TSPS-86 - connecting to leonardo client (#40)

* add logic to connect to Leonardo java client
* reorganize app and test folders
* add PR readme template

---------

Co-authored-by: Jose Soto <[email protected]>

README.md

@@ -104,4 +104,4 @@ The two tasks `report-to-sherlock` and `set-version-in-dev` will prompt Sherlock
 You can check the status of the deployment in [Beehive](https://beehive.dsp-devops.broadinstitute.org/apps/tsps) and in 
 [ArgoCD](https://ap-argocd.dsp-devops.broadinstitute.org/applications/ap-argocd/tsps-dev).
 
-For more information about deployment to dev, check out DevOps' [excellent documentation](https://docs.google.com/document/d/1lkUkN2KOpHKWufaqw_RIE7EN3vN4G2xMnYBU83gi8VA/).
+For more information about deployment to dev, check out DevOps' [excellent documentation](https://docs.google.com/document/d/1lkUkN2KOpHKWufaqw_RIE7EN3vN4G2xMnYBU83gi8VA/).

pull_request_template.md

@@ -0,0 +1,5 @@
+### Description 
+
+_Please replace this description with a concise description of this Pull Request._
+
+### Jira Ticket

service/build.gradle

@@ -35,9 +35,10 @@ dependencies {
     implementation 'org.apache.commons:commons-dbcp2:2.9.0'
     implementation 'org.springframework.boot:spring-boot-starter-data-jpa:2.7.0'
     implementation 'org.springframework.boot:spring-boot-starter-web:2.7.0'
-    implementation 'org.springframework.retry:spring-retry:1.3.3'
+    implementation 'org.springframework.retry:spring-retry:1.3.4'
 
     implementation 'org.broadinstitute.dsde.workbench:sam-client_2.12:0.1-61135c7'
+    implementation "org.broadinstitute.dsde.workbench:leonardo-client_2.13:1.3.6-66d9fcf"
     implementation 'javax.ws.rs:javax.ws.rs-api:2.1.1'
     implementation 'org.postgresql:postgresql:42.3.3'
     implementation 'javax.servlet:jstl:1.2'
@@ -65,6 +66,7 @@ dependencies {
         exclude group: 'com.vaadin.external.google', module: 'android-json'
     }
     testImplementation 'org.mockito:mockito-inline'
+    testImplementation 'org.apache.commons:commons-text:1.10.0'
 
     // dependencies for test containers
     testImplementation 'org.testcontainers:testcontainers:1.17.3'

service/src/main/java/bio/terra/pipelines/App.java

@@ -1,10 +1,6 @@
 package bio.terra.pipelines;
 
 import bio.terra.common.logging.LoggingInitializer;
-import com.fasterxml.jackson.databind.ObjectMapper;
-import com.fasterxml.jackson.datatype.jdk8.Jdk8Module;
-import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule;
-import com.fasterxml.jackson.module.paramnames.ParameterNamesModule;
 import javax.sql.DataSource;
 import org.springframework.boot.autoconfigure.SpringBootApplication;
 import org.springframework.boot.builder.SpringApplicationBuilder;
@@ -46,14 +42,6 @@ public App(DataSource dataSource) {
     this.dataSource = dataSource;
   }
 
-  @Bean("objectMapper")
-  public ObjectMapper objectMapper() {
-    return new ObjectMapper()
-        .registerModule(new ParameterNamesModule())
-        .registerModule(new Jdk8Module())
-        .registerModule(new JavaTimeModule());
-  }
-
   // This bean plus the @EnableTransactionManagement annotation above enables the use of the
   // @Transaction annotation to control the transaction properties of the data source.
   @Bean("transactionManager")

service/src/main/java/bio/terra/pipelines/app/StartupInitializer.java

@@ -1,7 +1,7 @@
 package bio.terra.pipelines.app;
 
 import bio.terra.common.migrate.LiquibaseMigrator;
-import bio.terra.pipelines.app.configuration.TspsDatabaseConfiguration;
+import bio.terra.pipelines.app.configuration.internal.TspsDatabaseConfiguration;
 import org.springframework.context.ApplicationContext;
 
 public final class StartupInitializer {

service/src/main/java/bio/terra/pipelines/app/configuration/external/LeonardoServerConfiguration.java

@@ -0,0 +1,44 @@
+package bio.terra.pipelines.app.configuration.external;
+
+import java.time.Duration;
+import java.util.List;
+import org.broadinstitute.dsde.workbench.client.leonardo.model.AppType;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.boot.context.properties.ConfigurationProperties;
+import org.springframework.boot.context.properties.ConstructorBinding;
+
+/**
+ * @param baseUri - Leonardo URI to send requests to
+ * @param wdsAppTypeNames - names used to signify what is the WDS app we want to use
+ * @param cbasAppTypeNames - names used to signify what is the cbas app we want to use
+ * @param dependencyUrlCacheTtl - how long (in seconds) to keep items in the cache
+ * @param debugApiLogging
+ */
+@ConfigurationProperties(prefix = "leonardo")
+public record LeonardoServerConfiguration(
+    String baseUri,
+    List<AppType> wdsAppTypeNames,
+    List<AppType> cbasAppTypeNames,
+    Duration dependencyUrlCacheTtl,
+    Boolean debugApiLogging) {
+
+  private static final Logger log = LoggerFactory.getLogger(LeonardoServerConfiguration.class);
+
+  @ConstructorBinding
+  public LeonardoServerConfiguration(
+      String baseUri,
+      List<String> wdsAppTypeNames,
+      List<String> cbasAppTypeNames,
+      long dependencyUrlCacheTtlSeconds,
+      Boolean debugApiLogging) {
+    this(
+        baseUri,
+        wdsAppTypeNames.stream().map(AppType::fromValue).toList(),
+        cbasAppTypeNames.stream().map(AppType::fromValue).toList(),
+        Duration.ofSeconds(dependencyUrlCacheTtlSeconds),
+        debugApiLogging);
+    log.info("Setting wdsAppTypes={}", wdsAppTypeNames);
+    log.info("Setting cbasAppTypeNames={}", cbasAppTypeNames);
+  }
+}

service/src/main/java/bio/terra/pipelines/config/SamConfiguration.java → service/src/main/java/bio/terra/pipelines/app/configuration/external/SamConfiguration.java

@@ -1,4 +1,4 @@
-package bio.terra.pipelines.config;
+package bio.terra.pipelines.app.configuration.external;
 
 import org.springframework.boot.context.properties.ConfigurationProperties;
 

service/src/main/java/bio/terra/pipelines/config/BeanConfig.java → service/src/main/java/bio/terra/pipelines/app/configuration/internal/BeanConfiguration.java

@@ -1,10 +1,8 @@
-package bio.terra.pipelines.config;
+package bio.terra.pipelines.app.configuration.internal;
 
-import com.fasterxml.jackson.annotation.JsonInclude;
-import com.fasterxml.jackson.databind.ObjectMapper;
-import com.fasterxml.jackson.datatype.jdk8.Jdk8Module;
-import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule;
-import com.fasterxml.jackson.module.paramnames.ParameterNamesModule;
+import bio.terra.common.iam.BearerToken;
+import bio.terra.common.iam.BearerTokenFactory;
+import javax.servlet.http.HttpServletRequest;
 import javax.sql.DataSource;
 import org.springframework.boot.context.properties.EnableConfigurationProperties;
 import org.springframework.context.annotation.Bean;
@@ -13,26 +11,30 @@
 import org.springframework.retry.annotation.EnableRetry;
 import org.springframework.transaction.PlatformTransactionManager;
 import org.springframework.transaction.annotation.EnableTransactionManagement;
+import org.springframework.web.context.annotation.RequestScope;
 
 @Configuration
 @EnableRetry
 @EnableTransactionManagement
 @EnableConfigurationProperties
-public class BeanConfig {
+public class BeanConfiguration {
 
   private final DataSource dataSource;
 
-  public BeanConfig(DataSource dataSource) {
+  public BeanConfiguration(DataSource dataSource) {
     this.dataSource = dataSource;
   }
 
-  @Bean("objectMapper")
-  public ObjectMapper objectMapper() {
-    return new ObjectMapper()
-        .registerModule(new ParameterNamesModule())
-        .registerModule(new Jdk8Module())
-        .registerModule(new JavaTimeModule())
-        .setDefaultPropertyInclusion(JsonInclude.Include.NON_ABSENT);
+  /**
+   * Taken from <a
+   * href="https://github.com/DataBiosphere/terra-data-catalog/blob/5cda83aef8548ff98e7cfbe2a6eaaed9ad1bff45/common/src/main/java/bio/terra/catalog/config/BeanConfig.java#L34-L38">Terra
+   * Data Catalog</a> Lasts for the duration of one request, and is injected into dependent beans,
+   * even singletons
+   */
+  @Bean("bearerToken")
+  @RequestScope
+  public BearerToken bearerToken(HttpServletRequest request) {
+    return new BearerTokenFactory().from(request);
   }
 
   // This bean plus the @EnableTransactionManagement annotation above enables the use of the

service/src/main/java/bio/terra/pipelines/app/configuration/internal/ImputationConfiguration.java

@@ -0,0 +1,7 @@
+package bio.terra.pipelines.app.configuration.internal;
+
+import org.springframework.boot.context.properties.ConfigurationProperties;
+
+/** configuration for all properties related to imputation */
+@ConfigurationProperties(prefix = "imputation")
+public record ImputationConfiguration(String workspaceId) {}

service/src/main/java/bio/terra/pipelines/app/configuration/PipelinesSpringConfiguration.java → service/src/main/java/bio/terra/pipelines/app/configuration/internal/PipelinesSpringConfiguration.java

@@ -1,4 +1,4 @@
-package bio.terra.pipelines.app.configuration;
+package bio.terra.pipelines.app.configuration.internal;
 
 import bio.terra.pipelines.app.StartupInitializer;
 import bio.terra.pipelines.generated.model.ApiVersionProperties;

service/src/main/java/bio/terra/pipelines/app/configuration/internal/RetryConfiguration.java

@@ -0,0 +1,51 @@
+package bio.terra.pipelines.app.configuration.internal;
+
+import bio.terra.pipelines.retry.RetryLoggingListener;
+import java.net.SocketTimeoutException;
+import javax.ws.rs.ProcessingException;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.retry.RetryListener;
+import org.springframework.retry.annotation.EnableRetry;
+import org.springframework.retry.backoff.FixedBackOffPolicy;
+import org.springframework.retry.policy.ExceptionClassifierRetryPolicy;
+import org.springframework.retry.policy.NeverRetryPolicy;
+import org.springframework.retry.policy.SimpleRetryPolicy;
+import org.springframework.retry.support.RetryTemplate;
+
+/** bean used to retry requests made by the system */
+@EnableRetry
+@Configuration
+public class RetryConfiguration {
+
+  @Bean(name = "listenerResetRetryTemplate")
+  public RetryTemplate listenerResetRetryTemplate() {
+    RetryTemplate retryTemplate = new RetryTemplate();
+
+    // Fixed delay of 1 second between retries
+    FixedBackOffPolicy fixedBackOffPolicy = new FixedBackOffPolicy();
+    fixedBackOffPolicy.setBackOffPeriod(1000L);
+
+    // Inner retry (assumping the classifier hits): up to 3 times
+    SimpleRetryPolicy srp = new SimpleRetryPolicy();
+    srp.setMaxAttempts(3);
+
+    ExceptionClassifierRetryPolicy ecrp = new ExceptionClassifierRetryPolicy();
+    ecrp.setExceptionClassifier(
+        exception -> {
+          if (exception instanceof ProcessingException
+              || exception instanceof SocketTimeoutException) {
+            return srp;
+          } else {
+            return new NeverRetryPolicy();
+          }
+        });
+
+    retryTemplate.setBackOffPolicy(fixedBackOffPolicy);
+    retryTemplate.setRetryPolicy(ecrp);
+    retryTemplate.setThrowLastExceptionOnExhausted(true);
+    retryTemplate.setListeners(new RetryListener[] {new RetryLoggingListener()});
+
+    return retryTemplate;
+  }
+}

service/src/main/java/bio/terra/pipelines/config/StatusCheckConfiguration.java → service/src/main/java/bio/terra/pipelines/app/configuration/internal/StatusCheckConfiguration.java

@@ -1,4 +1,4 @@
-package bio.terra.pipelines.config;
+package bio.terra.pipelines.app.configuration.internal;
 
 import org.springframework.boot.context.properties.ConfigurationProperties;
 

service/src/main/java/bio/terra/pipelines/app/configuration/TspsDatabaseConfiguration.java → service/src/main/java/bio/terra/pipelines/app/configuration/internal/TspsDatabaseConfiguration.java

@@ -1,4 +1,4 @@
-package bio.terra.pipelines.app.configuration;
+package bio.terra.pipelines.app.configuration.internal;
 
 import bio.terra.common.db.BaseDatabaseProperties;
 import bio.terra.common.db.DataSourceInitializer;

service/src/main/java/bio/terra/pipelines/config/VersionConfiguration.java → service/src/main/java/bio/terra/pipelines/app/configuration/internal/VersionConfiguration.java

@@ -1,4 +1,4 @@
-package bio.terra.pipelines.config;
+package bio.terra.pipelines.app.configuration.internal;
 
 import org.springframework.boot.context.properties.ConfigurationProperties;
 

service/src/main/java/bio/terra/pipelines/app/controller/JobsApiController.java

@@ -3,7 +3,7 @@
 import bio.terra.common.exception.ApiException;
 import bio.terra.common.iam.SamUser;
 import bio.terra.common.iam.SamUserFactory;
-import bio.terra.pipelines.config.SamConfiguration;
+import bio.terra.pipelines.app.configuration.external.SamConfiguration;
 import bio.terra.pipelines.db.entities.Job;
 import bio.terra.pipelines.db.exception.PipelineNotFoundException;
 import bio.terra.pipelines.generated.api.JobsApi;

service/src/main/java/bio/terra/pipelines/dependencies/common/HealthCheck.java

@@ -0,0 +1,8 @@
+package bio.terra.pipelines.dependencies.common;
+
+public interface HealthCheck {
+
+  record Result(boolean isOk, String message) {}
+
+  Result checkHealth();
+}