Test validation of module names

mdbenchmark/tests/test_generate.py

@@ -26,7 +26,7 @@
 
 
 @pytest.mark.parametrize('tpr_file', ('protein.tpr', 'protein'))
-def test_generate(cli_runner, tmpdir, tpr_file):
+def test_generate(cli_runner, monkeypatch, tmpdir, tpr_file):
     """Run an integration test on the generate function.
 
     Make sure that we accept both `protein` and `protein.tpr` as input files.
@@ -39,6 +39,28 @@ def test_generate(cli_runner, tmpdir, tpr_file):
                  'Creating a total of 4 benchmarks, with a run time of 15' \
                  ' minutes each.\nFinished generating all benchmarks.\nYou can' \
                  ' now submit the jobs with mdbenchmark submit.\n'
+
+        # Test that we get a warning, if no module name validation is performed.
+        result = cli_runner.invoke(cli.cli, [
+            'generate', '--module=gromacs/2016', '--host=draco',
+            '--max-nodes=4', '--gpu', '--name={}'.format(tpr_file)
+        ])
+        assert result.exit_code == 0
+        assert result.output == 'WARNING Not performing module name validation.\n' + output
+
+        # monkeypatch the output of the available modules
+        monkeypatch.setattr('mdbenchmark.generate.get_available_modules',
+                            lambda: {'gromacs': ['2016']})
+
+        # Test that we can skip module name validation, even if it actually works.
+        result = cli_runner.invoke(cli.cli, [
+            'generate', '--module=gromacs/2016', '--host=draco',
+            '--max-nodes=4', '--gpu', '--name={}'.format(tpr_file),
+            '--skip-validation'
+        ])
+        assert result.exit_code == 0
+        assert result.output == 'WARNING Not performing module name validation.\n' + output
+
         result = cli_runner.invoke(cli.cli, [
             'generate', '--module=gromacs/2016', '--host=draco',
             '--max-nodes=4', '--gpu', '--name={}'.format(tpr_file)
@@ -73,9 +95,13 @@ def test_generate(cli_runner, tmpdir, tpr_file):
                 'draco_gromacs/2016_gpu/{}/bench.job'.format(i))
 
 
-def test_generate_console_messages(cli_runner, tmpdir):
+def test_generate_console_messages(cli_runner, monkeypatch, tmpdir):
     """Test that the CLI for generate prints all error messages as expected."""
     with tmpdir.as_cwd():
+        # monkeypatch the output of the available modules
+        monkeypatch.setattr('mdbenchmark.generate.get_available_modules',
+                            lambda: {'gromacs': ['2016']})
+
         # Test that we get an error when not supplying a file name
         result = cli_runner.invoke(
             cli.cli, ['generate', '--module=gromacs/2016', '--host=draco'])
@@ -125,12 +151,16 @@ def test_generate_console_messages(cli_runner, tmpdir):
         assert result.output == output
 
 
-def test_generate_namd_experimental_warning(cli_runner, tmpdir):
+def test_generate_namd_experimental_warning(cli_runner, monkeypatch, tmpdir):
     """Test that we print the NAMD experimental warning."""
     with tmpdir.as_cwd():
         for f in ['md.namd', 'md.psf', 'md.pdb']:
             open(f, 'a').close()
 
+        # monkeypatch the output of the available modules
+        monkeypatch.setattr('mdbenchmark.generate.get_available_modules',
+                            lambda: {'namd': ['123']})
+
         result = cli_runner.invoke(cli.cli, [
             'generate', '--module=namd/123', '--host=draco', '--name=md'
         ])

mdbenchmark/tests/test_validate.py

@@ -0,0 +1,103 @@
+# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
+# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
+#
+# MDBenchmark
+# Copyright (c) 2017 Max Linke & Michael Gecht and contributors
+# (see the file AUTHORS for the full list of names)
+#
+# MDBenchmark is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# MDBenchmark is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with MDBenchmark.  If not, see <http://www.gnu.org/licenses/>.
+import os
+
+import click
+import pytest
+
+from mdbenchmark import validate
+from mdbenchmark.ext.click_test import cli_runner
+
+DIR_STRUCTURE = {
+    'applications': {
+        'gromacs': ['2016.4', '5.1.4-plumed2.3', '2018.1', '.12345-version'],
+        'namd': ['123', '456'],
+        'amber': ['13', '14', '15']
+    },
+    'visualization': {
+        'vmd': ['1.9.3', '1.9.4']
+    }
+}
+
+# @pytest.fixture
+# def dir_structure(request):
+#     class File(object):
+#         def __enter__(self, path, structure):
+#             self.path = path
+
+#             for k, v in dir_structure.items():
+#                 for k2, v2 in v.items():
+#                     os.makedirs(os.path.join(k, k2))
+#                     for v3 in v2:
+#                         open(os.path.join(k, k2, v3), 'a').close()
+
+#         def __exit__(self):
+#             os.remove(self.path)
+
+#     obj = File()
+#     request.addfinalizer(obj.__exit__)
+#     return obj
+
+
+def test_validation(monkeypatch, tmpdir, cli_runner):
+    """Test that we retrieve the correct module versions from a given path and can
+       validate module names and versions.
+    """
+
+    @click.group()
+    def test_cli():
+        pass
+
+    @test_cli.command()
+    def test():
+        validate.validate_module_name('wrong-format')
+
+    with tmpdir.as_cwd():
+        for k, v in DIR_STRUCTURE.items():
+            for k2, v2 in v.items():
+                os.makedirs(os.path.join(k, k2))
+                for v3 in v2:
+                    open(os.path.join(k, k2, v3), 'a').close()
+
+        # Make sure we return None when we cannot find the environment variable
+        assert validate.get_available_modules() == None
+        # Test the same thing for the `validate_module_name` function
+        assert validate.validate_module_name('gromacs/123') == None
+
+        # Prepare path variable that we are going to monkeypatch for
+        # `validate.get_available_modules`
+        dirs = ':'.join(
+            [os.path.join(os.getcwd(), x) for x in os.listdir(os.getcwd())])
+        monkeypatch.setenv('MODULEPATH', dirs)
+        modules = validate.get_available_modules()
+
+        # Assert that the correct modules and their versions are returned.
+        assert set(modules['gromacs']) == set(
+            ['2016.4', '5.1.4-plumed2.3', '2018.1'])
+        assert set(modules['namd']) == set(['123', '456'])
+
+        # Make sure we return a boolean if the module is available or not.
+        assert not validate.validate_module_name('gromacs/123')
+        assert validate.validate_module_name('gromacs/2018.1')
+
+        output = 'ERROR We were not able to determine the module name.\n'
+        result = cli_runner.invoke(test_cli, ['test'])
+        assert result.exit_code == 1
+        assert result.output == output