feat: e2e test suite for ega-dev env

Author: yasinmiran

e2eTests/build.gradle.kts

@@ -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.

e2eTests/docker-compose.template.yml

@@ -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
@@ -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
 

e2eTests/e2e-tests.Dockerfile

@@ -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"]

e2eTests/entrypoint.sh

@@ -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

e2eTests/env.sh

@@ -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=

e2eTests/src/test/java/no/elixir/e2eTests/EgaDevIntegrationTest.java

@@ -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();
+  }
+}

e2eTests/src/test/java/no/elixir/e2eTests/TokenUtilsTest.java

@@ -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-----
+                MIIEowIBAAKCAQEAsn+9in5AY3xOauxYljtWFocBEg/SVgTdGDQc/zLPHv2cwPeT
+                8sidSRofN0UTDH6logNmf5drZlpBUPNFE4lZ24DlLbPZzD1K+ubLAWAHEYUVaDz7
+                DjiVj5bBQUYMRqPXaz1/tfA5IMXfrmPCqhO2r+6OEXt6C9konsBRGNnGvfSCU8pP
+                VMxe3OSBz8f57OHjBa5ryZfEBrAFLAB09s3oicbvrfcUjVRxFjUiUW8tHv+gSPVM
+                8RDxpknwAvBDZ7kr0/xyIbRuNyuLQ7YQoPKf1M25EXqTR6uNaoHrJR9wX1T2757L
+                IeVjKBiGzNYBTqV8xEd1Ht2jfzAvKYbdcuglqQIDAQABAoIBAGj/uWg5QfkDi0Fc
+                S/P7bXWM7rVIN0tASypMpW383ld1ifr857ueBN+WjRw+9qiX6yi1ZVrSoGux1dAf
+                ede3KPN1C9rpe8mnmG6kym/BpAbLST9q96dy4492d7HE2b3H7RT5NSG58HD11NFJ
+                f536QLGW210vTCiiEkHoEQxUNpNPv/Fy+jRxl7TT/i+8wW60xBK0aDcfDNgNVsRq
+                yiCmfoHzbdDJy+4vaBhnB0UH6zPJlNjFNX1187TBZoh9ysN2+FBUfWQDkTHafB+A
+                frLNvnzdkNlbx6ZLEeEZHZYmBslPIG9bv5TMlZJofhInOK+5ep+HkWDlR/hXMWtC
+                er6Wcl0CgYEA5/W5Oudk4Rk1PeHYvtnRxEI7aDFJJcxL99M1iADysPGDCyw/ndDy
+                yX55DcIKmuw2SyPQhTLbkVdBorinKP2gO7dn6bVXUJro/TQnllnwh627CY2sLXEO
+                E3H2OkxcGD0FMLxfvOVSgYJVIBRmWoXA7i0yVykmdY8pUuRTnQVEYZsCgYEAxP+c
+                rFV5GdxxTxL2bZDwo4Zi3WADa7Fa6nqaSV4ORnyRYEq1eTg0pKORPNWujv/lChdZ
+                0sFXBCIU8ZCewgwApfRfegsL9BPbxcggbCM9PWU8H+MHEXg4ticyEm2MGGVQvSHy
+                SoyT+za0y6VczoJGqzsW8Zxy5vPdLDFpenkRHAsCgYB22w0fpqOlR9JlNA1otZnr
+                s3hXSjHOAWHHydy7JKk2i3n3RqQOTJurLXf/2bavbWvgkqhtKAMj9Q73vyBAO71X
+                /AFt2nK0JbxOyeOjAdDi5N1a5tIbsrtgsVtWwfvKm7HGKC/yTZs6KztNJcbQiYqz
+                QEt0J+zB/ipRhBdn9OP2EwKBgQCHwYrLa/+PZc2j63Js4QQj/Jkm62KQFWGM0r5+
+                LtXxlyhrzjAvAB+vEZUl8i9gFlJVWPAqf9giXgZGzh3JpZHQy438QZ6ULhc2vgox
+                2zr5k0kSxFX7oPib9njYICv6J9+y5rDc1PGpnfKLoEJLgZWHrKnMCL9aDtXs/YQt
+                xT6YLwKBgB2TBL6Z0kajrw77RTG5WPANGUEYLrDkfq5LPQcwJ/4rs56nUuW1jeeH
+                GVe1YDAIWEoCxYS/sRg8SuTxF1AZQ4rgeNZLJzgBepOQmie4tySlJYkoww7YvCwP
+                a/SdoUL52S2+Gl2N6qbgRaCvVKj5v8yStfMeFLzWcVxdlAnhZew1
+                -----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());
+  }
+}