Upgrade to Neo4j 5

compose.yaml

@@ -38,19 +38,18 @@ services:
         condition: service_healthy
 
   neo4j:
-    image: neo4j:4.4-community
+    image: neo4j:5-community
     ports:
       - '127.0.0.1:7474:7474' # HTTP
       #- '::1:7474:7474'
       - '127.0.0.1:7687:7687' # BOLT
       #- '::1:7687:7687'
     environment:
-      NEO4JLABS_PLUGINS: '["apoc"]'
+      NEO4J_PLUGINS: '["apoc", "apoc-extended"]'
       NEO4J_AUTH: none
-      NEO4J_dbms_mode: SINGLE
-      NEO4J_dbms_default__database: orkg
-      NEO4J_dbms_memory_heap_max__size: 4G
-      NEO4J_dbms_transaction_timeout: 30s
+      NEO4J_initial_dbms_default__database: orkg
+      NEO4J_server_memory_heap_max__size: 4G
+      NEO4J_db_transaction_timeout: 30s
     healthcheck:
       test: [ "CMD", "/var/lib/neo4j/bin/cypher-shell", "-u", "$${NEO4J_USERNAME}", "-p", "$${NEO4J_PASSWORD}", "MATCH () RETURN count(*) as count" ]
       interval: 5s

constants/build.gradle.kts

@@ -10,7 +10,7 @@ buildConfig {
     className("BuildConfig")
 
     buildConfigField("APP_NAME", rootProject.name)
-    buildConfigField("CONTAINER_IMAGE_NEO4J", "neo4j:4.4-community")
+    buildConfigField("CONTAINER_IMAGE_NEO4J", "neo4j:5-community")
     buildConfigField("CONTAINER_IMAGE_POSTGRES", "postgres:11")
     buildConfigField("CONTAINER_IMAGE_KEYCLOAK", "registry.gitlab.com/tibhannover/orkg/keycloak-docker-image:26.0.5")
 }

content-types/content-types-adapter-output-spring-data-neo4j-sdn6/src/main/kotlin/org/orkg/contenttypes/adapter/output/neo4j/internal/Neo4jPaperRepository.kt

@@ -18,7 +18,7 @@ interface Neo4jPaperRepository : Neo4jRepository<Neo4jResource, ThingId> {
 MATCH (r:Resource {id: $id})
 CALL apoc.path.expandConfig(r, {relationshipFilter: "<RELATED", labelFilter: "/Paper", uniqueness: "RELATIONSHIP_GLOBAL"})
 YIELD path
-WITH last(nodes(path)) AS paper, apoc.coll.reverse(apoc.coll.flatten([r in relationships(path) | [r, startNode(r)]])) AS path
+WITH last(nodes(path)) AS paper, reverse(apoc.coll.flatten([r in relationships(path) | [r, startNode(r)]])) AS path
 UNWIND path AS thing
 MATCH (t:Thing)
 WHERE t.id = thing.id

migrations/neo4j-migrations/build.gradle.kts

@@ -1,7 +1,7 @@
 import org.gradle.jvm.tasks.Jar
 
 plugins {
-    id("java-library")
+    id("org.orkg.gradle.kotlin-library")
 }
 
 tasks {

migrations/neo4j-migrations/src/main/kotlin/org/orkg/migrations/neo4j/AbstractCustomProcedureMigration.kt

@@ -0,0 +1,44 @@
+package org.orkg.migrations.neo4j
+
+import ac.simons.neo4j.migrations.core.JavaBasedMigration
+import ac.simons.neo4j.migrations.core.MigrationContext
+import java.lang.Thread.sleep
+import java.util.*
+
+abstract class AbstractCustomProcedureMigration(
+    private val migrationQuery: String,
+    private val validationQuery: String,
+    private val version: Long,
+    private val validationIntervalMs: Long = 100,
+) : JavaBasedMigration {
+    override fun apply(context: MigrationContext) {
+        val systemDBContext = context.getSessionConfig { it.withDatabase("system") }
+        context.driver.session(systemDBContext).executeWriteWithoutResult { tx ->
+            tx.run(migrationQuery)
+        }
+        val orkgDBContext = context.getSessionConfig { it.withDatabase("orkg") }
+        val validate = {
+            try {
+                context.driver.session(orkgDBContext).executeRead { tx ->
+                    tx.run(validationQuery).list().size
+                }
+            } catch (e: Exception) {
+                -1
+            }
+        }
+        var result = validate()
+        while (result == -1) {
+            sleep(validationIntervalMs)
+            result = validate()
+        }
+    }
+
+    override fun getOptionalDescription(): Optional<String> = Optional.ofNullable(
+        this::class.simpleName
+            ?.replace(Regex("""^[RV]\d+__"""), "")
+            ?.replace(Regex("""([A-Z])""")) { " " + it.value.lowercase() }
+            ?.trim()
+    )
+
+    override fun getChecksum(): Optional<String> = Optional.of(version.toString())
+}

migrations/neo4j-migrations/src/main/kotlin/org/orkg/migrations/neo4j/R0027__CreateCustomSubgraphProcedure.kt

@@ -0,0 +1,16 @@
+package org.orkg.migrations.neo4j
+
+@Suppress("ClassName")
+class R0027__CreateCustomSubgraphProcedure : AbstractCustomProcedureMigration(
+    """
+    CALL apoc.custom.installProcedure(
+        'subgraph(start :: ANY?, config :: MAP) :: (relationships :: LIST? OF RELATIONSHIP?)',
+        'CALL apoc.path.subgraphAll(${'$'}start, ${'$'}config) YIELD relationships WITH relationships UNWIND relationships AS rel WITH rel WHERE rel:RELATED RETURN COLLECT(rel) AS relationships',
+        'orkg',
+        'read',
+        'custom.subgraph(startNode <id>|Node|list, {maxLevel,relationshipFilter,labelFilter,bfs:true, filterStartNode:false, limit:-1, endNodes:[], terminatorNodes:[], sequence, beginSequenceAtStart:true}) yield relationships - expand the subgraph reachable from start node following relationships to max-level adhering to the label filters, returning all RELATED relationships within the subgraph'
+    );
+    """.trimIndent(),
+    validationQuery = "CALL custom.subgraph([], {})",
+    version = 1
+)

migrations/neo4j-migrations/src/main/kotlin/org/orkg/migrations/neo4j/R0031__CreateCustomTimestampParsingFunction.kt

@@ -0,0 +1,22 @@
+package org.orkg.migrations.neo4j
+
+import org.springframework.stereotype.Component
+
+@Component
+@Suppress("ClassName")
+class R0031__CreateCustomTimestampParsingFunction : AbstractCustomProcedureMigration(
+    """
+    CALL apoc.custom.installFunction(
+        'parseIsoOffsetDateTime(time :: STRING, unit = ms :: STRING) :: (INTEGER?)',
+        'WITH apoc.text.regreplace(${'$'}time, "(\.\d{1,3})\d*", "${'$'}1") AS time // limit fraction to 3 digits because parsing pattern only supports milliseconds (see java.text.SimpleDateFormat)
+        WITH apoc.text.regreplace(time, "(T\d{2}:\d{2})([+-]\d{2}:\d{2}|Z)${'$'}", "${'$'}1:00${'$'}2") AS time // insert seconds block if missing because parsing pattern does not support optional sections (see java.text.SimpleDateFormat)
+        WITH apoc.text.regreplace(time, "(T\d{2}:\d{2}:\d{2})([+-]\d{2}:\d{2}|Z)${'$'}", "${'$'}1.0${'$'}2") AS time // insert milliseconds block if missing because parsing pattern does not support optional sections (see java.text.SimpleDateFormat)
+        RETURN apoc.date.parse(time, ${'$'}unit, "yyyy-MM-dd\'T\'HH:mm:ss.SSSXXX")',
+        'orkg',
+        false,
+        'custom.parseIsoOffsetDateTime(\'2012-12-23T21:15:05.645313+02:00\', \'ms|s|m|h|d\') - parse date string as offset date time into the specified time unit'
+    );
+    """.trimIndent(),
+    validationQuery = "RETURN custom.parseIsoOffsetDateTime('2012-12-23T21:15:05.645313+02:00', 'ms')",
+    version = 1
+)

rest-api-server/src/main/resources/config/application.yml

@@ -109,6 +109,11 @@ management:
       enabled: true
 hawtio:
   authenticationEnabled: false
+org:
+  neo4j:
+    migrations:
+      packages-to-scan:
+        - "org.orkg.migrations.neo4j"
 ---
 spring:
   config:

scripts/reload-dump

@@ -4,7 +4,7 @@
 #
 set -e
 
-neo4j_version=4.4-community
+neo4j_version=5-community
 
 dump_volume=orkg-dumps
 source_dir=orkg-backend
@@ -47,7 +47,7 @@ docker compose stop neo4j
 # Load dump.
 # The double dash seems to be required to make the script work with "Git Bash" in Windows. :-/
 docker run -i --rm --entrypoint //bin/bash --volumes-from "${source_dir}-neo4j-1" --volume "${dump_volume}:/dumps" neo4j:$neo4j_version <<EOS
-neo4j-admin load --from=/dumps/neo4j-dump-latest.dump --database=orkg --force
+neo4j-admin database load orkg --overwrite-destination=true --from-stdin < /dumps/neo4j-dump-latest.dump
 EOS
 
 # Destroy database container. This is required to get rid of the logs, so the next step can wait successfully.

testing/spring/src/testFixtures/kotlin/org/orkg/testing/Neo4jContainerInitializer.kt

@@ -14,10 +14,11 @@ class Neo4jContainerInitializer : ApplicationContextInitializer<ConfigurableAppl
     // TODO: might be nice to aggregate values for debugging, if possible
 
     companion object {
-        val neo4jContainer: Neo4jContainer<*> =
-            Neo4jContainer(DockerImageName.parse(BuildConfig.CONTAINER_IMAGE_NEO4J))
+        val neo4jContainer: Neo4jContainer<*> = Neo4jContainer(DockerImageName.parse(BuildConfig.CONTAINER_IMAGE_NEO4J))
+            .withNeo4jConfig("initial.dbms.default_database", "orkg")
+            .withNeo4jConfig("apoc.custom.procedures.refresh", "100")
             .withoutAuthentication()
-            .withPlugins("apoc")
+            .withPlugins("apoc", "apoc-extended")
     }
 
     override fun initialize(applicationContext: ConfigurableApplicationContext) {

testing/spring/src/testFixtures/kotlin/org/orkg/testing/annotations/Annotations.kt

@@ -21,17 +21,20 @@ import org.springframework.core.annotation.AliasFor
 import org.springframework.data.neo4j.core.DatabaseSelectionProvider
 import org.springframework.data.neo4j.core.transaction.Neo4jTransactionManager
 import org.springframework.test.context.ContextConfiguration
+import org.springframework.test.context.TestPropertySource
 
 @SpringBootTest
 @ContextConfiguration(initializers = [Neo4jContainerInitializer::class])
 @ImportAutoConfiguration(MigrationsAutoConfiguration::class)
+@TestPropertySource(properties = ["org.neo4j.migrations.packages-to-scan=org.orkg.migrations.neo4j"])
 annotation class Neo4jContainerIntegrationTest
 
 @DataNeo4jTest
 @EnableAutoConfiguration
 @ContextConfiguration(initializers = [Neo4jContainerInitializer::class])
 @ImportAutoConfiguration(MigrationsAutoConfiguration::class)
 @Import(Neo4jTestConfiguration::class)
+@TestPropertySource(properties = ["org.neo4j.migrations.packages-to-scan=org.orkg.migrations.neo4j"])
 annotation class Neo4jContainerUnitTest(
     @get:AliasFor(annotation = ContextConfiguration::class, attribute = "classes")
     val classes: Array<KClass<*>> = [],