updating to new ontology repo

.circleci/requirements.txt

@@ -2,5 +2,6 @@
 git+https://github.com/KarrLab/log.git#egg=log
 
 # Karr Lab
+git+https://github.com/KarrLab/wc_onto.git#egg=wc_onto
 git+https://github.com/KarrLab/wc_utils.git#egg=wc_utils
 git+https://github.com/KarrLab/obj_model.git#egg=obj_model

requirements.txt

@@ -9,4 +9,5 @@ scipy
 setuptools
 six
 stringcase
+wc_onto
 wc_utils

tests/sbml/test_sbml_io.py

@@ -19,7 +19,7 @@
 from wc_lang.sbml import io as sbml_io
 from wc_lang.sbml import util as sbml_util
 from wc_lang.transform.prep_for_sbml import PrepForSbmlTransform
-from wc_utils.util.ontology import wcm_ontology
+from wc_onto import onto
 from wc_utils.util.units import unit_registry
 
 
@@ -56,13 +56,13 @@ def test_export_import(self):
 
     def test_SbmlExporter_error(self):
         model = Model(id='model')
-        model.submodels.create(id='Metabolism', framework=wcm_ontology['WCM:dynamic_flux_balance_analysis'])
-        model.submodels.create(id='Metabolism_2', framework=wcm_ontology['WCM:dynamic_flux_balance_analysis'])
+        model.submodels.create(id='Metabolism', framework=onto['WC:dynamic_flux_balance_analysis'])
+        model.submodels.create(id='Metabolism_2', framework=onto['WC:dynamic_flux_balance_analysis'])
         with self.assertRaisesRegex(ValueError, 'Only 1 submodel can be encoded'):
             sbml_io.SbmlExporter.run(model)
 
         model = Model(id='model')
-        submodel = model.submodels.create(id='Metabolism', framework=wcm_ontology['WCM:dynamic_flux_balance_analysis'])
+        submodel = model.submodels.create(id='Metabolism', framework=onto['WC:dynamic_flux_balance_analysis'])
         model.reactions.create(id='rxn_1', submodel=submodel, flux_bound_units=unit_registry.parse_units('M s^-1'))
         model.reactions.create(id='rxn_1', submodel=submodel, flux_bound_units=unit_registry.parse_units('M s^-1'))
         with self.assertRaisesRegex(sbml_util.LibSbmlError, 'Document is invalid'):
@@ -90,7 +90,7 @@ def test_writer_errors(self):
 
 class SbmlIoInCoreTestCase(unittest.TestCase):
     def test_Compartment_to_from_sbml(self):
-        c = Compartment(id='c', name='cytosol', geometry=wcm_ontology['WCM:3D_compartment'])
+        c = Compartment(id='c', name='cytosol', geometry=onto['WC:3D_compartment'])
 
         sbml_doc = sbml_util.LibSbmlInterface.create_doc()
         sbml_model = sbml_util.LibSbmlInterface.create_model(sbml_doc)
@@ -109,7 +109,7 @@ def test_Compartment_to_sbml_error(self):
         with self.assertRaisesRegex(ValueError, 'Unsupported geometry'):
             c.export_to_sbml(sbml_model)
 
-        c = Compartment(id='c', name='cytosol', geometry=wcm_ontology['WCM:3D_compartment'])
+        c = Compartment(id='c', name='cytosol', geometry=onto['WC:3D_compartment'])
         sbml_doc = sbml_util.LibSbmlInterface.create_doc()
         sbml_model = sbml_util.LibSbmlInterface.create_model(sbml_doc)
         sbml_c = c.export_to_sbml(sbml_model)

tests/test_io.py

@@ -20,7 +20,7 @@
 from wc_lang import io
 from wc_lang.io import Writer, Reader, convert, create_template
 from wc_utils.util.chem import EmpiricalFormula
-from wc_utils.util.ontology import wcm_ontology
+from wc_onto import onto
 from wc_utils.util.units import unit_registry
 from wc_utils.workbook.io import read as read_workbook, write as write_workbook
 import obj_model.io
@@ -68,7 +68,7 @@ def setUp(self):
             spec_type = mdl.species_types.create(
                 id='spec_type_{}'.format(i),
                 name='species type {}'.format(i),
-                type=wcm_ontology['WCM:metabolite'],
+                type=onto['WC:metabolite'],
                 structure='C' * (i + 1),
                 empirical_formula=EmpiricalFormula('C' + str(i + 1)),
                 molecular_weight=12 * (i + 1),
@@ -127,11 +127,11 @@ def get_or_create_species_coefficient(species=None, coefficient=None):
             functions.append(func)
 
         self.submdl_0 = submdl_0 = mdl.submodels.create(
-            id='submodel_0', name='submodel 0', framework=wcm_ontology['WCM:stochastic_simulation_algorithm'])
+            id='submodel_0', name='submodel 0', framework=onto['WC:stochastic_simulation_algorithm'])
         self.submdl_1 = submdl_1 = mdl.submodels.create(
-            id='submodel_1', name='submodel 1', framework=wcm_ontology['WCM:stochastic_simulation_algorithm'])
+            id='submodel_1', name='submodel 1', framework=onto['WC:stochastic_simulation_algorithm'])
         self.submdl_2 = submdl_2 = mdl.submodels.create(
-            id='submodel_2', name='submodel 2', framework=wcm_ontology['WCM:dynamic_flux_balance_analysis'])
+            id='submodel_2', name='submodel 2', framework=onto['WC:dynamic_flux_balance_analysis'])
         self.submodels = submodels = [submdl_0, submdl_1, submdl_2]
 
         self.rxn_0 = rxn_0 = submdl_0.reactions.create(

tests/test_merge.py

@@ -14,7 +14,7 @@
                           RateLawExpression, DfbaObjectiveExpression,
                           StopConditionExpression,
                           Evidence, DatabaseReference, Reference)
-from wc_utils.util.ontology import wcm_ontology
+from wc_onto import onto
 from wc_utils.util.units import unit_registry
 
 
@@ -158,21 +158,21 @@ def gen_models(self):
         models[3].parameters.create(id='p_6', units=unit_registry.parse_units('s^-1'))
 
         # submodels
-        models[0].submodels.create(id='submodel_11', framework=wcm_ontology['WCM:stochastic_simulation_algorithm'])
-        models[0].submodels.create(id='submodel_12', framework=wcm_ontology['WCM:dynamic_flux_balance_analysis'])
+        models[0].submodels.create(id='submodel_11', framework=onto['WC:stochastic_simulation_algorithm'])
+        models[0].submodels.create(id='submodel_12', framework=onto['WC:dynamic_flux_balance_analysis'])
 
-        models[1].submodels.create(id='submodel_21', framework=wcm_ontology['WCM:stochastic_simulation_algorithm'])
-        models[1].submodels.create(id='submodel_22', framework=wcm_ontology['WCM:dynamic_flux_balance_analysis'])
+        models[1].submodels.create(id='submodel_21', framework=onto['WC:stochastic_simulation_algorithm'])
+        models[1].submodels.create(id='submodel_22', framework=onto['WC:dynamic_flux_balance_analysis'])
 
-        models[2].submodels.create(id='submodel_11', framework=wcm_ontology['WCM:stochastic_simulation_algorithm'])
-        models[2].submodels.create(id='submodel_12', framework=wcm_ontology['WCM:dynamic_flux_balance_analysis'])
-        models[2].submodels.create(id='submodel_21', framework=wcm_ontology['WCM:stochastic_simulation_algorithm'])
-        models[2].submodels.create(id='submodel_22', framework=wcm_ontology['WCM:dynamic_flux_balance_analysis'])
+        models[2].submodels.create(id='submodel_11', framework=onto['WC:stochastic_simulation_algorithm'])
+        models[2].submodels.create(id='submodel_12', framework=onto['WC:dynamic_flux_balance_analysis'])
+        models[2].submodels.create(id='submodel_21', framework=onto['WC:stochastic_simulation_algorithm'])
+        models[2].submodels.create(id='submodel_22', framework=onto['WC:dynamic_flux_balance_analysis'])
 
-        models[3].submodels.create(id='submodel_11', framework=wcm_ontology['WCM:stochastic_simulation_algorithm'])
-        models[3].submodels.create(id='submodel_12', framework=wcm_ontology['WCM:dynamic_flux_balance_analysis'])
-        models[3].submodels.create(id='submodel_21', framework=wcm_ontology['WCM:stochastic_simulation_algorithm'])
-        models[3].submodels.create(id='submodel_22', framework=wcm_ontology['WCM:dynamic_flux_balance_analysis'])
+        models[3].submodels.create(id='submodel_11', framework=onto['WC:stochastic_simulation_algorithm'])
+        models[3].submodels.create(id='submodel_12', framework=onto['WC:dynamic_flux_balance_analysis'])
+        models[3].submodels.create(id='submodel_21', framework=onto['WC:stochastic_simulation_algorithm'])
+        models[3].submodels.create(id='submodel_22', framework=onto['WC:dynamic_flux_balance_analysis'])
 
         # reactions
         models[0].reactions.create(id='rxn_11', submodel=models[0].submodels[0])
@@ -581,7 +581,7 @@ def gen_models(self):
 
         for model in models:
             for ref in model.references:
-                ref.type = wcm_ontology['WCM:article']
+                ref.type = onto['WC:article']
 
         # generate ids
         for model in models:

tests/test_util.py

@@ -20,7 +20,7 @@
                           )
 from wc_lang import io
 from wc_lang import util
-from wc_utils.util.ontology import wcm_ontology
+from wc_onto import onto
 from wc_utils.util.units import unit_registry
 import obj_model.units
 import os.path
@@ -43,7 +43,7 @@ def setUp(self):
         self.species = species = []
         for i in range(8):
             spec_type = mdl.species_types.create(id='spec_type_{}'.format(
-                i), name='species type {}'.format(i), type=wcm_ontology['WCM:metabolite'])
+                i), name='species type {}'.format(i), type=onto['WC:metabolite'])
             species_types.append(spec_type)
 
             if i != 3:
@@ -58,9 +58,9 @@ def setUp(self):
             conc.id = conc.gen_id()
             conc.model = mdl
 
-        self.submdl_0 = submdl_0 = mdl.submodels.create(id='submdl_0', framework=wcm_ontology['WCM:stochastic_simulation_algorithm'])
-        self.submdl_1 = submdl_1 = mdl.submodels.create(id='submdl_1', framework=wcm_ontology['WCM:stochastic_simulation_algorithm'])
-        self.submdl_2 = submdl_2 = mdl.submodels.create(id='submdl_2', framework=wcm_ontology['WCM:dynamic_flux_balance_analysis'])
+        self.submdl_0 = submdl_0 = mdl.submodels.create(id='submdl_0', framework=onto['WC:stochastic_simulation_algorithm'])
+        self.submdl_1 = submdl_1 = mdl.submodels.create(id='submdl_1', framework=onto['WC:stochastic_simulation_algorithm'])
+        self.submdl_2 = submdl_2 = mdl.submodels.create(id='submdl_2', framework=onto['WC:dynamic_flux_balance_analysis'])
         self.submodels = [submdl_0, submdl_1, submdl_2]
 
         self.rxn_0 = rxn_0 = submdl_0.reactions.create(id='rxn_0', model=mdl)

tests/transform/test_transform_create_implicit_dfba_ex_rxns.py

@@ -10,7 +10,7 @@
 from wc_lang import Model
 from wc_lang.transform import CreateImplicitDfbaExchangeReactionsTransform
 from wc_utils.util.chem import EmpiricalFormula
-from wc_utils.util.ontology import wcm_ontology
+from wc_onto import onto
 import unittest
 import wc_lang.config.core
 
@@ -20,7 +20,7 @@ def test(self):
         config = wc_lang.config.core.get_config()['wc_lang']['dfba']
 
         model = Model()
-        submodel = model.submodels.create(id='submdl', name='submodel', framework=wcm_ontology['WCM:dynamic_flux_balance_analysis'])
+        submodel = model.submodels.create(id='submdl', name='submodel', framework=onto['WC:dynamic_flux_balance_analysis'])
 
         comps = [
             model.compartments.create(id='c', name='cytosol'),

tests/transform/test_transform_merge_submodels.py

@@ -10,7 +10,7 @@
                      Species, SpeciesCoefficient, Reaction,
                      DfbaObjective, DfbaObjectiveExpression, DfbaObjReaction)
 from wc_lang.transform import MergeAlgorithmicallyLikeSubmodelsTransform
-from wc_utils.util.ontology import wcm_ontology
+from wc_onto import onto
 import unittest
 
 
@@ -28,16 +28,16 @@ def test(self):
         species = []
         for i in range(5):
             st = mdl.species_types.create(id='spec_type_{}'.format(i),
-                                          type=wcm_ontology['WCM:metabolite'])
+                                          type=onto['WC:metabolite'])
             s = mdl.species.create(species_type=st,
                                    compartment=cmp)
             s.id = s.gen_id()
             species.append(s)
 
-        submdl_0 = mdl.submodels.create(id='submdl_0', framework=wcm_ontology['WCM:stochastic_simulation_algorithm'])
-        submdl_1 = mdl.submodels.create(id='submdl_1', framework=wcm_ontology['WCM:stochastic_simulation_algorithm'])
-        submdl_2 = mdl.submodels.create(id='submdl_2', framework=wcm_ontology['WCM:dynamic_flux_balance_analysis'])
-        submdl_3 = mdl.submodels.create(id='submdl_3', framework=wcm_ontology['WCM:dynamic_flux_balance_analysis'])
+        submdl_0 = mdl.submodels.create(id='submdl_0', framework=onto['WC:stochastic_simulation_algorithm'])
+        submdl_1 = mdl.submodels.create(id='submdl_1', framework=onto['WC:stochastic_simulation_algorithm'])
+        submdl_2 = mdl.submodels.create(id='submdl_2', framework=onto['WC:dynamic_flux_balance_analysis'])
+        submdl_3 = mdl.submodels.create(id='submdl_3', framework=onto['WC:dynamic_flux_balance_analysis'])
 
         rxn_0_0 = mdl.reactions.create(id='rxn_0_0', submodel=submdl_0)
         rxn_0_0.participants.add(SpeciesCoefficient(species=species[0], coefficient=-1))
@@ -119,8 +119,8 @@ def test(self):
         """ Merge algorithmically-like submodels """
         merged_mdl = mdl.copy()
         MergeAlgorithmicallyLikeSubmodelsTransform().run(merged_mdl)
-        merged_submdl_ssa = merged_mdl.submodels.get_one(framework=wcm_ontology['WCM:stochastic_simulation_algorithm'])
-        merged_submdl_fba = merged_mdl.submodels.get_one(framework=wcm_ontology['WCM:dynamic_flux_balance_analysis'])
+        merged_submdl_ssa = merged_mdl.submodels.get_one(framework=onto['WC:stochastic_simulation_algorithm'])
+        merged_submdl_fba = merged_mdl.submodels.get_one(framework=onto['WC:dynamic_flux_balance_analysis'])
 
         """ Test submodels merged corrected """
         self.assertEqual(len(merged_mdl.compartments), len(mdl.compartments))
@@ -142,8 +142,8 @@ def test(self):
             '{1}_{0}'.format(submdl_2.id, submdl_3.id),
         ])
 
-        self.assertEqual(merged_submdl_ssa.framework, wcm_ontology['WCM:stochastic_simulation_algorithm'])
-        self.assertEqual(merged_submdl_fba.framework, wcm_ontology['WCM:dynamic_flux_balance_analysis'])
+        self.assertEqual(merged_submdl_ssa.framework, onto['WC:stochastic_simulation_algorithm'])
+        self.assertEqual(merged_submdl_fba.framework, onto['WC:dynamic_flux_balance_analysis'])
 
         self.assertEqual(len(merged_submdl_ssa.get_children(kind='submodel', __type=Species)),
                          len(set(submdl_0.get_children(kind='submodel', __type=Species) +

tests/transform/test_transform_set_finite_dfba_flux_bounds.py

@@ -10,7 +10,7 @@
 from test.support import EnvironmentVarGuard
 from wc_lang import Model
 from wc_lang.transform.set_finite_dfba_flux_bounds import SetFiniteDfbaFluxBoundsTransform
-from wc_utils.util.ontology import wcm_ontology
+from wc_onto import onto
 from wc_utils.util.units import unit_registry
 import mock
 import unittest
@@ -19,7 +19,7 @@
 class SetFiniteDfbaFluxBoundsTransformTestCase(unittest.TestCase):
     def test(self):
         model = Model()
-        submodel = model.submodels.create(framework=wcm_ontology['WCM:dynamic_flux_balance_analysis'])
+        submodel = model.submodels.create(framework=onto['WC:dynamic_flux_balance_analysis'])
         rxn_1 = model.reactions.create(submodel=submodel, reversible=True,
                                        flux_min=None, flux_max=None)
         rxn_2 = model.reactions.create(submodel=submodel, reversible=False,

tests/transform/test_transform_split_reversible_reactions.py

@@ -11,7 +11,7 @@
 from wc_lang import (Model, Submodel, Reaction, Parameter, SpeciesType,
                      Species, Compartment, SpeciesCoefficient, RateLawDirection, RateLawExpression)
 from wc_lang.transform import SplitReversibleReactionsTransform
-from wc_utils.util.ontology import wcm_ontology
+from wc_onto import onto
 from wc_utils.util.units import unit_registry
 import unittest
 
@@ -22,9 +22,9 @@ def test(self):
 
         c = model.compartments.create(id='c')
 
-        t0 = model.species_types.create(id='s0', type=wcm_ontology['WCM:metabolite'])
-        t1 = model.species_types.create(id='s1', type=wcm_ontology['WCM:metabolite'])
-        t2 = model.species_types.create(id='s2', type=wcm_ontology['WCM:metabolite'])
+        t0 = model.species_types.create(id='s0', type=onto['WC:metabolite'])
+        t1 = model.species_types.create(id='s1', type=onto['WC:metabolite'])
+        t2 = model.species_types.create(id='s2', type=onto['WC:metabolite'])
 
         s0 = model.species.create(id='s0[c]', species_type=t0, compartment=c)
         s1 = model.species.create(id='s1[c]', species_type=t1, compartment=c)