ecmwf · mcakircali · Jun 13, 2024 · Jun 13, 2024 · Jun 17, 2024 · Jul 6, 2024
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -115,6 +115,12 @@ ecbuild_add_option( FEATURE SANDBOX
                     DESCRIPTION "build the sandbox stuff"
                     DEFAULT OFF	 )
 
+### Enables the FAM support for FDB. (https://openfam.github.io/)
+ecbuild_add_option( FEATURE FAMFDB
+                    CONDITION eckit_HAVE_OPENFAM
+                    DEFAULT ON
+                    DESCRIPTION "Enables the FAM support for FDB via OpenFAM API" )
+
 ### build the tools
 
 ecbuild_add_option( FEATURE BUILD_TOOLS

diff --git a/src/dummy_daos/daos.cc b/src/dummy_daos/daos.cc
@@ -30,8 +30,7 @@
 #include "eckit/types/UUID.h"
 #include "eckit/utils/MD5.h"
 
-#include "daos.h"
-#include "dummy_daos.h"
+#include "dummy_daos/dummy_daos.h"
 
 using eckit::PathName;
 

diff --git a/src/dummy_daos/daos/tests_lib.cc b/src/dummy_daos/daos/tests_lib.cc
@@ -14,7 +14,11 @@
  * @date   Jun 2022
  */
 
+#include "tests_lib.h"
+
 #include <unistd.h>
+#include "../dummy_daos.h"
+
 #include <cstring>
 
 #include "eckit/exception/Exceptions.h"

diff --git a/src/dummy_daos/daos/tests_lib.h b/src/dummy_daos/daos/tests_lib.h
@@ -17,7 +17,6 @@
 #pragma once
 
 #include <uuid/uuid.h>
-
 #include "../daos.h"
 
 //----------------------------------------------------------------------------------------------------------------------

diff --git a/src/fdb5/CMakeLists.txt b/src/fdb5/CMakeLists.txt
@@ -405,6 +405,10 @@ else()
     set( UUID_INCLUDE_DIRS "" )
 endif()
 
+if( HAVE_FAMFDB )
+    add_subdirectory( fam )
+endif()
+
 ecbuild_add_library(
 
     TARGET  fdb5
@@ -475,6 +479,12 @@ if ( HAVE_GRIB )
     )
 endif()
 
+if ( HAVE_FAMFDB )
+    list( APPEND fdb5_tools
+        fdb-fam
+    )
+endif()
+
 if ( HAVE_TOCFDB )
     list(APPEND fdb5_tools
         fdb-root

diff --git a/src/fdb5/LibFdb5.cc b/src/fdb5/LibFdb5.cc
@@ -12,8 +12,6 @@
 /// @author Tiago Quintino
 /// @date   Nov 2016
 
-#include <algorithm>
-
 #include "fdb5/LibFdb5.h"
 
 #include "eckit/config/LibEcKit.h"
@@ -23,9 +21,8 @@
 #include "eckit/exception/Exceptions.h"
 #include "eckit/log/Log.h"
 
-#include "fdb5/fdb5_version.h"
-
 #include "fdb5/config/Config.h"
+#include "fdb5/fdb5_version.h"
 
 namespace fdb5 {
 

diff --git a/src/fdb5/api/DistFDB.h b/src/fdb5/api/DistFDB.h
@@ -19,6 +19,8 @@
 #ifndef fdb5_api_DistFDB_H
 #define fdb5_api_DistFDB_H
 
+#include "eckit/utils/RendezvousHash.h"
+
 #include "fdb5/api/FDB.h"
 #include "fdb5/api/FDBFactory.h"
 

diff --git a/src/fdb5/api/FDB.cc b/src/fdb5/api/FDB.cc
@@ -13,7 +13,10 @@
  * (Project ID: 671951) www.nextgenio.eu
  */
 
+#include "fdb5/api/FDB.h"
+
 #include <cstddef>
+#include <memory>
 #include <sstream>
 #include <string>
 #include <vector>
@@ -28,7 +31,6 @@
 #include "eckit/message/Reader.h"
 
 #include "fdb5/LibFdb5.h"
-#include "fdb5/api/FDB.h"
 #include "fdb5/api/FDBFactory.h"
 #include "fdb5/api/helpers/FDBToolRequest.h"
 #include "fdb5/api/helpers/ListElement.h"
@@ -40,8 +42,6 @@
 #include "fdb5/message/MessageDecoder.h"
 #include "fdb5/types/Type.h"
 
-#include <memory>
-
 namespace fdb5 {
 
 //----------------------------------------------------------------------------------------------------------------------

diff --git a/src/fdb5/api/FDBFactory.cc b/src/fdb5/api/FDBFactory.cc
@@ -14,15 +14,13 @@
  */
 
 
-#include "eckit/config/YAMLConfiguration.h"
+#include "fdb5/api/FDBFactory.h"
+
 #include "eckit/log/Log.h"
-#include "eckit/message/Message.h"
 #include "eckit/thread/AutoLock.h"
 #include "eckit/thread/Mutex.h"
 
 #include "fdb5/LibFdb5.h"
-#include "fdb5/api/FDBFactory.h"
-#include "fdb5/api/helpers/FDBToolRequest.h"
 
 
 namespace fdb5 {
@@ -50,9 +48,6 @@ FDBBase::FDBBase(const Config& config, const std::string& name) : name_(name), c
     LOG_DEBUG_LIB(LibFdb5) << "FDBBase: " << config << std::endl;
 }
 
-
-FDBBase::~FDBBase() {}
-
 std::string FDBBase::id() const {
     std::stringstream ss;
     ss << config_;

diff --git a/src/fdb5/api/FDBFactory.h b/src/fdb5/api/FDBFactory.h
@@ -21,11 +21,8 @@
 
 #include <memory>
 
-#include "eckit/distributed/Transport.h"
 #include "eckit/memory/NonCopyable.h"
-#include "eckit/utils/Regex.h"
 
-#include "fdb5/api/FDBStats.h"
 #include "fdb5/api/helpers/AxesIterator.h"
 #include "fdb5/api/helpers/Callback.h"
 #include "fdb5/api/helpers/ControlIterator.h"
@@ -37,24 +34,24 @@
 #include "fdb5/api/helpers/StatusIterator.h"
 #include "fdb5/api/helpers/WipeIterator.h"
 #include "fdb5/config/Config.h"
-#include "fdb5/database/Catalogue.h"
 
 namespace eckit::message {
 
 class Message;
 
 }  // namespace eckit::message
 
-namespace metkit {
+namespace metkit::mars {
 
 class MarsRequest;
 
-}  // namespace metkit
+}  // namespace metkit::mars
 
 namespace fdb5 {
 
 class Key;
 class FDBToolRequest;
+class FieldLocation;
 
 //----------------------------------------------------------------------------------------------------------------------
 
@@ -65,7 +62,8 @@ class FDBBase : private eckit::NonCopyable, public CallbackRegistry {
 public:  // methods
 
     FDBBase(const Config& config, const std::string& name);
-    virtual ~FDBBase();
+
+    virtual ~FDBBase() = default;
 
     // -------------- Primary API functions ----------------------------
 

diff --git a/src/fdb5/api/LocalFDB.cc b/src/fdb5/api/LocalFDB.cc
@@ -13,21 +13,14 @@
  * (Project ID: 671951) www.nextgenio.eu
  */
 
+#include "fdb5/api/LocalFDB.h"
+
 #include "eckit/container/Queue.h"
 #include "eckit/log/Log.h"
 
 #include "fdb5/LibFdb5.h"
-#include "fdb5/api/LocalFDB.h"
 #include "fdb5/api/helpers/FDBToolRequest.h"
 #include "fdb5/api/helpers/ListIterator.h"
-#include "fdb5/database/Archiver.h"
-#include "fdb5/database/Catalogue.h"
-#include "fdb5/database/EntryVisitMechanism.h"
-#include "fdb5/database/Index.h"
-#include "fdb5/database/Inspector.h"
-#include "fdb5/database/Key.h"
-#include "fdb5/rules/Schema.h"
-
 #include "fdb5/api/local/AxesVisitor.h"
 #include "fdb5/api/local/ControlVisitor.h"
 #include "fdb5/api/local/DumpVisitor.h"
@@ -37,6 +30,11 @@
 #include "fdb5/api/local/StatsVisitor.h"
 #include "fdb5/api/local/StatusVisitor.h"
 #include "fdb5/api/local/WipeVisitor.h"
+#include "fdb5/database/Archiver.h"
+#include "fdb5/database/EntryVisitMechanism.h"
+#include "fdb5/database/Inspector.h"
+#include "fdb5/database/Key.h"
+#include "fdb5/rules/Schema.h"
 
 
 using namespace fdb5::api::local;

diff --git a/src/fdb5/api/LocalFDB.h b/src/fdb5/api/LocalFDB.h
@@ -20,12 +20,12 @@
 #define fdb5_api_LocalFDB_H
 
 #include "fdb5/api/FDBFactory.h"
+#include "fdb5/database/Inspector.h"
 #include "fdb5/database/Reindexer.h"
 
 
 namespace fdb5 {
 
-class Inspector;
 class Archiver;
 class FDB;
 

diff --git a/src/fdb5/api/RandomFDB.cc b/src/fdb5/api/RandomFDB.cc
@@ -13,6 +13,10 @@
  * (Project ID: 671951) www.nextgenio.eu
  */
 
+#include <stdlib.h>
+
+#include <random>
+
 #include "eckit/exception/Exceptions.h"
 #include "eckit/log/Log.h"
 

diff --git a/src/fdb5/api/SelectFDB.cc b/src/fdb5/api/SelectFDB.cc
@@ -13,6 +13,8 @@
  * (Project ID: 671951) www.nextgenio.eu
  */
 
+#include "fdb5/api/SelectFDB.h"
+
 #include "eckit/log/Log.h"
 #include "eckit/message/Message.h"
 #include "eckit/types/Types.h"

diff --git a/src/fdb5/api/helpers/FDBToolRequest.cc b/src/fdb5/api/helpers/FDBToolRequest.cc
@@ -17,12 +17,12 @@
 
 #include <algorithm>
 
+#include "eckit/exception/Exceptions.h"
+
 #include "metkit/mars/MarsExpension.h"
 #include "metkit/mars/MarsParser.h"
 #include "metkit/mars/MarsRequest.h"
 
-#include "eckit/exception/Exceptions.h"
-
 #include "fdb5/LibFdb5.h"
 
 

diff --git a/src/fdb5/api/helpers/WipeIterator.h b/src/fdb5/api/helpers/WipeIterator.h
@@ -19,10 +19,10 @@
 #ifndef fdb5_api_WipeIterator_H
 #define fdb5_api_WipeIterator_H
 
-#include "fdb5/api/helpers/APIIterator.h"
-
 #include <string>
 
+#include "fdb5/api/helpers/APIIterator.h"
+
 /*
  * Define a standard object which can be used to iterate the results of a
  * wipe() call on an arbitrary FDB object

diff --git a/src/fdb5/api/local/MoveVisitor.h b/src/fdb5/api/local/MoveVisitor.h
@@ -22,6 +22,10 @@
 
 #include "eckit/filesystem/PathName.h"
 
+#include "fdb5/api/helpers/MoveIterator.h"
+#include "fdb5/api/local/QueryVisitor.h"
+#include "fdb5/database/MoveVisitor.h"
+
 
 namespace fdb5 {
 namespace api {

diff --git a/src/fdb5/api/local/PurgeVisitor.h b/src/fdb5/api/local/PurgeVisitor.h
@@ -24,8 +24,6 @@
 #include "fdb5/database/PurgeVisitor.h"
 #include "fdb5/database/Store.h"
 
-#include "eckit/filesystem/PathName.h"
-
 
 namespace fdb5 {
 namespace api {

diff --git a/src/fdb5/api/local/QueueStringLogTarget.h b/src/fdb5/api/local/QueueStringLogTarget.h
@@ -19,12 +19,12 @@
 #ifndef fdb5_api_local_QueueStringLogTarget_H
 #define fdb5_api_local_QueueStringLogTarget_H
 
+#include <string>
+
 #include "eckit/container/Queue.h"
 #include "eckit/log/Channel.h"
 #include "eckit/log/LineBasedTarget.h"
 
-#include <string>
-
 namespace fdb5 {
 namespace api {
 namespace local {

diff --git a/src/fdb5/api/local/WipeVisitor.h b/src/fdb5/api/local/WipeVisitor.h
@@ -25,6 +25,10 @@
 
 #include "eckit/filesystem/PathName.h"
 
+#include "fdb5/api/helpers/WipeIterator.h"
+#include "fdb5/api/local/QueryVisitor.h"
+#include "fdb5/database/WipeVisitor.h"
+
 
 namespace fdb5 {
 namespace api {

diff --git a/src/fdb5/daos/DaosArrayHandle.cc b/src/fdb5/daos/DaosArrayHandle.cc
@@ -8,6 +8,8 @@
  * does it submit to any jurisdiction.
  */
 
+#include "fdb5/daos/DaosArrayHandle.h"
+
 #include <memory>
 
 #include "eckit/exception/Exceptions.h"

diff --git a/src/fdb5/daos/DaosArrayPartHandle.cc b/src/fdb5/daos/DaosArrayPartHandle.cc
@@ -8,6 +8,8 @@
  * does it submit to any jurisdiction.
  */
 
+#include "fdb5/daos/DaosArrayPartHandle.h"
+
 #include <memory>
 
 #include "eckit/exception/Exceptions.h"

diff --git a/src/fdb5/daos/DaosCatalogue.cc b/src/fdb5/daos/DaosCatalogue.cc
@@ -22,6 +22,7 @@
 #include "fdb5/daos/DaosName.h"
 #include "fdb5/daos/DaosSession.h"
 #include "fdb5/daos/DaosWipeVisitor.h"
+#include "fdb5/database/DatabaseNotFoundException.h"
 
 // using namespace eckit;
 

diff --git a/src/fdb5/daos/DaosCatalogueReader.cc b/src/fdb5/daos/DaosCatalogueReader.cc
@@ -16,6 +16,11 @@
 #include "fdb5/daos/DaosCatalogueReader.h"
 #include "fdb5/daos/DaosIndex.h"
 
+#include "fdb5/LibFdb5.h"
+#include "fdb5/daos/DaosIndex.h"
+#include "fdb5/daos/DaosName.h"
+#include "fdb5/daos/DaosSession.h"
+
 namespace fdb5 {
 
 //----------------------------------------------------------------------------------------------------------------------

diff --git a/src/fdb5/daos/DaosCommon.cc b/src/fdb5/daos/DaosCommon.cc
@@ -8,8 +8,6 @@
  * does it submit to any jurisdiction.
  */
 
-#include <algorithm>
-
 #include "fdb5/daos/DaosCommon.h"
 
 #include "eckit/config/Resource.h"