Merge branch 'master' into 559-update-link-validation

NeurodataWithoutBorders · Nov 28, 2024 · ee32dee · ee32dee
2 parents 055b617 + 7dfde02
commit ee32dee
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Showing 20 changed files with 1,577 additions and 1,056 deletions.
diff --git a/+file/Attribute.m b/+file/Attribute.m
@@ -48,7 +48,7 @@
             else
                 obj.value = [];
                 obj.readonly = false;
-            end            
+            end
 
             if isKey(source, 'dims')
                 obj.dimnames = source('dims');

diff --git a/+file/Dataset.m b/+file/Dataset.m
@@ -6,6 +6,8 @@
         dtype;
         isConstrainedSet;
         required;
+        value;
+        readonly; %determines whether value can be changed or not
         scalar;
         shape;
         dimnames;
@@ -22,12 +24,15 @@
             obj.type = '';
             obj.dtype = 'any';
             obj.required = true;
+            obj.value = [];
+            obj.readonly = false;
             obj.scalar = true;
             obj.definesType = false;
 
             obj.shape = {};
             obj.dimnames = {};
             obj.attributes = [];
+
 
             if nargin < 1
                 return;
@@ -42,6 +47,20 @@
             if isKey(source, nameKey)
                 obj.name = source(nameKey);
             end
+
+            % Todo: same as for attribute, should consolidate
+            valueKey = 'value';
+            defaultKey = 'default_value';
+            if isKey(source, defaultKey)
+                obj.value = source(defaultKey);
+                obj.readonly = false;
+            elseif isKey(source, valueKey)
+                obj.value = source(valueKey);
+                obj.readonly = true;
+            else
+                obj.value = [];
+                obj.readonly = false;
+            end
 
             typeKeys = {'neurodata_type_def', 'data_type_def'};
             parentKeys = {'neurodata_type_inc', 'data_type_inc'};

diff --git a/+file/fillClass.m b/+file/fillClass.m
@@ -33,16 +33,22 @@
             optional = [optional {propertyName}];
         end
 
-        if isa(prop, 'file.Attribute')
+        if isa(prop, 'file.Attribute') || isa(prop, 'file.Dataset') 
             if prop.readonly
                 readonly = [readonly {propertyName}];
             end
 
             if ~isempty(prop.value)
-                defaults = [defaults {propertyName}];
+                if isa(prop, 'file.Attribute') 
+                    defaults = [defaults {propertyName}];
+                else % file.Dataset
+                    if isRequired || all(isPropertyRequired)
+                        defaults = [defaults {propertyName}];
+                    end
+                end
             end
 
-            if ~isempty(prop.dependent)
+            if isa(prop, 'file.Attribute') && ~isempty(prop.dependent)
                 %extract prefix
                 parentName = strrep(propertyName, ['_' prop.name], '');
                 parent = classprops(parentName);

diff --git a/+file/fillValidators.m b/+file/fillValidators.m
@@ -4,7 +4,8 @@
         nm = propnames{i};
         prop = props(nm);
 
-        if isa(prop, 'file.Attribute') && prop.readonly && ~isempty(prop.value)
+        if (isa(prop, 'file.Attribute') || isa(prop, 'file.Dataset')) ...
+                && prop.readonly && ~isempty(prop.value)
             % Need to add a validator for inherited and readonly properties. In 
             % the superclass these properties might not be read only and due to
             % inheritance its not possible to change property attributes

diff --git a/+tests/+unit/TutorialTest.m b/+tests/+unit/TutorialTest.m
@@ -120,7 +120,8 @@ function inspectTutorialFileWithNwbInspector(testCase)
                     results = py.list(py.nwbinspector.inspect_nwbfile(nwbfile_path=nwbFilename));
                     results = testCase.convertNwbInspectorResultsToStruct(results);
                 elseif testCase.NWBInspectorMode == "CLI"
-                    [~, m] = system(sprintf('nwbinspector %s --levels importance', nwbFilename));
+                    [s, m] = system(sprintf('nwbinspector %s --levels importance', nwbFilename));
+                    testCase.assertEqual(s,0, 'Failed to run NWB Inspector using system command.')
                     results = testCase.parseNWBInspectorTextOutput(m);
                 end
 

diff --git a/+tests/+util/getPythonPath.m b/+tests/+util/getPythonPath.m
@@ -1,7 +1,7 @@
 function pythonPath = getPythonPath()
     envPath = fullfile('+tests', 'env.mat');
 
-    if isfile(envPath)
+    if isfile(fullfile(misc.getMatnwbDir, envPath))
         Env = load(envPath, '-mat');
         if isfield(Env, 'pythonPath')
             pythonPath = Env.pythonPath;

diff --git a/+types/+core/IZeroClampSeries.m b/+types/+core/IZeroClampSeries.m
@@ -6,7 +6,7 @@
 methods
     function obj = IZeroClampSeries(varargin)
         % IZEROCLAMPSERIES Constructor for IZeroClampSeries
-        varargin = [{'stimulus_description' 'N/A'} varargin];
+        varargin = [{'bias_current' types.util.correctType(0, 'single') 'bridge_balance' types.util.correctType(0, 'single') 'capacitance_compensation' types.util.correctType(0, 'single') 'stimulus_description' 'N/A'} varargin];
         obj = obj@types.core.CurrentClampSeries(varargin{:});
 
 
@@ -33,58 +33,25 @@
     %% VALIDATORS
 
     function val = validate_bias_current(obj, val)
-        val = types.util.checkDtype('bias_current', 'single', val);
-        if isa(val, 'types.untyped.DataStub')
-            if 1 == val.ndims
-                valsz = [val.dims 1];
-            else
-                valsz = val.dims;
-            end
-        elseif istable(val)
-            valsz = [height(val) 1];
-        elseif ischar(val)
-            valsz = [size(val, 1) 1];
+        if isequal(val, 0)
+            val = 0;
         else
-            valsz = size(val);
+            error('NWB:Type:ReadOnlyProperty', 'Unable to set the ''bias_current'' property of class ''<a href="matlab:doc types.core.IZeroClampSeries">IZeroClampSeries</a>'' because it is read-only.')
         end
-        validshapes = {[1]};
-        types.util.checkDims(valsz, validshapes);
     end
     function val = validate_bridge_balance(obj, val)
-        val = types.util.checkDtype('bridge_balance', 'single', val);
-        if isa(val, 'types.untyped.DataStub')
-            if 1 == val.ndims
-                valsz = [val.dims 1];
-            else
-                valsz = val.dims;
-            end
-        elseif istable(val)
-            valsz = [height(val) 1];
-        elseif ischar(val)
-            valsz = [size(val, 1) 1];
+        if isequal(val, 0)
+            val = 0;
         else
-            valsz = size(val);
+            error('NWB:Type:ReadOnlyProperty', 'Unable to set the ''bridge_balance'' property of class ''<a href="matlab:doc types.core.IZeroClampSeries">IZeroClampSeries</a>'' because it is read-only.')
         end
-        validshapes = {[1]};
-        types.util.checkDims(valsz, validshapes);
     end
     function val = validate_capacitance_compensation(obj, val)
-        val = types.util.checkDtype('capacitance_compensation', 'single', val);
-        if isa(val, 'types.untyped.DataStub')
-            if 1 == val.ndims
-                valsz = [val.dims 1];
-            else
-                valsz = val.dims;
-            end
-        elseif istable(val)
-            valsz = [height(val) 1];
-        elseif ischar(val)
-            valsz = [size(val, 1) 1];
+        if isequal(val, 0)
+            val = 0;
         else
-            valsz = size(val);
+            error('NWB:Type:ReadOnlyProperty', 'Unable to set the ''capacitance_compensation'' property of class ''<a href="matlab:doc types.core.IZeroClampSeries">IZeroClampSeries</a>'' because it is read-only.')
         end
-        validshapes = {[1]};
-        types.util.checkDims(valsz, validshapes);
     end
     function val = validate_stimulus_description(obj, val)
         if isequal(val, 'N/A')

diff --git a/+util/table2nwb.m b/+util/table2nwb.m
@@ -28,8 +28,8 @@
 
 for col = T
     if ~strcmp(col.Properties.VariableNames{1},'id')
-
-        if ~isempty(col.Properties.VariableDescriptions{1})
+        if ~isempty(col.Properties.VariableDescriptions) ...
+                && ~isempty(col.Properties.VariableDescriptions{1})
             description = col.Properties.VariableDescriptions{1};
         else
             description = 'no description provided';

diff --git a/tutorials/ecephys.mlx b/tutorials/ecephys.mlx