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fix(session): load and save data variables with function-based adapters #150

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21 changes: 6 additions & 15 deletions code/+nansen/+config/+varmodel/VariableModel.m
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Original file line number Diff line number Diff line change
Expand Up @@ -162,8 +162,6 @@ function updateDefaultValues(obj)
dlModel = nansen.DataLocationModel();
end

fileAdapterList = nansen.dataio.listFileAdapters();

for i = 1:numel(obj.Data)
if isempty( obj.Data(i).FileAdapter ) || strcmp(obj.Data(i).FileAdapter, str)
obj.Data(i).FileAdapter = 'Default';
Expand All @@ -179,15 +177,7 @@ function updateDefaultValues(obj)
if ~isfield(obj.Data, 'DataType') % Infer from file adapter
[obj.Data(:).DataType] = deal('');
for i = 1:numel(obj.Data)
if ~strcmp(obj.Data(i).FileAdapter, 'Default')
isMatch = strcmp({fileAdapterList.FileAdapterName}, obj.Data(i).FileAdapter);
if any(isMatch)
fileAdapterFcn = str2func(fileAdapterList(isMatch).FunctionName);
obj.Data(i).DataType = fileAdapterFcn().DataType;
else
% pass
end
end
obj.Data(i) = obj.updateVariableDataType(obj.Data(i));
end
else
% Normalize existing DataType to char. Todo: support string
Expand Down Expand Up @@ -659,15 +649,16 @@ function disableNotifications(obj)

methods (Static) % Todo: Should be moved to a data variable class
function variableItem = updateVariableDataType(variableItem)
% The list holds the data type of every file adapter, also of a
% function-based one, which is not a class that can be created
fileAdapterList = nansen.dataio.listFileAdapters();
if ~strcmp(variableItem.FileAdapter, 'Default')
isMatch = strcmp({fileAdapterList.FileAdapterName}, variableItem.FileAdapter);
if any(isMatch)
fileAdapterFcn = str2func(fileAdapterList(isMatch).FunctionName);

variableItem.DataType = fileAdapterFcn().DataType;
variableItem.DataType = char(fileAdapterList(find(isMatch, 1)).DataType);
else
% pass
% An adapter that is not in the current project keeps
% the data type the item has
end
end
end
Expand Down
8 changes: 6 additions & 2 deletions code/+nansen/+dataio/DynamicFileAdapter.m
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Expand Up @@ -47,11 +47,15 @@
end

methods (Access = protected)
function data = readData(obj)
function data = readData(obj, varargin)
% Session.loadData passes the variable name and name-value
% options to load; the read function takes the file only
data = obj.ReadFunction(obj.Filename);
end

function writeData(obj, data)
function writeData(obj, data, varargin)
% Session.saveData passes the variable name; the write
% function takes the file and the data only
if ~isempty(obj.WriteFunction)
obj.WriteFunction(obj.Filename, data)
else
Expand Down
12 changes: 11 additions & 1 deletion code/+nansen/+metadata/+type/Session.m
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Expand Up @@ -717,7 +717,17 @@ function updateSessionFolder(obj, dataLocationName, folderPath) %#ok<INUSD>
error('NANSEN:Session:MultipleFileAdapters', 'This is a bug. Please report')
end

fileAdapterFcn = str2func(fileAdapterList(isMatch).FunctionName);
fileAdapterInfo = fileAdapterList(isMatch);
if isfield(fileAdapterInfo, 'IsDynamic') && isequal(fileAdapterInfo.IsDynamic, true)
% A function-based file adapter is a folder with a
% fileadapter.json and read and write functions, not a
% class, and DynamicFileAdapter wraps it, as nansen.load does
functionName = fileAdapterInfo.FunctionName;
fileAdapterFcn = @(filePath, varargin) ...
nansen.dataio.DynamicFileAdapter(functionName, filePath);
else
fileAdapterFcn = str2func(fileAdapterInfo.FunctionName);
end
end

function viewDataVariable(obj, varName)
Expand Down
65 changes: 65 additions & 0 deletions tests/+nansen/+unittest/+session/FunctionBasedFileAdapterTest.m
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Original file line number Diff line number Diff line change
@@ -0,0 +1,65 @@
classdef FunctionBasedFileAdapterTest < matlab.unittest.TestCase
%FunctionBasedFileAdapterTest - Data variables whose file adapter is function-based
%
% A function-based file adapter is a folder with a fileadapter.json and
% read and write functions, such as MatFile of the core module. The mock
% project gets the variable Values, with the adapter MatFile, and a .mat
% file for it in the first session folder.
%
% Run tests:
% runtests('nansen.unittest.session.FunctionBasedFileAdapterTest')

properties
Project
Session
end

methods (TestClassSetup)
function setupProject(testCase)
testCase.applyFixture(nansen.fixture.ProjectFixture)
testCase.Project = nansen.getCurrentProject();

% The new item copies the fields of the mock project's item,
% which has fields that a default item lacks
variableModel = testCase.Project.VariableModel;
item = variableModel.Data(1);
item.VariableName = 'Values';
item.Uuid = nansen.util.getuuid();
item.FilePathPattern = '';
item.FileNameExpression = 'values';
item.FileType = '.mat';
item.FileAdapter = 'MatFile';
item.DataType = '';
variableModel.insertItem(item);
variableModel.save()

testCase.Session = testCase.Project.getSessionObjects( ...
testCase.Project.MetaTableCatalog.getMasterMetaTable('session').entries.sessionID{1});
Values = magic(3);
save(fullfile(testCase.Session.getSessionFolder('MockData'), 'values.mat'), 'Values')
end
end

methods (Test)
function testInsertedVariableGetsDataTypeOfAdapter(testCase)
item = testCase.Project.VariableModel.getItem('Values');

testCase.verifyEqual(item.DataType, 'struct')
end

function testLoadDataReadsWithFunctionBasedAdapter(testCase)
data = testCase.Session.loadData('Values');

testCase.verifyEqual(data.Values, magic(3))
end

function testSaveDataWritesWithFunctionBasedAdapter(testCase)
testCase.addTeardown(@() testCase.Session.saveData('Values', struct('Values', magic(3))))

testCase.Session.saveData('Values', struct('Values', magic(4)))

data = testCase.Session.loadData('Values');
testCase.verifyEqual(data.Values, magic(4))
end
end
end
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