Merge pull request #29 from MetOffice/feature/hofx_io_compare

Minor modifications to Monio::readState for HofX
MetOffice · Jan 5, 2024 · e406a1b · e406a1b
2 parents 083e3c1 + d65ea1f
commit e406a1b
Show file tree

Hide file tree

Showing 3 changed files with 32 additions and 9 deletions.
diff --git a/src/monio/Monio.cc b/src/monio/Monio.cc
@@ -61,7 +61,6 @@ void monio::Monio::readState(atlas::FieldSet& localFieldSet,
           if (mpiCommunicator_.rank() == mpiRankOwner_) {
             auto& functionSpace = globalField.functionspace();
             auto& grid = atlas::functionspace::NodeColumns(functionSpace).mesh().grid();
-
             // Initialise file
             int variableConvention = initialiseFile(grid.name(), filePath, true);
             // getFileData returns a copy of FileData (with required LFRic mesh data), so read data
@@ -72,13 +71,18 @@ void monio::Monio::readState(atlas::FieldSet& localFieldSet,
             if (variableConvention == consts::eJediConvention) {
               readName = fieldMetadata.jediName;
             }
-            oops::Log::debug() << "Monio::readState() processing data for> \"" <<
-                                  readName << "\"..." << std::endl;
-            // Read fields into memory
-            reader_.readDatumAtTime(fileData, readName, dateTime,
-                                    std::string(consts::kTimeDimName));
-            atlasReader_.populateFieldWithFileData(globalField, fileData, fieldMetadata, readName,
-                                                   variableConvention == consts::eLfricConvention);
+            if (utils::findInVector(consts::kMissingVariableNames, readName) == false) {
+              oops::Log::debug() << "Monio::readState() processing data for> \"" <<
+                                    readName << "\"..." << std::endl;
+              // Read fields into memory
+              reader_.readDatumAtTime(fileData, readName, dateTime,
+                                      std::string(consts::kTimeDimName));
+              atlasReader_.populateFieldWithFileData(globalField, fileData, fieldMetadata, readName,
+                                                    variableConvention == consts::eLfricConvention);
+            } else {
+              oops::Log::info() << "Monio::readState()> Variable \"" + fieldMetadata.jediName +
+                                   "\" not defined in LFRic. Skipping read..." << std::endl;
+            }
           }
           auto& functionSpace = globalField.functionspace();
           functionSpace.scatter(globalField, localField);

diff --git a/src/monio/Utils.cc b/src/monio/Utils.cc
@@ -8,7 +8,10 @@
 ******************************************************************************/
 #include "Utils.h"
 
+#include <stdio.h>
+
 #include <algorithm>
+#include <array>
 #include <fstream>
 #include <memory>
 
@@ -54,8 +57,22 @@ bool strToBool(std::string input) {
              (cleanStr.size() == 5 && cleanStr == "false")) {
     return false;
   } else {
-    throw std::invalid_argument("ERROR> Input value of \"" + input + "\" is not valid.");
+    throw std::invalid_argument("utils::strToBool> Input value of \"" + input + "\" is not valid.");
+  }
+}
+
+std::string exec(const std::string& cmd) {
+  std::array<char, 128> buffer;
+  std::string result;
+  std::string extCmd = "sh -c '" + cmd + "' 2>&1";
+  std::unique_ptr<FILE, decltype(&pclose)> pipe(popen(extCmd.c_str(), "r"), pclose);
+  if (!pipe) {
+    throw std::runtime_error("popen() failed!");
+  }
+  while (fgets(buffer.data(), buffer.size(), pipe.get()) != nullptr) {
+    result += buffer.data();
   }
+  return result;
 }
 
 bool fileExists(std::string path) {

diff --git a/src/monio/Utils.h b/src/monio/Utils.h
@@ -27,6 +27,8 @@ namespace utils {
   bool strToBool(std::string input);
   bool fileExists(std::string path);
 
+  std::string exec(const std::string& cmd);
+
   template<typename T1, typename T2>
   std::vector<T1> extractKeys(std::map<T1, T2> const& inputMap);