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

Install boost (compile or with package manager)
Install jsoncpp
Install/build mongoc library http://mongoc.org/libmongoc/current/installing.html
Install/build mongo-cxx lib https://mongodb.github.io/mongo-cxx-driver/mongocxx-v3/installation/
Download Ortanc sources or install orthanc-devel package

CentOS 7 Build Instructions

General Packages

yum -y install centos-release-scl centos-release-scl-rh epel-release
yum -y install make devtoolset-7 libuuid-devel openssl-devel cyrus-sasl-devel cmake3 zlib-devel

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
scl enable devtoolset-7 "./bootstrap.sh"
# following operations may exit 1 when some of the targets fail
scl enable devtoolset-7 "./b2 cflags=-fPIC" || :
scl enable devtoolset-7 "sudo ./b2 install --prefix=/usr/local" || :

Prerequisite: Mongo C Driver 1.12.x

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

curl -L --output mongo-c-driver-1.12.x.tar.gz https://github.com/mongodb/mongo-c-driver/archive/1.12.x.tar.gz
tar -xzf mongo-c-driver-1.12.x.tar.gz
mkdir -p mongo-c-driver-1.12.x/build
cd mongo-c-driver-1.12.x/build
scl enable devtoolset-7 "cmake3 -DCMAKE_CXX_FLAGS='-fPIC' -DCMAKE_INSTALL_PREFIX=/usr/local -DCMAKE_BUILD_TYPE=Release -DENABLE_AUTOMATIC_INIT_AND_CLEANUP=OFF .."
scl enable devtoolset-7 "make"
scl enable devtoolset-7 "sudo make install"

Prerequisite: MongoDB C++ Driver 3.3.x

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

curl -L --output mongo-cxx-driver-3.3.x.tar.gz https://github.com/mongodb/mongo-cxx-driver/archive/3.3.x.tar.gz
tar -xzf mongo-cxx-driver-3.3.x.tar.gz
mkdir -p mongo-cxx-driver-3.3.x/build
cd mongo-cxx-driver-r3.3.x/build
scl enable devtoolset-7 "cmake3 -DCMAKE_CXX_FLAGS='-fPIC' -DCMAKE_INSTALL_PREFIX=/usr/local -DCMAKE_BUILD_TYPE=Release -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
# so use sudo for make too
scl enable devtoolset-7 "sudo make"
scl enable devtoolset-7 "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-7 "cmake3 -DCMAKE_CXX_FLAGS='-fPIC' -DCMAKE_INSTALL_PREFIX=/usr/local -DCMAKE_BUILD_TYPE=Release .."
scl enable devtoolset-7 "make"
scl enable devtoolset-7 "sudo make install"

Build of this orthanc-mongodb plugin itself

mkdir -p orthanc-mongodb/build
cd orthanc-mongodb/build
scl enable devtoolset-7 "cmake3 -DCMAKE_CXX_FLAGS='-fPIC' -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=/usr/local -DORTHANC_ROOT=/usr/include .."
scl enable devtoolset-7 "make"
scl enable devtoolset-7 "sudo make install"

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:

ConnectionUri must contain the database name due to the bug in the mongocxx driver CXX-1187
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.

espakm / orthanc-mongodb