Stackification (#150)

* uimacpp_ros, robosherlock_msgs, rapidjson_ros part of  a stack now;

Author: bbferka

.gitignore

@@ -1,7 +1,7 @@
-cmake/robosherlock_config.cmake
-cmake/robosherlock.cmake
-data
-scripts/.*.modified
-scripts/*.pyc
-src/core/include/rs/types/*.h
-descriptors/typesystem/all_types.xml
+robosherlock/cmake/robosherlock_config.cmake
+robosherlock/cmake/robosherlock.cmake
+robosherlock/data
+robosherlock/scripts/.*.modified
+robosherlock/scripts/*.pyc
+robosherlock/src/core/include/rs/types/*.h
+robosherlock/descriptors/typesystem/all_types.xml

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "rapidjson_ros/include/rapidjson"]
+	path = rapidjson_ros/include/rapidjson
+	url = https://github.com/Tencent/rapidjson.git

.travis.yml

@@ -27,9 +27,8 @@ env:
 before_install:
   - sudo sh -c "echo \"deb http://packages.ros.org/ros/ubuntu $ROS_CI_DESKTOP main\" > /etc/apt/sources.list.d/ros-latest.list"
   - wget http://packages.ros.org/ros.key -O - | sudo apt-key add -
-  - sudo add-apt-repository ppa:robosherlock/ppa -y
   - sudo apt-get update -qq
-  - sudo apt-get install -y python-catkin-pkg python-rosdep python-wstool ros-kinetic-catkin ros-kinetic-libmongocxx-ros libxerces-c-dev libapr1-dev mongodb protobuf-compiler rapidjson lcov --force-yes
+  - sudo apt-get install -y python-catkin-pkg python-rosdep python-wstool ros-kinetic-catkin ros-kinetic-libmongocxx-ros libxerces-c-dev libapr1-dev mongodb protobuf-compiler lcov --force-yes
   - source /opt/ros/$ROS_DISTRO/setup.bash
   - sudo rosdep init
   - rosdep update
@@ -49,9 +48,6 @@ install:
   - ln -s $CI_SOURCE_PATH .
 
 before_script:
-  - cd ~/catkin_ws/src
-  - git clone https://github.com/RoboSherlock/robosherlock_msgs.git
-  - git clone https://github.com/RoboSherlock/uimacpp_ros.git
   - cd ~/catkin_ws
   - rosdep install -y --from-paths src --ignore-src --rosdistro $ROS_DISTRO
   - echo "export APR_HOME=/usr" >> ~/.bashrc
@@ -63,7 +59,7 @@ before_script:
 script:
   - cd ~/catkin_ws
   - source devel/setup.bash
-  - find -L /home/travis/catkin_ws/src/robosherlock  -name include -type d
+  - find -L /home/travis/catkin_ws/src/robosherlock/robosherlock  -name include -type d
   - catkin_make "$( [ -f $CATKIN_OPTIONS ] && cat $CATKIN_OPTIONS )"
   - source devel/setup.bash
   - cd ~/catkin_ws/src/robosherlock

rapidjson_ros/CMakeLists.txt

@@ -0,0 +1,113 @@
+cmake_minimum_required(VERSION 2.8.3)
+project(rapidjson_ros)
+
+## Compile as C++11, supported in ROS Kinetic and newer
+add_compile_options(-std=c++11)
+
+find_package(catkin REQUIRED)
+
+###################################
+## catkin specific configuration ##
+###################################
+## The catkin_package macro generates cmake config files for your package
+## Declare things to be passed to dependent projects
+## INCLUDE_DIRS: uncomment this if your package contains header files
+## LIBRARIES: libraries you create in this project that dependent projects also need
+## CATKIN_DEPENDS: catkin_packages dependent projects also need
+## DEPENDS: system dependencies of this project that dependent projects also need
+
+add_definitions(-DRAPIDJSON_HAS_STDSTRING)
+catkin_package(
+  INCLUDE_DIRS include/rapidjson/include
+#  LIBRARIES rapidjson_ros
+#  CATKIN_DEPENDS other_catkin_pkg
+#  DEPENDS system_lib
+)
+
+###########
+## Build ##
+###########
+
+## Specify additional locations of header files
+## Your package locations should be listed before other locations
+include_directories(
+ include/rapidjson/include
+)
+
+## Declare a C++ library
+# add_library(${PROJECT_NAME}
+#   src/${PROJECT_NAME}/rapidjson_ros.cpp
+# )
+
+## Add cmake target dependencies of the library
+## as an example, code may need to be generated before libraries
+## either from message generation or dynamic reconfigure
+# add_dependencies(${PROJECT_NAME} ${${PROJECT_NAME}_EXPORTED_TARGETS} ${catkin_EXPORTED_TARGETS})
+
+## Declare a C++ executable
+## With catkin_make all packages are built within a single CMake context
+## The recommended prefix ensures that target names across packages don't collide
+# add_executable(${PROJECT_NAME}_node src/rapidjson_ros_node.cpp)
+
+## Rename C++ executable without prefix
+## The above recommended prefix causes long target names, the following renames the
+## target back to the shorter version for ease of user use
+## e.g. "rosrun someones_pkg node" instead of "rosrun someones_pkg someones_pkg_node"
+# set_target_properties(${PROJECT_NAME}_node PROPERTIES OUTPUT_NAME node PREFIX "")
+
+## Add cmake target dependencies of the executable
+## same as for the library above
+# add_dependencies(${PROJECT_NAME}_node ${${PROJECT_NAME}_EXPORTED_TARGETS} ${catkin_EXPORTED_TARGETS})
+
+## Specify libraries to link a library or executable target against
+# target_link_libraries(${PROJECT_NAME}_node
+#   ${catkin_LIBRARIES}
+# )
+
+#############
+## Install ##
+#############
+
+# all install targets should use catkin DESTINATION variables
+# See http://ros.org/doc/api/catkin/html/adv_user_guide/variables.html
+
+## Mark executable scripts (Python etc.) for installation
+## in contrast to setup.py, you can choose the destination
+# install(PROGRAMS
+#   scripts/my_python_script
+#   DESTINATION ${CATKIN_PACKAGE_BIN_DESTINATION}
+# )
+
+## Mark executables and/or libraries for installation
+# install(TARGETS ${PROJECT_NAME} ${PROJECT_NAME}_node
+#   ARCHIVE DESTINATION ${CATKIN_PACKAGE_LIB_DESTINATION}
+#   LIBRARY DESTINATION ${CATKIN_PACKAGE_LIB_DESTINATION}
+#   RUNTIME DESTINATION ${CATKIN_PACKAGE_BIN_DESTINATION}
+# )
+
+## Mark cpp header files for installation
+# install(DIRECTORY include/${PROJECT_NAME}/
+#   DESTINATION ${CATKIN_PACKAGE_INCLUDE_DESTINATION}
+#   FILES_MATCHING PATTERN "*.h"
+#   PATTERN ".svn" EXCLUDE
+# )
+
+## Mark other files for installation (e.g. launch and bag files, etc.)
+# install(FILES
+#   # myfile1
+#   # myfile2
+#   DESTINATION ${CATKIN_PACKAGE_SHARE_DESTINATION}
+# )
+
+#############
+## Testing ##
+#############
+
+## Add gtest based cpp test target and link libraries
+# catkin_add_gtest(${PROJECT_NAME}-test test/test_rapidjson_ros.cpp)
+# if(TARGET ${PROJECT_NAME}-test)
+#   target_link_libraries(${PROJECT_NAME}-test ${PROJECT_NAME})
+# endif()
+
+## Add folders to be run by python nosetests
+# catkin_add_nosetests(test)

rapidjson_ros/include/rapidjson

@@ -0,0 +1,18 @@
+<?xml version="1.0"?>
+<package format="2">
+  <name>rapidjson_ros</name>
+  <version>0.0.1</version>
+  <description>The rapidjson_ros package; Wrapping rapidjson lib for Ubuntu 16.04/ROS Xenial</description>
+
+  <maintainer email="[email protected]">Ferenc Balint-Benczedi</maintainer>
+
+  <license>TODO</license>
+
+  <buildtool_depend>catkin</buildtool_depend>
+  <build_depend>roscpp</build_depend>
+
+  <export>
+    <!-- Other tools can request additional information be placed here -->
+
+  </export>
+</package>

rapidjson_ros/package.xml

@@ -55,7 +55,7 @@ find_package(catkin REQUIRED
  visualization_msgs cv_bridge image_transport
  image_geometry message_filters resource_retriever
  robosherlock_msgs std_srvs libmongocxx_ros
- uimacpp_ros)
+ uimacpp_ros rapidjson_ros)
 
 
 find_package(Eigen3 QUIET)
@@ -104,10 +104,10 @@ if(PROTOBUF_FOUND AND PROTOBUF_PROTOC_EXECUTABLE)
   set(RS_WEB_LIB rs_web)
 endif()
 
-find_package(RapidJSON REQUIRED)
-if(${RapidJSON_FOUND})
-    add_definitions(-DWITH_JSON -DRAPIDJSON_HAS_STDSTRING)
-endif()
+#find_package(RapidJSON REQUIRED)
+#if(${RapidJSON_FOUND})
+    add_definitions(-DRAPIDJSON_HAS_STDSTRING)
+#endif()
 
 find_package(json_prolog QUIET)
 option(WITH_JSON_PROLOG "build using json prolog" False)
@@ -134,7 +134,6 @@ endif()
 ## CMake variables                                                            ##
 ################################################################################
 
-add_definitions(-DDB_SCRIPTS_DIR="${PROJECT_SOURCE_DIR}/scripts/mongodb/")
 add_definitions(${PCL_DEFINITIONS})
 
 ################################################################################
@@ -157,7 +156,7 @@ set(RS_LIBS
 catkin_package(
   INCLUDE_DIRS ${RS_INCLUDE_DIRS_LIST} ${SWIPL_INCLUDE_DIRS} ${LIBAPR_INCLUDE_DIRS} ${Caffe_INCLUDE_DIRS} ${EIGEN3_INCLUDE_DIRS} ${OpenCV_INCLUDE_DIRS} ${PCL_INCLUDE_DIRS}
   LIBRARIES ${RS_LIBS}
-  CATKIN_DEPENDS pcl_ros cv_bridge libmongocxx_ros robosherlock_msgs uimacpp_ros
+  CATKIN_DEPENDS pcl_ros cv_bridge libmongocxx_ros robosherlock_msgs uimacpp_ros rapidjson_ros
   DEPENDS Boost OpenCV APR PCL ICUUC
   CFG_EXTRAS robosherlock.cmake ${PROJECT_NAME}_config.cmake
 )
@@ -178,19 +177,9 @@ include_directories(
   ${CMAKE_CURRENT_BINARY_DIR}
 )
 
-################################################################################
-## Update analysis engines, typesystem and include all relevant files         ##
-################################################################################
-
-## Update xml list of annotators inside analysis engines
-# update_analysis_engines()
-
 ## generate classes from the typesystem xml files
 generate_type_system()
 
-#find all relevant files
-find_additional_files(3rdparty)
-
 ################################################################################
 ## Sub Projects                                                               ##
 ################################################################################

CMakeLists.txt robosherlock/CMakeLists.txt

@@ -37,7 +37,8 @@
   <depend>uimacpp_ros                </depend>
   <depend>robosherlock_msgs          </depend>
   <depend>libmongocxx_ros            </depend>
-
+  
+  <depend>rapidjson_ros		     </depend>
   <depend>yaml-cpp                   </depend>
 
   <export>

cmake/FindAPR.cmake robosherlock/cmake/FindAPR.cmake

@@ -66,8 +66,6 @@ class Storage
   std::unordered_map<std::string,mongo::OID> camInfoOIDs;
   bool first;
 
-  void setupDBScripts();
-
   bool readArrayFS(uima::FeatureStructure fs, ::mongo::BSONObjBuilder &builderCAS, const ::mongo::OID &casOID, const std::string &sofaId, const std::string &dbCollection);
   bool readFS(uima::FeatureStructure fs, ::mongo::BSONObjBuilder &builderCAS, const ::mongo::OID &casOID, const std::string &sofaId, const std::string &dbCollection);
 

cmake/FindICUUC.cmake robosherlock/cmake/FindICUUC.cmake

@@ -61,12 +61,6 @@ Storage::Storage(const std::string &dbHost, const std::string &dbName, const boo
 
   db.connect(dbHost);
 
-#ifdef DB_SCRIPTS_DIR
-  if(setupScripts)
-  {
-    setupDBScripts();
-  }
-#endif
   if(clear)
   {
     std::list<std::string> names = db.getCollectionNames(dbName);
@@ -99,57 +93,6 @@ Storage &Storage::operator=(const Storage &other)
   return *this;
 }
 
-void Storage::setupDBScripts()
-{
-  std::vector<std::string> scripts;
-
-  DIR *dp;
-  struct dirent *dirp;
-
-  if((dp  = opendir(DB_SCRIPTS_DIR)) ==  nullptr)
-  {
-    outDebug("MongoDB script directory does not exist.");
-    return;
-  }
-
-  while((dirp = readdir(dp)) != nullptr)
-  {
-    if(dirp->d_type != DT_REG)
-    {
-      continue;
-    }
-
-    std::string filename = dirp->d_name;
-    if(filename.rfind(SCRIPT_EXT) != std::string::npos)
-    {
-      scripts.push_back(filename);
-    }
-  }
-  closedir(dp);
-
-  db.remove(dbScripts, mongo::Query());
-  for(size_t i = 0; i < scripts.size(); ++i)
-  {
-    std::string scriptFile = DB_SCRIPTS_DIR + scripts[i];
-    std::ifstream file(scriptFile);
-
-    if(!file.is_open())
-    {
-      outError("could not open: " << scriptFile);
-      continue;
-    }
-
-    std::string script((std::istreambuf_iterator<char>(file)), std::istreambuf_iterator<char>());
-    file.close();
-
-    outDebug("Evaluation JavaScript: " << scriptFile);
-    if(!db.eval(dbName, "function(){" + script + "}"))
-    {
-      outError("Error evaluating JavaScript: " << scriptFile);
-    }
-  }
-}
-
 bool Storage::readArrayFS(uima::FeatureStructure fs, mongo::BSONObjBuilder &builderCAS, const mongo::OID &casOID, const std::string &sofaId, const std::string &dbCollection)
 {
   uima::ArrayFS array;

cmake/FindMongoClientLibrary.cmake robosherlock/cmake/FindMongoClientLibrary.cmake

@@ -0,0 +1,38 @@
+cmake_minimum_required(VERSION 2.8.3)
+project(robosherlock_msgs)
+
+find_package(catkin REQUIRED COMPONENTS 
+  geometry_msgs 
+  shape_msgs
+  sensor_msgs
+  visualization_msgs
+  message_generation)
+
+add_message_files(
+  FILES
+  RSObjectDescriptions.msg
+  RSActiveAnnotatorList.msg
+)
+
+add_service_files(FILES
+  SetRSContext.srv
+  RSQueryService.srv
+  RSVisControl.srv
+  UpdateObjects.srv
+  ExecutePipeline.srv
+)
+
+generate_messages(
+  DEPENDENCIES
+  geometry_msgs
+  visualization_msgs
+  shape_msgs
+  sensor_msgs)
+
+catkin_package(
+  CATKIN_DEPENDS 
+    geometry_msgs 
+    shape_msgs 
+    sensor_msgs
+    message_runtime
+)

cmake/project_config.cmake.in robosherlock/cmake/project_config.cmake.in

@@ -0,0 +1,2 @@
+#list of active annotators (used for sending it to web frontend)
+string[] annotators

cmake/robosherlock.cmake.in robosherlock/cmake/robosherlock.cmake.in

@@ -0,0 +1 @@
+string[] obj_descriptions