Merge pull request #23 from FAIRDataPipeline/dev

Dev

CMakeLists.txt

@@ -61,7 +61,6 @@ INCLUDE( external/jsoncpp.cmake )
 INCLUDE( external/digestpp.cmake )
 INCLUDE( external/curl.cmake )
 INCLUDE( external/yaml_cpp.cmake )
-INCLUDE( external/spdlog.cmake )
 INCLUDE( external/toml11.cmake )
 INCLUDE( external/ghc.cmake )
 

README.md

@@ -33,6 +33,8 @@ $ cmake --build build --config=Release
 ## Outline
 The main class the user will interact with is `DataPipeline` which has only the required methods such as `link_read` etc. This class has a member which is a pointer to an underlying `DataPipelineImpl_` class which performs the various procedures required to handle the data. A logger has been used to give as much feedback to the user as possible, the verbosity being handled by a log level argument.
 
+### Logging
+The environment variable `FDP_LOG_LEVEL=[TRACE:DEBUG:INFO:WARN:ERROR:CRITICAL:OFF]` can be set to specify the logging output level.
 
 ## Unit Tests
 The unit tests use the local registry, this needs to be running prior to running the tests see: [the CLI documentation](https://github.com/FAIRDataPipeline/FAIR-CLI#registry)

external/digestpp.cmake

@@ -7,6 +7,7 @@ SET( DIGESTCPP_COMMIT "34ff2eeae397ed744d972d86b5a20f603b029fbd" )
 # So tell the compiler to exclude min and max macros in windows
 IF(WIN32)
     add_definitions(-DNOMINMAX)
+    add_definitions(-DNOGDI)
 ENDIF()
 
 MESSAGE( STATUS "[DigestCPP]" )

external/jsoncpp.cmake

@@ -4,6 +4,8 @@ MESSAGE( STATUS "[JsonCPP]" )
 MESSAGE( STATUS "\tJsonCpp Will be installed." )
 MESSAGE( STATUS "\tURL: ${JSONCPP_URL}" )
 
+SET (JSONCPP_WITH_TESTS OFF CACHE INTERNAL "Don't Build cpp tests")
+
 include(FetchContent)
 FetchContent_Declare(
     JsonCpp

include/fdp/exceptions.hxx

@@ -4,7 +4,7 @@
 #include <stdexcept>
 #include <string>
 
-namespace FDP {
+namespace FairDataPipeline {
 class config_parsing_error : public std::runtime_error {
 public:
   config_parsing_error(const std::string& message)
@@ -37,6 +37,6 @@ public:
   write_error(const std::string& message) : std::runtime_error(message) {}
 };
 
-}; // namespace FDP
+}; // namespace FairDataPipeline
 
 #endif

include/fdp/fdp.hxx

@@ -1,12 +1,11 @@
 #ifndef __FDP__
 #define __FDP__
 
-#include "spdlog/spdlog.h"
-#include <ghc/filesystem.hpp>
+#include "utilities/logging.hxx"
 
-//#include "fdp/registry/datapipeline.hxx"
+#include <ghc/filesystem.hpp>
 
-namespace FDP {
+namespace FairDataPipeline {
 /**
  * @brief DataPipeline Class:
  * A PIMPL Class for interacting the the FAIR Data Pipeline
@@ -15,31 +14,29 @@ namespace FDP {
     class DataPipeline {
 
         public:
+            typedef std::shared_ptr< DataPipeline > sptr;
   /**
    * @brief Construct a new Data Pipeline (PIMPL)
    * 
    * @param config_file_path 
    * @param script_file_path 
    * @param token 
-   * @param log_level 
    */
-            explicit DataPipeline(
+           static  sptr construct(
                     const std::string &config_file_path,
                     const std::string &script_file_path,
-                    std::string token = "",
-                    spdlog::level::level_enum log_level = spdlog::level::info);
+                    std::string token = "" );
+
 
   /**
    * @brief Destroy the Data Pipeline object
    * 
    */
             ~DataPipeline();
 
-            DataPipeline(DataPipeline &&rhs) noexcept;
-            DataPipeline &operator=(DataPipeline &&rhs) noexcept;
+            //DataPipeline(DataPipeline &&rhs) noexcept;
+            //DataPipeline &operator=(DataPipeline &&rhs) noexcept;
 
-            DataPipeline(const DataPipeline &rhs);
-            DataPipeline &operator=(const DataPipeline &rhs);
 
   /**
    * @brief Return a path to a given data product
@@ -68,10 +65,19 @@ namespace FDP {
             void finalise();
 
         private:
+            explicit DataPipeline(
+                    const std::string &config_file_path,
+                    const std::string &script_file_path,
+                    std::string token = ""
+                    );
+
+            DataPipeline(const DataPipeline &rhs) = delete;
+
+            DataPipeline &operator=(const DataPipeline &rhs) = delete;
+
             class impl;
 
             std::shared_ptr< DataPipeline::impl > pimpl_;
     };
-}; // namespace FDP
-
+}; // namespace FairDataPipeline
 #endif

include/fdp/objects/api_object.hxx

@@ -7,7 +7,7 @@
 
 #include "fdp/utilities/logging.hxx"
 
-namespace FDP {
+namespace FairDataPipeline {
     /**
      * @brief Class for API objects
      * 
@@ -49,7 +49,7 @@ namespace FDP {
              * @return int object id e.g. if the uri is http://127.0.0.1/object/1 
              * the object id will be 1
              */
-            int get_id();
+            int get_id() const ;
             /**
              * @brief Get the object type from the uri
              * 
@@ -58,7 +58,7 @@ namespace FDP {
              */
             static int get_id_from_string(std::string url);
 
-            std::string get_type();
+            std::string get_type() const ;
             /**
              * @brief Get the object uri
              * 

include/fdp/objects/config.hxx

@@ -25,12 +25,17 @@
 #include "fdp/objects/api_object.hxx"
 #include "fdp/objects/io_object.hxx"
 
-namespace FDP {
+namespace FairDataPipeline {
     /**
      * @brief class for interacting with confifurations
      * 
      */
     class Config {
+        public:
+            typedef std::shared_ptr< Config > sptr;
+
+            typedef std::map< std::string, IOObject > map_type;
+
         private:            
             const ghc::filesystem::path config_file_path_;
             const ghc::filesystem::path config_dir_;
@@ -59,11 +64,11 @@ namespace FDP {
 
             ApiObject::sptr code_run_;
 
-            std::map<std::string, IOObject> writes_;
-            std::map<std::string, IOObject> reads_;
+            map_type writes_;
+            map_type reads_;
 
-            std::map<std::string, IOObject> outputs_;
-            std::map<std::string, IOObject> inputs_;
+            map_type outputs_;
+            map_type inputs_;
 
             RESTAPI rest_api_location_ = RESTAPI::LOCAL;
 
@@ -87,7 +92,6 @@ namespace FDP {
 
 
         public:
-            typedef std::shared_ptr< Config > sptr;
 
             static Config::sptr construct(const ghc::filesystem::path &config_file_path,
                     const ghc::filesystem::path &script_file_path,
@@ -225,15 +229,15 @@ namespace FDP {
              * @param data_product 
              * @return ghc::filesystem::path 
              */
-            ghc::filesystem::path link_write(std::string &data_product);
+            ghc::filesystem::path link_write( const std::string &data_product);
 
             /**
              * @brief Return the filepath to a given data product
              * 
              * @param data_product 
              * @return ghc::filesystem::path 
              */
-            ghc::filesystem::path link_read(std::string &data_product);
+            ghc::filesystem::path link_read(const std::string& data_product);
 
             /**
              * @brief Finalise the pipeline

include/fdp/objects/io_object.hxx

@@ -8,7 +8,7 @@
 #include "fdp/utilities/logging.hxx"
 #include "fdp/objects/api_object.hxx"
 
-namespace FDP {
+namespace FairDataPipeline {
     /**
      * @brief Class for API objects
      * 
@@ -123,7 +123,7 @@ namespace FDP {
              * 
              * @return const std::string& 
              */
-            const std::string& get_use_namespace() {return use_namespace_;}
+            const std::string& get_use_namespace() const {return use_namespace_;}
 
             /**
              * @brief Get the path of the data product
@@ -144,7 +144,7 @@ namespace FDP {
              * 
              * @return std::string 
              */
-            const std::string& get_component_description() {return component_description_;}
+            const std::string& get_component_description() const {return component_description_;}
 
             /**
              * @brief Check whether the data product is public

include/fdp/objects/metadata.hxx

@@ -1,5 +1,5 @@
 /*! **************************************************************************
- * @file fdp/objects/metadata.hxx
+ * @file FairDataPipeline/objects/metadata.hxx
  * @author K. Zarebski (UKAEA)
  * @date 2021-05-05
  * @brief File containing methods for handling of metadata
@@ -29,7 +29,7 @@
    #include <unistd.h>
 #endif
 
-namespace FDP {
+namespace FairDataPipeline {
 /*! **************************************************************************
  * @brief calculates a hash from a given input file via SHA1
  *
@@ -94,6 +94,6 @@ bool file_exists( const std::string &Filename );
  */
 std::string read_token(const ghc::filesystem::path &token_path);
 
-}; // namespace FDP
+}; // namespace FairDataPipeline
 
 #endif

include/fdp/registry/api.hxx

@@ -1,10 +1,10 @@
 /*! **************************************************************************
- * @file fdp/registry/api.hxx
+ * @file FairDataPipeline/registry/api.hxx
  * @author K. Zarebski (UKAEA)
  * @date 2021-05-05
  * @brief File containing classes and methods for connecting to the RestAPI
  *
- * The classes and methods within this file are used to access the FDP
+ * The classes and methods within this file are used to access the FairDataPipeline
  * Data Pipeline RestAPI, they handle sending of requests and retrieval of
  * data as JSON strings
  ****************************************************************************/
@@ -27,7 +27,7 @@
 #include "fdp/utilities/json.hxx"
 #include "fdp/utilities/logging.hxx"
 
-namespace FDP {
+namespace FairDataPipeline {
 /*! **************************************************************************
  * @enum RESTAPI
  * @brief selection of either local or remote pipeline running
@@ -39,6 +39,7 @@ enum class RESTAPI {
   LOCAL   /*!< Run from local registry */
 };
 
+#if 0
 /*! **************************************************************************
  * @brief function for writing to file from a CURL call
  * @author K. Zarebski (UKAEA)
@@ -50,6 +51,7 @@ enum class RESTAPI {
  * @return size_t
  ****************************************************************************/
 size_t write_func_(void *ptr, size_t size, size_t nmemb, std::string *data);
+#endif 
 
 /*! **************************************************************************
  * @class API
@@ -70,8 +72,8 @@ public:
    *
    * @param url_root the root of the query address, e.g. localhost:8000/api
    ***************************************************************************/
-  API(std::string url_root)
-      : url_root_(API::append_with_forward_slash(url_root)) {}
+    static sptr construct( const std::string& url_root );
+
 
   /**
    * @brief sends the given 'packet' of information to the RestAPI
@@ -164,6 +166,9 @@ public:
   static std::string remove_leading_forward_slash(std::string str);
 
 private:
+  API( const std::string& url_root)
+      : url_root_(API::append_with_forward_slash(url_root)) {}
+
   std::string url_root_;
   CURL *setup_json_session_(std::string &addr_path, std::string *response,
                             long &http_code, std::string token = "");
@@ -181,8 +186,8 @@ private:
                      ghc::filesystem::path out_path);
 };
 
-std::string url_encode(std::string url);
+std::string url_encode(const std::string& url);
 
-}; // namespace FDP
+}; // namespace FairDataPipeline
 
 #endif

include/fdp/registry/data_io.hxx

@@ -1,5 +1,5 @@
 /*! **************************************************************************
- * @file fdp/registry/config.hxx
+ * @file FairDataPipeline/registry/config.hxx
  * @author K. Zarebski (UKAEA)
  * @date 2021-05-06
  * @brief File containing classes for interacting with the local file system
@@ -27,7 +27,7 @@
 #include "fdp/utilities/logging.hxx"
 #include "fdp/utilities/semver.hxx"
 
-namespace FDP {
+namespace FairDataPipeline {
 
 /*! ***************************************************************************
  * @brief read the value of a point estimate from a given TOML file
@@ -87,8 +87,10 @@ ghc::filesystem::path create_estimate(T &value,
 
   toml_out_.close();
 
-  APILogger->debug("FileSystem:CreateEstimate: Wrote point estimate to '{0}'",
-                   output_filename_.string());
+
+  auto the_logger = logger::get_logger();
+  the_logger->debug() 
+      <<  "FileSystem:CreateEstimate: Wrote point estimate to '" << output_filename_.string() << "'";
 
   return output_filename_;
 }
@@ -101,6 +103,6 @@ ghc::filesystem::path create_estimate(T &value,
  */
 std::string get_first_key_(const toml::value data_table);
 
-}; // namespace FDP
+}; // namespace FairDataPipeline
 
-#endif
+#endif