Feature/sina/hdf5 output support

src/axom/sina/CMakeLists.txt

@@ -50,10 +50,17 @@ blt_list_append( TO sina_headers ELEMENTS core/AdiakWriter.hpp IF AXOM_USE_ADIAK
 blt_list_append( TO sina_sources ELEMENTS core/AdiakWriter.cpp IF AXOM_USE_ADIAK )
 
 # Add fortran interface for Sina
+if(AXOM_USE_HDF5 AND ENABLE_FORTRAN)
+  set(AXOM_USE_HDF5_FORTRAN ".true.")
+else()
+  set(AXOM_USE_HDF5_FORTRAN ".false.")
+endif()
+
 if (ENABLE_FORTRAN)
   blt_list_append( TO sina_headers ELEMENTS interface/sina_fortran_interface.h)
   blt_list_append( TO sina_sources
-                   ELEMENTS interface/sina_fortran_interface.cpp interface/sina_fortran_interface.f)
+  ELEMENTS interface/sina_fortran_interface.cpp interface/sina_fortran_interface.f.in)
+  configure_file(interface/sina_fortran_interface.f.in interface/sina_fortran_interface.f @ONLY)
 endif()
 
 #------------------------------------------------------------------------------
@@ -87,4 +94,4 @@ endif()
 
 if(AXOM_ENABLE_EXAMPLES)
   add_subdirectory(examples)
-endif()
+endif()

src/axom/sina/core/Document.cpp

@@ -12,7 +12,6 @@
  *
  ******************************************************************************
  */
-
 #include "axom/sina/core/Document.hpp"
 
 #include "axom/config.hpp"
@@ -66,6 +65,21 @@ void protocolWarn(std::string const protocol, std::string const &name)
   }
 }
 
+std::string get_supported_file_types()
+{
+  std::string types = "[";
+  for(size_t i = 0; i < supported_types.size(); ++i)
+  {
+    types += supported_types[i];
+    if(i < supported_types.size() - 1)
+    {
+      types += ", ";
+    }
+  }
+  types += "]";
+  return types;
+}
+
 void Document::add(std::unique_ptr<Record> record)
 {
   records.emplace_back(std::move(record));
@@ -313,8 +327,11 @@ void saveDocument(Document const &document,
 #endif
   else
   {
-    throw std::invalid_argument(
-      "Invalid format choice. Please enter 'json' or 'hdf5'.");
+    std::ostringstream message;
+    message << "Invalid format choice. Please choose from one of the supported "
+               "protocols: "
+            << get_supported_file_types();
+    throw std::invalid_argument(message.str());
   }
 
   if(rename(tmpFileName.c_str(), fileName.c_str()) != 0)
@@ -347,16 +364,19 @@ Document loadDocument(std::string const &path,
     file_in.close();
     node.parse(file_contents.str(), "json");
     return Document {node, recordLoader};
-
 #ifdef AXOM_USE_HDF5
   case Protocol::HDF5:
     file_in.close();
     conduit::relay::io::load(path, "hdf5", node);
     restoreSlashes(node, modifiedNode);
     return Document {modifiedNode, recordLoader};
 #endif
-
   default:
+    std::ostringstream message;
+    message << "Invalid format choice. Please choose from one of the supported "
+               "protocols: "
+            << get_supported_file_types();
+    throw std::invalid_argument(message.str());
     break;
   }
 }

src/axom/sina/core/Document.hpp

@@ -36,14 +36,12 @@ namespace sina
 enum class Protocol
 {
   JSON,
-#ifdef AXOM_USE_HDF5
   HDF5
-#endif
 };
 
-const std::string supported_types[] = {"JSON",
+const std::vector<std::string> supported_types = {"JSON",
 #ifdef AXOM_USE_HDF5
-                                       "HDF5"
+                                                  "HDF5"
 #endif
 };
 
@@ -224,6 +222,13 @@ class Document
                      const std::string &pad = "",
                      const std::string &eoe = "") const;
 
+  /**
+    * \brief Get the list of file types currently supported by the implementation.
+    * 
+    * \return a string of supported file types
+    */
+  std::string get_supported_file_types();
+
 private:
   /**
      * Constructor helper method, extracts info from a conduit Node.
@@ -237,11 +242,12 @@ class Document
 /**
  * \brief Save the given Document to the specified location. If the given file exists,
  *        it will be overwritten.
- *
+ * 
  * \param document the Document to save
  * \param fileName the location of which to save the file
  * \param protocol the file type requested to save as contained in supported_types, default = JSON
  * \throws std::ios::failure if there are any IO errors
+ *         std::invalid_argument if the protocol given is an undefined, optional protocol
  */
 void saveDocument(Document const &document,
                   std::string const &fileName,
@@ -276,6 +282,7 @@ Document loadDocument(std::string const &path,
  * \param recordLoader the RecordLoader to use to load the different types
  *                     of records
  * \param protocol the type of file being loaded, default = JSON
+ * \throws std::invalid_argument if the protocol given is an undefined, optional protocol
  * \return the loaded Document
  */
 Document loadDocument(std::string const &path,

src/axom/sina/examples/CMakeLists.txt

@@ -27,7 +27,7 @@ set(sina_example_sources
     sina_view_datum_values.cpp
 )
 
-set(sina_example_depends sina conduit slic)
+set(sina_example_depends sina conduit::conduit slic)
 
 if (ENABLE_FORTRAN)
     blt_list_append( TO sina_example_sources ELEMENTS sina_fortran.f)
@@ -38,16 +38,26 @@ endif()
 #------------------------------------------------------------------------------
 foreach(src ${sina_example_sources})
     get_filename_component(exe_name ${src} NAME_WE)
+
+    if (exe_name STREQUAL "sina_fortran")
+        set(sina_mod_src ${CMAKE_CURRENT_BINARY_DIR}/../interface/sina_fortran_interface.f)
+    else()
+        set(sina_mod_src "")
+    endif()
+
     axom_add_executable(
         NAME       ${exe_name}_ex
-        SOURCES    ${src}
+        SOURCES    ${src} ${sina_mod_src}
         OUTPUT_DIR ${EXAMPLE_OUTPUT_DIRECTORY}
         DEPENDS_ON ${sina_example_depends}
         FOLDER     axom/sina/examples
-        )
+    )
+
+    if (exe_name STREQUAL "sina_fortran")
+        target_include_directories(${exe_name}_ex PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/../interface)
+    endif()
 
-    # Need to add this flag so XL will ignore trailing underscores in fortran function names
     if (${exe_name}_ex STREQUAL "sina_fortran_ex" AND CMAKE_Fortran_COMPILER_ID STREQUAL "XL")
         target_compile_options(${exe_name}_ex PRIVATE -qextname)
     endif()
-endforeach()
+endforeach()

src/axom/sina/examples/sina_fortran.f

@@ -1,5 +1,6 @@
 program example
   use sina_functions
+  use hdf5_config
   implicit none
 
   ! data types
@@ -57,7 +58,9 @@ program example
   full_path = make_cstring(wrk_dir//''//fle_nme)
   ofull_path = make_cstring(wrk_dir//''//ofle_nme)
   json_fn = make_cstring('sina_dump.json')
-  hdf5_fn = make_cstring('sina_dump.hdf5')
+  if (use_hdf5) then
+    hdf5_fn = make_cstring('sina_dump.hdf5')
+  end if
 
 
   mime_type = make_cstring('')
@@ -151,7 +154,9 @@ program example
   ! write out the Sina Document
   print *,'Writing out the Sina Document'
   call write_sina_document(json_fn)
-  call write_sina_document(hdf5_fn, 1)
+  if (use_hdf5) then
+    call write_sina_document(hdf5_fn, 1)
+  end if
 
 
 contains

src/axom/sina/interface/sina_fortran_interface.f → src/axom/sina/interface/sina_fortran_interface.f.in

@@ -144,4 +144,9 @@ subroutine save_without_protocol(fname)
     call write_sina_document_noprotocol(fname)
   end subroutine save_without_protocol
 
-end module 
+end module 
+
+module hdf5_config
+  implicit none
+  logical, parameter :: use_hdf5 = @AXOM_USE_HDF5_FORTRAN@
+end module hdf5_config

src/axom/sina/tests/sina_Document.cpp

@@ -410,7 +410,6 @@ TEST(Document, saveDocument_json)
   EXPECT_EQ("the type", readRecord["type"].as_string());
 }
 
-#ifdef AXOM_USE_HDF5
 TEST(Document, load_specifiedRecordLoader)
 {
   using RecordType = TestRecord<int>;
@@ -463,6 +462,7 @@ TEST(Document, load_defaultRecordLoaders)
   EXPECT_NE(nullptr, loadedRun);
 }
 
+#ifdef AXOM_USE_HDF5
 TEST(Document, create_fromJson_roundtrip_hdf5)
 {
   std::string orig_json =