#652[Feature request] Provide compartments as objects

cobra/__init__.py

@@ -10,7 +10,7 @@
 
 from cobra import flux_analysis, io
 from cobra.core import (
-    DictList, Gene, Metabolite, Model, Object, Reaction, Species)
+    DictList, Gene, Metabolite, Model, Object, Reaction, Species, Compartment)
 from cobra.util.version_info import show_versions
 
 __version__ = "0.11.3"

cobra/core/__init__.py

@@ -10,3 +10,4 @@
 from cobra.core.reaction import Reaction
 from cobra.core.solution import Solution, LegacySolution, get_solution
 from cobra.core.species import Species
+from cobra.core.compartment import Compartment

cobra/core/compartment.py

@@ -0,0 +1,40 @@
+# -*- coding: utf-8 -*-
+
+from __future__ import absolute_import
+
+from copy import deepcopy
+from cobra.util.util import format_long_string
+
+from cobra.core.object import Object
+
+
+class Compartment(Object):
+    """Compartment is a class for holding information regarding
+        a compartment in a cobra.Model object
+
+        Parameters
+        ----------
+        id : string
+           An identifier for the compartment
+        name : string
+           A human readable name.
+        """
+    def __init__(self, id=None, name=""):
+        Object.__init__(self, id, name)
+
+    def copy(self):
+        return deepcopy(self)
+
+    def _repr_html_(self):
+        return """
+        <table>
+            <tr>
+                <td><strong>Compartment identifier</strong></td><td>{id}</td>
+            </tr><tr>
+                <td><strong>Name</strong></td><td>{name}</td>
+            </tr><tr>
+                <td><strong>Memory address</strong></td>
+                <td>{address}</td>
+            </tr>
+        </table>""".format(id=self.id, name=format_long_string(self.name),
+                           address='0x0%x' % id(self))

cobra/core/model.py

@@ -16,6 +16,7 @@
 from cobra.exceptions import SolverNotFound
 from cobra.core.dictlist import DictList
 from cobra.core.object import Object
+from cobra.core.compartment import Compartment
 from cobra.core.reaction import separate_forward_and_reverse_bounds, Reaction
 from cobra.core.solution import get_solution
 from cobra.util.context import HistoryManager, resettable, get_context
@@ -90,7 +91,7 @@ def __init__(self, id_or_model=None, name=None):
             self.reactions = DictList()  # A list of cobra.Reactions
             self.metabolites = DictList()  # A list of cobra.Metabolites
             # genes based on their ids {Gene.id: Gene}
-            self._compartments = dict()
+            self._compartments = DictList()
             self._contexts = []
 
             # from cameo ...
@@ -163,29 +164,17 @@ def get_metabolite_compartments(self):
 
     @property
     def compartments(self):
-        return {met.compartment: self._compartments.get(met.compartment, '')
-                for met in self.metabolites if met.compartment is not None}
+        for met in self.metabolites:
+            if met.compartment is not None:
+                try:
+                    self._compartments.append(Compartment(met.compartment))
+                except Exception:
+                    pass
+        return self._compartments
 
     @compartments.setter
-    def compartments(self, value):
-        """Get or set the dictionary of current compartment descriptions.
-
-        Assigning a dictionary to this property updates the model's
-        dictionary of compartment descriptions with the new values.
-
-        Parameters
-        ----------
-        value : dict
-            Dictionary mapping compartments abbreviations to full names.
-
-        Examples
-        --------
-        >>> import cobra.test
-        >>> model = cobra.test.create_test_model("textbook")
-        >>> model.compartments = {'c': 'the cytosol'}
-        {'c': 'the cytosol', 'e': 'extracellular'}
-        """
-        self._compartments.update(value)
+    def compartments(self, compartments):
+        self._compartments = compartments
 
     @property
     def medium(self):
@@ -325,12 +314,42 @@ def copy(self):
         except Exception:  # pragma: no cover
             new._solver = copy(self.solver)  # pragma: no cover
 
+        try:
+            new.compartments = self.compartments
+        except Exception:
+            pass
+
         # it doesn't make sense to retain the context of a copied model so
         # assign a new empty context
         new._contexts = list()
 
         return new
 
+    def add_compartments(self, compartment_list):
+        if not hasattr(compartment_list, '__iter__'):
+            compartment_list = [compartment_list]
+        if len(compartment_list) == 0:
+            return None
+
+        # First check whether the compartments exist in the model
+        compartment_list = [x for x in compartment_list
+                            if x.id not in self.compartments]
+
+        bad_ids = [m for m in compartment_list
+                   if not isinstance(m.id, string_types) or len(m.id) < 1 or
+                   m is ' ']
+        if len(bad_ids) != 0:
+            raise ValueError('invalid identifiers in {}'.format(repr(bad_ids)))
+
+        self._compartments += compartment_list
+
+        context = get_context(self)
+        if context:
+            context(partial(self._compartments.__isub__, compartment_list))
+            for x in compartment_list:
+                # Do we care?
+                context(partial(setattr, x, '_model', None))
+
     def add_metabolites(self, metabolite_list):
         """Will add a list of metabolites to the model object and add new
         constraints accordingly.
@@ -863,6 +882,7 @@ def repair(self, rebuild_index=True, rebuild_relationships=True):
             self.reactions._generate_index()
             self.metabolites._generate_index()
             self.genes._generate_index()
+            self._compartments._generate_index()
         if rebuild_relationships:
             for met in self.metabolites:
                 met._reaction.clear()
@@ -1050,15 +1070,16 @@ def _repr_html_(self):
                 <td><strong>Objective expression</strong></td>
                 <td>{objective}</td>
             </tr><tr>
-                <td><strong>Compartments</strong></td>
+                <td><strong>{n_compartments} compartment(s)</strong></td>
                 <td>{compartments}</td>
             </tr>
-          </table>""".format(
+        </table>""".format(
             name=self.id,
             address='0x0%x' % id(self),
             num_metabolites=len(self.metabolites),
             num_reactions=len(self.reactions),
             objective=format_long_string(str(self.objective.expression), 100),
-            compartments=", ".join(
-                v if v else k for k, v in iteritems(self.compartments)
-            ))
+            n_compartments=len(self.compartments),
+            compartments=format_long_string(
+                ', '.join((r.id + " : " + r.name) for r in self._compartments),
+                200))

cobra/io/dict.py

@@ -8,7 +8,7 @@
 from numpy import bool_, float_
 from six import iteritems, string_types
 
-from cobra.core import Gene, Metabolite, Model, Reaction
+from cobra.core import Gene, Metabolite, Model, Reaction, Compartment
 from cobra.util.solver import set_objective
 
 _REQUIRED_REACTION_ATTRIBUTES = [
@@ -44,11 +44,17 @@
     "annotation": {},
 }
 
-_ORDERED_OPTIONAL_MODEL_KEYS = ["name", "compartments", "notes", "annotation"]
+_REQUIRED_COMPARTMENT_ATTRIBUTES = ["id", "name"]
+_ORDERED_OPTIONAL_COMPARTMENT_KEYS = ["notes", "annotation"]
+_OPTIONAL_COMPARTMENT_ATTRIBUTES = {
+    "notes": {},
+    "annotation": {},
+}
+
+_ORDERED_OPTIONAL_MODEL_KEYS = ["name", "notes", "annotation"]
 _OPTIONAL_MODEL_ATTRIBUTES = {
     "name": None,
     #  "description": None, should not actually be included
-    "compartments": [],
     "notes": {},
     "annotation": {},
 }
@@ -118,6 +124,23 @@ def gene_from_dict(gene):
     return new_gene
 
 
+def compartment_to_dict(compartment):
+    new_compartment = OrderedDict()
+    for key in _REQUIRED_COMPARTMENT_ATTRIBUTES:
+        new_compartment[key] = _fix_type(getattr(compartment, key))
+    _update_optional(compartment, new_compartment,
+                     _OPTIONAL_COMPARTMENT_ATTRIBUTES,
+                     _ORDERED_OPTIONAL_COMPARTMENT_KEYS)
+    return new_compartment
+
+
+def compartment_from_dict(compartment):
+    new_compartment = Compartment(compartment["id"])
+    for k, v in iteritems(compartment):
+        setattr(new_compartment, k, v)
+    return new_compartment
+
+
 def reaction_to_dict(reaction):
     new_reaction = OrderedDict()
     for key in _REQUIRED_REACTION_ATTRIBUTES:
@@ -174,6 +197,7 @@ def model_to_dict(model, sort=False):
     obj["metabolites"] = list(map(metabolite_to_dict, model.metabolites))
     obj["reactions"] = list(map(reaction_to_dict, model.reactions))
     obj["genes"] = list(map(gene_to_dict, model.genes))
+    obj["compartments"] = list(map(compartment_to_dict, model.compartments))
     obj["id"] = model.id
     _update_optional(model, obj, _OPTIONAL_MODEL_ATTRIBUTES,
                      _ORDERED_OPTIONAL_MODEL_KEYS)
@@ -182,6 +206,7 @@ def model_to_dict(model, sort=False):
         obj["metabolites"].sort(key=get_id)
         obj["reactions"].sort(key=get_id)
         obj["genes"].sort(key=get_id)
+        obj["compartments"].sort(key=get_id)
     return obj
 
 
@@ -211,6 +236,8 @@ def model_from_dict(obj):
     if 'reactions' not in obj:
         raise ValueError('Object has no reactions attribute. Cannot load.')
     model = Model()
+    model.add_compartments([compartment_from_dict(compartment) for
+                            compartment in obj['compartments']])
     model.add_metabolites(
         [metabolite_from_dict(metabolite) for metabolite in obj['metabolites']]
     )
@@ -225,6 +252,6 @@ def model_from_dict(obj):
         rxn in objective_reactions}
     set_objective(model, coefficients)
     for k, v in iteritems(obj):
-        if k in {'id', 'name', 'notes', 'compartments', 'annotation'}:
+        if k in {'id', 'name', 'notes', 'annotation'}:
             setattr(model, k, v)
     return model

cobra/io/json.py

@@ -229,10 +229,19 @@ def load_json_model(filename):
 
         },
         "compartments": {
-            "type": "object",
-            "patternProperties": {
-                "[a-z]{1,2}": {"type": "string"}
+            "type": "array",
+            "items": {
+                "type": "object",
+                "properties": {
+                    "id": {"type": "string"},
+                    "name": {"type": "string"},
+                    "notes": {"type": "object"},
+                    "annotation": {"type": "object"},
+                },
+                "required": ["id", "name"],
+                "additionalProperties": False,
             }
+
         },
         "notes": {"type": "object"},
         "annotation": {"type": "object"},

cobra/io/mat.py

@@ -11,7 +11,7 @@
 from numpy import array, inf, isinf
 from six import string_types
 
-from cobra.core import Metabolite, Model, Reaction
+from cobra.core import Metabolite, Model, Reaction, Compartment
 from cobra.util import create_stoichiometric_matrix
 from cobra.util.solver import set_objective
 
@@ -120,7 +120,8 @@ def create_mat_metabolite_id(model):
     for met in model.metabolites:
         if not _get_id_compartment(met.id) and met.compartment:
             yield '{}[{}]'.format(met.id,
-                                  model.compartments[met.compartment].lower())
+                                  model.compartments.get_by_id(
+                                      met.compartment).name.lower())
         else:
             yield met.id
 
@@ -204,12 +205,15 @@ def from_mat_struct(mat_struct, model_id=None, inf=inf):
             new_metabolite.compartment = m['comps'][0, 0][comp_index][0][0]
             if new_metabolite.compartment not in model.compartments:
                 comp_name = m['compNames'][0, 0][comp_index][0][0]
-                model.compartments[new_metabolite.compartment] = comp_name
+                model.add_compartments([
+                    Compartment(new_metabolite.compartment, comp_name)])
         else:
             new_metabolite.compartment = _get_id_compartment(new_metabolite.id)
-            if new_metabolite.compartment not in model.compartments:
-                model.compartments[
-                    new_metabolite.compartment] = new_metabolite.compartment
+            if new_metabolite.compartment not in model.compartments and \
+                    new_metabolite.compartment is not None:
+                model.add_compartments([
+                    Compartment(new_metabolite.compartment,
+                                new_metabolite.compartment)])
         try:
             new_metabolite.name = str(m["metNames"][0, 0][i][0][0])
         except (IndexError, ValueError):

cobra/io/sbml.py

@@ -9,7 +9,7 @@
 
 from six import iteritems
 
-from cobra.core import Metabolite, Model, Reaction
+from cobra.core import Metabolite, Model, Reaction, Compartment
 from cobra.util.solver import set_objective
 
 try:
@@ -123,6 +123,10 @@ def create_cobra_model_from_sbml_file(sbml_filename, old_sbml=False,
             [(v, k) for k, v in iteritems(compartment_dict)])
 
     cobra_model = Model(sbml_model_id)
+    # Populate the compartment list - This will be done based on
+    # cobra.Metabolites in cobra.Reactions in the future.
+    compartments = [Compartment(k, v) for k, v in iteritems(compartment_dict)]
+    cobra_model.add_compartments(compartments)
     metabolites = []
     metabolite_dict = {}
     # Convert sbml_metabolites to cobra.Metabolites
@@ -344,9 +348,6 @@ def create_cobra_model_from_sbml_file(sbml_filename, old_sbml=False,
 
     # Now, add all of the reactions to the model.
     cobra_model.id = sbml_model.getId()
-    # Populate the compartment list - This will be done based on
-    # cobra.Metabolites in cobra.Reactions in the future.
-    cobra_model.compartments = compartment_dict
 
     cobra_model.add_reactions(cobra_reaction_list)
     set_objective(cobra_model, coefficients)
@@ -460,14 +461,14 @@ def get_libsbml_document(cobra_model,
 
     # Add in the common compartment abbreviations.  If there are additional
     # compartments they also need to be added.
-    if not cobra_model.compartments:
-        cobra_model.compartments = {'c': 'cytosol',
-                                    'p': 'periplasm',
-                                    'e': 'extracellular'}
-    for the_key in cobra_model.compartments.keys():
+    if len(cobra_model.compartments) == 0:
+        cobra_model.add_compartments([Compartment('c', 'cytosol'),
+                                      Compartment('p', 'periplasm'),
+                                      Compartment('e', 'extracellular')])
+    for compartment in cobra_model.compartments:
         sbml_comp = sbml_model.createCompartment()
-        sbml_comp.setId(the_key)
-        sbml_comp.setName(cobra_model.compartments[the_key])
+        sbml_comp.setId(compartment.id)
+        sbml_comp.setName(compartment.name)
         sbml_comp.setSize(1)  # Just to get rid of warnings
 
     if print_time: