Clean whitespace

openMetadataInitiative · Nov 15, 2024 · 393b865 · 393b865
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Showing 37 changed files with 99 additions and 114 deletions.
diff --git a/code/+openminds/@Collection/Collection.m b/code/+openminds/@Collection/Collection.m
@@ -272,7 +272,7 @@ function updateLinks(obj)
                 obj openminds.Collection
                 savePath (1,1) string
                 options.SaveToSingleFile (1,1) logical = true
-                %options.IncludeEmptyProperties (1,1) logical = false
+                % options.IncludeEmptyProperties (1,1) logical = false
             end
 
             % Update links before saving
@@ -336,12 +336,11 @@ function load(obj, filePath)%, options)
         outputPaths = saveInstances(instance, filePath, options)
 
         instances = loadInstances(filePath)
-
     end
 
     methods (Access = protected)
 
-        %Add an instance to the Node container.
+        % Add an instance to the Node container.
         function addNode(obj, instance, options)
 
             arguments
@@ -362,7 +361,7 @@ function addNode(obj, instance, options)
 
             if isConfigured(obj.Nodes)
                 if isKey(obj.Nodes, instance.id)
-                    %warning('Node with id %s already exists in collection', instance.id)
+                    % warning('Node with id %s already exists in collection', instance.id)
                     if options.AbortIfNodeExists
                         return
                     end
@@ -389,7 +388,7 @@ function addNode(obj, instance, options)
             obj.addSubNodes(instance)
         end
 
-        %Add sub node instances (linked types) to the Node container.
+        % Add sub node instances (linked types) to the Node container.
         function addSubNodes(obj, instance)
             % Add links.
             linkedTypes = instance.getLinkedTypes();

diff --git a/code/+openminds/@Collection/loadInstances.m b/code/+openminds/@Collection/loadInstances.m
@@ -9,7 +9,7 @@
 
     arguments
         filePath (1,:) string = ""
-        %options.RecursionDepth = 1
+        % options.RecursionDepth = 1
     end
 
     import openminds.internal.serializer.JsonLdSerializer
@@ -39,7 +39,7 @@
 
                 if ~isfield(thisInstance, 'at_type')
                     continue % Todo: Why skip?
-                    %instances{i} = struct('id', thisInstance.at_id);
+                    % instances{i} = struct('id', thisInstance.at_id);
                 else
                     openMindsType = thisInstance.at_type;
                     className = openminds.internal.utility.string.type2class(openMindsType);

diff --git a/code/internal/+openminds/+abstract/ControlledTerm.m b/code/internal/+openminds/+abstract/ControlledTerm.m
@@ -113,7 +113,7 @@ function deserializeFromName(obj, instanceName)
                 end
             else
                 error('No matching instances were found for name "%s"', instanceName)
-                %error('Deserialization from user instance is not implemented yet')
+                % error('Deserialization from user instance is not implemented yet')
             end
             propNames = {'at_id', 'name', 'definition', 'description', 'interlexIdentifier', 'knowledgeSpaceLink', 'preferredOntologyIdentifier', 'synonym'};
 

diff --git a/code/internal/+openminds/+abstract/Schema.m b/code/internal/+openminds/+abstract/Schema.m
@@ -1,6 +1,6 @@
 classdef Schema < handle & openminds.internal.extern.uiw.mixin.AssignPVPairs & ...
                   openminds.internal.mixin.CustomInstanceDisplay & openminds.internal.mixin.StructAdapter
-%Schema Abstract base class shared by all concrete Schema classes
+% Schema Abstract base class shared by all concrete Schema classes
 
 % Todo:
 %   [ ] Validate schema. I.e are all required variables filled out
@@ -226,7 +226,7 @@
 
                     elseif numel(subs) > 1 && strcmp(subs(2).type, '()')
                         try
-                            %linkedObj = obj.subsref(subs(1:2));
+                            % linkedObj = obj.subsref(subs(1:2));
                             obj = builtin('subsasgn', obj, subs, value);
 
                         catch MECause
@@ -254,7 +254,7 @@
                                         error(errorStruct)
                                     end
 
-                                    %obj.subsasgn(subs, value);
+                                    % obj.subsasgn(subs, value);
                                 otherwise
                                     ME = MException('OPENMINDS_MATLAB:UnhandledIndexAssignment', ...
                                         'Unhandled index assignment, please report');
@@ -302,7 +302,7 @@
                     if obj.isSubsForPublicPropertyValue(subs)
                         evtData = PropertyValueChangedEventData(value, oldValue, false); % false for unlinked prop
                         obj.notify('InstanceChanged', evtData)
-                        %fprintf('Set unlinked property of %s\n', class(obj))
+                        % fprintf('Set unlinked property of %s\n', class(obj))
                     end
                 end
             end
@@ -370,7 +370,7 @@
                 if numel(subs) > 1
                     % Todo: Remove as this appears to be unused
                     if strcmp( subs(2).type, '()' ) && iscell(values)
-                        %subs(2).type = '{}';
+                        % subs(2).type = '{}';
                     end
 
                     if numOutputs > 0
@@ -569,7 +569,7 @@ function assignInstanceId(obj, id)
 
             import openminds.internal.utility.getSchemaDocLink
 
-            %annotation = obj.getSchemaShortName(class(obj));
+            % annotation = obj.getSchemaShortName(class(obj));
             annotation = getSchemaDocLink( class(obj) );
         end
 

diff --git a/code/internal/+openminds/+constant/BaseURI.m b/code/internal/+openminds/+constant/BaseURI.m
@@ -1,16 +1,16 @@
 function baseURI = BaseURI(version)
 % BaseURI Get the base URI for the specified OpenMINDS schema version
 %
-%   baseURI = openminds.constant.BaseURI(version) returns the base URI as a 
-%   string that corresponds to the specified OpenMINDS schema version. This 
-%   function dynamically selects the URI based on the version input. If no 
-%   version is specified, the version number for the active openMINDS version 
+%   baseURI = openminds.constant.BaseURI(version) returns the base URI as a
+%   string that corresponds to the specified OpenMINDS schema version. This
+%   function dynamically selects the URI based on the version input. If no
+%   version is specified, the version number for the active openMINDS version
 %   is selected.
 %
 %   Input:
-%       version - (optional) An instance of openminds.internal.utility.VersionNumber 
-%                 specifying the schema version. If no version is provided, 
-%                 the function automatically retrieves the current schema 
+%       version - (optional) An instance of openminds.internal.utility.VersionNumber
+%                 specifying the schema version. If no version is provided,
+%                 the function automatically retrieves the current schema
 %                 version using openminds.getSchemaVersion.
 %
 %   Output:

diff --git a/code/internal/+openminds/+constant/LATEST_VERSION.m b/code/internal/+openminds/+constant/LATEST_VERSION.m
@@ -1,3 +1,3 @@
 function str = LATEST_VERSION()
-    str = "4.0"; 
-end
+    str = "4.0";
+end
diff --git a/code/internal/+openminds/+internal/+abstract/LinkedCategory.m b/code/internal/+openminds/+internal/+abstract/LinkedCategory.m
@@ -201,7 +201,7 @@
 
             % Todo: Consider indicating that the array has mixed types,
             % i.e is heterogeneous-like...
-            %docLinkStr = sprintf('1x%d heterogeneous %s', numel(obj), docLinkStr);
+            % docLinkStr = sprintf('1x%d heterogeneous %s', numel(obj), docLinkStr);
 
             docLinkStr = sprintf('1x%d %s', numel(obj), docLinkStr);
             if isempty(obj)
@@ -234,8 +234,8 @@ function displayNonScalarObject(obj)
                 stringArray = strjoin( arrayfun(@(o) o.Instance.id, obj, 'UniformOutput', false), newline);
             else
                 repArray = arrayfun(@(o) o.Instance.compactRepresentationForSingleLine, obj, 'UniformOutput', false);
-                %stringArray = cellfun(@(r) r.Representation, repArray);
-                %rep = fullDataRepresentation(obj, displayConfiguration, 'StringArray', stringArray, 'Annotation', annotation');
+                % stringArray = cellfun(@(r) r.Representation, repArray);
+                % rep = fullDataRepresentation(obj, displayConfiguration, 'StringArray', stringArray, 'Annotation', annotation');
                 stringArray = cellfun(@(r) "    "+ r.PaddedDisplayOutput, repArray);
                 stringArray = strrep(stringArray, '[', '');
                 stringArray = strrep(stringArray, ']', '');
@@ -252,8 +252,8 @@ function displayNonScalarObject(obj)
 
         function stringArray = getStringArrayForSingleLine(obj)
             repArray = arrayfun(@(o) o.Instance.compactRepresentationForSingleLine, obj, 'UniformOutput', false);
-            %stringArray = cellfun(@(r) r.Representation, repArray);
-            %rep = fullDataRepresentation(obj, displayConfiguration, 'StringArray', stringArray, 'Annotation', annotation');
+            % stringArray = cellfun(@(r) r.Representation, repArray);
+            % rep = fullDataRepresentation(obj, displayConfiguration, 'StringArray', stringArray, 'Annotation', annotation');
 
             stringArray = cellfun(@(r) r.PaddedDisplayOutput, repArray);
             stringArray = strrep(stringArray, '[', '');

diff --git a/code/internal/+openminds/+internal/+extern/+fex/+filedownload/FileDownloadProgressMonitor.m b/code/internal/+openminds/+internal/+extern/+fex/+filedownload/FileDownloadProgressMonitor.m
@@ -77,7 +77,7 @@ function delete(obj)
 
         function set.Direction(obj, dir)
             obj.Direction = dir;
-            %fprintf('Direction set: %s\n', obj.Direction)
+            % fprintf('Direction set: %s\n', obj.Direction)
         end
 
         function set.Value(obj, value)

diff --git a/code/internal/+openminds/+internal/+generator/+abstract/ClassWriter.m b/code/internal/+openminds/+internal/+generator/+abstract/ClassWriter.m
@@ -147,7 +147,7 @@ function saveClassdef(obj)
             fwrite(fid, obj.ClassDefText);
             fclose(fid);
 
-            %fprintf('Saved class definition for %s to:\n"%s"\n', obj.ClassName, filePath)
+            % fprintf('Saved class definition for %s to:\n"%s"\n', obj.ClassName, filePath)
         end
 
         function appendLine(obj, numIndent, str)
@@ -319,7 +319,7 @@ function startFunctionBlock(obj, functionName, options)
         function endFunctionBlock(obj)
             numIndent = 2;
             obj.appendLine(numIndent, "end");
-            %obj.appendLine(numIndent, ""); % Add empty line
+            % obj.appendLine(numIndent, ""); % Add empty line
             obj.CurrentStep = "methods";
         end
     end

diff --git a/code/internal/+openminds/+internal/+generator/SchemaTranslator.m b/code/internal/+openminds/+internal/+generator/SchemaTranslator.m
@@ -54,7 +54,7 @@
 
             obj.saveClassdef()
 
-            %obj.saveAlias()
+            % obj.saveAlias()
 
             if ~nargout
                 clear obj
@@ -225,7 +225,7 @@ function assignOutputFile(obj)
         function saveAlias(obj)
             filePath = obj.getAliasFilePath();
 
-            %fullClassName = obj.getFullClassName();
+            % fullClassName = obj.getFullClassName();
             fullClassNameSimple = obj.getFullClassName("simple");
 
             folderPath = fullfile( openminds.internal.rootpath, 'internal', 'resources', 'templates' );
@@ -240,7 +240,6 @@ function saveAlias(obj)
             fid = fopen(filePath, 'w');
             fwrite(fid, str);
             fclose(fid);
-
         end
     end
 
@@ -447,11 +446,10 @@ function writeLinkedPropertyBlock(obj)
                     obj.appendLine(3, sprintf("'%s', {%s}%s", keyName, linkedTypesStr, lineBreak))
                 end
                 obj.appendLine(2, ')')
-
             end
 
             obj.endPropertyBlock()
-            %obj.writeLinkedPropertyBlo
+            % obj.writeLinkedPropertyBlo
         end
 
         function writeSchemaProperties(obj)
@@ -468,7 +466,6 @@ function writeSchemaProperties(obj)
                 end
                 obj.endPropertyBlock()
             else
-
             end
         end
 
@@ -573,18 +570,18 @@ function addSchemaProperty(obj, propertyName, propertyAttributes)
                 elseif numel(clsNames) == 1
                     dataType = clsNames{1};
                 else
-                    %dataType = 'cell';
-                    %validationFcnStr(end+1) = obj.getMultiTypeValidationFunctionString(propertyName, clsNames);
+                    % dataType = 'cell';
+                    % validationFcnStr(end+1) = obj.getMultiTypeValidationFunctionString(propertyName, clsNames);
 
                     dataType = createPropertyLinksetClass(obj.SchemaName, propertyName, clsNames, allowMultiple);
 
-                    %dataType = clsNames{1};
-                    %warning('Multiple schemas allowed for property %s of schema %s', propertyName, obj.SchemaName)
+                    % dataType = clsNames{1};
+                    % warning('Multiple schemas allowed for property %s of schema %s', propertyName, obj.SchemaName)
                 end
 
             elseif isfield(propertyAttributes, 'x_linkedCategories')
                 clsNames = cellfun(@(str) openminds.internal.utility.string.buildClassName(str, '', 'category'), propertyAttributes.x_linkedCategories, 'UniformOutput', false);
-                %dataType = sprintf('{%s}', strjoin(clsNames, ', '));
+                % dataType = sprintf('{%s}', strjoin(clsNames, ', '));
                 attributeNames = setdiff(attributeNames, 'x_linkedCategories');
                 dataType = clsNames{1};
                 if numel(clsNames) > 1
@@ -600,7 +597,6 @@ function addSchemaProperty(obj, propertyName, propertyAttributes)
                             dataType = itemDef.type;
                             itemFields = setdiff(itemFields, 'type');
                         else
-
                         end
                         % Todo: note: item is a nested attribute field....
                         if ~isempty(itemFields)
@@ -679,7 +675,7 @@ function addSchemaProperty(obj, propertyName, propertyAttributes)
                             end
                         case 'description'
                             % str = propertyAttributes.description;
-                            %disp(['description: ', str])
+                            % disp(['description: ', str])
                         otherwise
                             disp(['additional attributenames: ', attributeNames])
                     end
@@ -689,19 +685,19 @@ function addSchemaProperty(obj, propertyName, propertyAttributes)
             if isempty(validationFcnStr)
                 obj.addProperty(propertyName, 'Size', sizeAttribute, ...
                     'Type', dataType)
-                %newStr = sprintf('%s %s %s', propertyName, sizeAttribute, dataType);
+                % newStr = sprintf('%s %s %s', propertyName, sizeAttribute, dataType);
             else
 
                 validationFcnStr = sprintf("{%s}", strjoin(validationFcnStr, ", "));
 
                 obj.addProperty(propertyName, 'Size', sizeAttribute, ...
                     'Type', dataType, 'Validator', validationFcnStr)
-                %newStr = sprintf('%s %s %s %s', propertyName, sizeAttribute, dataType, validationFcnStr);
+                % newStr = sprintf('%s %s %s %s', propertyName, sizeAttribute, dataType, validationFcnStr);
             end
 
-            %newStr = obj.indentLine(newStr, 2);
-            %obj.appendLine(newStr)
-            %obj.appendLine('')
+            % newStr = obj.indentLine(newStr, 2);
+            % obj.appendLine(newStr)
+            % obj.appendLine('')
         end
     end
 
@@ -841,7 +837,7 @@ function writeEnumSwitchBlock(obj)
                 end
 
                 obj.appendLine(4, "")
-                %obj.writeEmptyLine()
+                % obj.writeEmptyLine()
             end
             obj.appendLine(3, 'end')
 

diff --git a/code/internal/+openminds/+internal/+generator/downloadSchemas.m b/code/internal/+openminds/+internal/+generator/downloadSchemas.m
@@ -46,5 +46,5 @@ function downloadSchemas(versionNumber)
     delete(tempPath)
 
     % Save the current commit ID
-    %openminds.internal.utility.git.saveCurrentSchemaCommitID()
+    % openminds.internal.utility.git.saveCurrentSchemaCommitID()
 end
diff --git a/code/internal/+openminds/+internal/+helper/listSchemasWithNonGenericLabel.m b/code/internal/+openminds/+internal/+helper/listSchemasWithNonGenericLabel.m
@@ -10,7 +10,7 @@
     tempsavepath = tempname;
     tempsavepath = [tempsavepath, '.mat'];
 
-    %disp(tempsavepath)
+    % disp(tempsavepath)
     cleanupObj = onCleanup(@(filepath)delete(tempsavepath));
 
     count = 0;
@@ -36,22 +36,22 @@
                 S.(iSchemaName).propertyName = "lookupLabel";
                 S.(iSchemaName).stringFormat = "sprintf('%s', lookupLabel)";
 
-                %pass
+                % pass
             elseif isprop(itemPreSave, 'fullName')
                 S.(iSchemaName).propertyName = 'fullName';
                 S.(iSchemaName).stringFormat = "sprintf('%s', fullName)";
 
-                %pass
+                % pass
             elseif isprop(itemPreSave, 'identifier')
                 S.(iSchemaName).propertyName = 'identifier';
                 S.(iSchemaName).stringFormat = "sprintf('%s', identifier)";
 
-                %pass
+                % pass
             elseif isprop(itemPreSave, 'name')
                 S.(iSchemaName).propertyName = 'name';
                 S.(iSchemaName).stringFormat = "sprintf('%s', name)";
 
-                %pass
+                % pass
             else
 
                 S.(iSchemaName).propertyName = '';
@@ -63,10 +63,9 @@
         catch ME
             fprintf('Could not create schema %s due to error:\n%s\n', ...
                 iSchemaName, ME.message)
-
         end
     end
 
-    %T = cell2table(C, 'VariableNames', {'SchemaName', 'Failure point', 'Error Message', 'Extended Error'});
-    %fprintf('Number of tests that failed: %d/%d\n', numTestsFailed, numTestsTotal)
+    % T = cell2table(C, 'VariableNames', {'SchemaName', 'Failure point', 'Error Message', 'Extended Error'});
+    % fprintf('Number of tests that failed: %d/%d\n', numTestsFailed, numTestsTotal)
 end