Merge pull request #104 from SynBioDex/develop

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SynBioDex · Dec 24, 2016 · 91bfb4d · 91bfb4d
2 parents 848ea2c + 614bd00
commit 91bfb4d
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diff --git a/.gitmodules b/.gitmodules
@@ -1,3 +1,3 @@
-[submodule "restbed"]
-	path = restbed
-	url = https://github.com/Corvusoft/restbed.git
+[submodule "jsconcpp"]
+    path = jsoncpp
+    url = https://github.com/open-source-parsers/jsoncpp
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,4 +1,5 @@
-set(CMAKE_OSX_DEPLOYMENT_TARGET "10.11")
+set(CMAKE_OSX_DEPLOYMENT_TARGET "10.9")
+set(CMAKE_OSX_SYSROOT /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk)
 
 CMAKE_MINIMUM_REQUIRED( VERSION 2.8 )
 PROJECT( SBOL )
@@ -37,13 +38,17 @@ endif()
 OPTION( SBOL_BUILD_PYTHON2  "Generate Python version 2 wrapper using SWIG" FALSE )
 OPTION( SBOL_BUILD_PYTHON3  "Generate Python version 3 wrapper using SWIG" FALSE )
 OPTION( SBOL_BUILD_MANUAL  "Generate SBOL documentation using Doxygen" FALSE )
-#OPTION( SBOL_BUILD_REST  "Generate RESTful API" FALSE )
+OPTION( SBOL_BUILD_JSON  "Build JsonCpp library (for Linux users primarily)" FALSE)
 
-# -fPIC from boost Python 
+# -fPIC from boost Python
 set (CMAKE_POSITION_INDEPENDENT_CODE TRUE)
 
-# build libSBOLc
-#ADD_SUBDIRECTORY( schema )
+# build examples
+IF( SBOL_BUILD_JSON )
+    ADD_SUBDIRECTORY( jsoncpp )
+ENDIF()
+
+# build libSBOL
 ADD_SUBDIRECTORY( source )
 
 # build examples
@@ -61,10 +66,6 @@ IF( SBOL_BUILD_MANUAL )
     ADD_SUBDIRECTORY( manual )
 ENDIF()
 
-IF( SBOL_BUILD_REST )
-    ADD_SUBDIRECTORY( restbed )
-ENDIF()
-
 IF( SBOL_BUILD_PYTHON2 OR SBOL_BUILD_PYTHON3 )
     ADD_SUBDIRECTORY( wrapper )
 ENDIF()

diff --git a/jsoncpp b/jsoncpp
diff --git a/manual/Doxyfile b/manual/Doxyfile
@@ -1905,7 +1905,7 @@ MAN_LINKS              = NO
 # captures the structure of the code including all documentation.
 # The default value is: NO.
 
-GENERATE_XML           = NO
+GENERATE_XML           = YES
 
 # The XML_OUTPUT tag is used to specify where the XML pages will be put. If a
 # relative path is entered the value of OUTPUT_DIRECTORY will be put in front of

diff --git a/restbed b/restbed
diff --git a/source/CMakeLists.txt b/source/CMakeLists.txt
@@ -4,6 +4,8 @@ ADD_SUBDIRECTORY( raptor )
 
 # gather headers
 include_directories( ${RAPTOR_INCLUDE_DIR})
+include_directories( ${JsonCpp_INCLUDE_DIR})
+include_directories( ${CURL_INCLUDE_DIR})
 
 # gather source files
 FILE(GLOB SBOL_HEADER_FILES
@@ -62,14 +64,16 @@ ENDIF()
 
 # link against raptor
 #ADD_DEFINITIONS( -DRAPTOR_STATIC -DLIBXML_STATIC)
-ADD_DEFINITIONS(-DLIBXML_STATIC -DRAPTOR_STATIC -DLIBXSLT_STATIC -DCURL_STATIC)
+ADD_DEFINITIONS(-DLIBXML_STATIC -DRAPTOR_STATIC -DLIBXSLT_STATIC -DCURL_STATIC -DCURL_STATICLIB)
 
 get_directory_property( DirDefs COMPILE_DEFINITIONS )
 #message( "COMPILE_DEFINITIONS = ${DirDefs}" )
 
-
+message("${INCLUDE_DIRECTORIES}")
 
 if (${CMAKE_SYSTEM_NAME} MATCHES "Windows")
+    include_directories( ${JSONCPP_INCLUDE_DIR}/..)
+    include_directories( ${CURL_INCLUDE_DIR}/..)
     if(SBOL_BUILD_32)
         message("Configuring for x86")
         set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /EHsc")
@@ -85,10 +89,12 @@ if (${CMAKE_SYSTEM_NAME} MATCHES "Windows")
                 ${SBOL_SOURCE_FILES})
         endif()
         target_link_libraries( sbol32
-            ${RAPTOR_LIBRARY}
-            ${LIBXML2_LIBRARIES}
+            ${raptor2}
+            ${xml2}
             ${zlib}
             ${iconv}
+            ${jsoncpp}
+            ${libcurl}
             Ws2_32.lib )
         install(TARGETS sbol32 DESTINATION lib)   # Installs to C:\Program Files (x86)\SBOL\lib
         install(DIRECTORY ${HEADER_OUTPUT_PATH} DESTINATION ${CMAKE_INSTALL_PREFIX}/include)
@@ -109,10 +115,12 @@ if (${CMAKE_SYSTEM_NAME} MATCHES "Windows")
                 ${SBOL_SOURCE_FILES})
         endif()
         target_link_libraries( sbol64
-            ${RAPTOR_LIBRARY}
-            ${LIBXML2_LIBRARIES}
+            ${raptor2}
+            ${xml2}
             ${zlib}
             ${iconv}
+            ${jsoncpp}
+            ${libcurl}
             Ws2_32.lib )
         install(TARGETS sbol64 DESTINATION lib)   # Installs to C:\Program Files (x86)\SBOL\lib
         install(DIRECTORY ${HEADER_OUTPUT_PATH} DESTINATION ${CMAKE_INSTALL_PREFIX}/include)
@@ -139,7 +147,8 @@ else ()  # If Mac OSX or Linux
         target_link_libraries( sbol32
             ${RAPTOR_LIBRARY}
             ${CURL_LIBRARY}
-            ${LIBXSLT_LIBRARIES})
+            ${LIBXSLT_LIBRARIES}
+            ${JsonCpp_LIBRARY})
         install(TARGETS sbol32 DESTINATION lib)  # Installs to /usr/local/lib
         install(DIRECTORY ${HEADER_OUTPUT_PATH} DESTINATION ${CMAKE_INSTALL_PREFIX}/include)
         set_target_properties(sbol32 PROPERTIES OUTPUT_NAME "sbol")
@@ -166,7 +175,8 @@ else ()  # If Mac OSX or Linux
                 target_link_libraries( _raptor
                     ${RAPTOR_LIBRARY}
                     ${CURL_LIBRARY}
-                    ${LIBXSLT_LIBRARIES})
+                    ${LIBXSLT_LIBRARIES}
+                    ${JsonCpp_LIBRARY})
                 #add_library( _raptor STATIC IMPORTED )
                 #set_property(TARGET _raptor PROPERTY IMPORTED_LOCATION ${RAPTOR_LIBRARY})
 
@@ -189,7 +199,8 @@ else ()  # If Mac OSX or Linux
         target_link_libraries( sbol64
             ${RAPTOR_LIBRARY}
             ${CURL_LIBRARY}
-            ${LIBXSLT_LIBRARIES})
+            ${LIBXSLT_LIBRARIES}
+            ${JsonCpp_LIBRARY})
         install(TARGETS sbol64 DESTINATION lib)  # Installs to /usr/local/lib
         install(DIRECTORY ${HEADER_OUTPUT_PATH} DESTINATION ${CMAKE_INSTALL_PREFIX}/include)
         set_target_properties(sbol64 PROPERTIES OUTPUT_NAME "sbol")

diff --git a/source/config.cpp b/source/config.cpp
@@ -3,13 +3,84 @@
 #include <string>
 #include <stdlib.h>     /* srand, rand */
 #include <time.h>
+#include <vector>
+#include <algorithm>
 
 using namespace sbol;
 using namespace std;
 
 extern Config& config = * new sbol::Config();  ///<  Global configuration object that governs library behavior, especially with regards to URI generation
 //Config& config = * new sbol::Config();  ///<  Global configuration object that governs library behavior, especially with regards to URI generation
 
+std::map<std::string, std::string> sbol::Config::options {
+    {"validate", "True"},
+    {"validatorURL", "http://www.async.ece.utah.edu/sbol-validator/endpoint.php"},
+    {"output", "SBOL2"},
+    {"diff", "False"},
+    {"noncompliantUrisAllowed", "False"},
+    {"incompleteDocumentsAllowed", "False"},
+    {"bestPracticesCheck", "False"},
+    {"failOnFirstError", "False"},
+    {"displayFullErrorStackTrace", "False"},
+    {"topLevelToConvert", ""},
+    {"uriPrefix", ""},
+    {"version", ""},
+    {"wantFileBack", "False"}
+};
+std::map<std::string, std::vector<std::string>> sbol::Config::valid_options {
+    {"validate", { "True", "False" }},
+    {"output", { "SBOL2", "FASTA", "GenBank" }},
+    {"diff", { "True", "False" }},
+    {"noncompliantUrisAllowed", { "True", "False" }},
+    {"incompleteDocumentsAllowed", { "True", "False" }},
+    {"bestPracticesCheck", { "True", "False" }},
+    {"failOnFirstError", { "True", "False" }},
+    {"displayFullErrorStackTrace", { "True", "False" }},
+    {"topLevelToConvert", {"", "True", "False" }},
+    {"wantFileBack", {"True", "False"}}
+};
+
+void sbol::Config::setOption(std::string option, std::string value)
+{
+    if (options.find(option) != options.end())
+    {
+        // Check if this option has valid arguments to validate against
+        if (valid_options.find(option) != valid_options.end())
+        {
+            // Set the option if a valid argument is provided
+            if (std::find(valid_options[option].begin(), valid_options[option].end(), value) != valid_options[option].end())
+                options[option] = value;
+            else
+            {
+                // Format error message
+                std::string msg;
+                for (auto const& arg : valid_options[option]) { msg += arg + ", "; }
+                msg[msg.size()-2] = '.';  // Replace last , with a .
+                throw SBOLError(SBOL_ERROR_INVALID_ARGUMENT, value + " not a valid value for this option. Valid options are " + msg);
+
+            }
+        }
+        else
+            // Any argument is valid, eg uriPrefix
+            options[option] = value;
+    }
+    else
+    {
+        throw SBOLError(SBOL_ERROR_INVALID_ARGUMENT, option + " not a valid configuration option for libSBOL");
+    }
+};
+
+std::string sbol::Config::getOption(std::string option)
+{
+    if (options.find(option) != options.end())
+    {
+        return options[option];
+    }
+    else
+    {
+        throw SBOLError(SBOL_ERROR_INVALID_ARGUMENT, option + " not a valid configuration option for libSBOL");
+    }
+};
 
 // @TODO move sbol_type TYPEDEF declaration to this file and use sbol_type instead of string for 2nd argument
 std::string sbol::constructCompliantURI(std::string sbol_type, std::string display_id, std::string version)

diff --git a/source/config.h b/source/config.h
@@ -3,13 +3,17 @@
 
 #include "sbolerror.h"
 #include <string>
+#include <map>
+#include <vector>
 
 namespace sbol
 {
     /// A class which contains global configuration variables for the libSBOL environment. Intended to be used like a static class, configuration variables are accessed through the `config' object.
     class Config
     {
     private:
+        static std::map<std::string, std::string> options;
+        static std::map<std::string, std::vector<std::string>> valid_options;
         std::string home; ///< The authoritative namespace for the Document. Setting the home namespace is like     signing a piece of paper.
         int SBOLCompliant; ///< Flag indicating whether to autoconstruct URI's consistent with SBOL's versioning scheme
         int SBOLCompliantTypes; ///< Flag indicating whether an object's type is included in SBOL-compliant URIs
@@ -33,6 +37,8 @@ namespace sbol
         int exceptionsEnabled();
         void setFileFormat(std::string file_format);
         std::string getFileFormat();
+        static void setOption(std::string option, std::string value);
+        static std::string getOption(std::string option);
     };
 
     void setHomespace(std::string ns); ///< Set the default namespace for autocreation of URIs when a new SBOL object is created