Updating PatchClampExperiment and other types

PyOpenWorm/channelworm.py

@@ -1,5 +1,6 @@
 from yarom.utils import slice_dict
 
+import six
 from .experiment import Experiment
 from .dataObject import DataObject, DatatypeProperty, ObjectProperty
 from .channel_common import CHANNEL_RDF_TYPE
@@ -9,90 +10,62 @@
 class PatchClampExperiment(Experiment):
     """
     Store experimental conditions for a patch clamp experiment.
+    """
 
-    Attributes
-    ----------
-    Ca_concentration : DatatypeProperty
-        Calcium concentration
-    Cl_concentration : DatatypeProperty
-        Chlorine concentration
-    blockers : DatatypeProperty
-        Channel blockers used for this experiment
-    cell : DatatypeProperty
-        The cell this experiment was performed on
-    cell_age : DatatypeProperty
-        Age of the cell
-    delta_t : DatatypeProperty
+    class_context = SCI_BIO_CTX.identifier
 
-    duration : DatatypeProperty
+    Ca_concentration = DatatypeProperty()
+    '''Calcium concentration'''
 
-    end_time : DatatypeProperty
+    Cl_concentration = DatatypeProperty()
+    '''Chlorine concentration'''
 
-    extra_solution : DatatypeProperty
+    blockers = DatatypeProperty()
+    '''Channel blockers used for this experiment'''
 
-    initial_voltage : DatatypeProperty
-        Starting voltage of the patch clamp
-    ion_channel : DatatypeProperty
-        The ion channel being clamped
-    membrane_capacitance : DatatypeProperty
-        Initial membrane capacitance
-    mutants : DatatypeProperty
-        Type(s) of mutants being used in this experiment
-    patch_type : DatatypeProperty
-        Type of patch clamp being used ('voltage' or 'current')
-    pipette_solution : DatatypeProperty
-        Type of solution in the pipette
-    protocol_end : DatatypeProperty
+    cell = DatatypeProperty()
+    '''The cell this experiment was performed on'''
 
-    protocol_start : DatatypeProperty
+    cell_age = DatatypeProperty()
+    '''Age of the cell'''
 
-    protocol_step : DatatypeProperty
+    delta_t = DatatypeProperty()
 
-    start_time : DatatypeProperty
+    duration = DatatypeProperty()
 
-    temperature : DatatypeProperty
+    end_time = DatatypeProperty()
 
-    type : DatatypeProperty
+    extra_solution = DatatypeProperty()
 
-    """
-    class_context = SCI_BIO_CTX.identifier
+    initial_voltage = DatatypeProperty()
+    '''Starting voltage of the patch clamp'''
+
+    ion_channel = DatatypeProperty()
+    '''The ion channel being clamped'''
+
+    membrane_capacitance = DatatypeProperty()
+    '''Initial membrane capacitance'''
+
+    mutants = DatatypeProperty()
+    '''Type(s) of mutants being used in this experiment'''
+
+    patch_type = DatatypeProperty()
+    '''Type of patch clamp being used ('voltage' or 'current')'''
+
+    pipette_solution = DatatypeProperty()
+    '''Type of solution in the pipette'''
+
+    protocol_end = DatatypeProperty()
+
+    protocol_start = DatatypeProperty()
+
+    protocol_step = DatatypeProperty()
+
+    start_time = DatatypeProperty()
+
+    temperature = DatatypeProperty()
 
-    conditions = [
-        'Ca_concentration',
-        'Cl_concentration',
-        'blockers',
-        'cell',
-        'cell_age',
-        'delta_t',
-        'duration',
-        'end_time',
-        'extra_solution',
-        'initial_voltage',
-        'ion_channel',
-        'membrane_capacitance',
-        'mutants',
-        'patch_type',
-        'pipette_solution',
-        'protocol_end',
-        'protocol_start',
-        'protocol_step',
-        'start_time',
-        'temperature',
-        'type',
-    ]
-
-    def __init__(self, reference=False, **kwargs):
-        conditions = slice_dict(kwargs, self.conditions)
-        kwargs = {k: kwargs[k] for k in kwargs if k not in conditions}
-        super(PatchClampExperiment, self).__init__(reference, **kwargs)
-
-        # enumerate conditions patch-clamp experiments should have
-
-        for c in self.conditions:
-            PatchClampExperiment.DatatypeProperty(c, self)
-
-        for c, v in conditions.items():
-            getattr(self, c).set(v)
+    type = DatatypeProperty()
 
 
 class ChannelModelType:
@@ -134,7 +107,7 @@ def __init__(self, modelType=None, *args, **kwargs):
         super(ChannelModel, self).__init__(*args, **kwargs)
 
         #Change modelType value to something from ChannelModelType class on init
-        if isinstance(modelType, str):
+        if isinstance(modelType, six.string_types):
             modelType = modelType.lower()
             if modelType in ('homology', ChannelModelType.homologyEstimate):
                 self.modelType(ChannelModelType.homologyEstimate)

PyOpenWorm/cli.py

@@ -10,11 +10,13 @@
 
 def additional_args(parser):
     'Add some additional options specific to CLI'
-    parser.add_argument('--output-mode', default='text')
+    parser.add_argument('--output-mode', default='text',
+            help='How to print the results of a command'
+            ' (if any). Either "json" or "text" (the default)')
     parser.add_argument('--text-field-separator', default='\t',
-            description='Separator to use between fields in text-mode output')
+            help='Separator to use between fields in text-mode output')
     parser.add_argument('--text-record-separator', default='\n',
-            description='Separator to use between records in text-mode output')
+            help='Separator to use between records in text-mode output')
 
 
 class NSHandler(object):

PyOpenWorm/experiment.py

@@ -24,10 +24,8 @@ class Experiment(DataObject):
 
     def __init__(self, reference=None, **kwargs):
         super(Experiment, self).__init__(**kwargs)
-        Experiment.ObjectProperty('reference',
-                                  owner=self,
-                                  value_type=Evidence,
-                                  multiple=True)
+        self.reference = Experiment.ObjectProperty(value_type=Evidence,
+                                                   multiple=True)
 
         if isinstance(reference, Evidence):
             #TODO: make this so the reference asserts this Experiment when it is added

tests/ChannelWormTest.py

@@ -0,0 +1,27 @@
+import unittest
+from PyOpenWorm.channelworm import PatchClampExperiment, ChannelModel, ChannelModelType
+
+
+class PatchClampExperimentTest(unittest.TestCase):
+
+    def test_cw_init(self):
+        PatchClampExperiment(cell='blah', delta_t=.002)
+
+
+class ChannelModelTest(unittest.TestCase):
+
+    def test_cm_init_pc_model_type(self):
+        cm = ChannelModel(modelType='patch-clamp')
+        self.assertEqual(ChannelModelType.patchClamp, cm.modelType.onedef())
+
+    def test_cm_init_homology_model_type(self):
+        cm = ChannelModel(modelType='homology')
+        self.assertEqual(ChannelModelType.homologyEstimate, cm.modelType.onedef())
+
+    def test_cm_init_unknown_model_type(self):
+        cm = ChannelModel(modelType='homolog')
+        self.assertIsNone(cm.modelType.onedef())
+
+    def test_cm_init_homoly_model_type(self):
+        cm = ChannelModel(modelType=23)
+        self.assertIsNone(cm.modelType.onedef())