Changes related to integration test

ega-data-api-commons/src/main/java/eu/elixir/ega/ebi/commons/config/MyAccessTokenConverter.java

@@ -228,6 +228,20 @@ public class MyAccessTokenConverter implements AccessTokenConverter {
                         .orElse(""));
     }
 
+    private Map<String, List<String>> getDatasetFileMap(final List<String> ga4ghDatasets) {
+        return ga4ghDatasets
+                .parallelStream()
+                .map(jwtService::parse)
+                .filter(Optional::isPresent)
+                .map(Optional::get)
+                .filter(jwtService::isValidSignature)
+                .filter(this::isValidToken)
+                .map(this::getDatasetId)
+                .filter(Optional::isPresent)
+                .map(Optional::get)
+                .collect(toMap(datasetId -> datasetId, fileDatasetService::getFileIds));
+    }
+
     private boolean isValidToken(final SignedJWT signedJWT) {
         try {
             return new Date(currentTimeMillis())
@@ -253,20 +267,6 @@ public class MyAccessTokenConverter implements AccessTokenConverter {
         return empty();
     }
 
-    private Map<String, List<String>> getDatasetFileMap(final List<String> ga4ghDatasets) {
-        return ga4ghDatasets
-                .parallelStream()
-                .map(jwtService::parse)
-                .filter(Optional::isPresent)
-                .map(Optional::get)
-                .filter(jwtService::isValidSignature)
-                .filter(this::isValidToken)
-                .map(this::getDatasetId)
-                .filter(Optional::isPresent)
-                .map(Optional::get)
-                .collect(toMap(datasetId -> datasetId, fileDatasetService::getFileIds));
-    }
-
     /**
      * Extracts the authentication audience (held in the 'AUD' key) from the
      * given authentication map.

ega-data-api-dataedge/src/main/java/eu/elixir/ega/ebi/dataedge/config/DataEdgeConfig.java

@@ -17,6 +17,11 @@
  */
 package eu.elixir.ega.ebi.dataedge.config;
 
+import com.nimbusds.jose.jwk.JWKSet;
+import eu.elixir.ega.ebi.commons.config.CachingMultipleRemoteTokenService;
+import eu.elixir.ega.ebi.commons.config.CachingRemoteTokenService;
+import eu.elixir.ega.ebi.commons.config.MyAccessTokenConverter;
+import eu.elixir.ega.ebi.commons.config.MyUserAuthenticationConverter;
 import eu.elixir.ega.ebi.commons.shared.service.FileDatasetService;
 import eu.elixir.ega.ebi.commons.shared.service.Ga4ghService;
 import eu.elixir.ega.ebi.commons.shared.service.JWTService;
@@ -28,11 +33,20 @@ import eu.elixir.ega.ebi.commons.shared.service.internal.UserDetailsServiceImpl;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Primary;
+import org.springframework.context.annotation.Profile;
+import org.springframework.core.annotation.Order;
 import org.springframework.core.task.TaskExecutor;
 import org.springframework.scheduling.annotation.EnableAsync;
 import org.springframework.scheduling.concurrent.ThreadPoolTaskExecutor;
+import org.springframework.security.oauth2.provider.token.AccessTokenConverter;
+import org.springframework.security.oauth2.provider.token.RemoteTokenServices;
 import org.springframework.web.client.RestTemplate;
+import org.springframework.web.cors.CorsConfiguration;
+import org.springframework.web.cors.UrlBasedCorsConfigurationSource;
+import org.springframework.web.filter.CorsFilter;
 
+import javax.servlet.http.HttpServletRequest;
 import java.io.IOException;
 import java.net.MalformedURLException;
 import java.net.URISyntaxException;
@@ -67,6 +81,7 @@ public class DataEdgeConfig {
         );
     }
 
+    @Profile("!integration-test")
     @Bean
     public JWTService initJWTServiceImpl(@Value("${ega.aai.public.jwk.url}") final String jwkPublicKeyURL,
                                          @Value("${ega.aai.public.jwk.connection-timeout}") final int connectTimeout,
@@ -83,6 +98,12 @@ public class DataEdgeConfig {
                 keyId);
     }
 
+    @Profile("integration-test")
+    @Bean
+    public JWTService initJWTServiceImplIntegrationTest() {
+        return new JWTServiceImpl(new JWKSet(), "rsa1");
+    }
+
     @Bean
     public FileDatasetService initFileDatasetServiceImpl(final RestTemplate restTemplate) {
         return new FileDatasetServiceImpl(restTemplate);
@@ -92,4 +113,90 @@ public class DataEdgeConfig {
     public UserDetailsService initUserDetailsServiceImpl(final RestTemplate restTemplate) {
         return new UserDetailsServiceImpl(restTemplate);
     }
+
+    /**
+     * This is a bit of a Hack! MitreID doesn't return 'user_name' but 'user_id',
+     * The customized User Authentication Converter simply changes the field name
+     * for extraction.
+     *
+     * @return The converted access token
+     */
+    @Bean
+    public AccessTokenConverter accessTokenConverter(final JWTService jwtService,
+                                                     final Ga4ghService ga4ghService,
+                                                     final FileDatasetService fileDatasetService,
+                                                     final UserDetailsService userDetailsService) {
+        return new MyAccessTokenConverter(
+                jwtService,
+                ga4ghService,
+                fileDatasetService,
+                new MyUserAuthenticationConverter(),
+                userDetailsService
+        );
+    }
+
+    /**
+     * Creates a combined token service including both EGA AAI and Elixir AAI
+     * authentication.
+     *
+     * @param request Unused
+     * @param checkTokenUrl EGA AAI token endpoint url
+     * @param clientId Client id for the EGA AAI
+     * @param clientSecret Client secret for the EGA AAI
+     * @param zuulCheckTokenUrl Elixir token endpoint url
+     * @param zuulClientId Elixir AAI ID
+     * @param zuulClientSecret Elixir AAI client
+     *
+     * @return A combined authentication token service
+     */
+    @Profile("enable-aai")
+    @Primary
+    @Bean
+    public RemoteTokenServices remoteTokenServices(HttpServletRequest request,
+                                                   final @Value("${auth.server.url}") String checkTokenUrl,
+                                                   final @Value("${auth.server.clientId}") String clientId,
+                                                   final @Value("${auth.server.clientsecret}") String clientSecret,
+                                                   final @Value("${auth.zuul.server.url}") String zuulCheckTokenUrl,
+                                                   final @Value("${auth.zuul.server.clientId}") String zuulClientId,
+                                                   final @Value("${auth.zuul.server.clientsecret}") String zuulClientSecret,
+                                                   final AccessTokenConverter accessTokenConverter) {
+
+        final CachingMultipleRemoteTokenService remoteTokenServices = new CachingMultipleRemoteTokenService();
+
+        // EGA AAI
+        CachingRemoteTokenService b = new CachingRemoteTokenService();
+        b.setCheckTokenEndpointUrl(checkTokenUrl);
+        b.setClientId(clientId);
+        b.setClientSecret(clientSecret);
+        b.setAccessTokenConverter(accessTokenConverter);
+        remoteTokenServices.addRemoteTokenService(b);
+
+        // ELIXIR AAI
+        CachingRemoteTokenService a = new CachingRemoteTokenService();
+        a.setCheckTokenEndpointUrl(zuulCheckTokenUrl);
+        a.setClientId(zuulClientId);
+        a.setClientSecret(zuulClientSecret);
+        a.setAccessTokenConverter(accessTokenConverter);
+        remoteTokenServices.addRemoteTokenService(a);
+
+        return remoteTokenServices;
+    }
+
+    /**
+     * Sets CORS headers to allow all methods and all hosts.
+     *
+     * @return CORSfilter
+     */
+    @Bean
+    @Order(0)
+    public CorsFilter corsFilter() {
+        UrlBasedCorsConfigurationSource source = new UrlBasedCorsConfigurationSource();
+        CorsConfiguration config = new CorsConfiguration();
+        config.setAllowCredentials(true);
+        config.addAllowedOrigin("*");
+        config.addAllowedHeader("*");
+        config.addAllowedMethod("*");
+        source.registerCorsConfiguration("/**", config);
+        return new CorsFilter(source);
+    }
 }

ega-data-api-dataedge/src/main/java/eu/elixir/ega/ebi/dataedge/config/OAuth2ResourceConfig.java

@@ -109,91 +109,4 @@ public class OAuth2ResourceConfig extends ResourceServerConfigurerAdapter {
                 .and()
                 .csrf().disable();
     }
-
-    /**
-     * This is a bit of a Hack! MitreID doesn't return 'user_name' but 'user_id',
-     * The customized User Authentication Converter simply changes the field name
-     * for extraction.
-     *
-     * @return The converted access token
-     */
-    @Bean
-    public AccessTokenConverter accessTokenConverter(final JWTService jwtService,
-                                                     final Ga4ghService ga4ghService,
-                                                     final FileDatasetService fileDatasetService,
-                                                     final UserDetailsService userDetailsService) {
-        return new MyAccessTokenConverter(
-                jwtService,
-                ga4ghService,
-                fileDatasetService,
-                new MyUserAuthenticationConverter(),
-                userDetailsService
-        );
-    }
-
-    /**
-     * Creates a combined token service including both EGA AAI and Elixir AAI
-     * authentication.
-     *
-     * @param request Unused
-     * @param checkTokenUrl EGA AAI token endpoint url
-     * @param clientId Client id for the EGA AAI
-     * @param clientSecret Client secret for the EGA AAI
-     * @param zuulCheckTokenUrl Elixir token endpoint url
-     * @param zuulClientId Elixir AAI ID
-     * @param zuulClientSecret Elixir AAI client
-     *
-     * @return A combined authentication token service
-     */
-    @Profile("enable-aai")
-    @Primary
-    @Bean
-    public RemoteTokenServices remoteTokenServices(HttpServletRequest request,
-                                                   final @Value("${auth.server.url}") String checkTokenUrl,
-                                                   final @Value("${auth.server.clientId}") String clientId,
-                                                   final @Value("${auth.server.clientsecret}") String clientSecret,
-                                                   final @Value("${auth.zuul.server.url}") String zuulCheckTokenUrl,
-                                                   final @Value("${auth.zuul.server.clientId}") String zuulClientId,
-                                                   final @Value("${auth.zuul.server.clientsecret}") String zuulClientSecret,
-                                                   final AccessTokenConverter accessTokenConverter) {
-
-        final CachingMultipleRemoteTokenService remoteTokenServices = new CachingMultipleRemoteTokenService();
-
-        // EGA AAI
-        CachingRemoteTokenService b = new CachingRemoteTokenService();
-        b.setCheckTokenEndpointUrl(checkTokenUrl);
-        b.setClientId(clientId);
-        b.setClientSecret(clientSecret);
-        b.setAccessTokenConverter(accessTokenConverter);
-        remoteTokenServices.addRemoteTokenService(b);
-
-        // ELIXIR AAI
-        CachingRemoteTokenService a = new CachingRemoteTokenService();
-        a.setCheckTokenEndpointUrl(zuulCheckTokenUrl);
-        a.setClientId(zuulClientId);
-        a.setClientSecret(zuulClientSecret);
-        a.setAccessTokenConverter(accessTokenConverter);
-        remoteTokenServices.addRemoteTokenService(a);
-
-        return remoteTokenServices;
-    }
-
-    /**
-     * Sets CORS headers to allow all methods and all hosts.
-     *
-     * @return CORSfilter
-     */
-    @Bean
-    @Order(0)
-    public CorsFilter corsFilter() {
-        UrlBasedCorsConfigurationSource source = new UrlBasedCorsConfigurationSource();
-        CorsConfiguration config = new CorsConfiguration();
-        config.setAllowCredentials(true);
-        config.addAllowedOrigin("*");
-        config.addAllowedHeader("*");
-        config.addAllowedMethod("*");
-        source.registerCorsConfiguration("/**", config);
-        return new CorsFilter(source);
-    }
-
 }

ega-data-api-dataedge/src/main/resources/application.yml

@@ -22,6 +22,9 @@ RES2:
 KEYSERVER:
   listOfServers: ${KEYS_SERVERS:keys}
 
+PERMISSIONSDATABASESERVER:
+  listOfServers: ${PERMISSIONS_DATABASE_SERVER:data}
+
 
 ega.ega.external.url:
 ega.ega.cram.fasta.a:
@@ -45,4 +48,8 @@ res:
     chunksize:
       header: 4096
       data: 20971520
-      index: 1048576
\ No newline at end of file
+      index: 1048576
+
+# EGA AAI proxy config
+ega.aai.proxy.url:
+ega.aai.proxy.basic-authorization:

extras/docker-compose.yml

@@ -6,12 +6,13 @@ services:
       - "9058:9058"
       - "5059:5059"
     environment:
-      - SPRING_PROFILES_ACTIVE=no-oss,LocalEGA
+      - SPRING_PROFILES_ACTIVE=no-oss,LocalEGA,integration-test
       - server.port=9058
       - JWTKEY=${JWTKEY}
       - FILEDATABASE.listOfServers=filedatabase:9051
       - RES2.listOfServers=resserver:9092
       - KEYSERVER.listOfServers=keyserver:9095
+      - PERMISSIONSDATABASESERVER.listOfServers=dataserver:9054
       - ega.ega.external.url=https://ega.ebi.ac.uk:8051/elixir/data/files/
       - ega.ega.cram.fasta=/homes/ega-prod/ngs_dev/Homo_sapiens_assembly38.fasta
       - ega.ega.cram.fasta.a=/homes/ega-prod/ngs_dev/Homo_sapiens_assembly38.fasta 
@@ -19,6 +20,9 @@ services:
       - ega.internal.filedatabase.url=https://FILEDATABASE
       - ega.internal.res.url=https://RES2
       - ega.internal.key.url=https://KEYSERVER
+      - ega.aai.proxy.url=https://ega.ebi.ac.uk:8053/ega-openid-connect-server
+      - ega.aai.proxy.basic-authorization=test-auth
+      - ega.internal.data.url=http://PERMISSIONSDATABASE
     volumes:
       - "$TRAVIS_BUILD_DIR/extras/certificate/rootCA.pem:/etc/ssl/certs/ca-certificates.crt"   
       - "$TRAVIS_BUILD_DIR/extras/certificate/server.p12:/dataedge.p12"