Merge pull request #217 from jonls/sbml-compartment

sbml: Parse compartment entries

psamm/datasource/entry.py

@@ -13,7 +13,7 @@
 # You should have received a copy of the GNU General Public License
 # along with PSAMM.  If not, see <http://www.gnu.org/licenses/>.
 #
-# Copyright 2016  Jon Lund Steffensen <jon_steffensen@uri.edu>
+# Copyright 2016-2017  Jon Lund Steffensen <jon_steffensen@uri.edu>
 
 """Representation of compound/reaction entries in models."""
 

psamm/datasource/sbml.py

@@ -31,7 +31,8 @@
 
 from .context import FileMark
 from .entry import (CompoundEntry as BaseCompoundEntry,
-                    ReactionEntry as BaseReactionEntry)
+                    ReactionEntry as BaseReactionEntry,
+                    CompartmentEntry as BaseCompartmentEntry)
 from ..reaction import Reaction, Compound, Direction
 from ..metabolicmodel import create_exchange_id
 from ..expression.boolean import Expression, And, Or, Variable
@@ -385,6 +386,29 @@ def filemark(self):
         return self._filemark
 
 
+class CompartmentEntry(_SBMLEntry, BaseCompartmentEntry):
+    """Compartment entry in the SBML file"""
+
+    def __init__(self, reader, root, filemark=None):
+        super(CompartmentEntry, self).__init__(reader, root)
+
+        self._name = self._root.get('name')
+        self._filemark = filemark
+
+    @property
+    def properties(self):
+        """All compartment properties as a dict."""
+        properties = {'id': self._id}
+        if self._name is not None:
+            properties['name'] = self._name
+
+        return properties
+
+    @property
+    def filemark(self):
+        return self._filemark
+
+
 class ObjectiveEntry(object):
     """Flux objective defined with FBC"""
 
@@ -582,6 +606,16 @@ def __init__(self, file, strict=False, ignore_boundary=False,
                         entry.reaction, [])
                     entries.append(entry)
 
+        # Compartments
+        self._model_compartments = {}
+        self._compartments = self._model.find(
+            self._sbml_tag('listOfCompartments'))
+        for compartment in self._compartments.iterfind(
+                self._sbml_tag('compartment')):
+            filemark = FileMark(self._context, None, 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'))
@@ -621,6 +655,10 @@ def __init__(self, file, strict=False, ignore_boundary=False,
 
                 self._active_objective = self._model_objectives[active]
 
+    def get_compartment(self, compartment_id):
+        """Return :class:`.CompartmentEntry` corresponding to id."""
+        return self._model_compartments[compartment_id]
+
     def get_reaction(self, reaction_id):
         """Return :class:`.ReactionEntry` corresponding to reaction_id"""
         return self._model_reactions[reaction_id]
@@ -636,6 +674,11 @@ def get_objective(self, objective_id):
     def get_active_objective(self):
         return self._active_objective
 
+    @property
+    def compartments(self):
+        """Iterator over :class:`.CompartmentEntry` entries."""
+        return itervalues(self._model_compartments)
+
     @property
     def reactions(self):
         """Iterator over :class:`ReactionEntries <.ReactionEntry>`"""

psamm/tests/test_datasource_sbml.py

@@ -75,6 +75,12 @@ def setUp(self):
     def test_model_name(self):
         self.assertEqual(self.reader.name, 'Test model')
 
+    def test_compartment_exists(self):
+        compartments = {entry.id: entry for entry in self.reader.compartments}
+        self.assertEqual(len(compartments), 1)
+        self.assertEqual(compartments['cell'].id, 'cell')
+        self.assertEqual(compartments['cell'].name, 'cell')
+
     def test_compounds_exist(self):
         species = {entry.id: entry for entry in self.reader.species}
         self.assertEqual(len(species), 5)
@@ -189,6 +195,12 @@ def test_model_name(self):
         self.assertEqual(self.reader.id, 'test_model')
         self.assertEqual(self.reader.name, 'Test model')
 
+    def test_compartment_exists(self):
+        compartments = {entry.id: entry for entry in self.reader.compartments}
+        self.assertEqual(len(compartments), 1)
+        self.assertEqual(compartments['C_c'].id, 'C_c')
+        self.assertEqual(compartments['C_c'].name, 'cell')
+
     def test_compounds_exist(self):
         species = {entry.id: entry for entry in self.reader.species}
         self.assertEqual(len(species), 5)
@@ -303,6 +315,12 @@ def test_model_name(self):
         self.assertEqual(self.reader.id, 'test_model')
         self.assertEqual(self.reader.name, 'Test model')
 
+    def test_compartment_exists(self):
+        compartments = {entry.id: entry for entry in self.reader.compartments}
+        self.assertEqual(len(compartments), 1)
+        self.assertEqual(compartments['C_c'].id, 'C_c')
+        self.assertEqual(compartments['C_c'].name, 'cell')
+
     def test_compounds_exist(self):
         species = {entry.id: entry for entry in self.reader.species}
         self.assertEqual(len(species), 5)
@@ -429,6 +447,12 @@ def test_model_name(self):
         self.assertEqual(self.reader.id, 'test_model')
         self.assertEqual(self.reader.name, 'Test model')
 
+    def test_compartment_exists(self):
+        compartments = {entry.id: entry for entry in self.reader.compartments}
+        self.assertEqual(len(compartments), 1)
+        self.assertEqual(compartments['C_c'].id, 'C_c')
+        self.assertEqual(compartments['C_c'].name, 'cell')
+
     def test_compounds_exist(self):
         species = {entry.id: entry for entry in self.reader.species}
         self.assertEqual(len(species), 5)
@@ -583,6 +607,12 @@ def test_model_name(self):
         self.assertEqual(self.reader.id, 'test_model')
         self.assertEqual(self.reader.name, 'Test model')
 
+    def test_compartment_exists(self):
+        compartments = {entry.id: entry for entry in self.reader.compartments}
+        self.assertEqual(len(compartments), 1)
+        self.assertEqual(compartments['C_c'].id, 'C_c')
+        self.assertEqual(compartments['C_c'].name, 'cell')
+
     def test_compounds_exist(self):
         species = {entry.id: entry for entry in self.reader.species}
         self.assertEqual(len(species), 5)