# **************************************************************************
# *
# * Authors: Carlos Oscar Sorzano (info@kinestat.com)
# *
# * Kinestat Pharma
# *
# * This program is free software; you can redistribute it and/or modify
# * it under the terms of the GNU General Public License as published by
# * the Free Software Foundation; either version 2 of the License, or
# * (at your option) any later version.
# *
# * This program is distributed in the hope that it will be useful,
# * but WITHOUT ANY WARRANTY; without even the implied warranty of
# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# * GNU General Public License for more details.
# *
# * You should have received a copy of the GNU General Public License
# * along with this program; if not, write to the Free Software
# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
# * 02111-1307 USA
# *
# * All comments concerning this program package may be sent to the
# * e-mail address 'info@kinestat.com'
# *
# **************************************************************************
import pyworkflow.protocol.params as params
from .protocol_pkpd import ProtPKPD
from pkpd.pkpd_units import PKPDUnit
# TESTED in test_workflow_gabrielsson_pk03.py
# TESTED in test_workflow_deconvolution.py
# TESTED in test_workflow_ivivc.py
# TESTED in test_workflow_ivivc2.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