cvtest.cpp

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//
// $Id: cvtest.cpp 4129 2012-11-20 00:05:37Z chambm $
//
//
// Original author: Darren Kessner <darren@proteowizard.org>
//
// Copyright 2007 Spielberg Family Center for Applied Proteomics
//   Cedars-Sinai Medical Center, Los Angeles, California  90048
//
// Licensed under the Apache License, Version 2.0 (the "License"); 
// you may not use this file except in compliance with the License. 
// You may obtain a copy of the License at 
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software 
// distributed under the License is distributed on an "AS IS" BASIS, 
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 
// See the License for the specific language governing permissions and 
// limitations under the License.
//


#include "pwiz/utility/misc/unit.hpp"
#include "cv.hpp"
#include "pwiz/utility/misc/Std.hpp"
#include "boost/thread/thread.hpp"
#include "boost/thread/barrier.hpp"
#include <cstring>


using namespace pwiz::cv;
using namespace pwiz::util;


ostream* os_ = 0;


void test()
{
    if (os_)
    {
        *os_ << "name: " << cvTermInfo(MS_sample_number).name << endl
             << "def: " << cvTermInfo(MS_sample_number).def << "\n\n";

        *os_ << "name: " << cvTermInfo(MS_polarity).name << endl
             << "def: " << cvTermInfo(MS_polarity).def << endl; 
    }

    // some simple tests
    unit_assert(cvTermInfo(MS_sample_number).name == "sample number");
    unit_assert(cvTermInfo(MS_contact_email).name == "contact email");
    unit_assert(cvTermInfo(MS_contact_email).def == "Email address of the contact person or organization.");

    unit_assert(cvTermInfo(MS_zlib_compression).parentsIsA.size() == 1 &&
                cvTermInfo(MS_zlib_compression).parentsIsA[0] == MS_binary_data_compression_type);

    unit_assert(cvTermInfo(MS_instrument_model).parentsPartOf.size() == 1 &&
                cvTermInfo(MS_instrument_model).parentsPartOf[0] == MS_instrument);

    unit_assert(cvTermInfo(MS_None_____OBSOLETE).isObsolete);
}


void testIsA()
{
    unit_assert(cvIsA(UO_dalton, UO_mass_unit));
    unit_assert(cvIsA(UO_mass_unit, UO_unit));
    unit_assert(cvIsA(UO_dalton, UO_unit));
    unit_assert(!cvIsA(UO_dalton, UO_energy_unit));
    unit_assert(cvIsA(MS_m_z, MS_m_z));
    unit_assert(cvIsA(MS_FT_ICR, MS_mass_analyzer_type));
    unit_assert(cvIsA(MS_ion_trap, MS_mass_analyzer_type));
    unit_assert(cvIsA(MS_linear_ion_trap, MS_mass_analyzer_type));
    unit_assert(cvIsA(MS_linear_ion_trap, MS_ion_trap));
    unit_assert(cvIsA(MS_radial_ejection_linear_ion_trap, MS_mass_analyzer_type));
    unit_assert(cvIsA(MS_radial_ejection_linear_ion_trap, MS_ion_trap));
    unit_assert(cvIsA(MS_radial_ejection_linear_ion_trap, MS_linear_ion_trap));
}


void testOtherRelations()
{
    const CVTermInfo& info = cvTermInfo(MS_accuracy);
    unit_assert(info.otherRelations.size() == 2);
    unit_assert(info.otherRelations.begin()->first == "has_units");
    unit_assert(info.otherRelations.begin()->second == MS_m_z);
    unit_assert(info.otherRelations.rbegin()->first == "has_units");
    unit_assert(info.otherRelations.rbegin()->second == UO_parts_per_million);

    const CVTermInfo& info2 = cvTermInfo(MS_Trypsin);
    unit_assert(info2.otherRelations.size() == 1);
    unit_assert(info2.otherRelations.begin()->first == "has_regexp");
    unit_assert(info2.otherRelations.begin()->second == MS______KR_____P_);
}


void testSynonyms()
{
    const CVTermInfo& info = cvTermInfo(MS_B);
    unit_assert(info.name == "magnetic field strength");
    unit_assert(info.exactSynonyms.size() == 1);
    unit_assert(info.exactSynonyms[0] == "B");
    unit_assert(cvTermInfo(MS_QIT).exactSynonyms.size() == 3);

    unit_assert(cvTermInfo(MS_chemical_ionization).shortName() == "CI");
    unit_assert(cvTermInfo(MS_FT_ICR).shortName() == "FT_ICR");
    unit_assert(cvTermInfo(MS_fourier_transform_ion_cyclotron_resonance_mass_spectrometer).shortName() == "FT_ICR");
    unit_assert(cvTermInfo(CVID_Unknown).shortName() == "Unknown");
}


void testIDTranslation()
{
    unit_assert(cvTermInfo("MS:1000025").cvid == MS_B);
    unit_assert(cvTermInfo("MS:1000042").cvid == MS_peak_intensity);
    unit_assert(cvTermInfo("UO:0000231").cvid == UO_information_unit);
    unit_assert(cvTermInfo("XX:0000231").cvid == CVID_Unknown);
    unit_assert(cvTermInfo("FOO:").cvid == CVID_Unknown);
    unit_assert(cvTermInfo(":FOO").cvid == CVID_Unknown);
    unit_assert(cvTermInfo("MS").cvid == CVID_Unknown);
}


void testPropertyValues()
{
    CVTermInfo phospho = cvTermInfo(UNIMOD_Phospho);

    unit_assert_operator_equal(1, phospho.propertyValues.count("delta_composition"));
    unit_assert_operator_equal("H O(3) P", phospho.propertyValues.find("delta_composition")->second);

    unit_assert_operator_equal(2, phospho.propertyValues.count("spec_1_site"));
    unit_assert_operator_equal("T", phospho.propertyValues.equal_range("spec_1_site").first->second);
    unit_assert_operator_equal("S", (--phospho.propertyValues.equal_range("spec_1_site").second)->second);

    unit_assert_operator_equal(1, phospho.propertyValues.count("spec_2_site"));
    unit_assert_operator_equal("Y", phospho.propertyValues.find("spec_2_site")->second);
}


void testThreadSafetyWorker(boost::barrier* testBarrier)
{
    testBarrier->wait(); // wait until all threads have started

    try
    {
        test();
        testIsA();
        testOtherRelations();
        testSynonyms();
        testIDTranslation();
        testPropertyValues();
    }
    catch (exception& e)
    {
        cerr << "Exception in worker thread: " << e.what() << endl;
    }
    catch (...)
    {
        cerr << "Unhandled exception in worker thread." << endl;
    }
}

void testThreadSafety(const int& testThreadCount)
{
    boost::barrier testBarrier(testThreadCount);
    boost::thread_group testThreadGroup;
    for (int i=0; i < testThreadCount; ++i)
        testThreadGroup.add_thread(new boost::thread(&testThreadSafetyWorker, &testBarrier));
    testThreadGroup.join_all();
}


int main(int argc, char* argv[])
{
    TEST_PROLOG(argc, argv)

    if (argc>1 && !strcmp(argv[1],"-v")) os_ = &cout; 

    try
    {
        //testThreadSafety(1); // does not test thread-safety of singleton initialization
        testThreadSafety(2);
        testThreadSafety(4);
        testThreadSafety(8);
        testThreadSafety(16);
    }
    catch (exception& e)
    {
        TEST_FAILED(e.what())
    }
    catch (...)
    {
        TEST_FAILED("Caught unknown exception.")
    }

    TEST_EPILOG
}