#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 +1,45 @@
+# -*- 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)
+        self._model = None
+
+    def copy(self):
+        return deepcopy(self)
+
+    @property
+    def model(self):
+        return (self._model)
+
+    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
@@ -52,13 +53,17 @@ class Model(Object):
         Gene
     solution : Solution
         The last obtained solution from optimizing the model.
+    compartment : DictList
+        A DictList where the key is the compartment identifier and the value a
+        Compartment
     """
 
     def __setstate__(self, state):
         """Make sure all cobra.Objects in the model point to the model.
         """
         self.__dict__.update(state)
-        for y in ['reactions', 'genes', 'metabolites']:
+        for y in ['reactions', 'genes', 'metabolites',
+                  'compartments']:
             for x in getattr(self, y):
                 x._model = self
         if not hasattr(self, "name"):
@@ -90,7 +95,7 @@ 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()  # A list of cobra.Compartments
             self._contexts = []
 
             # from cameo ...
@@ -161,32 +166,6 @@ def get_metabolite_compartments(self):
         return {met.compartment for met in self.metabolites
                 if met.compartment is not None}
 
-    @property
-    def compartments(self):
-        return {met.compartment: self._compartments.get(met.compartment, '')
-                for met in self.metabolites if met.compartment is not None}
-
-    @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)
-
     @property
     def medium(self):
 
@@ -272,14 +251,24 @@ def copy(self):
         than deepcopy
         """
         new = self.__class__()
-        do_not_copy_by_ref = {"metabolites", "reactions", "genes", "notes",
-                              "annotation"}
+        do_not_copy_by_ref = {"metabolites", "reactions", "genes",
+                              "compartments", "notes", "annotation"}
         for attr in self.__dict__:
             if attr not in do_not_copy_by_ref:
                 new.__dict__[attr] = self.__dict__[attr]
         new.notes = deepcopy(self.notes)
         new.annotation = deepcopy(self.annotation)
 
+        new.compartment = DictList()
+        for compartment in self.compartments:
+            new_compartment = compartment.__class__(None)
+            for attr, value in iteritems(compartment.__dict__):
+                if attr not in do_not_copy_by_ref:
+                    new_compartment.__dict__[attr] = copy(
+                        value) if attr == "formula" else value
+            new_compartment._model = new
+            new.compartments.append(new_compartment)
+
         new.metabolites = DictList()
         do_not_copy_by_ref = {"_reaction", "_model"}
         for metabolite in self.metabolites:
@@ -302,7 +291,8 @@ def copy(self):
             new.genes.append(new_gene)
 
         new.reactions = DictList()
-        do_not_copy_by_ref = {"_model", "_metabolites", "_genes"}
+        do_not_copy_by_ref = {"_model", "_metabolites", "_genes",
+                              "_compartments"}
         for reaction in self.reactions:
             new_reaction = reaction.__class__()
             for attr, value in iteritems(reaction.__dict__):
@@ -331,6 +321,41 @@ def copy(self):
 
         return new
 
+    def add_compartments(self, compartment_list):
+        """Will add a list of compartments to the model object
+
+        The change is reverted upon exit when using the model as a context.
+
+        Parameters
+        ----------
+        compartment_list : A list of `cobra.core.Compartment` objects
+
+        """
+        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]
+        if len(bad_ids) != 0:
+            raise ValueError('invalid identifiers in {}'.format(repr(bad_ids)))
+
+        for x in compartment_list:
+            x._model = self
+        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.
@@ -377,6 +402,19 @@ def add_metabolites(self, metabolite_list):
                 # Do we care?
                 context(partial(setattr, x, '_model', None))
 
+        # add compartments to cobra.Model
+        for met in metabolite_list:
+            compartment = Compartment(met.compartment)
+            if not self.compartments.has_id(compartment.id):
+                self.compartments += [compartment]
+                compartment._model = self
+
+                if context:
+                    # Remove the compartment later
+                    context(partial(self.compartments.__isub__,
+                                    [compartment]))
+                    context(partial(setattr, compartment, '_model', None))
+
     def remove_metabolites(self, metabolite_list, destructive=False):
         """Remove a list of metabolites from the the object.
 
@@ -863,6 +901,7 @@ 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()
@@ -874,7 +913,8 @@ def repair(self, rebuild_index=True, rebuild_relationships=True):
                 for gene in rxn._genes:
                     gene._reaction.add(rxn)
         # point _model to self
-        for l in (self.reactions, self.genes, self.metabolites):
+        for l in (self.reactions, self.genes, self.metabolites,
+                  self.compartments):
             for e in l:
                 e._model = self
 
@@ -1050,7 +1090,7 @@ 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(
@@ -1059,6 +1099,6 @@ def _repr_html_(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 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

@@ -229,14 +229,23 @@ 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"},
     },
-    "required": ["id", "reactions", "metabolites", "genes"],
+    "required": ["id", "reactions", "metabolites", "genes", "compartments"],
     "additionalProperties": False,
 }