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<section id="data-files-for-testing">
<span id="datafilesfortesting"></span><h1>Data Files for Testing<a class="headerlink" href="#data-files-for-testing" title="Link to this heading">#</a></h1>
<section id="summary">
<h2>Summary<a class="headerlink" href="#summary" title="Link to this heading">#</a></h2>
<p>This page gives an overview of how data files are managed within Mantid.</p>
</section>
<section id="motivation">
<h2>Motivation<a class="headerlink" href="#motivation" title="Link to this heading">#</a></h2>
<p>Some unit tests use a small amount of data that is created by the test harness and others load data
from a file. Take the example of <code class="docutils literal notranslate"><span class="pre">ApplyCalibrationTest</span></code>. In its first test, testSimple, it creates
a workspace with 10 detectors using <code class="docutils literal notranslate"><span class="pre">WorkspaceCreationHelper::create2DWorkspaceWithFullInstrument()</span></code>.
In the second test, testComplex, it reads a file <code class="docutils literal notranslate"><span class="pre">unit_testing/MAPS_Definition_Reduced.xml</span></code>, which contains
the definition of a MAPS instrument with the number of detectors reduced much to ensure it is read
quickly but preserving the other properties of this instrument. However, new tests should avoid even
loading of this nature unless there is a strong justification for doing so.</p>
<p><strong>Main issues:</strong></p>
<ul class="simple">
<li><p>Need to store data, mainly for testing, alongside the code</p></li>
<li><p>Some data needs to be versioned</p></li>
<li><p>Merging system tests back with main code requires handling large data
files</p></li>
<li><p>Git is bad at handling binary files</p></li>
</ul>
<p><strong>Implementation</strong></p>
<p>To avoid issues with storing large files in Git version control, Mantid uses CMake’s <a class="reference external" href="https://www.kitware.com/cmake-externaldata-using-large-files-with-distributed-version-control/">ExternalData</a> module.
Since CMake is already used as the build system, this does not introduce any additional Git-related workflow. ExternalData allows test data to be stored on a separate server while keeping only a reference to each file in the Git repository. Developers can add files to the data store, and CMake downloads them automatically when they are required for tests.</p>
</section>
<section id="cmake-s-external-data">
<h2>CMake’s External Data<a class="headerlink" href="#cmake-s-external-data" title="Link to this heading">#</a></h2>
<figure class="align-center" id="id1">
<img alt="Image originated at https://www.kitware.com/source/files/28_86189184.jpg" src="_images/ExternalDataSchematic.png" />
<figcaption>
<p><span class="caption-text">Image originated at <a class="reference external" href="https://www.kitware.com/source/files/28_86189184.jpg">https://www.kitware.com/source/files/28_86189184.jpg</a></span><a class="headerlink" href="#id1" title="Link to this image">#</a></p>
</figcaption>
</figure>
<p><strong>Terminology:</strong></p>
<ul class="simple">
<li><p>Content - the real data</p></li>
<li><p>Content link - text file containing a hash (MD5) of the real content.
The filename is the filename of the real data plus the <code class="docutils literal notranslate"><span class="pre">.md5</span></code>
extension</p></li>
<li><p>Object - a file that stores the real data and whose name is the <code class="docutils literal notranslate"><span class="pre">MD5</span></code>
hash of the content</p></li>
</ul>
<p><strong>Overview:</strong></p>
<ul class="simple">
<li><p>Git does not store any content, it only stores content links</p></li>
<li><p>Content is stored on a remote server that can be accessed via a
<code class="docutils literal notranslate"><span class="pre">http</span></code> link</p></li>
<li><p>Running cmake sets up build rules so that the content is downloaded
when dependent projects are built</p></li>
</ul>
</section>
<section id="local-object-store">
<h2>Local Object Store<a class="headerlink" href="#local-object-store" title="Link to this heading">#</a></h2>
<p>CMake does not download content directly but stores the content in a
<em>Local Object Store</em>, whose location is defined by the
<code class="docutils literal notranslate"><span class="pre">ExternalData_OBJECT_STORES</span></code> CMake variable. This allows it to share
content between build trees, especially useful for continuous
integration servers.</p>
</section>
<section id="binary-root">
<h2>Binary Root<a class="headerlink" href="#binary-root" title="Link to this heading">#</a></h2>
<p>The final step is to create the <em>real</em> filename and symbolic link (copy
on windows) it to the object in the local object store. The location of
the <em>real</em> filenames is controlled by the <code class="docutils literal notranslate"><span class="pre">ExternalData_BINARY_ROOT</span></code>
CMake variable and defaults to <code class="docutils literal notranslate"><span class="pre">build/ExternalData</span></code>.</p>
</section>
<section id="using-existing-data">
<h2>Using Existing Data<a class="headerlink" href="#using-existing-data" title="Link to this heading">#</a></h2>
<p>For unit testing, there are two places where files may be found:</p>
<ul class="simple">
<li><p><a class="reference external" href="https://github.com/mantidproject/mantid/tree/main/Testing/Data">…/Testing/Data/</a>
for <a class="reference internal" href="RunningTheUnitTests.html#runningtheunittests"><span class="std std-ref">unit test</span></a>, <a class="reference internal" href="Standards/DocumentationGuideForDevs.html#documentationguidefordevs"><span class="std std-ref">doc test</span></a>, and <a class="reference internal" href="SystemTests.html#systemtests"><span class="std std-ref">system test</span></a> data</p></li>
<li><p><a class="reference external" href="https://github.com/mantidproject/mantid/tree/main/instrument/unit_testing">…/instrument/unit_testing</a>
for test <a class="reference external" href="https://docs.mantidproject.org/nightly/concepts/InstrumentDefinitionFile.html#instrumentdefinitionfile" title="(in MantidProject v6.16)"><span class="xref std std-ref">IDF</span></a> files</p></li>
</ul>
<p>For system testing, there is one more location developers use to dump reference
data files:</p>
<ul class="simple">
<li><p><cite>…/Testing/SystemTests/tests/framework/reference</cite></p></li>
</ul>
<p>Generally speaking, the testing system will look for the default locations for
corresponding tests:</p>
<ul class="simple">
<li><p><cite>…/Testing/Data/DocTest</cite></p></li>
<li><p><cite>…/Testing/Data/SystemTest</cite></p></li>
<li><p><cite>…/Testing/Data/UnitTest</cite></p></li>
</ul>
<p>However, it is known that some developers like to reuse the same data files for different types of tests.
Therefore, sometimes the DocTest and SystemTest are using data from UnitTest, which means you should fetch
all testing data before trying to run any test locally. Furthermore, this location is mostly considered a
centralized location for all testing data. But some groups prefer to treat this location as storing <strong>input</strong>
testing data only; therefore the testing system will look for the reference folder mentioned above if it cannot
find the reference data here. There are many examples where the same data file has to be duplicated across multiple locations as required by the tests.
Overall, it is important to talk to the senior developers in your team to learn the
preferred location for storing testing data.</p>
</section>
<section id="adding-a-new-file-s">
<span id="datafilesfortesting-addinganewfile"></span><h2>Adding A New File(s)<a class="headerlink" href="#adding-a-new-file-s" title="Link to this heading">#</a></h2>
<p>A helper git command is defined called <code class="docutils literal notranslate"><span class="pre">add-test-data</span></code>. Before first use, the command must be
aliased using the procedure outlined <a class="reference internal" href="#datafilesfortesting-developersetup"><span class="std std-ref">below</span></a>. Once setup,
it would be called like this:</p>
<div class="highlight-sh notranslate"><div class="highlight"><pre><span></span>git<span class="w"> </span>add-test-data<span class="w"> </span>Testing/Data/UnitTest/INST12345.nxs
</pre></div>
</div>
<p>This does the following:</p>
<ul class="simple">
<li><p>Computes the MD5 hash of the data, e.g.
<code class="docutils literal notranslate"><span class="pre">d6948514d78db7fe251efb6cce4a9b83</span></code></p></li>
<li><p>Stores the MD5 hash in a file called
<code class="docutils literal notranslate"><span class="pre">Testing/Data/UnitTest/INST12345.nxs.md5</span></code></p></li>
<li><p>Renames the original data file to its MD5 sum
<code class="docutils literal notranslate"><span class="pre">Testing/Data/UnitTest/d6948514d78db7fe251efb6cce4a9b83</span></code></p></li>
<li><p>Runs <code class="docutils literal notranslate"><span class="pre">git</span> <span class="pre">add</span> <span class="pre">Testing/Data/UnitTest/INST12345.nxs.md5</span></code></p></li>
<li><p>Tells the user to upload the file(s),
<code class="docutils literal notranslate"><span class="pre">d6948514d78db7fe251efb6cce4a9b83</span></code>, to the <a class="reference external" href="https://testdata.mantidproject.org/ftp/external-data/upload">remote store</a></p></li>
</ul>
<p><strong>Notes:</strong></p>
<ul class="simple">
<li><p>For the change to have effect, re-run <code class="docutils literal notranslate"><span class="pre">cmake</span></code> in the build area</p></li>
<li><p>You need to use a shell to add & modify data files under Windows in
this way. Not every shell works as described, though <a class="reference external" href="https://windows.github.com/">Github for
Windows</a> shell would allow you to do
everything described here step by step without deviations.</p></li>
<li><p>Note, that ILL test data should be placed under <code class="docutils literal notranslate"><span class="pre">ILL/${INSTRUMENT}</span></code>
subdirectories (e.g. <code class="docutils literal notranslate"><span class="pre">ILL/IN16B</span></code>), and should not contain any
instrument prefix in the file name.</p></li>
</ul>
</section>
<section id="updating-file-s">
<h2>Updating File(s)<a class="headerlink" href="#updating-file-s" title="Link to this heading">#</a></h2>
<p>The workflow is the same as <a class="reference internal" href="#datafilesfortesting-addinganewfile"><span class="std std-ref">adding new files</span></a> except that
the developer must first put the new version of the file in the right place. For the example above,
it would be <code class="docutils literal notranslate"><span class="pre">Testing/Data/UnitTest/INST12345.nxs</span></code>. Then the new <code class="docutils literal notranslate"><span class="pre">.md5</span></code> file and associated renamed
file will be created. <code class="docutils literal notranslate"><span class="pre">git</span> <span class="pre">diff</span></code> will show that change to the contents of <code class="docutils literal notranslate"><span class="pre">Testing/Data/UnitTest/INST12345.nxs.md5</span></code>
and that there is an untracked file with the md5 sum for a name.</p>
</section>
<section id="developer-setup">
<span id="datafilesfortesting-developersetup"></span><h2>Developer Setup<a class="headerlink" href="#developer-setup" title="Link to this heading">#</a></h2>
<p>To add the <code class="docutils literal notranslate"><span class="pre">add-test-data</span></code> command alias to git run</p>
<div class="highlight-sh notranslate"><div class="highlight"><pre><span></span>git<span class="w"> </span>config<span class="w"> </span>alias.add-test-data<span class="w"> </span><span class="s1">'!bash -c "tools/Development/git/git-add-test-data $*"'</span>
</pre></div>
</div>
<p>in the git bash shell
(<a class="reference external" href="https://github.com/mantidproject/mantid/blob/main/tools/Development/git/git-add-test-data">script source</a>).
The single quotes are important so that bash doesn’t expand the exclamation mark as a variable.</p>
<p>It is advised that CMake is told where to put the “real” data as the
default is <code class="docutils literal notranslate"><span class="pre">$HOME/MantidExternalData</span></code> on Linux/Mac or
<code class="docutils literal notranslate"><span class="pre">C:/MantidExternalData</span></code> on Windows. Over time the store will grow so
it is recommended that it be placed on a disk with a large amount of
space. CMake uses the <code class="docutils literal notranslate"><span class="pre">MANTID_DATA_STORE</span></code> variable to define where the
data is stored.</p>
<p>The data itself can be downloaded from a local mirror as well to decrease build times.
This is controlled by the <code class="docutils literal notranslate"><span class="pre">DATA_STORE_MIRROR</span></code> variable which can be “all” (default), “none”, “ornl”, or “ral”.
The variable will insert additional data mirrors that facilities have created.
If the data is not found in a local mirror, it will be downloaded from the central data repository.</p>
<section id="example-cmake-command">
<h3>Example cmake command:<a class="headerlink" href="#example-cmake-command" title="Link to this heading">#</a></h3>
<p><strong>Linux/Mac:</strong></p>
<div class="highlight-sh notranslate"><div class="highlight"><pre><span></span>mkdir<span class="w"> </span>-p<span class="w"> </span>build
cmake<span class="w"> </span>-DMANTID_DATA_STORE<span class="o">=</span>/home/mgigg/Data/LocalObjectStore<span class="w"> </span>../Code/Mantid
</pre></div>
</div>
<p><strong>Windows:</strong></p>
<div class="highlight-sh notranslate"><div class="highlight"><pre><span></span>mkdir<span class="w"> </span>build
cmake<span class="w"> </span>-DMANTID_DATA_STORE<span class="o">=</span>D:/Data/LocalObjectStore<span class="w"> </span>../Code/Mantid
</pre></div>
</div>
</section>
<section id="setting-with-dropbox">
<h3>Setting With Dropbox:<a class="headerlink" href="#setting-with-dropbox" title="Link to this heading">#</a></h3>
<p>This is for people in the ORNL Dropbox share and has the effect of
reducing external network traffic. There is a <a class="reference external" href="http://gist.github.com/peterfpeterson/638490530e37c3d8dba5">gist</a> for
getting Dropbox running on Linux. Instead of defining the
<code class="docutils literal notranslate"><span class="pre">MANTID_DATA_STORE</span></code> in CMake, it is simplest to create a symbolic
link</p>
<div class="highlight-sh notranslate"><div class="highlight"><pre><span></span>ln<span class="w"> </span>-s<span class="w"> </span>~/Dropbox<span class="se">\ \(</span>ORNL<span class="se">\)</span>/MantidExternalData<span class="w"> </span>~
</pre></div>
</div>
<p>Then everything will happen automatically using CMake’s default behavior.</p>
</section>
<section id="proxy-settings">
<h3>Proxy Settings<a class="headerlink" href="#proxy-settings" title="Link to this heading">#</a></h3>
<p>If you are sitting behind a proxy server, then the shell or Visual Studio
needs to know about the proxy server. You must set the <code class="docutils literal notranslate"><span class="pre">http_proxy</span></code>
environment variable to <code class="docutils literal notranslate"><span class="pre">http://HOSTNAME:PORT</span></code>.</p>
<p>On Windows, go to <code class="docutils literal notranslate"><span class="pre">Control</span> <span class="pre">Panel->System</span></code> and
<code class="docutils literal notranslate"><span class="pre">Security->System->Advanced</span> <span class="pre">System</span> <span class="pre">settings->Environment</span> <span class="pre">Variables</span></code> and
click <code class="docutils literal notranslate"><span class="pre">New...</span></code> to add a variable.</p>
<p>On Linux/Mac you will need to set the variable in the shell profile or
on Linux you can set it system wide in <code class="docutils literal notranslate"><span class="pre">/etc/environment</span></code>.</p>
</section>
<section id="cmake-targets-for-downloading-test-data">
<h3>CMake targets for downloading test data<a class="headerlink" href="#cmake-targets-for-downloading-test-data" title="Link to this heading">#</a></h3>
<p>Currently there are four CMake targets defined at <a class="reference external" href="https://github.com/mantidproject/mantid/blob/main/buildconfig/CMake/SetupDataTargets.cmake">SetupDataTargets.cmake</a> (shown below) that download the test data when built. The corresponding data will appear in the path defined by the <code class="docutils literal notranslate"><span class="pre">ExternalData_BINARY_ROOT</span></code> CMake variable, which defaults to <code class="docutils literal notranslate"><span class="pre">build/ExternalData</span></code>.</p>
<ul class="simple">
<li><p><code class="docutils literal notranslate"><span class="pre">UnitTestData</span></code> - data required for the unit tests</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">DocTestData</span></code> - data required for the documentation tests</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">StandardTestData</span></code> - includes both data required by the unit tests and documentation tests</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">SystemTestData</span></code> - data required for the system tests.</p></li>
</ul>
</section>
<section id="troubleshooting">
<h3>Troubleshooting<a class="headerlink" href="#troubleshooting" title="Link to this heading">#</a></h3>
<blockquote>
<div><p>If you find that your tests cannot find the data they require check the
following gotchas:</p>
<ul class="simple">
<li><p>Check that you have re-run CMake in the build directory</p></li>
<li><p>Check that you have uploaded the original file renamed as a hash to
the Mantid file repository</p></li>
<li><p>Check that you have removed any user defined data search directories
in <code class="docutils literal notranslate"><span class="pre">~/.mantid</span></code></p></li>
<li><p>Check that you have rebuilt the test executable you’re trying to run.</p></li>
<li><p>Check that you have rebuilt the corresponding CMake target for the test you are trying to run.</p></li>
</ul>
</div></blockquote>
</section>
</section>
<section id="alternative-implementations">
<h2>Alternative Implementations<a class="headerlink" href="#alternative-implementations" title="Link to this heading">#</a></h2>
<p>Before selecting CMake’s ExternalData as the solution for handling large files used in testing, the following Git extensions were also considered:</p>
<ul class="simple">
<li><p><a class="reference external" href="https://github.com/jedbrown/git-fat">git-fat</a></p></li>
<li><p><a class="reference external" href="https://git-annex.branchable.com/">git-annex</a></p></li>
</ul>
</section>
</section>
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