CDirectory::~CDirectory()
{
CDirEntry *pEntry = m_pEntryList;
while (pEntry)
{
CDirEntry *pTmp = pEntry;
pEntry = pEntry->GetNext();
delete pTmp;
}
}
void CDirectory::AddEntry(struct dirent *de, CDirectory *pSubDir, const char *pHostName)
{
CDirEntry *pEntry = new CDirEntry;
pEntry->Create(de, pSubDir, pHostName);
pEntry->SetNext(m_pEntryList);
m_pEntryList = pEntry;
m_nbEntry++;
}
void CListProcess::UpdateStatus(int nItem)
{
wxString sTime;
bool bStartTime = false;
bool bStopTime = false;
long nMin;
long nMax;
long nCount = (long) m_pDirList->GetCount();
if(nItem >= 0)
{
nMin = (long) nItem;
nMax = nMin;
nMax++;
if(nMax > nCount)
{
nMax = nCount;
}
}
else
{
nMin = 0;
nMax = nCount;
}
wxListItem info;
CDirEntry *pDirEntry;
for(long i = nMin; i < nMax; i++)
{
pDirEntry = m_pDirList->At((size_t)i);
const wxString &sStatus(pDirEntry->GetStatusString());
sTime = pDirEntry->FormatStartTime();
SetItem(i,ITEM_START,sTime);
if(!sTime.IsEmpty())
{
bStartTime = true;
}
sTime = pDirEntry->FormatStopTime();
SetItem(i,ITEM_STOP,sTime);
if(!sTime.IsEmpty())
{
bStopTime = true;
}
SetItem(i,ITEM_STATUS,sStatus);
SetItemTextColour(i,pDirEntry->GetStatusColour());
}
if(bStartTime)
{
SetColumnWidth(ITEM_START,wxLIST_AUTOSIZE );
}
if(bStopTime)
{
SetColumnWidth(ITEM_STOP,wxLIST_AUTOSIZE );
}
SetColumnWidth(ITEM_STATUS,wxLIST_AUTOSIZE);
// Refresh();
}
MemHandle CPWad::Read (XString item)
{
CDirEntry *entry = (CDirEntry *)directory[item];
if (entry)
{
file.Seek (entry->Offset());
MemHandle data = file.Read ((size_t)entry->Size());
if (data.Size() == (size_t) entry->Size())
return data;
}
return 0;
}
void operator()( const CDirEntry & dirEntry ) {
//const static size_t kInvalidFileNumber = numeric_limits<size_t>::max();
if( ! dirEntry.IsFile() ) {
return;
}
CFile file(dirEntry);
string name = file.GetName();
if (NStr::EndsWith(name, ".txt") || NStr::StartsWith(name, ".")) {
return;
}
if (NStr::EndsWith(name, extKeep)) {
return;
}
// extract info from the file name
const string sFileName = file.GetName();
vector<string> vecFileNamePieces;
NStr::Split( sFileName, ".", vecFileNamePieces );
BOOST_REQUIRE(vecFileNamePieces.size() == 3);
string sTestName = vecFileNamePieces[0];
BOOST_REQUIRE(!sTestName.empty());
string sObjType = vecFileNamePieces[1];
BOOST_REQUIRE(!sObjType.empty());
string sFileType = vecFileNamePieces[2];
BOOST_REQUIRE(!sFileType.empty());
STestInfo & test_info_to_load =
(*m_pTestNameToInfoMap)[vecFileNamePieces[0]];
// assign object type contained in test input
if (sObjType == "entry" || sObjType == "annot") {
test_info_to_load.mObjType = sObjType;
}
else {
BOOST_FAIL("Unknown object type " << sObjType << ".");
}
// figure out what type of file we have and set appropriately
if (sFileType == mExtInput) {
BOOST_REQUIRE( test_info_to_load.mInFile.GetPath().empty() );
test_info_to_load.mInFile = file;
}
else if (sFileType == mExtOutput) {
BOOST_REQUIRE( test_info_to_load.mOutFile.GetPath().empty() );
test_info_to_load.mOutFile = file;
}
else if (sFileType == mExtErrors) {
BOOST_REQUIRE( test_info_to_load.mErrorFile.GetPath().empty() );
test_info_to_load.mErrorFile = file;
}
else {
BOOST_FAIL("Unknown file type " << sFileName << ".");
}
}
MemHandle CPWad::Read (XString map, XString item)
{
CDirEntry *entry = (CDirEntry *)directory[map];
if (entry)
{
entry = (CDirEntry *)entry->subdir[item];
if (entry)
{
file.Seek (entry->Offset());
MemHandle data = file.Read ((size_t)entry->Size());
if (data.Size() == (size_t) entry->Size())
{
cdebug.out << "Read From PWAD " << map << " " << item << " " << data.Size() << " bytes" << endl;
return data;
}
}
}
cerr << "Read From PWAD " << map << " " << item << " FAILED!! " << endl;
cdebug.out << "Read From PWAD " << map << " " << item << " FAILED!! " << endl;
return 0;
}
int CPWad::Write (MemHandle data, XString map, XString item)
{
CDirEntry *entry = (CDirEntry *)directory[map];
if (entry)
{
entry = (CDirEntry *)entry->subdir[item];
if (entry)
{
file.Seek (entry->Offset());
if (data.Size() == (size_t) entry->Size())
{
int status = file.Write (data);
cdebug.out << "Write to PWAD " << map << " " << item << " " << data.Size() << " bytes" << endl;
return status;
}
}
}
cerr << "Write to PWAD " << map << " " << item << " FAILED!! " << endl;
cdebug.out << "Write to PWAD " << map << " " << item << " FAILED!! " << endl;
return -1;
}
string g_FindDataFile(const CTempString& name, CDirEntry::EType type)
{
#ifdef NCBI_OS_MSWIN
static const char* kDelim = ";";
#else
static const char* kDelim = ":";
#endif
if ( !s_IgnoredDataFiles->empty()
&& CDirEntry::MatchesMask(name, *s_IgnoredDataFiles) ) {
return kEmptyStr;
}
list<string> dirs;
if (CDirEntry::IsAbsolutePath(name)) {
dirs.push_back(kEmptyStr);
} else {
TNCBIDataPath path;
TNCBIDataDir dir;
if ( !path.Get().empty() ) {
NStr::Split(path.Get(), kDelim, dirs);
}
if ( !dir.Get().empty() ) {
dirs.push_back(dir.Get());
}
}
CDirEntry candidate;
EFollowLinks fl = (type == CDirEntry::eLink) ? eIgnoreLinks : eFollowLinks;
ITERATE (list<string>, dir, dirs) {
candidate.Reset(CDirEntry::MakePath(*dir, name));
if (candidate.Exists() && candidate.GetType(fl) == type) {
return candidate.GetPath();
}
}
bool CListProcess::TransferDataToWindow()
{
wxString sTime;
bool bStartTime = false;
bool bStopTime = false;
bool bRtn = true;
bool bIsShown = IsShownOnScreen();
if(bIsShown)
{
Show(false);
}
size_t n = m_pDirList->GetCount();
long nItem;
CDirEntry *pDirEntry;
ClearAll();
InsertColumn(ITEM_DIR,_T("Directory"),wxLIST_FORMAT_LEFT);
InsertColumn(ITEM_START,_T("Start"),wxLIST_FORMAT_LEFT);
InsertColumn(ITEM_STOP,_T("Stop"),wxLIST_FORMAT_LEFT);
InsertColumn(ITEM_STATUS,_T("Status"),wxLIST_FORMAT_LEFT);
for(size_t i = 0; (i < n) && bRtn; i++)
{
pDirEntry = m_pDirList->At(i);
const wxString &sInput(pDirEntry->GetInputDir());
const wxString &sStatus(pDirEntry->GetStatusString());
nItem = InsertItem((long)i,sInput);
sTime = pDirEntry->FormatStartTime();
SetItem(nItem,ITEM_START,sTime);
if(!sTime.IsEmpty())
{
bStartTime = true;
}
sTime = pDirEntry->FormatStopTime();
SetItem(nItem,ITEM_STOP,sTime);
if(!sTime.IsEmpty())
{
bStopTime = true;
}
SetItem(nItem,ITEM_STATUS,sStatus);
SetItemTextColour(nItem,pDirEntry->GetStatusColour());
}
SetColumnWidth(ITEM_DIR,wxLIST_AUTOSIZE );
#define HEADER_SIZE 80
SetColumnWidth(ITEM_START,bStartTime ? wxLIST_AUTOSIZE : HEADER_SIZE);
SetColumnWidth(ITEM_STOP,bStopTime ? wxLIST_AUTOSIZE : HEADER_SIZE);
#undef HEADER_SIZE
SetColumnWidth(ITEM_STATUS,wxLIST_AUTOSIZE );
if(bIsShown)
{
Show(true);
}
Refresh();
return bRtn;
}
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 operator()( const CDirEntry & dirEntry ) {
if( ! dirEntry.IsFile() ) {
return;
}
CFile file(dirEntry);
string name = file.GetName();
if (NStr::EndsWith(name, ".txt") || NStr::StartsWith(name, ".")) {
return;
}
// extract info from the file name
const string sFileName = file.GetName();
vector<CTempString> vecFileNamePieces;
NStr::Split( sFileName, ".", vecFileNamePieces );
BOOST_REQUIRE(vecFileNamePieces.size() == 2);
CTempString tsTestName = vecFileNamePieces[0];
BOOST_REQUIRE(!tsTestName.empty());
CTempString tsFileType = vecFileNamePieces[1];
BOOST_REQUIRE(!tsFileType.empty());
STestInfo & test_info_to_load =
(*m_pTestNameToInfoMap)[vecFileNamePieces[0]];
// figure out what type of file we have and set appropriately
if (tsFileType == mExtInput) {
BOOST_REQUIRE( test_info_to_load.mInFile.GetPath().empty() );
test_info_to_load.mInFile = file;
}
else if (tsFileType == mExtOutput) {
BOOST_REQUIRE( test_info_to_load.mOutFile.GetPath().empty() );
test_info_to_load.mOutFile = file;
}
else if (tsFileType == mExtErrors) {
BOOST_REQUIRE( test_info_to_load.mErrorFile.GetPath().empty() );
test_info_to_load.mErrorFile = file;
}
else {
BOOST_FAIL("Unknown file type " << sFileName << ".");
}
}
void operator()( const CDirEntry & dirEntry ) {
const static size_t kInvalidFileNumber = numeric_limits<size_t>::max();
if( ! dirEntry.IsFile() ) {
return;
}
CFile file(dirEntry);
// skip the README file
if( file.GetName() == "README.txt" ) {
return;
}
// skip .svn files
if( NStr::Find(file.GetPath(), ".svn") != NPOS )
{
return;
}
const string sFilePath = file.GetPath();
cout << "Parsing file name: " << sFilePath << endl;
// extract info from the file name
const string sFileName = file.GetName();
vector<CTempString> vecFileNamePieces;
NStr::Tokenize( sFileName, ".", vecFileNamePieces );
BOOST_REQUIRE( vecFileNamePieces.size() == 2 ||
vecFileNamePieces.size() == 3 );
CTempString tsTestName = vecFileNamePieces[0];
BOOST_REQUIRE( ! tsTestName.empty() );
CTempString tsFileType = vecFileNamePieces[1];
size_t iFileNumber = kInvalidFileNumber;
if( vecFileNamePieces.size() > 2 ) {
iFileNumber = NStr::StringToUInt(vecFileNamePieces[2]);
}
STestInfo & test_info_to_load =
(*m_pTestNameToInfoMap)[vecFileNamePieces[0]];
// figure out what type of file we have and set appropriately
if( tsFileType == "agp" && iFileNumber == kInvalidFileNumber ) {
// handle agp file
// (and make sure we don't have duplicates)
BOOST_REQUIRE( test_info_to_load.m_AGPFile.GetPath().empty() );
test_info_to_load.m_AGPFile = file;
} else if( tsFileType == "expected_seq_entry" && iFileNumber != kInvalidFileNumber )
{
// handle expected seq-entry file
// (Note that the files could come in in any order)
vector<CFile> & vecExpectedSeqEntryFiles =
test_info_to_load.m_vecExpectedSeqEntryFiles;
if( vecExpectedSeqEntryFiles.size() <= iFileNumber ) {
// expand the vector to include this file number
vecExpectedSeqEntryFiles.resize( 1 + iFileNumber );
}
// make sure no duplicates
BOOST_REQUIRE( vecExpectedSeqEntryFiles[iFileNumber].GetPath().empty() );
vecExpectedSeqEntryFiles[iFileNumber] = file;
} else if( tsFileType == "flags" && iFileNumber == kInvalidFileNumber ) {
// handle flags file
BOOST_REQUIRE( test_info_to_load.m_FlagFile.GetPath().empty() );
test_info_to_load.m_FlagFile = file;
} else {
BOOST_FAIL("Unknown file type");
}
}
CPWad::CPWad (XString name)
: file (name, O_RDWR | O_BINARY), currentmap(0)
{
if (file.IsOpen())
{
// -=- read the pwad header -=-
cout << "Opened '" << name << "'" << endl;
cdebug.out << "Opened '" << name << "'" << endl;
file.Read (&header, sizeof(PWAD_HEADER));
swaplong((int *)&(header.dir_offset));
swaplong((int *)&(header.dir_entries));
if (memcmp ("PWAD", header.signature, 4) != 0)
{
cout << "Not a PWAD!" << "\n";
cdebug.out << "Not a PWAD!" << "\n";
Fail ();
return;
}
else
{
cdebug.out << "File size: " << file.Size() << endl;
cdebug.out << "Directory Offset: " << header.dir_offset << endl;
cdebug.out << "Directory Entries: " << header.dir_entries << endl;
}
// -=- read the directory -=-
file.Seek (header.dir_offset);
MemHandle dirbuff = file.Read ((size_t)(header.dir_entries * sizeof(DIR_ENTRY)));
if (dirbuff.Size () != (header.dir_entries * sizeof(DIR_ENTRY)))
{
cout << "Error Reading PWAD Directory." << endl;
cdebug.out << "Error Reading PWAD Directory." << endl;
Fail ();
}
else
{
cout << "Building directory...." << flush;
swap_lump_list((void *)dirbuff.Buffer(), header.dir_entries);
// -=- go through each dir entry and add it to our internal dir -=-
DIR_ENTRY *entry_ptr = (DIR_ENTRY *)dirbuff.Buffer();
for (int n = 0; n < header.dir_entries; n++)
{
AddEntry (entry_ptr[n]);
}
cout << "Done." << endl;
// -=- print out directory used for debugging -=-
CDirEntry *de;
CDirEntry *sde;
de = (CDirEntry *)directory.FirstItem ();
while (de)
{
cdebug.out << de->GetKey() << " " << de->Size() << " bytes\t @" << de->Offset() << endl;
sde = (CDirEntry *)de->subdir.FirstItem ();
while (sde)
{
cdebug.out << " " << sde->GetKey() << " " << sde->Size() << " bytes\t @" << sde->Offset() << endl;
sde = (CDirEntry *)sde->Next();
}
de = (CDirEntry *)de->Next();
}
// -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
}
}
else
{
cout << "Cannot open '" << name << "'" << endl;
cdebug.out << "Cannot open '" << name << "'" << endl;
Fail ();
}
}
