Some new code to check xvg files is introduced in the testutils.
For now it only checks the contents as doubles in case they are
lines with a number of columns of numbers. The tolerance for checking
should be specified by the caller. A test case is provided.
TODO
Add checks for legends.
Change-Id: I00e3c2768c520c8bc90cf7195870a23a1ad83b76
#include <string>
+#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/stringutil.h"
+
namespace gmx
{
{
}
+StringInputStream::StringInputStream(const std::string &input)
+ : input_(input), pos_(0)
+{
+}
+
+StringInputStream::StringInputStream(ConstArrayRef<const char *> const &input)
+ : input_(joinStrings(input.begin(), input.end(), "\n")), pos_(0)
+{
+ input_.append("\n");
+}
+
+bool StringInputStream::readLine(std::string *line)
+{
+ if (pos_ == input_.size())
+ {
+ line->clear();
+ return false;
+ }
+ else
+ {
+ size_t newpos = input_.find("\n", pos_);
+ if (newpos == std::string::npos)
+ {
+ newpos = input_.size();
+ }
+ else
+ {
+ // To include the newline as well!
+ newpos += 1;
+ }
+ line->assign(input_.substr(pos_, newpos-pos_));
+ pos_ = newpos;
+ return true;
+ }
+}
+
} // namespace gmx
#include <string>
-#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/textstream.h"
namespace gmx
std::string str_;
};
+template<typename T> class ConstArrayRef;
+
+/*! \libinternal \brief
+ * Helper class to convert static string data to a stream.
+ *
+ * Provides a text input stream that returns lines from a string
+ */
+class StringInputStream : public TextInputStream
+{
+ public:
+ /*! \brief
+ * Constructor that stores input lines in a string.
+ *
+ * The string is internally but no processing is done.
+ *
+ * \param[in] input String to be served by the stream.
+ */
+ explicit StringInputStream(const std::string &input);
+ /*! \brief
+ * Constructor that stores input lines in a string.
+ *
+ * The array of char * is stored as a string separated by newline.
+ *
+ * \param[in] input Array of char * to be served by the stream.
+ */
+ explicit StringInputStream(ConstArrayRef<const char *> const &input);
+
+ // From TextInputStream
+ virtual bool readLine(std::string *line);
+ virtual void close() {};
+ private:
+ std::string input_;
+ size_t pos_;
+};
+
} // namespace gmx
#endif
testfilemanager.cpp
testfileredirector.cpp
testinit.cpp
- testoptions.cpp)
+ testoptions.cpp
+ xvgtest.cpp)
add_library(testutils STATIC ${UNITTEST_TARGET_OPTIONS} ${TESTUTILS_SOURCES})
set(TESTUTILS_LIBS testutils)
#include "gromacs/commandline/cmdlineoptionsmodule.h"
#include "gromacs/commandline/cmdlineprogramcontext.h"
#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/filestream.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/stringutil.h"
#include "gromacs/utility/textreader.h"
#include "testutils/refdata.h"
#include "testutils/testfilemanager.h"
+#include "testutils/xvgtest.h"
namespace gmx
{
OutputFileInfo(const char *option, const std::string &path)
: option(option), path(path)
{
+ xvg = endsWith(path, ".xvg");
}
std::string option;
std::string path;
+ bool xvg;
};
typedef std::vector<OutputFileInfo> OutputFileList;
outfile != impl_->outputFiles_.end();
++outfile)
{
- std::string output = TextReader::readFileToString(outfile->path);
- outputChecker.checkStringBlock(output, outfile->option.c_str());
+ if (outfile->xvg)
+ {
+ TestReferenceChecker testChecker = checker.checkCompound("File",
+ outfile->option.c_str());
+ TextInputFile sis(outfile->path);
+ checkXvgFile(&sis, &testChecker);
+ }
+ else
+ {
+ std::string output = TextReader::readFileToString(outfile->path);
+ outputChecker.checkStringBlock(output, outfile->option.c_str());
+ }
}
}
}
* \p filename is given to TestTemporaryFileManager to make a unique
* filename for the temporary file, but is not otherwise used.
*
- * Currently, this method should not be called for an XVG file, because
- * the comments in the beginning of the file contain timestamps and
- * other variable information, causing the test to fail. Best used
- * only for custom data formats.
*/
void setOutputFile(CommandLine *args, const char *option,
const char *filename);
gmx_add_unit_test(TestUtilsUnitTests testutils-test
interactivetest.cpp
refdata_tests.cpp
- testasserts_tests.cpp)
+ testasserts_tests.cpp
+ xvgtest_tests.cpp)
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2015, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS 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
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Tests utilities for testing xvg files
+ *
+ * \author David van der Spoel <david.vanderspoel@icm.uu.se>
+ * \ingroup module_testutils
+ */
+#include "gmxpre.h"
+
+#include "testutils/xvgtest.h"
+
+#include <vector>
+
+#include <gtest/gtest.h>
+#include <gtest/gtest-spi.h>
+
+#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/stringstream.h"
+
+#include "testutils/refdata.h"
+#include "testutils/testasserts.h"
+
+namespace
+{
+//! Input testing data - an inline xvg file.
+const char * const input[] = {
+ "0 2905.86 -410.199",
+ "0.2 6656.67 -430.437",
+ "0.4 5262.44 -409.399",
+ "0.6 5994.69 -405.763",
+ "0.8 5941.37 -408.337",
+ "1 5869.87 -411.124"
+};
+
+TEST(XvgTests, CreateFile)
+{
+ {
+ // Create new data
+ gmx::test::TestReferenceData data(gmx::test::erefdataUpdateAll);
+ gmx::test::TestReferenceChecker checker(data.rootChecker());
+ // Convert char array to a stream and add it to the checker
+ gmx::StringInputStream sis(input);
+ gmx::test::checkXvgFile(&sis, &checker);
+ }
+ {
+ // Now read it back
+ gmx::test::TestReferenceData data(gmx::test::erefdataCompare);
+ gmx::test::TestReferenceChecker checker(data.rootChecker());
+ // Convert char array to a stream and add it to the checker
+ gmx::StringInputStream sis(input);
+ gmx::test::checkXvgFile(&sis, &checker);
+ }
+}
+
+TEST(XvgTests, CheckMissing)
+{
+ {
+ // Create new data
+ gmx::test::TestReferenceData data(gmx::test::erefdataUpdateAll);
+ gmx::test::TestReferenceChecker checker(data.rootChecker());
+ // Convert char array to a stream and add it to the checker
+ gmx::StringInputStream sis(input);
+ gmx::test::checkXvgFile(&sis, &checker);
+ }
+ {
+ const char * const input[] = {
+ "0 2905.86 -410.199",
+ "0.2 6656.67 -430.437",
+ "0.4 5262.44 -409.399"
+ };
+ // Now check with missing data
+ gmx::test::TestReferenceData data(gmx::test::erefdataCompare);
+ gmx::test::TestReferenceChecker checker(data.rootChecker());
+ gmx::StringInputStream sis(input);
+ EXPECT_NONFATAL_FAILURE(gmx::test::checkXvgFile(&sis, &checker), "absent");
+ }
+}
+
+TEST(XvgTests, CheckExtra)
+{
+ {
+ // Create new data
+ gmx::test::TestReferenceData data(gmx::test::erefdataUpdateAll);
+ gmx::test::TestReferenceChecker checker(data.rootChecker());
+ // Convert char array to a stream and add it to the checker
+ gmx::StringInputStream sis(input);
+ gmx::test::checkXvgFile(&sis, &checker);
+ }
+ {
+ const char * const input[] = {
+ "0 2905.86 -410.199",
+ "0.2 6656.67 -430.437",
+ "0.4 5262.44 -409.399",
+ "0.6 5994.69 -405.763",
+ "0.8 5941.37 -408.337",
+ "1 5869.87 -411.124",
+ "1.2 5889.87 -413.124"
+ };
+ // Now check with missing data
+ gmx::test::TestReferenceData data(gmx::test::erefdataCompare);
+ gmx::test::TestReferenceChecker checker(data.rootChecker());
+ gmx::StringInputStream sis(input);
+ EXPECT_NONFATAL_FAILURE(gmx::test::checkXvgFile(&sis, &checker), "Row6");
+ }
+}
+
+TEST(XvgTests, ReadIncorrect)
+{
+ {
+ // Create new data
+ gmx::test::TestReferenceData data(gmx::test::erefdataUpdateAll);
+ gmx::test::TestReferenceChecker checker(data.rootChecker());
+ // Convert char array to a stream and add it to the checker
+ gmx::StringInputStream sis(input);
+ gmx::test::checkXvgFile(&sis, &checker);
+ }
+ {
+ const char * const input[] = {
+ "0 2905.86 -410.199",
+ "0.2 6656.67 -430.437",
+ "0.4 5262.44 -409.399",
+ "0.6 5994.69 -405.763",
+ "0.8 5941.37 -408.337",
+ "1 5869.87 -421.124"
+ };
+ // Now check with incorrect data
+ gmx::test::TestReferenceData data(gmx::test::erefdataCompare);
+ gmx::test::TestReferenceChecker checker(data.rootChecker());
+ gmx::StringInputStream sis(input);
+ EXPECT_NONFATAL_FAILURE(gmx::test::checkXvgFile(&sis, &checker), "-411");
+ }
+}
+
+} // namespace
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2015, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS 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
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Implements routine to check the content of xvg files.
+ *
+ * \author David van der Spoel <david.vanderspoel@icm.uu.se>
+ * \ingroup module_testutils
+ */
+#include "gmxpre.h"
+
+#include "xvgtest.h"
+
+#include <cerrno>
+#include <cstdlib>
+
+#include <vector>
+
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/textstream.h"
+
+#include "testutils/refdata.h"
+#include "testutils/testasserts.h"
+
+namespace gmx
+{
+
+namespace test
+{
+
+void checkXvgFile(TextInputStream *input,
+ TestReferenceChecker *checker)
+{
+ std::string line;
+ int nrow = 0;
+
+ while (input->readLine(&line))
+ {
+ if (!((line.find("#") != line.npos) ||
+ (line.find("@") != line.npos)))
+ {
+ std::vector<std::string> split = splitString(line);
+ std::vector<real> row;
+
+ for (std::vector<std::string>::iterator si = split.begin();
+ (si < split.end()); ++si)
+ {
+ const char *ptr = si->c_str();
+ char *endptr;
+ errno = 0;
+ double dval = std::strtod(ptr, &endptr);
+ if (errno == ERANGE)
+ {
+ GMX_THROW(InvalidInputError("Invalid value: '" + *si
+ + "'; it causes an overflow/underflow"));
+ }
+ if (*ptr == '\0' || *endptr != '\0')
+ {
+ GMX_THROW(InvalidInputError("Invalid value: '" + *si
+ + "'; expected a number"));
+ }
+ row.push_back(dval);
+ }
+ std::string buf = formatString("Row%d", nrow++);
+ checker->checkSequence(row.begin(), row.end(), buf.c_str());
+ }
+ }
+ std::string buf = formatString("Row%d", nrow++);
+ checker->checkPresent(false, buf.c_str());
+}
+
+} // namespace test
+
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2015, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS 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
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ * \brief
+ * Declares function to add the content of an xvg file to a checker.
+ *
+ * \author David van der Spoel <david.vanderspoel@icm.uu.se>
+ * \inlibraryapi
+ * \ingroup module_testutils
+ */
+#ifndef GMX_TESTUTILS_XVGTESTS_H
+#define GMX_TESTUTILS_XVGTESTS_H
+
+#include <string>
+
+namespace gmx
+{
+
+class TextInputStream;
+
+namespace test
+{
+
+class TestReferenceChecker;
+
+/*! \brief
+ * Adds content of xvg file to TestReferenceChecker object.
+ *
+ * A stream of strings is parsed. The columns
+ * are analyzed with a relative tolerance provided by the input.
+ * Xmgrace formatting is ignored and only multi-column data is
+ * understood.
+ *
+ * \param[in] input Object returning the lines of the file/data
+ * one by one.
+ * \param[in,out] checker The checker object.
+ */
+void checkXvgFile(TextInputStream *input,
+ TestReferenceChecker *checker);
+
+
+} // namespace test
+
+} // namespace gmx
+
+#endif
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff