Loaders

This wiki page contains the description of all loaders in the intermine-neo4j sub project.

Neo4jLoader

Loads a mine into Neo4j using parameters in neo4jloader.properties.

./gradlew loader

Neo4jCompleter

Completes the references and collections for nodes that have only had attributes stored as a result of being loaded as references and collections by Neo4jLoader. This is very handy to fill out the graph without adding new nodes. neo4jloader.properties is used, especially loaded.classes to indicate which types of nodes you'd like completed.

./gradlew completer

Neo4jNodeLoader

Load a single node into Neo4j identified by its class and InterMine id. Other parameters are read from neo4jloader.properties.

./gradlew nodeLoader -PArgs=Gene,4295368

Neo4jEdgeLoader

Load edges into Neo4j given by source class, edge reference or collection, and target as referenced in the edge class. This converts IM objects which store relations, like Location, into Neo4j edges with properties. Since some target names, e.g. chromosomeLocation, refer to simpler-named classes, like Location, there are two parameters in neo4jloader.properties, intermine.edge.classes and neo4j.edge.types, which map IM classes to Neo4j edge types so that, for example, chromosomeLocation edges are given the type "location" in Neo4j.

./gradlew edgeLoader Gene chromosomeLocation locatedOn

InterMineModelXMLDumper

Simple utility dump an InterMine model in XML form to standard output.

./gradlew imModelXMLDumper -PArgs=http://www.synbiomine.org/synbiomine/service

Neo4jModelParser

Parses a Neo4j-annotated model XML file, which contains instructions like neo4j-include="true" in the class, attribute, reference and collection definitions to indicate that those items should be ignored in Neo4j loading. The main method takes an XML file as a parameter and spits out the data model with "X" denoting ignored items. Methods like isIgnored(ReferenceDescriptor) provide an easy way to see if a given reference (for example) should be ignored during loading.

gradlew modelParser <XML File> Gene.homologues