Source code for pkpd.protocols.protocol_pkpd_change_via

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# *
# * Authors:     Carlos Oscar Sorzano (info@kinestat.com)
# *
# * Kinestat Pharma
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# * This program is free software; you can redistribute it and/or modify
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import pyworkflow.protocol.params as params
from .protocol_pkpd import ProtPKPD
from pkpd.pkpd_units import PKPDUnit

# TESTED in test_workflow_gabrielsson_pk03.py, test_workflow_deconvolution.py

[docs]class ProtPKPDChangeVia(ProtPKPD): """ Change via of administration\n This protocol may also be used to change the bioavailability or the tlag Protocol created by http://www.kinestatpharma.com\n """ _label = 'change via' #--------------------------- DEFINE param functions -------------------------------------------- def _defineParams(self, form): form.addSection('Input') form.addParam('inputExperiment', params.PointerParam, label="Input experiment", pointerClass='PKPDExperiment', help='Select an experiment with samples') form.addParam('viaName', params.StringParam, label="Via name", help='Name of the via you want to change') form.addParam('newViaType', params.StringParam, label="New via type", help='New via type, leave it empty to keep current via. Valid vias are iv, ev0, ev1, ev01, evFractional, ' 'ev0tlag1, ev1-ev1Saturable, doubleWeibull, tripleWeibull, spline2, spline3, ..., spline20, ' 'splineXY2, splineXY3, ..., splineXY20') form.addParam('tlag', params.StringParam, label="New tlag", help='New tlag of the dose, leave it empty to let it free so that it can be optimized by an ODE model') form.addParam('bioavailability', params.StringParam, label="New bioavailability", help='New bioavailability of the dose, leave it empty to let it free so that it can be optimized by an ODE model') #--------------------------- INSERT steps functions -------------------------------------------- def _insertAllSteps(self): self._insertFunctionStep('runChange',self.inputExperiment.get().getObjId(),self.viaName.get(), self.newViaType.get(), self.tlag.get(),self.bioavailability.get()) self._insertFunctionStep('createOutputStep') #--------------------------- STEPS functions --------------------------------------------
[docs] def runChange(self, objId, viaName, newViaType, tlag, bioavailability): self.experiment = self.readExperiment(self.inputExperiment.get().fnPKPD) via = self.experiment.vias[viaName] if newViaType!="": via.via = newViaType if not tlag: if not 'tlag' in via.paramsToOptimize: via.paramsToOptimize.append("tlag") via.paramsUnitsToOptimize.append(PKPDUnit.UNIT_TIME_MIN) else: if 'tlag' in via.paramsToOptimize: idx=via.paramsToOptimize.index('tlag') del via.paramsToOptimize[idx] del via.paramsUnitsToOptimize[idx] via.tlag=float(tlag) if not bioavailability: if not 'bioavailability' in via.paramsToOptimize: via.paramsToOptimize.append("bioavailability") via.paramsUnitsToOptimize.append(PKPDUnit.UNIT_NONE) else: if 'bioavailability' in via.paramsToOptimize: idx=via.paramsToOptimize.index('bioavailability') del via.paramsToOptimize[idx] del via.paramsUnitsToOptimize[idx] via.bioavailability=float(bioavailability) self.experiment.write(self._getPath("experiment.pkpd"))
[docs] def createOutputStep(self): self._defineOutputs(outputExperiment=self.experiment) self._defineSourceRelation(self.inputExperiment, self.experiment)
#--------------------------- INFO functions -------------------------------------------- def _validate(self): errors = [] experiment = self.readExperiment(self.inputExperiment.get().fnPKPD) if not self.viaName.get() in experiment.vias: errors.append("%s is not a via of the experiment"%self.viaName.get()) return errors def _summary(self): msg=[] return msg