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@angeloprobst
angeloprobst committed Sep 19, 2024
1 parent 2ea66fb commit 20a6661
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1 change: 0 additions & 1 deletion hyperon_das_atomdb_cpp/src/.clang-format-ignore
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Original file line number Diff line number Diff line change
@@ -1,3 +1,2 @@
nanobind.cpp
main.cpp

288 changes: 133 additions & 155 deletions hyperon_das_atomdb_cpp/src/nanobind.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -55,180 +55,164 @@ NB_MODULE(hyperon_das_atomdb, m) {
.def_static("build_link_handle", &AtomDB::build_link_handle)
.def("node_exists", &AtomDB::node_exists)
.def("link_exists", &AtomDB::link_exists)
.def("get_atom",
[](
AtomDB& self,
const string& handle,
bool no_target_format = false,
bool targets_documents = false,
bool deep_representation = false,
const nb::kwargs _ = {}
) -> shared_ptr<const Atom> {
return self.get_atom(
handle,
{
no_target_format: no_target_format,
targets_documents: targets_documents,
deep_representation: deep_representation
}
);
},
"handle"_a,
nb::kw_only(),
"no_target_format"_a = false,
"targets_documents"_a = false,
"deep_representation"_a = false,
"_"_a = nb::kwargs()
)
.def(
"get_atom",
[](AtomDB& self,
const string& handle,
bool no_target_format = false,
bool targets_documents = false,
bool deep_representation = false,
const nb::kwargs _ = {}) -> shared_ptr<const Atom> {
return self.get_atom(handle, {
no_target_format : no_target_format,
targets_documents : targets_documents,
deep_representation : deep_representation
});
},
"handle"_a,
nb::kw_only(),
"no_target_format"_a = false,
"targets_documents"_a = false,
"deep_representation"_a = false,
"_"_a = nb::kwargs())
.def("get_node_handle", &AtomDB::get_node_handle)
.def("get_node_name", &AtomDB::get_node_name)
.def("get_node_type", &AtomDB::get_node_type)
.def("get_node_by_name", &AtomDB::get_node_by_name)
.def("get_atoms_by_field", &AtomDB::get_atoms_by_field)
.def("get_atoms_by_index", &AtomDB::get_atoms_by_index,
"index_id"_a, "query"_a, "cursor"_a = 0, "chunk_size"_a = 500
)
.def("get_atoms_by_text_field", &AtomDB::get_atoms_by_text_field,
"text_value"_a, "field"_a = "", "text_index_id"_a = ""
)
.def("get_atoms_by_index",
&AtomDB::get_atoms_by_index,
"index_id"_a,
"query"_a,
"cursor"_a = 0,
"chunk_size"_a = 500)
.def("get_atoms_by_text_field",
&AtomDB::get_atoms_by_text_field,
"text_value"_a,
"field"_a = "",
"text_index_id"_a = "")
.def("get_node_by_name_starting_with", &AtomDB::get_node_by_name_starting_with)
.def("get_all_nodes", &AtomDB::get_all_nodes, "node_type"_a, "names"_a = false)
.def("get_all_links",
[](
InMemoryDB& self,
const string& link_type,
const OptCursor cursor = nullopt,
const nb::kwargs _ = {}
) -> const pair<const OptCursor, const StringList> {
return self.get_all_links(link_type, { cursor: cursor });
},
"link_type"_a, nb::kw_only(), "cursor"_a = nullopt, "_"_a = nb::kwargs()
)
.def(
"get_all_links",
[](InMemoryDB& self,
const string& link_type,
const OptCursor cursor = nullopt,
const nb::kwargs _ = {}) -> const pair<const OptCursor, const StringList> {
return self.get_all_links(link_type, {cursor : cursor});
},
"link_type"_a,
nb::kw_only(),
"cursor"_a = nullopt,
"_"_a = nb::kwargs())
.def("get_link_handle", &AtomDB::get_link_handle)
.def("get_link_type", &AtomDB::get_link_type)
.def("get_link_targets", &AtomDB::get_link_targets)
.def("is_ordered", &AtomDB::is_ordered)
.def("get_incoming_links_handles",
[](
InMemoryDB& self,
const string& atom_handle,
const OptCursor cursor = nullopt,
const nb::kwargs _ = {}
) -> const pair<const OptCursor, const StringUnorderedSet> {
return self.get_incoming_links_handles(atom_handle, { cursor: cursor });
},
"atom_handle"_a, nb::kw_only(), "cursor"_a = nullopt, "_"_a = nb::kwargs()
)
.def("get_incoming_links_atoms",
[](
InMemoryDB& self,
const string& atom_handle,
const OptCursor cursor = nullopt,
bool no_target_format = false,
bool targets_documents = false,
bool deep_representation = false,
const nb::kwargs _ = {}
) -> const pair<const OptCursor, const vector<shared_ptr<const Atom>>> {
return self.get_incoming_links_atoms(
atom_handle,
{
no_target_format: no_target_format,
targets_documents: targets_documents,
deep_representation: deep_representation,
cursor: cursor
}
);
},
"atom_handle"_a,
nb::kw_only(),
"cursor"_a = nullopt,
"no_target_format"_a = false,
"targets_documents"_a = false,
"deep_representation"_a = false,
"_"_a = nb::kwargs()
)
.def("get_matched_links",
[](
InMemoryDB& self,
const string& link_type,
const StringList& target_handles,
const OptCursor cursor = nullopt,
bool toplevel_only = false,
const nb::kwargs _ = {}
) -> const pair<const OptCursor, const Pattern_or_Template_List> {
return self.get_matched_links(
link_type,
target_handles,
{ toplevel_only: toplevel_only, cursor: cursor }
);
},
"link_type"_a,
"target_handles"_a,
nb::kw_only(),
"cursor"_a = nullopt,
"toplevel_only"_a = false,
"_"_a = nb::kwargs()
)
.def("get_matched_type_template",
[](
InMemoryDB& self,
const ListOfAny& _template,
const OptCursor cursor = nullopt,
bool toplevel_only = false,
const nb::kwargs _ = {}
) -> const pair<const OptCursor, const Pattern_or_Template_List> {
return self.get_matched_type_template(
_template,
{ toplevel_only: toplevel_only, cursor: cursor }
);
},
"_template"_a,
nb::kw_only(),
"cursor"_a = nullopt,
"toplevel_only"_a = false,
"_"_a = nb::kwargs()
)
.def("get_matched_type",
[](
InMemoryDB& self,
const string& link_type,
const OptCursor cursor = nullopt,
bool toplevel_only = false,
const nb::kwargs _ = {}
) -> const pair<const OptCursor, const Pattern_or_Template_List> {
return self.get_matched_type(
link_type,
{ toplevel_only: toplevel_only, cursor: cursor }
);
},
"link_type"_a,
nb::kw_only(),
"cursor"_a = nullopt,
"toplevel_only"_a = false,
"_"_a = nb::kwargs()
)
.def(
"get_incoming_links_handles",
[](InMemoryDB& self,
const string& atom_handle,
const OptCursor cursor = nullopt,
const nb::kwargs _ = {}) -> const pair<const OptCursor, const StringUnorderedSet> {
return self.get_incoming_links_handles(atom_handle, {cursor : cursor});
},
"atom_handle"_a,
nb::kw_only(),
"cursor"_a = nullopt,
"_"_a = nb::kwargs())
.def(
"get_incoming_links_atoms",
[](InMemoryDB& self,
const string& atom_handle,
const OptCursor cursor = nullopt,
bool no_target_format = false,
bool targets_documents = false,
bool deep_representation = false,
const nb::kwargs _ = {})
-> const pair<const OptCursor, const vector<shared_ptr<const Atom>>> {
return self.get_incoming_links_atoms(atom_handle, {
no_target_format : no_target_format,
targets_documents : targets_documents,
deep_representation : deep_representation,
cursor : cursor
});
},
"atom_handle"_a,
nb::kw_only(),
"cursor"_a = nullopt,
"no_target_format"_a = false,
"targets_documents"_a = false,
"deep_representation"_a = false,
"_"_a = nb::kwargs())
.def(
"get_matched_links",
[](InMemoryDB& self,
const string& link_type,
const StringList& target_handles,
const OptCursor cursor = nullopt,
bool toplevel_only = false,
const nb::kwargs _ = {}) -> const pair<const OptCursor, const Pattern_or_Template_List> {
return self.get_matched_links(
link_type, target_handles, {toplevel_only : toplevel_only, cursor : cursor});
},
"link_type"_a,
"target_handles"_a,
nb::kw_only(),
"cursor"_a = nullopt,
"toplevel_only"_a = false,
"_"_a = nb::kwargs())
.def(
"get_matched_type_template",
[](InMemoryDB& self,
const ListOfAny& _template,
const OptCursor cursor = nullopt,
bool toplevel_only = false,
const nb::kwargs _ = {}) -> const pair<const OptCursor, const Pattern_or_Template_List> {
return self.get_matched_type_template(_template,
{toplevel_only : toplevel_only, cursor : cursor});
},
"_template"_a,
nb::kw_only(),
"cursor"_a = nullopt,
"toplevel_only"_a = false,
"_"_a = nb::kwargs())
.def(
"get_matched_type",
[](InMemoryDB& self,
const string& link_type,
const OptCursor cursor = nullopt,
bool toplevel_only = false,
const nb::kwargs _ = {}) -> const pair<const OptCursor, const Pattern_or_Template_List> {
return self.get_matched_type(link_type,
{toplevel_only : toplevel_only, cursor : cursor});
},
"link_type"_a,
nb::kw_only(),
"cursor"_a = nullopt,
"toplevel_only"_a = false,
"_"_a = nb::kwargs())
.def("get_atom_type", &AtomDB::get_atom_type)
.def("count_atoms", &AtomDB::count_atoms)
.def("clear_database", &AtomDB::clear_database)
.def("add_node", &AtomDB::add_node)
.def("add_link", &AtomDB::add_link, "link_params"_a, "toplevel"_a = true)
.def("reindex", &AtomDB::reindex)
.def("delete_atom", &AtomDB::delete_atom)
.def("create_field_index", &AtomDB::create_field_index,
.def("create_field_index",
&AtomDB::create_field_index,
"atom_type"_a,
"fields"_a,
"named_type"_a = "",
"composite_type"_a = nullopt,
"index_type"_a = FieldIndexType::BINARY_TREE
)
"index_type"_a = FieldIndexType::BINARY_TREE)
.def("bulk_insert", &AtomDB::bulk_insert)
.def("retrieve_all_atoms", &AtomDB::retrieve_all_atoms)
.def("commit", &AtomDB::commit);
// ---------------------------------------------------------------------------------------------
// adapters submodule --------------------------------------------------------------------------
nb::module_ adapters = m.def_submodule("adapters");
nb::class_<InMemoryDB, AtomDB>(adapters, "InMemoryDB")
.def(nb::init<>());
nb::class_<InMemoryDB, AtomDB>(adapters, "InMemoryDB").def(nb::init<>());
// ---------------------------------------------------------------------------------------------
// exceptions submodule ------------------------------------------------------------------------
nb::module_ exceptions = m.def_submodule("exceptions");
Expand All @@ -246,14 +230,12 @@ NB_MODULE(hyperon_das_atomdb, m) {
.def("to_string", &Atom::to_string)
.def("__str__", &Atom::to_string)
.def("__repr__", &Atom::to_string);
nb::class_<Node, Atom>(document_types, "Node")
.def_ro("name", &Node::name);
nb::class_<Node, Atom>(document_types, "Node").def_ro("name", &Node::name);
nb::class_<Link, Atom>(document_types, "Link")
.def_prop_ro("composite_type",
[](const Link& self) -> const nb::list {
return transformer::composite_type_to_pylist(self.composite_type);
}
)
})
.def_ro("named_type_hash", &Link::named_type_hash)
.def_ro("targets", &Link::targets)
.def_ro("is_top_level", &Link::is_top_level)
Expand All @@ -271,12 +253,8 @@ NB_MODULE(hyperon_das_atomdb, m) {
.def_rw("type", &LinkParams::type)
.def_rw("targets", &LinkParams::targets)
.def("add_target",
[](LinkParams& self, const LinkParams::Target& target) {
self.targets.push_back(target);
}
)
[](LinkParams& self, const LinkParams::Target& target) { self.targets.push_back(target); })
.def_static("is_node", &LinkParams::is_node)
.def_static("is_link", &LinkParams::is_link);
// ---------------------------------------------------------------------------------------------
}

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