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Upgrade dependencies to latest versions #100

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merged 3 commits into from
Nov 4, 2024
Merged

Upgrade dependencies to latest versions #100

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fc4363c
Upgrade dependencies to latest versions
rpoet-jh Nov 4, 2024
2f5d737
Disable spring cloud aws services
rpoet-jh Nov 4, 2024
5e8ed1b
Disable spring cloud aws cloudwatch
rpoet-jh Nov 4, 2024
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4 changes: 2 additions & 2 deletions pass-core-doi-service/pom.xml
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Expand Up @@ -29,8 +29,8 @@
</dependency>
<dependency>
<groupId>org.glassfish</groupId>
<artifactId>javax.json</artifactId>
<version>${javax.json.version}</version>
<artifactId>jakarta.json</artifactId>
<version>${jakarta.json.version}</version>
</dependency>
<dependency>
<groupId>com.squareup.okhttp3</groupId>
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4 changes: 2 additions & 2 deletions pass-core-doi-service/src/main/java/org/eclipse/pass/doi/service/ElideConnector.java
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Expand Up @@ -25,10 +25,10 @@
import java.util.Set;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import javax.json.JsonArray;
import javax.json.JsonObject;

import com.yahoo.elide.RefreshableElide;
import jakarta.json.JsonArray;
import jakarta.json.JsonObject;
import org.eclipse.pass.object.PassClient;
import org.eclipse.pass.object.PassClientResult;
import org.eclipse.pass.object.PassClientSelector;
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3 changes: 2 additions & 1 deletion pass-core-doi-service/src/main/java/org/eclipse/pass/doi/service/ExternalDoiService.java
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Expand Up @@ -24,7 +24,8 @@
import java.util.Set;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import javax.json.JsonObject;

import jakarta.json.JsonObject;

/**
* ExternalDoiService classes provide configuration needed for specific implementations'
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8 changes: 4 additions & 4 deletions ...e-doi-service/src/main/java/org/eclipse/pass/doi/service/ExternalDoiServiceConnector.java
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Expand Up @@ -21,11 +21,11 @@
import java.io.IOException;
import java.io.StringReader;
import java.util.Objects;
import javax.json.Json;
import javax.json.JsonObject;
import javax.json.JsonReader;
import javax.json.stream.JsonParsingException;

import jakarta.json.Json;
import jakarta.json.JsonObject;
import jakarta.json.JsonReader;
import jakarta.json.stream.JsonParsingException;
import okhttp3.Call;
import okhttp3.Headers;
import okhttp3.HttpUrl;
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4 changes: 2 additions & 2 deletions ...core-doi-service/src/main/java/org/eclipse/pass/doi/service/PassDoiServiceController.java
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Expand Up @@ -18,10 +18,10 @@

import java.io.IOException;
import java.io.OutputStream;
import javax.json.Json;
import javax.json.JsonObject;

import com.yahoo.elide.RefreshableElide;
import jakarta.json.Json;
import jakarta.json.JsonObject;
import jakarta.servlet.http.HttpServletRequest;
import jakarta.servlet.http.HttpServletResponse;
import org.slf4j.Logger;
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11 changes: 6 additions & 5 deletions pass-core-doi-service/src/main/java/org/eclipse/pass/doi/service/UnpaywallDoiService.java
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Expand Up @@ -20,11 +20,12 @@
import java.net.URI;
import java.net.URISyntaxException;
import java.util.HashMap;
import javax.json.Json;
import javax.json.JsonArray;
import javax.json.JsonArrayBuilder;
import javax.json.JsonObject;
import javax.json.JsonValue;

import jakarta.json.Json;
import jakarta.json.JsonArray;
import jakarta.json.JsonArrayBuilder;
import jakarta.json.JsonObject;
import jakarta.json.JsonValue;

/**
* The UnpaywallDoiService class is an implementation of the ExternalDoiService abstract class to interface with
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3 changes: 2 additions & 1 deletion pass-core-doi-service/src/main/java/org/eclipse/pass/doi/service/XrefDoiService.java
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Expand Up @@ -17,7 +17,8 @@
package org.eclipse.pass.doi.service;

import java.util.HashMap;
import javax.json.JsonObject;

import jakarta.json.JsonObject;

/**
* The XrefDoiService class is an implementation of the ExternalDoiService abstract class to interface with the Crossref
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6 changes: 3 additions & 3 deletions pass-core-doi-service/src/test/java/org/eclipse/pass/doi/service/ElideConnectorTest.java
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import static org.junit.jupiter.api.Assertions.assertTrue;

import java.io.StringReader;
import javax.json.Json;
import javax.json.JsonObject;
import javax.json.JsonReader;

import com.yahoo.elide.RefreshableElide;
import jakarta.json.Json;
import jakarta.json.JsonObject;
import jakarta.json.JsonReader;
import org.eclipse.pass.object.model.Journal;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.TestInstance;
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3 changes: 1 addition & 2 deletions ...i-service/src/test/java/org/eclipse/pass/doi/service/ExternalDoiServiceConnectorTest.java
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Expand Up @@ -19,8 +19,7 @@
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;

import javax.json.JsonObject;

import jakarta.json.JsonObject;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.TestInstance;
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7 changes: 4 additions & 3 deletions pass-core-doi-service/src/test/java/org/eclipse/pass/doi/service/JsonTestObjectsUtil.java
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Expand Up @@ -17,9 +17,10 @@
package org.eclipse.pass.doi.service;

import java.io.StringReader;
import javax.json.Json;
import javax.json.JsonObject;
import javax.json.JsonReader;

import jakarta.json.Json;
import jakarta.json.JsonObject;
import jakarta.json.JsonReader;

/**
* A utility class to provide real-life json responses
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1 change: 0 additions & 1 deletion pass-core-file-service/pom.xml
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Expand Up @@ -44,7 +44,6 @@
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>${apache.commons.io.version}</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.jsoup</groupId>
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30 changes: 23 additions & 7 deletions ...ile-service/src/main/java/org/eclipse/pass/file/service/storage/StorageConfiguration.java
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Expand Up @@ -39,9 +39,10 @@
import org.springframework.context.annotation.Configuration;
import software.amazon.awssdk.auth.credentials.DefaultCredentialsProvider;
import software.amazon.awssdk.regions.Region;
import software.amazon.awssdk.services.s3.S3Client;
import software.amazon.awssdk.services.s3.S3ClientBuilder;
import software.amazon.awssdk.services.s3.S3AsyncClient;
import software.amazon.awssdk.services.s3.S3AsyncClientBuilder;
import software.amazon.awssdk.services.s3.model.CreateBucketRequest;
import software.amazon.awssdk.transfer.s3.S3TransferManager;

/**
* The StorageConfiguration is responsible for handling the StorageProperties. The FileStorageService does not get the
Expand All @@ -60,35 +61,50 @@ public class StorageConfiguration {

@Bean
@ConditionalOnProperty(name = "pass.file-service.storage-type", havingValue = "S3")
public S3Client s3Client(StorageProperties storageProperties) throws IOException {
public S3TransferManager s3TransferManager() {
S3AsyncClient s3AsyncClient = S3AsyncClient.crtBuilder()
.credentialsProvider(DefaultCredentialsProvider.create())
.region(Region.of(awsRegion))
.build();

return S3TransferManager.builder()
.s3Client(s3AsyncClient)
.build();
}

@Bean
@ConditionalOnProperty(name = "pass.file-service.storage-type", havingValue = "S3")
public S3AsyncClient s3Client(StorageProperties storageProperties) throws IOException {
String bucketName = storageProperties.getBucketName().
orElseThrow(() -> new IOException("File Service: S3 bucket name is not set"));

S3ClientBuilder builder = S3Client.builder()
S3AsyncClientBuilder builder = S3AsyncClient.builder()
.credentialsProvider(DefaultCredentialsProvider.create())
.region(Region.of(awsRegion));

String endpoint = storageProperties.getS3Endpoint().orElse(null);
S3Client s3Client = StringUtils.isNotBlank(endpoint)
S3AsyncClient s3Client = StringUtils.isNotBlank(endpoint)
? builder.endpointOverride(URI.create(endpoint)).forcePathStyle(true).build()
: builder.build();

if (s3Client.listBuckets().buckets().stream().noneMatch(b -> b.name().equals(bucketName))) {
if (s3Client.listBuckets().join().buckets().stream().noneMatch(b -> b.name().equals(bucketName))) {
s3Client.createBucket(CreateBucketRequest.builder().bucket(bucketName).build());
}
return s3Client;
}

@Bean
@ConditionalOnProperty(name = "pass.file-service.storage-type", havingValue = "S3")
public OcflRepository ocflS3Repository(S3Client s3Client, StorageProperties storageProperties,
public OcflRepository ocflS3Repository(S3AsyncClient s3Client, S3TransferManager s3TransferManager,
StorageProperties storageProperties,
@Qualifier("rootPath") Path rootLoc) throws IOException {
String bucketName = storageProperties.getBucketName().
orElseThrow(() -> new IOException("File Service: S3 bucket name is not set"));
String repoPrefix = storageProperties.getS3RepoPrefix().orElse(null);

OcflS3Client.Builder builder = OcflS3Client.builder()
.s3Client(s3Client)
.transferManager(s3TransferManager)
.bucket(bucketName);
OcflS3Client ocflS3Client = StringUtils.isNotBlank(repoPrefix)
? builder.repoPrefix(repoPrefix).build()
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2 changes: 1 addition & 1 deletion pass-core-main/Dockerfile
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@@ -1,4 +1,4 @@
FROM eclipse-temurin:17.0.8_7-jre-jammy
FROM eclipse-temurin:17.0.13_11-jre-jammy

WORKDIR /app

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7 changes: 0 additions & 7 deletions pass-core-main/pom.xml
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Expand Up @@ -81,22 +81,16 @@
<dependency>
<groupId>org.liquibase</groupId>
<artifactId>liquibase-core</artifactId>
<version>${liquibase.version}</version>
<scope>runtime</scope>
</dependency>

<dependency>
<groupId>com.h2database</groupId>
<artifactId>h2</artifactId>
<version>${h2.version}</version>
<scope>runtime</scope>
</dependency>

<dependency>
<groupId>org.postgresql</groupId>
<artifactId>postgresql</artifactId>
<version>${postgres.version}</version>
<scope>runtime</scope>
</dependency>

<dependency>
Expand Down Expand Up @@ -175,7 +169,6 @@
<dependency>
<groupId>io.rest-assured</groupId>
<artifactId>rest-assured</artifactId>
<version>${rest-assured.version}</version>
<exclusions>
<exclusion>
<groupId>commons-logging</groupId>
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6 changes: 3 additions & 3 deletions pass-core-main/src/main/java/org/eclipse/pass/main/JmsConfiguration.java
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Expand Up @@ -20,8 +20,6 @@
import java.util.HashMap;
import java.util.Objects;
import java.util.Set;
import javax.json.Json;
import javax.json.JsonObjectBuilder;

import com.amazon.sqs.javamessaging.ProviderConfiguration;
import com.amazon.sqs.javamessaging.SQSConnectionFactory;
Expand All @@ -38,6 +36,8 @@
import com.yahoo.elide.jsonapi.JsonApiSettingsBuilderCustomizer;
import jakarta.jms.ConnectionFactory;
import jakarta.jms.TextMessage;
import jakarta.json.Json;
import jakarta.json.JsonObjectBuilder;
import jakarta.persistence.OptimisticLockException;
import org.apache.commons.lang3.StringUtils;
import org.eclipse.pass.main.repository.DepositRepository;
Expand Down Expand Up @@ -178,7 +178,7 @@ public EntityDictionary buildDictionary(Injector injector, ClassScanner scanner,
DepositRepository depositRepository) {

EntityDictionary dictionary = new EntityDictionary(new HashMap<>(), new HashMap<>(), injector,
CoerceUtil::lookup, entitiesToExclude, scanner);
CoerceUtil::lookup, entitiesToExclude, scanner, null);

setupHooks(dictionary, jms, userTokenFactory, submissionRepository, depositRepository);

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18 changes: 18 additions & 0 deletions pass-core-main/src/main/resources/application.yaml
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Expand Up @@ -25,6 +25,24 @@ elide:
spring:
application:
name: pass-core
cloud:
aws:
cloudwatch:
enabled: false
dynamodb:
enabled: false
parameterstore:
enabled: false
s3:
enabled: false
secretsmanager:
enabled: false
ses:
enabled: false
sns:
enabled: false
sqs:
enabled: false
jpa:
properties:
hibernate:
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6 changes: 3 additions & 3 deletions pass-core-main/src/test/java/org/eclipse/pass/doi/service/DoiServiceTest.java
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Expand Up @@ -5,11 +5,11 @@

import java.io.IOException;
import java.io.StringReader;
import javax.json.Json;
import javax.json.JsonObject;
import javax.json.JsonReader;

import com.yahoo.elide.RefreshableElide;
import jakarta.json.Json;
import jakarta.json.JsonObject;
import jakarta.json.JsonReader;
import okhttp3.Call;
import okhttp3.Credentials;
import okhttp3.HttpUrl;
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1 change: 1 addition & 0 deletions pass-core-main/src/test/java/org/eclipse/pass/main/AwsParamStoreConfigTest.java
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Expand Up @@ -37,6 +37,7 @@

@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT,
properties = {
"spring.cloud.aws.parameterstore.enabled=true",
"spring.cloud.aws.credentials.access-key=noop",
"spring.cloud.aws.credentials.secret-key=noop",
"spring.cloud.aws.region.static=us-east-1",
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8 changes: 4 additions & 4 deletions pass-core-main/src/test/java/org/eclipse/pass/main/JmsConfigurationTest.java
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Expand Up @@ -8,16 +8,16 @@
import java.net.URI;
import java.util.Collections;
import java.util.Enumeration;
import javax.json.Json;
import javax.json.JsonObject;
import javax.json.stream.JsonParser;
import javax.json.stream.JsonParser.Event;

import com.yahoo.elide.RefreshableElide;
import jakarta.jms.JMSException;
import jakarta.jms.QueueBrowser;
import jakarta.jms.Session;
import jakarta.jms.TextMessage;
import jakarta.json.Json;
import jakarta.json.JsonObject;
import jakarta.json.stream.JsonParser;
import jakarta.json.stream.JsonParser.Event;
import org.eclipse.pass.object.ElidePassClient;
import org.eclipse.pass.object.PassClient;
import org.eclipse.pass.object.model.Deposit;
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4 changes: 2 additions & 2 deletions pass-core-policy-service/pom.xml
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Expand Up @@ -30,8 +30,8 @@
</dependency>
<dependency>
<groupId>org.glassfish</groupId>
<artifactId>javax.json</artifactId>
<version>${javax.json.version}</version>
<artifactId>jakarta.json</artifactId>
<version>${jakarta.json.version}</version>
<scope>compile</scope>
</dependency>
</dependencies>
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10 changes: 5 additions & 5 deletions ...cy-service/src/main/java/org/eclipse/pass/policy/service/PassPolicyServiceController.java
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Expand Up @@ -20,13 +20,13 @@
import java.nio.charset.StandardCharsets;
import java.security.Principal;
import java.util.Set;
import javax.json.Json;
import javax.json.JsonArray;
import javax.json.JsonArrayBuilder;
import javax.json.JsonObject;
import javax.json.JsonObjectBuilder;

import com.yahoo.elide.RefreshableElide;
import jakarta.json.Json;
import jakarta.json.JsonArray;
import jakarta.json.JsonArrayBuilder;
import jakarta.json.JsonObject;
import jakarta.json.JsonObjectBuilder;
import jakarta.servlet.http.HttpServletRequest;
import jakarta.servlet.http.HttpServletResponse;
import org.eclipse.pass.object.model.Policy;
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6 changes: 3 additions & 3 deletions pass-core-user-service/pom.xml
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Expand Up @@ -35,9 +35,9 @@
</dependency>

<dependency>
<groupId>javax.json</groupId>
<artifactId>javax.json-api</artifactId>
<version>${javax.json.version}</version>
<groupId>jakarta.json</groupId>
<artifactId>jakarta.json-api</artifactId>
<version>${jakarta.json.version}</version>
</dependency>
</dependencies>
</project>
4 changes: 2 additions & 2 deletions pass-core-user-service/src/main/java/org/eclipse/pass/user/UserServiceController.java
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Expand Up @@ -3,10 +3,10 @@
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import java.security.Principal;
import javax.json.Json;
import javax.json.JsonObject;

import com.yahoo.elide.RefreshableElide;
import jakarta.json.Json;
import jakarta.json.JsonObject;
import jakarta.servlet.http.HttpServletRequest;
import jakarta.servlet.http.HttpServletResponse;
import org.eclipse.pass.object.PassClient;
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