# **************************************************************************
# *
# * 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
from itertools import zip_longest
[docs]class ProtPKPDCreateLabel(ProtPKPD):
""" Create label by performing calculations on already existing labels.\n
Protocol created by http://www.kinestatpharma.com\n """
_label = 'create label'
#--------------------------- DEFINE param functions --------------------------------------------
def _defineParams(self, form):
form.addSection('Input')
form.addParam('inputExperiment', params.PointerParam, label="Input experiment", important=True,
pointerClass='PKPDExperiment',
help='Select an experiment with samples')
form.addParam('labelToAdd', params.StringParam, label="Label(s) to add", default="",
help='Name of the variable to add. If several names are given, separated by semicolons.')
form.addParam('rewrite', params.BooleanParam, label="Rewrite labels", default=False,
help='Set this flag to true if you want to rewrite the content of existing labels.')
form.addParam('expression', params.StringParam, label="Expression(s) to calculate", default="",
help='For example, to normalize the apparent volume of distribution by the animal weight use $(Vd)/$(weight), a literal as "T1", or a constant 1.5. '\
'If several labels are created, separated by semicolons.')
form.addParam('units', params.StringParam, label="Units", default="None",
help='For example, L/kg. If several labels are created, separated by semicolons. '\
'Set to None for no units.')
form.addParam('comment', params.StringParam, label="Label comment(s)", default="",
help='For example, apparent volume of distribution per kilogram. '\
'If several labels are created, separated by semicolons.')
#--------------------------- INSERT steps functions --------------------------------------------
def _insertAllSteps(self):
self._insertFunctionStep('runCreate',self.inputExperiment.get().getObjId(), self.labelToAdd.get(),
self.expression.get(), self.comment.get())
self._insertFunctionStep('createOutputStep')
#--------------------------- STEPS functions --------------------------------------------
[docs] def runCreate(self, objId, labelToAdd, expression, comment):
self.experiment = self.readExperiment(self.inputExperiment.get().fnPKPD)
labels = self.labelToAdd.get().split(';')
expressions = self.expression.get().split(';')
units = self.units.get().split(';')
comments = self.comment.get().split(';')
for label, expression, unit, comment in zip_longest(labels,expressions,units,comments,fillvalue=""):
labelToAdd = label.strip().replace(' ',"_")
units = PKPDUnit(unit.strip())
for sampleName, sample in self.experiment.samples.items():
varValue = sample.evaluateExpression(expression.strip())
self.experiment.addParameterToSample(sampleName, labelToAdd, units.unit, comment.strip(), varValue,
self.rewrite.get())
self.writeExperiment(self.experiment,self._getPath("experiment.pkpd"))
[docs] def createOutputStep(self):
self._defineOutputs(outputExperiment=self.experiment)
self._defineSourceRelation(self.inputExperiment, self.experiment)
#--------------------------- INFO functions --------------------------------------------
def _summary(self):
msg=[]
labels = self.labelToAdd.get().split(';')
expressions = self.expression.get().split(';')
for label, expression in izip_longest(labels,expressions,fillvalue=""):
msg.append("%s created as %s"%(label.strip(),expression.strip()))
return msg