Source code for pkpd.protocols.protocol_pkpd_create_label

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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
from itertools import zip_longest

[docs]class ProtPKPDCreateLabel(ProtPKPD): """ Create label by performing calculations on already existing labels.\n Protocol created by\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