Source code for pkpd.protocols.protocol_pkpd_create_label_2exps

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# * Authors:     Carlos Oscar Sorzano (
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# * Kinestat Pharma
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import pyworkflow.protocol.params as params
from .protocol_pkpd import ProtPKPD
from pkpd.pkpd_units import PKPDUnit

[docs]class ProtPKPDCreateLabel2Exps(ProtPKPD): """ Create label by performing calculations on already existing labels from two different experiments.\n The protocol assumes that the same samples are present in both experiments and calculations are performed only on those samples with the same name in both experiments. Protocol created by\n """ _label = 'create label 2 Exps' #--------------------------- DEFINE param functions -------------------------------------------- def _defineParams(self, form): form.addSection('Input') form.addParam('inputExperiment1', params.PointerParam, label="Input experiment1", important=True, pointerClass='PKPDExperiment', help='Select an experiment with samples') form.addParam('inputExperiment2', params.PointerParam, label="Input experiment2", important=True, pointerClass='PKPDExperiment', help='Select an experiment with samples') form.addParam('labelToAdd', params.StringParam, label="Label to add", default="", help='Name of the variable to add') form.addParam('expression', params.StringParam, label="Expression to calculate", default="", help='For example, to estimate the Mean Absorption Time you may subtract the MRT of an intravenous experiment from the MRT of an oral experiment: $Exp1(MRT)-$Exp2(MRT)') form.addParam('units', params.StringParam, label="Units", default="None", help='For example, L/kg') form.addParam('comment', params.StringParam, label="Label comment", default="", help='For example, apparent volume of distribution per kilogram') #--------------------------- INSERT steps functions -------------------------------------------- def _insertAllSteps(self): self._insertFunctionStep('runCreate',self.inputExperiment1.get().getObjId(), self.inputExperiment2.get().getObjId(), self.labelToAdd.get(), self.expression.get(), self.comment.get()) self._insertFunctionStep('createOutputStep') #--------------------------- STEPS functions --------------------------------------------
[docs] def runCreate(self, objId1, objId2, labelToAdd, expression, comment): self.experiment1 = self.readExperiment(self.inputExperiment1.get().fnPKPD) self.experiment2 = self.readExperiment(self.inputExperiment2.get().fnPKPD) labelToAdd = self.labelToAdd.get().replace(' ',"_") units = PKPDUnit(self.units.get()) for sampleName, sample1 in self.experiment1.samples.items(): if sampleName in self.experiment2.samples: expression1 = sample1.substituteValuesInExpression(self.expression.get(),"Exp1") sample2 = self.experiment2.samples[sampleName] expression2 = sample2.substituteValuesInExpression(expression1,"Exp2") varValue = eval(expression2, {"__builtins__" : {"True": True, "False": False, "None": None} }, {}) self.experiment1.addParameterToSample(sampleName, labelToAdd, units.unit, self.comment.get(), varValue) else: # Remove this sample from the experiment because we cannot perform this calculation self.experiment1.samples.pop(sampleName) self.writeExperiment(self.experiment1,self._getPath("experiment.pkpd"))
[docs] def createOutputStep(self): self._defineOutputs(outputExperiment=self.experiment1) self._defineSourceRelation(self.inputExperiment1, self.experiment1) self._defineSourceRelation(self.inputExperiment2, self.experiment1)
#--------------------------- INFO functions -------------------------------------------- def _summary(self): msg=["%s created as %s"%(self.labelToAdd.get(),self.expression.get())] return msg