Source code for tellurium.teconverters.convert_phrasedml

from __future__ import print_function, division, absolute_import

import os
import re
try:
    import tesedml as libsedml
except ImportError:
    import libsedml

#Only load this class if phrasedml exists
try:
    import phrasedml



    class phrasedmlImporter(object):
    
        def __init__(self, sbml_map={}):
            """ Constructor. """
            self.sedml_str = None
            self.sedml_path = None
            self.sbml_map = sbml_map
    
    


        @classmethod
        def fromContent(cls, sedml_str, sbml_map={}):
    
            # FIXME: bad hack for https://github.com/fbergmann/libSEDML/issues/47
            # test for JWS quirks
            if 'xmlns="http://sed-ml.org/sed-ml/level1/version3"' in sedml_str:
                # import xml.etree.ElementTree as ElementTree
                # root = ElementTree.fromstring(sedml_str)
                # for p in root.findall('{http://sed-ml.org/sed-ml/level1/version3}plot2D'):
                #     if not 'logX' in p.attrib or not 'logY' in p.attrib:
                #         logX = False
                #         logY = False
                #         for l in p.findall('{http://sed-ml.org/sed-ml/level1/version3}listOfCurves'):
                #             for c in l.findall('{http://sed-ml.org/sed-ml/level1/version3}curve'):
                #                 if 'logX' in c.attrib and c.attrib['logX'].lower() == 'true':
                #                     logX = True
                #                 if 'logY' in c.attrib and c.attrib['logY'].lower() == 'true':
                #                     logY = True
                #         p.set('logX', logX)
                #         p.set('logY', logY)
                # sedml_str = (ElementTree.tostring(root, encoding='utf8', method='xml')).decode('utf8')
                while True:
                    p = sedml_str.find('plot2D')
                    if p < 0:
                        break
                    b = sedml_str.find('>', p)
                    if b < 0:
                        break
                    l = sedml_str.find('logX', p)
                    if l < 0 or b < l:
                        sedml_str = sedml_str[:p] + 'plot2D logX="false" logY="false" ' + sedml_str[p+len('plot2D'):]
                    else:
                        break
                print(sedml_str)
    
    
            importer = phrasedmlImporter(sbml_map)
            importer.sedml_str = sedml_str
            # test for errors
            result = importer.toPhrasedml()
            if result is None:
                # get errors from libsedml
                doc = libsedml.SedReader().readSedMLFromString(sedml_str)
                if doc.getNumErrors():
                    max_len = 100
                    message = doc.getError(doc.getNumErrors()-1).getMessage()
                    message = message[:max_len] + '...' if len(message) > max_len else message
                    raise RuntimeError('Errors reading SED-ML: {}'.format(message))
                else:
                    raise RuntimeError('Unable to read SED-ML.')
            return importer

    
    


        def isInRootDir(self, file):
            d = os.path.split(file)[0]
            return d == '' or d == '.'

    


        def removeFileExt(self, filename):
            return os.path.splitext(filename)[0]

    


        def formatResource(self, filename):
            """ Normalizes and also strips xml extension."""
            return self.removeFileExt(os.path.normpath(filename))

    


        def fixModelRefs(self, phrasedml_str):
            ''' Changes all references of type myModel.xml to myModel.'''
            model_ref = re.compile(r'^.*\s*model\s*"([^"]*)"\s*$')
            out_str = ''
            for line in phrasedml_str.splitlines():
                match = model_ref.match(line)
                if match:
                    filename = match.group(1)
                    if self.isInRootDir(filename):
                        line = line.replace(filename,self.formatResource(filename))
                out_str += line+'\n'
            return out_str

    


        def toPhrasedml(self):
            # assign sbml resources
            # print('toPhrasedml sbml resources:')
            phrasedml.clearReferencedSBML()
            for sbml_resource in self.sbml_map:
                # print('  {} -> {}'.format(sbml_resource, self.sbml_map[sbml_resource][:30]))
                phrasedml.setReferencedSBML(sbml_resource, self.sbml_map[sbml_resource])
            # convert to phrasedml
            if self.sedml_str:
                result = phrasedml.convertString(self.sedml_str)
                if result is None:
                    raise RuntimeError(phrasedml.getLastError())
                return self.fixModelRefs(phrasedml.getLastPhraSEDML())
            elif self.sedml_path:
                result = phrasedml.convertFile(self.sedml_str)
                if result is None:
                    raise RuntimeError(phrasedml.getLastError())
                return self.fixModelRefs(phrasedml.getLastPhraSEDML())



except:
    pass