ReaderTest.cpp File Reference

#include "pwiz/utility/misc/unit.hpp"
#include "pwiz/utility/misc/Std.hpp"
#include "pwiz/utility/misc/Filesystem.hpp"
#include "Reader.hpp"
#include "examples.hpp"
#include "MSDataFile.hpp"
#include "pwiz/data/vendor_readers/ExtendedReaderList.hpp"
#include <cstring>

Go to the source code of this file.

Classes
class	Reader1
struct	Reader1::ReaderConfig
class	Reader2
struct	Reader2::ReaderConfig

Functions
void	testGet ()
void	testAccept ()
void	testRead ()
void	testIdentifyFileFormat ()
void	test ()
int	main (int argc, char *argv[])

Variables
ostream *	os_ = 0

---

Function Documentation

void testGet

(

)

Definition at line 128 of file ReaderTest.cpp.

References Reader2::ReaderConfig::color, pwiz::msdata::ReaderList::get(), os_, Reader2::readerConfig, and unit_assert.

{
    if (os_) *os_ << "testGet()\n";

    ReaderList readers;
    readers.push_back(ReaderPtr(new Reader1));
    readers.push_back(ReaderPtr(new Reader2));

    unit_assert(readers.size() == 2);

    Reader1* reader1 = readers.get<Reader1>();
    unit_assert(reader1);
    if (os_) *os_ << "reader1 config: " << reader1->readerConfig.name << endl; 
    unit_assert(reader1->readerConfig.name == "default");
    reader1->readerConfig.name = "raw";
    if (os_) *os_ << "reader1 config: " << reader1->readerConfig.name << endl; 
    unit_assert(reader1->readerConfig.name == "raw");

    Reader2* reader2 = readers.get<Reader2>();
    unit_assert(reader2);
    if (os_) *os_ << "reader2 config: " << reader2->readerConfig.color << endl; 
    unit_assert(reader2->readerConfig.color == "orange");
    reader2->readerConfig.color = "purple";
    if (os_) *os_ << "reader2 config: " << reader2->readerConfig.color << endl; 
    unit_assert(reader2->readerConfig.color == "purple");

    const ReaderList& const_readers = readers;
    const Reader2* constReader2 = const_readers.get<Reader2>();
    unit_assert(constReader2);
    if (os_) *os_ << "constReader2 config: " << constReader2->readerConfig.color << endl; 

    if (os_) *os_ << endl;
}

void testAccept

(

)

Definition at line 163 of file ReaderTest.cpp.

References pwiz::msdata::Reader::accept(), os_, and unit_assert.

{
    if (os_) *os_ << "testAccept()\n";

    ReaderList readers;
    readers.push_back(ReaderPtr(new Reader1));
    readers.push_back(ReaderPtr(new Reader2));

    if (os_) *os_ << "accept 1:\n";
    unit_assert(readers.accept("1", "head"));
    if (os_) *os_ << "accept 2:\n";
    unit_assert(readers.accept("2", "head"));
    if (os_) *os_ << "accept 3:\n";
    unit_assert(!readers.accept("3", "head"));

    if (os_) *os_ << endl;
}

void testRead

(

)

Definition at line 182 of file ReaderTest.cpp.

References pwiz::msdata::Reader::accept(), Reader1::ReaderConfig::done, Reader2::ReaderConfig::done, pwiz::msdata::ReaderList::get(), os_, pwiz::msdata::ReaderList::read(), Reader1::readerConfig, Reader2::readerConfig, and unit_assert.

{
    if (os_) *os_ << "testRead()\n";

    ReaderList readers;
    readers.push_back(ReaderPtr(new Reader1));
    readers.push_back(ReaderPtr(new Reader2));

    MSData msd;

    // note: composite pattern with accept/read will cause two calls
    // to accept(); the alternative is to maintain state between accept()
    // and read(), which opens possibility for misuse. 

    unit_assert(readers.get<Reader1>()->readerConfig.done == false);
    if (readers.accept("1", "head"))
        readers.read("1", "head", msd);
    unit_assert(readers.get<Reader1>()->readerConfig.done == true);

    readers.get<Reader1>()->readerConfig.done = false;
    unit_assert(readers.get<Reader2>()->readerConfig.done == false);
    if (readers.accept("2", "head"))
        readers.read("2", "head", msd);
    unit_assert(readers.get<Reader1>()->readerConfig.done == false);
    unit_assert(readers.get<Reader2>()->readerConfig.done == true);

    if (os_) *os_ << endl;
}

void testIdentifyFileFormat

(

)

Definition at line 212 of file ReaderTest.cpp.

References pwiz::msdata::MSDataFile::WriteConfig::format, pwiz::msdata::identifyFileFormat(), pwiz::identdata::examples::initializeTiny(), MS_ABI_WIFF_file, MS_ISB_mzXML_file, MS_Mascot_MGF_file, MS_MS2_file, MS_mz5_file, MS_mzML_file, MS_Waters_raw_file, unit_assert_operator_equal, and write().

Referenced by test().

{
    ReaderPtr readers(new ExtendedReaderList);

    {ofstream fs("testSpectraDataFile.mzedML"); fs << "<?xml?><mzML>";}
    unit_assert_operator_equal(MS_mzML_file, identifyFileFormat(readers, "testSpectraDataFile.mzedML"));
    bfs::remove("testSpectraDataFile.mzedML");

    {ofstream fs("testSpectraDataFile.mzedXML"); fs << "<?xml?><mzXML>";}
    unit_assert_operator_equal(MS_ISB_mzXML_file, identifyFileFormat(readers, "testSpectraDataFile.mzedXML"));
    bfs::remove("testSpectraDataFile.mzedXML");

    
    {
        MSData msd;
        examples::initializeTiny(msd);
        MSDataFile::WriteConfig config;
        config.format = MSDataFile::Format_MZ5;
#ifndef WITHOUT_MZ5
        MSDataFile::write(msd, "testSpectraDataFile.Mz5", config);
        unit_assert_operator_equal(MS_mz5_file, identifyFileFormat(readers, "testSpectraDataFile.Mz5"));
#endif
    }
    bfs::remove("testSpectraDataFile.Mz5");

    {ofstream fs("testSpectraDataFile.mGF"); fs << "MGF";}
    unit_assert_operator_equal(MS_Mascot_MGF_file, identifyFileFormat(readers, "testSpectraDataFile.mGF"));
    bfs::remove("testSpectraDataFile.mGF");
    
    {ofstream fs("testSpectraDataFile.Ms2"); fs << "MS2";}
    unit_assert_operator_equal(MS_MS2_file, identifyFileFormat(readers, "testSpectraDataFile.Ms2"));
    bfs::remove("testSpectraDataFile.Ms2");
    
    {ofstream fs("testSpectraDataFile.wiFF"); fs << "WIFF";}
    unit_assert_operator_equal(MS_ABI_WIFF_file, identifyFileFormat(readers, "testSpectraDataFile.wiFF"));
    bfs::remove("testSpectraDataFile.wiFF");

    {ofstream fs("_FUNC42.DAT"); fs << "Life, the Universe, and Everything";}
    unit_assert_operator_equal(MS_Waters_raw_file, identifyFileFormat(readers, "."));
    bfs::remove("_FUNC42.DAT");
}

void test

(

)

Definition at line 255 of file ReaderTest.cpp.

References testAccept(), testGet(), testIdentifyFileFormat(), and testRead().

{
    testGet();
    testAccept();
    testRead();
    testIdentifyFileFormat();
}

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

Definition at line 264 of file ReaderTest.cpp.

References e(), os_, test(), TEST_EPILOG, TEST_FAILED, and TEST_PROLOG_EX.

{
    TEST_PROLOG_EX(argc, argv, "_MSData")

    try
    {
        if (argc==2 && !strcmp(argv[1],"-v")) os_ = &cout;
        test();
    }
    catch (exception& e)
    {
        TEST_FAILED(e.what())
    }
    catch (...)
    {
        TEST_FAILED("Caught unknown exception.")
    }

    TEST_EPILOG
}

---

Variable Documentation

ostream* os_ = 0

Definition at line 39 of file ReaderTest.cpp.