source: branches/0.13-stable/test/Suite.h @ 3431

#ifndef _theplu_yat_test_suite_
#define _theplu_yat_test_suite_

// $Id: Suite.h 3431 2015-10-26 07:09:34Z peter $

/*
  Copyright (C) 2008 Jari Häkkinen, Peter Johansson
  Copyright (C) 2009, 2010, 2011, 2013, 2014 Peter Johansson

  This file is part of the yat library, http://dev.thep.lu.se/yat

  The yat library 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.

  The yat library 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 yat. If not, see <http://www.gnu.org/licenses/>.
*/

// ensure that config.h always is included first
#ifndef YAT_VERSION
#error header 'config.h' not included
#endif

#include <yat/utility/config_public.h>

#define YAT_TEST_PROLOGUE "\n=== " << __func__ << " ===\n"

// used to tell automake that test should be skipped
#define EXIT_SKIP 77

// SKIP_BAM_TEST is defined if we should skip bam tests
#if !defined (YAT_HAVE_LIBBAM) || !defined (HAVE_SAMTOOLS_EXECUTABLE)
#define SKIP_BAM_TEST
#endif

#include <yat/utility/VectorMutable.h>
#include <yat/classifier/Target.h>

#include <boost/concept_archetype.hpp>
#include <boost/concept_check.hpp>
#include <boost/iterator/iterator_concepts.hpp>

#include <iosfwd>
#include <sstream>
#include <vector>

namespace theplu {
namespace yat {
namespace test {

  /**
     \internal utility class for tests
   */
  class Suite
  {
  public:
    Suite(int argc, char* argv[], bool require_bam=false);

    /**
     */
    ~Suite(void);

    /**
       set ok to 'b && ok' 

       \return b
    */
    bool add(bool b);

    /**
       \return In verbose mode std::cerr, else a ofstream to "/dev/null".
    */
    std::ostream& err(void) const;

    /**
       \return true if \f$ |a-b| <= N * \epsilon * min(|a|,|b|) \f$
       where \f$ \epsilon \f$ is std::numeric_limits<double>().epsilon()
    */
    bool equal(double a, double b, unsigned long int N=1);

    /**
       \return true if |\a a - \a b| <= \a margin 
    */
    bool equal_fix(double a, double b, double margin=0);

    /**
       \return true if \f$ |a-b| <= N * sqrt(\epsilon) * min(|a|,|b|) \f$
       where \f$ \epsilon \f$ is std::numeric_limits<double>().epsilon()
    */
    bool equal_sqrt(double a, double b, unsigned long int N=1);

    /**
       apply equal on ranges [first1, last1) and [first2, ...)
    */
    template<typename Iterator1, typename Iterator2>
    bool equal_range(Iterator1 first1, Iterator1 last1, Iterator2 first2,
                     unsigned int N=1);

    /**
       apply equal_fix on ranges [first1, last1) and [first2, ...)
    */
    template<typename Iterator1, typename Iterator2>
    bool equal_range_fix(Iterator1 first1, Iterator1 last1, Iterator2 first2,
                         double margin);

    /**
      \return true if test is ok
    */
    bool ok(void) const;

    /**
       \return In verbose mode std::cout, else a ofstream to "/dev/null".
    */
    std::ostream& out(void) const;

    /**
       In verbose mode a final message is sent to std::cout.

       If ok() is true: "Test is ok." otherwise
       "Test failed."

       \return 0 if ok.
     */
    int return_value(void) const;

    template<typename TrivialIterator>
    void test_trivial_iterator(const TrivialIterator&);

    template<typename InputIterator>
    void test_input_iterator(InputIterator&);

    template<typename OutputIterator>
    void test_output_iterator(OutputIterator&);

    template<typename ForwardIterator>
    void test_forward_iterator(ForwardIterator);

    template<typename BidirectionalIterator>
    void test_bidirectional_iterator(BidirectionalIterator);

    template<typename RandomAccessIterator>
    void test_random_access_iterator(RandomAccessIterator);

    template<typename Container2D>
    void test_concept_container2d(const Container2D&);

    template<typename MutableContainer2D>
    void test_concept_mutable_container2d(MutableContainer2D&);

    /**
       Function writes to a stream using operator<<, creates a new
       object using stream constructor, and the new object is written
       to another stream, and function check if the two outputs are
       equal.
    */
    template<class T>
    bool test_stream(const T&) const;

    /**
       This function is similar to add(bool) and could be used to
       detect/count known issues. When the issue is fixed, one can
       replace the call to xadd(bool) with a call to add(bool).

       If \a b is false a counter is incremented, which is used to in
       return_value() to generate some printout on how many known
       issues were detected.

       If \a b is true, ok_ is set to false, becasue the known issue
       is no longer an issue and one should replace the call with a
       call to add(bool).
     */
    bool xadd(bool b);

  private:
    unsigned int known_issues_;
    bool ok_;
  };

  /**
     \return absolute path to test src dir
  */
  std::string abs_srcdir(void);

  /**
     \return absolute path to file
     \param local_path path relative to srcdir
   */
  std::string filename(const std::string& local_path);

  /*
    class to test (at compile time) that a function (or class) works
    with a Container2D. Do not run any test using this class because
    the class is not really functional at run time.

    \see boost/concept_archetype.hpp
   */
  template<typename T>
  class container2d_archetype
  {
  public:
    typedef T value_type;
    typedef const T& const_reference;
    typedef const T* const_iterator;
    typedef const_iterator const_column_iterator;
    typedef const_iterator const_row_iterator;
    const_iterator begin(void) const { return &element_; }
    const_column_iterator begin_column(size_t) const { return &element_; }
    const_iterator begin_row(size_t) const { return &element_; }
    const_iterator end(void) const { return NULL; }
    const_column_iterator end_column(size_t) const { return NULL; }
    const_iterator end_row(size_t) const { return NULL; }
    size_t columns(void) const { return 0; }
    size_t rows(void) const { return 0; }
    const_reference operator()(size_t row, size_t column) const
    { return element_; }

  protected:
    T element_;
  };

  /*
    class to test (at compile time) that a function (or class) works
    with a MutableContainer2D. Do not run any test using this class because
    the class is not really functional at run time.

    \see boost/concept_archetype.hpp
   */
  template<typename T>
  class mutable_container2d_archetype : public container2d_archetype<T>
  {
  public:
    typedef T& reference;
    typedef T* iterator;
    typedef iterator column_iterator;
    typedef iterator row_iterator;
    iterator begin(void) { return &this->element_; }
    column_iterator begin_column(size_t) { return &this->element_; }
    iterator begin_row(size_t) { return &this->element_; }
    iterator end(void) { return NULL; }
    column_iterator end_column(size_t) { return NULL; }
    iterator end_row(size_t) { return NULL; }
    reference operator()(size_t row, size_t column)
    { return this->element_; }
  };

  /*
    class to test (at compile time) that a function (or class) works
    with a Distance. Do not run any test using this class because
    the class is not really functional at run time.

    \see boost/concept_archetype.hpp
   */
  class distance_archetype
  {
  public:
    /// class must be constructible somehow, but we don't wanna assume
    /// void constructor or any other common constructor so we use the
    /// signature to allow construction without assuming too much.
    distance_archetype(const boost::detail::dummy_constructor&) {};
    distance_archetype(const distance_archetype&) {};
    template<typename T1, typename T2>
    double operator()(T1 first1, T1 last1, T2 first2) const { return 0.0; }
  private:
    distance_archetype(void);
    distance_archetype& operator=(const distance_archetype&);
  };

  /*
    class to test (at compile time) that a function (or class) works
    with a NeighborWeighting. Do not run any test using this class because
    the class is not really functional at run time.

    \see boost/concept_archetype.hpp
   */
  class neighbor_weighting_archetype
  {
  public:
    neighbor_weighting_archetype(void) {}
    void operator()(const utility::VectorBase& distance,
                    const std::vector<size_t>& k_sorted,
                    const classifier::Target& target,
                    utility::VectorMutable& prediction) const {}
    neighbor_weighting_archetype& operator=(const neighbor_weighting_archetype&)
    { return *this; }
  private:
    neighbor_weighting_archetype(const neighbor_weighting_archetype&) {};
  };

  template<typename Iterator>
  void test_readable_iterator(Iterator iterator)
  {
    BOOST_CONCEPT_ASSERT((boost_concepts::ReadableIterator<Iterator>));
  }

  template<typename Iterator>
  void test_writable_iterator(Iterator iterator)
  {}

  template<typename Iterator>
  void test_swappable_iterator(Iterator iterator)
  {
    BOOST_CONCEPT_ASSERT((boost_concepts::SwappableIterator<Iterator>));
  }

  template<typename Iterator>
  void test_lvalue_iterator(Iterator iterator)
  {
    BOOST_CONCEPT_ASSERT((boost_concepts::LvalueIterator<Iterator>));
  }

  template<typename Iterator>
  void test_incrementable_iterator(Iterator iterator)
  {
    BOOST_CONCEPT_ASSERT((boost_concepts::IncrementableIterator<Iterator>));
  }

  template<typename Iterator>
  void test_single_pass_iterator(Iterator iterator)
  {
    BOOST_CONCEPT_ASSERT((boost_concepts::SinglePassIterator<Iterator>));
  }


  template<typename Iterator>
  void test_forward_traversal_iterator(Iterator iterator)
  {
    BOOST_CONCEPT_ASSERT((boost_concepts::ForwardTraversal<Iterator>));
  }


  template<typename Iterator>
  void test_bidirectional_traversal_iterator(Iterator iterator)
  {
    BOOST_CONCEPT_ASSERT((boost_concepts::BidirectionalTraversal<Iterator>));
  }


  template<typename Iterator>
  void test_random_access_traversal_iterator(Iterator iterator)
  {
    BOOST_CONCEPT_ASSERT((boost_concepts::RandomAccessTraversal<Iterator>));
  }

  // template implementations

  template<typename Iterator1, typename Iterator2>
  bool Suite::equal_range(Iterator1 first1, Iterator1 last1, Iterator2 first2,
                          unsigned int N)
  {
    while (first1!=last1){
      if (!this->equal(*first1, *first2, N) )  {
        return false;
      }
      ++first1;
      ++first2;
    }
    return true;
  }


  template<typename Iterator1, typename Iterator2>
  bool Suite::equal_range_fix(Iterator1 first1, Iterator1 last1, 
                              Iterator2 first2, double margin)
  {
    while (first1!=last1){
      if (!this->equal_fix(*first1, *first2, margin) )   {
        return false;
      }
      ++first1;
      ++first2;
    }
    return true;
  }


  // return true if we can write to a write-protected file
  bool run_as_root(void);

  // function that can be used to avoid warning: '-Wunused-but-set-variable'
  template<typename T>
  void avoid_compiler_warning(T) {}

  template<class T>
  bool Suite::test_stream(const T& t) const
  {
    this->err() << "Checking that output stream is valid as an input stream\n";
    std::stringstream ss;
    this->err() << "writing to output\n";
    ss << t;
    this->err() << "creating a new object from output\n";
    T t2(ss);
    std::stringstream ss2;
    this->err() << "writing to output\n";
    ss2 << t2;
    bool ok = ss2.str()==ss.str();
    if (!ok) {
      this->err() << "ERROR: first object gave following output:\n"
                  << ss.str() << "\n"
                  << "ERROR: and second object gave following output:\n"
                  << ss2.str() << "\n";
    }
    return ok;
  }

  template<typename TrivialIterator>
  void Suite::test_trivial_iterator(const TrivialIterator& iter)
  {
    err() << "  testing Trivial features" << std::endl;
    typename std::iterator_traits<TrivialIterator>::value_type tmp = *iter;
    add(tmp==*iter);
    TrivialIterator default_constructed;
    avoid_compiler_warning(default_constructed);
  }

  template<typename InputIterator>
  void Suite::test_input_iterator(InputIterator& iter)
  {
    BOOST_CONCEPT_ASSERT((boost::InputIterator<InputIterator>));
    test_trivial_iterator(iter);
    err() << "  testing Input features" << std::endl;
    // just to check compilation
    if (false) {
      ++iter;
      iter++;
    }
  }

  template<typename OutputIterator>
  void Suite::test_output_iterator(OutputIterator& iter)
  {
    err() << "  testing Output features" << std::endl;
    // OutputIterator should be default constructible and assignable
    OutputIterator oi;
    oi = iter;
    ++oi;
  }

  template<typename ForwardIterator>
  void Suite::test_forward_iterator(ForwardIterator iter)
  {
    BOOST_CONCEPT_ASSERT((boost::ForwardIterator<ForwardIterator>));
    test_output_iterator(iter);
    test_input_iterator(iter);
    err() << "  testing Forward features" << std::endl;

    typename std::iterator_traits<ForwardIterator>::value_type tmp = *iter;
    // testing multiple traversing is possible and does not change the data
    ForwardIterator iter1 = iter;
    ++iter1;
    add(iter!=iter1);
    ForwardIterator iter2 = iter;
    ++iter2;
    add(tmp==*iter);
  }

  template<typename BidirectionalIterator>
  void Suite::test_bidirectional_iterator(BidirectionalIterator iter)
  {
    BOOST_CONCEPT_ASSERT((boost::BidirectionalIterator<BidirectionalIterator>));
    test_forward_iterator(iter);
    bool ok_cached = ok();
    err() << "  testing Bidirectional features" << std::endl;
    const BidirectionalIterator i = iter;
    BidirectionalIterator tmp = iter++;
    if (!add(tmp==i)) {
      err() << "iter++ does not return iter\n";
    }
    if (!add(++tmp==iter)) {
      err() << "++iter failed\n";
    }
    if (!add(--tmp==i)) {
      err() << "--iter failed\n";
    }
    tmp = iter--;
    if (!add(--tmp==iter))
      err() << "iter-- failed" << std::endl;
    if (ok_cached && !ok())
      err() << "failed" << std::endl;
  }

  template<typename RandomAccessIterator>
  void Suite::test_random_access_iterator(RandomAccessIterator iter)
  {
    BOOST_CONCEPT_ASSERT((boost::RandomAccessIterator<RandomAccessIterator>));
    test_bidirectional_iterator(iter);
    err() << "  testing RandomAccess features" << std::endl;
    bool ok_cached = ok();
    RandomAccessIterator iter2 = iter;
    iter2 += 1;
    iter2 -= 1;
    RandomAccessIterator& iter3 = (iter2 += 1);
    RandomAccessIterator& iter4 = (iter3 -= 1);
    if (!add(iter2 == iter4))
      err() << "operator-(int) failed" << std::endl;
    add(++iter2 == iter3);

    RandomAccessIterator iter5 = iter + 0;
    RandomAccessIterator iter6 = 0 + iter;
    add(iter6 == iter5);

    RandomAccessIterator iter7 = iter - 0;
    add(iter7 == iter);
    add(iter7 - iter == 0);
    add(! (iter7<iter));

    typename RandomAccessIterator::value_type tmp = iter[0];
    typename RandomAccessIterator::value_type tmp2 = *iter;
    tmp = tmp; // avoid compiler warning
    if (!add(tmp == tmp2))
      err() << "operator[] failed" << std::endl;
    if (!add(iter[0] == *iter))
      err() << "operator[] failed" << std::endl;
    if (ok_cached && !ok())
      err() << "failed" << std::endl;
  }

  template<typename Container2D>
  void Suite::test_concept_container2d(const Container2D& c)
  {
    typedef typename Container2D::value_type value_type;
    typedef typename Container2D::const_reference const_reference;
    typedef typename Container2D::const_iterator const_iterator;
    typedef typename Container2D::const_column_iterator const_column_iterator;
    typedef typename Container2D::const_row_iterator const_row_iterator;
    const_iterator ci = c.begin();
    const_column_iterator cci = c.begin_column(0);
    const_row_iterator cri = c.begin_row(0);
    ci = c.end();
    cci = c.end_column(0);
    cri = c.end_row(0);
    size_t cols = c.columns();
    size_t rows = c.rows();
    // just to avoid compiler warning
    avoid_compiler_warning(cols);
    avoid_compiler_warning(rows);
    const_reference x = c(0,0);
    value_type y;
    y = x;
    avoid_compiler_warning(y);
  }

  template<typename MutableContainer2D>
  void Suite::test_concept_mutable_container2d(MutableContainer2D& mc)
  {
    test_concept_container2d(mc);
    typedef typename MutableContainer2D::reference reference;
    typedef typename MutableContainer2D::iterator iterator;
    typedef typename MutableContainer2D::column_iterator column_iterator;
    typedef typename MutableContainer2D::row_iterator row_iterator;
    iterator i = mc.begin();
    column_iterator ci = mc.begin_column(0);
    row_iterator ri = mc.begin_row(0);
    *i = *ci;
    *ci = *i;
    *ri = *i;
    i = mc.end();
    ci = mc.end_column(0);
    ri = mc.end_row(0);
    reference x = mc(0,0);
    x = *mc.begin();
  }

}}}

#endif