolutionError' if dxpy.api.container_list_folder raises an exception
This function returns a boolean value that indicates whether a folder of the
specified name exists at the specified path
Note: this function will NOT work on the root folder case, i.e. '/'
'''
if folder_name is None or path is None:
return False
try:
folder_list = dxpy.api.container_list_folder(project, {"folder": path, "only": "folders"})
except dxpy.exceptions.DXAPIError as e:
if e.name == 'ResourceNotFound':
raise ResolutionError(str(e.msg))
else:
raise e
target_folder = path + '/' + folder_name
# sanitize input if necessary
target_folder, _skip = clean_folder_path(target_folder, 'folder')
# Check that folder name exists in return from list folder API call
return target_folder in folder_list['folders'] | python | def check_folder_exists(project, path, folder_name):
'''
:param project: project id
:type project: string
:param path: path to where we should look for the folder in question
:type path: string
:param folder_name: name of the folder in question
:type folder_name: string
:returns: A boolean True or False whether the folder exists at the specified path
:type: boolean
:raises: :exc:'ResolutionError' if dxpy.api.container_list_folder raises an exception
This function returns a boolean value that indicates whether a folder of the
specified name exists at the specified path
Note: this function will NOT work on the root folder case, i.e. '/'
'''
if folder_name is None or path is None:
return False
try:
folder_list = dxpy.api.container_list_folder(project, {"folder": path, "only": "folders"})
except dxpy.exceptions.DXAPIError as e:
if e.name == 'ResourceNotFound':
raise ResolutionError(str(e.msg))
else:
raise e
target_folder = path + '/' + folder_name
# sanitize input if necessary
target_folder, _skip = clean_folder_path(target_folder, 'folder')
# Check that folder name exists in return from list folder API call
return target_folder in folder_list['folders'] | :param project: project id
:type project: string
:param path: path to where we should look for the folder in question
:type path: string
:param folder_name: name of the folder in question
:type folder_name: string
:returns: A boolean True or False whether the folder exists at the specified path
:type: boolean
:raises: :exc:'ResolutionError' if dxpy.api.container_list_folder raises an exception
This function returns a boolean value that indicates whether a folder of the
specified name exists at the specified path
Note: this function will NOT work on the root folder case, i.e. '/' | https://github.com/dnanexus/dx-toolkit/blob/74befb53ad90fcf902d8983ae6d74580f402d619/src/python/dxpy/utils/resolver.py#L1087-L1118 |
dnanexus/dx-toolkit | src/python/dxpy/utils/resolver.py | get_app_from_path | def get_app_from_path(path):
'''
:param path: A string to attempt to resolve to an app object
:type path: string
:returns: The describe hash of the app object if found, or None otherwise
:rtype: dict or None
This method parses a string that is expected to perhaps refer to
an app object. If found, its describe hash will be returned. For
more information on the contents of this hash, see the API
documentation. [TODO: external link here]
'''
alias = None
if not path.startswith('app-'):
path = 'app-' + path
if '/' in path:
alias = path[path.find('/') + 1:]
path = path[:path.find('/')]
try:
return dxpy.api.app_describe(path, alias=alias)
except dxpy.DXAPIError:
return None | python | def get_app_from_path(path):
'''
:param path: A string to attempt to resolve to an app object
:type path: string
:returns: The describe hash of the app object if found, or None otherwise
:rtype: dict or None
This method parses a string that is expected to perhaps refer to
an app object. If found, its describe hash will be returned. For
more information on the contents of this hash, see the API
documentation. [TODO: external link here]
'''
alias = None
if not path.startswith('app-'):
path = 'app-' + path
if '/' in path:
alias = path[path.find('/') + 1:]
path = path[:path.find('/')]
try:
return dxpy.api.app_describe(path, alias=alias)
except dxpy.DXAPIError:
return None | :param path: A string to attempt to resolve to an app object
:type path: string
:returns: The describe hash of the app object if found, or None otherwise
:rtype: dict or None
This method parses a string that is expected to perhaps refer to
an app object. If found, its describe hash will be returned. For
more information on the contents of this hash, see the API
documentation. [TODO: external link here] | https://github.com/dnanexus/dx-toolkit/blob/74befb53ad90fcf902d8983ae6d74580f402d619/src/python/dxpy/utils/resolver.py#L1120-L1142 |
dnanexus/dx-toolkit | src/python/dxpy/utils/resolver.py | get_global_workflow_from_path | def get_global_workflow_from_path(path):
'''
:param path: A string to attempt to resolve to a global workflow object
:type path: string
:returns: The describe hash of the global workflow object if found, or None otherwise
:rtype: dict or None
This method parses a string that is expected to perhaps refer to
a global workflow object. If found, its describe hash will be returned.
For more information on the contents of this hash, see the API
documentation. [TODO: external link here]
'''
alias = None
if not path.startswith('globalworkflow-'):
path = 'globalworkflow-' + path
if '/' in path:
alias = path[path.find('/') + 1:]
path = path[:path.find('/')]
try:
return dxpy.api.global_workflow_describe(path, alias=alias)
except dxpy.DXAPIError:
return None | python | def get_global_workflow_from_path(path):
'''
:param path: A string to attempt to resolve to a global workflow object
:type path: string
:returns: The describe hash of the global workflow object if found, or None otherwise
:rtype: dict or None
This method parses a string that is expected to perhaps refer to
a global workflow object. If found, its describe hash will be returned.
For more information on the contents of this hash, see the API
documentation. [TODO: external link here]
'''
alias = None
if not path.startswith('globalworkflow-'):
path = 'globalworkflow-' + path
if '/' in path:
alias = path[path.find('/') + 1:]
path = path[:path.find('/')]
try:
return dxpy.api.global_workflow_describe(path, alias=alias)
except dxpy.DXAPIError:
return None | :param path: A string to attempt to resolve to a global workflow object
:type path: string
:returns: The describe hash of the global workflow object if found, or None otherwise
:rtype: dict or None
This method parses a string that is expected to perhaps refer to
a global workflow object. If found, its describe hash will be returned.
For more information on the contents of this hash, see the API
documentation. [TODO: external link here] | https://github.com/dnanexus/dx-toolkit/blob/74befb53ad90fcf902d8983ae6d74580f402d619/src/python/dxpy/utils/resolver.py#L1144-L1167 |
dnanexus/dx-toolkit | src/python/dxpy/utils/resolver.py | resolve_global_executable | def resolve_global_executable(path, is_version_required=False):
"""
:param path: A string which is supposed to identify a global executable (app or workflow)
:type path: string
:param is_version_required: If set to True, the path has to specify a specific version/alias, e.g. "myapp/1.0.0"
:type is_version_required: boolean
:returns: The describe hash of the global executable object (app or workflow)
:raises: :exc:`ResolutionError` if it cannot be found
*path* is expected to have one of the following forms:
- hash ID, e.g. "globalworkflow-F85Z6bQ0xku1PKY6FjGQ011J", "app-FBZ3f200yfzkKYyp9JkFVQ97"
- named ID, e.g. "app-myapp", "globalworkflow-myworkflow"
- named ID with alias (version or tag), e.g. "myapp/1.2.0", "myworkflow/1.2.0"
- named ID with prefix and with alias (version or tag), e.g. "app-myapp/1.2.0", "globalworkflow-myworkflow/1.2.0"
"""
if not is_hashid(path) and is_version_required and "/" not in path:
raise ResolutionError('Version is required, e.g. "myexec/1.0.0"'.format())
# First, check if the prefix is provided, then we don't have to resolve the name
if path.startswith('app-'):
return resolve_app(path)
elif path.startswith('globalworkflow-'):
return resolve_global_workflow(path)
# If the path doesn't include a prefix, we must try describing
# as an app and, if that fails, as a global workflow
desc = get_app_from_path(path)
if not desc:
desc = get_global_workflow_from_path(path)
if desc is None:
raise ResolutionError(
'The given path "' + path + '" could not be resolved to an accessible global executable (app or workflow)')
return desc | python | def resolve_global_executable(path, is_version_required=False):
"""
:param path: A string which is supposed to identify a global executable (app or workflow)
:type path: string
:param is_version_required: If set to True, the path has to specify a specific version/alias, e.g. "myapp/1.0.0"
:type is_version_required: boolean
:returns: The describe hash of the global executable object (app or workflow)
:raises: :exc:`ResolutionError` if it cannot be found
*path* is expected to have one of the following forms:
- hash ID, e.g. "globalworkflow-F85Z6bQ0xku1PKY6FjGQ011J", "app-FBZ3f200yfzkKYyp9JkFVQ97"
- named ID, e.g. "app-myapp", "globalworkflow-myworkflow"
- named ID with alias (version or tag), e.g. "myapp/1.2.0", "myworkflow/1.2.0"
- named ID with prefix and with alias (version or tag), e.g. "app-myapp/1.2.0", "globalworkflow-myworkflow/1.2.0"
"""
if not is_hashid(path) and is_version_required and "/" not in path:
raise ResolutionError('Version is required, e.g. "myexec/1.0.0"'.format())
# First, check if the prefix is provided, then we don't have to resolve the name
if path.startswith('app-'):
return resolve_app(path)
elif path.startswith('globalworkflow-'):
return resolve_global_workflow(path)
# If the path doesn't include a prefix, we must try describing
# as an app and, if that fails, as a global workflow
desc = get_app_from_path(path)
if not desc:
desc = get_global_workflow_from_path(path)
if desc is None:
raise ResolutionError(
'The given path "' + path + '" could not be resolved to an accessible global executable (app or workflow)')
return desc | :param path: A string which is supposed to identify a global executable (app or workflow)
:type path: string
:param is_version_required: If set to True, the path has to specify a specific version/alias, e.g. "myapp/1.0.0"
:type is_version_required: boolean
:returns: The describe hash of the global executable object (app or workflow)
:raises: :exc:`ResolutionError` if it cannot be found
*path* is expected to have one of the following forms:
- hash ID, e.g. "globalworkflow-F85Z6bQ0xku1PKY6FjGQ011J", "app-FBZ3f200yfzkKYyp9JkFVQ97"
- named ID, e.g. "app-myapp", "globalworkflow-myworkflow"
- named ID with alias (version or tag), e.g. "myapp/1.2.0", "myworkflow/1.2.0"
- named ID with prefix and with alias (version or tag), e.g. "app-myapp/1.2.0", "globalworkflow-myworkflow/1.2.0" | https://github.com/dnanexus/dx-toolkit/blob/74befb53ad90fcf902d8983ae6d74580f402d619/src/python/dxpy/utils/resolver.py#L1220-L1253 |
dnanexus/dx-toolkit | src/python/dxpy/utils/resolver.py | resolve_to_objects_or_project | def resolve_to_objects_or_project(path, all_matching_results=False):
'''
:param path: Path to resolve
:type path: string
:param all_matching_results: Whether to return a list of all matching results
:type all_matching_results: boolean
A thin wrapper over :meth:`resolve_existing_path` which throws an
error if the path does not look like a project and doesn't match a
data object path.
Returns either a list of results or a single result (depending on
how many is expected; if only one, then an interactive picking of
a choice will be initiated if input is a tty, or else throw an error).
'''
# Attempt to resolve name
project, folderpath, entity_results = resolve_existing_path(path,
expected='entity',
allow_mult=True,
all_mult=all_matching_results)
if entity_results is None and not is_container_id(path):
if folderpath != None and folderpath != '/':
raise ResolutionError('Could not resolve "' + path + \
'''" to an existing data object or to only a project;
if you were attempting to refer to a project by name,
please append a colon ":" to indicate that it is a project.''')
return project, folderpath, entity_results | python | def resolve_to_objects_or_project(path, all_matching_results=False):
'''
:param path: Path to resolve
:type path: string
:param all_matching_results: Whether to return a list of all matching results
:type all_matching_results: boolean
A thin wrapper over :meth:`resolve_existing_path` which throws an
error if the path does not look like a project and doesn't match a
data object path.
Returns either a list of results or a single result (depending on
how many is expected; if only one, then an interactive picking of
a choice will be initiated if input is a tty, or else throw an error).
'''
# Attempt to resolve name
project, folderpath, entity_results = resolve_existing_path(path,
expected='entity',
allow_mult=True,
all_mult=all_matching_results)
if entity_results is None and not is_container_id(path):
if folderpath != None and folderpath != '/':
raise ResolutionError('Could not resolve "' + path + \
'''" to an existing data object or to only a project;
if you were attempting to refer to a project by name,
please append a colon ":" to indicate that it is a project.''')
return project, folderpath, entity_results | :param path: Path to resolve
:type path: string
:param all_matching_results: Whether to return a list of all matching results
:type all_matching_results: boolean
A thin wrapper over :meth:`resolve_existing_path` which throws an
error if the path does not look like a project and doesn't match a
data object path.
Returns either a list of results or a single result (depending on
how many is expected; if only one, then an interactive picking of
a choice will be initiated if input is a tty, or else throw an error). | https://github.com/dnanexus/dx-toolkit/blob/74befb53ad90fcf902d8983ae6d74580f402d619/src/python/dxpy/utils/resolver.py#L1320-L1346 |
dnanexus/dx-toolkit | src/python/dxpy/bindings/dxjob.py | new_dxjob | def new_dxjob(fn_input, fn_name, name=None, tags=None, properties=None, details=None,
instance_type=None, depends_on=None,
**kwargs):
'''
:param fn_input: Function input
:type fn_input: dict
:param fn_name: Name of the function to be called
:type fn_name: string
:param name: Name for the new job (default is "<parent job name>:<fn_name>")
:type name: string
:param tags: Tags to associate with the job
:type tags: list of strings
:param properties: Properties to associate with the job
:type properties: dict with string values
:param details: Details to set for the job
:type details: dict or list
:param instance_type: Instance type on which the job will be run, or a dict mapping function names to instance type requests
:type instance_type: string or dict
:param depends_on: List of data objects or jobs to wait that need to enter the "closed" or "done" states, respectively, before the new job will be run; each element in the list can either be a dxpy handler or a string ID
:type depends_on: list
:rtype: :class:`~dxpy.bindings.dxjob.DXJob`
Creates and enqueues a new job that will execute a particular
function (from the same app or applet as the one the current job is
running). Returns the :class:`~dxpy.bindings.dxjob.DXJob` handle for
the job.
Note that this function is shorthand for::
dxjob = DXJob()
dxjob.new(fn_input, fn_name, **kwargs)
.. note:: This method is intended for calls made from within
already-executing jobs or apps. If it is called from outside of
an Execution Environment, an exception will be thrown. To create
new jobs from outside the Execution Environment, use
:func:`dxpy.bindings.dxapplet.DXApplet.run` or
:func:`dxpy.bindings.dxapp.DXApp.run`.
.. note:: If the environment variable ``DX_JOB_ID`` is not set, this method assmes that it is running within the debug harness, executes the job in place, and provides a debug job handler object that does not have a corresponding remote API job object.
'''
dxjob = DXJob()
dxjob.new(fn_input, fn_name, name=name, tags=tags, properties=properties,
details=details, instance_type=instance_type, depends_on=depends_on, **kwargs)
return dxjob | python | def new_dxjob(fn_input, fn_name, name=None, tags=None, properties=None, details=None,
instance_type=None, depends_on=None,
**kwargs):
'''
:param fn_input: Function input
:type fn_input: dict
:param fn_name: Name of the function to be called
:type fn_name: string
:param name: Name for the new job (default is "<parent job name>:<fn_name>")
:type name: string
:param tags: Tags to associate with the job
:type tags: list of strings
:param properties: Properties to associate with the job
:type properties: dict with string values
:param details: Details to set for the job
:type details: dict or list
:param instance_type: Instance type on which the job will be run, or a dict mapping function names to instance type requests
:type instance_type: string or dict
:param depends_on: List of data objects or jobs to wait that need to enter the "closed" or "done" states, respectively, before the new job will be run; each element in the list can either be a dxpy handler or a string ID
:type depends_on: list
:rtype: :class:`~dxpy.bindings.dxjob.DXJob`
Creates and enqueues a new job that will execute a particular
function (from the same app or applet as the one the current job is
running). Returns the :class:`~dxpy.bindings.dxjob.DXJob` handle for
the job.
Note that this function is shorthand for::
dxjob = DXJob()
dxjob.new(fn_input, fn_name, **kwargs)
.. note:: This method is intended for calls made from within
already-executing jobs or apps. If it is called from outside of
an Execution Environment, an exception will be thrown. To create
new jobs from outside the Execution Environment, use
:func:`dxpy.bindings.dxapplet.DXApplet.run` or
:func:`dxpy.bindings.dxapp.DXApp.run`.
.. note:: If the environment variable ``DX_JOB_ID`` is not set, this method assmes that it is running within the debug harness, executes the job in place, and provides a debug job handler object that does not have a corresponding remote API job object.
'''
dxjob = DXJob()
dxjob.new(fn_input, fn_name, name=name, tags=tags, properties=properties,
details=details, instance_type=instance_type, depends_on=depends_on, **kwargs)
return dxjob | :param fn_input: Function input
:type fn_input: dict
:param fn_name: Name of the function to be called
:type fn_name: string
:param name: Name for the new job (default is "<parent job name>:<fn_name>")
:type name: string
:param tags: Tags to associate with the job
:type tags: list of strings
:param properties: Properties to associate with the job
:type properties: dict with string values
:param details: Details to set for the job
:type details: dict or list
:param instance_type: Instance type on which the job will be run, or a dict mapping function names to instance type requests
:type instance_type: string or dict
:param depends_on: List of data objects or jobs to wait that need to enter the "closed" or "done" states, respectively, before the new job will be run; each element in the list can either be a dxpy handler or a string ID
:type depends_on: list
:rtype: :class:`~dxpy.bindings.dxjob.DXJob`
Creates and enqueues a new job that will execute a particular
function (from the same app or applet as the one the current job is
running). Returns the :class:`~dxpy.bindings.dxjob.DXJob` handle for
the job.
Note that this function is shorthand for::
dxjob = DXJob()
dxjob.new(fn_input, fn_name, **kwargs)
.. note:: This method is intended for calls made from within
already-executing jobs or apps. If it is called from outside of
an Execution Environment, an exception will be thrown. To create
new jobs from outside the Execution Environment, use
:func:`dxpy.bindings.dxapplet.DXApplet.run` or
:func:`dxpy.bindings.dxapp.DXApp.run`.
.. note:: If the environment variable ``DX_JOB_ID`` is not set, this method assmes that it is running within the debug harness, executes the job in place, and provides a debug job handler object that does not have a corresponding remote API job object. | https://github.com/dnanexus/dx-toolkit/blob/74befb53ad90fcf902d8983ae6d74580f402d619/src/python/dxpy/bindings/dxjob.py#L45-L90 |
dnanexus/dx-toolkit | src/python/dxpy/bindings/dxjob.py | DXJob.new | def new(self, fn_input, fn_name, name=None, tags=None, properties=None, details=None,
instance_type=None, depends_on=None,
**kwargs):
'''
:param fn_input: Function input
:type fn_input: dict
:param fn_name: Name of the function to be called
:type fn_name: string
:param name: Name for the new job (default is "<parent job name>:<fn_name>")
:type name: string
:param tags: Tags to associate with the job
:type tags: list of strings
:param properties: Properties to associate with the job
:type properties: dict with string values
:param details: Details to set for the job
:type details: dict or list
:param instance_type: Instance type on which the job will be run, or a dict mapping function names to instance type requests
:type instance_type: string or dict
:param depends_on: List of data objects or jobs to wait that need to enter the "closed" or "done" states, respectively, before the new job will be run; each element in the list can either be a dxpy handler or a string ID
:type depends_on: list
Creates and enqueues a new job that will execute a particular
function (from the same app or applet as the one the current job
is running).
.. note:: This method is intended for calls made from within
already-executing jobs or apps. If it is called from outside
of an Execution Environment, an exception will be thrown. To
create new jobs from outside the Execution Environment, use
:func:`dxpy.bindings.dxapplet.DXApplet.run` or
:func:`dxpy.bindings.dxapp.DXApp.run`.
'''
final_depends_on = []
if depends_on is not None:
if isinstance(depends_on, list):
for item in depends_on:
if isinstance(item, DXJob) or isinstance(item, DXDataObject):
if item.get_id() is None:
raise DXError('A dxpy handler given in depends_on does not have an ID set')
final_depends_on.append(item.get_id())
elif isinstance(item, basestring):
final_depends_on.append(item)
else:
raise DXError('Expected elements of depends_on to only be either instances of DXJob or DXDataObject, or strings')
else:
raise DXError('Expected depends_on field to be a list')
if 'DX_JOB_ID' in os.environ:
req_input = {}
req_input["input"] = fn_input
req_input["function"] = fn_name
if name is not None:
req_input["name"] = name
if tags is not None:
req_input["tags"] = tags
if properties is not None:
req_input["properties"] = properties
if instance_type is not None:
req_input["systemRequirements"] = SystemRequirementsDict.from_instance_type(instance_type, fn_name).as_dict()
if depends_on is not None:
req_input["dependsOn"] = final_depends_on
if details is not None:
req_input["details"] = details
resp = dxpy.api.job_new(req_input, **kwargs)
self.set_id(resp["id"])
else:
self.set_id(queue_entry_point(function=fn_name, input_hash=fn_input,
depends_on=final_depends_on,
name=name)) | python | def new(self, fn_input, fn_name, name=None, tags=None, properties=None, details=None,
instance_type=None, depends_on=None,
**kwargs):
'''
:param fn_input: Function input
:type fn_input: dict
:param fn_name: Name of the function to be called
:type fn_name: string
:param name: Name for the new job (default is "<parent job name>:<fn_name>")
:type name: string
:param tags: Tags to associate with the job
:type tags: list of strings
:param properties: Properties to associate with the job
:type properties: dict with string values
:param details: Details to set for the job
:type details: dict or list
:param instance_type: Instance type on which the job will be run, or a dict mapping function names to instance type requests
:type instance_type: string or dict
:param depends_on: List of data objects or jobs to wait that need to enter the "closed" or "done" states, respectively, before the new job will be run; each element in the list can either be a dxpy handler or a string ID
:type depends_on: list
Creates and enqueues a new job that will execute a particular
function (from the same app or applet as the one the current job
is running).
.. note:: This method is intended for calls made from within
already-executing jobs or apps. If it is called from outside
of an Execution Environment, an exception will be thrown. To
create new jobs from outside the Execution Environment, use
:func:`dxpy.bindings.dxapplet.DXApplet.run` or
:func:`dxpy.bindings.dxapp.DXApp.run`.
'''
final_depends_on = []
if depends_on is not None:
if isinstance(depends_on, list):
for item in depends_on:
if isinstance(item, DXJob) or isinstance(item, DXDataObject):
if item.get_id() is None:
raise DXError('A dxpy handler given in depends_on does not have an ID set')
final_depends_on.append(item.get_id())
elif isinstance(item, basestring):
final_depends_on.append(item)
else:
raise DXError('Expected elements of depends_on to only be either instances of DXJob or DXDataObject, or strings')
else:
raise DXError('Expected depends_on field to be a list')
if 'DX_JOB_ID' in os.environ:
req_input = {}
req_input["input"] = fn_input
req_input["function"] = fn_name
if name is not None:
req_input["name"] = name
if tags is not None:
req_input["tags"] = tags
if properties is not None:
req_input["properties"] = properties
if instance_type is not None:
req_input["systemRequirements"] = SystemRequirementsDict.from_instance_type(instance_type, fn_name).as_dict()
if depends_on is not None:
req_input["dependsOn"] = final_depends_on
if details is not None:
req_input["details"] = details
resp = dxpy.api.job_new(req_input, **kwargs)
self.set_id(resp["id"])
else:
self.set_id(queue_entry_point(function=fn_name, input_hash=fn_input,
depends_on=final_depends_on,
name=name)) | :param fn_input: Function input
:type fn_input: dict
:param fn_name: Name of the function to be called
:type fn_name: string
:param name: Name for the new job (default is "<parent job name>:<fn_name>")
:type name: string
:param tags: Tags to associate with the job
:type tags: list of strings
:param properties: Properties to associate with the job
:type properties: dict with string values
:param details: Details to set for the job
:type details: dict or list
:param instance_type: Instance type on which the job will be run, or a dict mapping function names to instance type requests
:type instance_type: string or dict
:param depends_on: List of data objects or jobs to wait that need to enter the "closed" or "done" states, respectively, before the new job will be run; each element in the list can either be a dxpy handler or a string ID
:type depends_on: list
Creates and enqueues a new job that will execute a particular
function (from the same app or applet as the one the current job
is running).
.. note:: This method is intended for calls made from within
already-executing jobs or apps. If it is called from outside
of an Execution Environment, an exception will be thrown. To
create new jobs from outside the Execution Environment, use
:func:`dxpy.bindings.dxapplet.DXApplet.run` or
:func:`dxpy.bindings.dxapp.DXApp.run`. | https://github.com/dnanexus/dx-toolkit/blob/74befb53ad90fcf902d8983ae6d74580f402d619/src/python/dxpy/bindings/dxjob.py#L104-L173 |
dnanexus/dx-toolkit | src/python/dxpy/bindings/dxjob.py | DXJob.set_id | def set_id(self, dxid):
'''
:param dxid: New job ID to be associated with the handler (localjob IDs also accepted for local runs)
:type dxid: string
Discards the currently stored ID and associates the handler with *dxid*
'''
if dxid is not None:
if not (isinstance(dxid, basestring) and dxid.startswith('localjob-')):
# localjob IDs (which do not follow the usual ID
# syntax) should be allowed; otherwise, follow the
# usual syntax checking
verify_string_dxid(dxid, self._class)
self._dxid = dxid | python | def set_id(self, dxid):
'''
:param dxid: New job ID to be associated with the handler (localjob IDs also accepted for local runs)
:type dxid: string
Discards the currently stored ID and associates the handler with *dxid*
'''
if dxid is not None:
if not (isinstance(dxid, basestring) and dxid.startswith('localjob-')):
# localjob IDs (which do not follow the usual ID
# syntax) should be allowed; otherwise, follow the
# usual syntax checking
verify_string_dxid(dxid, self._class)
self._dxid = dxid | :param dxid: New job ID to be associated with the handler (localjob IDs also accepted for local runs)
:type dxid: string
Discards the currently stored ID and associates the handler with *dxid* | https://github.com/dnanexus/dx-toolkit/blob/74befb53ad90fcf902d8983ae6d74580f402d619/src/python/dxpy/bindings/dxjob.py#L175-L188 |
dnanexus/dx-toolkit | src/python/dxpy/bindings/dxjob.py | DXJob.describe | def describe(self, fields=None, io=None, **kwargs):
"""
:param fields: dict where the keys are field names that should
be returned, and values should be set to True (by default,
all fields are returned)
:type fields: dict
:param io: Include input and output fields in description;
cannot be provided with *fields*; default is True if
*fields* is not provided (deprecated)
:type io: bool
:returns: Description of the job
:rtype: dict
Returns a hash with key-value pairs containing information about
the job, including its state and (optionally) its inputs and
outputs, as described in the API documentation for the
`/job-xxxx/describe
<https://wiki.dnanexus.com/API-Specification-v1.0.0/Applets-and-Entry-Points#API-method:-/job-xxxx/describe>`_
method.
"""
if fields is not None and io is not None:
raise DXError('DXJob.describe: cannot provide non-None values for both fields and io')
describe_input = {}
if fields is not None:
describe_input['fields'] = fields
if io is not None:
describe_input['io'] = io
self._desc = dxpy.api.job_describe(self._dxid, describe_input, **kwargs)
return self._desc | python | def describe(self, fields=None, io=None, **kwargs):
"""
:param fields: dict where the keys are field names that should
be returned, and values should be set to True (by default,
all fields are returned)
:type fields: dict
:param io: Include input and output fields in description;
cannot be provided with *fields*; default is True if
*fields* is not provided (deprecated)
:type io: bool
:returns: Description of the job
:rtype: dict
Returns a hash with key-value pairs containing information about
the job, including its state and (optionally) its inputs and
outputs, as described in the API documentation for the
`/job-xxxx/describe
<https://wiki.dnanexus.com/API-Specification-v1.0.0/Applets-and-Entry-Points#API-method:-/job-xxxx/describe>`_
method.
"""
if fields is not None and io is not None:
raise DXError('DXJob.describe: cannot provide non-None values for both fields and io')
describe_input = {}
if fields is not None:
describe_input['fields'] = fields
if io is not None:
describe_input['io'] = io
self._desc = dxpy.api.job_describe(self._dxid, describe_input, **kwargs)
return self._desc | :param fields: dict where the keys are field names that should
be returned, and values should be set to True (by default,
all fields are returned)
:type fields: dict
:param io: Include input and output fields in description;
cannot be provided with *fields*; default is True if
*fields* is not provided (deprecated)
:type io: bool
:returns: Description of the job
:rtype: dict
Returns a hash with key-value pairs containing information about
the job, including its state and (optionally) its inputs and
outputs, as described in the API documentation for the
`/job-xxxx/describe
<https://wiki.dnanexus.com/API-Specification-v1.0.0/Applets-and-Entry-Points#API-method:-/job-xxxx/describe>`_
method. | https://github.com/dnanexus/dx-toolkit/blob/74befb53ad90fcf902d8983ae6d74580f402d619/src/python/dxpy/bindings/dxjob.py#L190-L219 |
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