diff --git a/arbor/include/arbor/mechcat.hpp b/arbor/include/arbor/mechcat.hpp
index 17cd7ef962917e55e913af6d66c154a4a7c8ef56..0018791f32818ef657a5ac2df0c74ed805e6ba70 100644
--- a/arbor/include/arbor/mechcat.hpp
+++ b/arbor/include/arbor/mechcat.hpp
@@ -106,7 +106,10 @@ public:
register_impl(std::type_index(typeid(B)), name, std::move(generic_proto));
}
- ~mechanism_catalogue();
+ // Copy over another catalogue's mechanism and attach a -- possibly empty -- prefix
+ void import(const mechanism_catalogue& other, const std::string& prefix);
+
+ ~mechanism_catalogue();
private:
std::unique_ptr<catalogue_state> state_;
@@ -119,5 +122,6 @@ private:
// Reference to global default mechanism catalogue.
const mechanism_catalogue& global_default_catalogue();
+const mechanism_catalogue& global_allen_catalogue();
} // namespace arb
diff --git a/arbor/mechcat.cpp b/arbor/mechcat.cpp
index 59b45df7943c0f666c925ce7d0bd63d3fa4ff468..4be6af12198e7debd9f861d613632e190e2b6703 100644
--- a/arbor/mechcat.cpp
+++ b/arbor/mechcat.cpp
@@ -123,25 +123,44 @@ struct catalogue_state {
catalogue_state() = default;
catalogue_state(const catalogue_state& other) {
- info_map_.clear();
+ import(other, "");
+ }
+
+ void import(const catalogue_state& other, const std::string& prefix) {
+ // Do all checks before adding anything, otherwise we might get inconsistent state.
+ auto assert_undefined = [&](const std::string& key) {
+ auto pkey = prefix+key;
+ if (defined(pkey)) {
+ throw duplicate_mechanism(pkey);
+ }
+ };
+
+ for (const auto& kv: other.info_map_) {
+ assert_undefined(kv.first);
+ }
+
+ for (const auto& kv: other.derived_map_) {
+ assert_undefined(kv.first);
+ }
+
for (const auto& kv: other.info_map_) {
- info_map_[kv.first] = make_unique<mechanism_info>(*kv.second);
+ auto key = prefix + kv.first;
+ info_map_[key] = make_unique<mechanism_info>(*kv.second);
}
- derived_map_.clear();
for (const auto& kv: other.derived_map_) {
+ auto key = prefix + kv.first;
const derivation& v = kv.second;
- derived_map_[kv.first] = {v.parent, v.globals, v.ion_remap, make_unique<mechanism_info>(*v.derived_info)};
+ derived_map_[key] = {prefix + v.parent, v.globals, v.ion_remap, make_unique<mechanism_info>(*v.derived_info)};
}
- impl_map_.clear();
for (const auto& name_impls: other.impl_map_) {
std::unordered_map<std::type_index, std::unique_ptr<mechanism>> impls;
for (const auto& tidx_mptr: name_impls.second) {
impls[tidx_mptr.first] = tidx_mptr.second->clone();
}
-
- impl_map_[name_impls.first] = std::move(impls);
+ auto key = prefix + name_impls.first;
+ impl_map_[key] = std::move(impls);
}
}
@@ -540,6 +559,10 @@ void mechanism_catalogue::derive(const std::string& name, const std::string& par
state_->bind(name, value(state_->derive(parent)));
}
+void mechanism_catalogue::import(const mechanism_catalogue& other, const std::string& prefix) {
+ state_->import(*other.state_, prefix);
+}
+
void mechanism_catalogue::remove(const std::string& name) {
if (!has(name)) {
throw no_such_mechanism(name);
diff --git a/mechanisms/CMakeLists.txt b/mechanisms/CMakeLists.txt
index a751dd25a97249bd71a3df5c67738059e96ae380..f72d7399874da1b2b2e070ba8c87619b4c66007d 100644
--- a/mechanisms/CMakeLists.txt
+++ b/mechanisms/CMakeLists.txt
@@ -1,8 +1,5 @@
include(BuildModules.cmake)
-set(mech_dir "${CMAKE_CURRENT_BINARY_DIR}/generated")
-file(MAKE_DIRECTORY "${mech_dir}")
-
set(external_modcc)
if(ARB_WITH_EXTERNAL_MODCC)
set(external_modcc MODCC ${modcc})
@@ -15,6 +12,8 @@ set(mech_sources "")
# ALLEN
set(allen_mechanisms CaDynamics Ca_HVA Ca_LVA Ih Im Im_v2 K_P K_T Kd Kv2like Kv3_1 NaTa NaTs NaV Nap SK)
set(allen_mod_srcdir "${CMAKE_CURRENT_SOURCE_DIR}/allen")
+set(mech_dir "${CMAKE_CURRENT_BINARY_DIR}/generated/allen")
+file(MAKE_DIRECTORY "${mech_dir}")
build_modules(
${allen_mechanisms}
@@ -53,6 +52,8 @@ endforeach()
# DEFAULT
set(default_mechanisms exp2syn expsyn hh kamt kdrmt nax nernst pas)
set(default_mod_srcdir "${CMAKE_CURRENT_SOURCE_DIR}/default")
+set(mech_dir "${CMAKE_CURRENT_BINARY_DIR}/generated/default")
+file(MAKE_DIRECTORY "${mech_dir}")
build_modules(
${default_mechanisms}
diff --git a/python/mechanism.cpp b/python/mechanism.cpp
index 0df5d95da1394ca7712f3a1e91075ee6d26e24d2..92515ef1e0e5a11e3fec446d12da29e6bb4196db 100644
--- a/python/mechanism.cpp
+++ b/python/mechanism.cpp
@@ -118,6 +118,10 @@ void register_mechanisms(pybind11::module& m) {
throw std::runtime_error(util::pprintf("\nKeyError: '{}'", name));
}
})
+ .def("import", &arb::mechanism_catalogue::import,
+ "other"_a, "Catalogue to import into self",
+ "prefix"_a, "Prefix for names in other",
+ "Import another catalogue, possibly with a prefix. Will overwrite in case of name collisions.")
.def("derive", &apply_derive,
"name"_a, "parent"_a,
"globals"_a=std::unordered_map<std::string, double>{},
@@ -130,6 +134,7 @@ void register_mechanisms(pybind11::module& m) {
return util::pprintf("<arbor.mechanism_catalogue>"); });
m.def("default_catalogue", [](){return arb::global_default_catalogue();});
+ m.def("allen_catalogue", [](){return arb::global_allen_catalogue();});
// arb::mechanism_desc
// For specifying a mechanism in the cable_cell interface.
diff --git a/test/unit/test_mechcat.cpp b/test/unit/test_mechcat.cpp
index 2d7ccac9432538b5f319bd9a4a30e2fe19945ab9..31526aa2c8e840861ace53879666658d94129ee5 100644
--- a/test/unit/test_mechcat.cpp
+++ b/test/unit/test_mechcat.cpp
@@ -443,4 +443,95 @@ TEST(mechcat, copy) {
EXPECT_EQ(typeid(*fleeb2_inst.mech.get()), typeid(*fleeb2_inst2.mech.get()));
}
+TEST(mechcat, import) {
+ auto cat = build_fake_catalogue();
+ mechanism_catalogue cat2;
+ cat2.import(cat, "fake_");
+
+ EXPECT_TRUE(cat.has("fleeb2"));
+ EXPECT_FALSE(cat.has("fake_fleeb2"));
+
+ EXPECT_TRUE(cat2.has("fake_fleeb2"));
+ EXPECT_FALSE(cat2.has("fleeb2"));
+
+ EXPECT_EQ(cat["fleeb2"], cat2["fake_fleeb2"]);
+
+ auto fleeb2_inst = cat.instance<foo_backend>("fleeb2");
+ auto fleeb2_inst2 = cat2.instance<foo_backend>("fake_fleeb2");
+
+ EXPECT_EQ(typeid(*fleeb2_inst.mech.get()), typeid(*fleeb2_inst2.mech.get()));
+}
+
+TEST(mechcat, import_collisions) {
+ {
+ auto cat = build_fake_catalogue();
+
+ mechanism_catalogue cat2;
+ EXPECT_NO_THROW(cat2.import(cat, "prefix:")); // Should have no collisions.
+ EXPECT_NO_THROW(cat.import(cat2, "prefix:")); // Should have no collisions here either.
+
+ // cat should have both original entries and copies with 'prefix:prefix:' prefixed.
+ ASSERT_TRUE(cat.has("fleeb2"));
+ ASSERT_TRUE(cat.has("prefix:prefix:fleeb2"));
+ }
+
+ // We should throw if there any collisions between base or derived mechanism
+ // names between the catalogues. If the import fails, the catalogue should
+ // remain unchanged.
+ {
+ // Collision between two base mechanisms.
+ {
+ auto cat = build_fake_catalogue();
+ mechanism_catalogue other;
+ other.add("fleeb", burble_info); // Note different mechanism info!
+
+ EXPECT_THROW(cat.import(other, ""), arb::duplicate_mechanism);
+ ASSERT_EQ(cat["fleeb"], fleeb_info);
+ }
+
+ // Collision derived vs base.
+ {
+ auto cat = build_fake_catalogue();
+
+ mechanism_catalogue other;
+ other.add("fleeb2", burble_info);
+
+ auto fleeb2_info = cat["fleeb2"];
+ EXPECT_THROW(cat.import(other, ""), arb::duplicate_mechanism);
+ EXPECT_EQ(cat["fleeb2"], fleeb2_info);
+ }
+
+ // Collision base vs derived.
+ {
+ auto cat = build_fake_catalogue();
+
+ mechanism_catalogue other;
+ other.add("zonkers", fleeb_info);
+ other.derive("fleeb", "zonkers", {{"plugh", 8.}});
+ ASSERT_FALSE(other["fleeb"]==fleeb_info);
+
+ ASSERT_FALSE(cat.has("zonkers"));
+ EXPECT_THROW(cat.import(other, ""), arb::duplicate_mechanism);
+ EXPECT_EQ(cat["fleeb"], fleeb_info);
+ EXPECT_FALSE(cat.has("zonkers"));
+ }
+
+ // Collision derived vs derived.
+ {
+ auto cat = build_fake_catalogue();
+
+ mechanism_catalogue other;
+ other.add("zonkers", fleeb_info);
+ other.derive("fleeb2", "zonkers", {{"plugh", 8.}});
+
+ auto fleeb2_info = cat["fleeb2"];
+ ASSERT_FALSE(other["fleeb2"]==fleeb2_info);
+
+ ASSERT_FALSE(cat.has("zonkers"));
+ EXPECT_THROW(cat.import(other, ""), arb::duplicate_mechanism);
+ EXPECT_EQ(cat["fleeb2"], fleeb2_info);
+ EXPECT_FALSE(cat.has("zonkers"));
+ }
+ }
+}