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feat: e2e suite for egadev environment #671

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14d49dc
test: update base test and methods for ega-dev
yasinmiran Sep 24, 2025
9801645
test: read test env vars from system env
yasinmiran Sep 24, 2025
b08705d
chore: sync 14.10.2025
yasinmiran Oct 14, 2025
59677c4
fix: export req and token
yasinmiran Oct 24, 2025
997d420
feat: add export/fega endpoint
yasinmiran Oct 24, 2025
adf2fbb
fix: optional accessToken or visaToken
yasinmiran Oct 24, 2025
b4c77f6
fix: token payload
yasinmiran Oct 24, 2025
3eb8f63
fix: use bouncycastle for keys
yasinmiran Dec 5, 2025
e399cf0
feat: download file via proxy
yasinmiran Dec 9, 2025
636ad0b
feat: compare downloaded file checksums
yasinmiran Dec 9, 2025
60c2f70
chore: add a descriptive log for export request response in e2e
yasinmiran Dec 11, 2025
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2 changes: 2 additions & 0 deletions e2eTests/build.gradle.kts
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Expand Up @@ -25,6 +25,8 @@ dependencies {
testImplementation("org.skyscreamer:jsonassert:1.5.3")
testCompileOnly("org.projectlombok:lombok:1.18.40")
testAnnotationProcessor("org.projectlombok:lombok:1.18.40")
implementation("org.bouncycastle:bcprov-jdk18on:1.82")
implementation("org.bouncycastle:bcpkix-jdk18on:1.82")
}

// Start setup scripts.
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26 changes: 23 additions & 3 deletions e2eTests/docker-compose.template.yml
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Expand Up @@ -644,8 +644,8 @@ services:
container_name: e2e-tests
hostname: e2e_tests
build:
context: .
dockerfile: e2e-tests.Dockerfile
context: ..
dockerfile: e2eTests/e2e-tests.Dockerfile
depends_on:
proxy:
condition: service_healthy
Expand All @@ -660,7 +660,27 @@ services:
file-orchestrator:
condition: service_healthy
environment:
- INTEGRATION=FEGA
- E2E_TESTS_RUNTIME=<<E2E_TESTS_RUNTIME>>
- E2E_TESTS_INTEGRATION=<<E2E_TESTS_INTEGRATION>>
- E2E_TESTS_PROXY_HOST=<<E2E_TESTS_PROXY_HOST>>
- E2E_TESTS_PROXY_PORT=<<E2E_TESTS_PROXY_PORT>>
- E2E_TESTS_SDA_DOA_HOST=<<E2E_TESTS_SDA_DOA_HOST>>
- E2E_TESTS_SDA_DOA_PORT=<<E2E_TESTS_SDA_DOA_PORT>>
- E2E_TESTS_CEGAMQ_CONN_STR=<<E2E_TESTS_CEGAMQ_CONN_STR>>
- E2E_TESTS_CEGAAUTH_USERNAME=<<E2E_TESTS_CEGAAUTH_USERNAME>>
- E2E_TESTS_CEGAAUTH_PASSWORD=<<E2E_TESTS_CEGAAUTH_PASSWORD>>
- E2E_TESTS_SDA_DB_HOST=<<E2E_TESTS_SDA_DB_HOST>>
- E2E_TESTS_SDA_DB_PORT=<<E2E_TESTS_SDA_DB_PORT>>
- E2E_TESTS_SDA_DB_USERNAME=<<E2E_TESTS_SDA_DB_USERNAME>>
- E2E_TESTS_SDA_DB_PASSWORD=<<E2E_TESTS_SDA_DB_PASSWORD>>
- E2E_TESTS_SDA_DB_DATABASE_NAME=<<E2E_TESTS_SDA_DB_DATABASE_NAME>>
- E2E_TESTS_TRUSTSTORE_PASSWORD=<<E2E_TESTS_TRUSTSTORE_PASSWORD>>
- E2E_TESTS_PROXY_TOKEN_AUDIENCE=<<E2E_TESTS_PROXY_TOKEN_AUDIENCE>>
- E2E_TESTS_PROXY_ADMIN_USERNAME=<<E2E_TESTS_PROXY_ADMIN_USERNAME>>
- E2E_TESTS_PROXY_ADMIN_PASSWORD=<<E2E_TESTS_PROXY_ADMIN_PASSWORD>>
# - E2E_TESTS_EGA_DEV_BASE_DIRECTORY=<<E2E_TESTS_EGA_DEV_BASE_DIRECTORY>>
# - E2E_TESTS_EGA_DEV_PUBLIC_KEY_FILENAME=<<E2E_TESTS_EGA_DEV_PUBLIC_KEY_FILENAME>>
# - E2E_TESTS_LSAAI_TOKEN=<<E2E_TESTS_LSAAI_TOKEN>>
volumes:
- storage:/storage

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25 changes: 18 additions & 7 deletions e2eTests/e2e-tests.Dockerfile
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@@ -1,19 +1,30 @@
# Use Temurin 21 as the base image for Java 21
FROM eclipse-temurin:21-jdk-alpine
FROM eclipse-temurin:21-jdk-alpine AS builder

WORKDIR /app

COPY build.gradle.kts settings.gradle.kts gradlew ./
COPY gradle/ ./gradle/
COPY buildSrc ./buildSrc
COPY lib/crypt4gh ./lib/crypt4gh
COPY e2eTests/ ./e2eTests

RUN ./gradlew :lib:crypt4gh:build :e2eTests:jar --no-daemon

FROM eclipse-temurin:21-jre-alpine

# Install bash
RUN apk add --no-cache bash

# Set the working directory in the container
WORKDIR /fega-norway

# Copy the application JAR and scripts
COPY /build/libs/e2eTests.jar /fega-norway/e2eTests.jar
COPY env.sh /fega-norway/env.sh
COPY entrypoint.sh /entrypoint.sh
# Copy the application JAR, env, and scripts
COPY --from=builder /app/e2eTests/build/libs/e2eTests.jar /fega-norway/e2eTests.jar
COPY --from=builder /app/e2eTests/entrypoint.sh /fega-norway/entrypoint.sh

# Make entrypoint executable
RUN chmod +x /entrypoint.sh
RUN chmod +x /fega-norway/entrypoint.sh

# Run the entrypoint using bash
CMD ["/bin/bash", "/entrypoint.sh"]
CMD ["/bin/bash", "/fega-norway/entrypoint.sh"]
17 changes: 11 additions & 6 deletions e2eTests/entrypoint.sh
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Expand Up @@ -10,21 +10,26 @@ if [ -f "/storage/certs/rootCA.pem" ]; then
-noprompt \
-storepass changeit
else
echo "Warning: /storage/certs/rootCA.pem not found, skipping certificate import."
echo "Info: /storage/certs/rootCA.pem not found, skipping certificate import."
fi

# Choose which test to run based on the INTEGRATION variable.
# NB! Must be present in the environment.
#
# Choose which test to run based on the E2E_TESTS_INTEGRATION variable.
# If set to "FEGA", run no.elixir.e2eTests.FEGAIntegrationTest.
# Otherwise, run no.elixir.e2eTests.GDIIntegrationTest.
# See the top-level classes in no.elixir.e2eTests for details.
if [ "$INTEGRATION" = "FEGA" ]; then
if [ "$E2E_TESTS_INTEGRATION" = "FEGA" ]; then
echo "Running FEGA integration tests"
exec java -jar e2eTests.jar --select-class no.elixir.e2eTests.FEGAIntegrationTest
elif [ "$INTEGRATION" = "GDI" ]; then
elif [ "$E2E_TESTS_INTEGRATION" = "GDI" ]; then
echo "Running GDI integration tests"
exec java -jar e2eTests.jar --select-class no.elixir.e2eTests.GDIIntegrationTest
elif [ "$E2E_TESTS_INTEGRATION" = "EGA_DEV" ]; then
echo "Running EGA_DEV integration tests"
exec java -jar e2eTests.jar --select-class no.elixir.e2eTests.EgaDevIntegrationTest
else
echo "Error: Unknown or unset INTEGRATION value: $INTEGRATION"
echo "Please set INTEGRATION=FEGA or INTEGRATION=GDI"
echo "Error: Unknown or unset E2E_TESTS_INTEGRATION value: $E2E_TESTS_INTEGRATION"
echo "Please set E2E_TESTS_INTEGRATION=FEGA or E2E_TESTS_INTEGRATION=GDI or E2E_TESTS_INTEGRATION=EGA_DEV"
exit 1
fi
46 changes: 28 additions & 18 deletions e2eTests/env.sh
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Expand Up @@ -200,38 +200,48 @@ export HEARTBEAT_REDIS_DB=0

# E2E Test
# ---------------------------------------------------------------------------

# Determines the runtime mode for the E2E tests.
# If set to "container", the entire test runs inside a Docker container.
# If set to "local", you can run the test using: `./gradlew :e2eTests:test`.
# Mainly used to switch the host/ports and file systems to fetch the certificates.
export E2E_RUNTIME=container
export E2E_TESTS_RUNTIME=container

# Determines which integration should be run.
# Either FEGA or GDI or EGA_DEV
export E2E_TESTS_INTEGRATION=FEGA

# Helper function to choose value based on runtime
function _runtime_() {
local container_value=$1
local local_value=$2

if [ "$E2E_RUNTIME" = "container" ]; then
if [ "$E2E_TESTS_RUNTIME" = "container" ]; then
echo "$container_value"
else
echo "$local_value"
fi
}

# Use the function for environment variable assignments
export E2E_PROXY_HOST=$(_runtime_ "proxy" "localhost")
export E2E_PROXY_PORT=$(_runtime_ "8080" "10443")
export E2E_SDA_DOA_HOST=$(_runtime_ "doa" "localhost")
export E2E_SDA_DOA_PORT=$(_runtime_ "8080" "80")
export E2E_CEGAMQ_CONN_STR="amqps://$CEGAMQ_USERNAME:$CEGAMQ_PASSWORD@$(_runtime_ $CEGAMQ_HOST "localhost"):$CEGAMQ_PORT/$CEGAMQ_VHOST"
export E2E_CEGAAUTH_USERNAME=$CEGAAUTH_CEGA_USERS_USER
export E2E_CEGAAUTH_PASSWORD=$CEGAAUTH_CEGA_USERS_PASSWORD
export E2E_SDA_DB_HOST=$(_runtime_ "$DB_HOST" "localhost")
export E2E_SDA_DB_PORT=$DB_PORT
export E2E_SDA_DB_USERNAME=$DB_POSTGRES_USER
export E2E_SDA_DB_PASSWORD=$DB_POSTGRES_PASSWORD
export E2E_SDA_DB_DATABASE_NAME=$DB_POSTGRES_DB
export E2E_TRUSTSTORE_PASSWORD=$KEYTOOL_TRUSTSTORE_PASSWORD
export E2E_PROXY_TOKEN_AUDIENCE=$PROXY_TOKEN_AUDIENCE
export E2E_PROXY_ADMIN_USERNAME=$PROXY_ADMIN_USER
export E2E_PROXY_ADMIN_PASSWORD=$PROXY_ADMIN_PASSWORD
export E2E_TESTS_PROXY_HOST=$(_runtime_ "proxy" "localhost")
export E2E_TESTS_PROXY_PORT=$(_runtime_ "8080" "10443")
export E2E_TESTS_SDA_DOA_HOST=$(_runtime_ "doa" "localhost")
export E2E_TESTS_SDA_DOA_PORT=$(_runtime_ "8080" "80")
export E2E_TESTS_CEGAMQ_CONN_STR="amqps://$CEGAMQ_USERNAME:$CEGAMQ_PASSWORD@$(_runtime_ $CEGAMQ_HOST "localhost"):$CEGAMQ_PORT/$CEGAMQ_VHOST"
export E2E_TESTS_CEGAAUTH_USERNAME=$CEGAAUTH_CEGA_USERS_USER
export E2E_TESTS_CEGAAUTH_PASSWORD=$CEGAAUTH_CEGA_USERS_PASSWORD
export E2E_TESTS_SDA_DB_HOST=$(_runtime_ "$DB_HOST" "localhost")
export E2E_TESTS_SDA_DB_PORT=$DB_PORT
export E2E_TESTS_SDA_DB_USERNAME=$DB_POSTGRES_USER
export E2E_TESTS_SDA_DB_PASSWORD=$DB_POSTGRES_PASSWORD
export E2E_TESTS_SDA_DB_DATABASE_NAME=$DB_POSTGRES_DB
export E2E_TESTS_TRUSTSTORE_PASSWORD=$KEYTOOL_TRUSTSTORE_PASSWORD
export E2E_TESTS_PROXY_TOKEN_AUDIENCE=$PROXY_TOKEN_AUDIENCE
export E2E_TESTS_PROXY_ADMIN_USERNAME=$PROXY_ADMIN_USER
export E2E_TESTS_PROXY_ADMIN_PASSWORD=$PROXY_ADMIN_PASSWORD

# New configs introduced for EGA DEV testing
# export E2E_TESTS_EGA_DEV_BASE_DIRECTORY=
# export E2E_TESTS_EGA_DEV_PUBLIC_KEY_FILENAME=
# export E2E_TESTS_LSAAI_TOKEN=
68 changes: 68 additions & 0 deletions e2eTests/src/test/java/no/elixir/e2eTests/EgaDevIntegrationTest.java
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@@ -0,0 +1,68 @@
package no.elixir.e2eTests;

import no.elixir.e2eTests.core.BaseE2ETest;
import no.elixir.e2eTests.features.*;
import no.elixir.e2eTests.utils.CommonUtils;
import org.junit.jupiter.api.*;

@TestMethodOrder(MethodOrderer.OrderAnnotation.class)
public class EgaDevIntegrationTest {

@BeforeAll
static void setup() throws Exception {
BaseE2ETest.setupEgaDevTestEnvironment();
}

@AfterAll
static void cleanup() {
BaseE2ETest.cleanupTestEnvironment();
}

@Test
@Order(1)
void UploadTest() throws Exception {
UploadTest.uploadThroughProxy();
// Wait for triggers to be set up at CEGA.
// Not really needed if using local CEGA container.
CommonUtils.waitForProcessing(5000);
}

@Test
@Order(2)
void IngestTest() throws Exception {
IngestTest.publishIngestionMessageToCEGA();
// Wait for the LEGA ingest and verify services
// to complete and update DB.
CommonUtils.waitForProcessing(5000);
}

@Test
@Order(3)
void AccessionTest() throws Exception {
AccessionTest.publishAccessionMessageOnBehalfOfCEGAToLocalEGA();
// Wait for LEGA finalize service to complete and update DB.
CommonUtils.waitForProcessing(5000);
}

@Test
@Order(4)
void MappingTest() throws Exception {
MappingTest.triggerMappingMessageFromCEGA();
// Wait for LEGA mapper service to store mapping
CommonUtils.waitForProcessing(1000);
}

@Test
@Order(5)
void ReleaseTest() throws Exception {
ReleaseTest.triggerReleaseMessageFromCEGA();
// Wait for LEGA mapper service to update dataset status
CommonUtils.waitForProcessing(1000);
}

@Test
@Order(6)
void DownloadTest() throws Exception {
DownloadWithExportRequestTest.testDownloadDatasetUsingFegaExportRequestAndVerifyResults();
}
}
77 changes: 77 additions & 0 deletions e2eTests/src/test/java/no/elixir/e2eTests/TokenUtilsTest.java
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@@ -0,0 +1,77 @@
package no.elixir.e2eTests;

import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;

import java.io.File;
import java.nio.charset.StandardCharsets;
import java.nio.file.Path;
import java.security.interfaces.RSAPrivateKey;
import java.security.interfaces.RSAPublicKey;
import no.elixir.e2eTests.utils.TokenUtils;
import org.apache.commons.io.FileUtils;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.io.TempDir;

public class TokenUtilsTest {

@TempDir Path tempDir;

@Test
void testPKCS1PrivateKey() throws Exception {
String pkcs1PrivateKey =
"""
-----BEGIN RSA PRIVATE KEY-----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-----END RSA PRIVATE KEY-----
""";
String publicKey =
"""
-----BEGIN PUBLIC KEY-----
MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAsn+9in5AY3xOauxYljtW
FocBEg/SVgTdGDQc/zLPHv2cwPeT8sidSRofN0UTDH6logNmf5drZlpBUPNFE4lZ
24DlLbPZzD1K+ubLAWAHEYUVaDz7DjiVj5bBQUYMRqPXaz1/tfA5IMXfrmPCqhO2
r+6OEXt6C9konsBRGNnGvfSCU8pPVMxe3OSBz8f57OHjBa5ryZfEBrAFLAB09s3o
icbvrfcUjVRxFjUiUW8tHv+gSPVM8RDxpknwAvBDZ7kr0/xyIbRuNyuLQ7YQoPKf
1M25EXqTR6uNaoHrJR9wX1T2757LIeVjKBiGzNYBTqV8xEd1Ht2jfzAvKYbdcugl
qQIDAQAB
-----END PUBLIC KEY-----
""";
// Write keys to temp files
File privKeyFile = new File(tempDir.toFile(), "pkcs1_private.pem");
File pubKeyFile = new File(tempDir.toFile(), "pkcs1_public.pem");
FileUtils.writeStringToFile(privKeyFile, pkcs1PrivateKey, StandardCharsets.UTF_8);
FileUtils.writeStringToFile(pubKeyFile, publicKey, StandardCharsets.UTF_8);
// Test loading PKCS#1 key (should be handled by BouncyCastle)
RSAPrivateKey privateKey = TokenUtils.getPrivateKey(privKeyFile.getAbsolutePath());
RSAPublicKey publicKey1 = TokenUtils.getPublicKey(pubKeyFile.getAbsolutePath());
assertNotNull(privateKey);
assertNotNull(publicKey1);
assertEquals("RSA", privateKey.getAlgorithm());
assertEquals("RSA", publicKey1.getAlgorithm());
}
}
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