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106 changes: 64 additions & 42 deletions doc/generateCore.html
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Expand Up @@ -6,7 +6,7 @@
<meta name="keywords" content="generateCore">
<meta name="description" content="GENERATECORE Generate Matlab classes from NWB core schema files">
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<meta name="generator" content="m2html v1.5 &copy; 2003-2005 Guillaume Flandin">
<meta name="generator" content="m2html &copy; 2003-2019 Guillaume Flandin">
<meta name="robots" content="index, follow">
<link type="text/css" rel="stylesheet" href="m2html.css">
</head>
Expand All @@ -24,16 +24,16 @@ <h2><a name="_name"></a>PURPOSE <a href="#_top"><img alt="^" border="0" src="up.
<div class="box"><strong>GENERATECORE Generate Matlab classes from NWB core schema files</strong></div>

<h2><a name="_synopsis"></a>SYNOPSIS <a href="#_top"><img alt="^" border="0" src="up.png"></a></h2>
<div class="box"><strong>function generateCore(varargin) </strong></div>
<div class="box"><strong>function generateCore(version, options) </strong></div>

<h2><a name="_description"></a>DESCRIPTION <a href="#_top"><img alt="^" border="0" src="up.png"></a></h2>
<div class="fragment"><pre class="comment"> GENERATECORE Generate Matlab classes from NWB core schema files
GENERATECORE() Generate classes (Matlab m-files) from the
NWB:N core namespace file.
NWB 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 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
Expand All @@ -42,12 +42,14 @@ <h2><a name="_description"></a>DESCRIPTION <a href="#_top"><img alt="^" border="
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('schema/core/nwb.namespace.yaml');
generateCore('schema/my_ext/myext.namespace.yaml');
generateCore('2.2.3');

See also <a href="generateExtension.html" class="code" title="function generateExtension(source)">GENERATEEXTENSION</a></pre></div>
See also <a href="generateExtension.html" class="code" title="function generateExtension(namespaceFilePath, options)">GENERATEEXTENSION</a></pre></div>

<!-- crossreference -->
<h2><a name="_cross"></a>CROSS-REFERENCE INFORMATION <a href="#_top"><img alt="^" border="0" src="up.png"></a></h2>
Expand All @@ -62,38 +64,58 @@ <h2><a name="_cross"></a>CROSS-REFERENCE INFORMATION <a href="#_top"><img alt="^


<h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" src="up.png"></a></h2>
<div class="fragment"><pre>0001 <a name="_sub0" href="#_subfunctions" class="code">function generateCore(varargin)</a>
0002 <span class="comment">% GENERATECORE Generate Matlab classes from NWB core schema files</span>
0003 <span class="comment">% GENERATECORE() Generate classes (Matlab m-files) from the</span>
0004 <span class="comment">% NWB:N core namespace file.</span>
0005 <span class="comment">%</span>
0006 <span class="comment">% GENERATECORE(core_or_extension_paths,...) Generate classes for the</span>
0007 <span class="comment">% core namespace as well as one or more extenstions. Each input filename</span>
0008 <span class="comment">% should be an NWB namespace file.</span>
0009 <span class="comment">%</span>
0010 <span class="comment">% A cache of schema data is generated in the 'namespaces' subdirectory in</span>
0011 <span class="comment">% the current working directory. This is for allowing cross-referencing</span>
0012 <span class="comment">% classes between multiple namespaces.</span>
0013 <span class="comment">%</span>
0014 <span class="comment">% Output files are generated placed in a '+types' subdirectory in the</span>
0015 <span class="comment">% current working directory.</span>
0016 <span class="comment">%</span>
0017 <span class="comment">% Example:</span>
0018 <span class="comment">% generateCore();</span>
0019 <span class="comment">% generateCore('schema/core/nwb.namespace.yaml');</span>
0020 <span class="comment">% generateCore('schema/my_ext/myext.namespace.yaml');</span>
0021 <span class="comment">%</span>
0022 <span class="comment">% See also GENERATEEXTENSION</span>
0023 <span class="keyword">if</span> nargin == 0
0024 [nwbLocation, ~, ~] = fileparts(mfilename(<span class="string">'fullpath'</span>));
0025 namespacePath = fullfile(nwbLocation, <span class="string">'schema'</span>, <span class="string">'core'</span>, <span class="string">'nwb.namespace.yaml'</span>);
0026 generateExtension(namespacePath);
0027 <span class="keyword">else</span>
0028 <span class="keyword">for</span> i=1:length(varargin)
0029 generateExtension(varargin{i});
0030 <span class="keyword">end</span>
0031 <span class="keyword">end</span>
0032 <span class="keyword">end</span></pre></div>
<hr><address>Generated on Fri 09-Aug-2019 14:27:49 by <strong><a href="http://www.artefact.tk/software/matlab/m2html/" title="Matlab Documentation in HTML">m2html</a></strong> &copy; 2005</address>
<div class="fragment"><pre>0001 <a name="_sub0" href="#_subfunctions" class="code">function generateCore(version, options)</a>
0002 <span class="comment">% GENERATECORE Generate Matlab classes from NWB core schema files</span>
0003 <span class="comment">% GENERATECORE() Generate classes (Matlab m-files) from the</span>
0004 <span class="comment">% NWB core namespace file. By default, generates off of the most recent nwb-schema</span>
0005 <span class="comment">% release.</span>
0006 <span class="comment">%</span>
0007 <span class="comment">% GENERATECORE(version) Generate classes for the</span>
0008 <span class="comment">% core namespace of the listed version.</span>
0009 <span class="comment">%</span>
0010 <span class="comment">% A cache of schema data is generated in the 'namespaces' subdirectory in</span>
0011 <span class="comment">% the current working directory. This is for allowing cross-referencing</span>
0012 <span class="comment">% classes between multiple namespaces.</span>
0013 <span class="comment">%</span>
0014 <span class="comment">% Output files are generated placed in a '+types' subdirectory in the</span>
0015 <span class="comment">% current working directory.</span>
0016 <span class="comment">%</span>
0017 <span class="comment">% GENERATECORE(__, 'savedir', saveDirectory) Generates the core class</span>
0018 <span class="comment">% files in the specified directory.</span>
0019 <span class="comment">%</span>
0020 <span class="comment">% Example:</span>
0021 <span class="comment">% generateCore();</span>
0022 <span class="comment">% generateCore('2.2.3');</span>
0023 <span class="comment">%</span>
0024 <span class="comment">% See also GENERATEEXTENSION</span>
0025
0026 arguments
0027 version (1,1) string {matnwb.common.mustBeValidSchemaVersion} = &quot;latest&quot;
0028 options.savedir (1,1) string = misc.getMatnwbDir()
0029 <span class="keyword">end</span>
0030
0031 <span class="keyword">if</span> version == &quot;latest&quot;
0032 version = matnwb.common.findLatestSchemaVersion();
0033 <span class="keyword">end</span>
0034
0035 schemaPath = fullfile(misc.getMatnwbDir(), &quot;nwb-schema&quot;, version);
0036 corePath = fullfile(schemaPath, &quot;core&quot;, &quot;nwb.namespace.yaml&quot;);
0037 commonPath = fullfile(schemaPath, <span class="keyword">...</span>
0038 &quot;hdmf-common-schema&quot;, <span class="keyword">...</span>
0039 &quot;common&quot;, <span class="keyword">...</span>
0040 &quot;namespace.yaml&quot;);
0041 assert(isfile(corePath), <span class="keyword">...</span>
0042 <span class="string">'NWB:GenerateCore:MissingCoreSchema'</span>, <span class="keyword">...</span>
0043 <span class="string">'Cannot find suitable core namespace for schema version `%s`'</span>, <span class="keyword">...</span>
0044 version);
0045
0046 namespaceFiles = corePath;
0047 <span class="keyword">if</span> isfile(commonPath)
0048 <span class="comment">% Important: generate common before core if common is available</span>
0049 namespaceFiles = [commonPath, namespaceFiles];
0050 <span class="keyword">end</span>
0051 generateExtension(namespaceFiles{:}, <span class="string">'savedir'</span>, options.savedir);
0052 <span class="keyword">end</span></pre></div>
<hr><address>Generated on Tue 19-Nov-2024 22:15:51 by <strong><a href="https://github.com/gllmflndn/m2html">m2html</a></strong> &copy; 2003-2022</address>
</body>
</html>
118 changes: 72 additions & 46 deletions doc/generateExtension.html
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Expand Up @@ -6,7 +6,7 @@
<meta name="keywords" content="generateExtension">
<meta name="description" content="GENERATEEXTENSION Generate Matlab classes from NWB extension schema file">
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<meta name="generator" content="m2html v1.5 &copy; 2003-2005 Guillaume Flandin">
<meta name="generator" content="m2html &copy; 2003-2019 Guillaume Flandin">
<meta name="robots" content="index, follow">
<link type="text/css" rel="stylesheet" href="m2html.css">
</head>
Expand All @@ -24,27 +24,26 @@ <h2><a name="_name"></a>PURPOSE <a href="#_top"><img alt="^" border="0" src="up.
<div class="box"><strong>GENERATEEXTENSION Generate Matlab classes from NWB extension schema file</strong></div>

<h2><a name="_synopsis"></a>SYNOPSIS <a href="#_top"><img alt="^" border="0" src="up.png"></a></h2>
<div class="box"><strong>function generateExtension(source) </strong></div>
<div class="box"><strong>function generateExtension(namespaceFilePath, options) </strong></div>

<h2><a name="_description"></a>DESCRIPTION <a href="#_top"><img alt="^" border="0" src="up.png"></a></h2>
<div class="fragment"><pre class="comment"> GENERATEEXTENSION Generate Matlab classes from NWB extension schema file
GENERATECORE(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
GENERATEEXTENSION(extension_path...) Generate classes
(Matlab m-files) from one or more NWB 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:
generateCore('schema\core\nwb.namespace.yaml');
generateExtension('schema\myext\myextension.namespace.yaml')

See also <a href="generateCore.html" class="code" title="function generateCore(varargin)">GENERATECORE</a></pre></div>
generateExtension('schema\myext\myextension.namespace.yaml', 'schema\myext2\myext2.namespace.yaml');

See also <a href="generateCore.html" class="code" title="function generateCore(version, options)">GENERATECORE</a></pre></div>

<!-- crossreference -->
<h2><a name="_cross"></a>CROSS-REFERENCE INFORMATION <a href="#_top"><img alt="^" border="0" src="up.png"></a></h2>
Expand All @@ -56,42 +55,69 @@ <h2><a name="_cross"></a>CROSS-REFERENCE INFORMATION <a href="#_top"><img alt="^
</ul>
<!-- crossreference -->


<h2><a name="_subfunctions"></a>SUBFUNCTIONS <a href="#_top"><img alt="^" border="0" src="up.png"></a></h2>
<ul style="list-style-image:url(matlabicon.gif)">
<li><a href="#_sub1" class="code">function mustBeYamlFile(filePath)</a></li></ul>

<h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" src="up.png"></a></h2>
<div class="fragment"><pre>0001 <a name="_sub0" href="#_subfunctions" class="code">function generateExtension(source)</a>
0002 <span class="comment">% GENERATEEXTENSION Generate Matlab classes from NWB extension schema file</span>
0003 <span class="comment">% GENERATECORE(extension_path...) Generate classes</span>
0004 <span class="comment">% (Matlab m-files) from one or more NWB:N schema extension namespace</span>
0005 <span class="comment">% files. A registry of already generated core types is used to resolve</span>
0006 <span class="comment">% dependent types.</span>
0007 <span class="comment">%</span>
0008 <span class="comment">% A cache of schema data is generated in the 'namespaces' subdirectory in</span>
0009 <span class="comment">% the current working directory. This is for allowing cross-referencing</span>
0010 <span class="comment">% classes between multiple namespaces.</span>
0011 <span class="comment">%</span>
0012 <span class="comment">% Output files are generated placed in a '+types' subdirectory in the</span>
0013 <span class="comment">% current working directory.</span>
0014 <span class="comment">%</span>
0015 <span class="comment">% Example:</span>
0016 <span class="comment">% generateCore('schema\core\nwb.namespace.yaml');</span>
0017 <span class="comment">% generateExtension('schema\myext\myextension.namespace.yaml')</span>
0018 <span class="comment">%</span>
0019 <span class="comment">% See also GENERATECORE</span>
0020 validateattributes(source, {<span class="string">'char'</span>, <span class="string">'string'</span>}, {<span class="string">'scalartext'</span>});
0021
0022 <span class="comment">%find jar from source and generate Schema</span>
0023 schema = spec.loadSchema();
0024
0025 [localpath, ~, ~] = fileparts(source);
0026 assert(2 == exist(source, <span class="string">'file'</span>),<span class="keyword">...</span>
0027 <span class="string">'MATNWB:FILE'</span>, <span class="string">'Path to file `%s` could not be found.'</span>, source);
0028 fid = fopen(source);
0029 namespace_map = schema.read(fread(fid, <span class="string">'*char'</span>) .');
0030 fclose(fid);
0031
0032 spec.generate(namespace_map, localpath);
0033 <span class="keyword">end</span></pre></div>
<hr><address>Generated on Fri 09-Aug-2019 14:27:49 by <strong><a href="http://www.artefact.tk/software/matlab/m2html/" title="Matlab Documentation in HTML">m2html</a></strong> &copy; 2005</address>
<div class="fragment"><pre>0001 <a name="_sub0" href="#_subfunctions" class="code">function generateExtension(namespaceFilePath, options)</a>
0002 <span class="comment">% GENERATEEXTENSION Generate Matlab classes from NWB extension schema file</span>
0003 <span class="comment">% GENERATEEXTENSION(extension_path...) Generate classes</span>
0004 <span class="comment">% (Matlab m-files) from one or more NWB schema extension namespace</span>
0005 <span class="comment">% files. A registry of already generated core types is used to resolve</span>
0006 <span class="comment">% dependent types.</span>
0007 <span class="comment">%</span>
0008 <span class="comment">% A cache of schema data is generated in the 'namespaces' subdirectory in</span>
0009 <span class="comment">% the current working directory. This is for allowing cross-referencing</span>
0010 <span class="comment">% classes between multiple namespaces.</span>
0011 <span class="comment">%</span>
0012 <span class="comment">% Output files are generated placed in a '+types' subdirectory in the</span>
0013 <span class="comment">% current working directory.</span>
0014 <span class="comment">%</span>
0015 <span class="comment">% Example:</span>
0016 <span class="comment">% generateExtension('schema\myext\myextension.namespace.yaml', 'schema\myext2\myext2.namespace.yaml');</span>
0017 <span class="comment">%</span>
0018 <span class="comment">% See also GENERATECORE</span>
0019
0020 arguments (Repeating)
0021 namespaceFilePath (1,1) string {<a href="#_sub1" class="code" title="subfunction mustBeYamlFile(filePath)">mustBeYamlFile</a>}
0022 <span class="keyword">end</span>
0023 arguments
0024 options.savedir (1,1) string = misc.getMatnwbDir()
0025 <span class="keyword">end</span>
0026
0027 assert( <span class="keyword">...</span>
0028 ~isempty(namespaceFilePath), <span class="keyword">...</span>
0029 <span class="string">'NWB:GenerateExtension:NamespaceMissing'</span>, <span class="keyword">...</span>
0030 <span class="string">'Please provide the file path to at least one namespace specification file.'</span> <span class="keyword">...</span>
0031 )
0032
0033 <span class="keyword">for</span> iNamespaceFiles = 1:length(namespaceFilePath)
0034
0035 source = namespaceFilePath{iNamespaceFiles};
0036 namespaceText = fileread(source);
0037
0038 [namespaceRootFolder, ~, ~] = fileparts(source);
0039 parsedNamespaceList = spec.generate(namespaceText, namespaceRootFolder);
0040
0041 <span class="keyword">for</span> iNamespace = 1:length(parsedNamespaceList)
0042 parsedNamespace = parsedNamespaceList(iNamespace);
0043 spec.saveCache(parsedNamespace, options.savedir);
0044 file.writeNamespace(parsedNamespace.name, options.savedir);
0045 <span class="keyword">end</span>
0046 <span class="keyword">end</span>
0047 rehash()
0048 <span class="keyword">end</span>
0049
0050 <a name="_sub1" href="#_subfunctions" class="code">function mustBeYamlFile(filePath)</a>
0051 arguments
0052 filePath (1,1) string {mustBeFile}
0053 <span class="keyword">end</span>
0054
0055 assert(endsWith(filePath, [&quot;.yaml&quot;, &quot;.yml&quot;], &quot;IgnoreCase&quot;, true), <span class="keyword">...</span>
0056 <span class="string">'NWB:GenerateExtension:MustBeYaml'</span>, <span class="keyword">...</span>
0057 <span class="string">'Expected file to point to a yaml file'</span>, filePath)
0058 <span class="keyword">end</span></pre></div>
<hr><address>Generated on Tue 19-Nov-2024 22:15:51 by <strong><a href="https://github.com/gllmflndn/m2html">m2html</a></strong> &copy; 2003-2022</address>
</body>
</html>
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