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DataONEorg/d1_python | lib_common/src/d1_common/cert/x509.py | extract_subject_from_dn | def extract_subject_from_dn(cert_obj):
"""Serialize a DN to a DataONE subject string.
Args:
cert_obj: cryptography.Certificate
Returns:
str:
Primary subject extracted from the certificate DN.
The certificate DN (DistinguishedName) is a sequence of RDNs
(RelativeDistinguishedName). Each RDN is a set of AVAs (AttributeValueAssertion /
AttributeTypeAndValue). A DataONE subject is a plain string. As there is no single
standard specifying how to create a string representation of a DN, DataONE selected
one of the most common ways, which yield strings such as:
CN=Some Name A123,O=Some Organization,C=US,DC=Some Domain,DC=org
In particular, the sequence of RDNs is reversed. Attribute values are escaped,
attribute type and value pairs are separated by "=", and AVAs are joined together
with ",". If an RDN contains an unknown OID, the OID is serialized as a dotted
string.
As all the information in the DN is preserved, it is not possible to create the
same subject with two different DNs, and the DN can be recreated from the subject.
"""
return ",".join(
"{}={}".format(
OID_TO_SHORT_NAME_DICT.get(v.oid.dotted_string, v.oid.dotted_string),
rdn_escape(v.value),
)
for v in reversed(list(cert_obj.subject))
) | python | def extract_subject_from_dn(cert_obj):
"""Serialize a DN to a DataONE subject string.
Args:
cert_obj: cryptography.Certificate
Returns:
str:
Primary subject extracted from the certificate DN.
The certificate DN (DistinguishedName) is a sequence of RDNs
(RelativeDistinguishedName). Each RDN is a set of AVAs (AttributeValueAssertion /
AttributeTypeAndValue). A DataONE subject is a plain string. As there is no single
standard specifying how to create a string representation of a DN, DataONE selected
one of the most common ways, which yield strings such as:
CN=Some Name A123,O=Some Organization,C=US,DC=Some Domain,DC=org
In particular, the sequence of RDNs is reversed. Attribute values are escaped,
attribute type and value pairs are separated by "=", and AVAs are joined together
with ",". If an RDN contains an unknown OID, the OID is serialized as a dotted
string.
As all the information in the DN is preserved, it is not possible to create the
same subject with two different DNs, and the DN can be recreated from the subject.
"""
return ",".join(
"{}={}".format(
OID_TO_SHORT_NAME_DICT.get(v.oid.dotted_string, v.oid.dotted_string),
rdn_escape(v.value),
)
for v in reversed(list(cert_obj.subject))
) | [
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Args:
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Returns:
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Primary subject extracted from the certificate DN.
The certificate DN (DistinguishedName) is a sequence of RDNs
(RelativeDistinguishedName). Each RDN is a set of AVAs (AttributeValueAssertion /
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DataONEorg/d1_python | lib_common/src/d1_common/cert/x509.py | create_d1_dn_subject | def create_d1_dn_subject(common_name_str):
"""Create the DN Subject for certificate that will be used in a DataONE environment.
The DN is formatted into a DataONE subject, which is used in authentication,
authorization and event tracking.
Args:
common_name_str: str
DataONE uses simple DNs without physical location information, so only the
``common_name_str`` (``CommonName``) needs to be specified.
For Member Node Client Side certificates or CSRs, ``common_name_str`` is the
``node_id``, e.g., ``urn:node:ABCD`` for production, or
``urn:node:mnTestABCD`` for the test environments.
For a local CA, something like ``localCA`` may be used.
For a locally trusted client side certificate, something like
``localClient`` may be used.
"""
return cryptography.x509.Name(
[
cryptography.x509.NameAttribute(
cryptography.x509.oid.NameOID.COUNTRY_NAME, "US"
),
cryptography.x509.NameAttribute(
cryptography.x509.oid.NameOID.STATE_OR_PROVINCE_NAME, "California"
),
cryptography.x509.NameAttribute(
cryptography.x509.oid.NameOID.LOCALITY_NAME, "San Francisco"
),
cryptography.x509.NameAttribute(
cryptography.x509.oid.NameOID.ORGANIZATION_NAME, "Root CA"
),
cryptography.x509.NameAttribute(
cryptography.x509.oid.NameOID.COMMON_NAME, "ca.ca.com"
),
]
) | python | def create_d1_dn_subject(common_name_str):
"""Create the DN Subject for certificate that will be used in a DataONE environment.
The DN is formatted into a DataONE subject, which is used in authentication,
authorization and event tracking.
Args:
common_name_str: str
DataONE uses simple DNs without physical location information, so only the
``common_name_str`` (``CommonName``) needs to be specified.
For Member Node Client Side certificates or CSRs, ``common_name_str`` is the
``node_id``, e.g., ``urn:node:ABCD`` for production, or
``urn:node:mnTestABCD`` for the test environments.
For a local CA, something like ``localCA`` may be used.
For a locally trusted client side certificate, something like
``localClient`` may be used.
"""
return cryptography.x509.Name(
[
cryptography.x509.NameAttribute(
cryptography.x509.oid.NameOID.COUNTRY_NAME, "US"
),
cryptography.x509.NameAttribute(
cryptography.x509.oid.NameOID.STATE_OR_PROVINCE_NAME, "California"
),
cryptography.x509.NameAttribute(
cryptography.x509.oid.NameOID.LOCALITY_NAME, "San Francisco"
),
cryptography.x509.NameAttribute(
cryptography.x509.oid.NameOID.ORGANIZATION_NAME, "Root CA"
),
cryptography.x509.NameAttribute(
cryptography.x509.oid.NameOID.COMMON_NAME, "ca.ca.com"
),
]
) | [
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DataONEorg/d1_python | lib_common/src/d1_common/cert/x509.py | serialize_cert_to_pem | def serialize_cert_to_pem(cert_obj):
"""Serialize certificate to PEM.
The certificate can be also be a Certificate Signing Request (CSR).
Args:
cert_obj: cryptography.Certificate
Returns:
bytes: PEM encoded certificate
"""
return cert_obj.public_bytes(
encoding=cryptography.hazmat.primitives.serialization.Encoding.PEM
) | python | def serialize_cert_to_pem(cert_obj):
"""Serialize certificate to PEM.
The certificate can be also be a Certificate Signing Request (CSR).
Args:
cert_obj: cryptography.Certificate
Returns:
bytes: PEM encoded certificate
"""
return cert_obj.public_bytes(
encoding=cryptography.hazmat.primitives.serialization.Encoding.PEM
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DataONEorg/d1_python | lib_common/src/d1_common/cert/x509.py | extract_subject_info_extension | def extract_subject_info_extension(cert_obj):
"""Extract DataONE SubjectInfo XML doc from certificate.
Certificates issued by DataONE may include an embedded XML doc containing
additional information about the subject specified in the certificate DN. If
present, the doc is stored as an extension with an OID specified by DataONE and
formatted as specified in the DataONE SubjectInfo schema definition.
Args:
cert_obj: cryptography.Certificate
Returns:
str : SubjectInfo XML doc if present, else None
"""
try:
subject_info_der = cert_obj.extensions.get_extension_for_oid(
cryptography.x509.oid.ObjectIdentifier(DATAONE_SUBJECT_INFO_OID)
).value.value
return str(pyasn1.codec.der.decoder.decode(subject_info_der)[0])
except Exception as e:
logging.debug('SubjectInfo not extracted. reason="{}"'.format(e)) | python | def extract_subject_info_extension(cert_obj):
"""Extract DataONE SubjectInfo XML doc from certificate.
Certificates issued by DataONE may include an embedded XML doc containing
additional information about the subject specified in the certificate DN. If
present, the doc is stored as an extension with an OID specified by DataONE and
formatted as specified in the DataONE SubjectInfo schema definition.
Args:
cert_obj: cryptography.Certificate
Returns:
str : SubjectInfo XML doc if present, else None
"""
try:
subject_info_der = cert_obj.extensions.get_extension_for_oid(
cryptography.x509.oid.ObjectIdentifier(DATAONE_SUBJECT_INFO_OID)
).value.value
return str(pyasn1.codec.der.decoder.decode(subject_info_der)[0])
except Exception as e:
logging.debug('SubjectInfo not extracted. reason="{}"'.format(e)) | [
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DataONEorg/d1_python | lib_common/src/d1_common/cert/x509.py | decode_der | def decode_der(cert_der):
"""Decode cert DER string to Certificate object.
Args:
cert_der : Certificate as a DER encoded string
Returns:
cryptography.Certificate()
"""
return cryptography.x509.load_der_x509_certificate(
data=cert_der, backend=cryptography.hazmat.backends.default_backend()
) | python | def decode_der(cert_der):
"""Decode cert DER string to Certificate object.
Args:
cert_der : Certificate as a DER encoded string
Returns:
cryptography.Certificate()
"""
return cryptography.x509.load_der_x509_certificate(
data=cert_der, backend=cryptography.hazmat.backends.default_backend()
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DataONEorg/d1_python | lib_common/src/d1_common/cert/x509.py | disable_cert_validation | def disable_cert_validation():
"""Context manager to temporarily disable certificate validation in the standard SSL
library.
Note: This should not be used in production code but is sometimes useful for
troubleshooting certificate validation issues.
By design, the standard SSL library does not provide a way to disable verification
of the server side certificate. However, a patch to disable validation is described
by the library developers. This context manager allows applying the patch for
specific sections of code.
"""
current_context = ssl._create_default_https_context
ssl._create_default_https_context = ssl._create_unverified_context
try:
yield
finally:
ssl._create_default_https_context = current_context | python | def disable_cert_validation():
"""Context manager to temporarily disable certificate validation in the standard SSL
library.
Note: This should not be used in production code but is sometimes useful for
troubleshooting certificate validation issues.
By design, the standard SSL library does not provide a way to disable verification
of the server side certificate. However, a patch to disable validation is described
by the library developers. This context manager allows applying the patch for
specific sections of code.
"""
current_context = ssl._create_default_https_context
ssl._create_default_https_context = ssl._create_unverified_context
try:
yield
finally:
ssl._create_default_https_context = current_context | [
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DataONEorg/d1_python | lib_common/src/d1_common/cert/x509.py | extract_issuer_ca_cert_url | def extract_issuer_ca_cert_url(cert_obj):
"""Extract issuer CA certificate URL from certificate.
Certificates may include a URL where the root certificate for the CA which was used
for signing the certificate can be downloaded. This function returns the URL if
present.
The primary use for this is to fix validation failure due to non-trusted issuer by
downloading the root CA certificate from the URL and installing it in the local
trust store.
Args:
cert_obj: cryptography.Certificate
Returns:
str: Issuer certificate URL if present, else None
"""
for extension in cert_obj.extensions:
if extension.oid.dotted_string == AUTHORITY_INFO_ACCESS_OID:
authority_info_access = extension.value
for access_description in authority_info_access:
if access_description.access_method.dotted_string == CA_ISSUERS_OID:
return access_description.access_location.value | python | def extract_issuer_ca_cert_url(cert_obj):
"""Extract issuer CA certificate URL from certificate.
Certificates may include a URL where the root certificate for the CA which was used
for signing the certificate can be downloaded. This function returns the URL if
present.
The primary use for this is to fix validation failure due to non-trusted issuer by
downloading the root CA certificate from the URL and installing it in the local
trust store.
Args:
cert_obj: cryptography.Certificate
Returns:
str: Issuer certificate URL if present, else None
"""
for extension in cert_obj.extensions:
if extension.oid.dotted_string == AUTHORITY_INFO_ACCESS_OID:
authority_info_access = extension.value
for access_description in authority_info_access:
if access_description.access_method.dotted_string == CA_ISSUERS_OID:
return access_description.access_location.value | [
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DataONEorg/d1_python | lib_common/src/d1_common/cert/x509.py | serialize_private_key_to_pem | def serialize_private_key_to_pem(private_key, passphrase_bytes=None):
"""Serialize private key to PEM.
Args:
private_key:
passphrase_bytes:
Returns:
bytes: PEM encoded private key
"""
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) | python | def serialize_private_key_to_pem(private_key, passphrase_bytes=None):
"""Serialize private key to PEM.
Args:
private_key:
passphrase_bytes:
Returns:
bytes: PEM encoded private key
"""
return private_key.private_bytes(
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DataONEorg/d1_python | lib_common/src/d1_common/cert/x509.py | generate_private_key | def generate_private_key(key_size=2048):
"""Generate a private key"""
return cryptography.hazmat.primitives.asymmetric.rsa.generate_private_key(
public_exponent=65537,
key_size=key_size,
backend=cryptography.hazmat.backends.default_backend(),
) | python | def generate_private_key(key_size=2048):
"""Generate a private key"""
return cryptography.hazmat.primitives.asymmetric.rsa.generate_private_key(
public_exponent=65537,
key_size=key_size,
backend=cryptography.hazmat.backends.default_backend(),
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DataONEorg/d1_python | lib_common/src/d1_common/cert/x509.py | load_csr | def load_csr(pem_path):
"""Load CSR from PEM encoded file"""
with open(pem_path, "rb") as f:
return cryptography.x509.load_pem_x509_csr(
data=f.read(), backend=cryptography.hazmat.backends.default_backend()
) | python | def load_csr(pem_path):
"""Load CSR from PEM encoded file"""
with open(pem_path, "rb") as f:
return cryptography.x509.load_pem_x509_csr(
data=f.read(), backend=cryptography.hazmat.backends.default_backend()
) | [
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DataONEorg/d1_python | lib_common/src/d1_common/cert/x509.py | load_private_key | def load_private_key(pem_path, passphrase_bytes=None):
"""Load private key from PEM encoded file"""
with open(pem_path, "rb") as f:
return cryptography.hazmat.primitives.serialization.load_pem_private_key(
data=f.read(),
password=passphrase_bytes,
backend=cryptography.hazmat.backends.default_backend(),
) | python | def load_private_key(pem_path, passphrase_bytes=None):
"""Load private key from PEM encoded file"""
with open(pem_path, "rb") as f:
return cryptography.hazmat.primitives.serialization.load_pem_private_key(
data=f.read(),
password=passphrase_bytes,
backend=cryptography.hazmat.backends.default_backend(),
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DataONEorg/d1_python | lib_common/src/d1_common/cert/x509.py | serialize_cert_to_der | def serialize_cert_to_der(cert_obj):
"""Serialize certificate to DER.
Args:
cert_obj: cryptography.Certificate
Returns:
bytes: DER encoded certificate
"""
return cert_obj.public_bytes(
cryptography.hazmat.primitives.serialization.Encoding.DER
) | python | def serialize_cert_to_der(cert_obj):
"""Serialize certificate to DER.
Args:
cert_obj: cryptography.Certificate
Returns:
bytes: DER encoded certificate
"""
return cert_obj.public_bytes(
cryptography.hazmat.primitives.serialization.Encoding.DER
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DataONEorg/d1_python | lib_common/src/d1_common/cert/x509.py | log_cert_info | def log_cert_info(logger, msg_str, cert_obj):
"""Dump basic certificate values to the log.
Args:
logger: Logger
Logger to which to write the certificate values.
msg_str: str
A message to write to the log before the certificate values.
cert_obj: cryptography.Certificate
Certificate containing values to log.
Returns:
None
"""
list(
map(
logger,
["{}:".format(msg_str)]
+ [
" {}".format(v)
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"Subject: {}".format(
_get_val_str(cert_obj, ["subject", "value"], reverse=True)
),
"Issuer: {}".format(
_get_val_str(cert_obj, ["issuer", "value"], reverse=True)
),
"Not Valid Before: {}".format(
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),
"Not Valid After: {}".format(cert_obj.not_valid_after.isoformat()),
"Subject Alt Names: {}".format(
_get_ext_val_str(
cert_obj, "SUBJECT_ALTERNATIVE_NAME", ["value", "value"]
)
),
"CRL Distribution Points: {}".format(
_get_ext_val_str(
cert_obj,
"CRL_DISTRIBUTION_POINTS",
["value", "full_name", "value", "value"],
)
),
"Authority Access Location: {}".format(
extract_issuer_ca_cert_url(cert_obj) or "<not found>"
),
]
],
)
) | python | def log_cert_info(logger, msg_str, cert_obj):
"""Dump basic certificate values to the log.
Args:
logger: Logger
Logger to which to write the certificate values.
msg_str: str
A message to write to the log before the certificate values.
cert_obj: cryptography.Certificate
Certificate containing values to log.
Returns:
None
"""
list(
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["{}:".format(msg_str)]
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),
"Issuer: {}".format(
_get_val_str(cert_obj, ["issuer", "value"], reverse=True)
),
"Not Valid Before: {}".format(
cert_obj.not_valid_before.isoformat()
),
"Not Valid After: {}".format(cert_obj.not_valid_after.isoformat()),
"Subject Alt Names: {}".format(
_get_ext_val_str(
cert_obj, "SUBJECT_ALTERNATIVE_NAME", ["value", "value"]
)
),
"CRL Distribution Points: {}".format(
_get_ext_val_str(
cert_obj,
"CRL_DISTRIBUTION_POINTS",
["value", "full_name", "value", "value"],
)
),
"Authority Access Location: {}".format(
extract_issuer_ca_cert_url(cert_obj) or "<not found>"
),
]
],
)
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A message to write to the log before the certificate values.
cert_obj: cryptography.Certificate
Certificate containing values to log.
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DataONEorg/d1_python | lib_common/src/d1_common/cert/x509.py | get_extension_by_name | def get_extension_by_name(cert_obj, extension_name):
"""Get a standard certificate extension by attribute name.
Args:
cert_obj: cryptography.Certificate
Certificate containing a standard extension.
extension_name : str
Extension name. E.g., 'SUBJECT_DIRECTORY_ATTRIBUTES'.
Returns:
Cryptography.Extension
"""
try:
return cert_obj.extensions.get_extension_for_oid(
getattr(cryptography.x509.oid.ExtensionOID, extension_name)
)
except cryptography.x509.ExtensionNotFound:
pass | python | def get_extension_by_name(cert_obj, extension_name):
"""Get a standard certificate extension by attribute name.
Args:
cert_obj: cryptography.Certificate
Certificate containing a standard extension.
extension_name : str
Extension name. E.g., 'SUBJECT_DIRECTORY_ATTRIBUTES'.
Returns:
Cryptography.Extension
"""
try:
return cert_obj.extensions.get_extension_for_oid(
getattr(cryptography.x509.oid.ExtensionOID, extension_name)
)
except cryptography.x509.ExtensionNotFound:
pass | [
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DataONEorg/d1_python | lib_common/src/d1_common/cert/x509.py | _get_val_list | def _get_val_list(obj, path_list, reverse=False):
"""Extract values from nested objects by attribute names.
Objects contain attributes which are named references to objects. This will descend
down a tree of nested objects, starting at the given object, following the given
path.
Args:
obj: object
Any type of object
path_list: list
Attribute names
reverse: bool
Reverse the list of values before concatenation.
Returns:
list of objects
"""
try:
y = getattr(obj, path_list[0])
except AttributeError:
return []
if len(path_list) == 1:
return [y]
else:
val_list = [x for a in y for x in _get_val_list(a, path_list[1:], reverse)]
if reverse:
val_list.reverse()
return val_list | python | def _get_val_list(obj, path_list, reverse=False):
"""Extract values from nested objects by attribute names.
Objects contain attributes which are named references to objects. This will descend
down a tree of nested objects, starting at the given object, following the given
path.
Args:
obj: object
Any type of object
path_list: list
Attribute names
reverse: bool
Reverse the list of values before concatenation.
Returns:
list of objects
"""
try:
y = getattr(obj, path_list[0])
except AttributeError:
return []
if len(path_list) == 1:
return [y]
else:
val_list = [x for a in y for x in _get_val_list(a, path_list[1:], reverse)]
if reverse:
val_list.reverse()
return val_list | [
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DataONEorg/d1_python | lib_common/src/d1_common/cert/x509.py | _get_val_str | def _get_val_str(obj, path_list=None, reverse=False):
"""Extract values from nested objects by attribute names and concatenate their
string representations.
Args:
obj: object
Any type of object
path_list: list
Attribute names
reverse: bool
Reverse the list of values before concatenation.
Returns:
str: Concatenated extracted values.
"""
val_list = _get_val_list(obj, path_list or [], reverse)
return "<not found>" if obj is None else " / ".join(map(str, val_list)) | python | def _get_val_str(obj, path_list=None, reverse=False):
"""Extract values from nested objects by attribute names and concatenate their
string representations.
Args:
obj: object
Any type of object
path_list: list
Attribute names
reverse: bool
Reverse the list of values before concatenation.
Returns:
str: Concatenated extracted values.
"""
val_list = _get_val_list(obj, path_list or [], reverse)
return "<not found>" if obj is None else " / ".join(map(str, val_list)) | [
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wilson-eft/wilson | wilson/translate/wet.py | _JMS_to_Bern_II | def _JMS_to_Bern_II(C, udlnu):
"""From JMS to BernII basis for charged current process semileptonic
operators. `udlnu` should be of the form 'udl_enu_tau', 'cbl_munu_e' etc."""
u = uflav[udlnu[0]]
d = dflav[udlnu[1]]
l = lflav[udlnu[4:udlnu.find('n')]]
lp = lflav[udlnu[udlnu.find('_',5)+1:len(udlnu)]]
ind = udlnu[0]+udlnu[1]+udlnu[4:udlnu.find('n')]+udlnu[udlnu.find('_',5)+1
:len(udlnu)]
return {
'1' + ind : C["VnueduLL"][lp, l, d, u].conj(),
'5' + ind : C["SnueduRL"][lp, l, d, u].conj(),
'1p' + ind : C["VnueduLR"][lp, l, d, u].conj(),
'5p' + ind : C["SnueduRR"][lp, l, d, u].conj(),
'7p' + ind : C["TnueduRR"][lp, l, d, u].conj()
} | python | def _JMS_to_Bern_II(C, udlnu):
"""From JMS to BernII basis for charged current process semileptonic
operators. `udlnu` should be of the form 'udl_enu_tau', 'cbl_munu_e' etc."""
u = uflav[udlnu[0]]
d = dflav[udlnu[1]]
l = lflav[udlnu[4:udlnu.find('n')]]
lp = lflav[udlnu[udlnu.find('_',5)+1:len(udlnu)]]
ind = udlnu[0]+udlnu[1]+udlnu[4:udlnu.find('n')]+udlnu[udlnu.find('_',5)+1
:len(udlnu)]
return {
'1' + ind : C["VnueduLL"][lp, l, d, u].conj(),
'5' + ind : C["SnueduRL"][lp, l, d, u].conj(),
'1p' + ind : C["VnueduLR"][lp, l, d, u].conj(),
'5p' + ind : C["SnueduRR"][lp, l, d, u].conj(),
'7p' + ind : C["TnueduRR"][lp, l, d, u].conj()
} | [
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wilson-eft/wilson | wilson/translate/wet.py | _Bern_to_JMS_II | def _Bern_to_JMS_II(C, udlnu):
"""From BernII to JMS basis for charged current process semileptonic
operators. `udlnu` should be of the form 'udl_enu_tau', 'cbl_munu_e' etc."""
u = uflav[udlnu[0]]
d = dflav[udlnu[1]]
l = lflav[udlnu[4:udlnu.find('n')]]
lp = lflav[udlnu[udlnu.find('_',5)+1:len(udlnu)]]
ind = udlnu[0]+udlnu[1]+udlnu[4:udlnu.find('n')]+udlnu[udlnu.find('_',5)+1
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return {
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"SnueduRL_{}{}{}{}".format(lp + 1, l + 1, d + 1, u + 1): C['5' + ind].conjugate(),
"VnueduLR_{}{}{}{}".format(lp + 1, l + 1, d + 1, u + 1): C['1p' + ind].conjugate(),
"SnueduRR_{}{}{}{}".format(lp + 1, l + 1, d + 1, u + 1): C['5p' + ind].conjugate(),
"TnueduRR_{}{}{}{}".format(lp + 1, l + 1, d + 1, u + 1): C['7p' + ind].conjugate()
} | python | def _Bern_to_JMS_II(C, udlnu):
"""From BernII to JMS basis for charged current process semileptonic
operators. `udlnu` should be of the form 'udl_enu_tau', 'cbl_munu_e' etc."""
u = uflav[udlnu[0]]
d = dflav[udlnu[1]]
l = lflav[udlnu[4:udlnu.find('n')]]
lp = lflav[udlnu[udlnu.find('_',5)+1:len(udlnu)]]
ind = udlnu[0]+udlnu[1]+udlnu[4:udlnu.find('n')]+udlnu[udlnu.find('_',5)+1
:len(udlnu)]
return {
"VnueduLL_{}{}{}{}".format(lp + 1, l + 1, d + 1, u + 1): C['1' + ind].conjugate(),
"SnueduRL_{}{}{}{}".format(lp + 1, l + 1, d + 1, u + 1): C['5' + ind].conjugate(),
"VnueduLR_{}{}{}{}".format(lp + 1, l + 1, d + 1, u + 1): C['1p' + ind].conjugate(),
"SnueduRR_{}{}{}{}".format(lp + 1, l + 1, d + 1, u + 1): C['5p' + ind].conjugate(),
"TnueduRR_{}{}{}{}".format(lp + 1, l + 1, d + 1, u + 1): C['7p' + ind].conjugate()
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wilson-eft/wilson | wilson/translate/wet.py | _BernII_to_Flavio_II | def _BernII_to_Flavio_II(C, udlnu, parameters):
"""From BernII to FlavioII basis
for charged current process semileptonic operators.
`udlnu` should be of the form 'udl_enu_tau', 'cbl_munu_e' etc."""
p = parameters
u = uflav[udlnu[0]]
d = dflav[udlnu[1]]
l = lflav[udlnu[4:udlnu.find('n')]]
lp = lflav[udlnu[udlnu.find('_',5)+1:len(udlnu)]]
ind = udlnu[0]+udlnu[1]+udlnu[4:udlnu.find('n')]+udlnu[udlnu.find('_',5)+1
:len(udlnu)]
ind2 = udlnu[1]+udlnu[0]+udlnu[4:udlnu.find('n')]+'nu'+udlnu[
udlnu.find('_',5)+1:len(udlnu)]
dic = {
'CVL_' + ind2 : C['1' + ind],
'CVR_'+ ind2 : C['1p' + ind],
'CSR_'+ ind2 : C['5' + ind],
'CSL_'+ ind2 : C['5p' + ind],
'CT_'+ ind2 : C['7p' + ind]
}
V = ckmutil.ckm.ckm_tree(p["Vus"], p["Vub"], p["Vcb"], p["delta"])
prefactor = -sqrt(2) / p['GF'] / V[u, d] / 4
return {k: prefactor * v for k, v in dic.items()} | python | def _BernII_to_Flavio_II(C, udlnu, parameters):
"""From BernII to FlavioII basis
for charged current process semileptonic operators.
`udlnu` should be of the form 'udl_enu_tau', 'cbl_munu_e' etc."""
p = parameters
u = uflav[udlnu[0]]
d = dflav[udlnu[1]]
l = lflav[udlnu[4:udlnu.find('n')]]
lp = lflav[udlnu[udlnu.find('_',5)+1:len(udlnu)]]
ind = udlnu[0]+udlnu[1]+udlnu[4:udlnu.find('n')]+udlnu[udlnu.find('_',5)+1
:len(udlnu)]
ind2 = udlnu[1]+udlnu[0]+udlnu[4:udlnu.find('n')]+'nu'+udlnu[
udlnu.find('_',5)+1:len(udlnu)]
dic = {
'CVL_' + ind2 : C['1' + ind],
'CVR_'+ ind2 : C['1p' + ind],
'CSR_'+ ind2 : C['5' + ind],
'CSL_'+ ind2 : C['5p' + ind],
'CT_'+ ind2 : C['7p' + ind]
}
V = ckmutil.ckm.ckm_tree(p["Vus"], p["Vub"], p["Vcb"], p["delta"])
prefactor = -sqrt(2) / p['GF'] / V[u, d] / 4
return {k: prefactor * v for k, v in dic.items()} | [
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wilson-eft/wilson | wilson/translate/wet.py | Flavio_to_Fierz_nunu | def Flavio_to_Fierz_nunu(C, ddll, parameters, norm_gf=True):
"""From Flavio semileptonic basis to semileptonic Fierz basis for Class V.
C should be the corresponding leptonic Fierz basis and
`ddll` should be of the form 'sbl_enu_tau', 'dbl_munu_e' etc."""
p = parameters
V = ckmutil.ckm.ckm_tree(p["Vus"], p["Vub"], p["Vcb"], p["delta"])
if ddll[:2] == 'sb':
xi = V[2, 2] * V[2, 1].conj()
elif ddll[:2] == 'db':
xi = V[2, 2] * V[2, 0].conj()
elif ddll[:2] == 'ds':
xi = V[2, 1] * V[2, 0].conj()
else:
raise ValueError("Unexpected flavours: {}".format(ddll[:2]))
q1, q2 = ddll[:2]
l1 = ddll[4:ddll.find('n')]
l2 = ddll[ddll.find('_', 5) + 1:]
ind = q1 + q2 + l1 + l2
# flavio has indices within currents inverted
indnu = q2 + q1 + 'nu' + l2 + 'nu' + l1
e = sqrt(4* pi * parameters['alpha_e'])
dic = {
'F' + ind + 'nu': C["CL_" + indnu] / ((8 * pi**2) / e**2),
'F' + ind + 'nup': C["CR_" + indnu] / ((8 * pi**2) / e**2),
}
if norm_gf:
prefactor = sqrt(2)/p['GF']/xi/4
else:
prefactor = 1 / xi
return {k: v / prefactor for k, v in dic.items()} | python | def Flavio_to_Fierz_nunu(C, ddll, parameters, norm_gf=True):
"""From Flavio semileptonic basis to semileptonic Fierz basis for Class V.
C should be the corresponding leptonic Fierz basis and
`ddll` should be of the form 'sbl_enu_tau', 'dbl_munu_e' etc."""
p = parameters
V = ckmutil.ckm.ckm_tree(p["Vus"], p["Vub"], p["Vcb"], p["delta"])
if ddll[:2] == 'sb':
xi = V[2, 2] * V[2, 1].conj()
elif ddll[:2] == 'db':
xi = V[2, 2] * V[2, 0].conj()
elif ddll[:2] == 'ds':
xi = V[2, 1] * V[2, 0].conj()
else:
raise ValueError("Unexpected flavours: {}".format(ddll[:2]))
q1, q2 = ddll[:2]
l1 = ddll[4:ddll.find('n')]
l2 = ddll[ddll.find('_', 5) + 1:]
ind = q1 + q2 + l1 + l2
# flavio has indices within currents inverted
indnu = q2 + q1 + 'nu' + l2 + 'nu' + l1
e = sqrt(4* pi * parameters['alpha_e'])
dic = {
'F' + ind + 'nu': C["CL_" + indnu] / ((8 * pi**2) / e**2),
'F' + ind + 'nup': C["CR_" + indnu] / ((8 * pi**2) / e**2),
}
if norm_gf:
prefactor = sqrt(2)/p['GF']/xi/4
else:
prefactor = 1 / xi
return {k: v / prefactor for k, v in dic.items()} | [
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wilson-eft/wilson | wilson/translate/wet.py | Fierz_to_EOS_lep | def Fierz_to_EOS_lep(C, ddll, parameters):
"""From semileptonic Fierz basis to EOS semileptonic basis for Class V.
C should be the corresponding leptonic Fierz basis and
`ddll` should be of the form 'sbl_enu_tau', 'dbl_munu_e' etc."""
p = parameters
V = ckmutil.ckm.ckm_tree(p["Vus"], p["Vub"], p["Vcb"], p["delta"])
Vtb = V[2,2]
Vts = V[2,1]
ind = ddll.replace('l_','').replace('nu_','')
ind2 = ddll.replace('l_','').replace('nu_','')[2::]
e = sqrt(4* pi * parameters['alpha_e'])
dic = {
'b->s' + ind2 + '::c9' : (16 * pi**2) / e**2 * C['F' + ind + '9'],
'b->s' + ind2 + "::c9'" : (16 * pi**2) / e**2 * C['F' + ind + '9p'],
'b->s' + ind2 + "::c10" : (16 * pi**2) / e**2 * C['F' + ind + '10'],
'b->s' + ind2 + "::c10'" : (16 * pi**2) / e**2 * C['F' + ind + '10p'],
'b->s' + ind2 + "::cS" : (16 * pi**2) / e**2 * C['F' + ind + 'S'],
'b->s' + ind2 + "::cS'" : (16 * pi**2) / e**2 * C['F' + ind + 'Sp'],
'b->s' + ind2 + "::cP" : (16 * pi**2) / e**2 * C['F' + ind + 'P'],
'b->s' + ind2 + "::cP'" : (16 * pi**2) / e**2 * C['F' + ind + 'Pp'],
'b->s' + ind2 + "::cT" : (16 * pi**2) / e**2 * C['F' + ind + 'T'],
'b->s' + ind2 + "::cT5" : (16 * pi**2) / e**2 * C['F' + ind + 'T5']
}
prefactor = sqrt(2)/p['GF']/Vtb/Vts.conj()/4
return {k: prefactor * v for k,v in dic.items()} | python | def Fierz_to_EOS_lep(C, ddll, parameters):
"""From semileptonic Fierz basis to EOS semileptonic basis for Class V.
C should be the corresponding leptonic Fierz basis and
`ddll` should be of the form 'sbl_enu_tau', 'dbl_munu_e' etc."""
p = parameters
V = ckmutil.ckm.ckm_tree(p["Vus"], p["Vub"], p["Vcb"], p["delta"])
Vtb = V[2,2]
Vts = V[2,1]
ind = ddll.replace('l_','').replace('nu_','')
ind2 = ddll.replace('l_','').replace('nu_','')[2::]
e = sqrt(4* pi * parameters['alpha_e'])
dic = {
'b->s' + ind2 + '::c9' : (16 * pi**2) / e**2 * C['F' + ind + '9'],
'b->s' + ind2 + "::c9'" : (16 * pi**2) / e**2 * C['F' + ind + '9p'],
'b->s' + ind2 + "::c10" : (16 * pi**2) / e**2 * C['F' + ind + '10'],
'b->s' + ind2 + "::c10'" : (16 * pi**2) / e**2 * C['F' + ind + '10p'],
'b->s' + ind2 + "::cS" : (16 * pi**2) / e**2 * C['F' + ind + 'S'],
'b->s' + ind2 + "::cS'" : (16 * pi**2) / e**2 * C['F' + ind + 'Sp'],
'b->s' + ind2 + "::cP" : (16 * pi**2) / e**2 * C['F' + ind + 'P'],
'b->s' + ind2 + "::cP'" : (16 * pi**2) / e**2 * C['F' + ind + 'Pp'],
'b->s' + ind2 + "::cT" : (16 * pi**2) / e**2 * C['F' + ind + 'T'],
'b->s' + ind2 + "::cT5" : (16 * pi**2) / e**2 * C['F' + ind + 'T5']
}
prefactor = sqrt(2)/p['GF']/Vtb/Vts.conj()/4
return {k: prefactor * v for k,v in dic.items()} | [
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wilson-eft/wilson | wilson/translate/wet.py | JMS_to_FormFlavor_lep | def JMS_to_FormFlavor_lep(C, dd):
"""From JMS to semileptonic Fierz basis for Classes V.
C should be the JMS basis and `ddll` should be of the
form 'sbl_eni_tau', 'dbl_munu_e' etc."""
b = dflav[dd[0]]
s = dflav[dd[1]]
return {
'CVLL_' + dd + 'mm' : C["VedLL"][1, 1, s, b],
'CVRR_' + dd + 'mm' : C["VedRR"][1, 1, s, b],
'CVLR_' + dd + 'mm' : C["VdeLR"][s, b, 1, 1],
'CVRL_' + dd + 'mm' : C["VedLR"][1, 1, s, b],
'CSLL_' + dd + 'mm' : C["SedRR"][1, 1, b, s].conj(),
'CSRR_' + dd + 'mm' : C["SedRR"][1, 1, s, b],
'CSLR_' + dd + 'mm' : C["SedRL"][1, 1, s, b],
'CSRL_' + dd + 'mm' : C["SedRL"][1, 1, b, s].conj(),
'CTLL_' + dd + 'mm' : C["TedRR"][1, 1, b, s].conj(),
'CTRR_' + dd + 'mm' : C["TedRR"][1, 1, s, b],
'CVLL_sdnn' : 1 / 3 * C["VnudLL"][0, 0, s-1, s]
+ 1 / 3 * C["VnudLL"][1, 1, s-1, s]
+ 1 / 3 * C["VnudLL"][2, 2, s-1, s],
'CVRL_sdnn' : 1 / 3 * C["VnudLR"][0, 0, s-1, s]
+ 1 / 3 * C["VnudLR"][1, 1, s-1, s]
+ 1 / 3 * C["VnudLR"][2, 2, s-1, s]
} | python | def JMS_to_FormFlavor_lep(C, dd):
"""From JMS to semileptonic Fierz basis for Classes V.
C should be the JMS basis and `ddll` should be of the
form 'sbl_eni_tau', 'dbl_munu_e' etc."""
b = dflav[dd[0]]
s = dflav[dd[1]]
return {
'CVLL_' + dd + 'mm' : C["VedLL"][1, 1, s, b],
'CVRR_' + dd + 'mm' : C["VedRR"][1, 1, s, b],
'CVLR_' + dd + 'mm' : C["VdeLR"][s, b, 1, 1],
'CVRL_' + dd + 'mm' : C["VedLR"][1, 1, s, b],
'CSLL_' + dd + 'mm' : C["SedRR"][1, 1, b, s].conj(),
'CSRR_' + dd + 'mm' : C["SedRR"][1, 1, s, b],
'CSLR_' + dd + 'mm' : C["SedRL"][1, 1, s, b],
'CSRL_' + dd + 'mm' : C["SedRL"][1, 1, b, s].conj(),
'CTLL_' + dd + 'mm' : C["TedRR"][1, 1, b, s].conj(),
'CTRR_' + dd + 'mm' : C["TedRR"][1, 1, s, b],
'CVLL_sdnn' : 1 / 3 * C["VnudLL"][0, 0, s-1, s]
+ 1 / 3 * C["VnudLL"][1, 1, s-1, s]
+ 1 / 3 * C["VnudLL"][2, 2, s-1, s],
'CVRL_sdnn' : 1 / 3 * C["VnudLR"][0, 0, s-1, s]
+ 1 / 3 * C["VnudLR"][1, 1, s-1, s]
+ 1 / 3 * C["VnudLR"][2, 2, s-1, s]
} | [
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wilson-eft/wilson | wilson/translate/wet.py | JMS_to_Fierz_chrom | def JMS_to_Fierz_chrom(C, qq):
"""From JMS to chromomagnetic Fierz basis for Class V.
qq should be of the form 'sb', 'ds' etc."""
if qq[0] in dflav:
s = dflav[qq[0]]
b = dflav[qq[1]]
return {
'F7gamma' + qq : C['dgamma'][s, b],
'F8g' + qq : C['dG'][s, b],
'F7pgamma' + qq : C['dgamma'][b, s].conj(),
'F8pg' + qq : C['dG'][b, s].conj()
}
else:
u = uflav[qq[0]]
c = uflav[qq[1]]
return {
'F7gamma' + qq : C['ugamma'][u, c],
'F8g' + qq : C['uG'][u, c],
'F7pgamma' + qq : C['ugamma'][c, u].conj(),
'F8pg' + qq : C['uG'][c, u].conj()
} | python | def JMS_to_Fierz_chrom(C, qq):
"""From JMS to chromomagnetic Fierz basis for Class V.
qq should be of the form 'sb', 'ds' etc."""
if qq[0] in dflav:
s = dflav[qq[0]]
b = dflav[qq[1]]
return {
'F7gamma' + qq : C['dgamma'][s, b],
'F8g' + qq : C['dG'][s, b],
'F7pgamma' + qq : C['dgamma'][b, s].conj(),
'F8pg' + qq : C['dG'][b, s].conj()
}
else:
u = uflav[qq[0]]
c = uflav[qq[1]]
return {
'F7gamma' + qq : C['ugamma'][u, c],
'F8g' + qq : C['uG'][u, c],
'F7pgamma' + qq : C['ugamma'][c, u].conj(),
'F8pg' + qq : C['uG'][c, u].conj()
} | [
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wilson-eft/wilson | wilson/translate/wet.py | Fierz_to_JMS_chrom | def Fierz_to_JMS_chrom(C, qq):
"""From chromomagnetic Fierz to JMS basis for Class V.
qq should be of the form 'sb', 'ds' etc."""
if qq[0] in dflav:
s = dflav[qq[0]] + 1
b = dflav[qq[1]] + 1
return {'dgamma_{}{}'.format(s, b): C['F7gamma' + qq],
'dG_{}{}'.format(s, b): C['F8g' + qq],
'dgamma_{}{}'.format(b, s): C['F7pgamma' + qq].conjugate(),
'dG_{}{}'.format(b, s): C['F8pg' + qq].conjugate(),
}
else:
u = uflav[qq[0]] + 1
c = uflav[qq[1]] + 1
return {'ugamma_{}{}'.format(u, c): C['F7gamma' + qq],
'uG_{}{}'.format(u, c): C['F8g' + qq],
'ugamma_{}{}'.format(c, u): C['F7pgamma' + qq].conjugate(),
'uG_{}{}'.format(c, u): C['F8pg' + qq].conjugate(),
} | python | def Fierz_to_JMS_chrom(C, qq):
"""From chromomagnetic Fierz to JMS basis for Class V.
qq should be of the form 'sb', 'ds' etc."""
if qq[0] in dflav:
s = dflav[qq[0]] + 1
b = dflav[qq[1]] + 1
return {'dgamma_{}{}'.format(s, b): C['F7gamma' + qq],
'dG_{}{}'.format(s, b): C['F8g' + qq],
'dgamma_{}{}'.format(b, s): C['F7pgamma' + qq].conjugate(),
'dG_{}{}'.format(b, s): C['F8pg' + qq].conjugate(),
}
else:
u = uflav[qq[0]] + 1
c = uflav[qq[1]] + 1
return {'ugamma_{}{}'.format(u, c): C['F7gamma' + qq],
'uG_{}{}'.format(u, c): C['F8g' + qq],
'ugamma_{}{}'.format(c, u): C['F7pgamma' + qq].conjugate(),
'uG_{}{}'.format(c, u): C['F8pg' + qq].conjugate(),
} | [
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] | 4164f55ff663d4f668c6e2b4575fd41562662cc9 | https://github.com/wilson-eft/wilson/blob/4164f55ff663d4f668c6e2b4575fd41562662cc9/wilson/translate/wet.py#L1331-L1349 | train | 45,423 |
wilson-eft/wilson | wilson/translate/wet.py | Fierz_to_Bern_chrom | def Fierz_to_Bern_chrom(C, dd, parameters):
"""From Fierz to chromomagnetic Bern basis for Class V.
dd should be of the form 'sb', 'ds' etc."""
e = sqrt(4 * pi * parameters['alpha_e'])
gs = sqrt(4 * pi * parameters['alpha_s'])
if dd == 'sb' or dd == 'db':
mq = parameters['m_b']
elif dd == 'ds':
mq = parameters['m_s']
else:
KeyError("Not sure what to do with quark mass for flavour {}".format(dd))
return {
'7gamma' + dd : gs**2 / e / mq * C['F7gamma' + dd ],
'8g' + dd : gs / mq * C['F8g' + dd ],
'7pgamma' + dd : gs**2 / e /mq * C['F7pgamma' + dd],
'8pg' + dd : gs / mq * C['F8pg' + dd]
} | python | def Fierz_to_Bern_chrom(C, dd, parameters):
"""From Fierz to chromomagnetic Bern basis for Class V.
dd should be of the form 'sb', 'ds' etc."""
e = sqrt(4 * pi * parameters['alpha_e'])
gs = sqrt(4 * pi * parameters['alpha_s'])
if dd == 'sb' or dd == 'db':
mq = parameters['m_b']
elif dd == 'ds':
mq = parameters['m_s']
else:
KeyError("Not sure what to do with quark mass for flavour {}".format(dd))
return {
'7gamma' + dd : gs**2 / e / mq * C['F7gamma' + dd ],
'8g' + dd : gs / mq * C['F8g' + dd ],
'7pgamma' + dd : gs**2 / e /mq * C['F7pgamma' + dd],
'8pg' + dd : gs / mq * C['F8pg' + dd]
} | [
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wilson-eft/wilson | wilson/translate/wet.py | Flavio_to_Fierz_chrom | def Flavio_to_Fierz_chrom(C, qq, parameters):
"""From Flavio to chromomagnetic Fierz basis for Class V.
qq should be of the form 'sb', 'db' etc."""
p = parameters
V = ckmutil.ckm.ckm_tree(p["Vus"], p["Vub"], p["Vcb"], p["delta"])
if qq == 'sb':
xi = V[2, 2] * V[2, 1].conj()
elif qq == 'db':
xi = V[2, 2] * V[2, 0].conj()
elif qq == 'ds':
xi = V[2, 1] * V[2, 0].conj()
elif qq == 'uc':
xi = V[1, 2].conj() * V[0, 2]
else:
raise ValueError("Unexpected flavours: {}".format(qq))
qqfl = qq[::-1]
e = sqrt(4 * pi * parameters['alpha_e'])
gs = sqrt(4 * pi * parameters['alpha_s'])
if qq == 'sb' or qq == 'db':
mq = parameters['m_b']
elif qq == 'ds':
mq = parameters['m_s']
elif qq == 'uc':
mq = parameters['m_c']
else:
KeyError("Not sure what to do with quark mass for flavour {}".format(qq))
dic = {
'F7gamma' + qq: C["C7_" + qqfl] / ((16 * pi**2) / e / mq),
'F8g' + qq: C["C8_" + qqfl] / ((16 * pi**2) / gs / mq),
'F7pgamma' + qq: C["C7p_" + qqfl] / ((16 * pi**2) / e / mq),
'F8pg' + qq: C["C8p_" + qqfl] / ((16 * pi**2) / gs / mq)
}
prefactor = sqrt(2)/p['GF']/xi/4
return {k: v / prefactor for k, v in dic.items()} | python | def Flavio_to_Fierz_chrom(C, qq, parameters):
"""From Flavio to chromomagnetic Fierz basis for Class V.
qq should be of the form 'sb', 'db' etc."""
p = parameters
V = ckmutil.ckm.ckm_tree(p["Vus"], p["Vub"], p["Vcb"], p["delta"])
if qq == 'sb':
xi = V[2, 2] * V[2, 1].conj()
elif qq == 'db':
xi = V[2, 2] * V[2, 0].conj()
elif qq == 'ds':
xi = V[2, 1] * V[2, 0].conj()
elif qq == 'uc':
xi = V[1, 2].conj() * V[0, 2]
else:
raise ValueError("Unexpected flavours: {}".format(qq))
qqfl = qq[::-1]
e = sqrt(4 * pi * parameters['alpha_e'])
gs = sqrt(4 * pi * parameters['alpha_s'])
if qq == 'sb' or qq == 'db':
mq = parameters['m_b']
elif qq == 'ds':
mq = parameters['m_s']
elif qq == 'uc':
mq = parameters['m_c']
else:
KeyError("Not sure what to do with quark mass for flavour {}".format(qq))
dic = {
'F7gamma' + qq: C["C7_" + qqfl] / ((16 * pi**2) / e / mq),
'F8g' + qq: C["C8_" + qqfl] / ((16 * pi**2) / gs / mq),
'F7pgamma' + qq: C["C7p_" + qqfl] / ((16 * pi**2) / e / mq),
'F8pg' + qq: C["C8p_" + qqfl] / ((16 * pi**2) / gs / mq)
}
prefactor = sqrt(2)/p['GF']/xi/4
return {k: v / prefactor for k, v in dic.items()} | [
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wilson-eft/wilson | wilson/translate/wet.py | Fierz_to_EOS_chrom | def Fierz_to_EOS_chrom(C, dd, parameters):
"""From Fierz to chromomagnetic EOS basis for Class V.
dd should be of the form 'sb', 'ds' etc."""
p = parameters
V = ckmutil.ckm.ckm_tree(p["Vus"], p["Vub"], p["Vcb"], p["delta"])
Vtb = V[2,2]
Vts = V[2,1]
e = sqrt(4 * pi * parameters['alpha_e'])
gs = sqrt(4 * pi * parameters['alpha_s'])
mb = parameters['m_b']
dic = {"b->s::c7": 16 * pi**2 / mb / e * C["F7gamma" + dd],
"b->s::c7'": 16 * pi**2 / mb / e * C["F7pgamma" + dd],
"b->s::c8": 16 * pi**2 / mb / gs * C["F8g" + dd],
"b->s::c8'": 16 * pi**2 / mb / gs * C["F8pg" + dd]
}
prefactor = sqrt(2)/p['GF']/Vtb/Vts.conj()/4
return {k: prefactor * v for k,v in dic.items()} | python | def Fierz_to_EOS_chrom(C, dd, parameters):
"""From Fierz to chromomagnetic EOS basis for Class V.
dd should be of the form 'sb', 'ds' etc."""
p = parameters
V = ckmutil.ckm.ckm_tree(p["Vus"], p["Vub"], p["Vcb"], p["delta"])
Vtb = V[2,2]
Vts = V[2,1]
e = sqrt(4 * pi * parameters['alpha_e'])
gs = sqrt(4 * pi * parameters['alpha_s'])
mb = parameters['m_b']
dic = {"b->s::c7": 16 * pi**2 / mb / e * C["F7gamma" + dd],
"b->s::c7'": 16 * pi**2 / mb / e * C["F7pgamma" + dd],
"b->s::c8": 16 * pi**2 / mb / gs * C["F8g" + dd],
"b->s::c8'": 16 * pi**2 / mb / gs * C["F8pg" + dd]
}
prefactor = sqrt(2)/p['GF']/Vtb/Vts.conj()/4
return {k: prefactor * v for k,v in dic.items()} | [
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wilson-eft/wilson | wilson/translate/wet.py | _JMS_to_Flavio_VII | def _JMS_to_Flavio_VII(C, parameters):
"""From JMS to flavio basis for class VII, i.e. flavour blind operators."""
d = {}
dtrans = json.loads(pkgutil.get_data('wilson', 'data/flavio_jms_vii.json').decode('utf8'))
for cj, cf in dtrans.items():
d[cf] = C.get(cj, 0)
gs = sqrt(4 * pi * parameters['alpha_s'])
e = sqrt(4 * pi * parameters['alpha_e'])
preC7 = 16 * pi**2 / e
preC8 = 16 * pi**2 / gs
d['C8_uu'] = preC8 / parameters['m_u'] * C.get('uG_11', 0)
d['C8_cc'] = preC8 / parameters['m_c'] * C.get('uG_22', 0)
d['C8_dd'] = preC8 / parameters['m_d'] * C.get('dG_11', 0)
d['C8_ss'] = preC8 / parameters['m_s'] * C.get('dG_22', 0)
d['C8_bb'] = preC8 / parameters['m_b'] * C.get('dG_33', 0)
d['C7_uu'] = preC7 / parameters['m_u'] * C.get('ugamma_11', 0)
d['C7_cc'] = preC7 / parameters['m_c'] * C.get('ugamma_22', 0)
d['C7_dd'] = preC7 / parameters['m_d'] * C.get('dgamma_11', 0)
d['C7_ss'] = preC7 / parameters['m_s'] * C.get('dgamma_22', 0)
d['C7_bb'] = preC7 / parameters['m_b'] * C.get('dgamma_33', 0)
d['C7_ee'] = preC7 / parameters['m_e'] * C.get('egamma_11', 0)
d['C7_mumu'] = preC7 / parameters['m_mu'] * C.get('egamma_22', 0)
d['C7_tautau'] = preC7 / parameters['m_tau'] * C.get('egamma_33', 0)
preGF = sqrt(2) / parameters['GF'] / 4
return {k: preGF * v for k,v in d.items()} | python | def _JMS_to_Flavio_VII(C, parameters):
"""From JMS to flavio basis for class VII, i.e. flavour blind operators."""
d = {}
dtrans = json.loads(pkgutil.get_data('wilson', 'data/flavio_jms_vii.json').decode('utf8'))
for cj, cf in dtrans.items():
d[cf] = C.get(cj, 0)
gs = sqrt(4 * pi * parameters['alpha_s'])
e = sqrt(4 * pi * parameters['alpha_e'])
preC7 = 16 * pi**2 / e
preC8 = 16 * pi**2 / gs
d['C8_uu'] = preC8 / parameters['m_u'] * C.get('uG_11', 0)
d['C8_cc'] = preC8 / parameters['m_c'] * C.get('uG_22', 0)
d['C8_dd'] = preC8 / parameters['m_d'] * C.get('dG_11', 0)
d['C8_ss'] = preC8 / parameters['m_s'] * C.get('dG_22', 0)
d['C8_bb'] = preC8 / parameters['m_b'] * C.get('dG_33', 0)
d['C7_uu'] = preC7 / parameters['m_u'] * C.get('ugamma_11', 0)
d['C7_cc'] = preC7 / parameters['m_c'] * C.get('ugamma_22', 0)
d['C7_dd'] = preC7 / parameters['m_d'] * C.get('dgamma_11', 0)
d['C7_ss'] = preC7 / parameters['m_s'] * C.get('dgamma_22', 0)
d['C7_bb'] = preC7 / parameters['m_b'] * C.get('dgamma_33', 0)
d['C7_ee'] = preC7 / parameters['m_e'] * C.get('egamma_11', 0)
d['C7_mumu'] = preC7 / parameters['m_mu'] * C.get('egamma_22', 0)
d['C7_tautau'] = preC7 / parameters['m_tau'] * C.get('egamma_33', 0)
preGF = sqrt(2) / parameters['GF'] / 4
return {k: preGF * v for k,v in d.items()} | [
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DataONEorg/d1_python | gmn/src/d1_gmn/app/revision.py | cut_from_chain | def cut_from_chain(sciobj_model):
"""Remove an object from a revision chain.
The object can be at any location in the chain, including the head or tail.
Preconditions:
- The object with the pid is verified to exist and to be a member of an
revision chain. E.g., with:
d1_gmn.app.views.asserts.is_existing_object(pid)
d1_gmn.app.views.asserts.is_in_revision_chain(pid)
Postconditions:
- The given object is a standalone object with empty obsoletes, obsoletedBy and
seriesId fields.
- The previously adjacent objects in the chain are adjusted to close any gap that
was created or remove dangling reference at the head or tail.
- If the object was the last object in the chain and the chain has a SID, the SID
reference is shifted over to the new last object in the chain.
"""
if _is_head(sciobj_model):
old_pid = sciobj_model.obsoletes.did
_cut_head_from_chain(sciobj_model)
elif _is_tail(sciobj_model):
old_pid = sciobj_model.obsoleted_by.did
_cut_tail_from_chain(sciobj_model)
else:
old_pid = sciobj_model.obsoleted_by.did
_cut_embedded_from_chain(sciobj_model)
_update_sid_to_last_existing_pid_map(old_pid) | python | def cut_from_chain(sciobj_model):
"""Remove an object from a revision chain.
The object can be at any location in the chain, including the head or tail.
Preconditions:
- The object with the pid is verified to exist and to be a member of an
revision chain. E.g., with:
d1_gmn.app.views.asserts.is_existing_object(pid)
d1_gmn.app.views.asserts.is_in_revision_chain(pid)
Postconditions:
- The given object is a standalone object with empty obsoletes, obsoletedBy and
seriesId fields.
- The previously adjacent objects in the chain are adjusted to close any gap that
was created or remove dangling reference at the head or tail.
- If the object was the last object in the chain and the chain has a SID, the SID
reference is shifted over to the new last object in the chain.
"""
if _is_head(sciobj_model):
old_pid = sciobj_model.obsoletes.did
_cut_head_from_chain(sciobj_model)
elif _is_tail(sciobj_model):
old_pid = sciobj_model.obsoleted_by.did
_cut_tail_from_chain(sciobj_model)
else:
old_pid = sciobj_model.obsoleted_by.did
_cut_embedded_from_chain(sciobj_model)
_update_sid_to_last_existing_pid_map(old_pid) | [
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DataONEorg/d1_python | gmn/src/d1_gmn/app/revision.py | resolve_sid | def resolve_sid(sid):
"""Get the PID to which the ``sid`` currently maps.
Preconditions:
- ``sid`` is verified to exist. E.g., with d1_gmn.app.views.asserts.is_sid().
"""
return d1_gmn.app.models.Chain.objects.get(sid__did=sid).head_pid.did | python | def resolve_sid(sid):
"""Get the PID to which the ``sid`` currently maps.
Preconditions:
- ``sid`` is verified to exist. E.g., with d1_gmn.app.views.asserts.is_sid().
"""
return d1_gmn.app.models.Chain.objects.get(sid__did=sid).head_pid.did | [
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DataONEorg/d1_python | gmn/src/d1_gmn/app/revision.py | is_obsoletes_pid | def is_obsoletes_pid(pid):
"""Return True if ``pid`` is referenced in the obsoletes field of any object.
This will return True even if the PID is in the obsoletes field of an object that
does not exist on the local MN, such as replica that is in an incomplete chain.
"""
return d1_gmn.app.models.ScienceObject.objects.filter(obsoletes__did=pid).exists() | python | def is_obsoletes_pid(pid):
"""Return True if ``pid`` is referenced in the obsoletes field of any object.
This will return True even if the PID is in the obsoletes field of an object that
does not exist on the local MN, such as replica that is in an incomplete chain.
"""
return d1_gmn.app.models.ScienceObject.objects.filter(obsoletes__did=pid).exists() | [
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DataONEorg/d1_python | gmn/src/d1_gmn/app/revision.py | is_obsoleted_by_pid | def is_obsoleted_by_pid(pid):
"""Return True if ``pid`` is referenced in the obsoletedBy field of any object.
This will return True even if the PID is in the obsoletes field of an object that
does not exist on the local MN, such as replica that is in an incomplete chain.
"""
return d1_gmn.app.models.ScienceObject.objects.filter(
obsoleted_by__did=pid
).exists() | python | def is_obsoleted_by_pid(pid):
"""Return True if ``pid`` is referenced in the obsoletedBy field of any object.
This will return True even if the PID is in the obsoletes field of an object that
does not exist on the local MN, such as replica that is in an incomplete chain.
"""
return d1_gmn.app.models.ScienceObject.objects.filter(
obsoleted_by__did=pid
).exists() | [
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DataONEorg/d1_python | gmn/src/d1_gmn/app/revision.py | _merge_chains | def _merge_chains(chain_model_a, chain_model_b):
"""Merge two chains.
For use when it becomes known that two chains that were created separately
actually are separate sections of the same chain
E.g.:
- A obsoleted by X is created. A has no SID. X does not exist yet. A chain is
created for A.
- B obsoleting Y is created. B has SID. Y does not exist yet. A chain is created
for B.
- C obsoleting X, obsoleted by Y is created. C tells us that X and Y are in the
same chain, which means that A and B are in the same chain. At this point, the
two chains need to be merged. Merging the chains causes A to take on the SID of
B.
"""
_set_chain_sid(
chain_model_a, d1_gmn.app.did.get_did_by_foreign_key(chain_model_b.sid)
)
for member_model in _get_all_chain_member_queryset_by_chain(chain_model_b):
member_model.chain = chain_model_a
member_model.save()
chain_model_b.delete() | python | def _merge_chains(chain_model_a, chain_model_b):
"""Merge two chains.
For use when it becomes known that two chains that were created separately
actually are separate sections of the same chain
E.g.:
- A obsoleted by X is created. A has no SID. X does not exist yet. A chain is
created for A.
- B obsoleting Y is created. B has SID. Y does not exist yet. A chain is created
for B.
- C obsoleting X, obsoleted by Y is created. C tells us that X and Y are in the
same chain, which means that A and B are in the same chain. At this point, the
two chains need to be merged. Merging the chains causes A to take on the SID of
B.
"""
_set_chain_sid(
chain_model_a, d1_gmn.app.did.get_did_by_foreign_key(chain_model_b.sid)
)
for member_model in _get_all_chain_member_queryset_by_chain(chain_model_b):
member_model.chain = chain_model_a
member_model.save()
chain_model_b.delete() | [
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DataONEorg/d1_python | gmn/src/d1_gmn/app/revision.py | _set_chain_sid | def _set_chain_sid(chain_model, sid):
"""Set or update SID for chain.
If the chain already has a SID, ``sid`` must either be None or match the existing
SID.
"""
if not sid:
return
if chain_model.sid and chain_model.sid.did != sid:
raise d1_common.types.exceptions.ServiceFailure(
0,
'Attempted to modify existing SID. '
'existing_sid="{}", new_sid="{}"'.format(chain_model.sid.did, sid),
)
chain_model.sid = d1_gmn.app.did.get_or_create_did(sid)
chain_model.save() | python | def _set_chain_sid(chain_model, sid):
"""Set or update SID for chain.
If the chain already has a SID, ``sid`` must either be None or match the existing
SID.
"""
if not sid:
return
if chain_model.sid and chain_model.sid.did != sid:
raise d1_common.types.exceptions.ServiceFailure(
0,
'Attempted to modify existing SID. '
'existing_sid="{}", new_sid="{}"'.format(chain_model.sid.did, sid),
)
chain_model.sid = d1_gmn.app.did.get_or_create_did(sid)
chain_model.save() | [
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DataONEorg/d1_python | gmn/src/d1_gmn/app/revision.py | _get_chain_by_pid | def _get_chain_by_pid(pid):
"""Find chain by pid.
Return None if not found.
"""
try:
return d1_gmn.app.models.ChainMember.objects.get(pid__did=pid).chain
except d1_gmn.app.models.ChainMember.DoesNotExist:
pass | python | def _get_chain_by_pid(pid):
"""Find chain by pid.
Return None if not found.
"""
try:
return d1_gmn.app.models.ChainMember.objects.get(pid__did=pid).chain
except d1_gmn.app.models.ChainMember.DoesNotExist:
pass | [
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DataONEorg/d1_python | gmn/src/d1_gmn/app/revision.py | _get_chain_by_sid | def _get_chain_by_sid(sid):
"""Return None if not found."""
try:
return d1_gmn.app.models.Chain.objects.get(sid__did=sid)
except d1_gmn.app.models.Chain.DoesNotExist:
pass | python | def _get_chain_by_sid(sid):
"""Return None if not found."""
try:
return d1_gmn.app.models.Chain.objects.get(sid__did=sid)
except d1_gmn.app.models.Chain.DoesNotExist:
pass | [
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DataONEorg/d1_python | gmn/src/d1_gmn/app/revision.py | _update_sid_to_last_existing_pid_map | def _update_sid_to_last_existing_pid_map(pid):
"""Set chain head PID to the last existing object in the chain to which ``pid``
belongs. If SID has been set for chain, it resolves to chain head PID.
Intended to be called in MNStorage.delete() and other chain manipulation.
Preconditions:
- ``pid`` must exist and be verified to be a PID.
d1_gmn.app.views.asserts.is_existing_object()
"""
last_pid = _find_head_or_latest_connected(pid)
chain_model = _get_chain_by_pid(last_pid)
if not chain_model:
return
chain_model.head_pid = d1_gmn.app.did.get_or_create_did(last_pid)
chain_model.save() | python | def _update_sid_to_last_existing_pid_map(pid):
"""Set chain head PID to the last existing object in the chain to which ``pid``
belongs. If SID has been set for chain, it resolves to chain head PID.
Intended to be called in MNStorage.delete() and other chain manipulation.
Preconditions:
- ``pid`` must exist and be verified to be a PID.
d1_gmn.app.views.asserts.is_existing_object()
"""
last_pid = _find_head_or_latest_connected(pid)
chain_model = _get_chain_by_pid(last_pid)
if not chain_model:
return
chain_model.head_pid = d1_gmn.app.did.get_or_create_did(last_pid)
chain_model.save() | [
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genialis/resolwe | resolwe/flow/migrations/0025_entity_type.py | populate_entity_type | def populate_entity_type(apps, schema_editor):
"""Populate entity type from attached descriptor schema."""
Entity = apps.get_model('flow', 'Entity')
for entity in Entity.objects.all():
if entity.descriptor_schema is not None:
entity.type = entity.descriptor_schema.slug
entity.save() | python | def populate_entity_type(apps, schema_editor):
"""Populate entity type from attached descriptor schema."""
Entity = apps.get_model('flow', 'Entity')
for entity in Entity.objects.all():
if entity.descriptor_schema is not None:
entity.type = entity.descriptor_schema.slug
entity.save() | [
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DataONEorg/d1_python | lib_common/src/d1_common/xml.py | deserialize | def deserialize(doc_xml, pyxb_binding=None):
"""Deserialize DataONE XML types to PyXB.
Args:
doc_xml: UTF-8 encoded ``bytes``
pyxb_binding: PyXB binding object. If not specified, the correct one should be
selected automatically.
Returns:
PyXB object
See Also:
``deserialize_d1_exception()`` for deserializing DataONE Exception types.
"""
pyxb_binding = pyxb_binding or d1_common.types.dataoneTypes
try:
return pyxb_binding.CreateFromDocument(doc_xml)
except pyxb.ValidationError as e:
raise ValueError(
'Unable to deserialize XML to PyXB. error="{}" xml="{}"'.format(
e.details(), doc_xml
)
)
except (pyxb.PyXBException, xml.sax.SAXParseException, Exception) as e:
raise ValueError(
'Unable to deserialize XML to PyXB. error="{}" xml="{}"'.format(
str(e), doc_xml
)
) | python | def deserialize(doc_xml, pyxb_binding=None):
"""Deserialize DataONE XML types to PyXB.
Args:
doc_xml: UTF-8 encoded ``bytes``
pyxb_binding: PyXB binding object. If not specified, the correct one should be
selected automatically.
Returns:
PyXB object
See Also:
``deserialize_d1_exception()`` for deserializing DataONE Exception types.
"""
pyxb_binding = pyxb_binding or d1_common.types.dataoneTypes
try:
return pyxb_binding.CreateFromDocument(doc_xml)
except pyxb.ValidationError as e:
raise ValueError(
'Unable to deserialize XML to PyXB. error="{}" xml="{}"'.format(
e.details(), doc_xml
)
)
except (pyxb.PyXBException, xml.sax.SAXParseException, Exception) as e:
raise ValueError(
'Unable to deserialize XML to PyXB. error="{}" xml="{}"'.format(
str(e), doc_xml
)
) | [
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DataONEorg/d1_python | lib_common/src/d1_common/xml.py | serialize_gen | def serialize_gen(
obj_pyxb, encoding='utf-8', pretty=False, strip_prolog=False, xslt_url=None
):
"""Serialize PyXB object to XML.
Args:
obj_pyxb: PyXB object
PyXB object to serialize.
encoding: str
Encoding to use for XML doc bytes
pretty: bool
True: Use pretty print formatting for human readability.
strip_prolog:
True: remove any XML prolog (e.g., ``<?xml version="1.0" encoding="utf-8"?>``),
from the resulting XML doc.
xslt_url: str
If specified, add a processing instruction to the XML doc that specifies the
download location for an XSLT stylesheet.
Returns:
XML document
"""
assert d1_common.type_conversions.is_pyxb(obj_pyxb)
assert encoding in (None, 'utf-8', 'UTF-8')
try:
obj_dom = obj_pyxb.toDOM()
except pyxb.ValidationError as e:
raise ValueError(
'Unable to serialize PyXB to XML. error="{}"'.format(e.details())
)
except pyxb.PyXBException as e:
raise ValueError('Unable to serialize PyXB to XML. error="{}"'.format(str(e)))
if xslt_url:
xslt_processing_instruction = obj_dom.createProcessingInstruction(
'xml-stylesheet', 'type="text/xsl" href="{}"'.format(xslt_url)
)
root = obj_dom.firstChild
obj_dom.insertBefore(xslt_processing_instruction, root)
if pretty:
xml_str = obj_dom.toprettyxml(indent=' ', encoding=encoding)
# Remove empty lines in the result caused by a bug in toprettyxml()
if encoding is None:
xml_str = re.sub(r'^\s*$\n', r'', xml_str, flags=re.MULTILINE)
else:
xml_str = re.sub(b'^\s*$\n', b'', xml_str, flags=re.MULTILINE)
else:
xml_str = obj_dom.toxml(encoding)
if strip_prolog:
if encoding is None:
xml_str = re.sub(r'^<\?(.*)\?>', r'', xml_str)
else:
xml_str = re.sub(b'^<\?(.*)\?>', b'', xml_str)
return xml_str.strip() | python | def serialize_gen(
obj_pyxb, encoding='utf-8', pretty=False, strip_prolog=False, xslt_url=None
):
"""Serialize PyXB object to XML.
Args:
obj_pyxb: PyXB object
PyXB object to serialize.
encoding: str
Encoding to use for XML doc bytes
pretty: bool
True: Use pretty print formatting for human readability.
strip_prolog:
True: remove any XML prolog (e.g., ``<?xml version="1.0" encoding="utf-8"?>``),
from the resulting XML doc.
xslt_url: str
If specified, add a processing instruction to the XML doc that specifies the
download location for an XSLT stylesheet.
Returns:
XML document
"""
assert d1_common.type_conversions.is_pyxb(obj_pyxb)
assert encoding in (None, 'utf-8', 'UTF-8')
try:
obj_dom = obj_pyxb.toDOM()
except pyxb.ValidationError as e:
raise ValueError(
'Unable to serialize PyXB to XML. error="{}"'.format(e.details())
)
except pyxb.PyXBException as e:
raise ValueError('Unable to serialize PyXB to XML. error="{}"'.format(str(e)))
if xslt_url:
xslt_processing_instruction = obj_dom.createProcessingInstruction(
'xml-stylesheet', 'type="text/xsl" href="{}"'.format(xslt_url)
)
root = obj_dom.firstChild
obj_dom.insertBefore(xslt_processing_instruction, root)
if pretty:
xml_str = obj_dom.toprettyxml(indent=' ', encoding=encoding)
# Remove empty lines in the result caused by a bug in toprettyxml()
if encoding is None:
xml_str = re.sub(r'^\s*$\n', r'', xml_str, flags=re.MULTILINE)
else:
xml_str = re.sub(b'^\s*$\n', b'', xml_str, flags=re.MULTILINE)
else:
xml_str = obj_dom.toxml(encoding)
if strip_prolog:
if encoding is None:
xml_str = re.sub(r'^<\?(.*)\?>', r'', xml_str)
else:
xml_str = re.sub(b'^<\?(.*)\?>', b'', xml_str)
return xml_str.strip() | [
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DataONEorg/d1_python | lib_common/src/d1_common/xml.py | serialize_for_transport | def serialize_for_transport(obj_pyxb, pretty=False, strip_prolog=False, xslt_url=None):
"""Serialize PyXB object to XML ``bytes`` with UTF-8 encoding for transport over the
network, filesystem storage and other machine usage.
Args:
obj_pyxb: PyXB object
PyXB object to serialize.
pretty: bool
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True: remove any XML prolog (e.g., ``<?xml version="1.0" encoding="utf-8"?>``),
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Returns:
bytes: UTF-8 encoded XML document
See Also:
``serialize_for_display()``
"""
return serialize_gen(obj_pyxb, 'utf-8', pretty, strip_prolog, xslt_url) | python | def serialize_for_transport(obj_pyxb, pretty=False, strip_prolog=False, xslt_url=None):
"""Serialize PyXB object to XML ``bytes`` with UTF-8 encoding for transport over the
network, filesystem storage and other machine usage.
Args:
obj_pyxb: PyXB object
PyXB object to serialize.
pretty: bool
True: Use pretty print formatting for human readability.
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True: remove any XML prolog (e.g., ``<?xml version="1.0" encoding="utf-8"?>``),
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xslt_url: str
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DataONEorg/d1_python | lib_common/src/d1_common/xml.py | serialize_to_xml_str | def serialize_to_xml_str(obj_pyxb, pretty=True, strip_prolog=False, xslt_url=None):
"""Serialize PyXB object to pretty printed XML ``str`` for display.
Args:
obj_pyxb: PyXB object
PyXB object to serialize.
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Returns:
str: Pretty printed XML document
"""
return serialize_gen(obj_pyxb, None, pretty, strip_prolog, xslt_url) | python | def serialize_to_xml_str(obj_pyxb, pretty=True, strip_prolog=False, xslt_url=None):
"""Serialize PyXB object to pretty printed XML ``str`` for display.
Args:
obj_pyxb: PyXB object
PyXB object to serialize.
pretty: bool
False: Disable pretty print formatting. XML will not have line breaks.
strip_prolog:
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xslt_url: str
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Returns:
str: Pretty printed XML document
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return serialize_gen(obj_pyxb, None, pretty, strip_prolog, xslt_url) | [
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DataONEorg/d1_python | lib_common/src/d1_common/xml.py | reformat_to_pretty_xml | def reformat_to_pretty_xml(doc_xml):
"""Pretty print XML doc.
Args:
doc_xml : str
Well formed XML doc
Returns:
str: Pretty printed XML doc
"""
assert isinstance(doc_xml, str)
dom_obj = xml.dom.minidom.parseString(doc_xml)
pretty_xml = dom_obj.toprettyxml(indent=' ')
# Remove empty lines in the result caused by a bug in toprettyxml()
return re.sub(r'^\s*$\n', r'', pretty_xml, flags=re.MULTILINE) | python | def reformat_to_pretty_xml(doc_xml):
"""Pretty print XML doc.
Args:
doc_xml : str
Well formed XML doc
Returns:
str: Pretty printed XML doc
"""
assert isinstance(doc_xml, str)
dom_obj = xml.dom.minidom.parseString(doc_xml)
pretty_xml = dom_obj.toprettyxml(indent=' ')
# Remove empty lines in the result caused by a bug in toprettyxml()
return re.sub(r'^\s*$\n', r'', pretty_xml, flags=re.MULTILINE) | [
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DataONEorg/d1_python | lib_common/src/d1_common/xml.py | are_equivalent | def are_equivalent(a_xml, b_xml, encoding=None):
"""Return True if two XML docs are semantically equivalent, else False.
- TODO: Include test for tails. Skipped for now because tails are not used in any
D1 types.
"""
assert isinstance(a_xml, str)
assert isinstance(b_xml, str)
a_tree = str_to_etree(a_xml, encoding)
b_tree = str_to_etree(b_xml, encoding)
return are_equal_or_superset(a_tree, b_tree) and are_equal_or_superset(
b_tree, a_tree
) | python | def are_equivalent(a_xml, b_xml, encoding=None):
"""Return True if two XML docs are semantically equivalent, else False.
- TODO: Include test for tails. Skipped for now because tails are not used in any
D1 types.
"""
assert isinstance(a_xml, str)
assert isinstance(b_xml, str)
a_tree = str_to_etree(a_xml, encoding)
b_tree = str_to_etree(b_xml, encoding)
return are_equal_or_superset(a_tree, b_tree) and are_equal_or_superset(
b_tree, a_tree
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DataONEorg/d1_python | lib_common/src/d1_common/xml.py | are_equal_or_superset | def are_equal_or_superset(superset_tree, base_tree):
"""Return True if ``superset_tree`` is equal to or a superset of ``base_tree``
- Checks that all elements and attributes in ``superset_tree`` are present and
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try:
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logger.debug(str(e))
return False
return True | python | def are_equal_or_superset(superset_tree, base_tree):
"""Return True if ``superset_tree`` is equal to or a superset of ``base_tree``
- Checks that all elements and attributes in ``superset_tree`` are present and
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- Can be used for checking if one XML document is based on another, as long as all
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"""
try:
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except CompareError as e:
logger.debug(str(e))
return False
return True | [
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DataONEorg/d1_python | lib_common/src/d1_common/xml.py | are_equal_xml | def are_equal_xml(a_xml, b_xml):
"""Normalize and compare XML documents for equality. The document may or may not be
a DataONE type.
Args:
a_xml: str
b_xml: str
XML documents to compare for equality.
Returns:
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"""
a_dom = xml.dom.minidom.parseString(a_xml)
b_dom = xml.dom.minidom.parseString(b_xml)
return are_equal_elements(a_dom.documentElement, b_dom.documentElement) | python | def are_equal_xml(a_xml, b_xml):
"""Normalize and compare XML documents for equality. The document may or may not be
a DataONE type.
Args:
a_xml: str
b_xml: str
XML documents to compare for equality.
Returns:
bool: ``True`` if the XML documents are semantically equivalent.
"""
a_dom = xml.dom.minidom.parseString(a_xml)
b_dom = xml.dom.minidom.parseString(b_xml)
return are_equal_elements(a_dom.documentElement, b_dom.documentElement) | [
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DataONEorg/d1_python | lib_common/src/d1_common/xml.py | are_equal_elements | def are_equal_elements(a_el, b_el):
"""Normalize and compare ElementTrees for equality.
Args:
a_el: ElementTree
b_el: ElementTree
ElementTrees to compare for equality.
Returns:
bool: ``True`` if the ElementTrees are semantically equivalent.
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if (
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):
return False
if a_child_el.nodeType == a_child_el.ELEMENT_NODE and not are_equal_elements(
a_child_el, b_child_el
):
return False
return True | python | def are_equal_elements(a_el, b_el):
"""Normalize and compare ElementTrees for equality.
Args:
a_el: ElementTree
b_el: ElementTree
ElementTrees to compare for equality.
Returns:
bool: ``True`` if the ElementTrees are semantically equivalent.
"""
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for a_child_el, b_child_el in zip(a_el.childNodes, b_el.childNodes):
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if (
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if a_child_el.nodeType == a_child_el.ELEMENT_NODE and not are_equal_elements(
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return True | [
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DataONEorg/d1_python | lib_common/src/d1_common/xml.py | sort_elements_by_child_values | def sort_elements_by_child_values(obj_pyxb, child_name_list):
"""In-place sort simple or complex elements in a PyXB object by values they contain
in child elements.
Args:
obj_pyxb: PyXB object
child_name_list: list of str
List of element names that are direct children of the PyXB object.
"""
obj_pyxb.sort(key=lambda x: [get_auto(getattr(x, n)) for n in child_name_list]) | python | def sort_elements_by_child_values(obj_pyxb, child_name_list):
"""In-place sort simple or complex elements in a PyXB object by values they contain
in child elements.
Args:
obj_pyxb: PyXB object
child_name_list: list of str
List of element names that are direct children of the PyXB object.
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obj_pyxb.sort(key=lambda x: [get_auto(getattr(x, n)) for n in child_name_list]) | [
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DataONEorg/d1_python | lib_common/src/d1_common/xml.py | format_diff_pyxb | def format_diff_pyxb(a_pyxb, b_pyxb):
"""Create a diff between two PyXB objects.
Args:
a_pyxb: PyXB object
b_pyxb: PyXB object
Returns:
str : `Differ`-style delta
"""
return '\n'.join(
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"""Create a diff between two PyXB objects.
Args:
a_pyxb: PyXB object
b_pyxb: PyXB object
Returns:
str : `Differ`-style delta
"""
return '\n'.join(
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DataONEorg/d1_python | lib_common/src/d1_common/xml.py | format_diff_xml | def format_diff_xml(a_xml, b_xml):
"""Create a diff between two XML documents.
Args:
a_xml: str
b_xml: str
Returns:
str : `Differ`-style delta
"""
return '\n'.join(
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"""Create a diff between two XML documents.
Args:
a_xml: str
b_xml: str
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str : `Differ`-style delta
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return '\n'.join(
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DataONEorg/d1_python | lib_common/src/d1_common/xml.py | get_opt_attr | def get_opt_attr(obj_pyxb, attr_str, default_val=None):
"""Get an optional attribute value from a PyXB element.
The attributes for elements that are optional according to the schema and
not set in the PyXB object are present and set to None.
PyXB validation will fail if required elements are missing.
Args:
obj_pyxb: PyXB object
attr_str: str
Name of an attribute that the PyXB object may contain.
default_val: any object
Value to return if the attribute is not present.
Returns:
str : Value of the attribute if present, else ``default_val``.
"""
v = getattr(obj_pyxb, attr_str, default_val)
return v if v is not None else default_val | python | def get_opt_attr(obj_pyxb, attr_str, default_val=None):
"""Get an optional attribute value from a PyXB element.
The attributes for elements that are optional according to the schema and
not set in the PyXB object are present and set to None.
PyXB validation will fail if required elements are missing.
Args:
obj_pyxb: PyXB object
attr_str: str
Name of an attribute that the PyXB object may contain.
default_val: any object
Value to return if the attribute is not present.
Returns:
str : Value of the attribute if present, else ``default_val``.
"""
v = getattr(obj_pyxb, attr_str, default_val)
return v if v is not None else default_val | [
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DataONEorg/d1_python | lib_common/src/d1_common/xml.py | get_opt_val | def get_opt_val(obj_pyxb, attr_str, default_val=None):
"""Get an optional Simple Content value from a PyXB element.
The attributes for elements that are optional according to the schema and
not set in the PyXB object are present and set to None.
PyXB validation will fail if required elements are missing.
Args:
obj_pyxb: PyXB object
attr_str: str
Name of an attribute that the PyXB object may contain.
default_val: any object
Value to return if the attribute is not present.
Returns:
str : Value of the attribute if present, else ``default_val``.
"""
try:
return get_req_val(getattr(obj_pyxb, attr_str))
except (ValueError, AttributeError):
return default_val | python | def get_opt_val(obj_pyxb, attr_str, default_val=None):
"""Get an optional Simple Content value from a PyXB element.
The attributes for elements that are optional according to the schema and
not set in the PyXB object are present and set to None.
PyXB validation will fail if required elements are missing.
Args:
obj_pyxb: PyXB object
attr_str: str
Name of an attribute that the PyXB object may contain.
default_val: any object
Value to return if the attribute is not present.
Returns:
str : Value of the attribute if present, else ``default_val``.
"""
try:
return get_req_val(getattr(obj_pyxb, attr_str))
except (ValueError, AttributeError):
return default_val | [
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genialis/resolwe | resolwe/flow/utils/exceptions.py | resolwe_exception_handler | def resolwe_exception_handler(exc, context):
"""Handle exceptions raised in API and make them nicer.
To enable this, you have to add it to the settings:
.. code:: python
REST_FRAMEWORK = {
'EXCEPTION_HANDLER': 'resolwe.flow.utils.exceptions.resolwe_exception_handler',
}
"""
response = exception_handler(exc, context)
if isinstance(exc, ValidationError):
if response is None:
response = Response({})
response.status_code = 400
response.data['error'] = exc.message
return response | python | def resolwe_exception_handler(exc, context):
"""Handle exceptions raised in API and make them nicer.
To enable this, you have to add it to the settings:
.. code:: python
REST_FRAMEWORK = {
'EXCEPTION_HANDLER': 'resolwe.flow.utils.exceptions.resolwe_exception_handler',
}
"""
response = exception_handler(exc, context)
if isinstance(exc, ValidationError):
if response is None:
response = Response({})
response.status_code = 400
response.data['error'] = exc.message
return response | [
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DataONEorg/d1_python | utilities/src/d1_util/jwt_token_tasks.py | validate_and_decode | def validate_and_decode(jwt_bu64, cert_obj):
"""Example for validating the signature of a JWT using only the cryptography
library.
Note that this does NOT validate the claims in the claim set.
"""
public_key = cert_obj.public_key()
message = '.'.join(d1_common.cert.jwt.get_bu64_tup(jwt_bu64)[:2])
signature = d1_common.cert.jwt.get_jwt_tup(jwt_bu64)[2]
try:
public_key.verify(
signature,
message,
cryptography.hazmat.primitives.asymmetric.padding.PKCS1v15(),
cryptography.hazmat.primitives.hashes.SHA256(),
)
except cryptography.exceptions.InvalidSignature as e:
raise Exception('Signature is invalid. error="{}"'.format(str(e)))
return d1_common.cert.jwt.get_jwt_dict(jwt_bu64) | python | def validate_and_decode(jwt_bu64, cert_obj):
"""Example for validating the signature of a JWT using only the cryptography
library.
Note that this does NOT validate the claims in the claim set.
"""
public_key = cert_obj.public_key()
message = '.'.join(d1_common.cert.jwt.get_bu64_tup(jwt_bu64)[:2])
signature = d1_common.cert.jwt.get_jwt_tup(jwt_bu64)[2]
try:
public_key.verify(
signature,
message,
cryptography.hazmat.primitives.asymmetric.padding.PKCS1v15(),
cryptography.hazmat.primitives.hashes.SHA256(),
)
except cryptography.exceptions.InvalidSignature as e:
raise Exception('Signature is invalid. error="{}"'.format(str(e)))
return d1_common.cert.jwt.get_jwt_dict(jwt_bu64) | [
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DataONEorg/d1_python | utilities/src/d1_util/jwt_token_tasks.py | find_valid_combinations | def find_valid_combinations(cert_file_name_list, jwt_file_name_list):
"""Given a list of cert and JWT file names, print a list showing each combination
along with indicators for combinations where the JWT signature was successfully
validated with the cert."""
for cert_file_name in cert_file_name_list:
cert_pem = '' # self.test_files.load_utf8_to_str(cert_file_name)
cert_obj = d1_common.cert.x509.deserialize_pem(cert_pem)
# d1_common.cert.x509.log_cert_info(logging.info, 'CERT', cert_obj)
for jwt_file_name in jwt_file_name_list:
jwt_bu64 = '' # self.test_files.load_utf8_to_str(jwt_file_name)
# d1_common.cert.jwt.log_jwt_bu64_info(logging.info, 'JWT', jwt_bu64)
is_ok = False
try:
d1_common.cert.jwt.validate_and_decode(jwt_bu64, cert_obj)
except d1_common.cert.jwt.JwtException as e:
logging.info('Invalid. msg="{}"'.format(str(e)))
else:
is_ok = True
logging.info(
'{} {} {}'.format(
'***' if is_ok else ' ', cert_file_name, jwt_file_name
)
) | python | def find_valid_combinations(cert_file_name_list, jwt_file_name_list):
"""Given a list of cert and JWT file names, print a list showing each combination
along with indicators for combinations where the JWT signature was successfully
validated with the cert."""
for cert_file_name in cert_file_name_list:
cert_pem = '' # self.test_files.load_utf8_to_str(cert_file_name)
cert_obj = d1_common.cert.x509.deserialize_pem(cert_pem)
# d1_common.cert.x509.log_cert_info(logging.info, 'CERT', cert_obj)
for jwt_file_name in jwt_file_name_list:
jwt_bu64 = '' # self.test_files.load_utf8_to_str(jwt_file_name)
# d1_common.cert.jwt.log_jwt_bu64_info(logging.info, 'JWT', jwt_bu64)
is_ok = False
try:
d1_common.cert.jwt.validate_and_decode(jwt_bu64, cert_obj)
except d1_common.cert.jwt.JwtException as e:
logging.info('Invalid. msg="{}"'.format(str(e)))
else:
is_ok = True
logging.info(
'{} {} {}'.format(
'***' if is_ok else ' ', cert_file_name, jwt_file_name
)
) | [
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DataONEorg/d1_python | lib_common/src/d1_common/url.py | parseUrl | def parseUrl(url):
"""Return a dict containing scheme, netloc, url, params, query, fragment keys.
query is a dict where the values are always lists. If the query key appears only
once in the URL, the list will have a single value.
"""
scheme, netloc, url, params, query, fragment = urllib.parse.urlparse(url)
query_dict = {
k: sorted(v) if len(v) > 1 else v[0]
for k, v in list(urllib.parse.parse_qs(query).items())
}
return {
'scheme': scheme,
'netloc': netloc,
'url': url,
'params': params,
'query': query_dict,
'fragment': fragment,
} | python | def parseUrl(url):
"""Return a dict containing scheme, netloc, url, params, query, fragment keys.
query is a dict where the values are always lists. If the query key appears only
once in the URL, the list will have a single value.
"""
scheme, netloc, url, params, query, fragment = urllib.parse.urlparse(url)
query_dict = {
k: sorted(v) if len(v) > 1 else v[0]
for k, v in list(urllib.parse.parse_qs(query).items())
}
return {
'scheme': scheme,
'netloc': netloc,
'url': url,
'params': params,
'query': query_dict,
'fragment': fragment,
} | [
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DataONEorg/d1_python | lib_common/src/d1_common/url.py | encodePathElement | def encodePathElement(element):
"""Encode a URL path element according to RFC3986."""
return urllib.parse.quote(
(
element.encode('utf-8')
if isinstance(element, str)
else str(element)
if isinstance(element, int)
else element
),
safe=d1_common.const.URL_PATHELEMENT_SAFE_CHARS,
) | python | def encodePathElement(element):
"""Encode a URL path element according to RFC3986."""
return urllib.parse.quote(
(
element.encode('utf-8')
if isinstance(element, str)
else str(element)
if isinstance(element, int)
else element
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safe=d1_common.const.URL_PATHELEMENT_SAFE_CHARS,
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DataONEorg/d1_python | lib_common/src/d1_common/url.py | encodeQueryElement | def encodeQueryElement(element):
"""Encode a URL query element according to RFC3986."""
return urllib.parse.quote(
(
element.encode('utf-8')
if isinstance(element, str)
else str(element)
if isinstance(element, int)
else element
),
safe=d1_common.const.URL_QUERYELEMENT_SAFE_CHARS,
) | python | def encodeQueryElement(element):
"""Encode a URL query element according to RFC3986."""
return urllib.parse.quote(
(
element.encode('utf-8')
if isinstance(element, str)
else str(element)
if isinstance(element, int)
else element
),
safe=d1_common.const.URL_QUERYELEMENT_SAFE_CHARS,
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DataONEorg/d1_python | lib_common/src/d1_common/url.py | urlencode | def urlencode(query, doseq=0):
"""Modified version of the standard urllib.urlencode that is conforms to RFC3986.
The urllib version encodes spaces as '+' which can lead to inconsistency. This
version will always encode spaces as '%20'.
Encode a sequence of two-element tuples or dictionary into a URL query string.
If any values in the query arg are sequences and doseq is true, each
sequence element is converted to a separate parameter.
If the query arg is a sequence of two-element tuples, the order of the
parameters in the output will match the order of parameters in the
input.
"""
if hasattr(query, "items"):
# Remove None parameters from query. Dictionaries are mutable, so we can
# remove the the items directly. dict.keys() creates a copy of the
# dictionary keys, making it safe to remove elements from the dictionary
# while iterating.
for k in list(query.keys()):
if query[k] is None:
del query[k]
# mapping objects
query = list(query.items())
else:
# Remove None parameters from query. Tuples are immutable, so we have to
# build a new version that does not contain the elements we want to remove,
# and replace the original with it.
query = list(filter((lambda x: x[1] is not None), query))
# it's a bother at times that strings and string-like objects are
# sequences...
try:
# non-sequence items should not work with len()
# non-empty strings will fail this
if len(query) and not isinstance(query[0], tuple):
raise TypeError
# zero-length sequences of all types will get here and succeed,
# but that's a minor nit - since the original implementation
# allowed empty dicts that type of behavior probably should be
# preserved for consistency
except TypeError:
ty, va, tb = sys.exc_info()
raise TypeError(
"not a valid non-string sequence or mapping object"
).with_traceback(tb)
l = []
if not doseq:
# preserve old behavior
for k, v in query:
k = encodeQueryElement(str(k))
v = encodeQueryElement(str(v))
l.append(k + '=' + v)
else:
for k, v in query:
k = encodeQueryElement(str(k))
if isinstance(v, str):
v = encodeQueryElement(v)
l.append(k + '=' + v)
elif isinstance(v, str):
# is there a reasonable way to convert to ASCII?
# encode generates a string, but "replace" or "ignore"
# lose information and "strict" can raise UnicodeError
v = encodeQueryElement(v.encode("ASCII", "replace"))
l.append(k + '=' + v)
else:
try:
# is this a sufficient test for sequence-ness?
len(v)
except TypeError:
# not a sequence
v = encodeQueryElement(str(v))
l.append(k + '=' + v)
else:
# loop over the sequence
for elt in v:
l.append(k + '=' + encodeQueryElement(str(elt)))
return '&'.join(sorted(l)) | python | def urlencode(query, doseq=0):
"""Modified version of the standard urllib.urlencode that is conforms to RFC3986.
The urllib version encodes spaces as '+' which can lead to inconsistency. This
version will always encode spaces as '%20'.
Encode a sequence of two-element tuples or dictionary into a URL query string.
If any values in the query arg are sequences and doseq is true, each
sequence element is converted to a separate parameter.
If the query arg is a sequence of two-element tuples, the order of the
parameters in the output will match the order of parameters in the
input.
"""
if hasattr(query, "items"):
# Remove None parameters from query. Dictionaries are mutable, so we can
# remove the the items directly. dict.keys() creates a copy of the
# dictionary keys, making it safe to remove elements from the dictionary
# while iterating.
for k in list(query.keys()):
if query[k] is None:
del query[k]
# mapping objects
query = list(query.items())
else:
# Remove None parameters from query. Tuples are immutable, so we have to
# build a new version that does not contain the elements we want to remove,
# and replace the original with it.
query = list(filter((lambda x: x[1] is not None), query))
# it's a bother at times that strings and string-like objects are
# sequences...
try:
# non-sequence items should not work with len()
# non-empty strings will fail this
if len(query) and not isinstance(query[0], tuple):
raise TypeError
# zero-length sequences of all types will get here and succeed,
# but that's a minor nit - since the original implementation
# allowed empty dicts that type of behavior probably should be
# preserved for consistency
except TypeError:
ty, va, tb = sys.exc_info()
raise TypeError(
"not a valid non-string sequence or mapping object"
).with_traceback(tb)
l = []
if not doseq:
# preserve old behavior
for k, v in query:
k = encodeQueryElement(str(k))
v = encodeQueryElement(str(v))
l.append(k + '=' + v)
else:
for k, v in query:
k = encodeQueryElement(str(k))
if isinstance(v, str):
v = encodeQueryElement(v)
l.append(k + '=' + v)
elif isinstance(v, str):
# is there a reasonable way to convert to ASCII?
# encode generates a string, but "replace" or "ignore"
# lose information and "strict" can raise UnicodeError
v = encodeQueryElement(v.encode("ASCII", "replace"))
l.append(k + '=' + v)
else:
try:
# is this a sufficient test for sequence-ness?
len(v)
except TypeError:
# not a sequence
v = encodeQueryElement(str(v))
l.append(k + '=' + v)
else:
# loop over the sequence
for elt in v:
l.append(k + '=' + encodeQueryElement(str(elt)))
return '&'.join(sorted(l)) | [
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DataONEorg/d1_python | lib_common/src/d1_common/url.py | makeCNBaseURL | def makeCNBaseURL(url):
"""Attempt to create a valid CN BaseURL when one or more sections of the URL are
missing."""
o = urllib.parse.urlparse(url, scheme=d1_common.const.DEFAULT_CN_PROTOCOL)
if o.netloc and o.path:
netloc = o.netloc
path = o.path
elif o.netloc:
netloc = o.netloc
path = d1_common.const.DEFAULT_CN_PATH
elif o.path:
s = o.path.split('/', 1)
netloc = s[0]
if len(s) == 1:
path = d1_common.const.DEFAULT_CN_PATH
else:
path = s[1]
else:
netloc = d1_common.const.DEFAULT_CN_HOST
path = d1_common.const.DEFAULT_CN_PATH
return urllib.parse.urlunparse(
(o.scheme, netloc, path, o.params, o.query, o.fragment)
) | python | def makeCNBaseURL(url):
"""Attempt to create a valid CN BaseURL when one or more sections of the URL are
missing."""
o = urllib.parse.urlparse(url, scheme=d1_common.const.DEFAULT_CN_PROTOCOL)
if o.netloc and o.path:
netloc = o.netloc
path = o.path
elif o.netloc:
netloc = o.netloc
path = d1_common.const.DEFAULT_CN_PATH
elif o.path:
s = o.path.split('/', 1)
netloc = s[0]
if len(s) == 1:
path = d1_common.const.DEFAULT_CN_PATH
else:
path = s[1]
else:
netloc = d1_common.const.DEFAULT_CN_HOST
path = d1_common.const.DEFAULT_CN_PATH
return urllib.parse.urlunparse(
(o.scheme, netloc, path, o.params, o.query, o.fragment)
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DataONEorg/d1_python | lib_common/src/d1_common/url.py | makeMNBaseURL | def makeMNBaseURL(url):
"""Attempt to create a valid MN BaseURL when one or more sections of the URL are
missing."""
o = urllib.parse.urlparse(url, scheme=d1_common.const.DEFAULT_MN_PROTOCOL)
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netloc = s[0]
if len(s) == 1:
path = d1_common.const.DEFAULT_MN_PATH
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netloc = d1_common.const.DEFAULT_MN_HOST
path = d1_common.const.DEFAULT_MN_PATH
return urllib.parse.urlunparse(
(o.scheme, netloc, path, o.params, o.query, o.fragment)
) | python | def makeMNBaseURL(url):
"""Attempt to create a valid MN BaseURL when one or more sections of the URL are
missing."""
o = urllib.parse.urlparse(url, scheme=d1_common.const.DEFAULT_MN_PROTOCOL)
if o.netloc and o.path:
netloc = o.netloc
path = o.path
elif o.netloc:
netloc = o.netloc
path = d1_common.const.DEFAULT_MN_PATH
elif o.path:
s = o.path.split('/', 1)
netloc = s[0]
if len(s) == 1:
path = d1_common.const.DEFAULT_MN_PATH
else:
path = s[1]
else:
netloc = d1_common.const.DEFAULT_MN_HOST
path = d1_common.const.DEFAULT_MN_PATH
return urllib.parse.urlunparse(
(o.scheme, netloc, path, o.params, o.query, o.fragment)
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DataONEorg/d1_python | lib_common/src/d1_common/url.py | find_url_mismatches | def find_url_mismatches(a_url, b_url):
"""Given two URLs, return a list of any mismatches.
If the list is empty, the URLs are equivalent. Implemented by parsing and comparing
the elements. See RFC 1738 for details.
"""
diff_list = []
a_parts = urllib.parse.urlparse(a_url)
b_parts = urllib.parse.urlparse(b_url)
# scheme
if a_parts.scheme.lower() != b_parts.scheme.lower():
diff_list.append(
'Schemes differ. a="{}" b="{}" differ'.format(
a_parts.scheme.lower(), b_parts.scheme.lower()
)
)
# netloc
if a_parts.netloc.lower() != b_parts.netloc.lower():
diff_list.append(
'Network locations differ. a="{}" b="{}"'.format(
a_parts.netloc.lower(), b_parts.netloc.lower
)
)
# path
if a_parts.path != b_parts.path:
diff_list.append(
'Paths differ: a="{}" b="{}"'.format(a_parts.path, b_parts.path)
)
# fragment
if a_parts.fragment != b_parts.fragment:
diff_list.append(
'Fragments differ. a="{}" b="{}"'.format(a_parts.fragment, b_parts.fragment)
)
# param
a_param_list = sorted(a_parts.params.split(";"))
b_param_list = sorted(b_parts.params.split(";"))
if a_param_list != b_param_list:
diff_list.append(
'Parameters differ. a="{}" b="{}"'.format(
', '.join(a_param_list), ', '.join(b_param_list)
)
)
# query
a_query_dict = urllib.parse.parse_qs(a_parts.query)
b_query_dict = urllib.parse.parse_qs(b_parts.query)
if len(list(a_query_dict.keys())) != len(list(b_query_dict.keys())):
diff_list.append(
'Number of query keys differs. a={} b={}'.format(
len(list(a_query_dict.keys())), len(list(b_query_dict.keys()))
)
)
for a_key in b_query_dict:
if a_key not in list(b_query_dict.keys()):
diff_list.append(
'Query key in first missing in second. a_key="{}"'.format(a_key)
)
elif sorted(a_query_dict[a_key]) != sorted(b_query_dict[a_key]):
diff_list.append(
'Query values differ. key="{}" a_value="{}" b_value="{}"'.format(
a_key, sorted(a_query_dict[a_key]), sorted(b_query_dict[a_key])
)
)
for b_key in b_query_dict:
if b_key not in a_query_dict:
diff_list.append(
'Query key in second missing in first. b_key="{}"'.format(b_key)
)
return diff_list | python | def find_url_mismatches(a_url, b_url):
"""Given two URLs, return a list of any mismatches.
If the list is empty, the URLs are equivalent. Implemented by parsing and comparing
the elements. See RFC 1738 for details.
"""
diff_list = []
a_parts = urllib.parse.urlparse(a_url)
b_parts = urllib.parse.urlparse(b_url)
# scheme
if a_parts.scheme.lower() != b_parts.scheme.lower():
diff_list.append(
'Schemes differ. a="{}" b="{}" differ'.format(
a_parts.scheme.lower(), b_parts.scheme.lower()
)
)
# netloc
if a_parts.netloc.lower() != b_parts.netloc.lower():
diff_list.append(
'Network locations differ. a="{}" b="{}"'.format(
a_parts.netloc.lower(), b_parts.netloc.lower
)
)
# path
if a_parts.path != b_parts.path:
diff_list.append(
'Paths differ: a="{}" b="{}"'.format(a_parts.path, b_parts.path)
)
# fragment
if a_parts.fragment != b_parts.fragment:
diff_list.append(
'Fragments differ. a="{}" b="{}"'.format(a_parts.fragment, b_parts.fragment)
)
# param
a_param_list = sorted(a_parts.params.split(";"))
b_param_list = sorted(b_parts.params.split(";"))
if a_param_list != b_param_list:
diff_list.append(
'Parameters differ. a="{}" b="{}"'.format(
', '.join(a_param_list), ', '.join(b_param_list)
)
)
# query
a_query_dict = urllib.parse.parse_qs(a_parts.query)
b_query_dict = urllib.parse.parse_qs(b_parts.query)
if len(list(a_query_dict.keys())) != len(list(b_query_dict.keys())):
diff_list.append(
'Number of query keys differs. a={} b={}'.format(
len(list(a_query_dict.keys())), len(list(b_query_dict.keys()))
)
)
for a_key in b_query_dict:
if a_key not in list(b_query_dict.keys()):
diff_list.append(
'Query key in first missing in second. a_key="{}"'.format(a_key)
)
elif sorted(a_query_dict[a_key]) != sorted(b_query_dict[a_key]):
diff_list.append(
'Query values differ. key="{}" a_value="{}" b_value="{}"'.format(
a_key, sorted(a_query_dict[a_key]), sorted(b_query_dict[a_key])
)
)
for b_key in b_query_dict:
if b_key not in a_query_dict:
diff_list.append(
'Query key in second missing in first. b_key="{}"'.format(b_key)
)
return diff_list | [
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DataONEorg/d1_python | client_cli/src/d1_cli/impl/command_processor.py | CommandProcessor.search | def search(self, line):
"""CN search."""
if self._session.get(d1_cli.impl.session.QUERY_ENGINE_NAME) == "solr":
return self._search_solr(line)
raise d1_cli.impl.exceptions.InvalidArguments(
"Unsupported query engine: {}".format(
self._session.get(d1_cli.impl.session.QUERY_ENGINE_NAME)
)
) | python | def search(self, line):
"""CN search."""
if self._session.get(d1_cli.impl.session.QUERY_ENGINE_NAME) == "solr":
return self._search_solr(line)
raise d1_cli.impl.exceptions.InvalidArguments(
"Unsupported query engine: {}".format(
self._session.get(d1_cli.impl.session.QUERY_ENGINE_NAME)
)
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DataONEorg/d1_python | client_cli/src/d1_cli/impl/command_processor.py | CommandProcessor.resolve | def resolve(self, pid):
"""Get Object Locations for Object."""
client = d1_cli.impl.client.CLICNClient(
**self._cn_client_connect_params_from_session()
)
object_location_list_pyxb = client.resolve(pid)
for location in object_location_list_pyxb.objectLocation:
d1_cli.impl.util.print_info(location.url) | python | def resolve(self, pid):
"""Get Object Locations for Object."""
client = d1_cli.impl.client.CLICNClient(
**self._cn_client_connect_params_from_session()
)
object_location_list_pyxb = client.resolve(pid)
for location in object_location_list_pyxb.objectLocation:
d1_cli.impl.util.print_info(location.url) | [
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DataONEorg/d1_python | client_cli/src/d1_cli/impl/command_processor.py | CommandProcessor.science_object_get | def science_object_get(self, pid, path):
"""First try the MN set in the session.
Then try to resolve via the CN set in the session.
"""
mn_client = d1_cli.impl.client.CLIMNClient(
**self._mn_client_connect_params_from_session()
)
try:
response = mn_client.get(pid)
except d1_common.types.exceptions.DataONEException:
pass
else:
self._output(response, path)
return
cn_client = d1_cli.impl.client.CLICNClient(
**self._cn_client_connect_params_from_session()
)
object_location_list_pyxb = cn_client.resolve(pid)
for location in object_location_list_pyxb.objectLocation:
try:
params = self._mn_client_connect_params_from_session()
params["base_url"] = location.baseURL
mn_client = d1_cli.impl.client.CLIMNClient(**params)
response = mn_client.get(pid)
except d1_common.types.exceptions.DataONEException:
pass
else:
self._output(response, path)
return
raise d1_cli.impl.exceptions.CLIError("Could not find object: {}".format(pid)) | python | def science_object_get(self, pid, path):
"""First try the MN set in the session.
Then try to resolve via the CN set in the session.
"""
mn_client = d1_cli.impl.client.CLIMNClient(
**self._mn_client_connect_params_from_session()
)
try:
response = mn_client.get(pid)
except d1_common.types.exceptions.DataONEException:
pass
else:
self._output(response, path)
return
cn_client = d1_cli.impl.client.CLICNClient(
**self._cn_client_connect_params_from_session()
)
object_location_list_pyxb = cn_client.resolve(pid)
for location in object_location_list_pyxb.objectLocation:
try:
params = self._mn_client_connect_params_from_session()
params["base_url"] = location.baseURL
mn_client = d1_cli.impl.client.CLIMNClient(**params)
response = mn_client.get(pid)
except d1_common.types.exceptions.DataONEException:
pass
else:
self._output(response, path)
return
raise d1_cli.impl.exceptions.CLIError("Could not find object: {}".format(pid)) | [
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DataONEorg/d1_python | client_cli/src/d1_cli/impl/command_processor.py | CommandProcessor.science_object_create | def science_object_create(self, pid, path, format_id=None):
"""Create a new Science Object on a Member Node."""
self._queue_science_object_create(pid, path, format_id) | python | def science_object_create(self, pid, path, format_id=None):
"""Create a new Science Object on a Member Node."""
self._queue_science_object_create(pid, path, format_id) | [
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DataONEorg/d1_python | client_cli/src/d1_cli/impl/command_processor.py | CommandProcessor.science_object_update | def science_object_update(self, pid_old, path, pid_new, format_id=None):
"""Obsolete a Science Object on a Member Node with a different one."""
self._queue_science_object_update(pid_old, path, pid_new, format_id) | python | def science_object_update(self, pid_old, path, pid_new, format_id=None):
"""Obsolete a Science Object on a Member Node with a different one."""
self._queue_science_object_update(pid_old, path, pid_new, format_id) | [
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DataONEorg/d1_python | client_cli/src/d1_cli/impl/command_processor.py | CommandProcessor._search_solr | def _search_solr(self, line):
"""Perform a SOLR search."""
try:
query_str = self._create_solr_query(line)
client = d1_cli.impl.client.CLICNClient(
**self._cn_client_connect_params_from_session()
)
object_list_pyxb = client.search(
queryType=d1_common.const.DEFAULT_SEARCH_ENGINE,
query=query_str,
start=self._session.get(d1_cli.impl.session.START_NAME),
rows=self._session.get(d1_cli.impl.session.COUNT_NAME),
)
d1_cli.impl.util.print_info(self._pretty(object_list_pyxb.toxml("utf-8")))
except d1_common.types.exceptions.ServiceFailure as e:
e = "%".join(str(e).splitlines()) # Flatten line
regexp = re.compile(
r"errorCode: (?P<error_code>\d+)%.*%Status code: (?P<status_code>\d+)"
)
result = regexp.search(e)
if (
(result is not None)
and (result.group("error_code") == "500")
and (result.group("status_code") == "400")
): # noqa: E129
result = re.search(
r"<b>description</b> <u>(?P<description>[^<]+)</u>", e
)
msg = re.sub(
"&([^;]+);",
lambda m: chr(html.entities.name2codepoint[m.group(1)]),
result.group("description"),
)
d1_cli.impl.util.print_info("Warning: %s" % msg)
else:
d1_cli.impl.util.print_error("Unexpected error:\n%s" % str(e)) | python | def _search_solr(self, line):
"""Perform a SOLR search."""
try:
query_str = self._create_solr_query(line)
client = d1_cli.impl.client.CLICNClient(
**self._cn_client_connect_params_from_session()
)
object_list_pyxb = client.search(
queryType=d1_common.const.DEFAULT_SEARCH_ENGINE,
query=query_str,
start=self._session.get(d1_cli.impl.session.START_NAME),
rows=self._session.get(d1_cli.impl.session.COUNT_NAME),
)
d1_cli.impl.util.print_info(self._pretty(object_list_pyxb.toxml("utf-8")))
except d1_common.types.exceptions.ServiceFailure as e:
e = "%".join(str(e).splitlines()) # Flatten line
regexp = re.compile(
r"errorCode: (?P<error_code>\d+)%.*%Status code: (?P<status_code>\d+)"
)
result = regexp.search(e)
if (
(result is not None)
and (result.group("error_code") == "500")
and (result.group("status_code") == "400")
): # noqa: E129
result = re.search(
r"<b>description</b> <u>(?P<description>[^<]+)</u>", e
)
msg = re.sub(
"&([^;]+);",
lambda m: chr(html.entities.name2codepoint[m.group(1)]),
result.group("description"),
)
d1_cli.impl.util.print_info("Warning: %s" % msg)
else:
d1_cli.impl.util.print_error("Unexpected error:\n%s" % str(e)) | [
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DataONEorg/d1_python | client_cli/src/d1_cli/impl/command_processor.py | CommandProcessor._create_solr_query | def _create_solr_query(self, line):
"""Actual search - easier to test. """
p0 = ""
if line:
p0 = line.strip()
p1 = self._query_string_to_solr_filter(line)
p2 = self._object_format_to_solr_filter(line)
p3 = self._time_span_to_solr_filter()
result = p0 + p1 + p2 + p3
return result.strip() | python | def _create_solr_query(self, line):
"""Actual search - easier to test. """
p0 = ""
if line:
p0 = line.strip()
p1 = self._query_string_to_solr_filter(line)
p2 = self._object_format_to_solr_filter(line)
p3 = self._time_span_to_solr_filter()
result = p0 + p1 + p2 + p3
return result.strip() | [
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genialis/resolwe | resolwe/flow/expression_engines/jinja/filters.py | apply_filter_list | def apply_filter_list(func, obj):
"""Apply `func` to list or tuple `obj` element-wise and directly otherwise."""
if isinstance(obj, (list, tuple)):
return [func(item) for item in obj]
return func(obj) | python | def apply_filter_list(func, obj):
"""Apply `func` to list or tuple `obj` element-wise and directly otherwise."""
if isinstance(obj, (list, tuple)):
return [func(item) for item in obj]
return func(obj) | [
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genialis/resolwe | resolwe/flow/expression_engines/jinja/filters.py | _get_data_attr | def _get_data_attr(data, attr):
"""Get data object field."""
if isinstance(data, dict):
# `Data` object's id is hydrated as `__id` in expression engine
data = data['__id']
data_obj = Data.objects.get(id=data)
return getattr(data_obj, attr) | python | def _get_data_attr(data, attr):
"""Get data object field."""
if isinstance(data, dict):
# `Data` object's id is hydrated as `__id` in expression engine
data = data['__id']
data_obj = Data.objects.get(id=data)
return getattr(data_obj, attr) | [
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genialis/resolwe | resolwe/flow/expression_engines/jinja/filters.py | input_ | def input_(data, field_path):
"""Return a hydrated value of the ``input`` field."""
data_obj = Data.objects.get(id=data['__id'])
inputs = copy.deepcopy(data_obj.input)
# XXX: Optimize by hydrating only the required field (major refactoring).
hydrate_input_references(inputs, data_obj.process.input_schema)
hydrate_input_uploads(inputs, data_obj.process.input_schema)
return dict_dot(inputs, field_path) | python | def input_(data, field_path):
"""Return a hydrated value of the ``input`` field."""
data_obj = Data.objects.get(id=data['__id'])
inputs = copy.deepcopy(data_obj.input)
# XXX: Optimize by hydrating only the required field (major refactoring).
hydrate_input_references(inputs, data_obj.process.input_schema)
hydrate_input_uploads(inputs, data_obj.process.input_schema)
return dict_dot(inputs, field_path) | [
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genialis/resolwe | resolwe/flow/expression_engines/jinja/filters.py | _get_hydrated_path | def _get_hydrated_path(field):
"""Return HydratedPath object for file-type field."""
# Get only file path if whole file object is given.
if isinstance(field, str) and hasattr(field, 'file_name'):
# field is already actually a HydratedPath object
return field
if isinstance(field, dict) and 'file' in field:
hydrated_path = field['file']
if not hasattr(hydrated_path, 'file_name'):
raise TypeError("Filter argument must be a valid file-type field.")
return hydrated_path | python | def _get_hydrated_path(field):
"""Return HydratedPath object for file-type field."""
# Get only file path if whole file object is given.
if isinstance(field, str) and hasattr(field, 'file_name'):
# field is already actually a HydratedPath object
return field
if isinstance(field, dict) and 'file' in field:
hydrated_path = field['file']
if not hasattr(hydrated_path, 'file_name'):
raise TypeError("Filter argument must be a valid file-type field.")
return hydrated_path | [
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genialis/resolwe | resolwe/flow/expression_engines/jinja/filters.py | get_url | def get_url(field):
"""Return file's url based on base url set in settings."""
hydrated_path = _get_hydrated_path(field)
base_url = getattr(settings, 'RESOLWE_HOST_URL', 'localhost')
return "{}/data/{}/{}".format(base_url, hydrated_path.data_id, hydrated_path.file_name) | python | def get_url(field):
"""Return file's url based on base url set in settings."""
hydrated_path = _get_hydrated_path(field)
base_url = getattr(settings, 'RESOLWE_HOST_URL', 'localhost')
return "{}/data/{}/{}".format(base_url, hydrated_path.data_id, hydrated_path.file_name) | [
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genialis/resolwe | resolwe/flow/expression_engines/jinja/filters.py | descriptor | def descriptor(obj, path=''):
"""Return descriptor of given object.
If ``path`` is specified, only the content on that path is
returned.
"""
if isinstance(obj, dict):
# Current object is hydrated, so we need to get descriptor from
# dict representation.
desc = obj['__descriptor']
else:
desc = obj.descriptor
resp = dict_dot(desc, path)
if isinstance(resp, list) or isinstance(resp, dict):
return json.dumps(resp)
return resp | python | def descriptor(obj, path=''):
"""Return descriptor of given object.
If ``path`` is specified, only the content on that path is
returned.
"""
if isinstance(obj, dict):
# Current object is hydrated, so we need to get descriptor from
# dict representation.
desc = obj['__descriptor']
else:
desc = obj.descriptor
resp = dict_dot(desc, path)
if isinstance(resp, list) or isinstance(resp, dict):
return json.dumps(resp)
return resp | [
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DataONEorg/d1_python | client_onedrive/src/d1_onedrive/impl/clients/onedrive_solr_client.py | OneDriveSolrClient._close_open_date_ranges | def _close_open_date_ranges(self, record):
"""If a date range is missing the start or end date, close it by copying the
date from the existing value."""
date_ranges = (('beginDate', 'endDate'),)
for begin, end in date_ranges:
if begin in record and end in record:
return
elif begin in record:
record[end] = record[begin]
elif end in record:
record[begin] = record[end] | python | def _close_open_date_ranges(self, record):
"""If a date range is missing the start or end date, close it by copying the
date from the existing value."""
date_ranges = (('beginDate', 'endDate'),)
for begin, end in date_ranges:
if begin in record and end in record:
return
elif begin in record:
record[end] = record[begin]
elif end in record:
record[begin] = record[end] | [
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DataONEorg/d1_python | client_onedrive/src/d1_onedrive/impl/drivers/dokan/solrclient.py | SolrConnection.getSolrType | def getSolrType(self, field):
"""Returns the SOLR type of the specified field name.
Assumes the convention of dynamic fields using an underscore + type character
code for the field name.
"""
ftype = 'string'
try:
ftype = self.fieldtypes[field]
return ftype
except Exception:
pass
fta = field.split('_')
if len(fta) > 1:
ft = fta[len(fta) - 1]
try:
ftype = self.fieldtypes[ft]
# cache the type so it's used next time
self.fieldtypes[field] = ftype
except Exception:
pass
return ftype | python | def getSolrType(self, field):
"""Returns the SOLR type of the specified field name.
Assumes the convention of dynamic fields using an underscore + type character
code for the field name.
"""
ftype = 'string'
try:
ftype = self.fieldtypes[field]
return ftype
except Exception:
pass
fta = field.split('_')
if len(fta) > 1:
ft = fta[len(fta) - 1]
try:
ftype = self.fieldtypes[ft]
# cache the type so it's used next time
self.fieldtypes[field] = ftype
except Exception:
pass
return ftype | [
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DataONEorg/d1_python | client_onedrive/src/d1_onedrive/impl/drivers/dokan/solrclient.py | SolrConnection.getftype | def getftype(self, name):
"""Returns the python type for the specified field name. The field list is
cached so multiple calls do not invoke a getFields request each time.
@param name(string) The name of the SOLR field
@returns Python type of the field.
"""
fields = self.getFields()
try:
fld = fields['fields'][name]
except Exception:
return str
if fld['type'] in ['string', 'text', 'stext', 'text_ws']:
return str
if fld['type'] in ['sint', 'integer', 'long', 'slong']:
return int
if fld['type'] in ['sdouble', 'double', 'sfloat', 'float']:
return float
if fld['type'] in ['boolean']:
return bool
return fld['type'] | python | def getftype(self, name):
"""Returns the python type for the specified field name. The field list is
cached so multiple calls do not invoke a getFields request each time.
@param name(string) The name of the SOLR field
@returns Python type of the field.
"""
fields = self.getFields()
try:
fld = fields['fields'][name]
except Exception:
return str
if fld['type'] in ['string', 'text', 'stext', 'text_ws']:
return str
if fld['type'] in ['sint', 'integer', 'long', 'slong']:
return int
if fld['type'] in ['sdouble', 'double', 'sfloat', 'float']:
return float
if fld['type'] in ['boolean']:
return bool
return fld['type'] | [
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genialis/resolwe | resolwe/process/fields.py | Field.clean | def clean(self, value):
"""Run validators and return the clean value."""
if value is None:
value = self.default
try:
value = self.to_python(value)
self.validate(value)
except ValidationError as error:
raise ValidationError("invalid value for {}: {}".format(
self.name,
error.args[0]
))
return value | python | def clean(self, value):
"""Run validators and return the clean value."""
if value is None:
value = self.default
try:
value = self.to_python(value)
self.validate(value)
except ValidationError as error:
raise ValidationError("invalid value for {}: {}".format(
self.name,
error.args[0]
))
return value | [
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genialis/resolwe | resolwe/process/fields.py | FileDescriptor.import_file | def import_file(self, imported_format=None, progress_from=0.0, progress_to=None):
"""Import field source file to working directory.
:param imported_format: Import file format (extracted, compressed or both)
:param progress_from: Initial progress value
:param progress_to: Final progress value
:return: Destination file path (if extracted and compressed, extracted path given)
"""
if not hasattr(resolwe_runtime_utils, 'import_file'):
raise RuntimeError('Requires resolwe-runtime-utils >= 2.0.0')
if imported_format is None:
imported_format = resolwe_runtime_utils.ImportedFormat.BOTH
return resolwe_runtime_utils.import_file(
src=self.file_temp,
file_name=self.path,
imported_format=imported_format,
progress_from=progress_from,
progress_to=progress_to
) | python | def import_file(self, imported_format=None, progress_from=0.0, progress_to=None):
"""Import field source file to working directory.
:param imported_format: Import file format (extracted, compressed or both)
:param progress_from: Initial progress value
:param progress_to: Final progress value
:return: Destination file path (if extracted and compressed, extracted path given)
"""
if not hasattr(resolwe_runtime_utils, 'import_file'):
raise RuntimeError('Requires resolwe-runtime-utils >= 2.0.0')
if imported_format is None:
imported_format = resolwe_runtime_utils.ImportedFormat.BOTH
return resolwe_runtime_utils.import_file(
src=self.file_temp,
file_name=self.path,
imported_format=imported_format,
progress_from=progress_from,
progress_to=progress_to
) | [
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genialis/resolwe | resolwe/process/fields.py | DataDescriptor._get | def _get(self, key):
"""Return given key from cache."""
self._populate_cache()
if key not in self._cache:
raise AttributeError("DataField has no member {}".format(key))
return self._cache[key] | python | def _get(self, key):
"""Return given key from cache."""
self._populate_cache()
if key not in self._cache:
raise AttributeError("DataField has no member {}".format(key))
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genialis/resolwe | resolwe/flow/managers/state.py | update_constants | def update_constants():
"""Recreate channel name constants with changed settings.
This kludge is mostly needed due to the way Django settings are
patched for testing and how modules need to be imported throughout
the project. On import time, settings are not patched yet, but some
of the code needs static values immediately. Updating functions such
as this one are then needed to fix dummy values.
"""
global MANAGER_CONTROL_CHANNEL, MANAGER_EXECUTOR_CHANNELS # pylint: disable=global-statement
global MANAGER_LISTENER_STATS, MANAGER_STATE_PREFIX # pylint: disable=global-statement
redis_prefix = getattr(settings, 'FLOW_MANAGER', {}).get('REDIS_PREFIX', '')
MANAGER_CONTROL_CHANNEL = '{}.control'.format(redis_prefix)
MANAGER_EXECUTOR_CHANNELS = ManagerChannelPair(
'{}.result_queue'.format(redis_prefix),
'{}.result_queue_response'.format(redis_prefix),
)
MANAGER_STATE_PREFIX = '{}.state'.format(redis_prefix)
MANAGER_LISTENER_STATS = '{}.listener_stats'.format(redis_prefix) | python | def update_constants():
"""Recreate channel name constants with changed settings.
This kludge is mostly needed due to the way Django settings are
patched for testing and how modules need to be imported throughout
the project. On import time, settings are not patched yet, but some
of the code needs static values immediately. Updating functions such
as this one are then needed to fix dummy values.
"""
global MANAGER_CONTROL_CHANNEL, MANAGER_EXECUTOR_CHANNELS # pylint: disable=global-statement
global MANAGER_LISTENER_STATS, MANAGER_STATE_PREFIX # pylint: disable=global-statement
redis_prefix = getattr(settings, 'FLOW_MANAGER', {}).get('REDIS_PREFIX', '')
MANAGER_CONTROL_CHANNEL = '{}.control'.format(redis_prefix)
MANAGER_EXECUTOR_CHANNELS = ManagerChannelPair(
'{}.result_queue'.format(redis_prefix),
'{}.result_queue_response'.format(redis_prefix),
)
MANAGER_STATE_PREFIX = '{}.state'.format(redis_prefix)
MANAGER_LISTENER_STATS = '{}.listener_stats'.format(redis_prefix) | [
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genialis/resolwe | resolwe/flow/managers/state.py | ManagerState.destroy_channels | def destroy_channels(self):
"""Destroy Redis channels managed by this state instance."""
for item_name in dir(self):
item = getattr(self, item_name)
if isinstance(item, self.RedisAtomicBase):
self.redis.delete(item.item_name) | python | def destroy_channels(self):
"""Destroy Redis channels managed by this state instance."""
for item_name in dir(self):
item = getattr(self, item_name)
if isinstance(item, self.RedisAtomicBase):
self.redis.delete(item.item_name) | [
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DataONEorg/d1_python | lib_common/src/d1_common/cert/subject_info_renderer.py | SubjectInfoRenderer.render_to_image_file | def render_to_image_file(
self, image_out_path, width_pixels=None, height_pixels=None, dpi=90
):
"""Render the SubjectInfo to an image file.
Args:
image_out_path : str
Path to where image image will be written. Valid extensions are
``.svg,`` ``.pdf``, and ``.png``.
width_pixels : int
Width of image to write.
height_pixels : int
Height of image to write, in pixels.
dpi:
Dots Per Inch to declare in image file. This does not change the
resolution of the image but may change the size of the image when
rendered.
Returns:
None
"""
self._render_type = "file"
self._tree.render(
file_name=image_out_path,
w=width_pixels,
h=height_pixels,
dpi=dpi,
units="px",
tree_style=self._get_tree_style(),
) | python | def render_to_image_file(
self, image_out_path, width_pixels=None, height_pixels=None, dpi=90
):
"""Render the SubjectInfo to an image file.
Args:
image_out_path : str
Path to where image image will be written. Valid extensions are
``.svg,`` ``.pdf``, and ``.png``.
width_pixels : int
Width of image to write.
height_pixels : int
Height of image to write, in pixels.
dpi:
Dots Per Inch to declare in image file. This does not change the
resolution of the image but may change the size of the image when
rendered.
Returns:
None
"""
self._render_type = "file"
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h=height_pixels,
dpi=dpi,
units="px",
tree_style=self._get_tree_style(),
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DataONEorg/d1_python | lib_common/src/d1_common/cert/subject_info_renderer.py | SubjectInfoRenderer.browse_in_qt5_ui | def browse_in_qt5_ui(self):
"""Browse and edit the SubjectInfo in a simple Qt5 based UI."""
self._render_type = "browse"
self._tree.show(tree_style=self._get_tree_style()) | python | def browse_in_qt5_ui(self):
"""Browse and edit the SubjectInfo in a simple Qt5 based UI."""
self._render_type = "browse"
self._tree.show(tree_style=self._get_tree_style()) | [
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DataONEorg/d1_python | lib_common/src/d1_common/cert/subject_info_renderer.py | SubjectInfoRenderer._gen_etetoolkit_tree | def _gen_etetoolkit_tree(self, node, subject_info_tree):
"""Copy SubjectInfoTree to a ETE Tree."""
for si_node in subject_info_tree.child_list:
if si_node.type_str == TYPE_NODE_TAG:
child = self._add_type_node(node, si_node.label_str)
elif si_node.type_str == SUBJECT_NODE_TAG:
child = self._add_subject_node(node, si_node.label_str)
else:
raise AssertionError(
'Unknown node type. type_str="{}"'.format(si_node.type_str)
)
self._gen_etetoolkit_tree(child, si_node) | python | def _gen_etetoolkit_tree(self, node, subject_info_tree):
"""Copy SubjectInfoTree to a ETE Tree."""
for si_node in subject_info_tree.child_list:
if si_node.type_str == TYPE_NODE_TAG:
child = self._add_type_node(node, si_node.label_str)
elif si_node.type_str == SUBJECT_NODE_TAG:
child = self._add_subject_node(node, si_node.label_str)
else:
raise AssertionError(
'Unknown node type. type_str="{}"'.format(si_node.type_str)
)
self._gen_etetoolkit_tree(child, si_node) | [
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DataONEorg/d1_python | lib_common/src/d1_common/cert/subject_info_renderer.py | SubjectInfoRenderer._add_type_node | def _add_type_node(self, node, label):
"""Add a node representing a SubjectInfo type."""
child = node.add_child(name=label)
child.add_feature(TYPE_NODE_TAG, True)
return child | python | def _add_type_node(self, node, label):
"""Add a node representing a SubjectInfo type."""
child = node.add_child(name=label)
child.add_feature(TYPE_NODE_TAG, True)
return child | [
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DataONEorg/d1_python | lib_common/src/d1_common/cert/subject_info_renderer.py | SubjectInfoRenderer._add_subject_node | def _add_subject_node(self, node, subj_str):
"""Add a node containing a subject string."""
child = node.add_child(name=subj_str)
child.add_feature(SUBJECT_NODE_TAG, True)
return child | python | def _add_subject_node(self, node, subj_str):
"""Add a node containing a subject string."""
child = node.add_child(name=subj_str)
child.add_feature(SUBJECT_NODE_TAG, True)
return child | [
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DataONEorg/d1_python | lib_common/src/d1_common/cert/subject_info_renderer.py | SubjectInfoRenderer._get_node_path | def _get_node_path(self, node):
"""Return the path from the root to ``node`` as a list of node names."""
path = []
while node.up:
path.append(node.name)
node = node.up
return list(reversed(path)) | python | def _get_node_path(self, node):
"""Return the path from the root to ``node`` as a list of node names."""
path = []
while node.up:
path.append(node.name)
node = node.up
return list(reversed(path)) | [
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DataONEorg/d1_python | lib_common/src/d1_common/cert/subject_info_renderer.py | SubjectInfoRenderer._layout | def _layout(self, node):
"""ETE calls this function to style each node before rendering.
- ETE terms:
- A Style is a specification for how to render the node itself
- A Face defines extra information that is rendered outside of the node
- Face objects are used here to provide more control on how to draw the nodes.
"""
def set_edge_style():
"""Set the style for edges and make the node invisible."""
node_style = ete3.NodeStyle()
node_style["vt_line_color"] = EDGE_COLOR
node_style["hz_line_color"] = EDGE_COLOR
node_style["vt_line_width"] = EDGE_WIDTH
node_style["hz_line_width"] = EDGE_WIDTH
node_style["size"] = 0
node.set_style(node_style)
def style_subject_node(color="Black"):
"""Specify the appearance of Subject nodes."""
face = ete3.TextFace(node.name, fsize=SUBJECT_NODE_FONT_SIZE, fgcolor=color)
set_face_margin(face)
node.add_face(face, column=0, position="branch-right")
def style_type_node(color="Black"):
"""Specify the appearance of Type nodes."""
face = ete3.CircleFace(
radius=TYPE_NODE_RADIUS,
color=TYPE_NODE_COLOR_DICT.get(node.name, "White"),
style="circle",
label={
"text": node.name,
"color": color,
"fontsize": (
TYPE_NODE_FONT_SIZE_FILE
if self._render_type == "file"
else TYPE_NODE_FONT_SIZE_BROWSE
),
},
)
set_face_margin(face)
node.add_face(face, column=0, position="branch-right")
def set_face_margin(face):
"""Add margins to Face object.
- Add space between inner_border and border on TextFace.
- Add space outside bounding area of CircleFace.
"""
face.margin_left = 5
face.margin_right = 5
# face.margin_top = 5
# face.margin_bottom = 5
set_edge_style()
if hasattr(node, SUBJECT_NODE_TAG):
style_subject_node()
elif hasattr(node, TYPE_NODE_TAG):
style_type_node()
else:
raise AssertionError("Unknown node type") | python | def _layout(self, node):
"""ETE calls this function to style each node before rendering.
- ETE terms:
- A Style is a specification for how to render the node itself
- A Face defines extra information that is rendered outside of the node
- Face objects are used here to provide more control on how to draw the nodes.
"""
def set_edge_style():
"""Set the style for edges and make the node invisible."""
node_style = ete3.NodeStyle()
node_style["vt_line_color"] = EDGE_COLOR
node_style["hz_line_color"] = EDGE_COLOR
node_style["vt_line_width"] = EDGE_WIDTH
node_style["hz_line_width"] = EDGE_WIDTH
node_style["size"] = 0
node.set_style(node_style)
def style_subject_node(color="Black"):
"""Specify the appearance of Subject nodes."""
face = ete3.TextFace(node.name, fsize=SUBJECT_NODE_FONT_SIZE, fgcolor=color)
set_face_margin(face)
node.add_face(face, column=0, position="branch-right")
def style_type_node(color="Black"):
"""Specify the appearance of Type nodes."""
face = ete3.CircleFace(
radius=TYPE_NODE_RADIUS,
color=TYPE_NODE_COLOR_DICT.get(node.name, "White"),
style="circle",
label={
"text": node.name,
"color": color,
"fontsize": (
TYPE_NODE_FONT_SIZE_FILE
if self._render_type == "file"
else TYPE_NODE_FONT_SIZE_BROWSE
),
},
)
set_face_margin(face)
node.add_face(face, column=0, position="branch-right")
def set_face_margin(face):
"""Add margins to Face object.
- Add space between inner_border and border on TextFace.
- Add space outside bounding area of CircleFace.
"""
face.margin_left = 5
face.margin_right = 5
# face.margin_top = 5
# face.margin_bottom = 5
set_edge_style()
if hasattr(node, SUBJECT_NODE_TAG):
style_subject_node()
elif hasattr(node, TYPE_NODE_TAG):
style_type_node()
else:
raise AssertionError("Unknown node type") | [
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genialis/resolwe | resolwe/flow/executors/local/prepare.py | FlowExecutorPreparer.extend_settings | def extend_settings(self, data_id, files, secrets):
"""Prevent processes requiring access to secrets from being run."""
process = Data.objects.get(pk=data_id).process
if process.requirements.get('resources', {}).get('secrets', False):
raise PermissionDenied(
"Process which requires access to secrets cannot be run using the local executor"
)
return super().extend_settings(data_id, files, secrets) | python | def extend_settings(self, data_id, files, secrets):
"""Prevent processes requiring access to secrets from being run."""
process = Data.objects.get(pk=data_id).process
if process.requirements.get('resources', {}).get('secrets', False):
raise PermissionDenied(
"Process which requires access to secrets cannot be run using the local executor"
)
return super().extend_settings(data_id, files, secrets) | [
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genialis/resolwe | resolwe/flow/finders.py | get_finder | def get_finder(import_path):
"""Get a process finder."""
finder_class = import_string(import_path)
if not issubclass(finder_class, BaseProcessesFinder):
raise ImproperlyConfigured(
'Finder "{}" is not a subclass of "{}"'.format(finder_class, BaseProcessesFinder))
return finder_class() | python | def get_finder(import_path):
"""Get a process finder."""
finder_class = import_string(import_path)
if not issubclass(finder_class, BaseProcessesFinder):
raise ImproperlyConfigured(
'Finder "{}" is not a subclass of "{}"'.format(finder_class, BaseProcessesFinder))
return finder_class() | [
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genialis/resolwe | resolwe/flow/finders.py | AppDirectoriesFinder._find_folders | def _find_folders(self, folder_name):
"""Return a list of sub-directories."""
found_folders = []
for app_config in apps.get_app_configs():
folder_path = os.path.join(app_config.path, folder_name)
if os.path.isdir(folder_path):
found_folders.append(folder_path)
return found_folders | python | def _find_folders(self, folder_name):
"""Return a list of sub-directories."""
found_folders = []
for app_config in apps.get_app_configs():
folder_path = os.path.join(app_config.path, folder_name)
if os.path.isdir(folder_path):
found_folders.append(folder_path)
return found_folders | [
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DataONEorg/d1_python | gmn/src/d1_gmn/app/views/assert_sysmeta.py | sanity | def sanity(request, sysmeta_pyxb):
"""Check that sysmeta_pyxb is suitable for creating a new object and matches the
uploaded sciobj bytes."""
_does_not_contain_replica_sections(sysmeta_pyxb)
_is_not_archived(sysmeta_pyxb)
_obsoleted_by_not_specified(sysmeta_pyxb)
if 'HTTP_VENDOR_GMN_REMOTE_URL' in request.META:
return
_has_correct_file_size(request, sysmeta_pyxb)
_is_supported_checksum_algorithm(sysmeta_pyxb)
_is_correct_checksum(request, sysmeta_pyxb) | python | def sanity(request, sysmeta_pyxb):
"""Check that sysmeta_pyxb is suitable for creating a new object and matches the
uploaded sciobj bytes."""
_does_not_contain_replica_sections(sysmeta_pyxb)
_is_not_archived(sysmeta_pyxb)
_obsoleted_by_not_specified(sysmeta_pyxb)
if 'HTTP_VENDOR_GMN_REMOTE_URL' in request.META:
return
_has_correct_file_size(request, sysmeta_pyxb)
_is_supported_checksum_algorithm(sysmeta_pyxb)
_is_correct_checksum(request, sysmeta_pyxb) | [
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DataONEorg/d1_python | gmn/src/d1_gmn/app/views/assert_sysmeta.py | is_valid_sid_for_new_standalone | def is_valid_sid_for_new_standalone(sysmeta_pyxb):
"""Assert that any SID in ``sysmeta_pyxb`` can be assigned to a new standalone
object."""
sid = d1_common.xml.get_opt_val(sysmeta_pyxb, 'seriesId')
if not d1_gmn.app.did.is_valid_sid_for_new_standalone(sid):
raise d1_common.types.exceptions.IdentifierNotUnique(
0,
'Identifier is already in use as {}. did="{}"'.format(
d1_gmn.app.did.classify_identifier(sid), sid
),
identifier=sid,
) | python | def is_valid_sid_for_new_standalone(sysmeta_pyxb):
"""Assert that any SID in ``sysmeta_pyxb`` can be assigned to a new standalone
object."""
sid = d1_common.xml.get_opt_val(sysmeta_pyxb, 'seriesId')
if not d1_gmn.app.did.is_valid_sid_for_new_standalone(sid):
raise d1_common.types.exceptions.IdentifierNotUnique(
0,
'Identifier is already in use as {}. did="{}"'.format(
d1_gmn.app.did.classify_identifier(sid), sid
),
identifier=sid,
) | [
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DataONEorg/d1_python | gmn/src/d1_gmn/app/views/assert_sysmeta.py | is_valid_sid_for_chain | def is_valid_sid_for_chain(pid, sid):
"""Assert that ``sid`` can be assigned to the single object ``pid`` or to the chain
to which ``pid`` belongs.
- If the chain does not have a SID, the new SID must be previously unused.
- If the chain already has a SID, the new SID must match the existing SID.
"""
if not d1_gmn.app.did.is_valid_sid_for_chain(pid, sid):
existing_sid = d1_gmn.app.revision.get_sid_by_pid(pid)
raise d1_common.types.exceptions.IdentifierNotUnique(
0,
'A different SID is already assigned to the revision chain to which '
'the object being created or updated belongs. A SID cannot be changed '
'once it has been assigned to a chain. '
'existing_sid="{}", new_sid="{}", pid="{}"'.format(existing_sid, sid, pid),
) | python | def is_valid_sid_for_chain(pid, sid):
"""Assert that ``sid`` can be assigned to the single object ``pid`` or to the chain
to which ``pid`` belongs.
- If the chain does not have a SID, the new SID must be previously unused.
- If the chain already has a SID, the new SID must match the existing SID.
"""
if not d1_gmn.app.did.is_valid_sid_for_chain(pid, sid):
existing_sid = d1_gmn.app.revision.get_sid_by_pid(pid)
raise d1_common.types.exceptions.IdentifierNotUnique(
0,
'A different SID is already assigned to the revision chain to which '
'the object being created or updated belongs. A SID cannot be changed '
'once it has been assigned to a chain. '
'existing_sid="{}", new_sid="{}", pid="{}"'.format(existing_sid, sid, pid),
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DataONEorg/d1_python | gmn/src/d1_gmn/app/views/assert_sysmeta.py | _does_not_contain_replica_sections | def _does_not_contain_replica_sections(sysmeta_pyxb):
"""Assert that ``sysmeta_pyxb`` does not contain any replica information."""
if len(getattr(sysmeta_pyxb, 'replica', [])):
raise d1_common.types.exceptions.InvalidSystemMetadata(
0,
'A replica section was included. A new object object created via '
'create() or update() cannot already have replicas. pid="{}"'.format(
d1_common.xml.get_req_val(sysmeta_pyxb.identifier)
),
identifier=d1_common.xml.get_req_val(sysmeta_pyxb.identifier),
) | python | def _does_not_contain_replica_sections(sysmeta_pyxb):
"""Assert that ``sysmeta_pyxb`` does not contain any replica information."""
if len(getattr(sysmeta_pyxb, 'replica', [])):
raise d1_common.types.exceptions.InvalidSystemMetadata(
0,
'A replica section was included. A new object object created via '
'create() or update() cannot already have replicas. pid="{}"'.format(
d1_common.xml.get_req_val(sysmeta_pyxb.identifier)
),
identifier=d1_common.xml.get_req_val(sysmeta_pyxb.identifier),
) | [
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DataONEorg/d1_python | gmn/src/d1_gmn/app/views/assert_sysmeta.py | _is_not_archived | def _is_not_archived(sysmeta_pyxb):
"""Assert that ``sysmeta_pyxb`` does not have have the archived flag set."""
if _is_archived(sysmeta_pyxb):
raise d1_common.types.exceptions.InvalidSystemMetadata(
0,
'Archived flag was set. A new object created via create() or update() '
'cannot already be archived. pid="{}"'.format(
d1_common.xml.get_req_val(sysmeta_pyxb.identifier)
),
identifier=d1_common.xml.get_req_val(sysmeta_pyxb.identifier),
) | python | def _is_not_archived(sysmeta_pyxb):
"""Assert that ``sysmeta_pyxb`` does not have have the archived flag set."""
if _is_archived(sysmeta_pyxb):
raise d1_common.types.exceptions.InvalidSystemMetadata(
0,
'Archived flag was set. A new object created via create() or update() '
'cannot already be archived. pid="{}"'.format(
d1_common.xml.get_req_val(sysmeta_pyxb.identifier)
),
identifier=d1_common.xml.get_req_val(sysmeta_pyxb.identifier),
) | [
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DataONEorg/d1_python | lib_common/src/d1_common/env.py | get_d1_env_by_base_url | def get_d1_env_by_base_url(cn_base_url):
"""Given the BaseURL for a CN, return the DataONE environment dict for the CN's
environemnt."""
for k, v in D1_ENV_DICT:
if v['base_url'].startswith(cn_base_url):
return D1_ENV_DICT[k] | python | def get_d1_env_by_base_url(cn_base_url):
"""Given the BaseURL for a CN, return the DataONE environment dict for the CN's
environemnt."""
for k, v in D1_ENV_DICT:
if v['base_url'].startswith(cn_base_url):
return D1_ENV_DICT[k] | [
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wilson-eft/wilson | wilson/match/smeft.py | match_all | def match_all(d_SMEFT, parameters=None):
"""Match the SMEFT Warsaw basis onto the WET JMS basis."""
p = default_parameters.copy()
if parameters is not None:
# if parameters are passed in, overwrite the default values
p.update(parameters)
C = wilson.util.smeftutil.wcxf2arrays_symmetrized(d_SMEFT)
C['vT'] = 246.22
C_WET = match_all_array(C, p)
C_WET = wilson.translate.wet.rotate_down(C_WET, p)
C_WET = wetutil.unscale_dict_wet(C_WET)
d_WET = wilson.util.smeftutil.arrays2wcxf(C_WET)
basis = wcxf.Basis['WET', 'JMS']
keys = set(d_WET.keys()) & set(basis.all_wcs)
d_WET = {k: d_WET[k] for k in keys}
return d_WET | python | def match_all(d_SMEFT, parameters=None):
"""Match the SMEFT Warsaw basis onto the WET JMS basis."""
p = default_parameters.copy()
if parameters is not None:
# if parameters are passed in, overwrite the default values
p.update(parameters)
C = wilson.util.smeftutil.wcxf2arrays_symmetrized(d_SMEFT)
C['vT'] = 246.22
C_WET = match_all_array(C, p)
C_WET = wilson.translate.wet.rotate_down(C_WET, p)
C_WET = wetutil.unscale_dict_wet(C_WET)
d_WET = wilson.util.smeftutil.arrays2wcxf(C_WET)
basis = wcxf.Basis['WET', 'JMS']
keys = set(d_WET.keys()) & set(basis.all_wcs)
d_WET = {k: d_WET[k] for k in keys}
return d_WET | [
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