Allow string inputs for most interfaces (#522)

* Support optional string arguments Can now provide double-quoted string paths and options to generate, export, and read functions. * Adds string checks for all filename references * Refactor generate, export, and read functions --------- Co-authored-by: Lawrence Niu <[email protected]>
NeurodataWithoutBorders · Jul 25, 2023 · 0d334ed · 0d334ed
1 parent 461c5c4
commit 0d334ed
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Showing 8 changed files with 320 additions and 285 deletions.
diff --git a/+types/+untyped/DataStub.m b/+types/+untyped/DataStub.m
@@ -16,8 +16,12 @@
 
     methods
         function obj = DataStub(filename, path)
-            obj.filename = filename;
-            obj.path = path;
+            validateattributes(filename, {'char', 'string'}, {'scalartext'} ...
+                , 'types.untyped.DataStub', 'filename', 1);
+            validateattributes(path, {'char', 'string'}, {'scalartext'} ...
+                , 'types.untyped.DataStub', 'path', 2);
+            obj.filename = char(filename);
+            obj.path = char(path);
         end
 
         function sid = get_space(obj)

diff --git a/+types/+untyped/ExternalLink.m b/+types/+untyped/ExternalLink.m
@@ -6,8 +6,12 @@
 
     methods
         function obj = ExternalLink(filename, path)
-            obj.filename = filename;
-            obj.path = path;
+            validateattributes(filename, {'char', 'string'}, {'scalartext'} ...
+                , 'types.untyped.ExternalLink', 'filename', 1);
+            validateattributes(path, {'char', 'string'}, {'scalartext'} ...
+                , 'types.untyped.ExternalLink', 'path', 2);
+            obj.filename = char(filename);
+            obj.path = char(path);
         end
 
         function data = deref(obj)

diff --git a/+types/+untyped/ObjectView.m b/+types/+untyped/ObjectView.m
@@ -23,10 +23,12 @@
             % target = A generated NWB object.
 
             if ischar(target) || isstring(target)
-                validateattributes(target, {'char', 'string'}, {'scalartext'});
-                obj.path = target;
+                validateattributes(target, {'char', 'string'}, {'scalartext'} ...
+                    , 'types.untyped.ObjectView', 'target string', 1);
+                obj.path = char(target);
             else
-                validateattributes(target, {'types.untyped.MetaClass'}, {'scalar'});
+                validateattributes(target, {'types.untyped.MetaClass'}, {'scalar'} ...
+                    , 'types.untyped.ObjectView', 'target object', 1);
                 obj.target = target;
             end
         end

diff --git a/+types/+untyped/SoftLink.m b/+types/+untyped/SoftLink.m
@@ -18,16 +18,19 @@
             % target = pre-generated NWB object.
 
             if ischar(target) || isstring(target)
-                validateattributes(target, {'char', 'string'}, {'scalartext'});
-                obj.path = target;
+                validateattributes(target, {'char', 'string'}, {'scalartext'} ...
+                    , 'types.untyped.SoftLink', 'target string', 1);
+                obj.path = char(target);
             else
-                validateattributes(target, {'types.untyped.MetaClass'}, {'scalar'});
+                validateattributes(target, {'types.untyped.MetaClass'}, {'scalar'} ...
+                    , 'types.untyped.SoftLink', 'target object', 2);
                 obj.target = target;
             end
         end
 
         function set.path(obj, val)
-            validateattributes(val, {'char', 'string'}, {'scalartext'});
+            validateattributes(val, {'char', 'string'}, {'scalartext'} ...
+                , '(types.untyped.SoftLink).path', 'path', 2);
             obj.path = val;
         end
 

diff --git a/generateCore.m b/generateCore.m
@@ -1,54 +1,55 @@
 function generateCore(varargin)
-% GENERATECORE Generate Matlab classes from NWB core schema files
-%   GENERATECORE()  Generate classes (Matlab m-files) from the
-%   NWB:N core namespace file. By default, generates off of the most recent nwb-schema
-%   release.
-%
-%   GENERATECORE(version)  Generate classes for the
-%   core namespace of the listed version.
-%
-%   A cache of schema data is generated in the 'namespaces' subdirectory in
-%   the current working directory.  This is for allowing cross-referencing
-%   classes between multiple namespaces.
-%
-%   Output files are generated placed in a '+types' subdirectory in the
-%   current working directory.
-%   
-%   GENERATECORE(__, 'savedir', saveDirectory) Generates the core class
-%   files in the specified directory.
-%
-%   Example:
-%      generateCore();
-%      generateCore('2.2.3');
-%
-%   See also GENERATEEXTENSION
-
-latestVersion = '2.6.0';
-
-if nargin == 0 || strcmp(varargin{1}, 'savedir')
-    version = latestVersion;
-else
-    version = varargin{1};
-    varargin = varargin(2:end);
-    validateattributes(version, {'char'}, {'scalartext'});
-end
-
-if strcmp(version, 'latest')
-    version = latestVersion;
-end
-
-schemaPath = fullfile(misc.getMatnwbDir(), 'nwb-schema', version);
-corePath = fullfile(schemaPath, 'core', 'nwb.namespace.yaml');
-commonPath = fullfile(schemaPath,...
-    'hdmf-common-schema', ...
-    'common',...
-    'namespace.yaml');
-assert(2 == exist(corePath, 'file'),...
-    'NWB:GenerateCore:MissingCoreSchema',...
-    'Cannot find suitable core namespace for schema version `%s`',...
-    version);
-if 2 == exist(commonPath, 'file')
-    generateExtension(commonPath, varargin{:});
-end
-generateExtension(corePath, varargin{:});
+    % GENERATECORE Generate Matlab classes from NWB core schema files
+    %   GENERATECORE()  Generate classes (Matlab m-files) from the
+    %   NWB:N core namespace file. By default, generates off of the most recent nwb-schema
+    %   release.
+    %
+    %   GENERATECORE(version)  Generate classes for the
+    %   core namespace of the listed version.
+    %
+    %   A cache of schema data is generated in the 'namespaces' subdirectory in
+    %   the current working directory.  This is for allowing cross-referencing
+    %   classes between multiple namespaces.
+    %
+    %   Output files are generated placed in a '+types' subdirectory in the
+    %   current working directory.
+    %
+    %   GENERATECORE(__, 'savedir', saveDirectory) Generates the core class
+    %   files in the specified directory.
+    %
+    %   Example:
+    %      generateCore();
+    %      generateCore('2.2.3');
+    %
+    %   See also GENERATEEXTENSION
+
+    latestVersion = '2.6.0';
+
+    if nargin == 0 || strcmp(varargin{1}, 'savedir')
+        version = latestVersion;
+    else
+        version = varargin{1};
+        validateattributes(version, {'char', 'string'}, {'scalartext'}, 'generateCore', 'version', 1);
+        version = char(version);
+        varargin = varargin(2:end);
+    end
+
+    if strcmp(version, 'latest')
+        version = latestVersion;
+    end
+
+    schemaPath = fullfile(misc.getMatnwbDir(), 'nwb-schema', version);
+    corePath = fullfile(schemaPath, 'core', 'nwb.namespace.yaml');
+    commonPath = fullfile(schemaPath,...
+        'hdmf-common-schema', ...
+        'common',...
+        'namespace.yaml');
+    assert(2 == exist(corePath, 'file'),...
+        'NWB:GenerateCore:MissingCoreSchema',...
+        'Cannot find suitable core namespace for schema version `%s`',...
+        version);
+    if 2 == exist(commonPath, 'file')
+        generateExtension(commonPath, varargin{:});
+    end
+    generateExtension(corePath, varargin{:});
 end
diff --git a/generateExtension.m b/generateExtension.m
@@ -1,56 +1,62 @@
 function generateExtension(varargin)
-% GENERATEEXTENSION Generate Matlab classes from NWB extension schema file
-%   GENERATEEXTENSION(extension_path...)  Generate classes
-%   (Matlab m-files) from one or more NWB:N schema extension namespace
-%   files.  A registry of already generated core types is used to resolve
-%   dependent types.
-%
-%   A cache of schema data is generated in the 'namespaces' subdirectory in
-%   the current working directory.  This is for allowing cross-referencing
-%   classes between multiple namespaces.
-%
-%   Output files are generated placed in a '+types' subdirectory in the
-%   current working directory.
-%
-%   Example:
-%      generateExtension('schema\myext\myextension.namespace.yaml', 'schema\myext2\myext2.namespace.yaml');
-%
-%   See also GENERATECORE
-assert(iscellstr(varargin),...
-    'NWB:GenerateExtension:InvalidArguments',...
-    'Must be a cell array of strings.'); %#ok<ISCLSTR>
-
-saveDirMask = strcmp(varargin, 'savedir');
-if any(saveDirMask)
-    assert(~saveDirMask(end),...
-        'NWB:GenerateExtenion:InvalidParameter',...
-        'savedir must be paired with the desired save directory.');
-    saveDir = varargin{find(saveDirMask, 1, 'last') + 1};
-    saveDirParametersMask = saveDirMask | circshift(saveDirMask, 1);
-    sourceList = varargin(~saveDirParametersMask);
-else
-    saveDir = misc.getMatnwbDir();
-    sourceList = varargin;
-end
-
-for iNamespaceFiles = 1:length(sourceList)
-    source = sourceList{iNamespaceFiles};
-    validateattributes(source, {'char', 'string'}, {'scalartext'});
+    % GENERATEEXTENSION Generate Matlab classes from NWB extension schema file
+    %   GENERATEEXTENSION(extension_path...)  Generate classes
+    %   (Matlab m-files) from one or more NWB:N schema extension namespace
+    %   files.  A registry of already generated core types is used to resolve
+    %   dependent types.
+    %
+    %   A cache of schema data is generated in the 'namespaces' subdirectory in
+    %   the current working directory.  This is for allowing cross-referencing
+    %   classes between multiple namespaces.
+    %
+    %   Output files are generated placed in a '+types' subdirectory in the
+    %   current working directory.
+    %
+    %   Example:
+    %      generateExtension('schema\myext\myextension.namespace.yaml', 'schema\myext2\myext2.namespace.yaml');
+    %
+    %   See also GENERATECORE
 
-    [localpath, ~, ~] = fileparts(source);
-    assert(2 == exist(source, 'file'),...
-        'NWB:GenerateExtension:FileNotFound', 'Path to file `%s` could not be found.', source);
-    fid = fopen(source);
-    namespaceText = fread(fid, '*char') .';
-    fclose(fid);
+    for iOption = 1:length(varargin)
+        option = varargin{iOption};
+        validateattributes(option, {'char', 'string'}, {'scalartext'} ...
+            , 'generateExtension', 'extension name', iOption);
+        if isstring(option)
+            varargin{iOption} = char(option);
+        end
+    end
 
-    Namespaces = spec.generate(namespaceText, localpath);
-
-    for iNamespace = 1:length(Namespaces)
-        Namespace = Namespaces(iNamespace);
-        spec.saveCache(Namespace, saveDir);
-        file.writeNamespace(Namespace.name, saveDir);
-        rehash();
+    saveDirMask = strcmp(varargin, 'savedir');
+    if any(saveDirMask)
+        assert(~saveDirMask(end),...
+            'NWB:GenerateExtenion:InvalidParameter',...
+            'savedir must be paired with the desired save directory.');
+        saveDir = varargin{find(saveDirMask, 1, 'last') + 1};
+        saveDirParametersMask = saveDirMask | circshift(saveDirMask, 1);
+        sourceList = varargin(~saveDirParametersMask);
+    else
+        saveDir = misc.getMatnwbDir();
+        sourceList = varargin;
+    end
+
+    for iNamespaceFiles = 1:length(sourceList)
+        source = sourceList{iNamespaceFiles};
+        validateattributes(source, {'char', 'string'}, {'scalartext'});
+
+        [localpath, ~, ~] = fileparts(source);
+        assert(2 == exist(source, 'file'),...
+            'NWB:GenerateExtension:FileNotFound', 'Path to file `%s` could not be found.', source);
+        fid = fopen(source);
+        namespaceText = fread(fid, '*char') .';
+        fclose(fid);
+
+        Namespaces = spec.generate(namespaceText, localpath);
+
+        for iNamespace = 1:length(Namespaces)
+            Namespace = Namespaces(iNamespace);
+            spec.saveCache(Namespace, saveDir);
+            file.writeNamespace(Namespace.name, saveDir);
+            rehash();
+        end
     end
-end
 end
diff --git a/nwbExport.m b/nwbExport.m
@@ -1,38 +1,44 @@
 function nwbExport(nwb, filenames)
-%NWBEXPORT Writes an NWB file.
-%  nwbRead(nwb,filename) Writes the nwb object to a file at filename.
-%
-%  Example:
-%    % Generate Matlab code for the NWB objects from the core schema.
-%    % This only needs to be done once.
-%    generateCore('schema\core\nwb.namespace.yaml');
-%    % Create some fake fata and write
-%    nwb = NwbFile;
-%    nwb.session_start_time = datetime('now');
-%    nwb.identifier = 'EMPTY';
-%    nwb.session_description = 'empty test file';
-%    nwbExport(nwb, 'empty.nwb');
-%
-%  See also GENERATECORE, GENERATEEXTENSION, NWBFILE, NWBREAD
-validateattributes(nwb, {'NwbFile'}, {'nonempty'});
-validateattributes(filenames, {'cell', 'string', 'char'}, {'nonempty'});
-if iscell(filenames)
-    assert(iscellstr(filenames), 'filename cell array must consist of strings');
-end
-if ~isscalar(nwb)
-    assert(~ischar(filenames) && length(filenames) == length(nwb), ...
-        'NwbFile and filename array dimensions must match.');
-end
-
-for i=1:length(nwb)
-    if iscellstr(filenames)
-        filename = filenames{i};
-    elseif isstring(filenames)
-        filename = filenames(i);
-    else
-        filename = filenames;
+    %NWBEXPORT Writes an NWB file.
+    %  nwbRead(nwb,filename) Writes the nwb object to a file at filename.
+    %
+    %  Example:
+    %    % Generate Matlab code for the NWB objects from the core schema.
+    %    % This only needs to be done once.
+    %    generateCore('schema\core\nwb.namespace.yaml');
+    %    % Create some fake fata and write
+    %    nwb = NwbFile;
+    %    nwb.session_start_time = datetime('now');
+    %    nwb.identifier = 'EMPTY';
+    %    nwb.session_description = 'empty test file';
+    %    nwbExport(nwb, 'empty.nwb');
+    %
+    %  See also GENERATECORE, GENERATEEXTENSION, NWBFILE, NWBREAD
+    validateattributes(nwb, {'NwbFile'}, {'nonempty'}, 'nwbExport', 'nwb', 1);
+    validateattributes(filenames, {'cell', 'string', 'char'}, {'nonempty'}, 'nwbExport', 'filenames', 2);
+    if isstring(filenames)
+        filenames = convertStringsToChars(filenames);
+    end
+    if iscell(filenames)
+        for iName = 1:length(filenames)
+            name = filenames{iName};
+            validateattributes(name, {'string', 'char'}, {'scalartext', 'nonempty'} ...
+                , 'nwbExport', 'filenames', 2);
+            filenames{iName} = char(name);
+        end
+    end
+    if ~isscalar(nwb)
+        assert(~ischar(filenames) && length(filenames) == length(nwb), ...
+            'NwbFile and filename array dimensions must match.');
     end
 
-    nwb(i).export(filename);
-end
+    for iFiles = 1:length(nwb)
+        if iscellstr(filenames)
+            filename = filenames{iFiles};
+        else
+            filename = filenames;
+        end
+
+        nwb(iFiles).export(filename);
+    end
 end