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| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Mon, 30 Mar 2020 20:37:49 +0200 |
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| 24 | 1 .. _postgresql: |
| 2 | |
| 3 | |
| 4 PostgreSQL plugins | |
| 5 ================== | |
| 6 | |
| 27 | 7 .. contents:: |
| 8 | |
| 9 The Orthanc project provides two **official** plugins to replace the | |
| 10 default storage area (on the filesystem) and the default SQLite index | |
| 11 by a PostgreSQL database. | |
| 12 | |
| 13 For general information, check out the `official homepage of the | |
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14 plugins <https://www.orthanc-server.com/static.php?page=postgresql>`__. |
| 27 | 15 |
| 16 | |
| 17 | |
| 18 Compilation | |
| 19 ----------- | |
| 20 | |
| 128 | 21 Static linking |
| 22 ^^^^^^^^^^^^^^ | |
| 23 | |
| 27 | 24 .. highlight:: text |
| 25 | |
| 154 | 26 The procedure to compile these plugins is similar to that for the |
| 27 | 27 :ref:`core of Orthanc <compiling>`. The following commands should work |
| 154 | 28 for most UNIX-like distribution (including GNU/Linux):: |
| 27 | 29 |
| 154 | 30 $ mkdir BuildPostgreSQL |
| 31 $ cd BuildPostgreSQL | |
| 32 $ cmake ../PostgreSQL -DSTATIC_BUILD=ON -DCMAKE_BUILD_TYPE=Release | |
| 27 | 33 $ make |
| 34 | |
| 35 The compilation will produce 2 shared libraries, each containing one plugin for Orthanc: | |
| 36 | |
| 37 * ``OrthancPostgreSQLIndex`` replaces the default SQLite index of Orthanc by PostgreSQL. | |
| 38 * ``OrthancPostgreSQLStorage`` makes Orthanc store the DICOM files it receives into PostgreSQL. | |
| 39 | |
| 128 | 40 |
| 41 Microsoft Windows and Apple OS X | |
| 42 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
| 43 | |
| 28 | 44 Pre-compiled binaries for Microsoft Windows `are also available |
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45 <https://www.orthanc-server.com/browse.php?path=/plugin-postgresql>`__. |
| 30 | 46 A package for `Apple's Mac OS X |
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47 <https://www.osimis.io/en/download.html>`__ |
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48 is available courtesy of `Osimis <https://www.osimis.io/>`__. |
| 27 | 49 |
| 50 | |
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51 .. _postgresql-ubuntu1604: |
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52 |
| 128 | 53 Dynamic linking on Ubuntu 16.04 |
| 54 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
| 55 | |
| 56 .. highlight:: text | |
| 57 | |
| 58 If static linking is not desired, here are build instructions for | |
| 59 Ubuntu 16.04 (provided build dependencies for the :ref:`core of | |
| 60 Orthanc <compiling>` have already been installed):: | |
| 61 | |
| 62 $ sudo apt-get install libpq-dev postgresql-server-dev-all | |
| 154 | 63 $ mkdir BuildPostgreSQL |
| 64 $ cd BuildPostgreSQL | |
| 65 $ cmake ../PostgreSQL -DCMAKE_BUILD_TYPE=Release \ | |
| 66 -DALLOW_DOWNLOADS=ON \ | |
| 67 -DUSE_SYSTEM_GOOGLE_TEST=OFF \ | |
| 68 -DUSE_SYSTEM_ORTHANC_SDK=OFF | |
| 128 | 69 $ make |
| 70 | |
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71 |
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72 .. _postgresql-cmake: |
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73 |
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74 Dynamic linking on other GNU/Linux distributions |
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75 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ |
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76 |
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77 .. highlight:: text |
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78 |
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79 The build instructions should always be very similar to those for |
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80 :ref:`Ubuntu 16.04 <postgresql-ubuntu1604>`. One difficulty that could |
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81 however arise is that it is possible that the CMake environment that |
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82 is shipped with the GNU/Linux distribution cannot locate a recent |
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83 version of the development headers for PostgreSQL. This leads to an |
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84 error while invoking CMake that looks like:: |
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85 |
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86 -- Could NOT find PostgreSQL (missing: PostgreSQL_TYPE_INCLUDE_DIR) |
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87 |
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88 In such a situation, please add your version of PostgreSQL to the |
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89 macro ``PostgreSQL_ADDITIONAL_VERSIONS`` that is defined at the end of |
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90 the `Resources/CMake/PostgreSQLConfiguration.cmake file |
| 361 | 91 <https://hg.orthanc-server.com/orthanc-databases/file/tip/Resources/CMake/PostgreSQLConfiguration.cmake>`__ |
| 92 in the sources of the project. | |
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93 |
| 128 | 94 |
| 27 | 95 Usage |
| 96 ----- | |
| 97 | |
| 98 .. highlight:: json | |
| 99 | |
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100 You of course first have to :ref:`install Orthanc <binaries>`, with a |
| 154 | 101 version above 0.9.5. You then have to **create a database** dedicated |
| 28 | 102 to Orthanc on some PostgreSQL server. Please refer to the `PostgreSQL |
| 103 documentation | |
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104 <https://www.postgresql.org/docs/current/tutorial-createdb.html>`__. |
| 27 | 105 |
| 106 Once Orthanc is installed and the database is created, you must add a | |
| 107 section in the :ref:`configuration file <configuration>` that | |
| 108 specifies the address of the **PostgreSQL server together with your | |
| 109 credentials**. You also have to tell Orthanc in which path it can find | |
| 110 the plugins: This is done by properly modifying the ``Plugins`` | |
| 111 option. You could for instance adapt the following configuration | |
| 112 file:: | |
| 113 | |
| 114 { | |
| 115 "Name" : "MyOrthanc", | |
| 116 "PostgreSQL" : { | |
| 117 "EnableIndex" : true, | |
| 118 "EnableStorage" : true, | |
| 119 "Host" : "localhost", | |
| 120 "Port" : 5432, | |
| 121 "Database" : "orthanc", | |
| 122 "Username" : "orthanc", | |
| 181 | 123 "Password" : "orthanc", |
| 124 "EnableSsl" : false // New in version 3.0 | |
| 27 | 125 }, |
| 126 "Plugins" : [ | |
| 154 | 127 "/home/user/orthanc-databases/BuildPostgreSQL/libOrthancPostgreSQLIndex.so", |
| 128 "/home/user/orthanc-databases/BuildPostgreSQL/libOrthancPostgreSQLStorage.so" | |
| 27 | 129 ] |
| 130 } | |
| 131 | |
| 154 | 132 **Important:** The ``EnableIndex`` and ``EnableStorage`` options must |
| 133 be explicitly set to ``true``, otherwise Orthanc will continue to use | |
| 134 its default SQLite back-end and the filesystem storage area. | |
| 27 | 135 |
| 181 | 136 **Remark 1:** When using the ``Storage`` PostgreSQL plugin, the DICOM |
| 154 | 137 files are stored as large objects in the database. This might |
| 138 actually consume more space than the DICOM file itself. We have | |
| 139 observed overhead up to 40%. However, it seems this overhead is | |
| 140 temporary and comes from Write-Ahead Logging. Check this `discussion | |
| 141 <https://groups.google.com/d/msg/orthanc-users/pPzHOpb--iw/QkKZ808gIgAJ>`__ | |
| 142 on the Orthanc Users group for more info). | |
| 118 | 143 |
| 181 | 144 **Remark 2:** A typical usage of the PostgreSQL plugin is to enable |
| 145 only the ``Index``, and to use the default filesystem storage for | |
| 146 DICOM files (on a NAS with proper disaster recovery strategies). This | |
| 147 setup provides best performance for large-scale databases. | |
| 148 | |
| 149 **Remark 3:** Setting the ``EnableSsl`` to ``true`` forces the use of | |
| 150 `SSL connections | |
| 151 <https://www.postgresql.org/docs/current/libpq-ssl.html>`__ between | |
| 152 Orthanc and the PostgreSQL server. It is a synonym for | |
| 153 ``sslmode=require`` in connections URI (see below). Setting | |
| 154 ``EnableSsl`` to ``false`` corresponds to ``sslmode=disable`` | |
| 155 (i.e. SSL is not used, even if it is both available in Orthanc and | |
| 156 PostgreSQL). To choose other values for the SSL mode (i.e. ``allow`` | |
| 157 and ``prefer``), please use connection URIs. | |
| 118 | 158 |
| 159 | |
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160 |
| 27 | 161 .. highlight:: text |
| 162 | |
| 163 Orthanc must of course be **restarted** after the modification of its | |
| 164 configuration file. The log will contain an output similar to:: | |
| 165 | |
| 166 $ ./Orthanc Configuration.json | |
| 167 W0212 16:30:34.576972 11285 main.cpp:632] Orthanc version: 0.8.6 | |
| 168 W0212 16:30:34.577386 11285 OrthancInitialization.cpp:80] Using the configuration from: Configuration.json | |
| 169 [...] | |
| 154 | 170 W0212 16:30:34.598053 11285 main.cpp:379] Registering a plugin from: /home/jodogne/Subversion/orthanc-databases/BuildPostgreSQL/libOrthancPostgreSQLIndex.so |
| 27 | 171 W0212 16:30:34.598470 11285 PluginsManager.cpp:258] Registering plugin 'postgresql-index' (version 1.0) |
| 172 W0212 16:30:34.598491 11285 PluginsManager.cpp:148] Using PostgreSQL index | |
| 154 | 173 W0212 16:30:34.608289 11285 main.cpp:379] Registering a plugin from: /home/jodogne/Subversion/orthanc-databases/BuildPostgreSQL/libOrthancPostgreSQLStorage.so |
| 27 | 174 W0212 16:30:34.608916 11285 PluginsManager.cpp:258] Registering plugin 'postgresql-storage' (version 1.0) |
| 175 W0212 16:30:34.608947 11285 PluginsManager.cpp:148] Using PostgreSQL storage area | |
| 176 [...] | |
| 177 W0212 16:30:34.674648 11285 main.cpp:530] Orthanc has started | |
| 178 | |
| 179 | |
| 180 .. highlight:: json | |
| 181 | |
| 182 Instead of specifying explicit authentication parameters, you can also | |
| 183 use the `PostgreSQL connection URIs syntax | |
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184 <https://www.postgresql.org/docs/current/libpq-connect.html#LIBPQ-CONNSTRING>`__. For |
| 27 | 185 instance:: |
| 186 | |
| 187 { | |
| 188 "Name" : "MyOrthanc", | |
| 189 "PostgreSQL" : { | |
| 190 "EnableIndex" : true, | |
| 191 "EnableStorage" : true, | |
| 181 | 192 "ConnectionUri" : "postgresql://username:password@localhost:5432/database?sslmode=prefer" |
| 27 | 193 }, |
| 194 "Plugins" : [ | |
| 154 | 195 "/home/user/orthanc-databases/BuildPostgreSQL/libOrthancPostgreSQLIndex.so", |
| 196 "/home/user/orthanc-databases/BuildPostgreSQL/libOrthancPostgreSQLStorage.so" | |
| 27 | 197 ] |
| 198 } | |
| 199 | |
| 200 | |
| 201 **Remark:** The Debian Med project maintains `another useful set of | |
| 202 instructions | |
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203 <https://salsa.debian.org/med-team/orthanc-postgresql/-/blob/master/debian/README.Debian>`__. |
| 27 | 204 |
| 205 | |
| 206 Advanced options | |
| 207 ---------------- | |
| 208 | |
| 209 Several advanced options are available as well to fine-tune the | |
| 210 configuration of the PostgreSQL plugins. They are documented below. | |
| 211 | |
| 212 | |
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213 .. _postgresql-lock: |
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214 |
| 27 | 215 Locking |
| 216 ^^^^^^^ | |
| 217 | |
| 218 .. highlight:: json | |
| 219 | |
| 220 By default, the plugins lock the database (using `PostgreSQL advisory | |
| 221 locks | |
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222 <https://www.postgresql.org/docs/current/functions-admin.html#FUNCTIONS-ADVISORY-LOCKS>`__) |
| 27 | 223 to prevent other instances of Orthanc from using the same PostgreSQL |
| 224 database. If you want several instances of Orthanc to share the same | |
| 225 database, set the ``Lock`` option to ``false`` in the configuration | |
| 226 file:: | |
| 227 | |
| 228 { | |
| 229 "Name" : "MyOrthanc", | |
| 230 "PostgreSQL" : { | |
| 231 "EnableIndex" : true, | |
| 232 "EnableStorage" : true, | |
| 233 "Lock" : false, | |
| 234 "ConnectionUri" : "postgresql://username:password@localhost:5432/database" | |
| 235 }, | |
| 236 "Plugins" : [ | |
| 154 | 237 "/home/user/orthanc-databases/BuildPostgreSQL/libOrthancPostgreSQLIndex.so", |
| 238 "/home/user/orthanc-databases/BuildPostgreSQL/libOrthancPostgreSQLStorage.so" | |
| 27 | 239 ] |
| 240 } | |
| 241 | |
| 242 Obviously, one must be very cautious when sharing the same database | |
| 243 between instances of Orthanc. In particular, all these instances | |
| 244 should share the same configuration. | |
| 245 | |
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246 Furthermore, the core of Orthanc does not currently support the replay |
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247 of database transactions, which is necessary to deal with conflicts |
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248 between several instances of Orthanc that would simultaneously write |
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249 to the database. |
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250 |
| 336 | 251 As a consequence, as of Orthanc 1.6.0, when connecting multiple |
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252 Orthanc to a single database by setting ``Lock`` to ``false``, there |
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253 should only be one instance of Orthanc acting as a writer and all the |
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254 other instances of Orthanc acting as readers only. Be careful to set |
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255 the option ``SaveJobs`` to ``false`` in the configuration file of all |
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256 the instances of Orthanc acting as readers. |
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257 |
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258 A refactoring is needed to improve the core of Orthanc in that |
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259 respect, for which we are looking for funding/donation from the |
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260 industry. Some issues reported in our bug tracker call for this |
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261 refactoring: `issue 83 |
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262 <https://bitbucket.org/sjodogne/orthanc/issues/83/>`__, `issue 121 |
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263 <https://bitbucket.org/sjodogne/orthanc/issues/121/>`__, `issue 151 |
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264 <https://bitbucket.org/sjodogne/orthanc/issues/151/>`__. |
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265 |
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266 |
| 27 | 267 |
| 268 Keep-alive | |
| 269 ^^^^^^^^^^ | |
| 270 | |
| 271 .. highlight:: text | |
| 272 | |
| 273 After some period of inactivity (users have reported 10 hours), you | |
| 274 might `experience an error | |
| 275 <https://bitbucket.org/sjodogne/orthanc/issues/15/postgresql-exceptions-after-time>`__ | |
| 276 such as:: | |
| 277 | |
| 278 E0220 03:20:51.562601 PluginsManager.cpp:163] Exception in database back-end: Error in PostgreSQL: server closed the connection unexpectedly. | |
| 279 This probably means the server terminated abnormally before or while processing the request. | |
| 280 E0220 06:51:03.924868 PluginsManager.cpp:163] Exception in database back-end: Error in PostgreSQL: no connection to the server | |
| 281 | |
| 282 This is due to a timeout in the PostgreSQL server. Please make sure to | |
| 283 `enable keep-alive | |
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284 <https://dba.stackexchange.com/questions/97534/is-there-a-timeout-option-for-remote-access-to-postgresql-database>`__ |
| 27 | 285 in the configuration of your PostgreSQL server |