Merge pull request #27 from EPFL-LCSB/dev

Dev: Hotfix v 0.9.0-b1

Author: realLCSB

doc/conf.py

@@ -95,7 +95,7 @@ def __getattr__(cls, name):
 version = '0.9'
 # The full version, including alpha/beta/rc tags.
 
-release = '0.9.0-b0'
+release = '0.9.0-b1'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

pytfa/core/model.py

@@ -14,6 +14,7 @@
 
 import pandas as pd
 from numpy import empty
+import optlang
 from optlang.exceptions import SolverError
 from cobra import DictList, Model
 from cobra.core.solution import Solution
@@ -63,6 +64,10 @@ def __init__(self, model, name, sloppy=False):
 
         self._cons_queue = list()
         self._var_queue = list()
+
+        self._var_dict = dict()
+        self._cons_dict = dict()
+
         self.sloppy=sloppy
 
 
@@ -182,26 +187,31 @@ def _remove_associated_consvar(self, all_cons_subclasses, all_var_subclasses,
                 try:
                     cons = self._cons_kinds[cons_type.__name__].get_by_id(strfy(element))
                     self.remove_constraint(cons)
-                except KeyError:
+                except KeyError as e:
                     pass
         for var_type in all_var_subclasses:
             for element in collection:
                 try:
                     var = self._var_kinds[var_type.__name__].get_by_id(strfy(element))
                     self.remove_variable(var)
-                except KeyError:
+                except KeyError as e:
                     pass
 
+
     def remove_variable(self, var):
         """
         Removes a variable
 
         :param var:
         :return:
         """
+        # Get the pytfa var object if an optlang variable is passed
+        if isinstance(var,optlang.Variable):
+            var = self._var_dict[var.name]
 
         self._var_dict.pop(var.name)
         self.remove_cons_vars(var.variable)
+        self.logger.debug('Removed variable {}'.format(var.name))
 
     def remove_constraint(self, cons):
         """
@@ -210,9 +220,13 @@ def remove_constraint(self, cons):
         :param cons:
         :return:
         """
+        # Get the pytfa var object if an optlang variable is passed
+        if isinstance(cons,optlang.Constraint):
+            cons = self._cons_dict[cons.name]
 
         self._cons_dict.pop(cons.name)
         self.remove_cons_vars(cons.constraint)
+        self.logger.debug('Removed constraint {}'.format(cons.name))
 
     def _push_queue(self):
         """
@@ -265,7 +279,10 @@ def regenerate_constraints(self):
         if hasattr(self, '_cons_kinds'):
             for k in self._cons_kinds:
                 attrname = camel2underscores(k)
-                delattr(self, attrname)
+                try:
+                    delattr(self, attrname)
+                except AttributeError:
+                    pass # The attribute may not have been set up yet
 
         _cons_kinds = defaultdict(DictList)
 

pytfa/io/dict.py

@@ -14,11 +14,13 @@
 
 from ..thermo.tmodel import ThermoModel
 
-from ..optim.variables import ReactionVariable, MetaboliteVariable
-from ..optim.constraints import ReactionConstraint, MetaboliteConstraint
+from ..optim.variables import ReactionVariable, MetaboliteVariable, ModelVariable
+from ..optim.constraints import ReactionConstraint, MetaboliteConstraint, ModelConstraint
 
 from optlang.util import expr_to_json, parse_expr
 
+from copy import copy
+
 
 def get_all_subclasses(cls):
     all_subclasses = []
@@ -34,10 +36,17 @@ def make_subclasses_dict(cls):
     the_dict[cls.__name__] = cls
     return the_dict
 
-REACTION_VARIABLE_SUBCLASSES    = make_subclasses_dict(ReactionVariable)
-REACTION_CONSTRAINT_SUBCLASSES  = make_subclasses_dict(ReactionConstraint)
-METABOLITE_VARIABLE_SUBCLASSES  = make_subclasses_dict(MetaboliteVariable)
-METABOLITE_CONSTRAINT_SUBCLASSES= make_subclasses_dict(MetaboliteConstraint)
+
+MODEL_VARIABLE_SUBCLASSES  = make_subclasses_dict(ModelVariable)
+MODEL_CONSTRAINT_SUBCLASSES= make_subclasses_dict(ModelConstraint)
+
+BASE_NAME2HOOK = {
+                    ReactionVariable    :'reactions',
+                    ReactionConstraint  :'reactions',
+                    MetaboliteVariable  :'metabolites',
+                    MetaboliteConstraint:'metabolites',
+                }
+
 
 SOLVER_DICT = {
     'optlang.gurobi_interface':'optlang-gurobi',
@@ -212,76 +221,79 @@ def _add_thermo_metabolite_info(met, met_dict):
     if hasattr(met, 'thermo'):
         met_dict['thermo'] = metabolite_thermo_to_dict(met)
 
-def model_from_dict(obj, solver=None):
+def model_from_dict(obj, solver=None, custom_hooks = None):
+    """
+    Custom_hooks looks like
+
+    .. code:: python
+
+        custom_hooks = {<EnzymeVariable Class at 0xffffff> : 'enzymes',
+                        ... }
+
+    :param obj:
+    :param solver:
+    :param custom_hooks:
+    :return:
+    """
     # Take advantage of cobra's serialization of mets and reactions
-    new = cbd.model_from_dict(obj)
+    cbm = cbd.model_from_dict(obj)
 
     if solver is not None:
         try:
-            new.solver = solver
+            cbm.solver = solver
         except SolverNotFound as snf:
             raise snf
     else:
         try:
-            new.solver = obj['solver']
+            cbm.solver = obj['solver']
         except KeyError:
             pass
 
+    if custom_hooks is None:
+        custom_hooks = dict()
+
+    custom_hooks.update(BASE_NAME2HOOK)
+
     if obj['kind'] == 'ThermoModel':
         new = ThermoModel(thermo_data=obj['thermo_data'],
-                          model=new,
+                          model=cbm,
                           name=obj['name'],
                           temperature=obj['temperature'],
                           min_ph=obj['min_ph'],
                           max_ph=obj['max_ph'])
         new = init_thermo_model_from_dict(new, obj)
+    else:
+        new = ThermoModel(model=cbm,
+                          name=obj['name'])
 
     new._push_queue()
 
+    name2class, name2hook = add_custom_classes(new,custom_hooks)
+
     for the_var_dict in obj['variables']:
         this_id = the_var_dict['id']
         classname = the_var_dict['kind']
         lb = the_var_dict['lb']
         ub = the_var_dict['ub']
         scaling_factor = the_var_dict['scaling_factor']
 
-        if classname in REACTION_VARIABLE_SUBCLASSES:
-            hook = new.reactions.get_by_id(this_id)
-            this_class = REACTION_VARIABLE_SUBCLASSES[classname]
-            nv = new.add_variable(kind=this_class,
-                                  hook=hook,
-                                  ub = ub,
-                                  lb = lb,
-                                  queue=True)
-
-        elif classname in METABOLITE_VARIABLE_SUBCLASSES:
-            hook = new.metabolites.get_by_id(this_id)
-            this_class = METABOLITE_VARIABLE_SUBCLASSES[classname]
-            nv = new.add_variable(kind=this_class,
-                                  hook=hook,
-                                  ub = ub,
-                                  lb = lb,
-                                  queue=True)
-
-        elif classname in ENZYME_VARIABLE_SUBCLASSES:
-            hook = new.enzymes.get_by_id(this_id)
-            this_class = ENZYME_VARIABLE_SUBCLASSES[classname]
+        if classname in MODEL_VARIABLE_SUBCLASSES:
+            hook = new
+            this_class = MODEL_VARIABLE_SUBCLASSES[classname]
             nv = new.add_variable(kind=this_class,
                                   hook=hook,
-                                  ub = ub,
-                                  lb = lb,
+                                  id_=this_id,
+                                  ub=ub,
+                                  lb=lb,
                                   queue=True)
-
-        elif classname in MODEL_VARIABLE_SUBCLASSES:
-            hook = new
-            this_class = MODEL_VARIABLE_SUBCLASSES[classname]
+        elif classname in name2class:
+            hook = name2hook[classname].get_by_id(this_id)
+            this_class = name2class[classname]
             nv = new.add_variable(kind=this_class,
                                   hook=hook,
-                                  id_ = this_id,
                                   ub = ub,
                                   lb = lb,
                                   queue=True)
-
         else:
             raise TypeError(
                 'Class {} serialization not handled yet' \
@@ -307,41 +319,24 @@ def model_from_dict(obj, solver=None):
         lb = the_cons_dict['lb']
         ub = the_cons_dict['ub']
 
-        if classname in REACTION_CONSTRAINT_SUBCLASSES:
-            hook = new.reactions.get_by_id(this_id)
-            this_class = REACTION_CONSTRAINT_SUBCLASSES[classname]
-            nc = new.add_constraint(kind=this_class, hook=hook,
-                                    expr=new_expr,
-                                    ub = ub,
-                                    lb = lb,
-                                    queue=True)
+        # Look for the corresponding class:
 
-        elif classname in METABOLITE_CONSTRAINT_SUBCLASSES:
-            hook = new.metabolites.get_by_id(this_id)
-            this_class = METABOLITE_CONSTRAINT_SUBCLASSES[classname]
+        if classname in MODEL_CONSTRAINT_SUBCLASSES:
+            hook=new
+            this_class = MODEL_CONSTRAINT_SUBCLASSES[classname]
             nc = new.add_constraint(kind=this_class, hook=hook,
-                                    expr=new_expr,
+                                    expr=new_expr, id_ = this_id,
                                     ub = ub,
                                     lb = lb,
                                     queue=True)
-
-        elif classname in ENZYME_CONSTRAINT_SUBCLASSES:
-            hook = new.enzymes.get_by_id(this_id)
-            this_class = ENZYME_CONSTRAINT_SUBCLASSES[classname]
+        elif classname in name2class:
+            hook = name2hook[classname].get_by_id(this_id)
+            this_class = name2class[classname]
             nc = new.add_constraint(kind=this_class, hook=hook,
                                     expr=new_expr,
                                     ub = ub,
                                     lb = lb,
                                     queue=True)
-
-        elif classname in MODEL_CONSTRAINT_SUBCLASSES:
-            hook=new
-            this_class = MODEL_CONSTRAINT_SUBCLASSES[classname]
-            nc = new.add_constraint(kind=this_class, hook=hook,
-                                    expr=new_expr, id_ = this_id,
-                                    ub = ub,
-                                    lb = lb,
-                                    queue=True)
         else:
             raise TypeError('Class {} serialization not handled yet' \
                             .format(classname))
@@ -356,6 +351,39 @@ def model_from_dict(obj, solver=None):
 
     return new
 
+def add_custom_classes(model, custom_hooks):
+    """
+    Allows custom variable serialization
+
+    :param model:
+    :param base_classes:
+    :param base_hooks:
+    :param custom_hooks:
+    :return:
+    """
+
+    base_classes = dict()
+    base_hooks = dict()
+
+    for this_class, hookname in custom_hooks.items():
+        # Build the subclass dict of the shape
+        # {'MyClass':<MyClass Object>}
+        this_subclass_dict = make_subclasses_dict(this_class)
+        base_classes.update(this_subclass_dict)
+
+        # Build the Hook dict, of the shape
+        # {'MySubClass':model.my_attr}
+        hooks = getattr(model,hookname)
+        this_hook_dict = {k:hooks for k in this_subclass_dict}
+        base_hooks.update(this_hook_dict)
+
+    return  base_classes, base_hooks
+
+
+def get_hook_dict(model,custom_hooks):
+
+    return {classname:getattr(model,hookname)
+            for classname, hookname in custom_hooks.items()}
 
 def init_thermo_model_from_dict(new, obj):
     for rxn_dict in obj['reactions']:

pytfa/optim/constraints.py

@@ -146,6 +146,45 @@ def model(self):
     def __repr__(self):
         return self.name + ': ' + self.constraint.expression.__repr__()
 
+class ModelConstraint(GenericConstraint):
+    """
+    Class to represent a variable attached to the model
+    """
+
+    def __init__(self, model, expr, id_, **kwargs):
+        GenericConstraint.__init__(self,
+                                   id_= id_,
+                                   expr=expr,
+                                   model=model,
+                                   hook=model,
+                                   **kwargs)
+
+
+class GeneConstraint(GenericConstraint):
+    """
+    Class to represent a variable attached to a enzyme
+    """
+
+    def __init__(self, gene, expr, **kwargs):
+        model = gene.model
+
+        GenericConstraint.__init__(self,
+                                   expr=expr,
+                                   model=model,
+                                   hook=gene,
+                                   **kwargs)
+
+    @property
+    def gene(self):
+        return self.hook
+
+    @property
+    def id(self):
+        return self.gene.id
+
+    @property
+    def model(self):
+        return self.gene.model
 
 class ReactionConstraint(GenericConstraint):
     """