//-------------------------------------------------------------------------------------
void Proxy::giveClientTo(Proxy* proxy)
{
if(clientMailbox_ == NULL || clientMailbox_->getChannel() == NULL)
{
char err[255];
kbe_snprintf(err, 255, "Proxy[%s]::giveClientTo: no has client.", getScriptName());
PyErr_SetString(PyExc_TypeError, err);
PyErr_PrintEx(0);
onGiveClientToFailure();
return;
}
Mercury::Channel* lpChannel = clientMailbox_->getChannel();
if(proxy)
{
EntityMailbox* mb = proxy->getClientMailbox();
if(mb != NULL)
{
ERROR_MSG(boost::format("Proxy::giveClientTo: %1%[%2%] give client to %3%[%4%], %5% have clientMailbox.\n") %
getScriptName() %
getID() %
proxy->getScriptName() %
proxy->getID() %
proxy->getScriptName());
onGiveClientToFailure();
return;
}
if(getCellMailbox())
{
// 通知cell丢失客户端
Mercury::Bundle* pBundle = Mercury::Bundle::ObjPool().createObject();
(*pBundle).newMessage(CellappInterface::onResetWitness);
(*pBundle) << this->getID();
getCellMailbox()->postMail((*pBundle));
Mercury::Bundle::ObjPool().reclaimObject(pBundle);
}
entitiesEnabled_ = false;
getClientMailbox()->addr(Mercury::Address::NONE);
Py_DECREF(getClientMailbox());
proxy->onGiveClientTo(lpChannel);
setClientMailbox(NULL);
addr(Mercury::Address::NONE);
if(proxy->getClientMailbox() != NULL)
{
// 通知client销毁当前entity
Mercury::Bundle* pBundle = Mercury::Bundle::ObjPool().createObject();
(*pBundle).newMessage(ClientInterface::onEntityDestroyed);
(*pBundle) << this->getID();
proxy->getClientMailbox()->postMail((*pBundle));
Mercury::Bundle::ObjPool().reclaimObject(pBundle);
}
}
}
void doSetUserRegions(struct sqlConnection *conn)
/* Respond to set regions button. */
{
char *oldPasted = cartUsualString(cart, hgtaEnteredUserRegions, "");
char *db = cartOptionalString(cart, hgtaUserRegionsDb);
if (db && !sameString(db, database))
oldPasted = "";
htmlOpen("Enter region definition\n");
hPrintf("<FORM ACTION=\"%s\" METHOD=POST "
" ENCTYPE=\"multipart/form-data\" NAME=\"mainForm\">\n", getScriptName());
cartSaveSession(cart);
hPrintf("<TABLE><TR><TD ALIGN=LEFT>\n");
hPrintf("Paste regions:");
hPrintf("</TD><TD ALIGN=RIGHT>");
hPrintf("Or upload file: <INPUT TYPE=FILE NAME=\"%s\"> <BR>\n",
hgtaEnteredUserRegionFile);
hPrintf("</TD></TR><TR><TD COLSPAN=2 ALIGN=LEFT>\n");
cgiMakeTextArea(hgtaEnteredUserRegions, oldPasted, 10, 70);
hPrintf("</TD></TR><TR><TD COLSPAN=2 ALIGN=LEFT>\n");
cgiMakeButton(hgtaDoSubmitUserRegions, "submit");
hPrintf(" ");
cgiMakeButton(hgtaDoClearSetUserRegionsText, "clear");
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
hPrintf("</TD></TR></TABLE>");
hPrintf("</FORM><BR>\n");
webIncludeHelpFile("hgTbUserRegionsHelp", FALSE);
htmlClose();
}
//-------------------------------------------------------------------------------------
void Proxy::onDefDataChanged(const PropertyDescription* propertyDescription,
PyObject* pyData)
{
uint32 flags = propertyDescription->getFlags();
if((flags & ED_FLAG_BASE_AND_CLIENT) <= 0 || clientMailbox_ == NULL)
return;
// 创建一个需要广播的模板流
MemoryStream* mstream = MemoryStream::ObjPool().createObject();
propertyDescription->getDataType()->addToStream(mstream, pyData);
Mercury::Bundle* pBundle = Mercury::Bundle::ObjPool().createObject();
(*pBundle).newMessage(ClientInterface::onUpdatePropertys);
(*pBundle) << getID();
if(scriptModule_->usePropertyDescrAlias())
(*pBundle) << propertyDescription->aliasIDAsUint8();
else
(*pBundle) << propertyDescription->getUType();
pBundle->append(*mstream);
g_privateClientEventHistoryStats.trackEvent(getScriptName(),
propertyDescription->getName(),
pBundle->currMsgLength());
sendToClient(ClientInterface::onUpdatePropertys, pBundle);
MemoryStream::ObjPool().reclaimObject(mstream);
}
void genomicFormatPage(struct sqlConnection *conn)
/* Put up page asking for what sort of genomic sequence. */
{
struct hTableInfo *hti = getHti(database, curTable, conn);
htmlOpen("%s Genomic Sequence", curTableLabel());
if (doGalaxy())
startGalaxyForm();
else
hPrintf("<FORM ACTION=\"%s\" METHOD=GET>\n", getScriptName());
cartSaveSession(cart);
hgSeqOptionsHtiCart(hti, cart);
hPrintf("<BR>\n");
if (doGalaxy())
{
/* pass parameter to get sequence to Galaxy */
cgiMakeHiddenVar(hgtaDoGenomicDna, "get sequence");
printGalaxySubmitButtons();
}
else
{
cgiMakeButton(hgtaDoGenomicDna, "get sequence");
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
hPrintf("</FORM>");
}
cgiDown(0.9);
htmlClose();
}
//-------------------------------------------------------------------------------------
PyObject* Proxy::pyClientAddr()
{
if(isDestroyed())
{
PyErr_Format(PyExc_AssertionError, "%s: %d is destroyed!\n",
getScriptName(), getID());
PyErr_PrintEx(0);
return 0;
}
PyObject* pyobj = PyTuple_New(2);
if(getClientMailbox() == NULL || getClientMailbox()->getChannel() == NULL ||
getClientMailbox()->getChannel()->endpoint() == NULL)
{
PyTuple_SetItem(pyobj, 0, PyLong_FromLong(0));
PyTuple_SetItem(pyobj, 1, PyLong_FromLong(0));
}
else
{
const Mercury::Address& addr = getClientMailbox()->getChannel()->endpoint()->addr();
PyTuple_SetItem(pyobj, 0, PyLong_FromUnsignedLong(addr.ip));
PyTuple_SetItem(pyobj, 1, PyLong_FromUnsignedLong(addr.port));
}
return pyobj;
}
void doUploadIdentifiers(struct sqlConnection *conn)
/* Respond to upload identifiers button. */
{
struct hTableInfo *hti = maybeGetHti(database, curTable, conn);
char *idField = getIdField(database, curTrack, curTable, hti);
htmlOpen("Upload Identifiers for %s", curTableLabel());
if (idField == NULL)
errAbort("Sorry, I can't tell which field of table %s to treat as the "
"identifier field.", curTable);
hPrintf("<FORM ACTION=\"%s\" METHOD=POST ENCTYPE=\"multipart/form-data\">\n",
getScriptName());
cartSaveSession(cart);
hPrintf("Please enter the name of a file from your computer that contains a ");
hPrintf("space, tab, or ");
hPrintf("line separated list of the items you want to include.\n");
explainIdentifiers(database, conn, idField);
hPrintf("<BR>\n");
hPrintf("<INPUT TYPE=FILE NAME=\"%s\"> ", hgtaPastedIdentifiers);
hPrintf("<BR>\n");
cgiMakeButton(hgtaDoPastedIdentifiers, "submit");
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
hPrintf("</FORM>");
cgiDown(0.9);
htmlClose();
}
//-------------------------------------------------------------------------------------
PyObject* Entity::pyTeleport(PyObject* nearbyMBRef, PyObject* pyposition, PyObject* pydirection)
{
if(!PySequence_Check(pyposition) || PySequence_Size(pyposition) != 3)
{
PyErr_Format(PyExc_Exception, "%s::teleport: %d position not is Sequence!\n", getScriptName(), getID());
PyErr_PrintEx(0);
S_Return;
}
if(!PySequence_Check(pydirection) || PySequence_Size(pydirection) != 3)
{
PyErr_Format(PyExc_Exception, "%s::teleport: %d direction not is Sequence!\n", getScriptName(), getID());
PyErr_PrintEx(0);
S_Return;
}
Position3D pos;
Direction3D dir;
PyObject* pyitem = PySequence_GetItem(pyposition, 0);
pos.x = (float)PyFloat_AsDouble(pyitem);
Py_DECREF(pyitem);
pyitem = PySequence_GetItem(pyposition, 1);
pos.y = (float)PyFloat_AsDouble(pyitem);
Py_DECREF(pyitem);
pyitem = PySequence_GetItem(pyposition, 2);
pos.z = (float)PyFloat_AsDouble(pyitem);
Py_DECREF(pyitem);
pyitem = PySequence_GetItem(pydirection, 0);
dir.roll = (float)PyFloat_AsDouble(pyitem);
Py_DECREF(pyitem);
pyitem = PySequence_GetItem(pydirection, 1);
dir.pitch = (float)PyFloat_AsDouble(pyitem);
Py_DECREF(pyitem);
pyitem = PySequence_GetItem(pydirection, 2);
dir.yaw = (float)PyFloat_AsDouble(pyitem);
Py_DECREF(pyitem);
teleport(nearbyMBRef, pos, dir);
S_Return;
}
//-------------------------------------------------------------------------------------
void Proxy::giveClientTo(Proxy* proxy)
{
Mercury::Channel* lpChannel = clientMailbox_->getChannel();
if(lpChannel == NULL)
{
char err[255];
kbe_snprintf(err, 255, "Proxy[%s]::giveClientTo: no has client.\n", getScriptName());
PyErr_SetString(PyExc_TypeError, err);
PyErr_PrintEx(0);
onGiveClientToFailure();
return;
}
if(proxy)
{
EntityMailbox* mb = proxy->getClientMailbox();
if(mb != NULL)
{
ERROR_MSG("Proxy::giveClientTo: %s[%ld] give client to %s[%ld], %s have clientMailbox.",
getScriptName(),
getID(),
proxy->getScriptName(),
proxy->getID(),
proxy->getScriptName());
onGiveClientToFailure();
return;
}
if(getCellMailbox())
{
// 通知cell丢失客户端
Mercury::Bundle* pBundle = Mercury::Bundle::ObjPool().createObject();
(*pBundle).newMessage(CellappInterface::onLoseWitness);
getCellMailbox()->postMail((*pBundle));
Mercury::Bundle::ObjPool().reclaimObject(pBundle);
}
getClientMailbox()->addr(Mercury::Address::NONE);
Py_DECREF(getClientMailbox());
proxy->onGiveClientTo(lpChannel);
setClientMailbox(NULL);
addr(Mercury::Address::NONE);
}
}
std::string
RotoItem::getFullyQualifiedName() const
{
std::string name = getScriptName();
boost::shared_ptr<RotoLayer> parent = getParentLayer();
if (parent) {
getScriptNameRecursive(parent.get(), &name);
}
return name;
}
//-------------------------------------------------------------------------------------
bool Entity::navigateStep(const Position3D& destination, float velocity, float maxMoveDistance, float maxDistance,
bool faceMovement, float girth, PyObject* userData)
{
DEBUG_MSG(boost::format("Entity[%1%:%2%]:destination=(%3%,%4%,%5%), velocity=%6%, maxMoveDistance=%7%, "
"maxDistance=%8%, faceMovement=%9%, girth=%10%, userData=%11%.\n") %
getScriptName() % id_ % destination.x % destination.y % destination.z % velocity % maxMoveDistance %
maxDistance % faceMovement % girth % userData);
return true;
}
//-------------------------------------------------------------------------------------
PyObject* Base::createCellEntity(PyObject* pyobj)
{
if(isDestroyed())
{
PyErr_Format(PyExc_Exception, "%s::createCellEntity: %d is destroyed!\n",
getScriptName(), getID());
PyErr_PrintEx(0);
S_Return;
}
if(Baseapp::getSingleton().findEntity(getID()) == NULL)
{
PyErr_Format(PyExc_Exception, "%s::createCellEntity: %d not found!\n", getScriptName(), getID());
PyErr_PrintEx(0);
S_Return;
}
if(creatingCell_ || this->getCellMailbox())
{
PyErr_Format(PyExc_Exception, "%s::createCellEntity: %d has a cell!\n", getScriptName(), getID());
PyErr_PrintEx(0);
S_Return;
}
if(!PyObject_TypeCheck(pyobj, EntityMailbox::getScriptType()))
{
PyErr_Format(PyExc_TypeError, "create %s arg1 is not cellMailbox!", this->getScriptName());
PyErr_PrintEx(0);
S_Return;
}
EntityMailboxAbstract* cellMailbox = static_cast<EntityMailboxAbstract*>(pyobj);
if(cellMailbox->getType() != MAILBOX_TYPE_CELL)
{
PyErr_Format(PyExc_TypeError, "create %s args1 not is a direct cellMailbox!", this->getScriptName());
PyErr_PrintEx(0);
S_Return;
}
creatingCell_ = true;
Baseapp::getSingleton().createCellEntity(cellMailbox, this);
S_Return;
}
//-------------------------------------------------------------------------------------
void Base::onRemoteMethodCall(Mercury::Channel* pChannel, MemoryStream& s)
{
// 如果是外部通道调用则判断来源性
if(pChannel->isExternal())
{
ENTITY_ID srcEntityID = pChannel->proxyID();
if(srcEntityID <= 0 || srcEntityID != this->getID())
{
WARNING_MSG("Base::onRemoteMethodCall: srcEntityID:%d, thisEntityID:%d.\n", srcEntityID, this->getID());
return;
}
}
if(isDestroyed())
{
ERROR_MSG("%s::onRemoteMethodCall: %d is destroyed!\n",
getScriptName(), getID());
s.read_skip(s.opsize());
return;
}
ENTITY_METHOD_UID utype = 0;
s >> utype;
MethodDescription* md = scriptModule_->findBaseMethodDescription(utype);
if(md == NULL)
{
ERROR_MSG("Base::onRemoteMethodCall: can't found method. utype=%u, callerID:%d.\n", utype, id_);
return;
}
DEBUG_MSG("Base::onRemoteMethodCall: entityID:%d, methodType:%s(%u).\n",
id_, md->getName(), utype);
md->currCallerID(this->getID());
PyObject* pyFunc = PyObject_GetAttrString(this, const_cast<char*>
(md->getName()));
if(md != NULL)
{
PyObject* pyargs = md->createFromStream(&s);
if(pyargs)
{
md->call(pyFunc, pyargs);
Py_XDECREF(pyargs);
}
else
{
SCRIPT_ERROR_CHECK();
}
}
Py_XDECREF(pyFunc);
}
//-------------------------------------------------------------------------------------
PyObject* Proxy::pyGetTimeSinceHeardFromClient()
{
if(isDestroyed())
{
PyErr_Format(PyExc_AssertionError, "%s: %d is destroyed!\n",
getScriptName(), getID());
PyErr_PrintEx(0);
return 0;
}
return PyFloat_FromDouble(this->getTimeSinceHeardFromClient());
}
//-------------------------------------------------------------------------------------
PyObject* Base::createInNewSpace(PyObject* params)
{
if(isDestroyed())
{
PyErr_Format(PyExc_Exception, "%s::createInNewSpace: %d is destroyed!\n",
getScriptName(), getID());
PyErr_PrintEx(0);
S_Return;
}
if(createdSpace_)
{
PyErr_Format(PyExc_Exception, "%s::createInNewSpace: %d has a space!\n", getScriptName(), getID());
PyErr_PrintEx(0);
S_Return;
}
createdSpace_ = true;
Baseapp::getSingleton().createInNewSpace(this, params);
S_Return;
}
static void genePredOptions(struct trackDb *track, char *type,
struct sqlConnection *conn)
/* Put up sequence type options for gene prediction tracks. */
{
char *predType = cartUsualString(cart, hgtaGeneSeqType, genePredMenu[0]);
char *dupType = cloneString(type);
char *typeWords[3];
int typeWordCount, typeIx;
/* Type field has 1-3 words which are in order:
* genePred pepTable mrnaTable */
typeWordCount = chopLine(dupType, typeWords);
/* TypeIx will be 0 (genomic) 1 (protein) 2(mrna). */
typeIx = stringArrayIx(predType, genePredMenu, typeWordCount);
if (typeIx < 0)
predType = genePredMenu[0];
htmlOpen("Select sequence type for %s", track->shortLabel);
hPrintf("<FORM ACTION=\"%s\" METHOD=GET>\n", getScriptName());
cartSaveSession(cart);
if (isRefGeneTrack(track->table))
{
/* RefGene covers all 3 types, but in it's own way. */
for (typeIx = 0; typeIx < 3; ++typeIx)
{
genePredTypeButton(genePredMenu[typeIx], predType);
hPrintf(" %s<BR>\n", genePredMenu[typeIx]);
}
}
else
{
/* Otherwise we always have genomic, and we have
* peptide/mrna only if there are corresponding table
* in the type field. */
for (typeIx = 0; typeIx < typeWordCount; ++typeIx)
{
if (typeIx == 0 || sqlTableExists(conn, typeWords[typeIx]))
{
genePredTypeButton(genePredMenu[typeIx], predType);
hPrintf(" %s<BR>\n", genePredMenu[typeIx]);
}
}
}
cgiMakeButton(hgtaDoGenePredSequence, "submit");
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
hPrintf("</FORM>\n");
cgiDown(0.9);
htmlClose();
freez(&dupType);
}
BOOL CModuleType::save()
{
char sysDirScripts [FILE_MAX_PATHLEN];
char sysDirModules [FILE_MAX_PATHLEN];
char sysDirIcons [FILE_MAX_PATHLEN];
if (RegKeyGetValue(REGKEY_SECTION_PATHNAME, REGKEY_KEY_SCRIPTS_PATHNAME, sysDirScripts) == FALSE)
strcpy(sysDirScripts, "scripts\\");
if (RegKeyGetValue(REGKEY_SECTION_PATHNAME, REGKEY_KEY_MODULES_PATHNAME, sysDirModules) == FALSE)
strcpy(sysDirModules, "modules\\");
if (RegKeyGetValue(REGKEY_SECTION_PATHNAME, REGKEY_KEY_ICONS_PATHNAME, sysDirIcons) == FALSE)
strcpy(sysDirIcons, "icons\\");
char outFnameScripts [FILE_MAX_FILENAME];
char outFnameModules [FILE_MAX_FILENAME];
char outFnameIcons [FILE_MAX_FILENAME];
sprintf(outFnameModules, "%s%s%s.%s", sysDirModules, getClassName(), getName(), MODULE_FILE_EXTENTION);
strcpy(outFnameScripts, getScriptName()); FileChangePathName(outFnameScripts, sysDirScripts);
sprintf(outFnameIcons, "%s%s%s.%s", sysDirIcons, getClassName(), getName(), ICON_FILE_EXTENTION);
// Copy a icon and script files into system directry.
BOOL bCopiedScriptFile = FileCopy(getScriptName(), outFnameScripts);
BOOL bCopiedIconFile = FileCopy(getIconName(), outFnameIcons);
if (!bCopiedScriptFile || !bCopiedIconFile)
return FALSE;
// Strip the directory name in a icon and scrpit file name.
char scriptFilename [FILE_MAX_FILENAME];
char iconFilename [FILE_MAX_FILENAME];
strcpy(scriptFilename, getScriptName()); FileStripPathName(scriptFilename); setScriptName(scriptFilename);
sprintf(iconFilename, "%s%s.%s", getClassName(), getName(), ICON_FILE_EXTENTION); setIconName(iconFilename);
// Save this module infomation into a file
return save(outFnameModules);
}
BOOL CModuleType::save(char *fname)
{
if (!isOK())
return FALSE;
ofstream fout(fname);
if (!fout)
return FALSE;
fout << "#CTB MODULETYPE V1.0" << endl;
fout << "CLASSNAME " << ((getClassName() && strlen(getClassName()) > 0) ? getClassName() : "NULL") << endl;
fout << "MODULENAME " << ((getName() && strlen(getName()) > 0) ? getName() : "NULL") << endl;
fout << "ATTRIBUTE " << ((getAttribure() == MODULETYPE_ATTRIBUTE_SYSTEM) ? "SYSTEM" : "USER") << endl;
fout << "SCRIPTNAME " << ((getScriptName() && strlen(getScriptName()) > 0) ? getScriptName() : "NULL") << endl;
fout << "ICONNAME " << ((getIconName() && strlen(getIconName()) > 0) ? getIconName() : "NULL") << endl;
int n;
for (n=0; n<MODULE_INOUTNODE_MAXNUM; n++) {
char *fieldTypeName = mEventInType[n]->getTypeName();
char *fieldName = mEventInType[n]->getName();
fout << "EVENTIN" << n << " " << (fieldTypeName ? fieldTypeName : "NULL") << " " << (fieldName ? fieldName : "NULL") << endl;
}
for (n=0; n<MODULE_INOUTNODE_MAXNUM; n++) {
char *fieldTypeName = mEventOutType[n]->getTypeName();
char *fieldName = mEventOutType[n]->getName();
fout << "EVENTOUT" << n << " " << (fieldTypeName ? fieldTypeName : "NULL") << " " << (fieldName ? fieldName : "NULL") << endl;
}
fout << "EXECUTIONNODE " << (hasExecutionNode() ? "TRUE" : "FALSE") << endl;
/*
fout << "TARGETNODE " << getTargetNodeFieldTypeName() << " " << getTargetNodeFieldName() << endl;
*/
return TRUE;
}
//-------------------------------------------------------------------------------------
void Entity::onRemoteMethodCall(Mercury::Channel* pChannel, MemoryStream& s)
{
SCOPED_PROFILE(SCRIPTCALL_PROFILE);
if(isDestroyed())
{
ERROR_MSG(boost::format("%1%::onRemoteMethodCall: %2% is destroyed!\n") %
getScriptName() % getID());
s.read_skip(s.opsize());
return;
}
ENTITY_METHOD_UID utype = 0;
s >> utype;
DEBUG_MSG(boost::format("Entity::onRemoteMethodCall: entityID %1%, methodType %2%.\n") %
id_ % utype);
MethodDescription* md = scriptModule_->findCellMethodDescription(utype);
if(md == NULL)
{
ERROR_MSG(boost::format("Entity::onRemoteMethodCall: can't found method. utype=%1%, callerID:%2%.\n") % utype % id_);
return;
}
md->currCallerID(this->getID());
PyObject* pyFunc = PyObject_GetAttrString(this, const_cast<char*>
(md->getName()));
if(md != NULL)
{
PyObject* pyargs = md->createFromStream(&s);
if(pyargs)
{
md->call(pyFunc, pyargs);
Py_XDECREF(pyargs);
}
else
{
SCRIPT_ERROR_CHECK();
}
}
Py_XDECREF(pyFunc);
}
NATRON_NAMESPACE_ENTER
void
TabWidgetI::toSerialization(SERIALIZATION_NAMESPACE::SerializationObjectBase* serializationBase)
{
SERIALIZATION_NAMESPACE::TabWidgetSerialization* serialization = dynamic_cast<SERIALIZATION_NAMESPACE::TabWidgetSerialization*>(serializationBase);
if (!serialization) {
return;
}
serialization->tabs = getTabScriptNames();
serialization->scriptName = getScriptName();
serialization->isAnchor = isAnchor();
serialization->currentIndex = activeIndex();
}
//-------------------------------------------------------------------------------------
PyObject* Proxy::pyGetEntitiesEnabled()
{
if(isDestroyed())
{
PyErr_Format(PyExc_AssertionError, "%s: %d is destroyed!\n",
getScriptName(), getID());
PyErr_PrintEx(0);
return 0;
}
if(this->entitiesEnabled())
{
Py_RETURN_TRUE;
}
Py_RETURN_FALSE;
}
//-------------------------------------------------------------------------------------
PyObject* Base::pyGetClientMailbox()
{
if(isDestroyed())
{
PyErr_Format(PyExc_Exception, "%s: %d is destroyed!\n",
getScriptName(), getID());
PyErr_PrintEx(0);
S_Return;
}
EntityMailbox* mailbox = getClientMailbox();
if(mailbox == NULL)
S_Return;
Py_INCREF(mailbox);
return mailbox;
}
//-------------------------------------------------------------------------------------
PyObject* Proxy::pyGiveClientTo(PyObject* pyOterProxy)
{
if(this->isDestroyed())
{
PyErr_Format(PyExc_AssertionError, "%s: %d is destroyed!\n",
getScriptName(), getID());
PyErr_PrintEx(0);
return 0;
}
// 如果为None 则设置为NULL
Proxy* oterProxy = NULL;
if(pyOterProxy != Py_None)
oterProxy = static_cast<Proxy*>(pyOterProxy);
giveClientTo(oterProxy);
S_Return;
}
void CGI::logCGIData(const QString& filename)
{
// create a QFile object to do the file I/O
QFile file(filename);
// open the file
if (file.open(QIODevice::WriteOnly))
{
// create a QTextStream object on the file
Q3TextStream textFile(&file);
// get the environment
textFile << "REQUEST_METHOD=" << getenv("REQUEST_METHOD") << endl;
textFile << "CONTENT_LENGTH=" << getenv("CONTENT_LENGTH") << endl;
// write the query string to the file
textFile << "QUERY_STRING=" << query_string << endl;
// write misc. CGI environment pieces
textFile << "AUTH_TYPE=" << getAuthType() << endl;
textFile << "GATEWAY_INTERFACE=" << getGatewayInterface() << endl;
textFile << "HTTP_ACCEPT=" << getHTTPAccept() << endl;
textFile << "HTTP_ACCEPT_ENCODING=" << getHTTPAcceptEncoding() << endl;
textFile << "HTTP_ACCEPT_LANGUAGE=" << getHTTPAcceptLanguage() << endl;
textFile << "HTTP_CONNECTION=" << getHTTPConnection() << endl;
textFile << "HTTP_REFERER=" << getHTTPReferer() << endl;
textFile << "HTTP_USER_AGENT=" << getHTTPUserAgent() << endl;
textFile << "REMOTE_HOST=" << getRemoteHost() << endl;
textFile << "REMOTE_ADDRESS=" << getRemoteAddress() << endl;
textFile << "REMOTE_PORT=" << getRemotePort() << endl;
textFile << "REQUEST_URI=" << getRequestURI() << endl;
textFile << "SCRIPT_NAME=" << getScriptName() << endl;
textFile << "SERVER_ADMIN=" << getServerAdmin() << endl;
textFile << "SERVER_NAME=" << getServerName() << endl;
textFile << "SERVER_PORT=" << getServerPort() << endl;
textFile << "SERVER_PROTOCOL=" << getServerProtocol() << endl;
textFile << "SERVER_SOFTWARE=" << getServerSoftware() << endl;
}
// close the file
file.close();
}
void doPasteIdentifiers(struct sqlConnection *conn)
/* Respond to paste identifiers button. */
{
struct sqlConnection *alternateConn = conn;
char *actualDb = database;
if (sameWord(curTable, WIKI_TRACK_TABLE))
{
alternateConn = wikiConnect();
actualDb = wikiDbName();
}
char *oldPasted = forCurTable() ?
cartUsualString(cart, hgtaPastedIdentifiers, "") : "";
struct hTableInfo *hti = maybeGetHti(actualDb, curTable, conn);
char *idField = getIdField(actualDb, curTrack, curTable, hti);
htmlOpen("Paste In Identifiers for %s", curTableLabel());
if (idField == NULL)
errAbort("Sorry, I can't tell which field of table %s to treat as the "
"identifier field.", curTable);
hPrintf("<FORM ACTION=\"%s\" METHOD=%s>\n", getScriptName(),
cartUsualString(cart, "formMethod", "POST"));
cartSaveSession(cart);
hPrintf("Please paste in the identifiers you want to include.\n");
if (sqlDatabaseExists("hgTemp"))
explainIdentifiers(actualDb, alternateConn, idField);
else
warn("No hgTemp database found for temporary tables.<br>Please src/product/README.mysql.setup for more information.");
hPrintf("<BR>\n");
cgiMakeTextArea(hgtaPastedIdentifiers, oldPasted, 10, 70);
hPrintf("<BR>\n");
cgiMakeButton(hgtaDoPastedIdentifiers, "submit");
hPrintf(" ");
cgiMakeButton(hgtaDoClearPasteIdentifierText, "clear");
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
hPrintf("</FORM>");
cgiDown(0.9);
htmlClose();
if (sameWord(curTable, WIKI_TRACK_TABLE))
wikiDisconnect(&alternateConn);
}
//-------------------------------------------------------------------------------------
PyObject* Base::pyDestroyEntity()
{
if(isDestroyed())
{
PyErr_Format(PyExc_Exception, "%s::destroy: %d is destroyed!\n",
getScriptName(), getID());
PyErr_PrintEx(0);
S_Return;
}
if(creatingCell_ || cellMailbox_ != NULL)
{
PyErr_Format(PyExc_Exception, "%s::destroy: id:%i has cell! creatingCell=%s\n", this->getScriptName(), this->getID(),
creatingCell_ ? "true" : "false");
PyErr_PrintEx(0);
}
else
destroyEntity();
S_Return;
}
//-------------------------------------------------------------------------------------
uint16 Entity::addProximity(float range)
{
if(range <= 0.0f)
{
ERROR_MSG(boost::format("Entity::addProximity: range(%1%) <= 0.0f! entity[%2%:%3%]\n") %
range % getScriptName() % getID());
return 0;
}
// 不允许范围大于cell边界
if(range > CELL_BORDER_WIDTH)
range = CELL_BORDER_WIDTH;
/*
// 在space中投放一个陷阱
Proximity* p = new Proximity(this, range, 0.0f);
trapMgr_.addProximity(p);
if(currChunk_ != NULL)
currChunk_->getSpace()->placeProximity(currChunk_, p);
return p->getID();*/
return 0;
}
void describeFields(char *db, char *table,
struct asObject *asObj, struct sqlConnection *conn)
/* Print out an HTML table showing table fields and types, and optionally
* offering histograms for the text/enum fields. */
{
struct sqlResult *sr;
char **row;
#define TOO_BIG_FOR_HISTO 500000
boolean tooBig = (sqlTableSize(conn, table) > TOO_BIG_FOR_HISTO);
char query[256];
struct slName *exampleList, *example;
boolean showItemRgb = FALSE;
showItemRgb=bedItemRgb(findTdbForTable(db, curTrack, table, ctLookupName));
// should we expect itemRgb instead of "reserved"
sqlSafef(query, sizeof(query), "select * from %s limit 1", table);
exampleList = storeRow(conn, query);
sqlSafef(query, sizeof(query), "describe %s", table);
sr = sqlGetResult(conn, query);
hTableStart();
hPrintf("<TR><TH>field</TH>");
if (exampleList != NULL)
hPrintf("<TH>example</TH>");
hPrintf("<TH>SQL type</TH> ");
if (!tooBig)
hPrintf("<TH>info</TH> ");
if (asObj != NULL)
hPrintf("<TH>description</TH> ");
puts("</TR>\n");
example = exampleList;
while ((row = sqlNextRow(sr)) != NULL)
{
if (showItemRgb && (sameWord(row[0],"reserved")))
hPrintf("<TR><TD><TT>itemRgb</TT></TD> ");
else
hPrintf("<TR><TD><TT>%s</TT></TD> ", row[0]);
if (exampleList != NULL)
{
hPrintf("<TD>");
if (example != NULL)
hPrintf("%s", cleanExample(example->name));
else
hPrintf("n/a");
hPrintf("</TD>");
}
// enums/sets with many items can make for painfully wide rows in the table --
// add spaces between quoted list values:
if (stringIn("','", row[1]))
{
struct dyString *spaced = dyStringSub(row[1], "','", "', '");
hPrintf("<TD><TT>%s</TT></TD>", spaced->string);
}
else
hPrintf("<TD><TT>%s</TT></TD>", row[1]);
if (!tooBig)
{
hPrintf(" <TD>");
if ((isSqlStringType(row[1]) && !sameString(row[1], "longblob")) ||
isSqlEnumType(row[1]) || isSqlSetType(row[1]))
{
hPrintf("<A HREF=\"%s", getScriptName());
hPrintf("?%s", cartSidUrlString(cart));
hPrintf("&%s=%s", hgtaDatabase, db);
hPrintf("&%s=%s", hgtaHistoTable, table);
hPrintf("&%s=%s", hgtaDoValueHistogram, row[0]);
hPrintf("\">");
hPrintf("values");
hPrintf("</A>");
}
else if (isSqlNumType(row[1]))
{
hPrintf("<A HREF=\"%s", getScriptName());
hPrintf("?%s", cartSidUrlString(cart));
hPrintf("&%s=%s", hgtaDatabase, db);
hPrintf("&%s=%s", hgtaHistoTable, table);
hPrintf("&%s=%s", hgtaDoValueRange, row[0]);
hPrintf("\">");
hPrintf("range");
hPrintf("</A>");
}
else
{
hPrintf(" ");
}
hPrintf("</TD>");
}
if (asObj != NULL)
{
struct asColumn *asCol = asColumnFind(asObj, row[0]);
hPrintf(" <TD>");
if (asCol != NULL)
hPrintf("%s", asCol->comment);
else
{
if (sameString("bin", row[0]))
hPrintf("Indexing field to speed chromosome range queries.");
else
hPrintf(" ");
}
hPrintf("</TD>");
}
puts("</TR>");
if (example != NULL)
example = example->next;
}
hTableEnd();
sqlFreeResult(&sr);
}
void doBedOrCtOptions(char *table, struct sqlConnection *conn,
boolean doCt)
/* Put up form to get options on BED or custom track output. */
/* (Taken from hgText.c/doBedCtOptions) */
{
char *table2 = NULL; /* For now... */
struct hTableInfo *hti = getHti(database, table, conn);
char buf[256];
char *setting;
htmlOpen("Output %s as %s", table, (doCt ? "Custom Track" : "BED"));
if (doGalaxy())
startGalaxyForm();
else if (doGreat())
{
verifyGreatAssemblies();
startGreatForm();
}
else
hPrintf("<FORM ACTION=\"%s\" METHOD=GET>\n", getScriptName());
cartSaveSession(cart);
if (!doGreat())
{
hPrintf("%s\n", "<TABLE><TR><TD>");
if (doCt)
{
hPrintf("%s\n", "</TD><TD>"
"<A HREF=\"../goldenPath/help/customTrack.html\" TARGET=_blank>"
"Custom track</A> header: </B>");
}
else
{
cgiMakeCheckBox(hgtaPrintCustomTrackHeaders,
cartCgiUsualBoolean(cart, hgtaPrintCustomTrackHeaders, FALSE));
hPrintf("%s\n", "</TD><TD> <B> Include "
"<A HREF=\"../goldenPath/help/customTrack.html\" TARGET=_blank>"
"custom track</A> header: </B>");
}
hPrintf("%s\n", "</TD></TR><TR><TD></TD><TD>name=");
safef(buf, sizeof(buf), "tb_%s", hti->rootName);
setting = cgiUsualString(hgtaCtName, buf);
cgiMakeTextVar(hgtaCtName, setting, 16);
hPrintf("%s\n", "</TD></TR><TR><TD></TD><TD>description=");
safef(buf, sizeof(buf), "table browser query on %s%s%s",
table, (table2 ? ", " : ""), (table2 ? table2 : ""));
setting = cgiUsualString(hgtaCtDesc, buf);
cgiMakeTextVar(hgtaCtDesc, setting, 50);
hPrintf("%s\n", "</TD></TR><TR><TD></TD><TD>visibility=");
if (isWiggle(database, table) || isBigWigTable(table))
{
setting = cartCgiUsualString(cart, hgtaCtVis, ctVisWigMenu[2]);
cgiMakeDropList(hgtaCtVis, ctVisWigMenu, ctVisWigMenuSize, setting);
}
else
{
setting = cartCgiUsualString(cart, hgtaCtVis, ctVisMenu[3]);
cgiMakeDropList(hgtaCtVis, ctVisMenu, ctVisMenuSize, setting);
}
hPrintf("%s\n", "</TD></TR><TR><TD></TD><TD>url=");
setting = cartCgiUsualString(cart, hgtaCtUrl, "");
cgiMakeTextVar(hgtaCtUrl, setting, 50);
hPrintf("%s\n", "</TD></TR><TR><TD></TD><TD>");
hPrintf("%s\n", "</TD></TR></TABLE>");
}
if (isWiggle(database, table) || isBedGraph(table) || isBigWigTable(table) )
{
char *setting = NULL;
hPrintf("<P> <B> Select type of data output: </B> <BR>\n");
setting = cartCgiUsualString(cart, hgtaCtWigOutType, outWigData);
cgiMakeRadioButton(hgtaCtWigOutType, outWigBed, sameString(setting, outWigBed));
hPrintf("BED format (no data value information, only position)<BR>\n");
cgiMakeRadioButton(hgtaCtWigOutType, outWigData, sameString(setting, outWigData));
hPrintf("DATA VALUE format (position and real valued data)</P>\n");
}
else
{
cgiDown(0.9);
hPrintf("<B> Create one BED record per: </B>\n");
if ((anyIntersection() && intersectionIsBpWise()) ||
(anySubtrackMerge(database, table) && subtrackMergeIsBpWise()))
{
/* The original table may have blocks/CDS, described in hti, but
* that info will be lost after base pair-wise operations. So make
* a temporary copy of hti with its flags tweaked: */
struct hTableInfo simplifiedHti;
memcpy(&simplifiedHti, hti, sizeof(simplifiedHti));
simplifiedHti.hasBlocks = FALSE;
simplifiedHti.hasCDS = FALSE;
fbOptionsHtiCart(&simplifiedHti, cart);
}
else
fbOptionsHtiCart(hti, cart);
}
if (doCt)
{
if (doGalaxy())
{
/* send the action parameter with the form as well */
cgiMakeHiddenVar(hgtaDoGetCustomTrackFile, "get custom track in file");
printGalaxySubmitButtons();
}
else
{
cgiMakeButton(hgtaDoGetCustomTrackTb, "get custom track in table browser");
hPrintf(" ");
cgiMakeButton(hgtaDoGetCustomTrackFile, "get custom track in file");
hPrintf("<BR>\n");
cgiMakeButton(hgtaDoGetCustomTrackGb, "get custom track in genome browser");
}
}
else
{
if (doGalaxy())
{
cgiMakeHiddenVar(hgtaDoGetBed, "get BED");
printGalaxySubmitButtons();
}
else if (doGreat())
{
cgiMakeHiddenVar(hgtaDoGetBed, "get BED");
printGreatSubmitButtons();
}
else
cgiMakeButton(hgtaDoGetBed, "get BED");
}
if (!doGalaxy() && !doGreat())
{
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
hPrintf("</FORM>\n");
}
cgiDown(0.9);
htmlClose();
}
void startGreatForm()
/* Start form for GREAT */
{
hPrintf("<FORM ACTION=\"%s\" NAME='greatForm' METHOD=POST>\n", getScriptName());
}
void doIntersectMore(struct sqlConnection *conn)
/* Continue working in intersect page. */
{
struct trackDb *iTrack;
char *name = curTableLabel();
char *iName, *iTable;
char *onChange = onChangeEither();
char *op, *setting;
boolean wigOptions = (isWiggle(database, curTable) || isBedGraph(curTable));
// Note - bigWig is purposely left out of wigOptions. It supports more intersection options
// than wig does.
struct hTableInfo *hti1 = maybeGetHti(database, curTable, conn), *hti2 = NULL;
htmlOpen("Intersect with %s", name);
hPrintf("<FORM ACTION=\"%s\" NAME=\"mainForm\" METHOD=GET>\n", getScriptName());
cartSaveSession(cart);
hPrintf("<TABLE BORDER=0>\n");
/* Print group and track line. */
hPrintf("Select a group, track and table to intersect with:\n");
iTrack = showGroupTrackRow(hgtaNextIntersectGroup, onChange,
hgtaNextIntersectTrack, onChange, conn);
iName = iTrack->shortLabel;
hPrintf("<TR><TD>\n");
iTable = showTableField(iTrack, hgtaNextIntersectTable, FALSE);
hti2 = maybeGetHti(database, iTable, conn);
hPrintf("</TD></TR>\n");
hPrintf("</TABLE>\n");
if (!wigOptions)
{
if (hti1 && hti1->hasBlocks)
hPrintf("<BR>Note: %s has gene/alignment structure. "
"Only the exons/blocks will be considered.\n", name);
if (hti2 && hti2->hasBlocks)
hPrintf("<BR>Note: %s has gene/alignment structure. "
"Only the bases covered by its exons/blocks will be "
"considered.\n", iName);
hPrintf("<H4>Intersect %s items with bases covered by %s:</H4>\n",
name, iName);
hPrintf("These combinations will maintain the names and "
"gene/alignment structure (if any) of %s: <P>\n",
name);
}
else
hPrintf("<P>\n");
op = cartUsualString(cart, hgtaNextIntersectOp, "any");
jsTrackingVar("op", op);
makeOpButton("any", op);
printf("All %s records that have any overlap with %s <BR>\n",
name, iName);
makeOpButton("none", op);
printf("All %s records that have no overlap with %s <BR>\n",
name, iName);
if (!wigOptions)
{
makeOpButton("more", op);
printf("All %s records that have at least ",
name);
setting = cartCgiUsualString(cart, hgtaNextMoreThreshold, "80");
cgiMakeTextVar(hgtaNextMoreThreshold, setting, 3);
printf(" %% overlap with %s <BR>\n", iName);
makeOpButton("less", op);
printf("All %s records that have at most ",
name);
setting = cartCgiUsualString(cart, hgtaNextLessThreshold, "80");
cgiMakeTextVar(hgtaNextLessThreshold, setting, 3);
printf(" %% overlap with %s <P>\n", iName);
}
else
{
/* keep javaScript onClick happy */
hPrintf("<input TYPE=HIDDEN NAME=\"hgta_nextMoreThreshold\" VALUE=80>\n");
hPrintf("<input TYPE=HIDDEN NAME=\"hgta_nextLessThreshold\" VALUE=80>\n");
hPrintf(" <P>\n");
}
if (!wigOptions)
{
boolean bigWig = isBigWigTable(curTable);
hPrintf("<H4>Intersect bases covered by %s and/or %s:</H4>\n",
name, iName);
if (!bigWig)
hPrintf("These combinations will discard the names and "
"gene/alignment structure (if any) of %s and produce a simple "
"list of position ranges.<P>\n",
name);
makeOpButton("and", op);
printf("Base-pair-wise intersection (AND) of %s and %s <BR>\n",
name, iName);
makeOpButton("or", op);
printf("Base-pair-wise union (OR) of %s and %s <P>\n",
name, iName);
hPrintf("Check the following boxes to complement one or both tables. "
"To complement a table means to include a base pair in the "
"intersection/union if it is <I>not</I> included in the table."
"<P>\n");
if (!bigWig)
{
jsMakeTrackingCheckBox(cart, hgtaNextInvertTable, "invertTable", FALSE);
printf("Complement %s before base-pair-wise intersection/union <BR>\n",
name);
}
jsMakeTrackingCheckBox(cart, hgtaNextInvertTable2, "invertTable2", FALSE);
printf("Complement %s before base-pair-wise intersection/union <P>\n",
iName);
}
else
{
/* keep javaScript onClick happy */
jsTrackingVar("op", op);
hPrintf("<SCRIPT>\n");
hPrintf("var invertTable=0;\n");
hPrintf("var invertTable2=0;\n");
hPrintf("</SCRIPT>\n");
hPrintf("(data track %s is not composed of gene records. Specialized intersection operations are not available.)<P>\n", name);
}
cgiMakeButton(hgtaDoIntersectSubmit, "submit");
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
hPrintf("</FORM>\n");
/* Hidden form - for benefit of javascript. */
{
static char *saveVars[32];
int varCount = ArraySize(nextVars);
memcpy(saveVars, nextVars, varCount * sizeof(saveVars[0]));
saveVars[varCount] = hgtaDoIntersectMore;
jsCreateHiddenForm(cart, getScriptName(), saveVars, varCount+1);
}
htmlClose();
}