From a1e27903f9a4f981ec15d360b659bb697e17bbac Mon Sep 17 00:00:00 2001
From: Geoff Hutchison <geoff.hutchison@gmail.com>
Date: Thu, 31 Aug 2023 15:41:48 -0400
Subject: [PATCH] Add support for a MessagePack variant to CJSON

Signed-off-by: Geoff Hutchison <geoff.hutchison@gmail.com>
---
 avogadro/io/cjsonformat.cpp       | 13 +++++++++++--
 avogadro/io/cjsonformat.h         |  5 +++--
 avogadro/io/cmsgpackformat.cpp    | 18 +++++++++++++++++-
 avogadro/io/cmsgpackformat.h      |  3 +++
 avogadro/io/fileformatmanager.cpp |  2 ++
 5 files changed, 36 insertions(+), 5 deletions(-)

diff --git a/avogadro/io/cjsonformat.cpp b/avogadro/io/cjsonformat.cpp
index a3a5b07ca6..c5221250e6 100644
--- a/avogadro/io/cjsonformat.cpp
+++ b/avogadro/io/cjsonformat.cpp
@@ -80,6 +80,11 @@ bool isBooleanArray(json& j)
 }
 
 bool CjsonFormat::read(std::istream& file, Molecule& molecule)
+{
+  return deserialize(file, molecule, true);
+}
+
+bool CjsonFormat::deserialize(std::istream& file, Molecule& molecule, bool isJson)
 {
   json jsonRoot = json::parse(file, nullptr, false);
   if (jsonRoot.is_discarded()) {
@@ -622,6 +627,11 @@ bool CjsonFormat::read(std::istream& file, Molecule& molecule)
 }
 
 bool CjsonFormat::write(std::ostream& file, const Molecule& molecule)
+{
+  return serialize(file, molecule, true);
+}
+
+bool CjsonFormat::serialize(std::ostream& file, const Molecule& molecule, bool isJson)
 {
   json opts;
   if (!options().empty())
@@ -1042,8 +1052,7 @@ bool CjsonFormat::write(std::ostream& file, const Molecule& molecule)
     root["layer"]["settings"][settings.first] = setting;
   }
 
-  // Write out the file, use a two space indent to "pretty print".
-  if (m_json)
+  if (isJson)
     file << std::setw(2) << root;
   else // write msgpack
     json::to_msgpack(root, file);
diff --git a/avogadro/io/cjsonformat.h b/avogadro/io/cjsonformat.h
index 556a78204a..e7e62a6528 100644
--- a/avogadro/io/cjsonformat.h
+++ b/avogadro/io/cjsonformat.h
@@ -50,8 +50,9 @@ class AVOGADROIO_EXPORT CjsonFormat : public FileFormat
   bool read(std::istream& in, Core::Molecule& molecule) override;
   bool write(std::ostream& out, const Core::Molecule& molecule) override;
 
-  // write JSON or MessagePack
-  bool m_json = true;
+  // internal - to allow JSON or MsgPack to be written
+  bool deserialize(std::istream& in, Core::Molecule& molecule, bool json);
+  bool serialize(std::ostream& out, const Core::Molecule& molecule, bool json);
 };
 
 } // end Io namespace
diff --git a/avogadro/io/cmsgpackformat.cpp b/avogadro/io/cmsgpackformat.cpp
index c4dcb4861f..5474832794 100644
--- a/avogadro/io/cmsgpackformat.cpp
+++ b/avogadro/io/cmsgpackformat.cpp
@@ -5,11 +5,16 @@
 
 #include "cmsgpackformat.h"
 
+#include <iostream>
+
 using namespace std;
 
 namespace Avogadro::Io {
 
-CMsgPackFormat::CMsgPackFormat() = default;
+CMsgPackFormat::CMsgPackFormat(): CjsonFormat()
+{
+  m_json = false;
+}
 
 CMsgPackFormat::~CMsgPackFormat() = default;
 
@@ -27,4 +32,15 @@ vector<std::string> CMsgPackFormat::mimeTypes() const
   return mime;
 }
 
+  bool CMsgPackFormat::read(std::istream& in, Core::Molecule& molecule)
+  {
+    return CjsonFormat::deserialize(in, molecule, false);
+  }
+
+  bool CMsgPackFormat::write(std::ostream& out, const Core::Molecule& molecule)
+  {
+    std::cerr << "CMsgPackFormat::write" << std::endl;
+    return CjsonFormat::serialize(out, molecule, false);
+  }
+
 } // namespace Avogadro::Io
diff --git a/avogadro/io/cmsgpackformat.h b/avogadro/io/cmsgpackformat.h
index ce92f1d672..8a8afca6fd 100644
--- a/avogadro/io/cmsgpackformat.h
+++ b/avogadro/io/cmsgpackformat.h
@@ -48,6 +48,9 @@ class AVOGADROIO_EXPORT CMsgPackFormat : public CjsonFormat
   std::vector<std::string> fileExtensions() const override;
   std::vector<std::string> mimeTypes() const override;
 
+  bool read(std::istream& in, Core::Molecule& molecule) override;
+  bool write(std::ostream& out, const Core::Molecule& molecule) override;
+
   // write MessagePack
   bool m_json = false;
 };
diff --git a/avogadro/io/fileformatmanager.cpp b/avogadro/io/fileformatmanager.cpp
index 1841213ee0..999a9c2c68 100644
--- a/avogadro/io/fileformatmanager.cpp
+++ b/avogadro/io/fileformatmanager.cpp
@@ -9,6 +9,7 @@
 
 #include "cjsonformat.h"
 #include "cmlformat.h"
+#include "cmsgpackformat.h"
 #include "dcdformat.h"
 #include "gromacsformat.h"
 #include "lammpsformat.h"
@@ -284,6 +285,7 @@ FileFormatManager::FileFormatManager()
 {
   addFormat(new CmlFormat);
   addFormat(new CjsonFormat);
+  addFormat(new CMsgPackFormat);
   addFormat(new DcdFormat);
   addFormat(new GromacsFormat);
   addFormat(new LammpsTrajectoryFormat);