Introduce SONATA support (#269)

.gitsubprojects

@@ -1,4 +1,5 @@
 # -*- mode: cmake -*-
+git_subproject(libsonata https://github.com/BlueBrain/libsonata.git ec58d16)
 git_subproject(Servus https://github.com/HBPVIS/Servus.git 170bd93)
 git_subproject(Lunchbox https://github.com/Eyescale/Lunchbox.git 9bd6a7d)
 git_subproject(Keyv https://github.com/BlueBrain/Keyv.git 8340fa2)

CMakeLists.txt

@@ -5,7 +5,7 @@
 #
 
 cmake_minimum_required(VERSION 3.1 FATAL_ERROR)
-project(Brion VERSION 3.0.0)
+project(Brion VERSION 3.1.0)
 set(Brion_VERSION_ABI 10)
 
 list(APPEND CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/CMake
@@ -43,6 +43,7 @@ common_find_package(PythonLibs)
 common_find_package(Servus REQUIRED)
 common_find_package(Sphinx 1.3)
 common_find_package(vmmlib REQUIRED)
+common_find_package(sonata REQUIRED)
 option(BRION_USE_ZEROEQ "Use ZeroEQ for plugin backend and morphologyServer" OFF)
 if(BRION_USE_ZEROEQ)
   git_subproject(ZeroEQ https://github.com/HBPVIS/ZeroEQ.git 1e66ee3)

brain/CMakeLists.txt

@@ -51,7 +51,7 @@ set(BRAIN_SOURCES
 set(BRAIN_PUBLIC_INCLUDE_DIRECTORIES ${Boost_INCLUDE_DIRS})
 set(BRAIN_LINK_LIBRARIES
   PUBLIC Brion vmmlib
-  PRIVATE Lunchbox ${Boost_FILESYSTEM_LIBRARIES}
+  PRIVATE sonata::sonata_shared Lunchbox ${Boost_FILESYSTEM_LIBRARIES}
 )
 
 if(TARGET Keyv)
@@ -65,6 +65,8 @@ if(TARGET MVDTool)
   list(APPEND BRAIN_LINK_LIBRARIES PRIVATE MVDTool)
 endif()
 
+#set(BRAIN_OMIT_EXPORT ON)
+
 common_library(Brain)
 if(TARGET MVDTool)
   target_compile_definitions(Brain PUBLIC BRAIN_USE_MVD3)

brain/circuit.cpp

@@ -23,8 +23,11 @@
 #include "circuit.h"
 #include "detail/circuit.h"
 
+#include "synapses.h"
 #include "synapsesStream.h"
 
+#include <bbp/sonata/edges.h>
+
 #include <servus/uint128_t.h>
 
 #include <boost/algorithm/string.hpp>
@@ -525,4 +528,44 @@ SynapsesStream Circuit::getProjectedSynapses(
 {
     return SynapsesStream(*this, preGIDs, postGIDs, prefetch);
 }
+
+uint32_ts Circuit::getProjectedEfferentGIDs(
+    const GIDSet& preGIDs, const std::string& projection) const
+{
+    const std::string projPath = _impl->getSynapseProjectionSource(projection);
+    if(projPath.find("sonata") == std::string::npos)
+    {
+        SynapsesStream ss = getExternalAfferentSynapses(preGIDs, projection);
+        auto future = ss.read(ss.getRemaining());
+        future.wait();
+        Synapses syn = future.get();
+        uint32_ts result (syn.preGIDs(), syn.preGIDs() + syn.size());
+        return result;
+    }
+    else
+    {
+        std::set<uint64_t> uniqueIds;
+        // Input ids must be decreased by 1
+        for(uint32_t oldId : preGIDs)
+        {
+            if(oldId > 0)
+                uniqueIds.insert(oldId - 1);
+        }
+
+        const size_ts nodeIds (uniqueIds.begin(), uniqueIds.end());
+        uint32_ts result;
+        const bbp::sonata::EdgeStorage edgeStorage (projPath);
+        for(const auto& name : edgeStorage.populationNames())
+        {
+            const bbp::sonata::EdgePopulation edges (projPath, "", name);
+            const bbp::sonata::Selection s = edges.efferentEdges(nodeIds);
+
+            for(auto gid : edges.targetNodeIDs(s))
+            {
+                result.push_back(static_cast<uint32_t>(gid) + 1);
+            }
+        }
+        return result;
+    }
+}
 }

brain/circuit.h

@@ -244,6 +244,16 @@ class Circuit
         const GIDSet& preGIDs, const GIDSet& postGIDs,
         SynapsePrefetch prefetch = SynapsePrefetch::none) const;
 
+    /**
+     * Return a list of efferent cells GIDs from a given projection
+     *
+     * @param preGIDs projection source cell IDs
+     * @param projection projection name
+     * @return list of efferent GIDs from inside the circuit
+     */
+    BRAIN_API uint32_ts getProjectedEfferentGIDs(
+        const GIDSet& preGIDs, const std::string& projection) const;
+
     class Impl; //!< @internal, public for inheritance MVD2/3 impls
 
 private:

brain/detail/circuit.h

@@ -414,6 +414,8 @@ class Circuit::Impl
     virtual URI getMorphologySource() const = 0;
 
     virtual MorphologyCache* getMorphologyCache() const { return nullptr; }
+    virtual std::string getSynapseSource() const = 0;
+    virtual std::string getSynapseProjectionSource(const std::string& name) const = 0;
     virtual SynapseCache* getSynapseCache() const { return nullptr; }
     virtual const brion::SynapseSummary& getSynapseSummary() const = 0;
     virtual const brion::Synapse& getSynapseAttributes(
@@ -679,6 +681,15 @@ class SonataCircuit : public Circuit::Impl
     }
 
     URI getMorphologySource() const final { return morphologySource; }
+    std::string getSynapseSource() const
+    {
+        return synapseSource.getPath();
+    }
+    std::string getSynapseProjectionSource(const std::string& name) const
+    {
+        (void)name;
+        LBTHROW(std::runtime_error("Unimplemented"));
+    }
     const brion::SynapseSummary& getSynapseSummary() const final
     {
         LBTHROW(std::runtime_error("Unimplemented"));
@@ -768,6 +779,20 @@ class BBPCircuit : public Circuit::Impl
         return nullptr;
     }
 
+    std::string getSynapseSource() const
+    {
+        return _synapseSource.getPath();
+    }
+
+    std::string getSynapseProjectionSource(const std::string& name) const
+    {
+        auto it = _afferentProjectionSources.find(name);
+        if(it == _afferentProjectionSources.end())
+            LBTHROW(std::runtime_error("Projection " + name + " not found"))
+
+        return it->second.getPath();
+    }
+
     SynapseCache* getSynapseCache() const final
     {
         if (_synapseCache)