Merge pull request #674 from EBISPOT/docker_heap_size

Make heap size configurale.

README.md

@@ -34,6 +34,10 @@ However, if you just want to try it out, this should get you going:
 
 You should now be able to access the OLS4 frontend at `http://localhost:8081`.
 
+If you need to set the heap size, you can do so using:
+
+    JAVA_OPTS="-Xms5G -Xmx25G"  docker compose up
+
 If you want to test it with your own ontology, copy the OWL or RDFS ontology file to the `testcases` folder (which is
 mounted in Docker). Then make a new config file for your ontology in `dataload/configs` (you can use `efo.json` as a
 template). For the `ontology_purl` property in the config, use e.g. `file:///opt/dataload/testcases/myontology.owl` if
@@ -174,6 +178,10 @@ or if you want to load all testcases, you can use
 
     ./dev-testing/teststack.sh ./testcases ./output
 
+If you need to set the Java heap size, you can set the environment the JAVA_OPTS variable as follows:
+
+     export JAVA_OPTS="-Xms5G -Xmx10G"
+
 Once Neo4J and Solr is up, to start the backend (REST API) you can run:
 
     ./dev-testing/start-backend.sh

dataload/create_datafiles.sh

@@ -15,8 +15,10 @@ JSON_PATH_LINKED=$OUTDIR/ontologies_linked.json
 
 rm -f $OUTDIR/*
 
+echo JAVA_OPTS=$JAVA_OPTS
+
 echo rdf2json
-java -DentityExpansionLimit=0 -DtotalEntitySizeLimit=0 -Djdk.xml.totalEntitySizeLimit=0 -Djdk.xml.entityExpansionLimit=0 -jar $SCRIPT_PATH/rdf2json/target/rdf2json-1.0-SNAPSHOT.jar --config "$CONFIG_URL" --output "$JSON_PATH" "${@:3}"
+java $JAVA_OPTS -DentityExpansionLimit=0 -DtotalEntitySizeLimit=0 -Djdk.xml.totalEntitySizeLimit=0 -Djdk.xml.entityExpansionLimit=0 -jar $SCRIPT_PATH/rdf2json/target/rdf2json-1.0-SNAPSHOT.jar --config "$CONFIG_URL" --output "$JSON_PATH" "${@:3}"
 
 echo linker
 java -jar $SCRIPT_PATH/linker/target/linker-1.0-SNAPSHOT.jar --input "$JSON_PATH" --output "$JSON_PATH_LINKED"

docker-compose.yml

@@ -1,6 +1,8 @@
 version: '3'
 services:
     ols4-dataload:
+      environment:
+        - JAVA_OPTS=${JAVA_OPTS}
       build: ./dataload
       volumes:
         - ols4-solr-data:/opt/solr/server/solr:rw