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[NOID] Exclude OpenCSV bean-dependencies
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OpenCSV has two variants, one of which parses CSV into beans. We never use this so it's safe to exclude those dependencies.
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@klaren
klaren committed Feb 29, 2024
1 parent 12a71ef commit 58652d8
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Showing 7 changed files with 47 additions and 48 deletions.
1 change: 0 additions & 1 deletion LICENSES.txt
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Expand Up @@ -29,7 +29,6 @@ Apache-2.0
commons-cli-1.2.jar
commons-codec-1.16.0.jar
commons-collections-3.2.2.jar
commons-collections4-4.4.jar
commons-compress-1.25.0.jar
commons-configuration2-2.9.0.jar
commons-csv-1.9.0.jar
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1 change: 0 additions & 1 deletion NOTICE.txt
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Expand Up @@ -59,7 +59,6 @@ Apache-2.0
commons-cli-1.2.jar
commons-codec-1.16.0.jar
commons-collections-3.2.2.jar
commons-collections4-4.4.jar
commons-compress-1.25.0.jar
commons-configuration2-2.9.0.jar
commons-csv-1.9.0.jar
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56 changes: 36 additions & 20 deletions common/src/main/java/apoc/ApocConfig.java
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Expand Up @@ -36,25 +36,28 @@
import java.io.IOException;
import java.lang.reflect.Field;
import java.net.URL;
import java.nio.file.Path;
import java.time.Duration;
import java.time.ZoneId;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Map;
import java.util.stream.Stream;
import org.apache.commons.configuration2.CombinedConfiguration;
import org.apache.commons.configuration2.Configuration;
import org.apache.commons.configuration2.EnvironmentConfiguration;
import org.apache.commons.configuration2.PropertiesConfiguration;
import org.apache.commons.configuration2.builder.combined.CombinedConfigurationBuilder;
import org.apache.commons.configuration2.builder.fluent.Parameters;
import org.apache.commons.configuration2.SystemConfiguration;
import org.apache.commons.configuration2.ex.ConfigurationException;
import org.apache.commons.configuration2.ex.ConversionException;
import org.apache.commons.configuration2.io.FileHandler;
import org.apache.commons.configuration2.tree.OverrideCombiner;
import org.neo4j.configuration.Config;
import org.neo4j.configuration.GraphDatabaseInternalSettings;
import org.neo4j.configuration.GraphDatabaseSettings;
import org.neo4j.dbms.api.DatabaseManagementService;
import org.neo4j.graphdb.GraphDatabaseService;
import org.neo4j.graphdb.Path;
import org.neo4j.graphdb.config.Setting;
import org.neo4j.graphdb.security.URLAccessChecker;
import org.neo4j.kernel.api.procedure.GlobalProcedures;
Expand Down Expand Up @@ -87,7 +90,7 @@ public class ApocConfig extends LifecycleAdapter {
APOC_IMPORT_FILE_ENABLED, false,
APOC_IMPORT_FILE_USE_NEO4J_CONFIG, true,
APOC_TRIGGER_ENABLED, false);
private static final List<Setting> NEO4J_DIRECTORY_CONFIGURATION_SETTING_NAMES = new ArrayList<>(Arrays.asList(
private static final List<Setting<?>> NEO4J_DIRECTORY_CONFIGURATION_SETTING_NAMES = new ArrayList<>(Arrays.asList(
data_directory,
load_csv_file_url_root,
logs_directory,
Expand Down Expand Up @@ -115,6 +118,7 @@ public class ApocConfig extends LifecycleAdapter {
private boolean expandCommands;

private Duration commandEvaluationTimeout;
private File apocConfFile;

public ApocConfig(
Config neo4jConfig,
Expand All @@ -134,7 +138,7 @@ public ApocConfig(
theInstance = this;

// expose this config instance via `@Context ApocConfig config`
globalProceduresRegistry.registerComponent((Class<ApocConfig>) getClass(), ctx -> this, true);
globalProceduresRegistry.registerComponent(ApocConfig.class, ctx -> this, true);
this.log.info("successfully registered ApocConfig for @Context");
}

Expand Down Expand Up @@ -169,11 +173,12 @@ private String evaluateIfCommand(String settingName, String entry) {
@Override
public void init() {
log.debug("called init");
// grab NEO4J_CONF from environment. If not set, calculate it from sun.java.command system property or Neo4j default
// grab NEO4J_CONF from environment. If not set, calculate it from sun.java.command system property or Neo4j
// default
String neo4jConfFolder = System.getenv().getOrDefault("NEO4J_CONF", determineNeo4jConfFolder());
System.setProperty("NEO4J_CONF", neo4jConfFolder);
log.info("system property NEO4J_CONF set to %s", neo4jConfFolder);
File apocConfFile = new File(neo4jConfFolder + "/apoc.conf");
apocConfFile = new File(neo4jConfFolder + "/apoc.conf");
// Command Expansion required check from Neo4j
if (apocConfFile.exists() && this.expandCommands) {
Config.Builder.validateFilePermissionForCommandExpansion(List.of(apocConfFile.toPath()));
Expand Down Expand Up @@ -211,15 +216,10 @@ protected String determineNeo4jConfFolder() {

/**
* use apache commons to load configuration
* classpath:/apoc-config.xml contains a description where to load configuration from
*/
protected void loadConfiguration() {
try {
URL resource = getClass().getClassLoader().getResource("apoc-config.xml");
log.info("loading apoc meta config from %s", resource.toString());
CombinedConfigurationBuilder builder = new CombinedConfigurationBuilder()
.configure(new Parameters().fileBased().setURL(resource));
config = builder.getConfiguration();
config = setupConfigurations(apocConfFile);

// Command Expansion if needed
config.getKeys()
Expand All @@ -237,7 +237,7 @@ protected void loadConfiguration() {
});

addDbmsDirectoriesMetricsSettings();
for (Setting s : NEO4J_DIRECTORY_CONFIGURATION_SETTING_NAMES) {
for (Setting<?> s : NEO4J_DIRECTORY_CONFIGURATION_SETTING_NAMES) {
Object value = neo4jConfig.get(s);
if (value != null) {
config.setProperty(s.name(), value.toString());
Expand All @@ -264,11 +264,29 @@ protected void loadConfiguration() {
}
}

private static Configuration setupConfigurations(File propertyFile) throws ConfigurationException {
PropertiesConfiguration configFile = new PropertiesConfiguration();
if (propertyFile.exists()) {
final FileHandler handler = new FileHandler(configFile);
handler.setFile(propertyFile);
handler.load();
}

// OverrideCombiner will evaluate keys in order, i.e. env before sys etc.
CombinedConfiguration combined = new CombinedConfiguration();
combined.setNodeCombiner(new OverrideCombiner());
combined.addConfiguration(new EnvironmentConfiguration());
combined.addConfiguration(new SystemConfiguration());
combined.addConfiguration(configFile);

return combined;
}

@SuppressWarnings("unchecked")
private void addDbmsDirectoriesMetricsSettings() {
try {
Class<?> metricsSettingsClass =
Class.forName("com.neo4j.kernel.impl.enterprise.configuration.MetricsSettings");
Field csvPathField = metricsSettingsClass.getDeclaredField("csvPath");
Class<?> metricsSettingsClass = Class.forName("com.neo4j.configuration.MetricsSettings");
Field csvPathField = metricsSettingsClass.getDeclaredField("csv_path");
Setting<Path> dbms_directories_metrics = (Setting<Path>) csvPathField.get(null);
NEO4J_DIRECTORY_CONFIGURATION_SETTING_NAMES.add(dbms_directories_metrics);
} catch (ClassNotFoundException | NoSuchFieldException | IllegalAccessException e) {
Expand Down Expand Up @@ -313,9 +331,7 @@ public void checkReadAllowed(String url, URLAccessChecker urlAccessChecker) thro

public void checkWriteAllowed(ExportConfig exportConfig, String fileName) {
if (!config.getBoolean(APOC_EXPORT_FILE_ENABLED)) {
if (exportConfig == null
|| (fileName != null && !fileName.equals(""))
|| !exportConfig.streamStatements()) {
if (exportConfig == null || (fileName != null && !fileName.isEmpty()) || !exportConfig.streamStatements()) {
throw new RuntimeException(EXPORT_TO_FILE_ERROR);
}
}
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14 changes: 0 additions & 14 deletions common/src/main/resources/apoc-config.xml
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This file was deleted.

5 changes: 4 additions & 1 deletion core/build.gradle
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Expand Up @@ -38,7 +38,10 @@ dependencies {

// These will be dependencies packaged with the .jar
implementation project(":common")
implementation group: 'com.opencsv', name: 'opencsv', version: '5.7.1'
implementation group: 'com.opencsv', name: 'opencsv', version: '5.7.1', {
exclude group: 'commons-beanutils', module: 'commons-beanutils'
exclude group: 'org.apache.commons', module: 'commons-collections4'
}
implementation group: 'org.roaringbitmap', name: 'RoaringBitmap', version: '0.7.17'

def arrowExclusions = {
Expand Down
2 changes: 1 addition & 1 deletion core/src/main/java/apoc/refactor/GraphRefactoring.java
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Expand Up @@ -142,7 +142,7 @@ public Stream<NodeRefactorResult> cloneNodes(
// If there was an error, the procedure still passes, but this node + its rels should not
// be created. Instead, an error is returned to the user in the output.
if (withRelationships) {
for (Relationship rel: newNode.getRelationships()) {
for (Relationship rel : newNode.getRelationships()) {
rel.delete();
}
}
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16 changes: 6 additions & 10 deletions core/src/test/java/apoc/refactor/GraphRefactoringTest.java
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Expand Up @@ -54,7 +54,6 @@
import java.util.Map;
import java.util.stream.Collectors;
import java.util.stream.StreamSupport;

import junit.framework.TestCase;
import org.apache.commons.lang3.exception.ExceptionUtils;
import org.hamcrest.Matchers;
Expand Down Expand Up @@ -1677,8 +1676,9 @@ public void testMergeRelsTrueAndProduceSelfRelFalse() {

@Test
public void issue3960WithCloneNodes() {
// Any node created in cloneNodes should not be committed if the entire query fails.
String query = """
// Any node created in cloneNodes should not be committed if the entire query fails.
String query =
"""
CREATE (original:Person {uid: "original"}), (original2:Person {uid: "original"})
WITH original, original2
CALL apoc.refactor.cloneNodes([original, original2], false, ["uid"])
Expand All @@ -1687,12 +1687,7 @@ public void issue3960WithCloneNodes() {
RETURN 1/0
""";

QueryExecutionException e = assertThrows(
QueryExecutionException.class,
() -> testCall(
db,
query,
(r) -> {}));
QueryExecutionException e = assertThrows(QueryExecutionException.class, () -> testCall(db, query, (r) -> {}));
Throwable except = ExceptionUtils.getRootCause(e);
TestCase.assertTrue(except instanceof RuntimeException);
TestCase.assertEquals("/ by zero", except.getMessage());
Expand All @@ -1704,7 +1699,8 @@ public void issue3960WithCloneNodes() {
public void ShouldErrorOnConstraintsFailedCommon() {
db.executeTransactionally(("CREATE CONSTRAINT unique_id FOR ()-[r:HAS_PET]-() REQUIRE r.id IS UNIQUE"));

String query = """
String query =
"""
CREATE (a:Person {name: 'Mark', city: 'London'})-[:HAS_PET {id: 1}]->(:Cat {name: "Mittens"})
WITH a
CALL apoc.refactor.cloneNodes([a], true, ["city"])
Expand Down

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