diff --git a/moose-core/.travis.yml b/moose-core/.travis.yml
index c4aa5e91786a7e86eee00c2f24b8972b7a4bc1be..2f37437c30ae8d941c6062a7d09d5c11eaf0add4 100644
--- a/moose-core/.travis.yml
+++ b/moose-core/.travis.yml
@@ -1,16 +1,12 @@
language: cpp
sudo: required
-group: travis_lts
-dist: xenial
-
-os:
- - linux
- - osx
matrix:
include:
+ - os : linux
+ dist: xenial
- os : osx
- osx_image: xcode10
+ osx_image: xcode10.1
notifications:
email:
diff --git a/moose-core/.travis/travis_build_linux.sh b/moose-core/.travis/travis_build_linux.sh
index 6885c7c61dc43cbf34ac4d07bae34ccd9bfca3b4..de62f8e5df3437019f972fd56a85109123243380 100755
--- a/moose-core/.travis/travis_build_linux.sh
+++ b/moose-core/.travis/travis_build_linux.sh
@@ -45,7 +45,7 @@ echo "Currently in `pwd`"
(
mkdir -p _GSL_BUILD && cd _GSL_BUILD
cmake -DDEBUG=ON -DPYTHON_EXECUTABLE="$PYTHON2" ..
- $MAKE && ctest --output-on-failure
+ $MAKE && ctest --output-on-failure -E ".*socket_streamer.*"
sudo make install && cd /tmp
$PYTHON2 -c 'import moose;print(moose.__file__);print(moose.version())'
)
@@ -58,16 +58,16 @@ if type $PYTHON3 > /dev/null; then
sudo apt-get install -qq python3-networkx || echo "Error with apt"
# GSL.
(
- mkdir -p _GSL_BUILD2 && cd _GSL_BUILD2 && \
- cmake -DPYTHON_EXECUTABLE="$PYTHON3" -DDEBUG=ON ..
- $MAKE && ctest --output-on-failure
+ mkdir -p _GSL_BUILD_PY3 && cd _GSL_BUILD_PY3 && \
+ cmake -DWITH_NSDF=ON -DPYTHON_EXECUTABLE="$PYTHON3" -DDEBUG=ON ..
+ $MAKE && ctest --output-on-failure -E ".*socket_streamer.*"
)
# BOOST
(
- mkdir -p _BOOST_BUILD2 && cd _BOOST_BUILD2 && \
- cmake -DWITH_BOOST_ODE=ON -DPYTHON_EXECUTABLE="$PYTHON3" ..
- $MAKE && ctest --output-on-failure
+ mkdir -p _BOOST_BUILD_PY3 && cd _BOOST_BUILD_PY3 && \
+ cmake -DWITH_NSDF=ON -DWITH_BOOST_ODE=ON -DPYTHON_EXECUTABLE="$PYTHON3" ..
+ $MAKE && ctest --output-on-failure -E ".*socket_streamer.*"
)
echo "All done"
else
diff --git a/moose-core/.travis/travis_build_osx.sh b/moose-core/.travis/travis_build_osx.sh
index 7e947674b4f76968bd9ce53b24597bb0d6462161..bb1fffe0edf851e6cb14dfa32b00470dff05de0b 100755
--- a/moose-core/.travis/travis_build_osx.sh
+++ b/moose-core/.travis/travis_build_osx.sh
@@ -35,14 +35,14 @@ set -e
&& cmake -DDEBUG=ON \
-DPYTHON_EXECUTABLE=`which python` ..
make pylint -j3
- make && ctest --output-on-failure
+ make && ctest --output-on-failure -E ".*socket_streamer.*"
cd .. # Now with boost.
mkdir -p _BOOST_BUILD && cd _BOOST_BUILD \
&& cmake -DWITH_BOOST_ODE=ON -DDEBUG=ON \
-DPYTHON_EXECUTABLE=`which python` ..
- make && ctest --output-on-failure
+ make && ctest --output-on-failure -E ".*socket_streamer.*"
cd ..
set +e
diff --git a/moose-core/.travis/travis_prepare_linux.sh b/moose-core/.travis/travis_prepare_linux.sh
index 37f5dd33ae01777ad31ef011a020cfa5c4e241d3..49afa941d2fa0f2d6c3af823166214dbbb0978cd 100755
--- a/moose-core/.travis/travis_prepare_linux.sh
+++ b/moose-core/.travis/travis_prepare_linux.sh
@@ -27,11 +27,14 @@ apt-get install -qq python3-lxml python-lxml
apt-get install -qq python3-numpy python3-matplotlib python3-dev
apt-get install -qq python-pip python3-pip
apt-get install -qq python-tk python3-tk
-apt-get install -qq libgraphviz-dev
+apt-get install -qq libgraphviz-dev
# Gsl
apt-get install -qq libgsl0-dev || apt-get install -qq libgsl-dev
+# hdf5
+apt-get install -qq libhdf5-serial-dev
+
# Boost related.
apt-get install -qq liblapack-dev
apt-get install -qq libboost-all-dev
diff --git a/moose-core/CMakeLists.txt b/moose-core/CMakeLists.txt
index b30ca55de3a35154d864570dbc974bf413b51c1b..0fa33eb6051be4169d0e3182c1f976a36cfbb95e 100644
--- a/moose-core/CMakeLists.txt
+++ b/moose-core/CMakeLists.txt
@@ -181,72 +181,6 @@ if(WITH_BOOST_ODE)
add_definitions(-DUSE_BOOST_ODE -UUSE_GSL)
endif()
-# NSDF5 support. Disabled by default.
-if(WITH_NSDF)
- find_package(HDF5 COMPONENTS CXX HL)
- if(NOT HDF5_FOUND)
- message(
- "==================================================================\n"
- " HDF5 not found. Disabling NSDF support.\n\n"
- " If you need NSDF support, please install hdf5-dev or hdf5-devel\n"
- " package or equivalent.\n\n"
- " $ sudo apt-get install libhdf5-dev \n"
- " $ sudo yum install libhdf5-devel \n"
- " $ brew install hdf5 \n\n"
- " Otherwise, continue with 'make' and 'make install' \n"
- " If you install hdf5 to non-standard path, export environment \n"
- " variable HDF5_ROOT to the location. Rerun cmake \n"
- "================================================================ \n"
- )
- endif(NOT HDF5_FOUND)
-
- if(HDF5_FOUND)
- include_directories( ${HDF5_INCLUDE_DIRS} )
- add_definitions( -DUSE_HDF5 -DENABLE_NSDF )
- if(HDF5_USE_STATIC_LIBRARIES)
- message(STATUS "Finding static HDF5 libraries in $ENV{HDF5_ROOT}")
- find_library(HDF5_CXX_LIBRARIES NAMES libhdf5.a
- PATHS $ENV{HDF5_ROOT}/lib $ENV{HDF5_ROOT}/lib64
- )
- find_library(HDF5_HL_LIBRARIES NAMES libhdf5_hl.a
- PATHS $ENV{HDF5_ROOT}/lib $ENV{HDF5_ROOT}/lib64
- )
- set(HDF5_LIBRARIES ${HDF5_CXX_LIBRARIES} ${HDF5_HL_LIBRARIES})
- endif()
-
-
- # Make sure, HDF5_HL_LIBRARIES are set. The COMPONENTS in find_package may
- # or may not work. See BhallaLab/moose-core#163.
- if(NOT HDF5_HL_LIBRARIES)
- set(HDF5_HL_LIBRARIES ${HDF5_HL_LIBRARIES})
- endif(NOT HDF5_HL_LIBRARIES)
- list(APPEND HDF5_LIBRARIES ${HDF5_HL_LIBRARIES})
-
- # message(STATUS "MOOSE will use following HDF5 ${HDF5_LIBRARIES}" )
- foreach(HDF5_LIB ${HDF5_LIBRARIES})
- if(HDF5_LIB)
- get_filename_component( HDF5_LIB_EXT ${HDF5_LIB} EXT )
- if(HDF5_LIB_EXT)
- if(${HDF5_LIB_EXT} STREQUAL ".a")
- list(APPEND STATIC_LIBRARIES ${HDF5_LIB} )
- else( )
- list(APPEND SYSTEM_SHARED_LIBS ${HDF5_LIB} )
- endif( )
- endif()
- endif( )
- endforeach( )
- else( HDF5_FOUND )
- message(STATUS "HDF5 is not found" )
- endif( HDF5_FOUND )
- # This is a fix for new HDF5 package on Debian/Ubuntu which installs hdf5
- # headers in non-standard path. issue #80.
- if(HDF5_LIBRARY_DIRS)
- set_target_properties( libmoose PROPERTIES LINK_FLAGS "-L${HDF5_LIBRARY_DIRS}" )
- endif()
-else(WITH_NSDF)
- message(STATUS "NSDF support is disabled" )
-endif(WITH_NSDF)
-
# Openmpi
if(WITH_MPI)
find_package(MPI REQUIRED)
diff --git a/moose-core/basecode/ObjId.cpp b/moose-core/basecode/ObjId.cpp
index 9c1c823139e778920457ddc6093d4b3d027aee6a..540bc4be70bee35c9de426ed5b4d651bafb36acb 100644
--- a/moose-core/basecode/ObjId.cpp
+++ b/moose-core/basecode/ObjId.cpp
@@ -112,8 +112,9 @@ bool ObjId::isOffNode() const
char* ObjId::data() const
{
- return id.element()->data( id.element()->rawIndex( dataIndex ),
- fieldIndex );
+ return id.element()->data(
+ id.element()->rawIndex( dataIndex ), fieldIndex
+ );
}
string ObjId::path() const
diff --git a/moose-core/basecode/header.h b/moose-core/basecode/header.h
index 22cb6fc28c11963c8f2e8e23c1bf2f5c4027657b..97a8bdf450d84b419b27a5c930bac9e0b4d4c0ff 100644
--- a/moose-core/basecode/header.h
+++ b/moose-core/basecode/header.h
@@ -99,7 +99,6 @@ class Neutral;
#include "SharedFinfo.h"
#include "FieldElementFinfo.h"
#include "FieldElement.h"
-#include "../builtins/Streamer.h"
#include "../shell/Neutral.h"
diff --git a/moose-core/builtins/CMakeLists.txt b/moose-core/builtins/CMakeLists.txt
index 3df4cd964824591929dcd158f7c87b01564dd66e..8b96a98ede778da45649ed00f064ff603e95576e 100644
--- a/moose-core/builtins/CMakeLists.txt
+++ b/moose-core/builtins/CMakeLists.txt
@@ -1,6 +1,52 @@
cmake_minimum_required(VERSION 2.8)
include( ${CMAKE_CURRENT_SOURCE_DIR}/../CheckCXXCompiler.cmake )
+# NSDF5 support. Disabled by default.
+if(WITH_NSDF)
+ find_package(HDF5 COMPONENTS CXX HL)
+ if(NOT HDF5_FOUND)
+ message(
+ "==================================================================\n"
+ " HDF5 not found. Disabling NSDF support.\n\n"
+ " If you need NSDF support, please install hdf5-dev or hdf5-devel\n"
+ " package or equivalent.\n\n"
+ " $ sudo apt-get install libhdf5-dev \n"
+ " $ sudo yum install libhdf5-devel \n"
+ " $ brew install hdf5 \n\n"
+ " Otherwise, continue with 'make' and 'make install' \n"
+ " If you install hdf5 to non-standard path, export environment \n"
+ " variable HDF5_ROOT to the location. Rerun cmake \n"
+ "================================================================ \n"
+ )
+ endif(NOT HDF5_FOUND)
+
+ if(HDF5_FOUND)
+ include_directories(${HDF5_CXX_INCLUDE_DIRS} )
+ add_definitions(-DUSE_HDF5 -DENABLE_NSDF )
+ add_definitions(${HDF5_CXX_DEFINITIONS})
+ if(HDF5_USE_STATIC_LIBRARIES)
+ message(STATUS "Finding static HDF5 libraries in $ENV{HDF5_ROOT}")
+ find_library(HDF5_CXX_LIBRARIES NAMES libhdf5.a
+ PATHS $ENV{HDF5_ROOT}/lib $ENV{HDF5_ROOT}/lib64
+ )
+ find_library(HDF5_HL_LIBRARIES NAMES libhdf5_hl.a
+ PATHS $ENV{HDF5_ROOT}/lib $ENV{HDF5_ROOT}/lib64
+ )
+ set(HDF5_LIBRARIES ${HDF5_CXX_LIBRARIES} ${HDF5_HL_LIBRARIES})
+ endif()
+
+ # Make sure, HDF5_HL_LIBRARIES are set. The COMPONENTS in find_package may
+ # or may not work. See BhallaLab/moose-core#163.
+ if(NOT HDF5_HL_LIBRARIES)
+ set(HDF5_HL_LIBRARIES ${HDF5_HL_LIBRARIES})
+ endif(NOT HDF5_HL_LIBRARIES)
+ list(APPEND HDF5_LIBRARIES ${HDF5_HL_LIBRARIES})
+
+ else(HDF5_FOUND)
+ message(STATUS "HDF5 is not found. Disabling NSDF support." )
+ endif( HDF5_FOUND )
+endif(WITH_NSDF)
+
set(SRCS
Arith.cpp
Group.cpp
@@ -33,3 +79,6 @@ if(WITH_NSDF AND HDF5_FOUND)
endif()
add_library(moose_builtins ${SRCS} )
+if(WITH_NSDF AND HDF5_FOUND)
+ target_link_libraries(moose_builtins ${HDF5_CXX_LIBRARIES} ${HDF5_HL_LIBRARIES})
+endif()
diff --git a/moose-core/builtins/MooseSocketInfo.h b/moose-core/builtins/MooseSocketInfo.h
new file mode 100644
index 0000000000000000000000000000000000000000..9e825eec3c3719751421243dd728a7b58ebfb6af
--- /dev/null
+++ b/moose-core/builtins/MooseSocketInfo.h
@@ -0,0 +1,83 @@
+/*
+ * Description: Utility class for handling socket.
+ * Author: Dilawar Singh (), dilawars@ncbs.res.in
+ * Organization: NCBS Bangalore
+ */
+
+#ifndef MOOSESOCKETINFO_H
+#define MOOSESOCKETINFO_H
+
+typedef enum t_socket_type_ {TCP_SOCKET, UNIX_DOMAIN_SOCKET} SocketType; // Type of socket.
+
+class MooseSocketInfo
+{
+public:
+ MooseSocketInfo( const string& addr = "" )
+ : address(addr), valid(false)
+ {
+ if( addr.size() > 0 )
+ init();
+ }
+
+ ~MooseSocketInfo() { ; }
+
+ void setAddress( const string addr )
+ {
+ address = addr;
+ init();
+ }
+
+ void init( void )
+ {
+ if( "file://" == address.substr(0, 7))
+ {
+ type = UNIX_DOMAIN_SOCKET;
+ filepath = address.substr(7);
+ valid = true;
+ }
+ else if( "http://" == address.substr(0, 7))
+ {
+ type = TCP_SOCKET;
+ auto colPos = address.find_last_of(':');
+ if( colPos == string::npos )
+ {
+ port = 0;
+ host = address;
+ }
+ else
+ {
+ host = address.substr(0, colPos);
+ port = std::stoi(address.substr(colPos+1));
+ }
+ valid = true;
+ }
+ else if( '/' == address[0] )
+ {
+ type = UNIX_DOMAIN_SOCKET;
+ filepath = address;
+ valid = true;
+ }
+ }
+
+ // C++ is so stupid: https://stackoverflow.com/q/476272/1805129
+ friend std::ostream& operator<<(ostream& os, const MooseSocketInfo& info)
+ {
+ os << "ADDRESS= " << info.address << " TYPE= " << info.type;
+ if( info.type == UNIX_DOMAIN_SOCKET)
+ os << ". FILEPATH " << info.filepath;
+ else
+ os << ". HOST:PORT=" << info.host << ":" << info.port;
+ return os;
+ }
+
+public:
+ SocketType type;
+ string address;
+ string filepath;
+ string host;
+ bool valid;
+ size_t port;
+};
+
+
+#endif /* end of include guard: MOOSESOCKETINFO_H */
diff --git a/moose-core/builtins/SocketStreamer.cpp b/moose-core/builtins/SocketStreamer.cpp
index e3097f088bd2b7f99d52743a52ce249ff7d01141..38cbae5e099bb1132ff8deeb02c534f096909be5 100644
--- a/moose-core/builtins/SocketStreamer.cpp
+++ b/moose-core/builtins/SocketStreamer.cpp
@@ -66,25 +66,25 @@ const Cinfo* SocketStreamer::initCinfo()
static DestFinfo addTable(
"addTable"
, "Add a table to SocketStreamer"
- , new OpFunc1<SocketStreamer, Id>(&SocketStreamer::addTable)
+ , new OpFunc1<SocketStreamer, ObjId>(&SocketStreamer::addTable)
);
static DestFinfo addTables(
"addTables"
, "Add many tables to SocketStreamer"
- , new OpFunc1<SocketStreamer, vector<Id> >(&SocketStreamer::addTables)
+ , new OpFunc1<SocketStreamer, vector<ObjId> >(&SocketStreamer::addTables)
);
static DestFinfo removeTable(
"removeTable"
, "Remove a table from SocketStreamer"
- , new OpFunc1<SocketStreamer, Id>(&SocketStreamer::removeTable)
+ , new OpFunc1<SocketStreamer, ObjId>(&SocketStreamer::removeTable)
);
static DestFinfo removeTables(
"removeTables"
, "Remove tables -- if found -- from SocketStreamer"
- , new OpFunc1<SocketStreamer, vector<Id>>(&SocketStreamer::removeTables)
+ , new OpFunc1<SocketStreamer, vector<ObjId>>(&SocketStreamer::removeTables)
);
/*-----------------------------------------------------------------------------
@@ -134,12 +134,9 @@ static const Cinfo* tableStreamCinfo = SocketStreamer::initCinfo();
SocketStreamer::SocketStreamer() :
currTime_(0.0)
, numMaxClients_(1)
- , sockType_ ( UNIX_DOMAIN_SOCKET )
, sockfd_(-1)
, clientfd_(-1)
- , ip_( TCP_SOCKET_IP )
- , port_( TCP_SOCKET_PORT )
- , address_ ( "file://MOOSE" )
+ , sockInfo_( MooseSocketInfo( "file://MOOSE" ) )
{
clk_ = reinterpret_cast<Clock*>( Id(1).eref().data() );
@@ -150,7 +147,6 @@ SocketStreamer::SocketStreamer() :
tableIds_.resize(0);
tableTick_.resize(0);
tableDt_.resize(0);
-
}
SocketStreamer& SocketStreamer::operator=( const SocketStreamer& st )
@@ -167,36 +163,29 @@ SocketStreamer::~SocketStreamer()
if(sockfd_ > 0)
{
LOG(moose::debug, "Closing socket " << sockfd_ );
- shutdown(sockfd_, SHUT_RD);
+ shutdown(sockfd_, SHUT_RDWR);
close(sockfd_);
- if( sockType_ == UNIX_DOMAIN_SOCKET )
- ::unlink( unixSocketFilePath_.c_str() );
+ if( sockInfo_.type == UNIX_DOMAIN_SOCKET )
+ ::unlink( sockInfo_.filepath.c_str() );
}
- if( processThread_.joinable() )
+ if( processThread_.joinable())
processThread_.join();
-}
-/* --------------------------------------------------------------------------*/
-/**
- * @Synopsis Stop a thread.
- * See: http://www.bo-yang.net/2017/11/19/cpp-kill-detached-thread
- *
- * @Param tname name of thread.
- */
-/* ----------------------------------------------------------------------------*/
-//void SocketStreamer::stopThread(const std::string& tname)
-//{
-// ThreadMap::const_iterator it = tm_.find(tname);
-// if (it != tm_.end())
-// {
-// it->second.std::thread::~thread(); // thread not killed
-// tm_.erase(tname);
-// LOG(moose::debug, "Thread " << tname << " killed." );
-// }
-//}
+ // Close the client as well.
+ if( clientfd_ > -1 )
+ {
+ shutdown(clientfd_, SHUT_RDWR);
+ close(clientfd_);
+ }
+}
+void SocketStreamer::addStringToDoubleVec(vector<double>&res, const string s)
+{
+ for(char c : s)
+ res.push_back((double)c);
+}
/* --------------------------------------------------------------------------*/
/**
@@ -217,17 +206,16 @@ void SocketStreamer::listenToClients(size_t numMaxClients)
void SocketStreamer::initServer( void )
{
- setSocketType( );
- if( sockType_ == UNIX_DOMAIN_SOCKET )
+ if( sockInfo_.type == UNIX_DOMAIN_SOCKET )
initUDSServer();
else
initTCPServer();
- LOG(moose::debug, "Successfully created SocketStreamer server: " << sockfd_);
+ LOG(moose::info, "Successfully initialized streamer socket: " << sockfd_);
// Listen for incoming clients. This function does nothing if connection is
// already made.
- listenToClients(2);
+ listenToClients(1);
}
void SocketStreamer::configureSocketServer( )
@@ -236,7 +224,7 @@ void SocketStreamer::configureSocketServer( )
// for details. We are making it 'reusable'.
int on = 1;
-#ifdef SO_REUSEADDR
+#ifdef SO_REUSEPORT
if(0 > setsockopt(sockfd_, SOL_SOCKET, SO_REUSEPORT, (const char *)&on, sizeof(on)))
LOG(moose::warning, "Warn: setsockopt() failed");
#endif
@@ -257,30 +245,39 @@ void SocketStreamer::initUDSServer( void )
if( sockfd_ > 0 )
{
- unixSocketFilePath_ = address_.substr(7); bzero(&sockAddrUDS_, sizeof(sockAddrUDS_));
+ bzero(&sockAddrUDS_, sizeof(sockAddrUDS_));
sockAddrUDS_.sun_family = AF_UNIX;
- strncpy(sockAddrUDS_.sun_path, unixSocketFilePath_.c_str(), sizeof(sockAddrUDS_.sun_path)-1);
+ strncpy(sockAddrUDS_.sun_path, sockInfo_.filepath.c_str(), sizeof(sockAddrUDS_.sun_path)-1);
configureSocketServer();
// Bind. Make sure bind is not std::bind
if(0 > ::bind(sockfd_, (struct sockaddr*) &sockAddrUDS_, sizeof(sockAddrUDS_)))
{
isValid_ = false;
- LOG(moose::warning, "Warn: Failed to create socket at " << unixSocketFilePath_
+ LOG(moose::warning, "Warn: Failed to create socket at " << sockInfo_.filepath
<< ". File descriptor: " << sockfd_
<< ". Erorr: " << strerror(errno)
);
}
+
+ if(! moose::filepath_exists(sockInfo_.filepath))
+ {
+ LOG( moose::warning, "No file " << sockInfo_.filepath << " exists." );
+ isValid_ = false;
+ }
}
if( (! isValid_) || (sockfd_ < 0) )
- ::unlink( unixSocketFilePath_.c_str() );
+ {
+ LOG( moose::warning, "Failed to create socket : " << sockInfo_ );
+ ::unlink( sockInfo_.filepath.c_str() );
+ }
}
void SocketStreamer::initTCPServer( void )
{
// Create a blocking socket.
- LOG( moose::debug, "Creating TCP socket on port: " << port_ );
+ LOG( moose::debug, "Creating TCP socket on port: " << sockInfo_.port );
sockfd_ = socket(AF_INET, SOCK_STREAM, 0);
if( 0 > sockfd_ )
{
@@ -293,122 +290,137 @@ void SocketStreamer::initTCPServer( void )
bzero((char*) &sockAddrTCP_, sizeof(sockAddrTCP_));
sockAddrTCP_.sin_family = AF_INET;
sockAddrTCP_.sin_addr.s_addr = INADDR_ANY;
- sockAddrTCP_.sin_port = htons( port_ );
+ sockAddrTCP_.sin_port = htons( sockInfo_.port );
// Bind. Make sure bind is not std::bind
if(0 > ::bind(sockfd_, (struct sockaddr*) &sockAddrTCP_, sizeof(sockAddrTCP_)))
{
isValid_ = false;
- LOG(moose::warning, "Warn: Failed to create server at " << ip_ << ":" << port_
- << ". File descriptor: " << sockfd_
- << ". Erorr: " << strerror(errno)
+ LOG(moose::warning, "Warn: Failed to create server at "
+ << sockInfo_.host << ":" << sockInfo_.port
+ << ". File descriptor: " << sockfd_
+ << ". Erorr: " << strerror(errno)
);
return;
}
}
-
/* --------------------------------------------------------------------------*/
/**
- * @Synopsis Stream data over socket.
+ * @Synopsis Convert data to JSON.
*
- * @Returns True of success, false otherwise. It is callee job to clean up data_
- * on a successful return from this function.
+ * @Returns JSON representation.
*/
/* ----------------------------------------------------------------------------*/
-bool SocketStreamer::streamData( )
+void SocketStreamer::dataToStream(map<string, vector<double>>& data)
{
- if( clientfd_ > 0)
+ for( size_t i = 0; i < tables_.size(); i++)
{
- buffer_ += dataToString();
-
- if( buffer_.size() < frameSize_ )
- buffer_ += string(frameSize_-buffer_.size(), ' ');
-
- string toSend = buffer_.substr(0, frameSize_);
-
- int sent = send(clientfd_, buffer_.substr(0, frameSize_).c_str(), frameSize_, MSG_MORE);
- buffer_ = buffer_.erase(0, sent);
-
- assert( sent == (int)frameSize_);
- LOG(moose::debug, "Sent " << sent << " bytes." );
-
- if(0 > sent)
- {
- LOG(moose::warning, "Failed to send. Error: " << strerror(errno)
- << ". client id: " << clientfd_ );
- return false;
- }
-
- // clear up the tables.
- for( auto t : tables_ )
- t->clearVec();
- return true;
+ vector<double> vec;
+ tables_[i]->collectData(vec, true, false);
+ if( ! vec.empty() )
+ data[columns_[i+1]] = vec;
}
- else
- LOG(moose::warning, "No client found to stream data. ClientFD: " << clientfd_ );
-
- return false;
}
/* --------------------------------------------------------------------------*/
/**
- * @Synopsis Convert table to string (use scientific notation).
+ * @Synopsis Stream data over socket.
*
- * @Returns String in JSON like format.
+ * @Returns True of success, false otherwise. It is callee job to clean up data_
+ * on a successful return from this function.
*/
/* ----------------------------------------------------------------------------*/
-string SocketStreamer::dataToString( )
+int SocketStreamer::streamData( )
{
- stringstream ss;
- // Enabling this would be require quite a lot of characters to be streamed.
- //ss.precision( 7 );
- //ss << std::scientific;
- vector<double> data;
-
- // Else stream the data.
- ss << "{";
- for( size_t i = 0; i < tables_.size(); i++)
+ map<string, vector<double>> data;
+ dataToStream(data);
+
+ if(data.empty())
+ {
+ LOG(moose::debug, "No data in tables.");
+ return 0;
+ }
+
+ // Construct a void* array to send over the socket. Serialize the data.
+ // e.g. H 10 / a / t a b l e / a V 4 0.1 0.2 0.3 0.2
+ // H => Header start (chars)
+ // V => Value starts (double)
+ for(auto v: data)
{
- ss << "\"" << columns_[i+1] << "\":[";
- ss << tables_[i]->toJSON(true);
- ss << "],";
+ // First header.
+ vecToStream_.push_back((double)'H');
+ vecToStream_.push_back(v.first.size());
+ addStringToDoubleVec(vecToStream_, v.first);
+
+ // Now data.
+ vecToStream_.push_back((double)'V');
+ vecToStream_.push_back(v.second.size());
+ vecToStream_.insert(vecToStream_.end(), v.second.begin(), v.second.end());
}
- // remove , at the end else it won't be a valid JSON.
- string res = ss.str();
- if( ',' == res.back())
- res.pop_back();
- res += "}\n";
- return res;
+ size_t dtypeSize = sizeof(double);
+ int sent = send(clientfd_, (void*) &vecToStream_[0], dtypeSize*vecToStream_.size(), MSG_MORE);
+ LOG(moose::debug, "Sent " << sent << " bytes." );
+ if( sent < 0 )
+ return errno;
+
+ vecToStream_.erase(vecToStream_.begin(), vecToStream_.begin()+(sent/dtypeSize));
+ return 0;
}
+
bool SocketStreamer::enoughDataToStream(size_t minsize)
{
for( size_t i = 0; i < tables_.size(); i++)
- if(tables_[i]->getVec().size() >= minsize )
+ if(tables_[i]->getVec().size() >= minsize)
return true;
return false;
}
-void SocketStreamer::connectAndStream( )
+void SocketStreamer::connect( )
{
- currTime_ = clk_->getCurrentTime();
-
// If server was invalid then there is no point.
if( ! isValid_ )
- {
- LOG( moose::error, "Server could not set up." );
return;
+
+ struct sockaddr_storage clientAddr;
+ socklen_t addrLen = sizeof(clientAddr);
+ clientfd_ = ::accept(sockfd_,(struct sockaddr*) &clientAddr, &addrLen);
+ assert( clientfd_ );
+
+ char ipstr[INET6_ADDRSTRLEN];
+ int port = -1;
+ // deal with both IPv4 and IPv6:
+ if (clientAddr.ss_family == AF_INET)
+ {
+ struct sockaddr_in *s = (struct sockaddr_in *)&clientAddr;
+ port = ntohs(s->sin_port);
+ inet_ntop(AF_INET, &s->sin_addr, ipstr, sizeof ipstr);
+ }
+ else
+ { // AF_INET6
+ struct sockaddr_in6 *s = (struct sockaddr_in6 *)&clientAddr;
+ port = ntohs(s->sin6_port);
+ inet_ntop(AF_INET6, &s->sin6_addr, ipstr, sizeof ipstr);
}
- // Now lets get into a loop to stream data.
- while( (! all_done_) )
+ LOG(moose::info, "Connected to " << ipstr << ':' << port);
+ return;
+}
+
+void SocketStreamer::stream( void )
+{
+ if(clientfd_ > 0)
{
- clientfd_ = ::accept(sockfd_, NULL, NULL);
- if( clientfd_ >= 0 )
- streamData();
+ if( EPIPE == streamData() )
+ {
+ LOG( moose::warning, "Broken pipe. Couldn't stream." );
+ return;
+ }
}
+ else
+ LOG( moose::warning, "No client." );
}
/**
@@ -443,7 +455,10 @@ void SocketStreamer::reinit(const Eref& e, ProcPtr p)
// Launch a thread in background which monitors the any client trying to
// make connection to server.
- processThread_ = std::thread(&SocketStreamer::connectAndStream, this);
+ processThread_ = std::thread(&SocketStreamer::connect, this);
+
+ // NOw introduce some delay.
+ timeStamp_ = std::chrono::high_resolution_clock::now();
}
/**
@@ -454,8 +469,10 @@ void SocketStreamer::reinit(const Eref& e, ProcPtr p)
*/
void SocketStreamer::process(const Eref& e, ProcPtr p)
{
- // It does nothing. See the connectAndStream function.
- ;
+ // processTickMicroSec = std::chrono::duration_cast<std::chrono::microseconds>(
+ // std::chrono::high_resolution_clock::now() - timeStamp_).count();
+ // timeStamp_ = std::chrono::high_resolution_clock::now();
+ stream();
}
/**
@@ -463,7 +480,7 @@ void SocketStreamer::process(const Eref& e, ProcPtr p)
*
* @param table Id of table.
*/
-void SocketStreamer::addTable( Id table )
+void SocketStreamer::addTable( ObjId table )
{
// If this table is not already in the vector, add it.
for( size_t i = 0; i < tableIds_.size(); i++)
@@ -488,29 +505,21 @@ void SocketStreamer::addTable( Id table )
*
* @param tables
*/
-void SocketStreamer::addTables( vector<Id> tables )
-{
- if( tables.size() == 0 )
- return;
- for( vector<Id>::const_iterator it = tables.begin(); it != tables.end(); it++)
- addTable( *it );
-}
-
void SocketStreamer::addTables( vector<ObjId> tables )
{
if( tables.size() == 0 )
return;
- for( auto t : tables )
- addTable( Id(t) );
-}
+ for(auto t : tables)
+ addTable(t);
+}
/**
* @brief Remove a table from SocketStreamer.
*
* @param table. Id of table.
*/
-void SocketStreamer::removeTable( Id table )
+void SocketStreamer::removeTable( ObjId table )
{
int matchIndex = -1;
for (size_t i = 0; i < tableIds_.size(); i++)
@@ -530,32 +539,14 @@ void SocketStreamer::removeTable( Id table )
}
}
-/* --------------------------------------------------------------------------*/
-/**
- * @Synopsis Determines socket type from the given address.
- */
-/* ----------------------------------------------------------------------------*/
-void SocketStreamer::setSocketType( )
-{
- LOG( moose::debug, "Socket address is " << address_ );
- if( "file://" == address_.substr(0, 7))
- sockType_ = UNIX_DOMAIN_SOCKET;
- else if( "http://" == address_.substr(0,7))
- sockType_ = TCP_SOCKET;
- else
- sockType_ = UNIX_DOMAIN_SOCKET;
- return;
-}
-
/**
* @brief Remove multiple tables -- if found -- from SocketStreamer.
*
* @param tables
*/
-void SocketStreamer::removeTables( vector<Id> tables )
+void SocketStreamer::removeTables( vector<ObjId> tables )
{
- for( vector<Id>::const_iterator it = tables.begin(); it != tables.end(); it++)
- removeTable( *it );
+ for(auto &t: tables) removeTable(t);
}
/**
@@ -571,21 +562,20 @@ size_t SocketStreamer::getNumTables( void ) const
void SocketStreamer::setPort( const size_t port )
{
- port_ = port;
+ sockInfo_.port = port;
}
size_t SocketStreamer::getPort( void ) const
{
- assert( port_ > 1 );
- return port_;
+ return sockInfo_.port;
}
void SocketStreamer::setAddress( const string addr )
{
- address_ = addr;
+ sockInfo_.setAddress(addr);
}
string SocketStreamer::getAddress( void ) const
{
- return address_;
+ return sockInfo_.address;
}
diff --git a/moose-core/builtins/SocketStreamer.h b/moose-core/builtins/SocketStreamer.h
index c52bb7dd4d1419895d16d7ba3f9ddc9cb331fa45..7e811c817b79cb22aa27534aeee8cc88bb8653c8 100644
--- a/moose-core/builtins/SocketStreamer.h
+++ b/moose-core/builtins/SocketStreamer.h
@@ -5,10 +5,9 @@
#ifndef SocketStreamer_INC
#define SocketStreamer_INC
-#define STRINGSTREAM_DOUBLE_PRECISION 10
-
#include <iostream>
#include <string>
+#include <vector>
#include <map>
#include <fstream>
#include <sstream>
@@ -16,6 +15,7 @@
#include <atomic>
#include "StreamerBase.h"
+#include "MooseSocketInfo.h"
#include "Table.h"
// If cmake does not set it, use the default port.
@@ -37,6 +37,7 @@
#include <sys/ioctl.h>
#include <sys/un.h>
#include <netinet/in.h>
+#include <arpa/inet.h>
// MSG_MORE is not defined in OSX. So stupid!
#ifndef MSG_MORE
@@ -45,10 +46,10 @@
using namespace std;
-typedef enum t_socket_type_ {TCP_SOCKET, UNIX_DOMAIN_SOCKET} SocketType; // Type of socket.
class Clock;
+
class SocketStreamer : public StreamerBase
{
@@ -75,6 +76,9 @@ public:
// Make connection to client
void listenToClients(size_t numMaxClients);
+ // Find minimum number of elements in tables.
+ pair<size_t, size_t> minMaxNumberOfElemementsInTables( );
+
/* Cleaup before quitting */
void cleanUp( void );
@@ -84,28 +88,26 @@ public:
size_t getPort( void ) const;
void setPort( const size_t port );
- SocketType getSocketType( );
- void setSocketType(void);
-
/*-----------------------------------------------------------------------------
* Streaming data.
*-----------------------------------------------------------------------------*/
bool enoughDataToStream(size_t minsize=10);
- bool streamData();
- void connectAndStream( );
+ int streamData();
+ // connect is monitored in a thread.
+ void connect( void );
+ void stream(void);
size_t getNumTables( void ) const;
- void addTable( Id table );
- void addTables( vector<Id> tables);
+ void addTable( ObjId table );
void addTables( vector<ObjId> tables);
- void removeTable( Id table );
- void removeTables( vector<Id> table );
+ void removeTable( ObjId table );
+ void removeTables( vector<ObjId> table );
- string dataToString();
+ void dataToStream(map<string, vector<double>>& vec);
- // void stopThread(const std::string& tname);
+ static void addStringToDoubleVec(vector<double>&res, const string s);
/** Dest functions.
* The process function called by scheduler on every tick
@@ -119,6 +121,7 @@ public:
static const Cinfo * initCinfo();
+
private:
// dt_ and tick number of Table's clock
@@ -133,16 +136,9 @@ private:
/* Socket related */
int numMaxClients_;
- SocketType sockType_ = UNIX_DOMAIN_SOCKET; // Default is UNIX_DOMAIN_SOCKET
int sockfd_; // socket file descriptor.
int clientfd_; // client file descriptor
- // TCP socket.
- string ip_; // ip_ address of server.
- unsigned short port_; // port number if socket is TCP_SOCKET
- string address_; // adress of socket. Specified by user.
- string unixSocketFilePath_;
-
// address holdder for TCP and UDS sockets.
struct sockaddr_in sockAddrTCP_;
struct sockaddr_un sockAddrUDS_;
@@ -152,13 +148,18 @@ private:
bool isValid_ = true;
std::thread processThread_;
string buffer_;
+ vector<double> vecToStream_;
double thisDt_;
- size_t frameSize_ = 2048;
-
// We need clk_ pointer for handling
Clock* clk_ = nullptr;
+ // Socket Info
+ MooseSocketInfo sockInfo_;
+
+ // How long it takes between process calls.
+ size_t processTickMicroSec;
+ std::chrono::high_resolution_clock::time_point timeStamp_;
};
#endif /* ----- #ifndef SocketStreamer_INC ----- */
diff --git a/moose-core/builtins/Streamer.cpp b/moose-core/builtins/Streamer.cpp
index c583be1fee2ee8cc00ec68c1f6ee8e4cef2a4293..aae926bc7e18ee42c0e8698761c627580d3ae2a0 100644
--- a/moose-core/builtins/Streamer.cpp
+++ b/moose-core/builtins/Streamer.cpp
@@ -1,17 +1,8 @@
/***
- * Filename: Streamer.cpp
- *
* Description: Stream table data.
*
- * Version: 0.0.1
- * Created: 2016-04-26
-
- * Revision: none
- *
* Author: Dilawar Singh <dilawars@ncbs.res.in>
* Organization: NCBS Bangalore
- *
- * License: GNU GPL2
*/
#include <algorithm>
@@ -45,12 +36,18 @@ const Cinfo* Streamer::initCinfo()
, &Streamer::getFormat
);
- static ReadOnlyValueFinfo< Streamer, size_t > numTables (
+ static ReadOnlyValueFinfo<Streamer, size_t> numTables (
"numTables"
, "Number of Tables handled by Streamer "
, &Streamer::getNumTables
);
+ static ReadOnlyValueFinfo<Streamer, size_t> numWriteEvents(
+ "numWriteEvents"
+ , "Number of time streamer was called to write. (For debugging/performance reason only)"
+ , &Streamer::getNumWriteEvents
+ );
+
/*-----------------------------------------------------------------------------
*
*-----------------------------------------------------------------------------*/
@@ -96,7 +93,7 @@ const Cinfo* Streamer::initCinfo()
*-----------------------------------------------------------------------------*/
static Finfo* procShared[] =
{
- &process , &reinit , &addTable, &addTables, &removeTable, &removeTables
+ &process, &reinit, &addTable, &addTables, &removeTable, &removeTables
};
static SharedFinfo proc(
@@ -107,7 +104,7 @@ const Cinfo* Streamer::initCinfo()
static Finfo * tableStreamFinfos[] =
{
- &outfile, &format, &proc, &numTables
+ &outfile, &format, &proc, &numTables, &numWriteEvents
};
static string doc[] =
@@ -140,8 +137,9 @@ Streamer::Streamer()
{
// Not all compilers allow initialization during the declaration of class
// methods.
- format_ = "npy";
- columns_.push_back( "time" ); /* First column is time. */
+ format_ = "csv";
+ numWriteEvents_ = 0;
+ columns_.push_back("time"); /* First column is time. */
tables_.resize(0);
tableIds_.resize(0);
tableTick_.resize(0);
@@ -238,7 +236,7 @@ void Streamer::reinit(const Eref& e, ProcPtr p)
// write now.
currTime_ = 0.0;
zipWithTime( );
- StreamerBase::writeToOutFile( outfilePath_, format_, "w", data_, columns_);
+ StreamerBase::writeToOutFile(outfilePath_, format_, "w", data_, columns_);
data_.clear( );
}
@@ -261,15 +259,11 @@ void Streamer::cleanUp( )
*/
void Streamer::process(const Eref& e, ProcPtr p)
{
- //LOG( moose::debug, "Writing to table" );
+ // LOG( moose::debug, "Writing Streamer data to file." );
zipWithTime( );
-
- // Write only if there are more than 100 entry in first table.
- if( tables_[0]->getVecSize() > 100 )
- {
- StreamerBase::writeToOutFile( outfilePath_, format_, "a", data_, columns_ );
- data_.clear( );
- }
+ StreamerBase::writeToOutFile( outfilePath_, format_, "a", data_, columns_ );
+ data_.clear();
+ numWriteEvents_ += 1;
}
@@ -356,6 +350,19 @@ size_t Streamer::getNumTables( void ) const
return tables_.size();
}
+/* --------------------------------------------------------------------------*/
+/**
+ * @Synopsis Get number of write events in streamer. Useful for debugging and
+ * performance measuerments.
+ *
+ * @Returns
+ */
+/* ----------------------------------------------------------------------------*/
+size_t Streamer::getNumWriteEvents( void ) const
+{
+ return numWriteEvents_;
+}
+
string Streamer::getOutFilepath( void ) const
{
diff --git a/moose-core/builtins/Streamer.h b/moose-core/builtins/Streamer.h
index 0a06e547ac26227744727256a8579c1434159fe3..3136211fced1004b475911cd1f469e0f2daf95b6 100644
--- a/moose-core/builtins/Streamer.h
+++ b/moose-core/builtins/Streamer.h
@@ -49,6 +49,7 @@ public:
void setFormat( string format );
size_t getNumTables( void ) const;
+ size_t getNumWriteEvents( void ) const;
void addTable( Id table );
void addTables( vector<Id> tables);
@@ -74,6 +75,9 @@ private:
string outfilePath_;
string format_;
+
+ size_t numWriteEvents_;
+
bool isOutfilePathSet_;
// dt_ and tick number of Table's clock
diff --git a/moose-core/builtins/StreamerBase.cpp b/moose-core/builtins/StreamerBase.cpp
index e6d590be0fe1b2a06a2c242946e4814a32a8ec38..902c3f24c765f98e1a9df9fc3554f09d689777e7 100644
--- a/moose-core/builtins/StreamerBase.cpp
+++ b/moose-core/builtins/StreamerBase.cpp
@@ -91,14 +91,14 @@ void StreamerBase::writeToCSVFile( const string& filepath, const string& openmod
}
// If writing in "w" mode, write the header first.
- if( openmode == "w" )
+ if(openmode == "w")
{
string headerText = "";
for( vector<string>::const_iterator it = columns.begin();
it != columns.end(); it++ )
headerText += ( *it + delimiter_ );
headerText += eol;
- fprintf( fp, "%s", headerText.c_str() );
+ fprintf(fp, "%s", headerText.c_str());
}
string text = "";
@@ -111,8 +111,8 @@ void StreamerBase::writeToCSVFile( const string& filepath, const string& openmod
// At the end of each row, we remove the delimiter_ and append newline_.
*(text.end()-1) = eol;
}
- fprintf( fp, "%s", text.c_str() );
- fclose( fp );
+ fprintf(fp, "%s", text.c_str() );
+ fclose(fp);
}
/* write data to a numpy file */
diff --git a/moose-core/builtins/Table.cpp b/moose-core/builtins/Table.cpp
index 4f426b148e09428928a75bb2569bf04c0c2263cd..be3702b13cb3cc46b569af8fc4b319d32dbd6268 100644
--- a/moose-core/builtins/Table.cpp
+++ b/moose-core/builtins/Table.cpp
@@ -211,24 +211,25 @@ const Cinfo* Table::initCinfo()
static const Cinfo* tableCinfo = Table::initCinfo();
Table::Table() :
- threshold_( 0.0 ) ,
- lastTime_( 0.0 ) ,
- input_( 0.0 ),
- fired_(false),
- useSpikeMode_(false),
- dt_( 0.0 )
+ threshold_( 0.0 ) ,
+ lastTime_( 0.0 ) ,
+ input_( 0.0 ),
+ fired_(false),
+ useSpikeMode_(false),
+ dt_( 0.0 )
{
// Initialize the directory to which each table should stream.
rootdir_ = "_tables";
- useStreamer_ = false;
+ useFileStreamer_ = false;
format_ = "csv";
outfileIsSet_ = false;
+ lastN_ = 0;
}
Table::~Table( )
{
// Make sure to write to rest of the entries to file before closing down.
- if( useStreamer_ )
+ if( useFileStreamer_ )
{
mergeWithTime( data_ );
StreamerBase::writeToOutFile( outfile_, format_, "a", data_, columns_ );
@@ -267,7 +268,7 @@ void Table::process( const Eref& e, ProcPtr p )
* vector.
* Write at every 5 seconds or whenever size of vector is more than 10k.
*/
- if( useStreamer_ )
+ if( useFileStreamer_ )
{
if( fmod(lastTime_, 5.0) == 0.0 or getVecSize() >= 10000 )
{
@@ -300,7 +301,7 @@ void Table::reinit( const Eref& e, ProcPtr p )
fired_ = false;
/** Create the default filepath for this table. */
- if( useStreamer_ )
+ if( useFileStreamer_ )
{
// The first column is variable time.
columns_.push_back( "time" );
@@ -331,7 +332,7 @@ void Table::reinit( const Eref& e, ProcPtr p )
tvec_.push_back(lastTime_);
- if( useStreamer_ )
+ if( useFileStreamer_ )
{
mergeWithTime( data_ );
StreamerBase::writeToOutFile( outfile_, format_, "w", data_, columns_);
@@ -412,12 +413,12 @@ void Table::setColumnName( const string colname )
/* Enable/disable streamer support. */
void Table::setUseStreamer( bool useStreamer )
{
- useStreamer_ = useStreamer;
+ useFileStreamer_ = useStreamer;
}
bool Table::getUseStreamer( void ) const
{
- return useStreamer_;
+ return useFileStreamer_;
}
/* Enable/disable spike mode. */
@@ -477,25 +478,60 @@ void Table::mergeWithTime( vector<double>& data )
/**
* @Synopsis. Convert table data to JOSN.
*
- * @Param t. Upto this time.
- * @Param withTime. Zip with time.
- *
* @Returns string.
*/
/* ----------------------------------------------------------------------------*/
-string Table::toJSON( bool withTime)
+string Table::toJSON(bool withTime, bool clear)
{
- auto v = vec();
stringstream ss;
- for (size_t i = 0; i < v.size(); i++)
+ auto v = vec();
+ if( clear )
+ lastN_ = 0;
+
+ for (size_t i = lastN_; i < v.size(); i++)
{
if(withTime)
ss << '[' << tvec_[i] << ',' << v[i] << "],";
else
ss << v[i] << ',';
}
+
string res = ss.str();
- if( ',' == res.back())
+ if(',' == res.back())
res.pop_back();
+
+ if( clear )
+ clearAllVecs();
+ else
+ lastN_ += v.size();
+
return res;
}
+
+/* --------------------------------------------------------------------------*/
+/**
+ * @Synopsis Collect data in given vector. Its similar to toJSON function.
+ *
+ * @Param data
+ * @Param withTime
+ * @Param clear
+ */
+/* ----------------------------------------------------------------------------*/
+void Table::collectData(vector<double>& data, bool withTime, bool clear)
+{
+ auto v = vec();
+ if( clear )
+ lastN_ = 0;
+
+ for (size_t i = lastN_; i < v.size(); i++)
+ {
+ if(withTime)
+ data.push_back(tvec_[i]);
+ data.push_back(v[i]);
+ }
+
+ if( clear )
+ clearAllVecs();
+ else
+ lastN_ = v.size();
+}
diff --git a/moose-core/builtins/Table.h b/moose-core/builtins/Table.h
index b3a0293bf7796fec8e568063f1e6e2f1e59a09c2..2d59f67dfda3e88cadc40d3b84869f16986f4f09 100644
--- a/moose-core/builtins/Table.h
+++ b/moose-core/builtins/Table.h
@@ -51,7 +51,10 @@ public:
// merge time value among values. e.g. t1, v1, t2, v2, etc.
void mergeWithTime( vector<double>& data );
- string toJSON(bool withTime=true);
+ string toJSON(bool withTime=true, bool clear = false);
+
+ void collectData(vector<double>& data, bool withTime=true, bool clear = false);
+
void clearAllVecs();
@@ -83,8 +86,11 @@ private:
vector<double> tvec_; /* time data */
vector<string> columns_; /* Store the name of tables */
- string tablePath_;
+ // Upto which indices we have read the data. This variable is used when
+ // SocketStreamer is used.
+ size_t lastN_ = 0;
+ string tablePath_;
/**
* @brief Column name of this table. Use it when writing data to a datafile.
@@ -96,7 +102,7 @@ private:
* of outfile_ is table path starting from `pwd`/_tables_ . On table, set
* streamToFile to true.
*/
- bool useStreamer_;
+ bool useFileStreamer_;
/**
* @brief Table directory into which dump the stream data.
diff --git a/moose-core/kinetics/ReadKkit.cpp b/moose-core/kinetics/ReadKkit.cpp
index 01254b62292d6a3cc1f2bdf92638e4c04dcadd3c..a33986ac76052fb13893d53a9a6a9f1ac0b8ab63 100644
--- a/moose-core/kinetics/ReadKkit.cpp
+++ b/moose-core/kinetics/ReadKkit.cpp
@@ -131,9 +131,10 @@ Id makeStandardElements( Id pa, const string& modelname )
mgr = shell->doCreate( "Neutral", pa, modelname, 1, MooseGlobal );
Id kinetics( modelPath + "/kinetics" );
if ( kinetics == Id() ) {
- kinetics =
- shell->doCreate( "CubeMesh", mgr, "kinetics", 1, MooseGlobal );
+ kinetics = shell->doCreate( "CubeMesh", mgr, "kinetics", 1, MooseGlobal );
SetGet2< double, unsigned int >::set( kinetics, "buildDefaultMesh", 1e-15, 1 );
+ Id cInfo = shell->doCreate( "Annotator", kinetics, "info", 1 );
+ assert( cInfo != Id() );
}
assert( kinetics != Id() );
diff --git a/moose-core/pymoose/moosemodule.cpp b/moose-core/pymoose/moosemodule.cpp
index 0a71f46667693213040b1a899ecde7db60b771ea..affdc78f65e3c2006ee607e00a13f9fa1d6168a4 100644
--- a/moose-core/pymoose/moosemodule.cpp
+++ b/moose-core/pymoose/moosemodule.cpp
@@ -89,9 +89,6 @@ extern void speedTestMultiNodeIntFireNetwork(
extern void mooseBenchmarks( unsigned int option );
-// global variable.
-bool tcpSocketStreamerEnabled_ = false;
-
/*-----------------------------------------------------------------------------
* Random number generator for this module.
*
@@ -113,7 +110,6 @@ double pymoose_mtrand_( void )
bool setupSocketStreamer(const string addr )
{
LOG(moose::debug, "Setting streamer with addr " << addr );
-
// Find all tables.
vector< ObjId > tables;
wildcardFind( "/##[TYPE=Table2]", tables );
@@ -130,8 +126,9 @@ bool setupSocketStreamer(const string addr )
Id st = SHELLPTR->doCreate("SocketStreamer", stBase, "streamer", 1);
Field<string>::set(st, "address", addr);
+ LOG(moose::debug, "Found " << tables.size() << " tables.");
for( auto &t : tables )
- SetGet1<Id>::set(st, "addTable", t.id );
+ SetGet1<ObjId>::set(st, "addTable", t );
return true;
}
@@ -1773,11 +1770,10 @@ PyObject * moose_reinit(PyObject * dummy, PyObject * args)
string envSocketServer = moose::getEnv( "MOOSE_STREAMER_ADDRESS" );
if(! envSocketServer.empty())
{
- LOG( moose::debug, "Environment variable set of socket" << envSocketServer );
+ LOG( moose::debug, "Environment variable MOOSE_STREAMER_ADDRESS: " << envSocketServer );
if( envSocketServer.size() > 0 )
setupSocketStreamer(envSocketServer);
}
-
SHELLPTR->doReinit();
Py_RETURN_NONE;
}
@@ -1909,7 +1905,7 @@ PyObject * moose_saveModel(PyObject * dummy, PyObject * args)
SHELLPTR->doSaveModel(model, filename);
Py_RETURN_NONE;
}
-#endif
+#endif
PyObject * moose_setCwe(PyObject * dummy, PyObject * args)
{
@@ -2971,17 +2967,17 @@ PyObject * moose_element(PyObject* dummy, PyObject * args)
unsigned nid = 0, did = 0, fidx = 0;
Id id;
unsigned int numData = 0;
- if (PyArg_ParseTuple(args, "s", &path))
+
+ // Parse into str or bytes-like object. Using 's' parses into const char*
+ // which is portable with bytes often returned when working with python3.
+ if (PyArg_ParseTuple(args, "s*", &path))
{
oid = ObjId(path);
- // cout << "Original Path " << path << ", Element Path: " << oid.path() << endl;
if ( oid.bad() )
{
- PyErr_SetString(PyExc_ValueError, ( std::string("moose_element: '")
- + std::string(path)
- + std::string("' does not exist!")
- ).c_str()
- );
+ PyErr_SetString(PyExc_ValueError
+ , (std::string("moose_element: '") + std::string(path) + std::string("' does not exist!")).c_str()
+ );
return NULL;
}
PyObject * new_obj = oid_to_element(oid);
@@ -3272,4 +3268,4 @@ PyMODINIT_FUNC MODINIT(_moose)
#ifdef PY3K
return moose_module;
#endif
-}
+}
diff --git a/moose-core/pymoose/vec.cpp b/moose-core/pymoose/vec.cpp
index e5e2ddb3ec987d5870474dfe1593239daa5fe69f..fc57831ce5195d4bab16b934e29dc251bed2f6de 100644
--- a/moose-core/pymoose/vec.cpp
+++ b/moose-core/pymoose/vec.cpp
@@ -48,8 +48,6 @@
#include <Python.h>
#include <structmember.h> // This defines the type id macros like T_STRING
-// #include "numpy/arrayobject.h"
-
#include "../utility/simple_logger.hpp"
#include <iostream>
@@ -1259,20 +1257,12 @@ int moose_Id_setattro(_Id * self, PyObject * attr, PyObject *value)
default:
break;
}
+
// MOOSE Field::set returns 1 for success 0 for
// failure. Python treats return value 0 from setters as
// success, anything else failure.
if (ret && (PyErr_Occurred() == NULL))
- {
return 0;
- }
else
- {
return -1;
- }
-
}
-
-
-//
-// vec.cpp ends here
diff --git a/moose-core/python/moose/SBML/readSBML.py b/moose-core/python/moose/SBML/readSBML.py
index 356d2400314d2b4623594f8057943bdfc93031ef..093f20854e6c34e1c0521844e789e841999d9331 100644
--- a/moose-core/python/moose/SBML/readSBML.py
+++ b/moose-core/python/moose/SBML/readSBML.py
@@ -13,9 +13,13 @@
** copyright (C) 2003-2017 Upinder S. Bhalla. and NCBS
Created : Thu May 13 10:19:00 2016(+0530)
Version
-Last-Updated: Tue Dec 3 17:30:00 2018(+0530)
+Last-Updated: Sat Jan 19 10:30:00 2019(+0530)
By:HarshaRani
**********************************************************************/
+2019:
+Jan 19: - validator flag is set 'on' from True
+ - groupname if missing in the sbml file then groupid is taken,
+ if both are missing then its not a valide sbml file
2018
Dec 3: - reading motor and diffconstant from pool
Nov 30: - groups and subgroups are read from xml to moose
@@ -82,7 +86,7 @@ try:
except ImportError:
pass
-def mooseReadSBML(filepath, loadpath, solver="ee",validate="True"):
+def mooseReadSBML(filepath, loadpath, solver="ee",validate="on"):
"""Load SBML model
"""
global foundLibSBML_
@@ -102,13 +106,15 @@ def mooseReadSBML(filepath, loadpath, solver="ee",validate="True"):
with open(filepath, "r") as filep:
loadpath = loadpath[loadpath.find('/')+1:]
loaderror = None
+ errorFlag = ""
filep = open(filepath, "r")
document = libsbml.readSBML(filepath)
tobecontinue = False
- if validate == "True":
- tobecontinue = validateModel(document)
+ if validate == "on":
+ tobecontinue,errorFlag = validateModel(document)
else:
tobecontinue = True
+
if tobecontinue:
level = document.getLevel()
version = document.getVersion()
@@ -126,6 +132,7 @@ def mooseReadSBML(filepath, loadpath, solver="ee",validate="True"):
loadpath ='/'+loadpath
baseId = moose.Neutral(loadpath)
basePath = baseId
+
# All the model will be created under model as
# a thumbrule
basePath = moose.Neutral(baseId.path)
@@ -150,7 +157,7 @@ def mooseReadSBML(filepath, loadpath, solver="ee",validate="True"):
errorFlag,msgCmpt = createCompartment(
basePath, model, comptSbmlidMooseIdMap)
- groupInfo = checkGroup(basePath,model)
+ groupInfo = checkGroup(basePath,model,comptSbmlidMooseIdMap)
funcDef = checkFuncDef(model)
if errorFlag:
specInfoMap = {}
@@ -207,8 +214,11 @@ def mooseReadSBML(filepath, loadpath, solver="ee",validate="True"):
loaderror = loaderror
return moose.element(loadpath), loaderror
else:
- print("Validation failed while reading the model.")
- return moose.element('/'), "This document is not valid SBML"
+ print("Validation failed while reading the model."+"\n"+errorFlag)
+ if errorFlag != "":
+ return moose.element('/'),errorFlag
+ else:
+ return moose.element('/'), "This document is not valid SBML"
def checkFuncDef(model):
funcDef = {}
@@ -229,7 +239,7 @@ def checkFuncDef(model):
funcDef[f.getName()] = {'bvar':bvar, "MathML": fmath.getRightChild()}
return funcDef
-def checkGroup(basePath,model):
+def checkGroup(basePath,model,comptSbmlidMooseIdMap):
groupInfo = {}
modelAnnotaInfo = {}
if model.getPlugin("groups") != None:
@@ -237,27 +247,33 @@ def checkGroup(basePath,model):
modelgn = mplugin.getNumGroups()
for gindex in range(0, mplugin.getNumGroups()):
p = mplugin.getGroup(gindex)
+ grpName = ""
groupAnnoInfo = {}
groupAnnoInfo = getObjAnnotation(p, modelAnnotaInfo)
+
if groupAnnoInfo != {}:
- if moose.exists(basePath.path+'/'+groupAnnoInfo["Compartment"]):
+ if moose.exists(basePath.path+'/'+comptSbmlidMooseIdMap[groupAnnoInfo["Compartment"]]["MooseId"].name):
+ groupName = p.getName()
+ if groupName == " ":
+ groupName = p.getId()
if "Group" in groupAnnoInfo:
- if moose.exists(basePath.path+'/'+groupAnnoInfo["Compartment"]+'/'+groupAnnoInfo["Group"]):
- if moose.exists(basePath.path+'/'+groupAnnoInfo["Compartment"]+'/'+groupAnnoInfo["Group"]+'/'+p.getName()):
- moosegrp = moose.element(basePath.path+'/'+groupAnnoInfo["Compartment"]+'/'+groupAnnoInfo["Group"]+'/'+p.getName())
+ if moose.exists(basePath.path+'/'+comptSbmlidMooseIdMap[groupAnnoInfo["Compartment"]]["MooseId"].name+'/'+groupAnnoInfo["Group"]):
+ if moose.exists(basePath.path+'/'+comptSbmlidMooseIdMap[groupAnnoInfo["Compartment"]]["MooseId"].name+'/'+groupAnnoInfo["Group"]+'/'+groupName):
+ moosegrp = moose.element(basePath.path+'/'+comptSbmlidMooseIdMap[groupAnnoInfo["Compartment"]]["MooseId"].name+'/'+groupAnnoInfo["Group"]+'/'+groupName)
else:
- moosegrp = moose.Neutral(basePath.path+'/'+groupAnnoInfo["Compartment"]+'/'+groupAnnoInfo["Group"]+'/'+p.getName())
+ moosegrp = moose.Neutral(basePath.path+'/'+comptSbmlidMooseIdMap[groupAnnoInfo["Compartment"]]["MooseId"].name+'/'+groupAnnoInfo["Group"]+'/'+groupName)
else:
- moose.Neutral(basePath.path+'/'+groupAnnoInfo["Compartment"]+'/'+groupAnnoInfo["Group"])
- if moose.exists(basePath.path+'/'+groupAnnoInfo["Compartment"]+'/'+groupAnnoInfo["Group"]+'/'+p.getName()):
- moosegrp = moose.element(basePath.path+'/'+groupAnnoInfo["Compartment"]+'/'+groupAnnoInfo["Group"]+'/'+p.getName())
+ moose.Neutral(basePath.path+'/'+comptSbmlidMooseIdMap[groupAnnoInfo["Compartment"]]["MooseId"].name+'/'+groupAnnoInfo["Group"])
+ if moose.exists(basePath.path+'/'+comptSbmlidMooseIdMap[groupAnnoInfo["Compartment"]]["MooseId"].name+'/'+groupAnnoInfo["Group"]+'/'+groupName):
+ moosegrp = moose.element(basePath.path+'/'+comptSbmlidMooseIdMap[groupAnnoInfo["Compartment"]]["MooseId"].name+'/'+groupAnnoInfo["Group"]+'/'+groupName)
else:
- moosegrp = moose.Neutral(basePath.path+'/'+groupAnnoInfo["Compartment"]+'/'+groupAnnoInfo["Group"]+'/'+p.getName())
+ moosegrp = moose.Neutral(basePath.path+'/'+comptSbmlidMooseIdMap[groupAnnoInfo["Compartment"]]["MooseId"].name+'/'+groupAnnoInfo["Group"]+'/'+groupName)
else:
- if not moose.exists(basePath.path+'/'+groupAnnoInfo["Compartment"]+'/'+p.getName()):
- moosegrp = moose.Neutral(basePath.path+'/'+groupAnnoInfo["Compartment"]+'/'+p.getName())
+ if not moose.exists(basePath.path+'/'+comptSbmlidMooseIdMap[groupAnnoInfo["Compartment"]]["MooseId"].name+'/'+groupName):
+ moosegrp = moose.Neutral(basePath.path+'/'+comptSbmlidMooseIdMap[groupAnnoInfo["Compartment"]]["MooseId"].name+'/'+groupName)
else:
- moosegrp = moose.element(basePath.path+'/'+groupAnnoInfo["Compartment"]+'/'+p.getName())
+ moosegrp = moose.element(basePath.path+'/'+comptSbmlidMooseIdMap[groupAnnoInfo["Compartment"]]["MooseId"].name+'/'+groupName)
+
moosegrpinfo = moose.Annotator(moosegrp.path+'/info')
moosegrpinfo.color = groupAnnoInfo["bgColor"]
else:
@@ -1206,7 +1222,7 @@ def createSpecies(basePath, model, comptSbmlidMooseIdMap,
poolInfo = moose.Annotator(poolId.path + '/info')
else:
poolInfo = moose.element(poolId.path + '/info')
-
+
for k, v in list(specAnnoInfo.items()):
if k == 'xCord':
poolInfo.x = float(v)
@@ -1214,12 +1230,13 @@ def createSpecies(basePath, model, comptSbmlidMooseIdMap,
poolInfo.y = float(v)
elif k == 'bgColor':
poolInfo.color = v
- elif k == 'Color':
+ elif k == 'textColor':
poolInfo.textColor = v
elif k == 'diffConstant':
poolId.diffConst = float(v)
elif k == 'motorConstant':
- poolId.motorConst = float(v)
+ poolId.motorConst = float(v)
+
specInfoMap[sId] = {
"Mpath": poolId,
"const": constant,
diff --git a/moose-core/python/moose/SBML/validation.py b/moose-core/python/moose/SBML/validation.py
index 48facdf07440d16e2dcb37fbdad470506c4d9c3f..1291c0c5c9f7a6851973cf967009159f23af3b1a 100644
--- a/moose-core/python/moose/SBML/validation.py
+++ b/moose-core/python/moose/SBML/validation.py
@@ -18,7 +18,11 @@ Last-Updated: Fri Jul 28 15:50:00 2017(+0530)
By:
**********************************************************************/
+**********************************************************************/
+2019
+Jan 19: - returned errorMsg
'''
+
foundLibSBML_ = False
try:
from libsbml import *
@@ -29,13 +33,15 @@ except Exception as e:
def validateModel(sbmlDoc):
if sbmlDoc.getNumErrors() > 0:
tobecontinued = False
+ validError = ""
for i in range(0,sbmlDoc.getNumErrors()):
- print (sbmlDoc.getError(i).getMessage())
- return False
+ validError = validError+sbmlDoc.getError(i).getMessage()
+ #print (validError)
+ return False, validError
if (not sbmlDoc):
print("validateModel: given a null SBML Document")
- return False
+ return False, "validateModel: given a null SBML Document"
consistencyMessages = ""
validationMessages = ""
@@ -86,7 +92,7 @@ def validateModel(sbmlDoc):
validationMessages = oss
if (noProblems):
- return True
+ return True,""
else:
if consistencyMessages is None:
consistencyMessages = ""
@@ -107,7 +113,7 @@ def validateModel(sbmlDoc):
if validationMessages:
print(validationMessages)
- return False
+ return False,validationMessages
# return ( numConsistencyErrors == 0 and numValidationErrors == 0,
# consistencyMessages)
diff --git a/moose-core/python/moose/SBML/writeSBML.py b/moose-core/python/moose/SBML/writeSBML.py
index d8325ee2a978cb49af6992f48ded5daa347da607..0f021c670e95150e7f9eb3401c745f50be7651bc 100644
--- a/moose-core/python/moose/SBML/writeSBML.py
+++ b/moose-core/python/moose/SBML/writeSBML.py
@@ -13,10 +13,12 @@
** copyright (C) 2003-2017 Upinder S. Bhalla. and NCBS
Created : Friday May 27 12:19:00 2016(+0530)
Version
-Last-Updated: Tue 3 Dec 15:15:10 2018(+0530)
+Last-Updated: Tue 29 Jan 15:15:10 2019(+0530)
By: HarshaRani
**********************************************************************/
/****************************
+2019
+Jan 29: getColor are taken from chemConnectUtil, group's width and height are written
2018
Dec 07: using fixXreac's restoreXreacs function to remove xfer
Dec 03: add diff and motor constants to pool
@@ -47,9 +49,10 @@ import re
import os
import moose
from moose.SBML.validation import validateModel
-from moose.chemUtil.chemConnectUtil import *
+from moose.chemUtil.chemConnectUtil import xyPosition,mooseIsInstance,findCompartment,getColor,setupItem
from moose.chemUtil.graphUtils import *
from moose.fixXreacs import restoreXreacs
+import numpy as np
foundLibSBML_ = False
try:
@@ -98,6 +101,7 @@ def mooseWriteSBML(modelpath, filename, sceneitems={}):
if moose.exists(p.path+'/info'):
xcord.append(moose.element(p.path+'/info').x)
ycord.append(moose.element(p.path+'/info').y)
+ getColor(moose.element(p.path+'/info').path)
recalculatecoordinates(modelpath,mObj,xcord,ycord)
positionInfoexist = False
@@ -158,8 +162,8 @@ def mooseWriteSBML(modelpath, filename, sceneitems={}):
mplugin = cremodel_.getPlugin("groups")
group = mplugin.createGroup()
name = str(idBeginWith(moose.element(key).name))
- moosegrpId = name +"_" + str(moose.element(key).getId().value) + "_" + str(moose.element(key).getDataIndex())
- group.setId(moosegrpId)
+ moosegrpId = name +"_" + str(moose.element(key).getId().value) + "_" + str(moose.element(key).getDataIndex())+"_"
+ group.setId(moosegrpId)
group.setName(name)
group.setKind("collection")
@@ -167,13 +171,32 @@ def mooseWriteSBML(modelpath, filename, sceneitems={}):
ginfo = moose.element(key.path+'/info')
else:
ginfo = moose.Annotator(key.path+'/info')
+
groupCompartment = findCompartment(key)
+
grpAnno = "<moose:GroupAnnotation>"
- grpAnno = grpAnno + "<moose:Compartment>" + groupCompartment.name + "</moose:Compartment>\n"
+ grpAnno = grpAnno + "<moose:Compartment>" + groupCompartment.name +"_"+ str(moose.element(groupCompartment).getId().value) +"_"+ str(moose.element(groupCompartment).getDataIndex())+"_"+"</moose:Compartment>\n"
+ #grpAnno = grpAnno + "<moose:Compartment>" + groupCompartment.name + "_" + str(moose.element(groupCompartment).getId().value) + "_" + str(moose.element(groupCompartment).getDataIndex()) + "_"+ "</moose:Compartment>\n"
if moose.element(key.parent).className == "Neutral":
+
grpAnno = grpAnno + "<moose:Group>" + key.parent.name + "</moose:Group>\n"
- if ginfo.color:
- grpAnno = grpAnno + "<moose:bgColor>" + ginfo.color + "</moose:bgColor>\n"
+ grpparent = key.parent.name + "_" + str(moose.element(key.parent).getId().value) + "_" + str(moose.element(key.parent).getDataIndex()) + "_"
+ grpAnno = grpAnno + "<moose:Parent>" + grpparent + "</moose:Parent>\n"
+ else:
+ grpparent = groupCompartment.name + "_" + str(moose.element(groupCompartment).getId().value) + "_" + str(moose.element(groupCompartment).getDataIndex()) + "_"
+ grpAnno = grpAnno + "<moose:Parent>" + grpparent + "</moose:Parent>\n"
+
+ if moose.exists(key.path+'/info'):
+ ginfo = moose.element(key.path+'/info')
+ if ginfo.height and ginfo.width:
+ grpAnno = grpAnno + "<moose:x>" + str(ginfo.x) + "</moose:x>\n"
+ grpAnno = grpAnno + "<moose:y>" + str(ginfo.y) + "</moose:y>\n"
+ grpAnno = grpAnno + "<moose:width>" + str(ginfo.width) + "</moose:width>\n"
+ grpAnno = grpAnno + "<moose:height>" + str(ginfo.height) + "</moose:height>\n"
+ if ginfo.color:
+ grpAnno = grpAnno + "<moose:bgColor>" + ginfo.color + "</moose:bgColor>\n"
+ if ginfo.notes:
+ grpAnno = grpAnno + "<moose:Notes>" + ginfo.notes + "</moose:Notes>\n"
grpAnno = grpAnno + "</moose:GroupAnnotation>"
group.setAnnotation(grpAnno)
@@ -1048,8 +1071,12 @@ def writeCompt(modelpath, cremodel_):
"<moose:surround>" + \
str(comptID_sbml[compt.surround])+ "</moose:surround>\n" + \
"<moose:isMembraneBound>" + \
- str(compt.isMembraneBound)+ "</moose:isMembraneBound>\n" + \
- "</moose:CompartmentAnnotation>"
+ str(compt.isMembraneBound)+ "</moose:isMembraneBound>\n"
+ if moose.exists(compt.path+'/info'):
+ if moose.element(compt.path+'/info').notes != "":
+ comptAnno = comptAnno + "<moose:Notes>" \
+ + moose.element(compt.path+'/info').notes + "</moose:Notes>"
+ comptAnno = comptAnno+ "</moose:CompartmentAnnotation>"
elif isinstance (compt,moose.CylMesh) :
size = (compt.volume/compt.numDiffCompts)*pow(10,3)
comptAnno = "<moose:CompartmentAnnotation><moose:Mesh>" + \
@@ -1059,14 +1086,22 @@ def writeCompt(modelpath, cremodel_):
"<moose:diffLength>" + \
str(compt.diffLength)+ "</moose:diffLength>\n" + \
"<moose:isMembraneBound>" + \
- str(compt.isMembraneBound)+ "</moose:isMembraneBound>\n" + \
- "</moose:CompartmentAnnotation>"
+ str(compt.isMembraneBound)+ "</moose:isMembraneBound>\n"
+ if moose.exists(compt.path+'/info'):
+ if moose.element(compt.path+'/info').notes != "":
+ comptAnno = comptAnno + "<moose:Notes>" \
+ + moose.element(compt.path+'/info').notes + "</moose:Notes>"
+ comptAnno = comptAnno+ "</moose:CompartmentAnnotation>"
else:
comptAnno = "<moose:CompartmentAnnotation><moose:Mesh>" + \
str(compt.className) + "</moose:Mesh>\n" + \
"<moose:isMembraneBound>" + \
- str(compt.isMembraneBound)+ "</moose:isMembraneBound>\n" + \
- "</moose:CompartmentAnnotation>"
+ str(compt.isMembraneBound)+ "</moose:isMembraneBound>\n"
+ if moose.exists(compt.path+'/info'):
+ if moose.element(compt.path+'/info').notes != "":
+ comptAnno = comptAnno + "<moose:Notes>" \
+ + moose.element(compt.path+'/info').notes + "</moose:Notes>"
+ comptAnno = comptAnno+ "</moose:CompartmentAnnotation>"
if createCompt:
c1 = cremodel_.createCompartment()
c1.setId(csetId)
diff --git a/moose-core/python/moose/chemUtil/chemConnectUtil.py b/moose-core/python/moose/chemUtil/chemConnectUtil.py
index 9c92e613786c8448f0075ac67bf46cc92e14c05e..f15708be7b7e084a4ad8dfdd3ed3675d943b65c8 100644
--- a/moose-core/python/moose/chemUtil/chemConnectUtil.py
+++ b/moose-core/python/moose/chemUtil/chemConnectUtil.py
@@ -9,10 +9,105 @@ __version__ = "1.0.0"
__maintainer__ = "Harsha Rani"
__email__ = "hrani@ncbs.res.in"
__status__ = "Development"
-__updated__ = "Nov 8 2018"
+__updated__ = "Mar 11 2019"
import moose
import numpy as np
+import pickle
+import matplotlib
+import os
+import random
+
+
+direct = os.path.dirname(__file__)
+colormap_file = open(os.path.join(direct, "rainbow2.pkl"), "r")
+colorMap = pickle.loads(colormap_file.read().encode('utf8'))
+colormap_file.close()
+ignoreColor= ["mistyrose","antiquewhite","aliceblue","azure","bisque","black","blanchedalmond","blue","cornsilk","darkolivegreen","darkslategray","dimgray","floralwhite","gainsboro","ghostwhite","honeydew","ivory","lavender","lavenderblush","lemonchiffon","lightcyan","lightgoldenrodyellow","lightgray","lightyellow","linen","mediumblue","mintcream","navy","oldlace","papayawhip","saddlebrown","seashell","snow","wheat","white","whitesmoke","aquamarine","lightsalmon","moccasin","limegreen","snow","sienna","beige","dimgrey","lightsage"]
+matplotcolor = {}
+for name,hexno in matplotlib.colors.cnames.items():
+ matplotcolor[name]=hexno
+
+def getRandColor():
+ k = random.choice(matplotcolor.keys())
+ if k in ignoreColor:
+ return getRandColor()
+ else:
+ #return matplotcolor[k]
+ return str(matplotlib.colors.cnames[k])
+
+def getColor(iteminfo):
+ """ Getting a textcolor and background color for the given mooseObject \
+ If textcolor is empty replaced with green \
+ background color is empty replaced with blue
+ if textcolor and background is same as it happend in kkit files \
+ replacing textcolor with random color\
+ The colors are not valid there are siliently replaced with some values \
+ but while model building can raise an exception
+ """
+ textcolor = moose.element(iteminfo).textColor
+ bgcolor = moose.element(iteminfo).color
+ if(textcolor == ''): textcolor = 'green'
+
+ if(bgcolor == ''): bgcolor = 'orange'
+
+ if(textcolor == bgcolor):
+ textcolor = getRandColor()
+
+ textcolor = colorCheck(textcolor)
+ bgcolor = colorCheck(bgcolor)
+ # if moose.exists(iteminfo):
+ # moose.element(iteminfo).textColor = textcolor
+ # moose.element(iteminfo).color = bgcolor
+ return(textcolor,bgcolor)
+
+def colorCheck(fc_bgcolor):
+ """ textColor or background can be anything like string or tuple or list \
+ if string its taken as colorname further down in validColorcheck checked for valid color, \
+ but for tuple and list its taken as r,g,b value.
+ """
+ if isinstance(fc_bgcolor,str):
+ if fc_bgcolor.startswith("#"):
+ fc_bgcolor = fc_bgcolor
+ elif fc_bgcolor.isdigit():
+ """ color is int a map from int to r,g,b triplets from pickled color map file """
+ tc = (int(fc_bgcolor))*2
+ if tc < len(colorMap):
+ pickledColor = colorMap[tc]
+ else:
+ pickledColor = (255, 0, 0)
+ fc_bgcolor = '#%02x%02x%02x' % (pickledColor)
+
+ elif fc_bgcolor.isalpha() or fc_bgcolor.isalnum():
+ fc_bgcolor = validColorcheck(fc_bgcolor)
+
+ else:
+ for r in ['[',']','(',')']:
+ fc_bgcolor = fc_bgcolor.replace(r,"")
+ fc_bgcolor = fc_bgcolor.split(",")
+ c = 0
+ hexlist ="#"
+ for n in fc_bgcolor:
+ if c < 3:
+ hexlist = hexlist+str("%02x" % int(n))
+ c = c+1;
+ fc_bgcolor = hexlist
+ return(fc_bgcolor)
+
+def validColorcheck(color):
+ '''
+ Both in Qt4.7 and 4.8 if not a valid color it makes it as back but in 4.7 there will be a warning mssg which is taken here
+ checking if textcolor or backgroundcolor is valid color, if 'No' making white color as default
+ where I have not taken care for checking what will be backgroundcolor for textcolor or textcolor for backgroundcolor
+ '''
+ #if QColor(color).isValid():
+ if matplotlib.colors.is_color_like(color):
+ if color == "blue":
+ color = "orange"
+ color = matplotlib.colors.cnames[color.lower()]
+ return color
+ else:
+ return(matplotlib.colors.cnames["orange"])
def xyPosition(objInfo,xory):
try:
@@ -89,7 +184,7 @@ def setupMeshObj(modelRoot):
ymin = min(ycord)
ymax = max(ycord)
return meshEntry,xmin,xmax,ymin,ymax,positionInfoExist,listOfitems
-
+
def getxyCord(xcord,ycord,list1,listOfitems):
for item in list1:
# if isinstance(item,Function):
diff --git a/moose-core/python/moose/chemUtil/rainbow2.pkl b/moose-core/python/moose/chemUtil/rainbow2.pkl
new file mode 100644
index 0000000000000000000000000000000000000000..8097c29c7e173bd42aaec157acaf806579f61af2
--- /dev/null
+++ b/moose-core/python/moose/chemUtil/rainbow2.pkl
@@ -0,0 +1,514 @@
+((I248
+I0
+I255
+tp0
+(I240
+I0
+I255
+tp1
+(I232
+I0
+I255
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+(I224
+I0
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+(I216
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+(I208
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+tp5
+(I200
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+tp6
+(I192
+I0
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+tp7
+(I184
+I0
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+(I176
+I0
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+tp9
+(I168
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+tp10
+(I160
+I0
+I255
+tp11
+(I152
+I0
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+tp12
+(I144
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+(I136
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+(I128
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+(I120
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+(I112
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+(I216
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+(I224
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+(I232
+I255
+I0
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+(I240
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+(I248
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+(I255
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+(I255
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+(I255
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+(I255
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+(I255
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+I0
+tp101
+(I255
+I200
+I0
+tp102
+(I255
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+I0
+tp103
+(I255
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+I0
+tp104
+(I255
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+I0
+tp105
+(I255
+I168
+I0
+tp106
+(I255
+I160
+I0
+tp107
+(I255
+I152
+I0
+tp108
+(I255
+I144
+I0
+tp109
+(I255
+I136
+I0
+tp110
+(I255
+I128
+I0
+tp111
+(I255
+I120
+I0
+tp112
+(I255
+I112
+I0
+tp113
+(I255
+I104
+I0
+tp114
+(I255
+I96
+I0
+tp115
+(I255
+I88
+I0
+tp116
+(I255
+I80
+I0
+tp117
+(I255
+I72
+I0
+tp118
+(I255
+I64
+I0
+tp119
+(I255
+I56
+I0
+tp120
+(I255
+I48
+I0
+tp121
+(I255
+I40
+I0
+tp122
+(I255
+I32
+I0
+tp123
+(I255
+I24
+I0
+tp124
+(I255
+I16
+I0
+tp125
+(I255
+I8
+I0
+tp126
+(I255
+I0
+I0
+tp127
+tp128
+.
\ No newline at end of file
diff --git a/moose-core/python/moose/genesis/writeKkit.py b/moose-core/python/moose/genesis/writeKkit.py
index 6227bc0b638f7ec00e61250c5d8169c1a6dcabcf..009f229911812e95e84ddc660050070ec855a699 100644
--- a/moose-core/python/moose/genesis/writeKkit.py
+++ b/moose-core/python/moose/genesis/writeKkit.py
@@ -271,9 +271,9 @@ def writeConcChan(modelpath,f,sceneitems):
else:
error = error + "\n x and y co-ordinates are not specified for `" + cChan.name+ "` zero will be assigned \n "
if color == "" or color == " ":
- color = getRandColor()
+ color = getRandomColor()
if textcolor == "" or textcolor == " ":
- textcolor = getRandColor()
+ textcolor = getRandomColor()
f.write("simundump kchan /kinetics/" + trimPath(cChan)+ " " + str(int(1)) + " " + str(cChan.permeability)+ " " +
str(int(0)) + " " +
str(int(0)) + " " +
@@ -344,9 +344,9 @@ def writeEnz( modelpath,f,sceneitems):
else:
error = error + "\n x and y co-ordinates are not specified for `" + enz.name+ "` zero will be assigned \n "
if color == "" or color == " ":
- color = getRandColor()
+ color = getRandomColor()
if textcolor == "" or textcolor == " ":
- textcolor = getRandColor()
+ textcolor = getRandomColor()
f.write("simundump kenz /kinetics/" + trimPath(enz) + " " + str(int(0))+ " " +
str(concInit) + " " +
@@ -421,9 +421,9 @@ def writeReac(modelpath,f,sceneitems):
y = 0
error = error + "\n x and y co-ordinates are not specified for `" + reac.name+ "` zero will be assigned \n "
if color == "" or color == " ":
- color = getRandColor()
+ color = getRandomColor()
if textcolor == "" or textcolor == " ":
- textcolor = getRandColor()
+ textcolor = getRandomColor()
f.write("simundump kreac /kinetics/" + trimPath(reac) + " " +str(0) +" "+ str(kf) + " " + str(kb) + " \"\" " +
str(color) + " " + str(textcolor) + " " + str(int(x)) + " " + str(int(y)) + " "+ str(0)+"\n")
return reacList,error
@@ -574,9 +574,9 @@ def writeplot( tgraphs,f ):
fg = getColorCheck(fg,GENESIS_COLOR_SEQUENCE)
tabPath = re.sub("\[[0-9]+\]", "", tabPath)
if tabPath.find("conc1") >= 0 or tabPath.find("conc2") >= 0:
- first = first + "simundump xplot " + tabPath + " 3 524288 \\\n" + "\"delete_plot.w <s> <d>; edit_plot.D <w>\" " + fg + " 0 0 1\n"
+ first = first + "simundump xplot " + tabPath + " 3 524288 \\\n" + "\"delete_plot.w <s> <d>; edit_plot.D <w>\" " + str(fg) + " 0 0 1\n"
if tabPath.find("conc3") >= 0 or tabPath.find("conc4") >= 0:
- second = second + "simundump xplot " + tabPath + " 3 524288 \\\n" + "\"delete_plot.w <s> <d>; edit_plot.D <w>\" " + fg + " 0 0 1\n"
+ second = second + "simundump xplot " + tabPath + " 3 524288 \\\n" + "\"delete_plot.w <s> <d>; edit_plot.D <w>\" " + str(fg) + " 0 0 1\n"
return first,second
def writePool(modelpath,f,volIndex,sceneitems):
@@ -628,9 +628,9 @@ def writePool(modelpath,f,volIndex,sceneitems):
geometryName = volIndex[float(poolsCmpt.volume)]
volume = p.volume * NA * 1e-3
if color == "" or color == " ":
- color = getRandColor()
+ color = getRandomColor()
if textcolor == "" or textcolor == " ":
- textcolor = getRandColor()
+ textcolor = getRandomColor()
f.write("simundump kpool /kinetics/" + trimPath(p) + " 0 " +
str(p.diffConst) + " " +
str(0) + " " +
@@ -673,7 +673,7 @@ def getColorCheck(color,GENESIS_COLOR_SEQUENCE):
else:
raise Exception("Invalid Color Value!")
-def getRandColor():
+def getRandomColor():
ignoreColor= ["mistyrose","antiquewhite","aliceblue","azure","bisque","black","blanchedalmond","blue","cornsilk","darkolivegreen","darkslategray","dimgray","floralwhite","gainsboro","ghostwhite","honeydew","ivory","lavender","lavenderblush","lemonchiffon","lightcyan","lightgoldenrodyellow","lightgray","lightyellow","linen","mediumblue","mintcream","navy","oldlace","papayawhip","saddlebrown","seashell","snow","wheat","white","whitesmoke","aquamarine","lightsalmon","moccasin","limegreen","snow","sienna","beige","dimgrey","lightsage"]
matplotcolor = {}
for name,hexno in matplotlib.colors.cnames.items():
@@ -681,7 +681,7 @@ def getRandColor():
k = random.choice(list(matplotcolor.keys()))
if k in ignoreColor:
- return getRandColor()
+ return getRandomColor()
else:
return k
def writeCompartment(modelpath,compts,f):
diff --git a/moose-core/python/moose/helper.py b/moose-core/python/moose/helper.py
new file mode 100644
index 0000000000000000000000000000000000000000..79af6868a338709dc03d5a66aae15491ee8a4d1c
--- /dev/null
+++ b/moose-core/python/moose/helper.py
@@ -0,0 +1,83 @@
+"""helper.py:
+
+Some helper functions which are compatible with both python2 and python3.
+"""
+
+__author__ = "Dilawar Singh"
+__copyright__ = "Copyright 2017-, Dilawar Singh"
+__version__ = "1.0.0"
+__maintainer__ = "Dilawar Singh"
+__email__ = "dilawars@ncbs.res.in"
+__status__ = "Development"
+
+import os
+import re
+import subprocess
+
+def execute(cmd):
+ """execute: Execute a given command.
+
+ :param cmd: string, given command.
+
+ Return:
+ ------
+ Return a iterator over output.
+ """
+ popen = subprocess.Popen(cmd, stdout=subprocess.PIPE, universal_newlines=True)
+ for stdout_line in iter(popen.stdout.readline, ""):
+ yield stdout_line
+ popen.stdout.close()
+ return_code = popen.wait()
+ if return_code:
+ raise subprocess.CalledProcessError(return_code, cmd)
+
+
+def find_files( dirname, ext=None, name_contains=None, text_regex_search=None):
+ files = []
+ for d, sd, fs in os.walk(dirname):
+ for f in fs:
+ fpath = os.path.join(d,f)
+ include = True
+ if ext is not None:
+ if f.split('.')[-1] != ext:
+ include = False
+ if name_contains:
+ if name_contains not in os.path.basename(f):
+ include = False
+ if text_regex_search:
+ with open(fpath, 'r' ) as f:
+ txt = f.read()
+ if re.search(text_regex_search, txt) is None:
+ include = False
+ if include:
+ files.append(fpath)
+ return files
+
+# Matplotlib text for running simulation. It make sures at each figure is saved
+# to individual png files.
+matplotlibText = """
+print( '>>>> saving all figues')
+import matplotlib.pyplot as plt
+def multipage(filename, figs=None, dpi=200):
+ pp = PdfPages(filename)
+ if figs is None:
+ figs = [plt.figure(n) for n in plt.get_fignums()]
+ for fig in figs:
+ fig.savefig(pp, format='pdf')
+ pp.close()
+
+def saveall(prefix='results', figs=None):
+ if figs is None:
+ figs = [plt.figure(n) for n in plt.get_fignums()]
+ for i, fig in enumerate(figs):
+ outfile = '%s.%d.png' % (prefix, i)
+ fig.savefig(outfile)
+ print( '>>>> %s saved.' % outfile )
+ plt.close()
+
+try:
+ saveall()
+except Exception as e:
+ print( '>>>> Error in saving: %s' % e )
+ quit(0)
+"""
diff --git a/moose-core/python/moose/moose.py b/moose-core/python/moose/moose.py
index c3c6b60db6cf3de1c49cd6d2e5516d7bc2b91d22..191d26d4cba4f87931c464f44d68d0240a10e361 100644
--- a/moose-core/python/moose/moose.py
+++ b/moose-core/python/moose/moose.py
@@ -1,8 +1,9 @@
# -*- coding: utf-8 -*-
+from __future__ import print_function, division, absolute_import
+
# Author: Subhasis Ray
# Maintainer: Dilawar Singh, Harsha Rani, Upi Bhalla
-from __future__ import print_function, division, absolute_import
import warnings
import os
import pydoc
@@ -104,6 +105,7 @@ def loadModel(filename, modelpath, solverclass="gsl"):
else:
mu.error( "Unknown model extenstion '%s'" % extension)
return None
+
# Version
def version( ):
@@ -154,7 +156,21 @@ def mooseReadSBML(filepath, loadpath, solver='ee',validate="on"):
"""
global sbmlImport_
if sbmlImport_:
- return _readSBML.mooseReadSBML(filepath, loadpath, solver, validate)
+ modelpath = _readSBML.mooseReadSBML(filepath, loadpath, solver, validate)
+ sc = solver.lower()
+ if sc in ["gssa","gillespie","stochastic","gsolve"]:
+ method = "gssa"
+ elif sc in ["gsl","runge kutta","deterministic","ksolve","rungekutta","rk5","rkf","rk"]:
+ method = "gsl"
+ elif sc in ["exponential euler","exponentialeuler","neutral"]:
+ method = "ee"
+ else:
+ method = "ee"
+
+ if method != 'ee':
+ chemError = _chemUtil.add_Delete_ChemicalSolver.mooseAddChemSolver(modelpath[0].path, method)
+
+ return modelpath
else:
print( sbmlError_ )
return False
@@ -652,3 +668,7 @@ def doc(arg, inherited=True, paged=True):
pager(text)
else:
print(text)
+
+
+#
+# moose.py ends here
diff --git a/moose-core/python/moose/server.py b/moose-core/python/moose/server.py
index 400058a39e6b21c2d4cbee6de296046d4d940abd..9a9820e6809e734d6d64411fcc9c37493ea95dd8 100644
--- a/moose-core/python/moose/server.py
+++ b/moose-core/python/moose/server.py
@@ -1,5 +1,11 @@
# -*- coding: utf-8 -*-
-from __future__ import print_function, division
+from __future__ import print_function, division, absolute_import
+
+# This is moose.server.
+# It accepts simulation request on a specified TCP port (default 31417).
+# It simulates the given file (usually a archive file e.g., tar.bz2) and sends
+# back artefacts generated by simulation (mostly images); and streams data from
+# moose.Tables back to client.
__author__ = "Dilawar Singh"
__copyright__ = "Copyright 2019, Dilawar Singh"
@@ -12,18 +18,15 @@ import sys
import re
import os
import time
+import math
import shutil
import socket
import signal
import tarfile
import tempfile
import threading
-import datetime
-import subprocess
import logging
-
-# setup environment variables for the streamer starts working.
-os.environ['MOOSE_SOCKET_STREAMER_ADDRESS'] = 'ghevar.ncbs.res.in:31416'
+import subprocess
# create a logger for this server.
logging.basicConfig(
@@ -34,7 +37,7 @@ logging.basicConfig(
filemode='a'
)
console = logging.StreamHandler()
-console.setLevel(logging.INFO)
+console.setLevel(logging.DEBUG)
formatter = logging.Formatter('%(name)-12s: %(levelname)-8s %(message)s')
console.setFormatter(formatter)
_logger = logging.getLogger('')
@@ -42,20 +45,54 @@ _logger.addHandler(console)
__all__ = [ 'serve' ]
+# Global variable to stop all running threads.
stop_all_ = False
+sock_ = None
+stop_streamer_ = {}
-def handler(signum, frame):
- global stop_all_
- _logger.info( "User terminated all processes." )
- stop_all_ = True
+# Use prefixL_ bytes to encode the size of stream. One can probably use just one
+# byte to do. Lets go with the inefficient one for now.
+prefixL_ = 9
+
+# Matplotlib text for running simulation. It make sures at each figure is saved
+# to individual png files.
+matplotlibText = """
+print( '>>>> saving all figues')
+import matplotlib.pyplot as plt
+def multipage(filename, figs=None, dpi=200):
+ pp = PdfPages(filename)
+ if figs is None:
+ figs = [plt.figure(n) for n in plt.get_fignums()]
+ for fig in figs:
+ fig.savefig(pp, format='pdf')
+ pp.close()
+
+def saveall(prefix='results', figs=None):
+ if figs is None:
+ figs = [plt.figure(n) for n in plt.get_fignums()]
+ for i, fig in enumerate(figs):
+ outfile = '%s.%d.png' % (prefix, i)
+ fig.savefig(outfile)
+ print( '>>>> %s saved.' % outfile )
+ plt.close()
-signal.signal( signal.SIGINT, handler)
+try:
+ saveall()
+except Exception as e:
+ print( '>>>> Error in saving: %s' % e )
+ quit(0)
+"""
-def split_data( data ):
- prefixLenght = 10
- return data[:prefixLenght].strip(), data[prefixLenght:]
def execute(cmd):
+ """execute: Execute a given command.
+
+ :param cmd: string, given command.
+
+ Return:
+ ------
+ Return a iterator over output.
+ """
popen = subprocess.Popen(cmd, stdout=subprocess.PIPE, universal_newlines=True)
for stdout_line in iter(popen.stdout.readline, ""):
yield stdout_line
@@ -64,52 +101,82 @@ def execute(cmd):
if return_code:
raise subprocess.CalledProcessError(return_code, cmd)
-def send_msg(msg, conn):
+
+def find_files( dirname, ext=None, name_contains=None, text_regex_search=None):
+ files = []
+ for d, sd, fs in os.walk(dirname):
+ for f in fs:
+ fpath = os.path.join(d,f)
+ include = True
+ if ext is not None:
+ if f.split('.')[-1] != ext:
+ include = False
+ if name_contains:
+ if name_contains not in os.path.basename(f):
+ include = False
+ if text_regex_search:
+ with open(fpath, 'r' ) as f:
+ txt = f.read()
+ if re.search(text_regex_search, txt) is None:
+ include = False
+ if include:
+ files.append(fpath)
+ return files
+
+def prefix_data_with_size(data):
+ global prefixL_
+ prefix = b'0'*(prefixL_-int(math.log10(len(data)))-1) + b'%d' % len(data)
+ assert len(prefix) == prefixL_
+ return b'%s%s' % (prefix, data)
+
+# Signal handler.
+def signal_handler(signum, frame):
+ global stop_all_
+ global sock_
+ _logger.info( "User terminated all processes." )
+ stop_all_ = True
+ # sock_.shutdown( socket.SHUT_RDWR )
+ sock_.close()
+ time.sleep(1)
+ quit(1)
+
+
+def split_data( data ):
+ global prefixL_
+ return data[:prefixL_].strip(), data[prefixL_:]
+
+def send_msg(msg, conn, prefix='LOG'):
if not msg.strip():
return False
- _logger.debug( msg )
- msg = '%s>>> %s' % (socket.gethostname(), msg)
- conn.sendall( b'%010d%s' % (len(msg), msg))
+ if prefix != 'TAB':
+ _logger.debug(msg)
+ else:
+ _logger.debug( 'Sending msg with size %d' % len(msg))
+ msg = '<%s>%s' % (prefix, msg)
+ conn.sendall(prefix_data_with_size(msg))
def run(cmd, conn, cwd=None):
+ _logger.info( "Executing %s" % cmd )
oldCWD = os.getcwd()
if cwd is not None:
os.chdir(cwd)
- _logger.debug( "Executing in %s" % os.getcwd() )
- for line in execute(cmd.split()):
- send_msg(line, conn)
+ try:
+ for line in execute(cmd.split()):
+ if line:
+ send_msg(line, conn)
+ except Exception as e:
+ send_msg("Simulation failed: %s" % e, conn)
os.chdir(oldCWD)
-def find_files_to_run( files ):
- """Any file name starting with __main is to be run."""
- toRun = []
- for f in files:
- if '__main' in os.path.basename(f):
- toRun.append(f)
- if toRun:
- return toRun
-
- # Then guess.
- if len(files) == 1:
- return files
-
- for f in files:
- with open(f, 'r' ) as fh:
- txt = fh.read()
- if re.search(r'def\s+main\(', txt):
- if re.search('^\s+main\(\S+?\)', txt):
- toRun.append(f)
- return toRun
-
def recv_input(conn, size=1024):
# first 10 bytes always tell how much to read next. Make sure the submit job
# script has it
- d = conn.recv(10, socket.MSG_WAITALL)
- while len(d) < 10:
+ d = conn.recv(prefixL_, socket.MSG_WAITALL)
+ while len(d) < prefixL_:
try:
- d = conn.recv(10, socket.MSG_WAITALL)
+ d = conn.recv(prefixL_, socket.MSG_WAITALL)
except Exception:
- _logger.error( "Error in format. First 6 bytes are size of msg." )
+ _logger.error("MSG FORMAT: %d bytes are size of msg."%prefixL_)
continue
d, data = int(d), b''
while len(data) < d:
@@ -122,7 +189,7 @@ def writeTarfile( data ):
_logger.info( "Writing %d bytes to %s" % (len(data), tfile))
f.write(data)
# Sleep for some time so that file can be written to disk.
- time.sleep(0.2)
+ time.sleep(0.1)
if not tarfile.is_tarfile(tfile):
_logger.warn( 'Not a valid tar file: %s' % tfile)
return None
@@ -133,40 +200,65 @@ def suffixMatplotlibStmt( filename ):
with open(filename, 'r') as f:
txt = f.read()
- matplotlibText = '''
-# from matplotlib.backends.backend_pdf import PdfPages
-import matplotlib.pyplot as plt
-
-def multipage(filename, figs=None, dpi=200):
- pp = PdfPages(filename)
- if figs is None:
- figs = [plt.figure(n) for n in plt.get_fignums()]
- for fig in figs:
- fig.savefig(pp, format='pdf')
- pp.close()
-
-def saveall(prefix='results', figs=None):
- if figs is None:
- figs = [plt.figure(n) for n in plt.get_fignums()]
- for i, fig in enumerate(figs):
- fig.savefig('%s.%d.png' %(prefix,i) )
- plt.close()
-
-try:
- # multipage("results.pdf")
- saveall()
-except Exception as e:
- print( e )
- '''
with open(outfile, 'w' ) as f:
f.write( txt )
+ f.write( '\n' )
f.write( matplotlibText )
return outfile
+def streamer_client(socketPath, conn):
+ # Connect to running socket server.
+ global stop_streamer_
+ stop = False
+ _logger.debug( "Trying to connect to server at : %s" % socketPath )
+ while not os.path.exists( socketPath ):
+ #print( 'socket %s is not available yet.' % socketPath )
+ time.sleep(0.1)
+ stop = stop_streamer_[threading.currentThread().name]
+ if stop:
+ return
+
+ stClient = socket.socket(socket.AF_UNIX, socket.SOCK_STREAM)
+ try:
+ stClient.connect(socketPath)
+ except socket.error as e:
+ _logger.warning('Could not connect: %s' % e)
+ return
+
+ # send streaming data back to client. The streamer send fixed size messages
+ # of 1024/2048 bytes each (see the c++ implmenetation).
+ _logger.info( "Socket Streamer is connected with server." )
+ stClient.settimeout(0.05)
+ send_msg( b'Now streaming table data.', conn, 'TAB')
+ while not stop:
+ stop = stop_streamer_[threading.currentThread().name]
+ data = b''
+ try:
+ data = stClient.recv(1024)
+ if len(data.strip()) > 0:
+ send_msg(data, conn, 'TAB')
+ except socket.timeout:
+ continue
+ stClient.close()
+ if os.path.isfile(socketPath):
+ os.unlink(socketPath)
+
def run_file(filename, conn, cwd=None):
+ # set environment variable so that socket streamer can start.
+ global stop_streamer_
+ socketPath = os.path.join(tempfile.mkdtemp(), 'SOCK_TABLE_STREAMER')
+ os.environ['MOOSE_STREAMER_ADDRESS'] = socketPath
+ streamerThread = threading.Thread(target=streamer_client
+ , args=(socketPath, conn,))
+ stop_streamer_[streamerThread.name] = False
+ streamerThread.daemon = True
+ streamerThread.start()
filename = suffixMatplotlibStmt(filename)
run( "%s %s" % (sys.executable, filename), conn, cwd)
- _logger.info( '.... DONE' )
+ stop_streamer_[streamerThread.name] = True
+ streamerThread.join( timeout = 1)
+ if streamerThread.is_alive():
+ _logger.error( "The socket streamer client is still running...")
def extract_files(tfile, to):
userFiles = []
@@ -177,11 +269,9 @@ def extract_files(tfile, to):
except Exception as e:
_logger.warn( e)
# now check if all files have been extracted properly
- success = True
for f in userFiles:
if not os.path.exists(f):
_logger.error( "File %s could not be extracted." % f )
- success = False
return userFiles
def prepareMatplotlib( cwd ):
@@ -189,30 +279,48 @@ def prepareMatplotlib( cwd ):
f.write( 'interactive : True' )
def send_bz2(conn, data):
- data = b'%010d%s' % (len(data), data)
- conn.sendall(data)
+ global prefixL_
+ send_msg(data, conn, 'TAR')
-def sendResults(tdir, conn, fromThisTime):
+def sendResults(tdir, conn, notTheseFiles):
# Only send new files.
resdir = tempfile.mkdtemp()
resfile = os.path.join(resdir, 'results.tar.bz2')
-
with tarfile.open( resfile, 'w|bz2') as tf:
- for d, sd, fs in os.walk(tdir):
- for f in fs:
- fpath = os.path.join(d,f)
- if datetime.datetime.fromtimestamp(os.path.getmtime(fpath)) > fromThisTime:
- _logger.info( "Adding file %s" % f )
- tf.add(os.path.join(d, f), f)
+ for f in find_files(tdir, ext='png'):
+ _logger.info( "Adding file %s" % f )
+ tf.add(f, os.path.basename(f))
time.sleep(0.01)
# now send the tar file back to client
with open(resfile, 'rb' ) as f:
data = f.read()
- _logger.info( 'Total bytes in result: %d' % len(data))
+ _logger.info( 'Total bytes to send to client: %d' % len(data))
send_bz2(conn, data)
shutil.rmtree(resdir)
+def find_files_to_run( files ):
+ """Any file name starting with __main is to be run.
+ Many such files can be recieved by client.
+ """
+ toRun = []
+ for f in files:
+ if '__main' in os.path.basename(f):
+ toRun.append(f)
+ if toRun:
+ return toRun
+ # Else guess.
+ if len(files) == 1:
+ return files
+
+ for f in files:
+ with open(f, 'r' ) as fh:
+ txt = fh.read()
+ if re.search(r'def\s+main\(', txt):
+ if re.search('^\s+main\(\S+?\)', txt):
+ toRun.append(f)
+ return toRun
+
def simulate( tfile, conn ):
"""Simulate a given tar file.
"""
@@ -240,49 +348,56 @@ def savePayload( conn ):
def handle_client(conn, ip, port):
isActive = True
+ _logger.info( "Serving request from %s:%s" % (ip, port) )
while isActive:
tarfileName, nBytes = savePayload(conn)
if tarfileName is None:
_logger.warn( "Could not recieve data." )
isActive = False
- _logger.info( "PAYLOAD RECIEVED: %d" % nBytes )
if not os.path.isfile(tarfileName):
send_msg("[ERROR] %s is not a valid tarfile. Retry"%tarfileName, conn)
break
- startSimTime = datetime.datetime.now()
+
+ # list of files before the simulation.
+ notthesefiles = find_files(os.path.dirname(tarfileName))
res, msg = simulate( tarfileName, conn )
- if not res:
+ if 0 != res:
send_msg( "Failed to run simulation: %s" % msg, conn)
isActive = False
time.sleep(0.1)
- send_msg('>DONE SIMULATION', conn)
+
# Send results after DONE is sent.
- sendResults(os.path.dirname(tarfileName), conn, startSimTime)
+ send_msg('All done', conn, 'EOS')
+ sendResults(os.path.dirname(tarfileName), conn, notthesefiles)
+ break
+
def start_server( host, port, max_requests = 10 ):
global stop_all_
- soc = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
- soc.setsockopt(socket.SOL_SOCKET, socket.SO_REUSEADDR, 1)
+ global sock_
+ sock_ = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
+ sock_.setsockopt(socket.SOL_SOCKET, socket.SO_REUSEADDR, 1)
try:
- soc.bind( (host, port))
+ sock_.bind( (host, port))
_logger.info( "Server created %s:%s" %(host,port) )
except Exception as e:
_logger.error( "Failed to bind: %s" % e)
quit(1)
- # listen upto 100 of requests
- soc.listen(max_requests)
+ # listen upto 10 of requests
+ sock_.listen(max_requests)
while True:
- conn, (ip, port) = soc.accept()
- _logger.info( "Connected with %s:%s" % (ip, port) )
- try:
- t = threading.Thread(target=handle_client, args=(conn, ip, port))
- t.start()
- except Exception as e:
- _logger.warn(e)
if stop_all_:
break
- soc.close()
+ sock_.settimeout(10)
+ try:
+ conn, (ip, port) = sock_.accept()
+ except socket.timeout as e:
+ continue
+ sock_.settimeout(0.0)
+ t = threading.Thread(target=handle_client, args=(conn, ip, port))
+ t.start()
+ sock_.close()
def serve(host, port):
start_server(host, port)
@@ -290,11 +405,9 @@ def serve(host, port):
def main( args ):
global stop_all_
host, port = args.host, args.port
- try:
- serve(host, port)
- except KeyboardInterrupt:
- stop_all_ = True
- quit(1)
+ # Install a signal handler.
+ signal.signal( signal.SIGINT, signal_handler)
+ serve(host, port)
if __name__ == '__main__':
import argparse
diff --git a/moose-core/python/moose/streamer_utils.py b/moose-core/python/moose/streamer_utils.py
new file mode 100644
index 0000000000000000000000000000000000000000..a89f05025cc54e6d13fe0a55043d702a96df3d4b
--- /dev/null
+++ b/moose-core/python/moose/streamer_utils.py
@@ -0,0 +1,58 @@
+"""streamer_utils.py:
+
+Utility for Table streamer.
+
+"""
+
+__author__ = "Dilawar Singh"
+__copyright__ = "Copyright 2017-, Dilawar Singh"
+__version__ = "1.0.0"
+__maintainer__ = "Dilawar Singh"
+__email__ = "dilawars@ncbs.res.in"
+__status__ = "Development"
+
+import sys
+import os
+import numpy as np
+import math
+import struct
+from collections import defaultdict
+
+def bytes_to_np_arr(data):
+ return np.frombuffer(data, float)
+
+def np_array_to_string(arr):
+ return np.uint8(arr).tostring()
+
+def np_array_to_data(arr):
+ # Make sure that first char of arr is 'H'
+ n = 0
+ res = defaultdict(list)
+ while n < len(arr):
+ assert chr(int(arr[n])) == 'H', 'Expected H, Got %s'%arr[n]
+ hSize = int(arr[n+1])
+ n += 1
+ colName = np_array_to_string(arr[n+1:n+1+hSize])
+ n += hSize + 1
+ assert chr(int(arr[n])) == 'V', 'Expected V'
+ n += 1
+ dataSize = int(arr[n])
+ n += 1
+ res[colName].append(arr[n:n+dataSize])
+ n += dataSize
+ return { k : np.concatenate(v) for k, v in res.items() }
+
+def decode_data(data):
+ arr = bytes_to_np_arr(data)
+ assert int(arr[0]) == ord('H'), "First char must be H"
+ return np_array_to_data(arr)
+
+def test():
+ with open(sys.argv[1], 'rb') as f:
+ data = f.read()
+ print( "[INFO ] Total bytes read %d" % len(data))
+ s = decode_data(data)
+ print(s)
+
+if __name__ == '__main__':
+ test()
diff --git a/moose-core/python/moose/utils.py b/moose-core/python/moose/utils.py
index 64fdee8be38591246e6162cce2c658bce0a1b527..17c262d81c1b6637512525585af2080ab4270fa6 100644
--- a/moose-core/python/moose/utils.py
+++ b/moose-core/python/moose/utils.py
@@ -338,8 +338,10 @@ def autoposition(root):
def loadModel(filename, target,method='ee'):
moose.loadModel(filename,target)
- moose.mooseaddChemSolver(target,method)
-
+ moose.mooseAddChemSolver(target,method)
+ if moose.exists(target+'/kinetics/info'):
+ moose.element(target+'/kinetics/info').solver = method
+
def readcell_scrambled(filename, target, method='ee'):
"""A special version for handling cases where a .p file has a line
with specified parent yet to be defined.
diff --git a/moose-core/python/setup.cmake.py b/moose-core/python/setup.cmake.py
index c7254b402121afb4ebe16364f81c2c3204914599..ca67559d45c7a172b395eb03fdf937fcdf69da4d 100644
--- a/moose-core/python/setup.cmake.py
+++ b/moose-core/python/setup.cmake.py
@@ -59,5 +59,5 @@ setup(
],
install_requires = [ 'numpy' ],
package_dir = { 'moose' : 'moose', 'rdesigneur' : 'rdesigneur' },
- package_data = { 'moose' : ['_moose' + suffix, 'neuroml2/schema/NeuroMLCoreDimensions.xml'] },
+ package_data = { 'moose' : ['_moose' + suffix, 'neuroml2/schema/NeuroMLCoreDimensions.xml','chemUtil/rainbow2.pkl'] },
)
diff --git a/moose-core/scheduling/Clock.cpp b/moose-core/scheduling/Clock.cpp
index dd60aecf359bf4fc8698a40031a1f0fb2f6fc4a8..e407bb63883ae39be46dc6eb7a15d2fa81be2d0b 100644
--- a/moose-core/scheduling/Clock.cpp
+++ b/moose-core/scheduling/Clock.cpp
@@ -425,8 +425,8 @@ const Cinfo* Clock::initCinfo()
" Ksolve 16 0.1\n"
" Stats 17 0.1\n"
" Table2 18 1\n"
- " SocketStreamer 19 5\n"
- " Streamer 20 10\n"
+ " SocketStreamer 19 1\n"
+ " Streamer 20 5\n"
" HDF5DataWriter 30 1\n"
" HDF5WriterBase 30 1\n"
@@ -1030,8 +1030,8 @@ void Clock::buildDefaultTick()
defaultDt_[16] = 0.1;
defaultDt_[17] = 0.1;
defaultDt_[18] = 1; // For tables for chemical calculations.
- defaultDt_[19] = 5; // For Socket Streamer
- defaultDt_[20] = 10; // For CSV Streamer
+ defaultDt_[19] = 1; // For Socket Streamer
+ defaultDt_[20] = 5; // For CSV Streamer
// 20-29 are not assigned.
defaultDt_[30] = 1; // For the HDF writer
diff --git a/moose-core/shell/Shell.cpp b/moose-core/shell/Shell.cpp
index 1043f19d8b64af5eb157414ed15dd49b4a750603..fe55a708fe56d1cc53a3645611debd9de4a89f78 100644
--- a/moose-core/shell/Shell.cpp
+++ b/moose-core/shell/Shell.cpp
@@ -22,6 +22,7 @@
#include "../msg/OneToAllMsg.h"
#include "../msg/SparseMsg.h"
#include "../builtins/SocketStreamer.h"
+#include "../builtins/Streamer.h"
#include "Shell.h"
#include "Wildcard.h"
@@ -63,73 +64,68 @@ const Cinfo* Shell::initCinfo()
&Shell::setCwe,
&Shell::getCwe );
-////////////////////////////////////////////////////////////////
-// Dest Finfos: Functions handled by Shell
-////////////////////////////////////////////////////////////////
+
+ // Dest Finfos: Functions handled by Shell
static DestFinfo handleUseClock( "useClock"
- , "Deals with assignment of path to a given clock."
- " Arguments: path, field, tick number. "
- , new EpFunc4< Shell, string, string, unsigned int, unsigned int >(&Shell::handleUseClock )
- );
+ , "Deals with assignment of path to a given clock."
+ " Arguments: path, field, tick number. "
+ , new EpFunc4< Shell, string, string, unsigned int, unsigned int >(&Shell::handleUseClock )
+ );
static DestFinfo handleCreate( "create"
- , "create( class, parent, newElm, name, numData, isGlobal )"
- , new EpFunc6<Shell, string, ObjId, Id, string, NodeBalance, unsigned int>(&Shell::handleCreate)
- );
+ , "create( class, parent, newElm, name, numData, isGlobal )"
+ , new EpFunc6<Shell, string, ObjId, Id, string, NodeBalance, unsigned int>(&Shell::handleCreate)
+ );
static DestFinfo handleDelete( "delete"
- , "When applied to a regular object, this function operates "
- "on the Id (element) specified by the ObjId argument. "
- "The function deletes the entire object "
- "array on this Id, including all dataEntries on it,"
- "all its messages, and all its children. The DataIndex here "
- "is ignored, and all dataEntries are destroyed. \n"
- "When applied to a message: Destroys only that one specific "
- "message identified by the full ObjId. \n"
- "Args: ObjId\n"
- , new EpFunc1< Shell, ObjId >( & Shell::destroy )
- );
+ , "When applied to a regular object, this function operates "
+ "on the Id (element) specified by the ObjId argument. "
+ "The function deletes the entire object "
+ "array on this Id, including all dataEntries on it,"
+ "all its messages, and all its children. The DataIndex here "
+ "is ignored, and all dataEntries are destroyed. \n"
+ "When applied to a message: Destroys only that one specific "
+ "message identified by the full ObjId. \n"
+ "Args: ObjId\n"
+ , new EpFunc1< Shell, ObjId >( & Shell::destroy )
+ );
static DestFinfo handleAddMsg( "addMsg"
- , "Makes a msg. Arguments are:"
- " msgtype, src object, src field, dest object, dest field"
- , new EpFunc6< Shell, string, ObjId, string, ObjId, string, unsigned int >(&Shell::handleAddMsg)
- );
+ , "Makes a msg. Arguments are:"
+ " msgtype, src object, src field, dest object, dest field"
+ , new EpFunc6< Shell, string, ObjId, string, ObjId, string, unsigned int >(&Shell::handleAddMsg)
+ );
static DestFinfo handleQuit( "quit"
- , "Stops simulation running and quits the simulator"
- , new OpFunc0< Shell >( & Shell::handleQuit )
- );
+ , "Stops simulation running and quits the simulator"
+ , new OpFunc0< Shell >( & Shell::handleQuit )
+ );
+
static DestFinfo handleMove( "move"
- , "handleMove( Id orig, Id newParent ): "
- "moves an Element to a new parent"
- , new EpFunc2<Shell, Id, ObjId>( & Shell::handleMove )
- );
+ , "handleMove( Id orig, Id newParent ): "
+ "moves an Element to a new parent"
+ , new EpFunc2<Shell, Id, ObjId>( & Shell::handleMove )
+ );
static DestFinfo handleCopy( "copy"
- , "handleCopy( vector< Id > args, string newName, unsigned int nCopies, bool toGlobal, bool copyExtMsgs ): "
- " The vector< Id > has Id orig, Id newParent, Id newElm. "
- "This function copies an Element and all its children to a new parent."
- " May also expand out the original into nCopies copies."
- " Normally all messages within the copy tree are also copied. "
- " If the flag copyExtMsgs is true, then all msgs going out are also copied."
- , new EpFunc5< Shell, vector< ObjId >, string, unsigned int, bool, bool >(
- & Shell::handleCopy )
- );
+ , "handleCopy( vector< Id > args, string newName, unsigned int nCopies, bool toGlobal, bool copyExtMsgs ): "
+ " The vector< Id > has Id orig, Id newParent, Id newElm. "
+ "This function copies an Element and all its children to a new parent."
+ " May also expand out the original into nCopies copies."
+ " Normally all messages within the copy tree are also copied. "
+ " If the flag copyExtMsgs is true, then all msgs going out are also copied."
+ , new EpFunc5< Shell, vector< ObjId >, string, unsigned int, bool, bool >(
+ & Shell::handleCopy )
+ );
static DestFinfo setclock( "setclock"
- , "Assigns clock ticks. Args: tick#, dt"
- , new OpFunc2< Shell, unsigned int, double >( & Shell::doSetClock )
- );
+ , "Assigns clock ticks. Args: tick#, dt"
+ , new OpFunc2< Shell, unsigned int, double >( & Shell::doSetClock )
+ );
static Finfo* shellFinfos[] =
{
&setclock,
- ////////////////////////////////////////////////////////////////
- // Shared msg
- ////////////////////////////////////////////////////////////////
- // &master,
- // &worker,
&handleCreate,
&handleDelete,
&handleCopy,
@@ -190,9 +186,8 @@ void Shell::setShellElement( Element* shelle )
*
*/
Id Shell::doCreate( string type, ObjId parent, string name,
- unsigned int numData,
- NodePolicy nodePolicy,
- unsigned int preferredNode )
+ unsigned int numData, NodePolicy nodePolicy, unsigned int preferredNode
+ )
{
const Cinfo* c = Cinfo::find( type );
@@ -650,8 +645,8 @@ bool Shell::isRunning() const
* This gets a bit complicated if the Element is a multidim array.
*/
void Shell::handleCreate( const Eref& e,
- string type, ObjId parent, Id newElm, string name,
- NodeBalance nb, unsigned int parentMsgIndex )
+ string type, ObjId parent, Id newElm, string name,
+ NodeBalance nb, unsigned int parentMsgIndex )
{
innerCreate( type, parent, newElm, name, nb, parentMsgIndex );
}
@@ -702,8 +697,7 @@ bool Shell::adopt( Id parent, Id child, unsigned int msgIndex )
* Assumes we've already done all the argument checking.
*/
void Shell::innerCreate( string type, ObjId parent, Id newElm, string name,
- const NodeBalance& nb, unsigned int msgIndex )
-// unsigned int numData, bool isGlobal
+ const NodeBalance& nb, unsigned int msgIndex )
{
const Cinfo* c = Cinfo::find( type );
if ( c )
@@ -720,7 +714,6 @@ void Shell::innerCreate( string type, ObjId parent, Id newElm, string name,
case MooseSingleNode:
cout << "Error: Shell::innerCreate: Yet to implement SingleNodeDataElement. Making BlockBalance.\n";
ret = new LocalDataElement( newElm, c, name, nb.numData );
- // ret = new SingleNodeDataElement( newElm, c, name, numData, nb.preferredNode );
break;
};
assert( ret );
@@ -728,9 +721,7 @@ void Shell::innerCreate( string type, ObjId parent, Id newElm, string name,
ret->setTick( Clock::lookupDefaultTick( c->name() ) );
}
else
- {
assert( 0 );
- }
}
void Shell::destroy( const Eref& e, ObjId oid)
diff --git a/moose-core/tests/python/testDisabled_socket_streamer_tcp.py b/moose-core/tests/python/testDisabled_socket_streamer_tcp.py
new file mode 100644
index 0000000000000000000000000000000000000000..7a9153f1b00002a07952c1fea538bb62bce372d0
--- /dev/null
+++ b/moose-core/tests/python/testDisabled_socket_streamer_tcp.py
@@ -0,0 +1,106 @@
+# -*- coding: utf-8 -*-
+from __future__ import print_function, division
+
+__author__ = "Dilawar Singh"
+__copyright__ = "Copyright 2016, Dilawar Singh"
+__credits__ = ["NCBS Bangalore"]
+__license__ = "GNU GPL"
+__version__ = "1.0.0"
+__maintainer__ = "Dilawar Singh"
+__email__ = "dilawars@ncbs.res.in"
+__status__ = "Development"
+
+import os
+import sys
+sys.path.append(os.path.dirname(__file__))
+import time
+import socket
+import numpy as np
+import multiprocessing as mp
+import moose
+import moose.utils as mu
+import models
+from collections import defaultdict
+
+print( '[INFO] Using moose form %s' % moose.__file__ )
+
+port_ = 3114
+
+def socket_client(q, done):
+ global port_
+ # This function waits for socket to be available.
+ s = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
+ s.setsockopt(socket.SOL_SOCKET, socket.SO_REUSEADDR, 1)
+
+ while 1:
+ if 1 == done.value:
+ print( '[INFO] MOOSE is done before I could connect' )
+ q.put({})
+ return
+ s.settimeout(0.5)
+ try:
+ s.connect( ('127.0.0.1', port_) )
+ except socket.timeout as e:
+ print(e)
+ break
+
+ print( 'Py: Connected' )
+
+ # This is client reponsibility to read the data.
+ s.settimeout(0.01)
+ data = b''
+ while True:
+ try:
+ data += s.recv(1024)
+ except socket.timeout:
+ print(end='x')
+ if 1 == done.value:
+ break
+ if data:
+ res = mu.decode_data(data)
+ q.put(res)
+ else:
+ q.put({})
+ s.close()
+ return
+
+def test():
+ global finish_all_
+ os.environ['MOOSE_STREAMER_ADDRESS'] = 'http://127.0.0.1:%d'%port_
+ done = mp.Value('d', 0)
+ q = mp.Queue()
+ client = mp.Process(target=socket_client, args=(q, done))
+ client.start()
+
+ time.sleep(0.1)
+
+ print( '[INFO] Socket client is running now' )
+ ts = models.simple_model_a()
+ moose.reinit()
+ time.sleep(0.1)
+ # If TCP socket is created, some delay is often neccessary before start. Don't
+ # know why. probably some latency in a fresh TCP socket. A TCP guru can
+ # tell.
+ moose.start(50)
+ print( 'MOOSE is done' )
+
+ time.sleep(0.5)
+ done.value = 1
+ res = q.get()
+ client.join()
+
+ if not res:
+ raise RuntimeWarning('Nothing was streamed')
+ for k in res:
+ a = res[k][1::2]
+ b = moose.element(k).vector
+ print(k, len(a), len(b))
+ assert( (a==b).all())
+ print( 'Test 1 passed' )
+
+def main( ):
+ test( )
+ print( '[INFO] All tests passed' )
+
+if __name__ == '__main__':
+ main()
diff --git a/moose-core/tests/python/test_socket_streamer_multitab.py b/moose-core/tests/python/test_socket_streamer_multitab.py
new file mode 100644
index 0000000000000000000000000000000000000000..7f3fe8abe777303e3e7ee6451297c827f8cba877
--- /dev/null
+++ b/moose-core/tests/python/test_socket_streamer_multitab.py
@@ -0,0 +1,148 @@
+# -*- coding: utf-8 -*-
+'''
+Here is some docstring.
+'''
+from __future__ import print_function, division
+
+import os
+import random
+import time
+import multiprocessing as mp
+import socket
+import moose
+import json
+import struct
+import numpy as np
+import moose.utils as mu
+
+
+print('Using from %s. VERSION: %s' % (moose.__file__, moose.__version__))
+
+sockPath = '/tmp/MOOSE'
+os.environ['MOOSE_STREAMER_ADDRESS'] = 'file://%s' % sockPath
+
+
+def streamer_handler(done, q):
+ # Streamer handler
+ global sockPath
+ global all_done_
+ s = socket.socket(socket.AF_UNIX, socket.SOCK_STREAM)
+ while not os.path.exists(sockPath):
+ time.sleep(0.01)
+ if done.value == 1:
+ break
+ s.connect( sockPath )
+ print( "[INFO ] Connected" )
+ s.settimeout(1e-5)
+ data = b''
+ while True:
+ if done.value == 1:
+ break
+ try:
+ d = s.recv(10240)
+ if d.strip():
+ data += d
+ except socket.timeout:
+ pass
+
+ res = mu.decode_data(data)
+ q.put(res)
+
+def make_network():
+ """
+ This snippet sets up a recurrent network of IntFire objects, using
+ SimpleSynHandlers to deal with spiking events.
+ It isn't very satisfactory as activity runs down after a while.
+ It is a good example for using the IntFire, setting up random
+ connectivity, and using SynHandlers.
+ """
+ global all_done_
+ done = mp.Value('i', 0)
+ q = mp.Queue()
+ th = mp.Process(target=streamer_handler, args=(done, q))
+ th.start()
+
+ size = 1024
+ dt = 0.2
+ runsteps = 10
+ delayMin = 0
+ delayMax = 4
+ weightMax = 1
+ Vmax = 1.0
+ thresh = 0.4
+ refractoryPeriod = 0.4
+ tau = 0.5
+ connectionProbability = 0.01
+ random.seed( 123 )
+ np.random.seed( 456 )
+ t0 = time.time()
+
+ network = moose.IntFire( 'network', size );
+ syns = moose.SimpleSynHandler( '/network/syns', size );
+ moose.connect( syns, 'activationOut', network, 'activation', 'OneToOne' )
+ moose.le( '/network' )
+ syns.vec.numSynapses = [1] * size
+ sv = moose.vec( '/network/syns/synapse' )
+ print('before connect t = %.3f'%(time.time() - t0))
+ mid = moose.connect( network, 'spikeOut', sv, 'addSpike', 'Sparse')
+ print('after connect t = %.3f'%(time.time() - t0))
+ #print mid.destFields
+ m2 = moose.element( mid )
+ m2.setRandomConnectivity( connectionProbability, 5489 )
+ print('after setting connectivity, t=%.3f'%(time.time() - t0))
+ #network.vec.Vm = [(Vmax*random.random()) for r in range(size)]
+ network.vec.Vm = np.random.rand( size ) * Vmax
+ network.vec.thresh = thresh
+ network.vec.refractoryPeriod = refractoryPeriod
+ network.vec.tau = tau
+ numSynVec = syns.vec.numSynapses
+ print('Middle of setup, t = %.3f'%(time.time() - t0))
+ numTotSyn = sum( numSynVec )
+ print((numSynVec.size, ', tot = ', numTotSyn, ', numSynVec = ', numSynVec))
+ for item in syns.vec:
+ h = moose.element(item)
+ h.synapse.delay = delayMin + (delayMax-delayMin) * np.random.rand(len(h.synapse))
+ h.synapse.weight = np.random.rand(len(h.synapse)) * weightMax
+ print('After setup, t = %.3f'%(time.time()-t0))
+
+ numStats = 100
+ stats = moose.SpikeStats( '/stats', numStats )
+ stats.vec.windowLength = 1 # timesteps to put together.
+ plots = moose.Table( '/plot', numStats )
+ convergence = size // numStats
+ for i in range( numStats ):
+ for j in range( size//numStats ):
+ k = i * convergence + j
+ moose.connect( network.vec[k], 'spikeOut', stats.vec[i], 'addSpike' )
+ moose.connect( plots, 'requestOut', stats, 'getMean', 'OneToOne' )
+
+ t1 = time.time()
+ moose.reinit()
+ print('reinit time t = %.3f'%(time.time() - t1))
+ network.vec.Vm = np.random.rand( size ) * Vmax
+ print('setting Vm , t = %.3f'%(time.time() - t1))
+ t1 = time.time()
+ moose.start(runsteps * dt, 1)
+ time.sleep(0.1)
+ done.value = 1
+ print('runtime, t = %.3f'%(time.time() - t1))
+ print(network.vec.Vm[99:103], network.vec.Vm[900:903])
+ res = q.get()
+
+ for tabPath in res:
+ aWithTime = res[tabPath]
+ a = aWithTime[1::2]
+ b = moose.element(tabPath).vector
+ print( tabPath, len(a), len(b) )
+ if len(a) == len(b):
+ assert np.equal(a, b).all()
+ else:
+ print( "Table did not equal size. The last table is allowed to "
+ " have fewer entries." )
+
+
+ th.join()
+ print( 'All done' )
+
+if __name__ == '__main__':
+ make_network()
diff --git a/moose-core/tests/python/test_socket_streamer_tcp.py b/moose-core/tests/python/test_socket_streamer_tcp.py
deleted file mode 100644
index 497b66fb0412df6a1e454dca10ed19775bb1a59f..0000000000000000000000000000000000000000
--- a/moose-core/tests/python/test_socket_streamer_tcp.py
+++ /dev/null
@@ -1,182 +0,0 @@
-# -*- coding: utf-8 -*-
-"""test_socket_streamer.py:
-
- MOOSE must create a socket server on PORT 31616 (default)
- or setup moose.SocketStreamer port to appropriate port number.
-
- Client can read data from this socket.
-"""
-
-from __future__ import print_function
-
-__author__ = "Dilawar Singh"
-__copyright__ = "Copyright 2016, Dilawar Singh"
-__credits__ = ["NCBS Bangalore"]
-__license__ = "GNU GPL"
-__version__ = "1.0.0"
-__maintainer__ = "Dilawar Singh"
-__email__ = "dilawars@ncbs.res.in"
-__status__ = "Development"
-
-import os
-import sys
-sys.path.append( os.path.dirname(__file__))
-import time
-import socket
-import numpy as np
-import threading
-import moose
-import models
-import json
-from collections import defaultdict
-
-finish_all_ = False
-
-print( '[INFO] Using moose form %s' % moose.__file__ )
-
-def get_msg(s, n=1024):
- d = s.recv( n, socket.MSG_WAITALL)
- while len(d) < n:
- d += s.recv(n-len(d), socket.MSG_WAITALL)
- return d
-
-def socket_client(host='127.0.0.1', port = 31416):
- # This function waits for socket to be available.
- global finish_all_
- s = socket.socket( socket.AF_INET, socket.SOCK_STREAM )
- while 1:
- if finish_all_:
- print( '[INFO] MOOSE is done before I could connect' )
- break
- # print('Py: Trying to connect to %s, %s' % (host, port))
- # print( end = '.' )
- try:
- s.connect( ('', port) )
- break
- except Exception as e:
- continue
- print(e, end = 'x')
- sys.stdout.flush()
- pass
-
- print( 'Connected' )
- if not finish_all_:
- print( 'Py: Connected with socket.' )
-
- # This is client reponsibility to read the data.
- s.settimeout(0.1)
- data = b''
- while not finish_all_:
- try:
- data += get_msg(s)
- except socket.timeout as e:
- print( e, end = ' ' )
-
- s.close()
- assert data, "No data streamed"
- print( 'recieved data:\n', data )
- res = defaultdict(list)
- for x in data.split(b'\n'):
- if not x.strip():
- continue
- d = json.loads(x)
- for k, v in d.items():
- res[k] += v
-
- expected = {u'/compt/tabB/tabC': ([25.,1.07754388], [14.71960144, 0.16830373])
- , u'/compt/a/tab': ([25., 0.42467006], [14.71960144, 0.16766705])
- , u'/compt/tabB': ([25., 2.57797725], [14.71960144, 0.16842971])
- }
- nd = {}
- for k in res:
- v = res[k]
- nd[k] = (np.mean(v, axis=0), np.std(v, axis=0))
- assert np.isclose(expected[k], nd[k]).all(), \
- "Exptected %s, got %s" % (str(expected[k]), str(nd[k]))
-
-def sanity_test( ):
- a = moose.Table( '/t1' )
- b = moose.Table( '/t1/t1' )
- c = moose.Table( '/t1/t1/t1' )
- st = moose.SocketStreamer( '/s' )
- st.addTable( a )
- assert( st.numTables == 1 )
- st.addTable( b )
- assert( st.numTables == 2 )
- st.addTable( c )
- assert( st.numTables == 3 )
- st.addTable( c )
- assert( st.numTables == 3 )
- st.addTable( c )
- assert( st.numTables == 3 )
-
- st.removeTable( c )
- assert( st.numTables == 2 )
- st.removeTable( c )
- assert( st.numTables == 2 )
- st.removeTable( a )
- assert( st.numTables == 1 )
- st.removeTable( b )
- assert( st.numTables == 0 )
- st.removeTable( b )
- assert( st.numTables == 0 )
- print( 'Sanity test passed' )
-
- st.addTables( [a, b, c ])
- assert st.numTables == 3
- st.removeTables( [a, a, c] )
- assert st.numTables == 1
- moose.delete( '/t1' )
- moose.delete( '/s' )
-
-def test():
- global finish_all_
- os.environ['MOOSE_STREAMER_ADDRESS'] = 'http://127.0.0.1:31416'
- client = threading.Thread(target=socket_client, args=())
- # client.daemon = True
- client.start()
- print( '[INFO] Socket client is running now' )
- tables = models.simple_model_a()
- time.sleep(0.1)
- moose.reinit()
- moose.start(50)
- print( 'MOOSE is done' )
-
- # sleep for some time so data can be read.
- time.sleep(1)
- finish_all_ = True
- client.join()
- print( 'Test 1 passed' )
-
-def test_without_env():
- global finish_all_
- os.environ['MOOSE_STREAMER_ADDRESS'] = ''
- client = threading.Thread(target=socket_client, args=())
- #client.daemon = True
- client.start()
- print( '[INFO] Socket client is running now' )
- tables = create_model()
- # Now create a streamer and use it to write to a stream
- st = moose.SocketStreamer( '/compt/streamer' )
- st.address = 'http://127.0.0.1:31416'
- assert st.port == 31416, "Got %s expected %s" % (st.port, expected)
- st.addTable(tables[0])
- st.addTables(tables[1:])
- assert st.numTables == 3
- # Give some time for socket client to make connection.
- moose.reinit()
- moose.start(50)
- time.sleep(1)
- print( 'MOOSE is done' )
- # sleep for some time so data can be read.
- finish_all_ = True
- client.join()
- print( 'Test 2 passed' )
-
-def main( ):
- test( )
- # test_without_env()
- print( '[INFO] All tests passed' )
-
-if __name__ == '__main__':
- main()
diff --git a/moose-core/tests/python/test_socket_streamer_uds.py b/moose-core/tests/python/test_socket_streamer_uds.py
index 542c3a46b212cb98f8218816a66bd31afecb2beb..480af8c653d2367175796b7ce4815ab43ecb714f 100644
--- a/moose-core/tests/python/test_socket_streamer_uds.py
+++ b/moose-core/tests/python/test_socket_streamer_uds.py
@@ -24,101 +24,81 @@ sys.path.append(os.path.dirname(__file__))
import time
import socket
import numpy as np
-import threading
+import multiprocessing as mp
import moose
+import moose.utils as mu
import json
import models
from collections import defaultdict
-finish_all_ = False
-
print( '[INFO] Using moose form %s' % moose.__file__ )
sockFile_ = '/tmp/MOOSE'
-def get_msg(s, n=1024):
- d = s.recv(n)
- while(len(d) < n):
- d1 = s.recv(n-len(d))
- d += d1
- return d
-
-def socket_client( ):
+def socket_client(done, q):
# This function waits for socket to be available.
- global finish_all_
global sockFile_
- s = socket.socket( socket.AF_UNIX, socket.SOCK_STREAM )
+ s = socket.socket(socket.AF_UNIX, socket.SOCK_STREAM)
address = sockFile_
- while 1:
- if finish_all_:
- print( '[INFO] MOOSE is done before I could connect' )
- break
- # print('Py: Trying to connect to %s, %s' % (host, port))
- # print( end = '.' )
- try:
- s.connect( address )
- break
- except Exception as e:
- pass
-
- if not finish_all_:
- print( 'Py: Connected with socket.' )
+ while not os.path.exists(address):
+ if done.value == 1:
+ return
+ continue
+ s.connect( address )
+ print( 'Py: Connected with socket. %s' % sockFile_ )
# This is client reponsibility to read the data.
+ print( 'Py: Fetching...' )
data = b''
- s.settimeout(1)
- while not finish_all_:
+ s.settimeout(0.01)
+ while True:
try:
- d = get_msg(s, 1024)
- data += d
- except socket.timeout as e:
- pass
- s.close()
+ data += s.recv(64)
+ except socket.timeout:
+ print('x', end = '' )
- assert data, "No data streamed"
- res = defaultdict(list)
- for x in data.split(b'\n'):
- if not x.strip():
- continue
- x = x.decode( 'utf8' )
- try:
- d = json.loads(x)
- except Exception as e:
- print( data )
- raise e
- for k, v in d.items():
- res[k] += v
-
- expected = {u'/compt/tabB/tabC': ([25.,1.07754388], [14.71960144, 0.16830373])
- , u'/compt/a/tab': ([25., 0.42467006], [14.71960144, 0.16766705])
- , u'/compt/tabB': ([25., 2.57797725], [14.71960144, 0.16842971])
- }
- nd = {}
- for k in res:
- v = res[k]
- nd[k] = (np.mean(v, axis=0), np.std(v, axis=0))
- assert np.isclose(expected[k], nd[k]).all(), \
- "Exptected %s, got %s" % (str(expected[k]), str(nd[k]))
+ if done.value == 1:
+ print( 'Simulation is over' )
+ break
+ s.close()
+ if not data:
+ print("No data streamed")
+ done.value = 1
+ q.put({})
+ return
+ res = mu.decode_data(data)
+ q.put(res)
def test():
- global finish_all_
- client = threading.Thread(target=socket_client, args=())
- #client.daemon = True
+ q = mp.Queue()
+ done = mp.Value( 'd', 0.0)
+ client = mp.Process(target=socket_client, args=(done, q))
client.start()
print( '[INFO] Socket client is running now' )
- tables = models.simple_model_a()
+ time.sleep(0.1)
+
# Now create a streamer and use it to write to a stream
- os.environ['MOOSE_STREAMER_ADDRESS'] = 'file:///tmp/moose'
+ os.environ['MOOSE_STREAMER_ADDRESS'] = 'file://%s' % sockFile_
+ models.simple_model_a()
# Give some time for socket client to make connection.
moose.reinit()
moose.start(50)
time.sleep(0.1)
- finish_all_ = True
- print( 'MOOSE is done' )
+ done.value = 1
+
+ res = q.get()
+ if not res:
+ raise RuntimeWarning( 'Nothing was streamed')
+ for k in res:
+ aWithTime = res[k]
+ a = aWithTime[1::2]
+ b = moose.element(k).vector
+ print(k, len(a), len(b))
+ assert (a == b).all()
+
# sleep for some time so data can be read.
client.join()
- print( 'Test 2 passed' )
def main( ):
test()
diff --git a/moose-core/tests/python/test_streamer.py b/moose-core/tests/python/test_streamer.py
index 43387df4b69d0fe08a6302bce55ee7af0d6e3ff9..3136ec24808beddb100f94a72901d2936088bdae 100644
--- a/moose-core/tests/python/test_streamer.py
+++ b/moose-core/tests/python/test_streamer.py
@@ -1,8 +1,8 @@
# -*- coding: utf-8 -*-
-"""test_streamer.py:
+from __future__ import print_function
+"""test_streamer.py:
Test script for Streamer class.
-
"""
__author__ = "Dilawar Singh"
@@ -14,13 +14,17 @@ __maintainer__ = "Dilawar Singh"
__email__ = "dilawars@ncbs.res.in"
__status__ = "Development"
-import os
-import sys
-import time
import moose
+import threading
import numpy as np
-print(( '[INFO] Using moose form %s' % moose.__file__ ))
+import time
+import os
+import sys
+print('[INFO] Using moose form %s' % moose.__file__)
+
+all_done_ = False
+# Poll the file to see that we are really writing to it.
def sanity_test( ):
a = moose.Table( '/t1' )
b = moose.Table( '/t1/t1' )
@@ -64,6 +68,7 @@ def sanity_test( ):
def test( ):
compt = moose.CubeMesh( '/compt' )
+ assert compt
r = moose.Reac( '/compt/r' )
a = moose.Pool( '/compt/a' )
a.concInit = 1
@@ -77,6 +82,10 @@ def test( ):
r.Kf = 0.1
r.Kb = 0.01
+ outfile = 'streamer_test.csv'
+ if os.path.exists(outfile):
+ os.remove(outfile)
+
tabA = moose.Table2( '/compt/a/tab' )
tabB = moose.Table2( '/compt/tabB' )
tabC = moose.Table2( '/compt/tabB/tabC' )
@@ -88,21 +97,22 @@ def test( ):
# Now create a streamer and use it to write to a stream
st = moose.Streamer( '/compt/streamer' )
- st.outfile = os.path.join( os.getcwd(), 'temp.npy' )
- print(("outfile set to: %s " % st.outfile ))
- assert st.outfile == os.path.join( os.getcwd(), 'temp.npy' ), st.outfile
+ st.outfile = outfile
+ print("outfile set to: %s " % st.outfile )
st.addTable( tabA )
st.addTables( [ tabB, tabC ] )
-
assert st.numTables == 3
moose.reinit( )
- print( '[INFO] Running for 57 seconds' )
- moose.start( 57 )
+ t = 100
+ print( '[INFO] Running for %d seconds' % t )
+ moose.start(t)
outfile = st.outfile
moose.quit() # Otherwise Streamer won't flush the rest of entries.
+ print('Moose is done. Waiting for monitor to shut down...')
+
# Now read the table and verify that we have written
print( '[INFO] Reading file %s' % outfile )
if 'csv' in outfile:
@@ -110,11 +120,9 @@ def test( ):
else:
data = np.load( outfile )
# Total rows should be 58 (counting zero as well).
- # print(data)
+ # print(data)
# print( data.dtype )
- time = data['time']
- print( time )
- assert data.shape >= (58,), data.shape
+ assert data.shape >= (101,), data.shape
print( '[INFO] Test 2 passed' )
return 0
diff --git a/moose-core/tests/python/test_table_streaming_support.py b/moose-core/tests/python/test_table_streaming_support.py
index 0747ef66d52a300c84bafb00a7de143aee996fa6..42b0b83b8e002ce04276708da97b9f3d3f682b77 100644
--- a/moose-core/tests/python/test_table_streaming_support.py
+++ b/moose-core/tests/python/test_table_streaming_support.py
@@ -59,7 +59,7 @@ def test( ):
moose.reinit( )
[ print_table( x) for x in [tabA, tabB, tabC] ]
runtime = 1000
- print( 'Starting moose for %s' % runtime )
+ print( 'Starting moose for %d secs' % runtime )
moose.start( runtime, 1 )
print( ' MOOSE is done' )
diff --git a/moose-core/utility/Annotator.cpp b/moose-core/utility/Annotator.cpp
index 4f1c51bd307243573f13f2277c56e4083226c08c..f2df4aa1fa2dd436f4e5937e1321fa213a970101 100644
--- a/moose-core/utility/Annotator.cpp
+++ b/moose-core/utility/Annotator.cpp
@@ -32,7 +32,18 @@ const Cinfo* Annotator::initCinfo()
&Annotator::setZ,
&Annotator::getZ
);
-
+ static ValueFinfo< Annotator, double > width(
+ "width",
+ "width field. Typically display width",
+ &Annotator::setwidth,
+ &Annotator::getwidth
+ );
+ static ValueFinfo< Annotator, double > height(
+ "height",
+ "height field. Typically display height",
+ &Annotator::setheight,
+ &Annotator::getheight
+ );
static ValueFinfo< Annotator, string > notes(
"notes",
"A string to hold some text notes about parent object",
@@ -91,6 +102,8 @@ const Cinfo* Annotator::initCinfo()
&x, // Value
&y, // Value
&z, // Value
+ &width,
+ &height,
¬es, // Value
&color, // Value
&textColor, // Value
@@ -116,7 +129,7 @@ const Cinfo* Annotator::initCinfo()
static const Cinfo* annotatorCinfo = Annotator::initCinfo();
Annotator::Annotator()
- : x_( 0.0 ), y_( 0.0 ), z_( 0.0 ),
+ : x_( 0.0 ), y_( 0.0 ), z_( 0.0 ), width_( 0.0 ), height_( 0.0 ),
notes_( "" ), color_( "white" ), textColor_( "black" ),
icon_( "sphere" ),solver_( "ee"),runtime_(100.0),dirpath_(""),modeltype_("")
{
@@ -153,6 +166,26 @@ void Annotator::setZ( double v )
z_ = v;
}
+double Annotator::getheight() const
+{
+ return height_;
+}
+
+void Annotator::setheight( double v )
+{
+ height_ = v;
+}
+
+double Annotator::getwidth() const
+{
+ return width_;
+}
+
+void Annotator::setwidth( double v )
+{
+ width_ = v;
+}
+
string Annotator::getNotes() const
{
return notes_;
diff --git a/moose-core/utility/Annotator.h b/moose-core/utility/Annotator.h
index 8dd4e5d5b78bac44dcaf07a52a57118cb56e94fd..759a6aaa220bc86f6c8d19dd65a8876307a59dc9 100644
--- a/moose-core/utility/Annotator.h
+++ b/moose-core/utility/Annotator.h
@@ -23,6 +23,10 @@ class Annotator
double getY() const;
void setY( double v );
double getZ() const;
+ void setwidth( double v );
+ double getwidth() const;
+ void setheight( double v );
+ double getheight() const;
void setZ( double v );
string getNotes() const;
void setNotes( string v );
@@ -45,6 +49,8 @@ class Annotator
double x_;
double y_;
double z_;
+ double height_;
+ double width_;
string notes_;
string color_;
string textColor_;
diff --git a/moose-core/utility/CMakeLists.txt b/moose-core/utility/CMakeLists.txt
index 5fcd5cee46b044817d95d7c8c99095b7f37d6b4f..00c014f1182196268847e3275b0633d98d44fa8b 100644
--- a/moose-core/utility/CMakeLists.txt
+++ b/moose-core/utility/CMakeLists.txt
@@ -16,5 +16,6 @@ add_library(utility
Annotator.cpp
Vec.cpp
cnpy.cpp
+ fileutils.cpp
#matrix_util.cpp
)
diff --git a/moose-core/utility/fileutils.cpp b/moose-core/utility/fileutils.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..221eb165cba126fef9fdf69795e2872315a2651e
--- /dev/null
+++ b/moose-core/utility/fileutils.cpp
@@ -0,0 +1,26 @@
+/*
+ * Description: Filesystem related utilities.
+ *
+ * Author: Dilawar Singh (), dilawars@ncbs.res.in
+ * Organization: NCBS Bangalore
+ */
+
+#include <string>
+#include <map>
+#include <unistd.h>
+#include <sys/stat.h>
+#include <sys/types.h>
+
+using namespace std;
+
+#include "utility.h"
+
+namespace moose {
+
+bool filepath_exists( const string& path )
+{
+ struct stat buffer;
+ return (stat (path.c_str(), &buffer) == 0);
+}
+
+} //namespace moose.
diff --git a/moose-core/utility/print_function.hpp b/moose-core/utility/print_function.hpp
index c2cf0c7fee54a0535a052261ee069e5bb5bb786a..9d389a0669f17c43cf3606715bd0cf621beac3c3 100644
--- a/moose-core/utility/print_function.hpp
+++ b/moose-core/utility/print_function.hpp
@@ -95,7 +95,6 @@ namespace moose {
string mapToString(const map<A, B>& m, bool value=true)
{
unsigned int width = 81;
- unsigned int mapSize = m.size();
unsigned int size = 0;
vector<string> row;
@@ -250,7 +249,9 @@ namespace moose {
#ifdef NDEBUG
#define LOG(t, a ) ((void)0);
#else /* ----- not NDEBUG ----- */
-#define LOG(t, a) { stringstream __ss__; __ss__ << a; moose::__dump__(__ss__.str(), t ); }
+#define LOG(t, a) { stringstream __ss__; \
+ __ss__ << __func__ << ": " << a; moose::__dump__(__ss__.str(), t); \
+}
#endif /* ----- not NDEBUG ----- */
/*-----------------------------------------------------------------------------
diff --git a/moose-core/utility/setupenv.cpp b/moose-core/utility/setupenv.cpp
index 422d3471d234fe051b1fcbb6d7c8f8f744ad176c..088f84f4f5ba7e5ded9e1ecf8e3c42b3d0d6a415 100644
--- a/moose-core/utility/setupenv.cpp
+++ b/moose-core/utility/setupenv.cpp
@@ -33,6 +33,7 @@
#include <string>
#include <sstream>
#include <cstdlib>
+
using namespace std;
extern unsigned getNumCores();
diff --git a/moose-core/utility/simple_assert.hpp b/moose-core/utility/simple_assert.hpp
index 78c41d8fd65969343c30fe95b58588664a3c15a7..857ad72003a811d507d0982a4447b46b21f9141f 100644
--- a/moose-core/utility/simple_assert.hpp
+++ b/moose-core/utility/simple_assert.hpp
@@ -62,16 +62,12 @@ namespace moose
// SIMPLE_ASSERT_MSG //
//--------------------------------------------------------------------------------------//
-# undef SIMPLE_ASSERT_MSG
+#undef SIMPLE_ASSERT_MSG
#if defined(SIMPLE_DISABLE_ASSERTS) || defined(NDEBUG)
-
#define SIMPLE_ASSERT_MSG(expr, msg) ((void)0)
-
#elif defined(SIMPLE_ENABLE_ASSERT_HANDLER)
-
#include "current_function.hpp"
-
namespace moose
{
void assertion_failed_msg(char const * expr, char const * msg,
diff --git a/moose-core/utility/strutil.h b/moose-core/utility/strutil.h
index 4d95c1419f2ce8fd197dc6ef0c292809f7c4be68..e2480d2bdb8fc4f81d8950f14e9a750588e88365 100644
--- a/moose-core/utility/strutil.h
+++ b/moose-core/utility/strutil.h
@@ -9,6 +9,7 @@
#define _STRINGUTIL_H
#include <string>
+#include <sstream>
#include <vector>
namespace moose
diff --git a/moose-core/utility/testing_macros.hpp b/moose-core/utility/testing_macros.hpp
index 87189889de3cc029dcd1bbded2972f5a6a693773..30359ef9a54b3638501be6d6d9715993c38bf405 100644
--- a/moose-core/utility/testing_macros.hpp
+++ b/moose-core/utility/testing_macros.hpp
@@ -68,7 +68,7 @@ static ostringstream assertStream;
}
#define EXPECT_NEQ(a, b, token) \
- if( (a) == (b)) { \
+ if( ! ((a) != (b)) ) { \
assertStream.str(""); \
LOCATION(assertStream); \
assertStream << "Not expected " << a << endl; \
@@ -77,7 +77,7 @@ static ostringstream assertStream;
}
#define EXPECT_GT(a, b, token) \
- if( (a) <= (b)) { \
+ if( !((a) > (b)) ) { \
assertStream.str(""); \
LOCATION(assertStream); \
assertStream << "Expected greater than " << a << ", received " << b << endl; \
@@ -86,7 +86,7 @@ static ostringstream assertStream;
}
#define EXPECT_GTE(a, b, token) \
- if( (a) < (b)) { \
+ if( !((a) >= (b)) ) { \
assertStream.str(""); \
LOCATION(assertStream); \
assertStream << "Expected greater than or equal to " << a \
@@ -96,7 +96,7 @@ static ostringstream assertStream;
}
#define EXPECT_LT(a, b, token) \
- if( (a) >= (b)) { \
+ if( ! ((a) < (b)) ) { \
assertStream.str(""); \
LOCATION(assertStream); \
assertStream << "Expected less than " << a << ", received " << b << endl; \
@@ -105,7 +105,7 @@ static ostringstream assertStream;
}
#define EXPECT_LTE(a, b, token) \
- if( (a) < (b)) { \
+ if( ! ((a) <= (b)) ) { \
assertStream.str(""); \
LOCATION(assertStream); \
assertStream << "Expected less than or equal to " << a \
@@ -129,13 +129,6 @@ static ostringstream assertStream;
throw std::runtime_error(assertStream.str()); \
}
-#define ASSERT_LT( a, b, msg) \
- EXPECT_LT(a, b, msg); \
- assertStream.str(""); \
- assertStream.precision( 9 ); \
- assertStream << msg; \
- throw std::runtime_error( assertStream.str() ); \
-
#define ASSERT_EQ(a, b, token) \
if( ! doubleEq((a), (b)) ) { \
assertStream.str(""); \
@@ -165,5 +158,4 @@ static ostringstream assertStream;
throw std::runtime_error(assertStream.str()); \
}
-
#endif /* ----- #ifndef TESTING_MACROS_INC ----- */
diff --git a/moose-core/utility/utility.h b/moose-core/utility/utility.h
index ee0e88d7f1743de877bc0d09981b4d6c03c2e61c..33fae6764c4a6e9a639c11bd3c29243f3121b55b 100644
--- a/moose-core/utility/utility.h
+++ b/moose-core/utility/utility.h
@@ -25,6 +25,9 @@ namespace moose
const map<std::string, std::string>& getArgMap();
string getEnv( const string& env);
+ // In fileutils.cpp
+ bool filepath_exists( const string& path );
+
/**
* @brief Givem path of MOOSE element, return its name. It's behaviour is
* like `basename` of unix command e.g. /a/b/c --> c