def verify(self, xml_file_name) -> str:
""" verify xmldsig and return signerCertificate """
moaspss_conf = os.path.join(PROJDIR_ABS,
'conf/moa-spss/MOASPSSConfiguration.xml')
log4j_conf = os.path.join(PROJDIR_ABS, 'conf/log4j.properties')
sig_doc = xml_file_name
logging.debug(
'verifying signature of %s using moa-sp, config path=%s' %
(sig_doc, moaspss_conf))
try:
os.environ['PYJNIUS_ACTIVATE']
pvzdverifysig = self.pywrapper(moaspss_conf, log4j_conf, sig_doc)
response = pvzdverifysig.verify()
if response.pvzdCode != 'OK':
logging.debug("Signature verification failed, code=" +
response.pvzdCode + "; " + response.pvzdMessage)
raise ValidationError("Signature verification failed, code=" +
response.pvzdCode + "; " +
response.pvzdMessage)
except KeyError:
import javabridge
# constructor takes three string parameters
pvzdverifysig = javabridge.make_instance(
self.pvzd_verify_sig,
"(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)V",
moaspss_conf, log4j_conf, sig_doc)
# method verify returns response object
response = javabridge.call(
pvzdverifysig, "verify", "()" + "L" +
self.pvzd_verify_sig_pkg + "/" + "PvzdVerifySigResponse;")
if javabridge.get_field(response, "pvzdCode",
"Ljava/lang/String;") != 'OK':
raise ValidationError(
"Signature verification failed, code=" +
javabridge.get_field(response, "pvzdCode",
"Ljava/lang/String;") + "; " +
javabridge.get_field(response, "pvzdMessage",
"Ljava/lang/String;"))
# Following "see-what-you-signed" principle use returned data from sig library
signed_data_str = response.referencedata
try:
os.environ['PYJNIUS_ACTIVATE']
r = XmlSigVerifyerResponse(signed_data_str,
response.signerCertificateEncoded)
except KeyError:
import javabridge
r = XmlSigVerifyerResponse(
signed_data_str,
javabridge.get_field(response, "signerCertificateEncoded",
"Ljava/lang/String;"))
return r
def missing_count(self):
"""
The number of missing values.
:return: The number of missing values
:rtype: int
"""
return javabridge.get_field(self.jobject, "missingCount", "I")
def int_count(self):
"""
The number of int-like values.
:return: The number of int-like values
:rtype: int
"""
return javabridge.get_field(self.jobject, "intCount", "I")
def nominal_counts(self):
"""
Counts of each nominal value.
:return: Counts of each nominal value
:rtype: ndarray
"""
return javabridge.get_env().get_int_array_elements(javabridge.get_field(self.jobject, "nominalCounts", "[I"))
def unique_count(self):
"""
The number of values that only appear once.
:return: The number of values that only appear once
:rtype: int
"""
return javabridge.get_field(self.jobject, "uniqueCount", "I")
def distinct_count(self):
"""
The number of distinct values.
:return: The number of distinct values
:rtype: int
"""
return javabridge.get_field(self.jobject, "distinctCount", "I")
def int_count(self):
"""
The number of int-like values.
:return: The number of int-like values
:rtype: int
"""
return javabridge.get_field(self.jobject, "intCount", "I")
def test_09_03_set_field(self):
class_name = "org/cellprofiler/javabridge/test/RealRect"
o = javabridge.make_instance(class_name, "()V")
test_cases = (
("f_boolean", "Z", True), # <AK> added
("f_char", "C", "A"),
("f_byte", "B", 3),
("f_short", "S", 15),
("f_int", "I", 392),
("f_long", "J", -14),
("f_float", "F", 1.03),
("f_double", "D", -889.1),
("f_object", "Ljava/lang/Object;",
javabridge.make_instance("java/lang/Integer", "(I)V", 15)),
("f_object", "Ljava/lang/Object;", None))
for field_name, signature, value in test_cases:
javabridge.set_field(o, field_name, signature, value)
v = javabridge.get_field(o, field_name, signature)
if isinstance(value, float):
self.assertAlmostEqual(v, value)
elif isinstance(value, javabridge.JB_Object):
self.assertTrue(
javabridge.call(value, "equals", "(Ljava/lang/Object;)Z",
v))
else:
self.assertEqual(v, value)
def stddev(self):
"""
The std deviation of values at the last calculateDerived() call
:return: The std deviation of values at the last calculateDerived() call
:rtype: float
"""
return javabridge.get_field(self.jobject, "stdDev", "D")
def stddev(self):
"""
The std deviation of values at the last calculateDerived() call
:return: The std deviation of values at the last calculateDerived() call
:rtype: float
"""
return javabridge.get_field(self.jobject, "stdDev", "D")
def sumsq(self):
"""
The sum of values squared seen.
:return: The sum of values squared seen
:rtype: float
"""
return javabridge.get_field(self.jobject, "sumSq", "D")
def max(self):
"""
The maximum value seen, or Double.NaN if no values seen.
:return: The maximum value seen, or Double.NaN if no values seen
:rtype: float
"""
return javabridge.get_field(self.jobject, "max", "D")
def mean(self):
"""
The mean of values at the last calculateDerived() call.
:return: The mean of values at the last calculateDerived() call
:rtype: float
"""
return javabridge.get_field(self.jobject, "mean", "D")
def count(self):
"""
The number of values seen.
:return: The number of values seen
:rtype: float
"""
return javabridge.get_field(self.jobject, "count", "D")
def unique_count(self):
"""
The number of values that only appear once.
:return: The number of values that only appear once
:rtype: int
"""
return javabridge.get_field(self.jobject, "uniqueCount", "I")
def total_count(self):
"""
The total number of values.
:return: The total number of values
:rtype: int
"""
return javabridge.get_field(self.jobject, "totalCount", "I")
def sumsq(self):
"""
The sum of values squared seen.
:return: The sum of values squared seen
:rtype: float
"""
return javabridge.get_field(self.jobject, "sumSq", "D")
def mean(self):
"""
The mean of values at the last calculateDerived() call.
:return: The mean of values at the last calculateDerived() call
:rtype: float
"""
return javabridge.get_field(self.jobject, "mean", "D")
def missing_count(self):
"""
The number of missing values.
:return: The number of missing values
:rtype: int
"""
return javabridge.get_field(self.jobject, "missingCount", "I")
def max(self):
"""
The maximum value seen, or Double.NaN if no values seen.
:return: The maximum value seen, or Double.NaN if no values seen
:rtype: float
"""
return javabridge.get_field(self.jobject, "max", "D")
def count(self):
"""
The number of values seen.
:return: The number of values seen
:rtype: float
"""
return javabridge.get_field(self.jobject, "count", "D")
def distinct_count(self):
"""
The number of distinct values.
:return: The number of distinct values
:rtype: int
"""
return javabridge.get_field(self.jobject, "distinctCount", "I")
def total_count(self):
"""
The total number of values.
:return: The total number of values
:rtype: int
"""
return javabridge.get_field(self.jobject, "totalCount", "I")
def numeric_stats(self):
"""
Stats on numeric value distributions.
:return: Stats on numeric value distributions
:rtype: NumericStats
"""
return Stats(javabridge.get_field(self.jobject, "numericStats", "Lweka/experiment/Stats;"))
def nominal_counts(self):
"""
Counts of each nominal value.
:return: Counts of each nominal value
:rtype: ndarray
"""
return javabridge.get_env().get_int_array_elements(
javabridge.get_field(self.jobject, "nominalCounts", "[I"))
def nominal_weights(self):
"""
Weight mass for each nominal value.
:return: Weight mass for each nominal value
:rtype: ndarray
"""
return javabridge.get_env().get_double_array_elements(
javabridge.get_field(self.jobject, "nominalWeights", "[D"))
def nominal_weights(self):
"""
Weight mass for each nominal value.
:return: Weight mass for each nominal value
:rtype: ndarray
"""
return javabridge.get_env().get_double_array_elements(
javabridge.get_field(self.jobject, "nominalWeights", "[D"))
def numeric_stats(self):
"""
Stats on numeric value distributions.
:return: Stats on numeric value distributions
:rtype: NumericStats
"""
return Stats(
javabridge.get_field(self.jobject, "numericStats",
"Lweka/experiment/Stats;"))
def test_11_07_get_selection_bounds(self):
display_svc = ij2.get_display_service(self.context)
overlay_svc = ij2.get_overlay_service(self.context)
i, j = np.mgrid[0:15, 0:1900:100]
image = i+j
ds = ij2.create_dataset(self.context, image, "Foo")
display = display_svc.createDisplay("Foo", ds)
mask = np.zeros(i.shape, bool)
islice = slice(2,-3)
jslice = slice(3,-4)
mask[islice, jslice] = True
overlay = ij2.create_overlay(self.context, mask)
overlay_svc.addOverlays(display, J.make_list([overlay]))
ij2.select_overlay(display.o, overlay)
rect = overlay_svc.getSelectionBounds(display)
self.assertEqual(J.get_field(rect, "x", "D"), 3)
self.assertEqual(J.get_field(rect, "y", "D"), 2)
self.assertEqual(J.get_field(rect, "width", "D"), 11)
self.assertEqual(J.get_field(rect, "height", "D"), 9)
def test_11_07_get_selection_bounds(self):
display_svc = ij2.get_display_service(self.context)
overlay_svc = ij2.get_overlay_service(self.context)
i, j = np.mgrid[0:15, 0:1900:100]
image = i + j
ds = ij2.create_dataset(self.context, image, "Foo")
display = display_svc.createDisplay("Foo", ds)
mask = np.zeros(i.shape, bool)
islice = slice(2, -3)
jslice = slice(3, -4)
mask[islice, jslice] = True
overlay = ij2.create_overlay(self.context, mask)
overlay_svc.addOverlays(display, J.make_list([overlay]))
ij2.select_overlay(display.o, overlay)
rect = overlay_svc.getSelectionBounds(display)
self.assertEqual(J.get_field(rect, "x", "D"), 3)
self.assertEqual(J.get_field(rect, "y", "D"), 2)
self.assertEqual(J.get_field(rect, "width", "D"), 11)
self.assertEqual(J.get_field(rect, "height", "D"), 9)
def verify(self, xml_file_name) -> str:
""" verify xmldsig and return signerCertificate """
moaspss_conf = os.path.join(PROJDIR_ABS, 'conf/moa-spss/MOASPSSConfiguration.xml')
log4j_conf = os.path.join(PROJDIR_ABS, 'conf/log4j.properties')
sig_doc = xml_file_name
logging.debug('verifying signature of %s using moa-sp, config path=%s' % (sig_doc, moaspss_conf))
try:
os.environ['PYJNIUS_ACTIVATE']
pvzdverifysig = self.pywrapper(
moaspss_conf,
log4j_conf,
sig_doc)
response = pvzdverifysig.verify()
if response.pvzdCode != 'OK':
logging.debug("Signature verification failed, code=" +
response.pvzdCode + "; " + response.pvzdMessage)
raise ValidationError("Signature verification failed, code=" +
response.pvzdCode + "; " + response.pvzdMessage)
except KeyError:
import javabridge
# constructor takes three string parameters
pvzdverifysig = javabridge.make_instance(self.pvzd_verify_sig,
"(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)V",
moaspss_conf, log4j_conf, sig_doc)
# method verify returns response object
response = javabridge.call(pvzdverifysig, "verify",
"()" + "L" + self.pvzd_verify_sig_pkg + "/" + "PvzdVerifySigResponse;")
if javabridge.get_field(response, "pvzdCode", "Ljava/lang/String;") != 'OK':
raise ValidationError("Signature verification failed, code=" +
javabridge.get_field(response, "pvzdCode", "Ljava/lang/String;") + "; " +
javabridge.get_field(response, "pvzdMessage", "Ljava/lang/String;"))
# Following "see-what-you-signed" principle use returned data from sig library
signed_data_str = response.referencedata
try:
os.environ['PYJNIUS_ACTIVATE']
r = XmlSigVerifyerResponse(signed_data_str, response.signerCertificateEncoded)
except KeyError:
import javabridge
r = XmlSigVerifyerResponse(signed_data_str, javabridge.get_field(response, "signerCertificateEncoded", "Ljava/lang/String;"))
return r
def __getattr__(self, name):
try:
jfield = self.klass.getField(name)
except:
raise AttributeError()
STATIC = J.get_static_field("java/lang/reflect/Modifier", "STATIC", "I")
if (J.call(jfield, "getModifiers", "()I") & STATIC) == STATIC:
raise AttributeError()
klass = J.call(jfield, "getType", "()Ljava/lang/Class;")
result = J.get_field(self.o, name, sig(klass))
if isinstance(result, J.JB_Object):
result = JWrapper(result)
return result
def __getattr__(self, name):
try:
jfield = self.klass.getField(name)
except:
raise AttributeError()
STATIC = J.get_static_field("java/lang/reflect/Modifier", "STATIC",
"I")
if (J.call(jfield, "getModifiers", "()I") & STATIC) == STATIC:
raise AttributeError()
klass = J.call(jfield, "getType", "()Ljava/lang/Class;")
result = J.get_field(self.o, name, sig(klass))
if isinstance(result, J.JB_Object):
result = JWrapper(result)
return result
def p(self, *args):
"""
Gets the p-value for r2
Signatures:
float p()
Returns:
The p value
"""
try:
p = self._p()
return p
except javabridge.JavaException:
return javabridge.get_field(self.o, "p","F")
def dPrime(self, *args):
"""
Gets the D' value
Signatures:
float dPrime()
Returns:
The D' value
"""
try:
dPrime = self._dPrime()
return dPrime
except javabridge.JavaException:
return javabridge.get_field(self.o, "dprime","F")
def r2(self, *args):
"""
Gets the r2 value
Signatures:
float r2()
Returns:
The r2 value
"""
try:
r2 = self._r2()
return r2
except javabridge.JavaException:
return javabridge.get_field(self.o, "r2","F")
def n(self, *args):
"""
Gets the number of individuals used to calculate LD
Signatures:
int n()
Returns:
The number of individuals used to calculate LD
"""
try:
n = self._n()
return n
except javabridge.JavaException:
return javabridge.get_field(self.o, "n","I")
def __getattr__(self, name):
if name in ("o", "class_wrapper", "methods"):
raise AttributeError()
if not hasattr(self, "methods"):
# not initialized
raise AttributeError()
try:
jfield = self.class_wrapper.getField(name)
except:
raise AttributeError()
STATIC = J.get_static_field("java/lang/reflect/Modifier", "STATIC", "I")
if (J.call(jfield, "getModifiers", "()I") & STATIC) == STATIC:
raise AttributeError()
klass = J.call(jfield, "getType", "()Ljava/lang/Class;")
result = J.get_field(self.o, name, sig(klass))
if isinstance(result, J.JB_Object):
result = JWrapper(result)
return result
def __getattr__(self, name):
if name in ("o", "class_wrapper", "methods"):
raise AttributeError()
if not hasattr(self, "methods"):
# not initialized
raise AttributeError()
try:
jfield = self.class_wrapper.getField(name)
except:
raise AttributeError()
STATIC = J.get_static_field("java/lang/reflect/Modifier", "STATIC",
"I")
if (J.call(jfield, "getModifiers", "()I") & STATIC) == STATIC:
raise AttributeError()
klass = J.call(jfield, "getType", "()Ljava/lang/Class;")
result = J.get_field(self.o, name, sig(klass))
if isinstance(result, J.JB_Object):
result = JWrapper(result)
return result
def test_09_03_set_field(self):
class_name = "org/cellprofiler/javabridge/test/RealRect"
o = javabridge.make_instance(class_name, "()V")
test_cases = (
("f_char", "C", "A"),
("f_byte", "B", 3),
("f_short", "S", 15),
("f_int", "I", 392),
("f_long", "J", -14),
("f_float", "F", 1.03),
("f_double", "D", -889.1),
("f_object", "Ljava/lang/Object;",
javabridge.make_instance("java/lang/Integer", "(I)V", 15)),
("f_object", "Ljava/lang/Object;", None))
for field_name, signature, value in test_cases:
javabridge.set_field(o, field_name, signature, value)
v = javabridge.get_field(o, field_name, signature)
if isinstance(value, float):
self.assertAlmostEqual(v, value)
elif isinstance(value, javabridge.JB_Object):
self.assertTrue(javabridge.call(
value, "equals", "(Ljava/lang/Object;)Z", v))
else:
self.assertEqual(v, value)
def fn():
o = javabridge.make_instance("java/lang/Object", "()V")
javabridge.get_field(o, "NoSuchField", "I")
def test_09_01_00_get_field(self):
o = javabridge.make_instance(
"org/cellprofiler/javabridge/test/RealRect", "(DDDD)V", 1, 2, 3, 4)
self.assertEqual(javabridge.get_field(o, "x", "D"), 1)
def fn():
o = javabridge.make_instance("java/lang/Object", "()V")
javabridge.get_field(o, "NoSuchField", "I")
def test_09_01_00_get_field(self):
o = javabridge.make_instance("org/cellprofiler/javabridge/test/RealRect", "(DDDD)V", 1, 2, 3, 4)
self.assertEqual(javabridge.get_field(o, "x", "D"), 1)