Setup

MaSyMoS can be used as a standalone or as a plugin for the Neo4J WebServer.

If you want to run MaSyMoS from it's source locally on your computer, please follow the steps described in Getting Started to setup an development environment.

Build Jar files

Build Jar files with Docker

The easiest way of creating the MaSyMoS-jar-files is to use our MaSyMos-Docker-Project.

1. clone the repository
2. run the jar-builder/maven-build-masymos-jars.sh bash file
3. find all jar files in jar-builder/masymos-builds

Find further information on the docker repository and how to tweak it on the documentation page Docker Documentation.

Build Jar files locally

To create a local standalone you need masymos-core and masymos-cli.

To create it locally, clone the repositories, get the dependencies via Maven and build the jar. You need to take care of the java version, you are using. Find more information on the Getting Started.

Find the instructions on how to use the command line interface in the CLI.

Setup Server

Setup Server with Docker

The easiest way of using the MaSyMoS Morre Neo4J Plugin is to use our MaSyMos-Docker-Project.

1. clone the repository
2. copy your local database into a docker volume with $ ./server-integration/copy_own_data_into_docker_volume.sh /path/to/neo4j/databases/my_database
3. run the server with server-integration/run-neo4j-server.sh

Find detailed usage information on the documentation page Docker Documentation.

Find the instructions on how to use masymos morre in the MORRE.

Setup Server locally

If you want to use MaSyMoS as a search server for models you will have to set up the server version. To do so, start by downloading Neo4J WebServer. Please check the Neo4J-vesion in pom.xml (<groupId>org.neo4j</groupId>) before downloading the server. You might want to make sure to compile MaSyMoS with the same version as the downloaded server. Follow the Neo4J setup instructions.

To create a Server-MaSyMoS you need masymos-core and masymos-morre. Then follow these steps:

1. Use Maven to compile masymos-core (mvn install) without dependencies and do the same with masymos-morre (mvn package). You must use the same Java version used for Neo4J.

2. Copy the JAR for masymos-more into $Neo4jRoot/plugins.

3. Open $Neo4JRoot/conf/neo4j.conf and set:

   Arguments

   Key	Value	Description
   dbms.active_database	…	points the path of your database
   dbms.allow_upgrade (v3.3+) dbms.allow_format_migration (<v3.3)	true	if you are using a server with a higher version then the one the DB was created with
   dbms.security.auth_enabled	false	or configure the authentication
   dbms.unmanaged_extension_classes	de.unirostock.morre.server.plugin=/morre	to allow MaSyMoS plugin to be loaded

   • you might also want to uncomment dbms.connector.http.address=0.0.0.0:7474 to accept non-localhost connections

4. You will also need some additional libraries for the server, easiest way is to create masymos-core and masymos-morre without dependencies and let Maven pack all necessary libraries in a directory next to the generated JAR.

   • ℹ packing all the libraries inside the morre-package (fat jar) is not a good idea, even having the libs inside the core package will not work, because neo4j may has other versions running.

   • To get all the libraries, please follow these steps

     1. look up the target/lib-directory after the build in masymos-core and masymos-morre. (There is maven goal copy-dependencies for this in the pom, running automatically.)

        • copy all the libraries into $Neo4jRoot/lib/ext (you may need to create it).

     2. Avoid unpredictable behaviour based on java-library complications

        1. Delete all libraries from lib/ext, that are in lib i.e. with bash in lib/ext: for f in ./../*; do rm -v "./$(basename $f)"; done.

        2. Delete the following files from lib/ext:

           • *.pom
           • neo4j-*.jar
           • server-*.jar

   • The result in $Neo4JRoot/lib/ext may look like this (list is maybe outdated)

   click here to show the list

   activation-1.1.jar
   animal-sniffer-annotations-1.14.jar
   axis-1.4.jar
   axis-jaxrpc-1.4.jar
   axis-saaj-1.4.jar
   axis-wsdl4j-1.5.1.jar
   BFLog-1.3.7.jar
   BFUtils-0.5.7.jar
   biojava-ontology-4.0.0.jar
   BiVeS-CellML-1.8.0.jar
   BiVeS-Core-1.9.1.jar
   caffeine-2.6.1.jar
   collections-generic-4.01.jar
   commons-cli-1.3.jar
   commons-codec-1.11.jar
   commons-csv-1.0.jar
   commons-discovery-0.2.jar
   commons-lang3-3.9.jar
   commons-logging-1.2.jar
   commons-rdf-api-0.5.0.jar
   dom4j-1.6.1.jar
   error_prone_annotations-2.0.18.jar
   fluent-hc-4.5.5.jar
   gson-2.8.6.jar
   guava-22.0.jar
   hamcrest-core-1.3.jar
   hppcrt-0.7.5.jar
   httpclient-4.5.10.jar
   httpclient-cache-4.5.2.jar
   httpclient-osgi-4.5.5.jar
   httpcore-4.4.12.jar
   httpcore-nio-4.4.9.jar
   httpcore-osgi-4.4.9.jar
   httpmime-4.5.5.jar
   j2objc-annotations-1.1.jar
   jackson-annotations-2.9.10.jar
   jackson-core-2.9.10.jar
   jackson-databind-2.9.10.jar
   javax.inject-1.jar
   javax.ws.rs-api-2.0.jar
   jaxen-1.1.1.jar
   jcl-over-slf4j-1.7.22.jar
   jCOMODI-1.0.2.jar
   jdom2-2.0.5.jar
   jdom-1.0.jar
   jdom-1.1.3.jar
   jdom-contrib-1.1.3.jar
   jena-arq-3.0.0.jar
   jena-base-3.0.0.jar
   jena-core-3.0.0.jar
   jena-iri-3.0.0.jar
   jena-shaded-guava-3.0.0.jar
   jena-tdb-3.0.0.jar
   jfact-5.0.3.jar
   jigsaw-2.2.6.jar
   jlibsedml-2.2.3.jar
   jmathml-2.2.1.jar
   jms-1.1.jar
   jmxri-1.2.1.jar
   jmxtools-1.2.1.jar
   joda-time-2.9.7.jar
   jsbml-1.5.jar
   jsbml-arrays-1.5.jar
   jsbml-comp-1.5.jar
   jsbml-core-1.5.jar
   jsbml-distrib-1.5.jar
   jsbml-dyn-1.5.jar
   jsbml-fbc-1.5.jar
   jsbml-groups-1.5.jar
   jsbml-layout-1.5.jar
   jsbml-multi-1.5.jar
   jsbml-qual-1.5.jar
   jsbml-render-1.5.jar
   jsbml-req-1.5.jar
   jsbml-spatial-1.5.jar
   jsbml-tidy-1.5.jar
   jsonld-java-0.12.0.jar
   json-simple-1.1.1.jar
   jsoup-1.12.1.jar
   jsr305-3.0.2.jar
   jtidy-r938.jar
   jul-to-slf4j-1.7.25.jar
   junit-4.12.jar
   libthrift-0.9.2.jar
   log4j-1.2.15.jar
   log4j-1.2-api-2.3.jar
   log4j-api-2.8.2.jar
   log4j-core-2.8.2.jar
   log4j-slf4j-impl-2.1.jar
   mail-1.4.jar
   masymos-core-1.0.2.jar
   metainf-services-1.8.jar
   miriam-lib-1.1.6.jar
   netty-all-4.1.32.Final.jar
   owlapi-api-5.1.12.jar
   owlapi-apibinding-5.1.12.jar
   owlapi-compatibility-5.1.12.jar
   owlapi-distribution-5.1.12.jar
   owlapi-impl-5.1.12.jar
   owlapi-oboformat-5.1.12.jar
   owlapi-parsers-5.1.12.jar
   owlapi-rio-5.1.12.jar
   owlapi-tools-5.1.12.jar
   paxtools-core-5.1.0.jar
   rdf4j-model-2.3.2.jar
   rdf4j-rio-api-2.3.2.jar
   rdf4j-rio-binary-2.3.2.jar
   rdf4j-rio-datatypes-2.3.2.jar
   rdf4j-rio-jsonld-2.3.2.jar
   rdf4j-rio-languages-2.3.2.jar
   rdf4j-rio-n3-2.3.2.jar
   rdf4j-rio-nquads-2.3.2.jar
   rdf4j-rio-ntriples-2.3.2.jar
   rdf4j-rio-rdfjson-2.3.2.jar
   rdf4j-rio-rdfxml-2.3.2.jar
   rdf4j-rio-trig-2.3.2.jar
   rdf4j-rio-trix-2.3.2.jar
   rdf4j-rio-turtle-2.3.2.jar
   rdf4j-util-2.3.2.jar
   RoaringBitmap-0.6.32.jar
   slf4j-api-1.7.13.jar
   slf4j-log4j12-1.7.12.jar
   stax2-api-3.1.4.jar
   staxmate-2.3.0.jar
   trove4j-3.0.3.jar
   woodstox-core-5.0.1.jar
   xalan-2.7.0.jar
   xercesImpl-2.8.0.jar
   xml-apis-1.3.03.jar
   xmlpull-1.1.3.1.jar
   xmlutils-0.6.13.jar
   xom-1.3.2.jar
   xpp3_min-1.1.4c.jar
   xstream-1.4.9.jar
   xz-1.6.jar
   zstd-proxy-3.5.13.jar
   

5. Finally, we need to add $Neo4JRoot/lib/ext to the servers classpath.

   • Linux

     • Open $Neo4JRoot/bin/neo4j and add :${NEO4J_LIB}/ext/* to CLASSPATH variable

     build_classpath() {
         CLASSPATH="${NEO4J_PLUGINS}:${NEO4J_CONF}:${NEO4J_LIB}/*:${NEO4J_LIB}/ext/*:${NEO4J_PLUGINS}/*"
         # …
     

   • Windows

     • Open $Neo4JRoot/bin/Neo4j-Management/Get-Java.ps1 and add ;$($Neo4jServer.Home)/lib/ext/* to the Java command line:

     # Build the Java command line
     $ClassPath="$($Neo4jServer.Home)/lib/*;$($Neo4jServer.Home)/plugins/*;$($Neo4jServer.Home)/lib/ext/*"
     

• Well done, you can now try to start MaSyMoS with ./bin/neo4j console!
• Read about how to work with the server on MORRE.