Merge pull request #247 from NeurodataWithoutBorders/242-schema-selector

Schema Selector

+tests/+system/NwbTestInterface.m

@@ -15,12 +15,8 @@ function setupClass(testCase)
 
     methods (TestMethodSetup)
         function setupMethod(testCase)
-            testCase.applyFixture(matlab.unittest.fixtures.WorkingFolderFixture);
-            schemaPath = fullfile(testCase.root, 'nwb-schema');
-
-            generateCore(...
-                fullfile(schemaPath, 'hdmf-common-schema', 'common', 'namespace.yaml'),...
-                fullfile(schemaPath, 'core', 'nwb.namespace.yaml'));
+            testCase.applyFixture(matlab.unittest.fixtures.WorkingFolderFixture);            
+            generateCore();
             testCase.file = NwbFile( ...
                 'session_description', 'a test NWB File', ...
                 'identifier', 'TEST123', ...

.gitmodules

@@ -0,0 +1,18 @@
+[submodule "nwb-schema/2.2.5"]
+	path = nwb-schema/2.2.5
+	url = https://github.com/NeurodataWithoutBorders/nwb-schema
+[submodule "nwb-schema/2.2.4"]
+	path = nwb-schema/2.2.4
+	url = https://github.com/NeurodataWithoutBorders/nwb-schema
+[submodule "nwb-schema/2.2.3"]
+	path = nwb-schema/2.2.3
+	url = https://github.com/NeurodataWithoutBorders/nwb-schema
+[submodule "nwb-schema/2.2.2"]
+	path = nwb-schema/2.2.2
+	url = https://github.com/NeurodataWithoutBorders/nwb-schema
+[submodule "nwb-schema/2.2.1"]
+	path = nwb-schema/2.2.1
+	url = https://github.com/NeurodataWithoutBorders/nwb-schema
+[submodule "nwb-schema/2.2.0"]
+	path = nwb-schema/2.2.0
+	url = https://github.com/NeurodataWithoutBorders/nwb-schema

README.md

@@ -9,7 +9,7 @@ A Matlab interface for reading and writing Neurodata Without Borders (NWB) 2.0 f
 Download the current release of MatNWB from the [MatNWB releases page](https://github.com/NeurodataWithoutBorders/matnwb/releases) or from the [![View NeurodataWithoutBorders/matnwb on File Exchange](https://www.mathworks.com/matlabcentral/images/matlab-file-exchange.svg)](https://www.mathworks.com/matlabcentral/fileexchange/67741-neurodatawithoutborders-matnwb). You can also check out the latest development version via 
 
 ```bash
-git clone https://github.com/NeurodataWithoutBorders/matnwb.git
+git clone --recurse-submodules https://github.com/NeurodataWithoutBorders/matnwb.git
 ```
 
 ### Step 2: Generate the API
@@ -19,37 +19,32 @@ From the Matlab command line, add MatNWB to the Matlab path and generate the cor
 ```matlab
 cd matnwb
 addpath(genpath(pwd));
-generateCore(); % generate core namespace located in the repository.
+generateCore(); % generate the most recent nwb-schema release.
 ```
 
 ### Optional: Generate MatNWB code for extensions
 
-The `generateCore` command also takes variable arguments from any extensions.
+The `generateExtension` command generates extension classes given a file path to the extension's namespace.
 
 ```matlab
-generateCore('schema/core/nwb.namespace.yaml', '.../my_extensions1.namespace.yaml',...);
-```
-
-You can also generate extensions without generating the core classes in this way:
-
-```matlab
-generateExtension('my_extension.namespace.yaml');
+generateExtension('schema/core/nwb.namespace.yaml', '.../my_extensions1.namespace.yaml',...);
 ```
 
 Generated Matlab code will be put a `+types` subdirectory.  This is a Matlab package.  When the `+types` folder is accessible to the Matlab path, the generated code will be used for reading NWBFiles.
 
 ```matlab
-nwb=nwbRead('data.nwb');
+nwb = nwbRead('data.nwb');
 ```
 
-### Optional: Download the NWB format schema
+### Optional: Generate an older core schema
 
-Download the current release of the NWB format schema from the [nwb-schema releases page](https://github.com/NeurodataWithoutBorders/nwb-schema/releases) or check out the latest development via 
+The `generateCore` command can generate older versions of the nwb schema.
 
-```bash
-git clone --recursive https://github.com/NeurodataWithoutBorders/nwb-schema.git
+```matlab
+generateCore('2.2.1'); % generate schema 2.2.1
 ```
-Then re-run `generateCore()` to update the API from the updated schema.
+
+Currently, only schemas 2.2.x are supported (2.1.0 and 2.0.1 are not supported at this time).
 
 ## Tutorials
 

generateCore.m

@@ -1,11 +1,11 @@
-function generateCore(varargin)
+function generateCore(version)
 % GENERATECORE Generate Matlab classes from NWB core schema files
 %   GENERATECORE()  Generate classes (Matlab m-files) from the
-%   NWB:N core namespace file.
+%   NWB:N core namespace file. By default, generates off of the most recent nwb-schema
+%   release.
 %
-%   GENERATECORE(core_or_extension_paths,...)  Generate classes for the
-%   core namespace as well as one or more extenstions.  Each input filename
-%   should be an NWB namespace file.
+%   GENERATECORE(version)  Generate classes for the
+%   core namespace of that version
 %
 %   A cache of schema data is generated in the 'namespaces' subdirectory in
 %   the current working directory.  This is for allowing cross-referencing
@@ -16,25 +16,30 @@ function generateCore(varargin)
 %
 %   Example:
 %      generateCore();
-%      generateCore('schema/core/nwb.namespace.yaml');
-%      generateCore('schema/my_ext/myext.namespace.yaml');
+%      generateCore('2.2.3');
 %
 %   See also GENERATEEXTENSION
+
 if nargin == 0
-    [nwbLocation, ~, ~] = fileparts(mfilename('fullpath'));
-    schemaPath = fullfile(nwbLocation, 'nwb-schema');
-    corePath = fullfile(schemaPath, 'core', 'nwb.namespace.yaml');
-    commonPath = fullfile(schemaPath, 'hdmf-common-schema', ...
-        'common', 'namespace.yaml');
-
-    if 2 == exist(commonPath, 'file')
-        generateExtension(commonPath);
-    end
-
-    generateExtension(corePath);
+    version = '2.2.5';
 else
-    for i=1:length(varargin)
-        generateExtension(varargin{i});
-    end
+    validateattributes(version, {'char'}, {'scalartext'});
 end
+
+[nwbLocation, ~, ~] = fileparts(mfilename('fullpath'));
+schemaPath = fullfile(nwbLocation, 'nwb-schema', version);
+corePath = fullfile(schemaPath, 'core', 'nwb.namespace.yaml');
+commonPath = fullfile(schemaPath,...
+    'hdmf-common-schema', ...
+    'common',...
+    'namespace.yaml');
+assert(2 == exist(corePath, 'file'),...
+    'MATNWB:nwbread:missingSpec',...
+    'Cannot find suitable core namespace for schema version `%s`',...
+    version);
+
+if 2 == exist(commonPath, 'file')
+    generateExtension(commonPath);
+end
+generateExtension(corePath);
 end

generateExtension.m

@@ -1,6 +1,6 @@
-function generateExtension(source)
+function generateExtension(varargin)
 % GENERATEEXTENSION Generate Matlab classes from NWB extension schema file
-%   GENERATECORE(extension_path...)  Generate classes
+%   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.
@@ -13,19 +13,22 @@ function generateExtension(source)
 %   current working directory.
 %
 %   Example:
-%      generateCore('schema\core\nwb.namespace.yaml');
-%      generateExtension('schema\myext\myextension.namespace.yaml')
+%      generateExtension('schema\myext\myextension.namespace.yaml', 'schema\myext2\myext2.namespace.yaml');
 %
 %   See also GENERATECORE
-validateattributes(source, {'char', 'string'}, {'scalartext'});
-
-[localpath, ~, ~] = fileparts(source);
-assert(2 == exist(source, 'file'),...
-    'MATNWB:FILE', 'Path to file `%s` could not be found.', source);
-fid = fopen(source);
-namespaceText = fread(fid, '*char') .';
-fclose(fid);
-
-Namespace = spec.generate(namespaceText, localpath);
-file.writeNamespace(Namespace.name);
+for i = 1:length(varargin)
+    source = varargin{i};
+    validateattributes(source, {'char', 'string'}, {'scalartext'});
+
+    [localpath, ~, ~] = fileparts(source);
+    assert(2 == exist(source, 'file'),...
+        'MATNWB:FILE', 'Path to file `%s` could not be found.', source);
+    fid = fopen(source);
+    namespaceText = fread(fid, '*char') .';
+    fclose(fid);
+
+    Namespace = spec.generate(namespaceText, localpath);
+    file.writeNamespace(Namespace.name);
+    rehash();
+end
 end