Graphdb SE Documentation Release 8.5
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GraphDB SE Documentation Release 8.5 Ontotext Jun 17, 2019 CONTENTS 1 General 1 1.1 About GraphDB...........................................2 1.2 Architecture & components.....................................2 1.2.1 Architecture.........................................2 1.2.1.1 RDF4J.......................................3 1.2.1.2 The Sail API....................................4 1.2.2 Components.........................................4 1.2.2.1 Engine.......................................4 1.2.2.2 Connectors.....................................5 1.2.2.3 Workbench.....................................5 1.3 GraphDB SE.............................................5 1.3.1 Comparison of GraphDB Free and GraphDB SE......................6 1.4 Connectors..............................................6 1.5 Workbench..............................................6 2 Quick start guide 9 2.1 Run GraphDB as a stand-alone server................................9 2.1.1 Running GraphDB.....................................9 2.1.1.1 Options...................................... 10 2.1.2 Configuring GraphDB................................... 10 2.1.2.1 Paths and network settings............................ 10 2.1.2.2 Java virtual machine settings........................... 10 2.1.3 Stopping the database.................................... 11 2.2 Set up your license.......................................... 11 2.3 Create a repository.......................................... 13 2.4 Load your data............................................ 13 2.4.1 Load data through the GraphDB Workbench........................ 14 2.4.2 Load data through SPARQL or RDF4J API........................ 15 2.4.3 Load data through the GraphDB LoadRDF tool...................... 15 2.5 Explore your data and class relationships.............................. 16 2.5.1 Explore instances...................................... 16 2.5.2 Create your own visual graph................................ 19 2.5.3 Class hierarchy....................................... 20 2.5.4 Domain-Range graph.................................... 22 2.5.5 Class relationships..................................... 24 2.6 Query your data........................................... 27 2.6.1 Query data through the Workbench............................. 27 2.6.2 Query data programmatically................................ 31 2.7 Additional resources......................................... 31 3 Installation 33 3.1 Requirements............................................. 33 3.1.1 Minimum.......................................... 33 3.1.2 Hardware sizing....................................... 33 i 3.1.3 Licensing.......................................... 34 3.2 Running GraphDB.......................................... 34 3.2.1 Run GraphDB as a stand-alone server........................... 34 3.2.1.1 Running GraphDB................................. 34 3.2.1.2 Configuring GraphDB............................... 35 3.2.1.3 Stopping the database............................... 36 3.3 Configuring GraphDB........................................ 36 3.3.1 Directories......................................... 36 3.3.1.1 GraphDB Home.................................. 36 3.3.1.2 Checking the configured directories........................ 37 3.3.2 Configuration........................................ 37 3.3.2.1 Config properties................................. 37 3.3.2.2 Configuring logging................................ 39 3.3.3 Best practices........................................ 39 3.3.3.1 Step by step guide................................. 39 3.4 Distribution package......................................... 39 3.5 Using Maven artifacts........................................ 39 3.5.1 Public Maven repository.................................. 40 3.5.2 Distribution......................................... 40 3.5.3 GraphDB JAR file for embedding the database or plugin development.......... 41 3.5.4 I want to proxy the repository in my nexus......................... 41 4 Administration 43 4.1 Administration tasks......................................... 43 4.2 Administration tools......................................... 43 4.2.1 Workbench......................................... 44 4.2.2 JMX interface........................................ 44 4.2.2.1 Configuring the JMX endpoint.......................... 44 4.3 Setting up licenses.......................................... 44 4.3.1 Setting up licenses through the Workbench........................ 45 4.3.2 Setting up licenses through a file.............................. 46 4.3.2.1 Custom file path property............................. 46 4.3.3 Order of preference..................................... 47 4.3.4 Deprecated methods.................................... 47 4.4 Creating locations.......................................... 47 4.4.1 Active location....................................... 47 4.4.2 Inactive location...................................... 50 4.4.3 Connect to a remote location................................ 50 4.4.4 Configure a data location.................................. 51 4.5 Creating a repository......................................... 51 4.5.1 Create a repository..................................... 52 4.5.1.1 Using the Workbench............................... 52 4.5.1.2 Using the RDF4J console............................. 52 4.5.2 Manage repositories..................................... 53 4.5.2.1 Select a repository................................. 53 4.5.2.2 Make it a default repository............................ 53 4.5.2.3 Edit a repository.................................. 54 4.6 Configuring a repository....................................... 54 4.6.1 Plan a repository configuration............................... 54 4.6.2 Configure a repository through the GraphDB Workbench................. 55 4.6.3 Edit a repository...................................... 55 4.6.4 Configure a repository programmatically.......................... 56 4.6.5 Configuration parameters.................................. 57 4.6.6 Configure GraphDB memory................................ 60 4.6.6.1 Configure Java heap memory........................... 60 4.6.6.2 Single global page cache............................. 60 4.6.6.3 Configure Entity pool memory.......................... 61 4.6.6.4 Sample memory configuration.......................... 61 ii 4.6.7 Reconfigure a repository.................................. 61 4.6.7.1 Using the Workbench............................... 62 4.6.7.2 In the SYSTEM repository.............................. 62 4.6.7.3 Global overrides.................................. 62 4.6.8 Rename a repository.................................... 62 4.6.8.1 Using the workbench............................... 62 4.6.8.2 Editing of the SYSTEM repository......................... 62 4.7 Access rights and security...................................... 63 4.7.1 Managing users’ access................................... 63 4.7.1.1 User roles..................................... 64 4.7.1.2 Login and default credentials........................... 64 4.7.1.3 Free access..................................... 65 4.8 Application settings......................................... 65 4.9 Backing up and restoring a repository................................ 66 4.9.1 Backup a repository..................................... 66 4.9.1.1 Export repository to an RDF file......................... 67 4.9.1.2 Backup GraphDB by copying the binary image.................. 68 4.9.2 Restore a repository..................................... 68 4.10 Query monitoring and termination.................................. 69 4.10.1 Query monitoring and termination using the workbench.................. 69 4.10.2 Query monitoring and termination using the JMX interface................ 70 4.10.2.1 Query monitoring................................. 70 4.10.2.2 Terminating a query................................ 71 4.10.3 Terminating a transaction.................................. 71 4.10.4 Automatically prevent long running queries........................ 72 4.11 Troubleshooting........................................... 72 4.11.1 Database health checks................................... 72 4.11.1.1 Possible values for health checks and their meaning............... 72 4.11.1.2 Default health checks for the different GraphDB editions............ 72 4.11.1.3 Running the health checks............................. 73 4.11.2 System metrics monitoring................................. 73 4.11.2.1 Page cache metrics................................. 74 4.11.2.2 Entity pool metrics................................ 74 4.11.3 Diagnosing and reporting critical errors.......................... 75 4.11.3.1 Report....................................... 75 4.11.3.2 Logs........................................ 77 4.11.4 Storage tool......................................... 78 4.11.4.1 Options...................................... 78 4.11.4.2 Supported commands............................... 78 4.11.4.3 Examples..................................... 78 5 Usage 81 5.1 Loading data............................................. 81 5.1.1 Loading data using the Workbench............................. 81 5.1.1.1 Import settings................................... 82 5.1.1.2 Importing local files................................ 83 5.1.1.3 Importing server files............................... 84 5.1.1.4 Importing remote content............................. 84 5.1.1.5 Importing RDF data from a text snippet...................... 84 5.1.1.6 Import data with