TVB-2663 Remove tvb.adapter dependency from model_operation.py

AmoghJohri · Jun 17, 2020 · 04abf94 · 04abf94
1 parent bce4854
commit 04abf94
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Showing 7 changed files with 107 additions and 71 deletions.
diff --git a/framework_tvb/tvb/adapters/simulator/form_with_ranges.py b/framework_tvb/tvb/adapters/simulator/form_with_ranges.py
@@ -29,7 +29,7 @@
 #
 from abc import abstractmethod
 from tvb.basic.neotraits.api import NArray
-from tvb.adapters.simulator.range_parameter import RangeParameter
+from tvb.core.entities.transient.range_parameter import RangeParameter
 from tvb.core.neotraits.forms import Form
 
 

diff --git a/framework_tvb/tvb/adapters/simulator/noise_forms.py b/framework_tvb/tvb/adapters/simulator/noise_forms.py
@@ -28,13 +28,13 @@
 #
 #
 from tvb.adapters.simulator.equation_forms import get_form_for_equation
-from tvb.adapters.simulator.subforms_mapping import SubformsEnum, get_ui_name_to_equation_dict, Linear
+from tvb.adapters.simulator.form_with_ranges import FormWithRanges
+from tvb.adapters.simulator.subforms_mapping import SubformsEnum, get_ui_name_to_equation_dict
 from tvb.basic.neotraits.api import Attr, Range
+from tvb.core.entities.transient.range_parameter import RangeParameter
+from tvb.core.neotraits.forms import ScalarField, ArrayField, SelectField
 from tvb.datatypes.equations import Equation
 from tvb.simulator.noise import Noise, Additive, Multiplicative
-from tvb.adapters.simulator.form_with_ranges import FormWithRanges
-from tvb.adapters.simulator.range_parameter import RangeParameter
-from tvb.core.neotraits.forms import ScalarField, ArrayField, SelectField
 
 
 def get_form_for_noise(noise_class):

diff --git a/...tvb/adapters/simulator/range_parameter.py → ...vb/adapters/simulator/range_parameters.py b/...tvb/adapters/simulator/range_parameter.py → ...vb/adapters/simulator/range_parameters.py
@@ -27,61 +27,16 @@
 #   Frontiers in Neuroinformatics (7:10. doi: 10.3389/fninf.2013.00010)
 #
 #
-import json
-import numpy
 from collections import OrderedDict
-from tvb.basic.neotraits.api import HasTraits, NArray, Range
+
+from tvb.basic.neotraits.api import NArray, Range
+from tvb.core.entities.transient.range_parameter import RangeParameter
 from tvb.datatypes.connectivity import Connectivity
 from tvb.datatypes.surfaces import Surface
 from tvb.simulator.integrators import IntegratorStochastic
 from tvb.simulator.simulator import Simulator
 
 
-class RangeParameter(object):
-    KEY_FLOAT_LO = 'lo'
-    KEY_FLOAT_STEP = 'step'
-    KEY_FLOAT_HI = 'hi'
-
-    def __init__(self, name, type, range_definition, is_array=False, range_values=None):
-        self.name = name
-        self.type = type
-        self.is_array = is_array
-        # range_definition is a Range object when type=float and a FilterChain otherwise
-        self.range_definition = range_definition
-        self.range_values = range_values
-
-    def to_json(self):
-        if self.type is float:
-            return json.dumps([self.name, {self.KEY_FLOAT_LO: self.range_definition.lo,
-                                           self.KEY_FLOAT_STEP: self.range_definition.step,
-                                           self.KEY_FLOAT_HI: self.range_definition.hi}])
-
-        return json.dumps([self.name, self.range_definition])
-
-    @staticmethod
-    def from_json(range_json):
-        range_list = json.loads(range_json)
-        if isinstance(range_list[1], dict):
-            return RangeParameter(range_list[0], float,
-                                  Range(range_list[1][RangeParameter.KEY_FLOAT_LO],
-                                        range_list[1][RangeParameter.KEY_FLOAT_HI],
-                                        range_list[1][RangeParameter.KEY_FLOAT_STEP]))
-
-        return RangeParameter(range_list[0], HasTraits, range_list[1])
-
-    def get_range_values(self):
-        if self.type is float:
-            self.range_values = self.range_definition.to_array()
-            if self.is_array:
-                self.range_values = [numpy.array([value]) for value in self.range_values]
-        return self.range_values
-
-    def fill_from_default(self, range_param):
-        # type: (RangeParameter) -> None
-        self.type = range_param.type
-        self.is_array = range_param.is_array
-
-
 class SimulatorRangeParameters(object):
 
     def __init__(self, connectivity_filters=None, surface_filters=None, coupling=None, model=None,

diff --git a/framework_tvb/tvb/adapters/simulator/simulator_fragments.py b/framework_tvb/tvb/adapters/simulator/simulator_fragments.py
@@ -29,29 +29,30 @@
 #
 
 import uuid
+
 import formencode
 from formencode import validators
+from tvb.adapters.datatypes.db.local_connectivity import LocalConnectivityIndex
+from tvb.adapters.datatypes.db.patterns import StimuliRegionIndex, SpatioTemporalPatternIndex
+from tvb.adapters.datatypes.db.region_mapping import RegionMappingIndex
+from tvb.adapters.datatypes.db.surface import SurfaceIndex
 from tvb.adapters.simulator.integrator_forms import get_form_for_integrator
+from tvb.adapters.simulator.model_forms import get_ui_name_to_model
+from tvb.adapters.simulator.monitor_forms import get_ui_name_to_monitor_dict, get_monitor_to_ui_name_dict
 from tvb.adapters.simulator.subforms_mapping import get_ui_name_to_integrator_dict
-from tvb.core.entities.filters.chain import FilterChain
 from tvb.basic.neotraits.api import Attr, Range, List
+from tvb.core.adapters.abcadapter import ABCAdapterForm
+from tvb.core.entities.filters.chain import FilterChain
+from tvb.core.entities.transient.range_parameter import RangeParameter
+from tvb.core.neocom import h5
+from tvb.core.neotraits.forms import DataTypeSelectField, ScalarField, ArrayField, SimpleFloatField, \
+    SimpleHiddenField, SelectField, MultiSelectField
 from tvb.core.neotraits.view_model import Str
 from tvb.datatypes.cortex import Cortex
 from tvb.datatypes.surfaces import CORTICAL
 from tvb.simulator.integrators import Integrator
 from tvb.simulator.models.base import Model
 from tvb.simulator.simulator import Simulator
-from tvb.adapters.simulator.model_forms import get_ui_name_to_model
-from tvb.adapters.simulator.monitor_forms import get_ui_name_to_monitor_dict, get_monitor_to_ui_name_dict
-from tvb.adapters.simulator.range_parameter import RangeParameter
-from tvb.core.adapters.abcadapter import ABCAdapterForm
-from tvb.adapters.datatypes.db.local_connectivity import LocalConnectivityIndex
-from tvb.adapters.datatypes.db.patterns import StimuliSurfaceIndex, StimuliRegionIndex, SpatioTemporalPatternIndex
-from tvb.adapters.datatypes.db.region_mapping import RegionMappingIndex
-from tvb.adapters.datatypes.db.surface import SurfaceIndex
-from tvb.core.neotraits.forms import DataTypeSelectField, ScalarField, ArrayField, SimpleFloatField, \
-    SimpleHiddenField, SelectField, MultiSelectField
-from tvb.core.neocom import h5
 
 
 class SimulatorSurfaceFragment(ABCAdapterForm):

diff --git a/framework_tvb/tvb/core/entities/model/model_operation.py b/framework_tvb/tvb/core/entities/model/model_operation.py
@@ -36,18 +36,19 @@
 .. moduleauthor:: Yann Gordon <yann@tvb.invalid>
 """
 
-import json
 import datetime
-from sqlalchemy.orm import relationship, backref
+import json
+
 from sqlalchemy import Boolean, Integer, String, DateTime, Column, ForeignKey
+from sqlalchemy.orm import relationship, backref
 from tvb.basic.logger.builder import get_logger
-from tvb.adapters.simulator.range_parameter import RangeParameter
 from tvb.config import TVB_IMPORTER_CLASS, TVB_IMPORTER_MODULE
-from tvb.core.neotraits.db import Base
-from tvb.core.utils import string2date, generate_guid
 from tvb.core.entities.exportable import Exportable
 from tvb.core.entities.model.model_project import Project, User
+from tvb.core.entities.transient.range_parameter import RangeParameter
+from tvb.core.neotraits.db import Base
 from tvb.core.utils import string2bool, date2string, LESS_COMPLEX_TIME_FORMAT
+from tvb.core.utils import string2date, generate_guid
 
 LOG = get_logger(__name__)
 

diff --git a/framework_tvb/tvb/core/entities/transient/range_parameter.py b/framework_tvb/tvb/core/entities/transient/range_parameter.py
@@ -0,0 +1,79 @@
+# -*- coding: utf-8 -*-
+#
+#
+# TheVirtualBrain-Framework Package. This package holds all Data Management, and
+# Web-UI helpful to run brain-simulations. To use it, you also need do download
+# TheVirtualBrain-Scientific Package (for simulators). See content of the
+# documentation-folder for more details. See also http://www.thevirtualbrain.org
+#
+# (c) 2012-2020, Baycrest Centre for Geriatric Care ("Baycrest") and others
+#
+# This program is free software: you can redistribute it and/or modify it under the
+# terms of the GNU General Public License as published by the Free Software Foundation,
+# either version 3 of the License, or (at your option) any later version.
+# This program is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.  See the GNU General Public License for more details.
+# You should have received a copy of the GNU General Public License along with this
+# program.  If not, see <http://www.gnu.org/licenses/>.
+#
+#
+#   CITATION:
+# When using The Virtual Brain for scientific publications, please cite it as follows:
+#
+#   Paula Sanz Leon, Stuart A. Knock, M. Marmaduke Woodman, Lia Domide,
+#   Jochen Mersmann, Anthony R. McIntosh, Viktor Jirsa (2013)
+#       The Virtual Brain: a simulator of primate brain network dynamics.
+#   Frontiers in Neuroinformatics (7:10. doi: 10.3389/fninf.2013.00010)
+#
+#
+
+import json
+
+import numpy
+from tvb.basic.neotraits.api import HasTraits, Range
+
+
+class RangeParameter(object):
+    KEY_FLOAT_LO = 'lo'
+    KEY_FLOAT_STEP = 'step'
+    KEY_FLOAT_HI = 'hi'
+
+    def __init__(self, name, type, range_definition, is_array=False, range_values=None):
+        self.name = name
+        self.type = type
+        self.is_array = is_array
+        # range_definition is a Range object when type=float and a FilterChain otherwise
+        self.range_definition = range_definition
+        self.range_values = range_values
+
+    def to_json(self):
+        if self.type is float:
+            return json.dumps([self.name, {self.KEY_FLOAT_LO: self.range_definition.lo,
+                                           self.KEY_FLOAT_STEP: self.range_definition.step,
+                                           self.KEY_FLOAT_HI: self.range_definition.hi}])
+
+        return json.dumps([self.name, self.range_definition])
+
+    @staticmethod
+    def from_json(range_json):
+        range_list = json.loads(range_json)
+        if isinstance(range_list[1], dict):
+            return RangeParameter(range_list[0], float,
+                                  Range(range_list[1][RangeParameter.KEY_FLOAT_LO],
+                                        range_list[1][RangeParameter.KEY_FLOAT_HI],
+                                        range_list[1][RangeParameter.KEY_FLOAT_STEP]))
+
+        return RangeParameter(range_list[0], HasTraits, range_list[1])
+
+    def get_range_values(self):
+        if self.type is float:
+            self.range_values = self.range_definition.to_array()
+            if self.is_array:
+                self.range_values = [numpy.array([value]) for value in self.range_values]
+        return self.range_values
+
+    def fill_from_default(self, range_param):
+        # type: (RangeParameter) -> None
+        self.type = range_param.type
+        self.is_array = range_param.is_array
diff --git a/framework_tvb/tvb/interfaces/web/controllers/simulator_controller.py b/framework_tvb/tvb/interfaces/web/controllers/simulator_controller.py
@@ -35,7 +35,7 @@
 from tvb.adapters.simulator.equation_forms import get_form_for_equation
 from tvb.adapters.simulator.model_forms import get_form_for_model
 from tvb.adapters.simulator.noise_forms import get_form_for_noise
-from tvb.adapters.simulator.range_parameter import SimulatorRangeParameters
+from tvb.adapters.simulator.range_parameters import SimulatorRangeParameters
 from tvb.adapters.simulator.simulator_adapter import SimulatorAdapterForm
 from tvb.adapters.simulator.simulator_fragments import *
 from tvb.adapters.simulator.monitor_forms import get_form_for_monitor