Merge pull request #197 from overture-stack/develop

release 3.8.0
- add ability to customize server url in spring doc swagger to support reverse proxy rewrite path 
- ISO format dates in painless script to avoid date transformer issue in es rest client

.mvn/maven.config

@@ -1,3 +1,3 @@
--Drevision=3.7.0
+-Drevision=3.8.0
 -Dsha1=
 -Dchangelist=-SNAPSHOT

maestro-app/src/main/java/bio/overture/maestro/app/infra/adapter/outbound/indexing/elasticsearch/AnalysisCentricElasticSearchAdapter.java

@@ -15,6 +15,7 @@
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.fasterxml.jackson.databind.ObjectWriter;
 import com.fasterxml.jackson.databind.PropertyNamingStrategy;
+import com.fasterxml.jackson.databind.util.StdDateFormat;
 import io.github.resilience4j.retry.Retry;
 import io.github.resilience4j.retry.RetryConfig;
 import java.io.IOException;
@@ -146,16 +147,15 @@ private List<AnalysisCentricDocument> getAnalysisCentricDocuments(
   private UpdateRequest mapAnalysisToUpsertRepositoryQuery(
       AnalysisCentricDocument analysisCentricDocument) {
     val mapper = new ObjectMapper().setPropertyNamingStrategy(PropertyNamingStrategy.SNAKE_CASE);
-
     val paramsBuilder = new HashMap<String, Object>();
     paramsBuilder.put(
         "repository",
         mapper.convertValue(analysisCentricDocument.getRepositories().get(0), Map.class));
     paramsBuilder.put("analysis_state", analysisCentricDocument.getAnalysisState());
-    paramsBuilder.put("updated_at", analysisCentricDocument.getUpdatedAt());
+    paramsBuilder.put("updated_at", getDateIso(analysisCentricDocument.getUpdatedAt()));
     if (analysisCentricDocument.getPublishedAt()
         != null) { // Nullable as may not have been published
-      paramsBuilder.put("published_at", analysisCentricDocument.getPublishedAt());
+      paramsBuilder.put("published_at", getDateIso(analysisCentricDocument.getPublishedAt()));
     }
 
     val parameters = unmodifiableMap(paramsBuilder);

maestro-app/src/main/java/bio/overture/maestro/app/infra/adapter/outbound/indexing/elasticsearch/ElasticSearchConfig.java

@@ -72,7 +72,7 @@ CommandLineRunner analysisElasticsearchBootstrapper(AnalysisCentricElasticSearch
     return (args) -> adapter.initialize();
   }
 
-  @Bean
+  @Bean("ES_CLIENT")
   RestHighLevelClient client(ApplicationProperties properties) {
     val httpHostArrayList =
         new ArrayList<HttpHost>(

maestro-app/src/main/java/bio/overture/maestro/app/infra/adapter/outbound/indexing/elasticsearch/FileCentricElasticSearchAdapter.java

@@ -266,14 +266,21 @@ private List<FileCentricDocument> getFileCentricDocuments(
   private UpdateRequest mapFileToUpsertRepositoryQuery(FileCentricDocument fileCentricDocument) {
     val mapper = new ObjectMapper().setPropertyNamingStrategy(PropertyNamingStrategy.SNAKE_CASE);
 
+    // this ISO date format is added because in one instance where maestro was deployed
+    // an error to transform java.util.date was raised:
+    // cannot write time value xcontent for unknown value of type class java.util.Date
+    // there seem to be a class loader issue that cannot load the date transfomers in
+    // org.elasticsearch.common.xcontent.XContentBuilder
+    // root cause not found.
     val paramsBuilder = new HashMap<String, Object>();
     paramsBuilder.put(
         "repository", mapper.convertValue(fileCentricDocument.getRepositories().get(0), Map.class));
     paramsBuilder.put("analysis_state", fileCentricDocument.getAnalysis().getAnalysisState());
-    paramsBuilder.put("updated_at", fileCentricDocument.getAnalysis().getUpdatedAt());
+    paramsBuilder.put("updated_at", getDateIso(fileCentricDocument.getAnalysis().getUpdatedAt()));
     if (fileCentricDocument.getAnalysis().getPublishedAt()
         != null) { // Nullable as may not have been published
-      paramsBuilder.put("published_at", fileCentricDocument.getAnalysis().getPublishedAt());
+      paramsBuilder.put(
+          "published_at", getDateIso(fileCentricDocument.getAnalysis().getPublishedAt()));
     }
 
     val parameters = unmodifiableMap(paramsBuilder);

maestro-app/src/main/java/bio/overture/maestro/app/infra/adapter/outbound/indexing/elasticsearch/SearchAdapterHelper.java

@@ -7,6 +7,8 @@
 import io.github.resilience4j.retry.RetryConfig;
 import io.vavr.control.Try;
 import java.io.IOException;
+import java.text.DateFormat;
+import java.text.SimpleDateFormat;
 import java.time.Duration;
 import java.util.*;
 import java.util.function.Function;
@@ -234,4 +236,11 @@ private static UpdateRequest prepareUpdate(UpdateRequest req) {
     Assert.notNull(req.id(), "No Id define for Query");
     return req;
   }
+
+  static String getDateIso(Date date)
+  {
+    DateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss.SSS'Z'");
+    dateFormat.setTimeZone(TimeZone.getTimeZone("UTC"));
+    return dateFormat.format(date);
+  }
 }

maestro-app/src/main/java/bio/overture/maestro/app/infra/config/RootConfiguration.java

@@ -29,12 +29,18 @@
 import bio.overture.maestro.app.infra.config.properties.PropertiesConfig;
 import bio.overture.maestro.domain.api.DomainApiConfig;
 import com.fasterxml.jackson.databind.ObjectMapper;
+import io.swagger.v3.oas.models.OpenAPI;
+import io.swagger.v3.oas.models.servers.Server;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Import;
 import org.springframework.context.annotation.Primary;
 import org.springframework.web.reactive.function.client.WebClient;
 
+import java.util.List;
+
 /** Aggregates all configuration in one place */
 @Configuration
 @Import({
@@ -97,4 +103,12 @@ class WebConfig {
   public ObjectMapper objectMapper() {
     return new ObjectMapper();
   }
+
+  @Bean
+  @ConditionalOnProperty(name = "springdoc.serverOverride.enabled", havingValue = "true")
+  public OpenAPI maestroOpenApi(@Value("${springdoc.serverOverride.value}") String serverOverride) {
+    return new OpenAPI()
+        .servers(List.of(new Server().url(serverOverride)));
+  }
+
 }

maestro-app/src/main/resources/config/application.yml

@@ -172,5 +172,13 @@ spring:
             maxAttempts: 1
 
 springdoc:
+  ## The reason this was added to support reverse proxy url rewrites like: http://xyz.com/maestro
+  ## otherwise the swagger urls will not be sent to the correct url since swagger ui depends
+  ## on the server definition and springdoc needs forward headers to be enabled by spring
+  ## enabling forward headers in maestro caused it to conflict with disabling kafka
+  ## and forced an autoconfigure for kafka client.
+  serverOverride:
+    enabled: false
+    value: http://localhost:11235/custom
   swagger-ui:
-    path: /api-docs
+    path: /api-docs