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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

It is possible to install all dependencies manually (below you will find instructions) or you could try to use AUTO_INSTALL_DEPENDENCIES flag for cmake. In this way some dependencies will be installed automaticaly for orthanc-mongodb project. For more details refer to docs folder -> autoconfig.md file.

CentOS 7 Build Instructions

General Packages

yum -y install centos-release-scl centos-release-scl-rh epel-release
yum -y install make devtoolset-8 libuuid-devel openssl-devel cyrus-sasl-devel cmake3 zlib-devel

Prerequisite: Mongo C Driver 1.15.x

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

curl -L --output mongo-c-driver-1.15.x.tar.gz https://github.com/mongodb/mongo-c-driver/archive/1.15.x.tar.gz
tar -xzf mongo-c-driver-1.15.x.tar.gz
mkdir -p mongo-c-driver-1.15.x/build
cd mongo-c-driver-1.15.x/build
scl enable devtoolset-8 "cmake3 -DCMAKE_C_FLAGS='-fPIC' -DCMAKE_INSTALL_PREFIX=/usr/local -DCMAKE_BUILD_TYPE=Release -DENABLE_AUTOMATIC_INIT_AND_CLEANUP=OFF .."
scl enable devtoolset-8 "make"
scl enable devtoolset-8 "sudo make install"

Prerequisite: MongoDB C++ Driver 3.4.x

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

curl -L --output mongo-cxx-driver-3.4.x.tar.gz https://github.com/mongodb/mongo-cxx-driver/archive/3.4.x.tar.gz
tar -xzf mongo-cxx-driver-3.4.x.tar.gz
mkdir -p mongo-cxx-driver-3.4.x/build
cd mongo-cxx-driver-r3.4.x/build
scl enable devtoolset-8 "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-8 "sudo make"
scl enable devtoolset-8 "sudo make install"

Prerequisite: JsonCpp (1.8.0 exact)

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-8 "cmake3 -DCMAKE_CXX_FLAGS='-fPIC' -DCMAKE_INSTALL_PREFIX=/usr/local -DCMAKE_BUILD_TYPE=Release .."
scl enable devtoolset-8 "make"
scl enable devtoolset-8 "sudo make install"

Build of this orthanc-mongodb plugin itself

mkdir -p orthanc-mongodb/build
cd orthanc-mongodb/build
scl enable devtoolset-8 "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-8 "make"
scl enable devtoolset-8 "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

Debian 9 Build Instructions (static build)

General Packages

apt -y install build-essential unzip cmake make libsasl2-dev uuid-dev libssl-dev zlib1g-dev git curl

Prerequisite: Mongo C Driver 1.15.x

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

curl -L --output mongo-c-driver-1.15.x.tar.gz https://github.com/mongodb/mongo-c-driver/archive/1.15.x.tar.gz
tar -xzf mongo-c-driver-1.15.x.tar.gz
mkdir -p mongo-c-driver-1.15.x/build
cd mongo-c-driver-1.15.x/build
cmake -DCMAKE_C_FLAGS='-fPIC' -DCMAKE_INSTALL_PREFIX=/usr/local -DCMAKE_BUILD_TYPE=Release -DENABLE_STATIC=ON -DENABLE_AUTOMATIC_INIT_AND_CLEANUP=OFF -DENABLE_ICU=OFF ../mongo-c-driver-1.15.x
make
sudo make install

Prerequisite: MongoDB C++ Driver 3.4.x

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

curl -L --output mongo-cxx-driver-3.4.x.tar.gz https://github.com/mongodb/mongo-cxx-driver/archive/3.4.x.tar.gz
tar -xzf mongo-cxx-driver-3.4.x.tar.gz
mkdir -p mongo-cxx-driver-3.4.x/build
cd mongo-cxx-driver-r3.4.x/build
cmake -DCMAKE_CXX_FLAGS='-fPIC' -DCMAKE_INSTALL_PREFIX=/usr/local -DCMAKE_BUILD_TYPE=Release -DBUILD_SHARED_LIBS=OFF -DLIBBSON_DIR=/usr/local -DLIBMONGOC_DIR=/usr/local ..
sudo make
sudo make install

Prerequisite: JsonCpp (1.8.0 exact)

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
cmake -DCMAKE_CXX_FLAGS='-fPIC' -DCMAKE_INSTALL_PREFIX=/usr/local -DBUILD_STATIC_LIBS=ON -DBUILD_SHARED_LIBS=OFF -DCMAKE_BUILD_TYPE=Release ..
make
sudo make install

Build of this orthanc-mongodb plugin itself

mkdir -p orthanc-mongodb/build
cd orthanc-mongodb/build

cmake -DCMAKE_CXX_FLAGS='-fPIC' -DCMAKE_INSTALL_PREFIX=/usr -DLINK_STATIC_LIBS=TRUE -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=/usr/local ..
make

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.