Orthanc MongoDB plugin
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Thomas Fromm
Latest commit 5e56b55 May 25, 2018

README.md

MongoDB plugins for Orthanc DICOM Server

See: https://github.com/Doc-Cirrus/orthanc-mongodb

OVERVIEW

The repository contains two plugins to store the data in MongoDB database.

Installation

This chapter describes the process of installation with not too much details and not necessarily contain all how-to to resolve possible problems that might appear.

Prerequisites

CentOS Build Instructions

General Packages

yum -y install centos-release-scl centos-release-scl-rh epel-release
yum -y install gcc gcc-c++ devtoolset-4 cmake boost-devel libuuid-devel openssl-devel cyrus-sasl-devel cmake3

Prerequisite: Orthanc 1.2.0

Its not nessesary to build Orthanc, if you have orthanc-devel packages installed. At the moment there exists no package for Orthanc 1.2.0 in any offical repository for CentOS 6.

yum -y install python curl-devel dcmtk-devel gtest-devel jsoncpp-devel libjpeg-devel libpng-devel sqlite-devel lua-devel >= 5.1.0 mongoose-devel openssl-devel pugixml-devel
curl -L --output Orthanc-1.2.0.tar.gz http://www.orthanc-server.com/downloads/get.php?path=/orthanc/Orthanc-1.2.0.tar.gz
tar -xzf Orthanc-1.2.0.tar.gz
mkdir Orthanc-1.2.0/build
cd Orthanc-1.2.0/build
cmake .. \
	-DCMAKE_BUILD_TYPE=Release \
	-DDCMTK_LIBRARIES=CharLS \
	-DSTANDALONE_BUILD:BOOL=ON \
	-DSTATIC_BUILD:BOOL=ON \
	-DALLOW_DOWNLOADS:BOOL=ON \
	-DUSE_SYSTEM_SQLITE:BOOL=OFF \
	-DUSE_SYSTEM_BOOST:BOOL=OFF \
	-DUSE_SYSTEM_CURL:BOOL=OFF \
	-DSYSTEM_MONGOOSE_USE_CALLBACKS=OFF \
	-DUNIT_TESTS_WITH_HTTP_CONNEXIONS=OFF
make
sudo make install

Prerequisite: Mongo C Driver 1.9.x

https://github.com/mongodb/mongo-c-driver/releases

cd mongo-c-driver-1.9.x
./configure --enable-static --with-pic --disable-automatic-init-and-cleanup
make
sudo make install

Prerequisite: boost 1.60+

curl -L --output boost_1_63_0.tar.gz https://sourceforge.net/projects/boost/files/boost/1.63.0/boost_1_63_0.tar.gz/download
tar -xzf boost_1_63_0.tar.gz
cd boost_1_63_0
./bootstrap.sh
# following operations may exit 1 when some of the targets fail
./b2 cflags=-fPIC -j 2 || :
sudo ./b2 install || :

Prerequisite: MongoDB C++ Driver 3.2.x

https://github.com/mongodb/mongo-cxx-driver/releases

cd mongo-cxx-driver-r3.2.x/build
scl enable devtoolset-4 "export CXXFLAGS=-fPIC && cmake3 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/usr/local -DLIBBSON_DIR=/usr/local -DLIBMONGOC_DIR=/usr/local .."
# for any reason it requires write permissions to /usr/local/include/bsoncxx/v_noabi/bsoncxx/third_party/mnmlstc/share/cmake/core
# use sudo for make too in this case
scl enable devtoolset-4 "sudo make"
scl enable devtoolset-4 "sudo make install"

Prerequisite: JsonCpp

curl -L --output jsoncpp-1.8.0.tar.gz https://github.com/open-source-parsers/jsoncpp/archive/1.8.0.tar.gz
tar -xzf jsoncpp-1.8.0.tar.gz
mkdir -p jsoncpp-1.8.0/build
cd jsoncpp-1.8.0/build
scl enable devtoolset-4 "export CXXFLAGS=-fPIC && cmake3 -DCMAKE_BUILD_TYPE=Release .."
scl enable devtoolset-4 "make"
scl enable devtoolset-4 "sudo make install"

Build of this orthanc-mongodb plugin itself

mkdir -p orthanc-mongodb/build
cd orthanc-mongodb/build
scl enable devtoolset-4 "export PKG_CONFIG_PATH=/usr/local/lib/pkgconfig && cmake3 -DCMAKE_BUILD_TYPE=Release -DORTHANC_ROOT=/usr/include .."
scl enable devtoolset-4 "make"
  • ORTHANC_ROOT - the Orthanc server sources root to include the orthanc/OrthancCPlugin.h
  • BUILD_TESTS - option to build tests, default off
  • BUILD_WITH_GCOV - option to include coverage default off

Plugin configuration setup

Add plugins in the Ortahc json configuration file:

    ...
  "Plugins" : [
    "libOrthancMongoDBIndex.dylib",
    "libOrthancMongoDBStorage.dylib"
  ],
  // MongoDB plugin confihuration section:
  "MongoDB" : {
    "EnableIndex" : true, // false to use default SQLite 
    "EnableStorage" : true, // false to use default SQLite 
    "ConnectionUri" : "mongodb://localhost:27017/orthanc_db",
    "ChunkSize" : 261120
  },
  ...

Also it's possible to configure the plugin with separate config options:

    "Plugins" : [
    "libOrthancMongoDBIndex.dylib",
    "libOrthancMongoDBStorage.dylib"
    ],
    "MongoDB" : {
        "host" : "customhost",
        "port" : 27001,
        "user" : "user",
        "database" : "database",
        "password" : "password",
        "authenticationDatabase" : "admin",
        "ChunkSize" : 261120
    }

NOTE: Setting up the ConnectionUri overrides the host, port, database params. So if the ConnectionUri is set, the other parameters except the ChunkSize will be ignored.

Testing is described with more details in here

Known Issues:

  1. ConnectionUri must contain the database name due to the bug in the mongocxx driver CXX-1187
  2. The Orthanc server should be compiled in Release or RelWithDebInfo mode to turn off assertions. There are asserts like that `./OrthancServer/ServerIndex.cpp: assert(index_.currentStorageSize_ == index_.db_.GetTotalCompressedSize());``` it involves full collection scan to aggregate the total AttachedFiles significantly slows the performance down.