Merge pull request #245 from jonls/sbml-celementtree

sbml: Use cElementTree if possible

psamm/datasource/sbml.py

@@ -19,14 +19,20 @@
 
 from __future__ import unicode_literals
 
-import xml.etree.ElementTree as ET
 from decimal import Decimal
 from fractions import Fraction
 from functools import partial
 import logging
 import re
 import json
 
+# Import ElementTree XML parser. The lxml etree implementation may also be
+# used with SBMLReader but has compatiblity issues with SBMLWriter.
+try:
+    import xml.etree.cElementTree as ET
+except ImportError:
+    import xml.etree.ElementTree as ET
+
 from six import itervalues, iteritems, text_type, PY3
 
 from .context import FileMark
@@ -640,23 +646,26 @@ def __init__(self, file, strict=False, ignore_boundary=True,
             self._sbml_tag('listOfCompartments'))
         for compartment in self._compartments.iterfind(
                 self._sbml_tag('compartment')):
-            filemark = FileMark(self._context, None, None)
+            filemark = FileMark(
+                self._context, self._get_sourceline(compartment), None)
             entry = CompartmentEntry(self, compartment, filemark=filemark)
             self._model_compartments[entry.id] = entry
 
         # Species
         self._model_species = {}
         self._species = self._model.find(self._sbml_tag('listOfSpecies'))
         for species in self._species.iterfind(self._sbml_tag('species')):
-            filemark = FileMark(self._context, None, None)
+            filemark = FileMark(
+                self._context, self._get_sourceline(species), None)
             entry = SpeciesEntry(self, species, filemark=filemark)
             self._model_species[entry.id] = entry
 
         # Reactions
         self._model_reactions = {}
         self._reactions = self._model.find(self._sbml_tag('listOfReactions'))
         for reaction in self._reactions.iterfind(self._sbml_tag('reaction')):
-            filemark = FileMark(self._context, None, None)
+            filemark = FileMark(
+                self._context, self._get_sourceline(reaction), None)
             entry = ReactionEntry(self, reaction, filemark=filemark)
             self._model_reactions[entry.id] = entry
 
@@ -700,6 +709,10 @@ def __init__(self, file, strict=False, ignore_boundary=True,
 
                 self._active_objective = self._model_objectives[active]
 
+    def _get_sourceline(self, element):
+        """Get source line of element (only supported by lxml)."""
+        return getattr(element, 'sourceline', None)
+
     def get_compartment(self, compartment_id):
         """Return :class:`.CompartmentEntry` corresponding to id."""
         return self._model_compartments[compartment_id]

psamm/tests/test_command.py

@@ -20,7 +20,6 @@
 import sys
 import os
 import argparse
-import codecs
 import shutil
 import tempfile
 from contextlib import contextmanager
@@ -103,6 +102,7 @@ class MockSolverCommand(SolverCommandMixin, Command):
     """
     def run(self):
         solver = self._get_solver()
+        print(solver)
 
 
 class BaseCommandTest(object):
@@ -579,7 +579,7 @@ def test_command_argument_error(self):
 
 class TestSBMLCommandMain(unittest.TestCase, BaseCommandTest):
     def setUp(self):
-        doc = StringIO('''<?xml version="1.0" encoding="UTF-8"?>
+        doc = BytesIO('''<?xml version="1.0" encoding="UTF-8"?>
 <sbml xmlns="http://www.sbml.org/sbml/level3/version1/core"
       xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version1"
       xmlns:html="http://www.w3.org/1999/xhtml"
@@ -631,7 +631,7 @@ def setUp(self):
    <fbc:fluxBound fbc:reaction="R_Biomass" fbc:operation="lessEqual" fbc:value="1000"/>
   </fbc:listOfFluxBounds>
  </model>
-</sbml>''')
+</sbml>'''.encode('utf-8'))
 
         reader = sbml.SBMLReader(doc)
         self._model = reader.create_model()

psamm/tests/test_datasource_sbml.py

@@ -16,21 +16,23 @@
 #
 # Copyright 2014-2017  Jon Lund Steffensen <jon_steffensen@uri.edu>
 
+from __future__ import unicode_literals
+
 import unittest
 
 from psamm.datasource import sbml
 from psamm.reaction import Reaction, Compound, Direction
 
 from decimal import Decimal
 from fractions import Fraction
-from six import StringIO
+from six import BytesIO
 
 
 class TestSBMLDatabaseL1V2(unittest.TestCase):
     """Test parsing of a simple level 1 version 2 SBML file"""
 
     def setUp(self):
-        self.doc = StringIO('''<?xml version="1.0" encoding="UTF-8"?>
+        self.doc = BytesIO('''<?xml version="1.0" encoding="UTF-8"?>
 <sbml xmlns="http://www.sbml.org/sbml/level1"
       xmlns:html="http://www.w3.org/1999/xhtml"
       level="1" version="2">
@@ -70,7 +72,7 @@ def setUp(self):
    </reaction>
   </listOfReactions>
  </model>
-</sbml>''')
+</sbml>'''.encode('utf-8'))
 
     def test_model_name(self):
         reader = sbml.SBMLReader(self.doc)
@@ -169,7 +171,7 @@ class TestSBMLDatabaseL2V5(unittest.TestCase):
     """Test parsing of a simple level 2 version 5 SBML file"""
 
     def setUp(self):
-        self.doc = StringIO('''<?xml version="1.0" encoding="UTF-8"?>
+        self.doc = BytesIO('''<?xml version="1.0" encoding="UTF-8"?>
 <sbml xmlns="http://www.sbml.org/sbml/level2/version5"
       xmlns:html="http://www.w3.org/1999/xhtml"
       level="2" version="5">
@@ -209,7 +211,7 @@ def setUp(self):
    </reaction>
   </listOfReactions>
  </model>
-</sbml>''')
+</sbml>'''.encode('utf-8'))
 
     def test_model_name(self):
         reader = sbml.SBMLReader(self.doc)
@@ -309,7 +311,7 @@ class TestSBMLDatabaseL3V1(unittest.TestCase):
     """Test parsing of a simple level 3 version 1 SBML file"""
 
     def setUp(self):
-        self.doc = StringIO('''<?xml version="1.0" encoding="UTF-8"?>
+        self.doc = BytesIO('''<?xml version="1.0" encoding="UTF-8"?>
 <sbml xmlns="http://www.sbml.org/sbml/level3/version1/core"
       xmlns:html="http://www.w3.org/1999/xhtml"
       level="3" version="1">
@@ -349,7 +351,7 @@ def setUp(self):
    </reaction>
   </listOfReactions>
  </model>
-</sbml>''')
+</sbml>'''.encode('utf-8'))
 
     def test_model_name(self):
         reader = sbml.SBMLReader(self.doc)
@@ -446,7 +448,7 @@ class TestSBMLDatabaseL3V1WithFBCV1(unittest.TestCase):
     """Test parsing of a level 3 version 1 SBML file with FBC version 1"""
 
     def setUp(self):
-        self.doc = StringIO('''<?xml version="1.0" encoding="UTF-8"?>
+        self.doc = BytesIO('''<?xml version="1.0" encoding="UTF-8"?>
 <sbml xmlns="http://www.sbml.org/sbml/level3/version1/core"
       xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version1"
       xmlns:html="http://www.w3.org/1999/xhtml"
@@ -498,7 +500,7 @@ def setUp(self):
    <fbc:fluxBound fbc:reaction="R_Biomass" fbc:operation="lessEqual" fbc:value="1000"/>
   </fbc:listOfFluxBounds>
  </model>
-</sbml>''')
+</sbml>'''.encode('utf-8'))
 
     def test_model_name(self):
         reader = sbml.SBMLReader(self.doc)
@@ -616,7 +618,7 @@ class TestSBMLDatabaseL3V1WithFBCV2(unittest.TestCase):
     """Test parsing of a level 3 version 1 SBML file with FBC version 2"""
 
     def setUp(self):
-        self.doc = StringIO('''<?xml version="1.0" encoding="UTF-8"?>
+        self.doc = BytesIO('''<?xml version="1.0" encoding="UTF-8"?>
 <sbml xmlns="http://www.sbml.org/sbml/level3/version1/core"
       xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2"
       xmlns:html="http://www.w3.org/1999/xhtml"
@@ -667,7 +669,7 @@ def setUp(self):
    </fbc:objective>
   </fbc:listOfObjectives>
  </model>
-</sbml>''')
+</sbml>'''.encode('utf-8'))
 
     def test_model_name(self):
         reader = sbml.SBMLReader(self.doc)