Source code for cadbiom.models.guard_transitions.TestModelExtraction

# -*- coding: utf-8 -*-
## Filename    : extract_visitor.py
## Author(s)   : Michel Le Borgne
## Created     : 5 nov. 2012
## Revision    :
## Source      :
##
## Copyright 2009 - 2012 - 2020 IRISA/IRSET
##
## This library 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 2.1 of the License, or
## any later version.
##
## This library 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.  The software and
## documentation provided hereunder is on an "as is" basis, and IRISA has
## no obligations to provide maintenance, support, updates, enhancements
## or modifications.
## In no event shall IRISA be liable to any party for direct, indirect,
## special, incidental or consequential damages, including lost profits,
## arising out of the use of this software and its documentation, even if
## IRISA have been advised of the possibility of such damage.  See
## the GNU General Public License for more details.
##
## You should have received a copy of the GNU General Public License
## along with this library; if not, write to the Free Software Foundation,
## Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
##
## The original code contained here was initially developed by:
##
##     Michel Le Borgne.
##     IRISA
##     Symbiose team
##     IRISA  Campus de Beaulieu
##     35042 RENNES Cedex, FRANCE
##
##
##     http:
##     mailto:
##
## Contributor(s): Geoffroy Andrieux
##
"""
Test Visitors for extracting submodels.
PathExtractor : abstract a trajectory as a set of path in the transition graph
"""
from __future__ import print_function
import unittest
import sys
import pkg_resources

from antlr4 import FileStream, CommonTokenStream

from cadbiom.models.guard_transitions.translators.chart_xml_pid import MakeModelFromPidFile
from cadbiom.models.guard_transitions.translators.chart_lang import LangVisitor

from cadbiom.models.guard_transitions.extract_visitor import PathExtractor
from cadbiom.models.guard_transitions.analyser.ana_visitors import TableVisitor
from cadbiom.models.guard_transitions.translators.cadlangLexer import cadlangLexer
from cadbiom.models.guard_transitions.translators.cadlangParser import cadlangParser
from cadbiom.models.guard_transitions.chart_model import ChartModel

import cadbiom.commons as cm

LOGGER = cm.logger()


class Reporter(object):
    """
    Simple reporter for tests
    """
    def __init__(self):
        self.error = False
        self.mess = ""

    def display(self,  mes):
        """
        print message
        """
        self.error = True
        self.mess += "ERROR -> "+mes
        LOGGER.error("ModelExtraction: %s", self.mess)


class TestExtractVisitors(unittest.TestCase):
    """
    Test visitor for model extraction
    """
    @unittest.skip("Test files not provided")
    def test_exec1(self):
        """
        Test on simple exp
        """
        file_name = 'translators/tests/ext1.cal'
        reporter = Reporter()
        readf = FileStream(file_name)
        lexer = cadlangLexer(readf)
        lexer.set_error_reporter(reporter)
        parser = cadlangParser(CommonTokenStream(lexer))
        parser.set_error_reporter(reporter)
        model = ChartModel('test1')
        parser.cad_model(model)
        model = parser.model

        target = ['C_D']
        frontier = ['F1', 'F2','F3']
        pex = PathExtractor(model, target, frontier, reporter)
        model.accept(pex)
        # decompiler visitor
        lvi = LangVisitor(sys.stdout)
        pex.extract_model.accept(lvi)

    def test_exec2(self):
        """
        test visitor execution
        """

        file_name = pkg_resources.resource_filename(
            __name__, # package name
            './translators/tests/tgf_cano.xml'
        )
        reporter = Reporter()
        parser = MakeModelFromPidFile(file_name, reporter)
        if reporter.error:
            raise Exception("Error in reading file '%s'" % file_name)

        model = parser.model
        tvi = TableVisitor(reporter)
        model.accept(tvi)

        target = ['TRAP_1']
        frontier = ['TGFBR2__dimer___active_intToMb',
                    'TGFBfamily__dimer___active_exCellRegion', 'CTGF']
        pex = PathExtractor(model, target, frontier, reporter)
        model.accept(pex)
        # decompiler visitor
        lvi = LangVisitor(sys.stdout)
        pex.extract_model.accept(lvi)
        # Note extracted model is the extract_model attribute of PathExtractor