ProteomeDataFileTest.cpp File Reference

#include "ProteomeDataFile.hpp"
#include "Diff.hpp"
#include "examples.hpp"
#include "Reader_FASTA.hpp"
#include "pwiz/utility/misc/unit.hpp"
#include "pwiz/utility/misc/Filesystem.hpp"
#include "pwiz/utility/misc/Std.hpp"
#include <boost/iostreams/filtering_stream.hpp>
#include <boost/iostreams/filter/gzip.hpp>
#include <boost/iostreams/device/file_descriptor.hpp>
#include <boost/iostreams/copy.hpp>

Go to the source code of this file.

Classes
class	TestReader

Functions
void	validateWriteRead (const ProteomeDataFile::WriteConfig &writeConfig, const DiffConfig diffConfig)
void	test ()
void	testReader ()
int	main (int argc, char *argv[])

Variables
ostream *	os_ = 0
string	filenameBase_ = "temp.ProteomeDataFileTest"

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Function Documentation

void validateWriteRead	(	const ProteomeDataFile::WriteConfig &	writeConfig,
		const DiffConfig	diffConfig
	)

Definition at line 49 of file ProteomeDataFileTest.cpp.

References diff(), filename1, filenameBase_, pwiz::proteome::ProteomeDataFile::WriteConfig::format, Format_FASTA, pwiz::proteome::Reader_FASTA::Config::indexed, pwiz::proteome::ProteomeDataFile::WriteConfig::indexed, pwiz::identdata::examples::initializeTiny(), os_, unit_assert, pwiz::proteome::ProteomeDataFile::write(), and write().

{
    if (os_) *os_ << "validateWriteRead()\n  " << writeConfig << endl; 

    string filename1 = filenameBase_ + "1.fasta";
    string filename2 = filenameBase_ + "2.fasta";

    {
        // create ProteomeData object in memory
        ProteomeData tiny;
        examples::initializeTiny(tiny);

        // write to file #1 (static)
        ProteomeDataFile::write(tiny, filename1, writeConfig);

        shared_ptr<Reader> reader;
        if (writeConfig.format == ProteomeDataFile::Format_FASTA)
        {
            // Reader_FASTA creates the index in the read() call
            Reader_FASTA::Config config;
            config.indexed = writeConfig.indexed;
            reader.reset(new Reader_FASTA(config));
        }

        // read back into an ProteomeDataFile object
        ProteomeDataFile pd1(filename1, *reader);

        // compare
        Diff<ProteomeData, DiffConfig> diff(tiny, pd1, diffConfig);
        if (diff && os_) *os_ << diff << endl;
        unit_assert(!diff);

        // write to file #2 (member)
        pd1.write(filename2, writeConfig);

        // read back into another ProteomeDataFile object
        ProteomeDataFile pd2(filename2, *reader);

        // compare
        diff(tiny, pd2);
        if (diff && os_) *os_ << diff << endl;
        unit_assert(!diff);

        // now give the gzip read a workout
        bio::filtering_istream tinyGZ(bio::gzip_compressor() | bio::file_descriptor_source(filename1));
        bio::copy(tinyGZ, bio::file_descriptor_sink(filename1+".gz", ios::out|ios::binary));

        ProteomeDataFile pd3(filename1+".gz", *reader);

        // compare
        diff(tiny, pd3);
        if (diff && os_) *os_ << diff << endl;
        unit_assert(!diff);
        }

    // remove temp files
    bfs::remove(filename1);
    bfs::remove(filename2);
    bfs::remove(filename1 + ".gz");

    bool index1Exists = bfs::exists(filename1 + ".index");
    bool index2Exists = bfs::exists(filename2 + ".index");
    bool index3Exists = bfs::exists(filename1 + ".gz.index");

    bool indexShouldExist = writeConfig.indexed;
    unit_assert(!indexShouldExist || index1Exists);
    unit_assert(!indexShouldExist || index2Exists);
    unit_assert(!indexShouldExist || index3Exists);

    if (index1Exists) bfs::remove(filename1 + ".index");
    if (index2Exists) bfs::remove(filename2 + ".index");
    if (index3Exists) bfs::remove(filename1 + ".gz.index");
}

void test

(

)

Definition at line 124 of file ProteomeDataFileTest.cpp.

References pwiz::proteome::ProteomeDataFile::WriteConfig::indexed, and validateWriteRead().

{
    ProteomeDataFile::WriteConfig writeConfig;
    DiffConfig diffConfig;

    // test FASTA with binary stream index
    validateWriteRead(writeConfig, diffConfig);

    // test FASTA with memory index
    writeConfig.indexed = false;
    validateWriteRead(writeConfig, diffConfig);
}

void testReader

(

)

Definition at line 172 of file ProteomeDataFileTest.cpp.

References TestReader::count, filenameBase_, os_, and unit_assert.

{
    // create a file
    string filename = filenameBase_ + ".fAsTa";
    ofstream os(filename.c_str());
    os << ">Id Description\nSEQUENCE\n";
    os.close();

    // open the file with our Reader
    TestReader reader;
    ProteomeDataFile pd(filename, reader);

    // verify that our reader got called properly
    unit_assert(reader.count == 2);

    // remove temp file
    boost::filesystem::remove(filename);

    if (os_) *os_ << endl;
}

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

Definition at line 194 of file ProteomeDataFileTest.cpp.

References e(), os_, test(), TEST_EPILOG, TEST_FAILED, TEST_PROLOG, and pwiz::util::testReader().

{
    TEST_PROLOG(argc, argv)

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

    TEST_EPILOG
}

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Variable Documentation

ostream* os_ = 0

Definition at line 43 of file ProteomeDataFileTest.cpp.

string filenameBase_ = "temp.ProteomeDataFileTest"

Definition at line 46 of file ProteomeDataFileTest.cpp.