void sRunTest(const string &sTestName, const STestInfo & testInfo, bool keep)
{
    cerr << "Testing " << testInfo.mInFile.GetName() << " against " <<
        testInfo.mOutFile.GetName() << " and " <<
        testInfo.mErrorFile.GetName() << endl;

    string logName = CDirEntry::GetTmpName();
    CErrorLogger logger(logName);

    CGvfReader reader(0);
    CNcbiIfstream ifstr(testInfo.mInFile.GetPath().c_str());

    typedef CGff2Reader::TAnnotList ANNOTS;
    ANNOTS annots;
    try {
        reader.ReadSeqAnnots(annots, ifstr, &logger);
    }
    catch (...) {
        BOOST_ERROR("Error: " << sTestName << " failed during conversion.");
        ifstr.close();
        return;
    }

    string resultName = CDirEntry::GetTmpName();
    CNcbiOfstream ofstr(resultName.c_str());
    for (ANNOTS::iterator cit = annots.begin(); cit != annots.end(); ++cit){
        ofstr << MSerial_AsnText << **cit;
        ofstr.flush();
    }
    ifstr.close();
    ofstr.close();

    bool success = testInfo.mOutFile.CompareTextContents(resultName, CFile::eIgnoreWs);
    if (!success) {
        CDirEntry deResult = CDirEntry(resultName);
        if (keep) {
            deResult.Copy(testInfo.mOutFile.GetPath() + "." + extKeep);
        }
        deResult.Remove();
        CDirEntry(logName).Remove();
        BOOST_ERROR("Error: " << sTestName << " failed due to post processing diffs.");
    }
    CDirEntry(resultName).Remove();

    success = testInfo.mErrorFile.CompareTextContents(logName, CFile::eIgnoreWs);
    CDirEntry deErrors = CDirEntry(logName);
    if (!success  &&  keep) {
        deErrors.Copy(testInfo.mErrorFile.GetPath() + "." + extKeep);
    }
    deErrors.Remove();
    if (!success) {
        BOOST_ERROR("Error: " << sTestName << " failed due to error handling diffs.");
    }
};
示例#2
0
//  ----------------------------------------------------------------------------
void CMultiReaderApp::xProcessVcf(
    const CArgs& args,
    CNcbiIstream& istr,
    CNcbiOstream& ostr)
//  ----------------------------------------------------------------------------
{
    typedef vector<CRef<CSeq_annot> > ANNOTS;
    ANNOTS annots;

    CVcfReader reader( m_iFlags );
    reader.ReadSeqAnnots(annots, istr, m_pErrors);
    for (ANNOTS::iterator cit = annots.begin(); cit != annots.end(); ++cit){
        xWriteObject(**cit, ostr);
    }
}
示例#3
0
//  ----------------------------------------------------------------------------
void CMultiReaderApp::xProcessGff3(
    const CArgs& args,
    CNcbiIstream& istr,
    CNcbiOstream& ostr)
//  ----------------------------------------------------------------------------
{
    typedef vector<CRef<CSeq_annot> > ANNOTS;
    ANNOTS annots;
    
    if (args["format"].AsString() == "gff2") { // process as plain GFF2
        return xProcessGff2(args, istr, ostr);
    }
    CGff3Reader reader(m_iFlags, m_AnnotName, m_AnnotTitle);
    reader.ReadSeqAnnots(annots, istr, m_pErrors);
    for (ANNOTS::iterator cit = annots.begin(); cit != annots.end(); ++cit){
        xWriteObject(**cit, ostr);
    }
}
void sUpdateCase(CDir& test_cases_dir, const string& test_name)
{   
    string input = CDir::ConcatPath( test_cases_dir.GetPath(), test_name + "." + extInput);
    string output = CDir::ConcatPath( test_cases_dir.GetPath(), test_name + "." + extOutput);
    string errors = CDir::ConcatPath( test_cases_dir.GetPath(), test_name + "." + extErrors);
    if (!CFile(input).Exists()) {
         BOOST_FAIL("input file " << input << " does not exist.");
    }
    cerr << "Creating new test case from " << input << " ..." << endl;

    CErrorLogger logger(errors);
    CGvfReader reader(0);
    CNcbiIfstream ifstr(input.c_str());

    typedef CGff2Reader::TAnnotList ANNOTS;
    ANNOTS annots;
    try {
        reader.ReadSeqAnnots(annots, ifstr, &logger);
    }
    catch (...) {
        ifstr.close();
        BOOST_FAIL("Error: " << input << " failed during conversion.");
    }
    ifstr.close();
    cerr << "    Produced new error listing " << output << "." << endl;

    CNcbiOfstream ofstr(output.c_str());
    for (ANNOTS::iterator cit = annots.begin(); cit != annots.end(); ++cit){
        ofstr << MSerial_AsnText << **cit;
        ofstr.flush();
    }
    ofstr.close();
    cerr << "    Produced new ASN1 file " << output << "." << endl;

    cerr << " ... Done." << endl;
}