upgrade neo4j to 2025.03.0

README.md

@@ -241,12 +241,11 @@ First, make sure the configuration files (that determine which ontologies to loa
 
 Run Neo4j `import` command:
 
-    ./neo4j-admin import \
+    ./neo4j-admin database import full \
     --ignore-empty-strings=true \
     --legacy-style-quoting=false \
     --array-delimiter="|" \
     --multiline-fields=true \
-    --database=neo4j \
     --read-buffer-size=134217728 \
     $(<LOCAL_DIR>/make_csv_import_cmd.sh)
 

dataload/Dockerfile

@@ -3,7 +3,7 @@
 # This image, once built, should allow any arbitrary config to be loaded and output neo4j/solr datafiles
 
 
-FROM maven:3.8-jdk-11
+FROM maven:3.8-eclipse-temurin-21
 
 RUN addgroup --system --gid 1000 ols && adduser --system --uid 1000 --ingroup ols ols
 
@@ -13,13 +13,13 @@ RUN addgroup --system --gid 1000 ols && adduser --system --uid 1000 --ingroup ol
 # and Solr servers are the standard images specified in docker-compose.yml
 #
 RUN mkdir /opt/neo4j && \
-    curl https://dist.neo4j.org/neo4j-community-4.4.9-unix.tar.gz | tar -xz --strip-components=1 -C /opt/neo4j
+    curl https://dist.neo4j.org/neo4j-community-2025.03.0-unix.tar.gz | tar -xz --strip-components=1 -C /opt/neo4j
 
 RUN mkdir /opt/solr && \
     curl https://archive.apache.org/dist/solr/solr/9.0.0/solr-9.0.0.tgz | tar -xz --strip-components=1 -C /opt/solr
 
 RUN echo "dbms.security.auth_enabled=false" >> /opt/neo4j/conf/neo4j.conf
-RUN echo "dbms.jvm.additional=-Dorg.neo4j.kernel.impl.index.schema.GenericNativeIndexPopulator.blockBasedPopulation=true" >> /opt/neo4j/conf/neo4j.conf
+RUN echo "server.jvm.additional=-Dorg.neo4j.kernel.impl.index.schema.GenericNativeIndexPopulator.blockBasedPopulation=true" >> /opt/neo4j/conf/neo4j.conf
 
 # Copy all the code for dataload into /opt/dataload and build the JARs
 #

dataload/README.md

@@ -25,14 +25,13 @@ You can now convert this huge JSON file to a CSV file ready for Neo4j, using jso
 
 ## Step 3: CSV to Neo4j
 
-Now (after 5-10 mins) you should have a directory full of CSV files. These files are formatted especially for Neo4j. You can load them using `neo4j-admin import`, but you'll need to provide the filename of every single CSV file on the command line, which is boring, so included in this repo is a script called `make_csv_import_cmd.sh` that generates the command line for you.
+Now (after 5-10 mins) you should have a directory full of CSV files. These files are formatted especially for Neo4j. You can load them using `neo4j-admin database import full`, but you'll need to provide the filename of every single CSV file on the command line, which is boring, so included in this repo is a script called `make_csv_import_cmd.sh` that generates the command line for you.
 
-    neo4j-admin import \
+    neo4j-admin database import full \
 	    --ignore-empty-strings=true \
 	    --legacy-style-quoting=false \
 	    --multiline-fields=true \
 	    --array-delimiter="|" \
-	    --database=neo4j \
 	    $(./make_csv_import_cmd.sh)
 
 Now you should have a Neo4j database ready to start!

dataload/create_neo4j_indexes.sh

@@ -5,7 +5,7 @@ if [ $# == 0 ]; then
     exit 1
 fi
 
-$1/bin/neo4j start
+$1/bin/neo4j start --verbose
 sleep 20
 
 echo Creating neo4j indexes...

dataload/load_into_neo4j.sh

@@ -8,14 +8,13 @@ fi
 rm -rf $1/data/databases/neo4j
 rm -rf $1/data/transactions/neo4j
 
-$1/bin/neo4j-admin import \
+$1/bin/neo4j-admin database import full \
         --ignore-empty-strings=true \
         --legacy-style-quoting=false \
         --multiline-fields=true \
         --read-buffer-size=16777216 \
         --array-delimiter="|" \
-        --database=neo4j \
-        --processors=16 \
+        --threads=32 \
         $(./make_csv_import_cmd.sh $2)
 
 

dev-testing/load_test_into_neo4j.sh

@@ -5,12 +5,11 @@ if [ $# == 0 ]; then
     exit 1
 fi
 
-$NEO4J_HOME/bin/neo4j-admin import \
+$NEO4J_HOME/bin/neo4j-admin database import full \
         --ignore-empty-strings=true \
         --legacy-style-quoting=false \
         --multiline-fields=true \
         --array-delimiter="|" \
-        --database=neo4j \
-        --processors=2 \
+        --threads=4 \
         --read-buffer-size=134217728 \
         $($OLS4_HOME/dev-testing/make_csv_import_cmd.sh $1)

docker-compose.yml

@@ -26,7 +26,7 @@ services:
         ols4-dataload:
           condition: service_completed_successfully
     ols4-neo4j:
-      image: neo4j:4.4.9-community
+      image: neo4j:2025.03.0-community
       ports:
         - 7474:7474
         - 7687:7687

frontend/src/pages/Downloads.tsx

@@ -98,7 +98,7 @@ const data: any[] = [
   },
   {
     description:
-      "The neo4j database generated from ontologies_linked.json by the OLS json2neo tool, after creating db indexes (Requires Neo4j community 4.4.9)",
+      "The neo4j database generated from ontologies_linked.json by the OLS json2neo tool, after creating db indexes (Requires Neo4j community 2025.03.0)",
     downloadLabel: "neo4j.tgz",
     downloadLink:
       "https://ftp.ebi.ac.uk/pub/databases/spot/ols/latest/neo4j.tgz",

k8chart-dev/ols4/templates/ols4-neo4j-deployment.yaml

@@ -29,7 +29,7 @@ spec:
             claimName: {{ .Release.Name }}-neo4j-pvc
       containers:
         - name: neo4j
-          image: ghcr.io/ebispot/ols4-neo4j:4.4.9-community
+          image: neo4j:2025.03.0-community
           volumeMounts:
             - mountPath: "/data"
               name: {{ .Release.Name }}-neo4j-storage

k8chart/ols4/templates/ols4-neo4j-deployment.yaml

@@ -30,7 +30,7 @@ spec:
             claimName: {{ .Release.Name }}-neo4j-pvc
       containers:
         - name: neo4j
-          image: ghcr.io/ebispot/ols4-neo4j:4.4.9-community
+          image: neo4j:2025.03.0-community
           volumeMounts:
             - mountPath: "/data"
               name: {{ .Release.Name }}-neo4j-storage