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INSTRUCTIONS.md

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About this document

This is a quick overview on how to setup a Java server for the MolecularModelManager (Minerva).

Building the server

Prerequisites to build the code

  • Java (JDK 1.8 or later) as compiler
  • Maven (3.0.x) Build-Tool

Building the Minerva Server

 ./build-server.sh

Running the Minerva Server

Prerequisites

  • go-lego.owl (GO-SVN/trunk/ontology/extensionx/go-lego.owl) and catalog.xml to local copies
  • folder with model files (GO-SVN/trunk/experimental/lego/server/owl-models/)

Start the MolecularModelManager server from the command line

  • Build the code, will result in a jar
  • Check memory settings in start-m3-server.sh, change as needed.
  • The start script is in the bin folder: start-m3-server.sh

The Minerva server expects parameters for:

  -g path-to/go-lego.owl
  -f path-to/owl-models
  [--port 6800]
  [-c path-to/catalog.xml]

For more details and options, please check the source code of owltools.gaf.lego.server.StartUpTool

Full example using a catalog.xml, IRIs and assumes a full GO-SVN trunk checkout:

start-m3-server.sh -c go-trunk/ontology/extensions/catalog-v001.xml \
-g http://purl.obolibrary.org/obo/go/extensions/go-lego \
-f go-trunk/experimental/lego/server/owl-models \
--port 6800

Start Server via Eclipse:

  • Requires all data (go and models)
  • Build in eclipse, start as main with appropriate parameters.

Automatically create a catalog file pointing to local copies of the imported ontologies

If you have ROBOT installed, you can easily create a local mirror of an OWL imports chain, so that large imported ontologies don't need to be repeatedly downloaded while you are developing locally:

robot mirror --input my-ontology.owl --directory my-cache --output my-catalog.xml

(instead of --input, you can also use -I and directly provide the ontology IRI rather than a filename)

Then provide the my-catalog.xml file to Minerva when starting the server, using the -c option.

Running Tests

	mvn -Dtest=FindGoCodesTest.testFindShortEvidence,LegoToGeneAnnotationTranslatorTest.testZfinExample test

Failing Tests

mvn -e -DfailIfNoTests=false -Dtest=FindGoCodesTest test

https://raw.githubusercontent.com/evidenceontology/evidenceontology/master/gaf-eco-mapping.txt

Maven CLI

Quick Test via curl

This assumes you are in the minerva/ directory, which is the parent of minerva-server/.

curl localhost:6800/`cat minerva-server/src/test/resources/server-test/long-get.txt`

Sonarqube

Run sonarqube server locally using docker and ensure it is up and running by visiting http://localhost:9000

docker run -d --rm --name sonarqube -p 9000:9000 sonarqube:7.9.6-community

For static analysis:

mvn clean package sonar:sonar -DskipTests

For static analysis and code coverage:

mvn clean package sonar:sonar

Stopping sonarqube docker container. This would automatically remove the container since the --rm option was used above.

docker stop sonarqube

Obtaining owl-models and go-lego.owl

See Monarch Ontology and use the instructions there to generate a catalog-v001.xml.

  • ftp://ftp.geneontology.org/pub/go//experimental/lego/server/owl-models
  • ftp://ftp.geneontology.org/pub/go//ontology/extensions/go-lego.owl

Useful source files for learning

  • /minerva-server/src/main/java/org/geneontology/minerva/server/handler/M3BatchHandler.java

Using the Blazegraph model store

Create a new Blazegraph journal from a directory of existing model files

minerva-cli.sh --import-owl-models -j blazegraph.jnl -f models

Dump model files from a Blazegraph journal that is not in use

minerva-cli.sh --dump-owl-models -j blazegraph.jnl -f models

Start the Minerva Server with configuration for Blazegraph journal and model dump folder

java "-Xmx$MINERVA_MEMORY" -jar minerva-server.jar -c catalog-v001.xml -g http://purl.obolibrary.org/obo/go/extensions/go-lego.owl -f blazegraph.jnl --export-folder exported-models --port 9999 --use-request-logging --slme-elk --skip-class-id-validation --set-important-relation-parent http://purl.obolibrary.org/obo/LEGOREL_0000000

Note the options -f blazegraph.jnl for specifying the journal file and --export-folder exported-models for specifying where to write OWL models in response to a export-all operation request.

Request an OWL dump of all models from a running Minerva Server

curl 'http://localhost:3400/api/minerva_local/m3Batch?token=&intention=query&requests=%5B%7B%22entity%22%3A%22meta%22%2C%22operation%22%3A%22export-all%22%2C%22arguments%22%3A%7B%7D%7D%5D'

This will output to the folder configured in the startup arguments.

Run a SPARQL Update against the triples in the database

This should be handled with care since direct changes to triples will bypass any validations that typically occur when data are edited via the standard Minerva server API.

SPARQL Update is useful for various bulk maintenance operations that may periodically be necessary, e.g. updating all uses of an obsolete property to the current preferred IRI. Before running the update, the server should be stopped, since the Blazegraph journal can only be used from one Java process at a time. Then simply run the command like this:

java -jar minerva-cli.jar --sparql-update -j blazegraph.jnl -f update.rq

where update.rq is a file containing the SPARQL update. For example:

PREFIX directly_activates: <http://purl.obolibrary.org/obo/RO_0002406>
PREFIX directly_positively_regulates: <http://purl.obolibrary.org/obo/RO_0002629>
DELETE { 
    GRAPH ?g { ?s directly_activates: ?o . }
}
INSERT { 
    GRAPH ?g { ?s directly_positively_regulates: ?o . }
}
WHERE {
    GRAPH ?g { ?s directly_activates: ?o . }
}

Migrate obsolete class assertions via term_replaced_by

This command will update all class assertions which reference an obsolete term, whenever there is a term_replaced_by annotation found in the ontology. The database is directly modified via a SPARQL Update. The instance node will have its modified date updated, and an rdfs:comment will be added to the node, describing the change.

java -jar minerva-cli.jar --replace-obsolete -j blazegraph.jnl --ontology file:go-lego-reacto.owl

The model ontology node will also receive the updated date and the change comment.

Migrate class and object property assertions via TSV

This command will migrate class assertions and object property assertions from one term to another according to provide TSV mappings. The database is directly modified via a SPARQL Update. As for obsoletions, the relevant axiom and model nodes will receive updated dates and a comment describing the change. The input files should have a header row, and at least two columns, where the replaced term is the first column and the replacement term is the second column.

java -jar minerva-cli.jar --replace-terms -j blazegraph.jnl --replacement-classes class-replacements.tsv --replacement-properties property-replacements.tsv

SPARQL endpoint service

Minerva provides a read-only SPARQL query service at the /sparql path. Using GET, a URL-encoded query can be submitted as a value for the query parameter. Alternatively, POST can be used to submit form data with a query parameter, or to submit a SPARQL query directly, using the application/sparql-query MIME type.

SPARQL endpoint configuration

The only configurable aspect of the SPARQL endpoint is the query timeout. This can be set with a command-line option to the Minerva server at startup: --sparql-endpoint-timeout 10. The value is the time in seconds; the default is 10.