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.");
}
};
// ----------------------------------------------------------------------------
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);
}
}
// ----------------------------------------------------------------------------
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;
}