Merge pull request #26 from MetOffice/feature/file_closure

Feature/file closure
MetOffice · Oct 24, 2023 · 94662e8 · 94662e8
2 parents 45c1e65 + 28dc225
commit 94662e8
Show file tree

Hide file tree

Showing 22 changed files with 131 additions and 42 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,7 +1,7 @@
 ###############################################################################
 # MONIO - Met Office NetCDF Input Output                                      #
 #                                                                             #
-# (C) Crown Copyright 2023 Met Office                                         #
+# (C) Crown Copyright 2023, Met Office.                                       #
 #                                                                             #
 # This software is licensed under the terms of the Apache Licence Version 2.0 #
 # which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.        #

diff --git a/ci/CMakeLists.txt b/ci/CMakeLists.txt
@@ -1,3 +1,12 @@
+###############################################################################
+# MONIO - Met Office NetCDF Input Output                                      #
+#                                                                             #
+# (C) Crown Copyright 2023, Met Office.                                       #
+#                                                                             #
+# This software is licensed under the terms of the Apache Licence Version 2.0 #
+# which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.        #
+###############################################################################
+
 cmake_minimum_required( VERSION 3.20 FATAL_ERROR )
 
 project( monio-ci VERSION 0.0.1 LANGUAGES C CXX Fortran )

diff --git a/ci/build-and-lint b/ci/build-and-lint
@@ -1,7 +1,12 @@
 #!/bin/bash
-#
-# (C) Crown Copyright 2023, the Met Office. All rights reserved.
-#
+###############################################################################
+# MONIO - Met Office NetCDF Input Output                                      #
+#                                                                             #
+# (C) Crown Copyright 2023, Met Office.                                       #
+#                                                                             #
+# This software is licensed under the terms of the Apache Licence Version 2.0 #
+# which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.        #
+###############################################################################
 set -euo pipefail
 
 finally() {

diff --git a/ci/build-and-test b/ci/build-and-test
@@ -1,7 +1,12 @@
 #!/bin/bash
-#
-# (C) Crown Copyright 2023, the Met Office. All rights reserved.
-#
+###############################################################################
+# MONIO - Met Office NetCDF Input Output                                      #
+#                                                                             #
+# (C) Crown Copyright 2023, Met Office.                                       #
+#                                                                             #
+# This software is licensed under the terms of the Apache Licence Version 2.0 #
+# which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.        #
+###############################################################################
 set -euxo pipefail
 
 finally() {

diff --git a/ci/get-ref-branch b/ci/get-ref-branch
@@ -1,4 +1,12 @@
 #!/bin/bash
+###############################################################################
+# MONIO - Met Office NetCDF Input Output                                      #
+#                                                                             #
+# (C) Crown Copyright 2023, Met Office.                                       #
+#                                                                             #
+# This software is licensed under the terms of the Apache Licence Version 2.0 #
+# which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.        #
+###############################################################################
 set -euxo pipefail
 repo="$1"  # expect path to a repo clone
 

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
@@ -1,7 +1,7 @@
 ###############################################################################
 # MONIO - Met Office NetCDF Input Output                                      #
 #                                                                             #
-# (C) Crown Copyright 2023 Met Office                                         #
+# (C) Crown Copyright 2023, Met Office.                                       #
 #                                                                             #
 # This software is licensed under the terms of the Apache Licence Version 2.0 #
 # which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.        #

diff --git a/src/monio/AtlasReader.cc b/src/monio/AtlasReader.cc
@@ -12,6 +12,7 @@
 
 #include "Utils.h"
 #include "UtilsAtlas.h"
+#include "Monio.h"
 
 monio::AtlasReader::AtlasReader(const eckit::mpi::Comm& mpiCommunicator,
                                     const int mpiRankOwner):
@@ -59,6 +60,7 @@ void monio::AtlasReader::populateFieldWithDataContainer(atlas::Field& field,
       break;
     }
     default: {
+        Monio::get().closeFiles();
         utils::throwException("AtlasReader::populateFieldWithDataContainer()> "
                                  "Data type not coded for...");
       }
@@ -91,6 +93,7 @@ void monio::AtlasReader::populateFieldWithDataContainer(atlas::Field& field,
       break;
     }
     default: {
+        Monio::get().closeFiles();
         utils::throwException("AtlasReader::populateFieldWithDataContainer()> "
                                  "Data type not coded for...");
       }
@@ -107,6 +110,7 @@ void monio::AtlasReader::populateField(atlas::Field& field,
   auto fieldView = atlas::array::make_view<T, 2>(field);
   // Field with noFirstLevel == true should have been adjusted to have 70 levels.
   if (noFirstLevel == true && field.levels() == consts::kVerticalFullSize) {
+    Monio::get().closeFiles();
     utils::throwException("AtlasReader::populateField()> Field levels misconfiguration...");
   // Only valid case for field with noFirstLevel == true. Field is adjusted to have 70 levels but
   // read data still has enough to fill 71.
@@ -118,6 +122,7 @@ void monio::AtlasReader::populateField(atlas::Field& field,
         if (std::size_t(index) <= dataVec.size()) {
           fieldView(i, j - 1) = dataVec[index];
         } else {
+          Monio::get().closeFiles();
           utils::throwException("AtlasReader::populateField()> Calculated index exceeds size of "
                                 "data for field \"" + field.name() + "\".");
         }
@@ -132,6 +137,7 @@ void monio::AtlasReader::populateField(atlas::Field& field,
         if (std::size_t(index) <= dataVec.size()) {
           fieldView(i, j) = dataVec[index];
         } else {
+          Monio::get().closeFiles();
           utils::throwException("AtlasReader::populateField()> Calculated index exceeds size of "
                                 "data for field \"" + field.name() + "\".");
         }
@@ -170,6 +176,7 @@ void monio::AtlasReader::populateField(atlas::Field& field,
       if (std::size_t(index) <= dataVec.size()) {
         fieldView(i, j) = dataVec[index];
       } else {
+        Monio::get().closeFiles();
         utils::throwException("AtlasReader::populateField()> "
                               "Calculated index exceeds size of data.");
       }
@@ -192,6 +199,7 @@ atlas::Field monio::AtlasReader::getReadField(atlas::Field& field,
     if (atlasType != atlasType.KIND_REAL64 &&
         atlasType != atlasType.KIND_REAL32 &&
         atlasType != atlasType.KIND_INT32) {
+        Monio::get().closeFiles();
         utils::throwException("AtlasReader::getReadField())> Data type not coded for...");
     }
     atlas::util::Config atlasOptions = atlas::option::name(field.name()) |

diff --git a/src/monio/AtlasWriter.cc b/src/monio/AtlasWriter.cc
@@ -17,6 +17,7 @@
 #include "DataContainerFloat.h"
 #include "DataContainerInt.h"
 #include "Metadata.h"
+#include "Monio.h"
 #include "Utils.h"
 #include "UtilsAtlas.h"
 #include "Writer.h"
@@ -202,7 +203,8 @@ void monio::AtlasWriter::populateDataContainerWithField(
         break;
       }
       default: {
-        utils::throwException("AtlasWriter::populateDataContainerWithField()> "
+        Monio::get().closeFiles();
+utils::throwException("AtlasWriter::populateDataContainerWithField()> "
                                  "Data type not coded for...");
       }
     }
@@ -254,7 +256,8 @@ void monio::AtlasWriter::populateDataContainerWithField(
       break;
     }
     default: {
-        utils::throwException("AtlasWriter::populateDataContainerWithField()> "
+        Monio::get().closeFiles();
+utils::throwException("AtlasWriter::populateDataContainerWithField()> "
                                  "Data type not coded for...");
       }
     }
@@ -268,7 +271,8 @@ void monio::AtlasWriter::populateDataVec(std::vector<T>& dataVec,
   oops::Log::debug() << "AtlasWriter::populateDataVec() " << field.name() << std::endl;
   int numLevels = field.levels();
   if ((lfricToAtlasMap.size() * numLevels) != dataVec.size()) {
-    utils::throwException("AtlasWriter::populateDataVec()> "
+    Monio::get().closeFiles();
+utils::throwException("AtlasWriter::populateDataVec()> "
                           "Data container is not configured for the expected data...");
   }
   auto fieldView = atlas::array::make_view<T, 2>(field);
@@ -323,10 +327,12 @@ atlas::Field monio::AtlasWriter::getWriteField(atlas::Field& field,
   if (atlasType != atlasType.KIND_REAL64 &&
       atlasType != atlasType.KIND_REAL32 &&
       atlasType != atlasType.KIND_INT32) {
+      Monio::get().closeFiles();
       utils::throwException("AtlasWriter::getWriteField())> Data type not coded for...");
   }
   // Erroneous case. For noFirstLevel == true field should have 70 levels
   if (noFirstLevel == true && field.levels() == consts::kVerticalFullSize) {
+    Monio::get().closeFiles();
     utils::throwException("AtlasWriter::getWriteField()> Field levels misconfiguration...");
   }
   // WARNING - This name-check is an LFRic-Lite specific convention...
@@ -350,6 +356,7 @@ atlas::Field monio::AtlasWriter::getWriteField(atlas::Field& field,
       field.metadata().set("name", writeName);
     }
   } else {
+    Monio::get().closeFiles();
     utils::throwException("AtlasWriter::getWriteField()> Field write name misconfiguration...");
   }
   return field;

diff --git a/src/monio/AtlasWriter.h b/src/monio/AtlasWriter.h
@@ -1,10 +1,10 @@
 /******************************************************************************
 * MONIO - Met Office NetCDF Input Output                                      *
 *                                                                             *
-* (C) Crown Copyright 2023, Met Office. All rights reserved.                  *
+* (C) Crown Copyright 2023 Met Office                                         *
 *                                                                             *
-* This software is licensed under the terms of the 3-Clause BSD License       *
-* which can be obtained from https://opensource.org/license/bsd-3-clause/.    *
+* This software is licensed under the terms of the Apache Licence Version 2.0 *
+* which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.        *
 ******************************************************************************/
 #pragma once
 

diff --git a/src/monio/Data.cc b/src/monio/Data.cc
@@ -17,6 +17,7 @@
 #include "DataContainerDouble.h"
 #include "DataContainerFloat.h"
 #include "DataContainerInt.h"
+#include "Monio.h"
 #include "Utils.h"
 
 namespace {
@@ -142,6 +143,7 @@ std::shared_ptr<monio::DataContainerBase>
   if (it != dataContainers_.end()) {
     return it->second;
   } else {
+    Monio::get().closeFiles();
     utils::throwException("DataContainer named \"" + name + "\" was not found.");
   }
 }

diff --git a/src/monio/DataContainerDouble.cc b/src/monio/DataContainerDouble.cc
@@ -11,6 +11,7 @@
 #include <stdexcept>
 
 #include "Constants.h"
+#include "Monio.h"
 #include "Utils.h"
 
 monio::DataContainerDouble::DataContainerDouble(const std::string& name) :
@@ -30,6 +31,7 @@ const std::vector<double>& monio::DataContainerDouble::getData() const {
 
 const double& monio::DataContainerDouble::getDatum(const size_t index) {
   if (index > dataVector_.size()) {
+    Monio::get().closeFiles();
     utils::throwException("DataContainerDouble::getDatum()> Passed index exceeds vector size...");
   }
 

diff --git a/src/monio/DataContainerFloat.cc b/src/monio/DataContainerFloat.cc
@@ -11,6 +11,7 @@
 #include <stdexcept>
 
 #include "Constants.h"
+#include "Monio.h"
 #include "Utils.h"
 
 monio::DataContainerFloat::DataContainerFloat(const std::string& name) :
@@ -30,6 +31,7 @@ const std::vector<float>& monio::DataContainerFloat::getData() const {
 
 const float& monio::DataContainerFloat::getDatum(const size_t index) {
   if (index > dataVector_.size()) {
+    Monio::get().closeFiles();
     utils::throwException("DataContainerFloat::getDatum()> Passed index exceeds vector size...");
   }
   return dataVector_[index];

diff --git a/src/monio/DataContainerInt.cc b/src/monio/DataContainerInt.cc
@@ -11,6 +11,7 @@
 #include <stdexcept>
 
 #include "Constants.h"
+#include "Monio.h"
 #include "Utils.h"
 
 monio::DataContainerInt::DataContainerInt(const std::string& name) :
@@ -30,6 +31,7 @@ const std::vector<int>& monio::DataContainerInt::getData() const {
 
 const int& monio::DataContainerInt::getDatum(const size_t index) {
   if (index > dataVector_.size()) {
+    Monio::get().closeFiles();
     utils::throwException("DataContainerInt::getDatum()> Passed index exceeds vector size...");
   }
   return dataVector_[index];

diff --git a/src/monio/File.cc b/src/monio/File.cc
@@ -254,8 +254,8 @@ void monio::File::readAttributes(Metadata& metadata) {
       metadata.addGlobalAttr(globAttr->getName(), globAttr);
     }
   } else {
-    utils::throwException(
-        "File::readAttributes()> Write file accessed for reading...");
+    close();
+    utils::throwException("File::readAttributes()> Write file accessed for reading...");
   }
 }
 

diff --git a/src/monio/Metadata.cc b/src/monio/Metadata.cc
@@ -20,6 +20,7 @@
 #include "AttributeDouble.h"
 #include "AttributeInt.h"
 #include "AttributeString.h"
+#include "Monio.h"
 #include "Utils.h"
 
 monio::Metadata::Metadata() {
@@ -142,6 +143,7 @@ int monio::Metadata::getDimension(const std::string& dimName) {
   if (isDimDefined(dimName) == true) {
     return dimensions_.at(dimName);
   } else {
+    Monio::get().closeFiles();
     utils::throwException("Metadata::getDimension()> dimension \"" + dimName + "\" not found...");
   }
 }
@@ -170,6 +172,7 @@ std::shared_ptr<monio::Variable> monio::Metadata::getVariable(const std::string&
   if (it != variables_.end()) {
     return variables_.at(varName);
   } else {
+    Monio::get().closeFiles();
     utils::throwException("Metadata::getVariable()> variable \"" + varName + "\" not found...");
   }
 }
@@ -182,6 +185,7 @@ const std::shared_ptr<monio::Variable>
   if (it != variables_.end()) {
     return variables_.at(varName);
   } else {
+    Monio::get().closeFiles();
     utils::throwException("Metadata::getVariable()> variable \"" + varName + "\" not found...");
   }
 }
@@ -223,6 +227,7 @@ const std::vector<std::string> monio::Metadata::getVarStrAttrs(
       varStrAttrs.push_back(attr);
   }
   if (varNames.size() != varStrAttrs.size()) {
+    Monio::get().closeFiles();
     utils::throwException("Metadata::getVarStrAttrs()> "
         "Unmatched number of variables and attributes...");
   }
@@ -361,6 +366,7 @@ void monio::Metadata::deleteVariable(const std::string& varName) {
   if (it != variables_.end()) {
     variables_.erase(varName);
   } else {
+    Monio::get().closeFiles();
     utils::throwException("Metadata::deleteVariable()> Variable \"" + varName + "\" not found...");
   }
 }
@@ -432,6 +438,7 @@ void monio::Metadata::printVariables() {
           break;
         }
         default: {
+          Monio::get().closeFiles();
           utils::throwException("Metadata::printGlobalAttrs()> Data type not coded for...");
         }
       }
@@ -464,6 +471,7 @@ void monio::Metadata::printGlobalAttrs() {
         break;
       }
       default: {
+        Monio::get().closeFiles();
         utils::throwException("Metadata::printGlobalAttrs()> Data type not coded for...");
       }
     }