new schema.jar now works with default generateCore and generateExtens…

…ion. file export is now possible.

+spec/getNamespaceInfo.m

@@ -0,0 +1,38 @@
+%returns sources given namespace java object
+function s = getNamespaceInfo(namespaceMap)
+errid = 'MATNWB:INVALIDFILE';
+errmsg = 'Could not read namespace file.  Invalid format.';
+
+assert(namespaceMap.containsKey('namespaces'), errid, errmsg);
+namespaceIter = namespaceMap.get('namespaces').iterator();
+
+%spawn empty struct.  Produce struct array of all defined namespaces
+s = struct('filenames', {}, 'name', {}, 'dependencies', {}, 'version', {});
+sidx = 1;
+while namespaceIter.hasNext()
+    namespace = namespaceIter.next();
+    assert(namespace.containsKey('name')...
+        && namespace.containsKey('schema')...
+        && namespace.containsKey('version'),...
+        errid, errmsg);
+    name = namespace.get('name');
+    version = namespace.get('version');
+    filenames = {};
+    dependencies = {};
+    schemaIter = namespace.get('schema').iterator();
+    while schemaIter.hasNext()
+        schemaFile = schemaIter.next();
+        if schemaFile.containsKey('source')
+            filenames{end+1} = schemaFile.get('source');
+        elseif schemaFile.containsKey('namespace')
+            dependencies{end+1} = schemafile.get('namespace');
+        else
+            error(errid, errmsg);
+        end
+    end
+    s(sidx) = struct('name', name,...
+        'filenames', {filenames},...
+        'dependencies', {dependencies},...
+        'version', version);
+end
+end

+spec/getSourceInfo.m

@@ -0,0 +1,17 @@
+function processed = getSourceInfo(classmap)
+%given containers.Map of (file/module)->(string) returns (file/module)->HashMap
+% representing the schema file.
+processed = containers.Map;
+schema = Schema();
+classkeys = keys(classmap);
+
+for i=1:length(classkeys)
+    ck = classkeys{i};
+    cval = classmap(ck);
+    try
+        processed(ck) = schema.read(cval);
+    catch ME
+        error('MATNWB:INVALIDFILE',...
+            'Data for namespace source `%s` is invalid', ck);
+    end
+end

generateExtension.m

@@ -14,7 +14,7 @@ function generateExtension(source)
 %   
 %   Example:
 %      generateCore('schema\core\nwb.namespace.yaml');
-%      generateExtension('schema\core\myextension.namespace.yaml')
+%      generateExtension('schema\myext\myextension.namespace.yaml')
 % 
 %   See also GENERATECORE
 validateattributes(source, {'char', 'string'}, {'scalartext'});
@@ -25,10 +25,28 @@ function generateExtension(source)
 if ~any(strcmp(javaclasspath(), javapath))
     javaaddpath(javapath);
 end
+schema = Schema();
 [localpath, ~, ~] = fileparts(source);
-[filenames, nm, dep] = yaml.getNamespaceInfo(source);
-schema = yaml.getSourceInfo(localpath, filenames{:});
-extSchema = struct('name', nm, 'schema', schema, 'dependencies', {dep});
+assert(2 == exist(source, 'file'),...
+    'MATNWB:FILE', 'Path to file `%s` could not be found.', source);
+fid = fopen(source);
+namespace_map = schema.read(fread(fid, '*char') .');
+fclose(fid);
+namespace = spec.getNamespaceInfo(namespace_map);
+
+schema_map = containers.Map;
+for i=1:length(namespace.filenames)
+    filename = namespace.filenames{i};
+    fid = fopen(fullfile(localpath, filename));
+    schema_map(filename) = fread(fid, '*char') .';
+    fclose(fid);
+end
+schema = spec.getSourceInfo(schema_map);
+
+extSchema = struct('name', namespace.name,...
+    'schema', schema,...
+    'dependencies', {namespace.dependencies},...
+    'version', namespace.version);
 namespacePath = fullfile(nwbloc, 'namespaces');
 if 7 ~= exist(namespacePath, 'dir')
     mkdir(namespacePath);

nwbExport.m

@@ -3,14 +3,15 @@ function nwbExport(nwb, filename)
 %  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.
+%    % 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
+%    % Create some fake fata and write
 %    nwb = nwbfile;
-%    nwb.epochs = types.core.Epochs;
-%    nwb.epochs.stim = types.Epoch;
-%    nwbExport(nwb, 'epoch.nwb');
+%    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'});