Merge pull request #120 from overture-stack/rc/0.14.0

Release 0.14.0
refactor to run in server mode with custom domain
fix port -1 in ego and song swaggers
upgrade maestro to fix the elasticsearch exception
fix ego health check in server mode

README.md

@@ -31,6 +31,11 @@ docker exec -it $(docker service ps ego-db --no-trunc --format '{{ .Name }}.{{.I
 11. Run `make start-transfer-shell`. This will automatically run the `genomic-transfer-helper` and load the contents of `jwt.txt` as the JWT to allow authorized access to song and score.
 12. Once logged into the container, you can use the score and song clients. Run `./song-client/bin/sing ping` and `curl $(curl -sL http://score-api:8080/download/ping)` to do a health check.
 
+## Gateway
+The gateway is based on nginx.
+the config template file is under ./nginx/path-based, there is also a docker file
+tagging the gateway is done in Jenkinsfile, it will always have a new tag with the same version as the dms version.
+
 ## Tips
 ### Checking for OOM messages when a container/service is killed
 Sometimes, if the reserved/limit memory is too low, a container will get killed by the kernel. To find out if this is the case, run

pom.xml

@@ -10,7 +10,7 @@
 	</parent>
 	<groupId>bio.overture</groupId>
 	<artifactId>dms</artifactId>
-  	<version>0.13.1</version>
+  	<version>0.14.0</version>
 	<name>dms</name>
 	<description>Overture Data Management System</description>
 

src/main/java/bio/overture/dms/cli/questionnaire/DmsQuestionnaire.java

@@ -74,12 +74,12 @@ public DmsConfig buildDmsConfig() {
             .getAnswer();
 
     GatewayConfig gatewayConfig = null;
-    URL dmsGatewayUrl = new URL("http://localhost:80");
+    URL dmsGatewayUrl;
     int gatewayPort = 80;
     if (clusterRunMode == SERVER) {
       dmsGatewayUrl =
           questionFactory
-              .newUrlSingleQuestion("What is the base DMS Gateway URL (example: dms.cancercollaboratory.org)?",
+              .newUrlSingleQuestion("What is the base DMS Gateway URL (example: http://dms.cancercollaboratory.org)?",
                   false,
                   null
               ).getAnswer();

src/main/java/bio/overture/dms/compose/deployment/ego/EgoHelper.java

@@ -76,16 +76,8 @@ public void waitForEgoApiHealthy(ClusterRunModes clusterRunMode, EgoConfig egoCo
             .restClientFactory(basicRestClientFactory)
             .build();
 
-    EgoClient egoClient = null;
-    if (clusterRunMode == LOCAL) {
-      egoClient =
+    EgoClient egoClient =
           egoClientFactory2.buildNoAuthEgoClient(getLocalEgoApiUrl(egoConfig.getApi()).toString());
-    } else if (clusterRunMode == SERVER) {
-      egoClient = egoClientFactory2.buildNoAuthEgoClient(egoConfig.getApi().getUrl().toString());
-    } else {
-      throw buildIllegalStateException(
-          "The clusterRunMode '%s' could not be processed", clusterRunMode);
-    }
 
     // Attempt to get the public key several times
     Failsafe.with(RETRY_POLICY).get(egoClient::getPublicKey);

src/main/java/bio/overture/dms/compose/deployment/score/ScoreApiDeployer.java

@@ -99,15 +99,7 @@ private void provisionS3Buckets(ClusterRunModes clusterRunMode, ScoreConfig scor
 
   @SneakyThrows
   private URI resolveS3Endpoint(ClusterRunModes clusterRunMode, ScoreS3Config scoreS3Config) {
-    if (clusterRunMode == SERVER) {
-      return scoreS3Config.getUrl().toURI();
-    } else if (clusterRunMode == LOCAL) {
-      return resolveS3LocalUrl(scoreS3Config);
-    } else {
-      throw new IllegalStateException(
-          format(
-              "The clusterRunMode '%s' is unknown and cannot be processed", clusterRunMode.name()));
-    }
+    return resolveS3LocalUrl(scoreS3Config);
   }
 
   @SneakyThrows

src/main/resources/templates/servicespec/ego-api.yaml.vm

@@ -15,12 +15,14 @@ TaskTemplate:
     - DEFAULT_USER_FIRSTUSERASADMIN=true
     - SPRING_DATASOURCE_PASSWORD=$dmsConfig.ego.db.databasePassword
     - SPRING_DATASOURCE_URL=jdbc:postgresql://${composeServiceResources.EGO_DB.toString()}:5432/ego?stringtype=unspecified
+#if($dmsConfig.ego.api.url.port > 0)
     - SWAGGER_HOST=$dmsConfig.ego.api.url.host:$dmsConfig.ego.api.url.port
+#else
+    - SWAGGER_HOST=$dmsConfig.ego.api.url.host
+#end
     - SWAGGER_BASEURL=#if($dmsConfig.ego.api.url.path == '')/#{else}$dmsConfig.ego.api.url.path#end
-#if( $dmsConfig.clusterRunMode == 'LOCAL')
     - LOGIN_NONCE_SECURE=false
     - LOGIN_NONCE_SAMESITE=lax
-#end
     - INITIALIZATION_ENABLED=true
     - INITIALIZATION_APPLICATIONS_0_NAME=$dmsConfig.ego.api.dmsAppCredential.name
     - INITIALIZATION_APPLICATIONS_0_TYPE=ADMIN

src/main/resources/templates/servicespec/gateway.yaml.vm

@@ -5,7 +5,6 @@
 Name: gateway
 TaskTemplate:
   ContainerSpec:
-    # todo change this to point to a version
     Image: "ghcr.io/overture-stack/dms-gateway:0.13.0"
     Env:
       - NGINX_PORT=80

src/main/resources/templates/servicespec/maestro.yaml.vm

@@ -5,7 +5,7 @@
 Name: maestro
 TaskTemplate:
   ContainerSpec:
-    Image: "ghcr.io/overture-stack/maestro:3.8.0-993b837"
+    Image: "ghcr.io/overture-stack/maestro:3.8.0"
     Env:
     - management.health.elasticsearch.enabled=false
     - MAESTRO.ELASTICSEARCH.CLUSTERNODES=${composeServiceResources.ELASTICSEARCH.toString()}:9200
@@ -20,7 +20,6 @@ TaskTemplate:
     - SPRING_CODEC_MAXINMEMORYSIZE=-1
     - MAESTRO_REPOSITORIES_0_ORGANIZATION=local_song_organization
     - MAESTRO_REPOSITORIES_0_COUNTRY=local_song_country
-    #- springdoc.api-docs.path=/v3/api-docs
     - springdoc.swagger-ui.url=/maestro/v3/api-docs
     - springdoc.webjars.prefix=/maestro/webjars
     - springdoc.swagger-ui.path=/api-docs

src/main/resources/templates/servicespec/song-api.yaml.vm

@@ -23,7 +23,11 @@ TaskTemplate:
       - AUTH_SERVER_SCOPE_SYSTEM=SONG.WRITE
       - AUTH_JWT_PUBLICKEYURL=http://${composeServiceResources.EGO_API.toString()}:8080/oauth/token/public_key
       - ID_USELOCAL=true
+#if($dmsConfig.song.api.url.port > 0)
       - SWAGGER_HOST=$dmsConfig.song.api.url.host:$dmsConfig.song.api.url.port
+#else
+      - SWAGGER_HOST=$dmsConfig.song.api.url.host
+#end
       - SWAGGER_BASEPATH=#if($dmsConfig.song.api.url.path == '')/#{else}$dmsConfig.song.api.url.path#end
       - SCORE_URL=http://${composeServiceResources.SCORE_API.toString()}:8080
       - SCORE_CLIENTCREDENTIALS_ID=$dmsConfig.song.api.appCredential.clientId