# **************************************************************************
# *
# * Authors: David Herreros Calero (dherreros@cnb.csic.es)
# *
# * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
# *
# * 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 'scipion@cnb.csic.es'
# *
# **************************************************************************
import pyworkflow as pw
from pyworkflow.mapper.sqlite_db import SqliteDb
from pyworkflow.utils.properties import Message
import pwem.objects.data_flexhub as pwobj
# FIXME: Do not use this methods and remove in the future
[docs]class ProtFlexBase:
def _createSet(self, SetClass, template, suffix, **kwargs):
""" Create a set and set the filename using the suffix.
If the file exists, it will be deleted. """
setFn = self._getPath(template % suffix)
# Close the connection to the database if
# it is open before deleting the file
pw.utils.cleanPath(setFn)
SqliteDb.closeConnection(setFn)
setObj = SetClass(filename=setFn, **kwargs)
return setObj
def _createSetOfParticlesFlex(self, suffix='', **kwargs):
return self._createSet(pwobj.SetOfParticlesFlex,
'flexparticles%s.sqlite', suffix, **kwargs)
def _createSetOfClassesFlex(self, flexParticles, suffix='', **kwargs):
classes = self._createSet(pwobj.SetOfClassesFlex,
'flexClasses%s.sqlite', suffix, **kwargs)
classes.setImages(flexParticles)
return classes
def _createSetOfClassesStructFlex(self, flexParticles, suffix='', **kwargs):
classes = self._createSet(pwobj.SetOfClassesStructFlex,
'flexClassesStruct%s.sqlite', suffix, **kwargs)
classes.setImages(flexParticles)
return classes
def _createSetOfVolumesFlex(self, suffix='', **kwargs):
return self._createSet(pwobj.SetOfVolumesFlex,
'flexvolumes%s.sqlite', suffix, **kwargs)
def _createSetOfAtomStructFlex(self, suffix='', **kwargs):
return self._createSet(pwobj.SetOfAtomStructFlex,
'flexstructs%s.sqlite', suffix, **kwargs)
def _getOutputSuffix(self, cls):
""" Get the name to be used for a new output.
For example: output3DCoordinates7.
It should take into account previous outputs
and number with a higher value.
"""
maxCounter = -1
for attrName, _ in self.iterOutputAttributes(cls):
suffix = attrName.replace(self.OUTPUT_PREFIX, '')
try:
counter = int(suffix)
except:
counter = 1 # when there is not number assume 1
maxCounter = max(counter, maxCounter)
return str(maxCounter+1) if maxCounter > 0 else '' # empty if not output