upgrade neo4j to 4.0.6

hetnet/neo4j/docker/Dockerfile

@@ -1,21 +1,23 @@
-FROM neo4j:3.5.12
+FROM neo4j:4.0.6
 MAINTAINER Daniel Himmelstein, <[email protected]>
 
-COPY scripts /
-RUN chmod +x /get_data_run_neo4j.sh
-
-COPY files/neo4j.conf /var/lib/neo4j/conf/
-COPY files/piwik.html /
-COPY files/neo4j-guide-extension-3.2.3.jar /var/lib/neo4j/plugins
-COPY guides /guides
-
 # Update or install packages
 RUN apt-get update && apt-get install --yes \
   bzip2 \
   curl \
   tar \
+  nano \
   zip
 
+COPY scripts /
+RUN chmod +x /get_data_run_neo4j.sh
+
+COPY files/neo4j.conf /var/lib/neo4j/conf/
+COPY files/piwik.html /
+# https://github.com/neo4j-contrib/neo4j-guides
+# COPY files/neo4j-guide-extension-3.2.3.jar /var/lib/neo4j/plugins
+# COPY guides /guides
+
 # Install Neo4j APOC plugin
 # RUN wget --quiet --directory-prefix=/var/lib/neo4j/plugins \
 #  https://github.com/neo4j-contrib/neo4j-apoc-procedures/releases/download/3.0.4.1/apoc-3.0.4.1-all.jar

hetnet/neo4j/docker/README.md

@@ -11,7 +11,7 @@ The contents of this repository are mostly included in the Docker image. However
 Build the image using the following command:
 
 ```sh
-TAG="dhimmel/hetionet:hetionet-v1.0_neo4j-3.5.12"
+TAG="dhimmel/hetionet:hetionet-v1.0_neo4j-4.0.6"
 docker build --tag dhimmel/hetionet:latest --tag $TAG --file Dockerfile .
 ```
 
@@ -37,6 +37,32 @@ docker run \
   dhimmel/hetionet
 ```
 
+## DELETE
+
+```
+TAG="dhimmel/hetionet:hetionet-v1.0_neo4j-4.0.6"
+docker build --tag $TAG --file Dockerfile .
+```
+
+```sh
+docker run \
+  --name=hetionet-container \
+  --rm \
+  --publish=7474:7474 \
+  --publish=7687:7687 \
+  --volume=$HOME/neo4j/hetionet-data:/data \
+  --volume=$HOME/neo4j/hetionet-logs:/logs \
+  --interactive --tty \
+  dhimmel/hetionet:hetionet-v1.0_neo4j-4.0.6 bash
+```
+
+```
+DB_URL="https://github.com/hetio/hetionet/raw/030e44430f168d934c44860ad5a9512deb7c7175/hetnet/neo4j/hetionet-v1.0-neo4j.dump"
+neo4j-admin load --from=data/hetionet-v1.0-neo4j.dump --database=hetionet
+
+Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.neo4j.dbms.database.DefaultSystemGraphInitializer@6b760460' was successfully initialized, but failed to start. Please see the attached cause exception "Unknown store version 'AF4.3.0'".
+```
+
 ## Deploying the docker
 
 From the cloud host, first pull the docker `docker pull dhimmel/hetionet` and then start the docker `sh ~/run-docker.sh`. `run-docker.sh` should be copied from [`host/run-docker.sh`](host/run-docker.sh) in this repository into $HOME on the cloud host.

hetnet/neo4j/docker/files/neo4j.conf

@@ -5,8 +5,8 @@
 # https://neo4j.com/docs/operations-manual/current/reference/configuration-settings/
 #*****************************************************************
 
-# The name of the database to mount (deprecated argument)
-dbms.active_database=graph.db
+# The name of the database to mount
+dbms.default_database=hetionet
 
 # This setting constrains all `LOAD CSV` import files to be under the `import` directory. Remove or comment it out to
 # allow files to be loaded from anywhere in the filesystem; this introduces possible security problems. See the
@@ -20,13 +20,15 @@ dbms.security.auth_enabled=false
 # Enable this to be able to upgrade a store from an older version.
 dbms.allow_upgrade=true
 
+# unsupported.dbms.tx_log.fail_on_corrupted_log_files=false
+
 #*****************************************************************
 # Network connector configuration
 #*****************************************************************
 
 # With default configuration Neo4j only accepts local connections.
 # To accept non-local connections, uncomment this line:
-dbms.connectors.default_listen_address=0.0.0.0
+dbms.default_listen_address=0.0.0.0
 
 # You can also choose a specific network interface, and configure a non-default
 # port for each connector, by setting their individual listen_address.
@@ -50,7 +52,8 @@ dbms.connector.http.enabled=true
 #dbms.connector.http.listen_address=:7474
 
 # HTTPS Connector. There can be zero or one HTTPS connectors.
-dbms.connector.https.enabled=true
+# https://community.neo4j.com/t5/neo4j-graph-platform/after-neo4j-v4-0-0-upgrade-https-set-to-enabled-but-no-ssl/m-p/32648/highlight/true#M17238
+# dbms.connector.https.enabled=false
 #dbms.connector.https.listen_address=:7473
 
 # Number of Neo4j worker threads.
@@ -90,7 +93,7 @@ dbms.logs.http.enabled=true
 #dbms.logs.debug.rotation.keep_number=7
 
 # Log executed queries that takes longer than the configured threshold. Enable by uncommenting this line.
-dbms.logs.query.enabled=true
+dbms.logs.query.enabled=INFO
 
 # If the execution of query takes more time than this threshold, the query is logged. If set to zero then all queries
 # are logged.
@@ -142,8 +145,8 @@ dbms.transaction.timeout=120s
 
 # Configure the guide-extension
 # https://github.com/jexp/neo4j-guides/tree/master/guide-extension
-dbms.unmanaged_extension_classes=extension.web=/guides
-org.neo4j.server.guide.directory=data/guides
+# dbms.unmanaged_extension_classes=extension.web=/guides
+# org.neo4j.server.guide.directory=data/guides
 
 # Enable remote content (guides) from anywhere
 # In Neo4j 3.2.1, only available in enterprise (https://github.com/neo4j/neo4j/issues/9534)

hetnet/neo4j/docker/scripts/get_data.sh

@@ -6,14 +6,19 @@ set -o errexit
 cd /data
 
 mkdir -p databases
-if [ ! -d "databases/graph.db" ]; then
-  echo "Downloading and extracting database"
-  DB_URL="https://github.com/hetio/hetionet/raw/e319b1b50639b845a35e31fbc16afcbe9b8c2dfd/hetnet/neo4j/hetionet-v1.0.db.tar.bz2"
-  curl --silent --location $DB_URL | tar --extract --bzip2 --directory=databases
+HETIONET_DUMP=hetionet-v1.0-neo4j.dump
+if [ ! -f "$HETIONET_DUMP" ]; then
+  echo "Downloading database dump"
+  DB_URL="https://github.com/hetio/hetionet/raw/030e44430f168d934c44860ad5a9512deb7c7175/hetnet/neo4j/$HETIONET_DUMP"
+  wget "$DB_URL"
+  # curl --silent --location $DB_URL | neo4j-admin load --from=- --database=hetionet --force
 else
   echo "Not retrieving database as it already exists"
 fi
 
+# Loading takes seconds, so 
+neo4j-admin load --from="$HETIONET_DUMP" --database=hetionet --force
+
 if [ ! -d "guides" ]; then
   echo "Downloading and extracting guides"
   cp --recursive /guides ./

hetnet/neo4j/docker/scripts/get_data_run_neo4j.sh

@@ -1,3 +1,4 @@
 #!/bin/sh
 sh /get_data.sh
+export NEO4J_EDITION=community
 /docker-entrypoint.sh neo4j