From 1a6bca654bf7a619fd9d712f4ea11e74b4f565c6 Mon Sep 17 00:00:00 2001
From: "uri.akavia" <uri.akavia@mcgill.ca>
Date: Wed, 29 Jun 2022 22:11:33 -0400
Subject: [PATCH] now almost all of the tests work

---
 src/cobra/io/dict.py                  | 49 ---------------------------
 tests/test_core/test_udconstraints.py |  6 ++--
 2 files changed, 3 insertions(+), 52 deletions(-)

diff --git a/src/cobra/io/dict.py b/src/cobra/io/dict.py
index fc5241605..0c0a47a15 100644
--- a/src/cobra/io/dict.py
+++ b/src/cobra/io/dict.py
@@ -1,19 +1,16 @@
 """Provide functions for cobrapy objects to generic Python objects and vice-versa."""
 import itertools
-import re
 from collections import OrderedDict, defaultdict
 from typing import TYPE_CHECKING, Dict, List, Sequence, Set, Tuple, Union
 
 import numpy as np
 
 from ..core import (
-    ConstraintComponent,
     Gene,
     Group,
     Metabolite,
     Model,
     Reaction,
-    UserDefinedConstraint,
 )
 from ..io.sbml import (
     F_GENE,
@@ -520,52 +517,6 @@ def group_from_dict(
     new_group.add_members(cobra_members)
     return new_group
 
-def const_comp_to_dict(component: ConstraintComponent) -> Dict:
-    new_const_comp = OrderedDict()
-    for key in _REQUIRED_CONSTRAINT_COMP_ATTRIBUTES:
-        new_const_comp[key] = _fix_type(getattr(component, key))
-    _update_optional(
-        component,
-        new_const_comp,
-        _OPTIONAL_CONSTRAINT_COMP_ATTRIBUTES,
-        _ORDERED_OPTIONAL_CONSTRAINT_COMP_KEYS,
-    )
-    return new_const_comp
-
-
-def user_defined_const_to_dict(constraint: UserDefinedConstraint) -> Dict:
-    new_const = OrderedDict()
-    for key in _REQUIRED_CONSTRAINT_ATTRIBUTES:
-        if key != "constraint_comps":
-            new_const[key] = _fix_type(getattr(constraint, key))
-            continue
-        new_const["constraint_comps"] = list(
-            map(const_comp_to_dict, constraint.constraint_comps)
-        )
-    _update_optional(
-        constraint,
-        new_const,
-        _OPTIONAL_CONSTRAINT_ATTRIBUTES,
-        _ORDERED_OPTIONAL_CONSTRAINT_KEYS,
-    )
-    return new_const
-
-
-def user_defined_const_from_dict(constraint: Dict) -> UserDefinedConstraint:
-    new_user_defined_const = UserDefinedConstraint()
-    for k, v in constraint.items():
-        if k == "constraint_comps":
-            for comp in v:
-                new_comp = ConstraintComponent(**comp)
-                new_user_defined_const.add_constraint_comps([new_comp])
-        elif k == "annotation":
-            continue
-        elif k == "notes":
-            continue
-        else:
-            setattr(new_user_defined_const, k, v)
-    return new_user_defined_const
-
 
 def model_to_dict(
     model: Model, sort: bool = False, f_replace: dict = F_REPLACE  # noqa:    W0102
diff --git a/tests/test_core/test_udconstraints.py b/tests/test_core/test_udconstraints.py
index 496f0f77f..0156bf717 100644
--- a/tests/test_core/test_udconstraints.py
+++ b/tests/test_core/test_udconstraints.py
@@ -88,8 +88,8 @@ def test_user_defined_constraints_on_single_variable():
 
 
 def test_json_reading_writing(model, tmp_path):
-    cc1 = Variable("FBA")
-    cc2 = Variable('NH4t')
+    cc1 = model.reactions.get_by_id('FBA').flux_expression
+    cc2 = model.reactions.get_by_id('NH4t').flux_expression
     cc3 = Variable('difference')
     c1 = Constraint(cc1 - cc2 - cc3, lb=0, ub=0, name='c1')
 
@@ -109,7 +109,7 @@ def test_json_reading_writing(model, tmp_path):
     variable_names = {var.name for var in const_1.variables}
     assert 'FBA' in variable_names
     solution2 = model.optimize()
-    assert solution1 == pytest.approx(solution2)
+    assert solution1.objective_value == pytest.approx(solution2.objective_value)
 
 
 def test_user_defined_constraints_read_write_json(data_directory, tmp_path):