def run_string_conversions1(self):
basestr = 200000 * b" "
li = []
for i in range(1000):
if (i + 1) % 100 == 0:
show_mem("%4d runs" % i)
dv = pyopenms.DataValue(basestr)
dv = pyopenms.DataValue(basestr)
li.append(dv)
del li
def run_string_lists(self):
basestr = 10000 * b" "
li = []
for i in range(100):
if (i + 1) % 100 == 0:
show_mem("%4d runs" % i)
sl = pyopenms.DataValue([basestr] * 30)
sl = pyopenms.DataValue([basestr] * 30)
li.append(sl)
del sl
del li
def getModelDefaults(default_model):
params = pms.Param()
params.setValue("type", pms.DataValue(default_model), "Type of model")
model_types = [ "linear", "b_spline", "interpolated"]
if default_model not in model_types:
model_types.insert(0, default_model)
params.setValidStrings("type", model_types)
model_params = pms.Param()
pms.TransformationModelLinear.getDefaultParameters(model_params)
params.insert("linear:", model_params)
params.setSectionDescription("linear", "Parameters for 'linear' model")
pms.TransformationModelBSpline.getDefaultParameters(model_params)
params.insert("b_spline:", model_params)
params.setSectionDescription("b_spline", "Parameters for 'b_spline' model")
pms.TransformationModelInterpolated.getDefaultParameters(model_params)
entry = model_params.getEntry("interpolation_type")
interpolation_types = entry.valid_strings
if "polynomial" in interpolation_types:
interpolation_types.remove("polynomial")
model_params.setValidStrings("interpolation_type", interpolation_types)
params.insert("interpolated:", model_params)
params.setSectionDescription("interpolated", "Parameters for 'interpolated' model")
return params
def _addDataProcessing(item, params):
dp = item.getDataProcessing()
p = pms.DataProcessing()
p.setProcessingActions(set([pms.ProcessingAction.ALIGNMENT]))
sw = p.getSoftware()
sw.setName(os.path.basename(sys.argv[0]))
sw.setVersion(pms.VersionInfo.getVersion())
p.setSoftware(sw)
p.setCompletionTime(pms.DateTime.now())
for k, v in params.asDict().items():
p.setMetaValue("parameter: "+k, pms.DataValue(v))
dp.append(p)
item.setDataProcessing(dp)
return item
def testDataValue():
"""
@tests:
DataValue.__init__
DataValue.isEmpty
DataValue.toDoubleList
DataValue.toDouble
DataValue.toInt
DataValue.toIntList
DataValue.toString
DataValue.toStringList
DataValue.valueType
"""
a = pyopenms.DataValue()
assert a.isEmpty()
a = pyopenms.DataValue(1)
assert not a.isEmpty()
assert a.toInt() == 1
assert a.valueType() == pyopenms.DataType.INT_VALUE
a = pyopenms.DataValue(1.0)
assert not a.isEmpty()
assert a.toDouble() == 1.0
assert a.valueType() == pyopenms.DataType.DOUBLE_VALUE
a = pyopenms.DataValue("1")
assert not a.isEmpty()
assert a.toString() == "1"
assert a.valueType() == pyopenms.DataType.STRING_VALUE
a = pyopenms.DataValue([1])
assert not a.isEmpty()
assert a.toIntList() == [1]
assert a.valueType() == pyopenms.DataType.INT_LIST
a = pyopenms.DataValue([1.0])
assert not a.isEmpty()
assert a.toDoubleList() == [1.0]
assert a.valueType() == pyopenms.DataType.DOUBLE_LIST
a = pyopenms.DataValue(["1.0"])
assert not a.isEmpty()
assert a.toStringList() == ["1.0"]
assert a.valueType() == pyopenms.DataType.STRING_LIST
def _testMetaInfoInterface(what):
#void getKeys(libcpp_vector[String] & keys)
#void getKeys(libcpp_vector[unsigned int] & keys)
#DataValue getMetaValue(unsigned int) nogil except +
#DataValue getMetaValue(String) nogil except +
#void setMetaValue(unsigned int, DataValue) nogil except +
#void setMetaValue(String, DataValue) nogil except +
#bool metaValueExists(String) nogil except +
#bool metaValueExists(unsigned int) nogil except +
#void removeMetaValue(String) nogil except +
#void removeMetaValue(unsigned int) nogil except +
what.setMetaValue("key", pyopenms.DataValue(42))
what.setMetaValue("key2", pyopenms.DataValue(42))
keys = []
what.getKeys(keys)
keys = [0]
what.getKeys(keys)
assert len(keys) and all(isinstance(k, (long, int)) for k in keys)
assert what.getMetaValue(keys[0]).toInt() == 42
keys = [""]
what.getKeys(keys)
assert len(keys) and all(isinstance(k, str) for k in keys)
assert what.getMetaValue(keys[0]).toInt() == 42
assert what.metaValueExists("key")
what.removeMetaValue("key")
what.setMetaValue(1024, pyopenms.DataValue(42))
keys = []
what.getKeys(keys)
keys = [0]
what.getKeys(keys)
assert len(keys) and all(isinstance(k, (long, int)) for k in keys)
assert what.getMetaValue(keys[0]).toInt() == 42
keys = [""]
what.getKeys(keys)
assert len(keys) and all(isinstance(k, str) for k in keys)
assert what.getMetaValue(keys[0]).toInt() == 42
what.setMetaValue("key", pyopenms.DataValue(42))
what.setMetaValue("key2", pyopenms.DataValue(42))
assert what.metaValueExists("key")
what.removeMetaValue("key")
keys = []
what.getKeys(keys)
assert len(keys) == 2
what.removeMetaValue("key2")
keys = []
what.getKeys(keys)
assert len(keys) == 1
what.clearMetaInfo()
keys = []
what.getKeys(keys)
assert len(keys) == 0