feat(openchallenges): add coverage tools to OC organization service (#…

…2344)

* Configure test to use h2 db

* Disable hibernate and elastic in unit test

* Fix unit tests

* Upgrade to Gradle v8.4

* Exclude some files from the test

apps/openchallenges/organization-service/build.gradle

@@ -23,8 +23,6 @@ repositories {
 }
 
 dependencies {
-  implementation "org.hibernate.search:hibernate-search-mapper-orm:${hibernateSearchVersion}"
-  implementation "org.hibernate.search:hibernate-search-backend-elasticsearch:${hibernateSearchVersion}"
   annotationProcessor "org.projectlombok:lombok:${lombokVersion}"
   compileOnly "org.projectlombok:lombok:${lombokVersion}"
   implementation 'com.google.code.findbugs:jsr305:3.0.2'
@@ -35,6 +33,8 @@ dependencies {
   implementation "com.fasterxml.jackson.datatype:jackson-datatype-jsr310:${fasterxmlVersion}"
   implementation "org.flywaydb:flyway-core:${flywaydbVersion}"
   implementation "org.flywaydb:flyway-mysql:${flywaydbVersion}"
+  implementation "org.hibernate.search:hibernate-search-backend-elasticsearch:${hibernateSearchVersion}"
+  implementation "org.hibernate.search:hibernate-search-mapper-orm:${hibernateSearchVersion}"
   implementation "org.keycloak:keycloak-admin-client:${keycloakVersion}"
   implementation "org.keycloak:keycloak-spring-boot-starter:${keycloakVersion}"
   implementation "org.sagebionetworks:util:${openchallengesVersion}"
@@ -45,10 +45,11 @@ dependencies {
   implementation "org.springframework.boot:spring-boot-starter-validation:${springBootVersion}"
   implementation "org.springframework.boot:spring-boot-starter-web:${springBootVersion}"
   implementation "org.springframework.cloud:spring-cloud-starter-netflix-eureka-client:${springCloudVersion}"
+  implementation "org.springframework.cloud:spring-cloud-starter-openfeign:${springCloudVersion}"
   implementation "org.springframework.data:spring-data-commons:${springDataVersion}"
   runtimeOnly 'mysql:mysql-connector-java:8.0.30'
   testImplementation "org.springframework.boot:spring-boot-starter-test:${springBootVersion}"
-  implementation "org.springframework.cloud:spring-cloud-starter-openfeign:${springCloudVersion}"
+  testRuntimeOnly 'com.h2database:h2:2.1.214'
 
   // Enable distributed tracing
   implementation "org.springframework.cloud:spring-cloud-starter-sleuth:${springCloudVersion}"
@@ -78,8 +79,7 @@ bootBuildImage {
 }
 
 test {
-  // This instruction makes the test fail
-	// useJUnitPlatform()
+	useJUnitPlatform()
 
   testLogging.showStandardStreams = true
 
@@ -100,6 +100,24 @@ jacocoTestReport {
   reports {
     xml.required = true
   }
+
+  afterEvaluate {
+    def autoGenerated = [
+      '**/api/*.*',
+      '**/configuration/EnumConverterConfiguration*.*',
+      '**/configuration/Flyway*.*',
+      '**/configuration/HibernateSearch*.*',
+      '**/configuration/HomeController*.*',
+      '**/configuration/Keycloak*.*',
+      '**/configuration/SpringDocConfiguration*.*',
+      '**/model/dto/**',
+      '**/RFC3339DateFormat.*'
+    ]
+    classDirectories.setFrom(files(classDirectories.files.collect {
+        fileTree(dir: it, exclude: autoGenerated
+        )
+    }))
+  }
 }
 
 sonar {

apps/openchallenges/organization-service/gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,7 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.3-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.4-bin.zip
+networkTimeout=10000
+validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

apps/openchallenges/organization-service/gradlew

@@ -55,7 +55,7 @@
 #       Darwin, MinGW, and NonStop.
 #
 #   (3) This script is generated from the Groovy template
-#       https://github.com/gradle/gradle/blob/master/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
+#       https://github.com/gradle/gradle/blob/HEAD/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
 #       within the Gradle project.
 #
 #       You can find Gradle at https://github.com/gradle/gradle/.
@@ -80,13 +80,11 @@ do
     esac
 done
 
-APP_HOME=$( cd "${APP_HOME:-./}" && pwd -P ) || exit
-
-APP_NAME="Gradle"
+# This is normally unused
+# shellcheck disable=SC2034
 APP_BASE_NAME=${0##*/}
-
-# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
+# Discard cd standard output in case $CDPATH is set (https://github.com/gradle/gradle/issues/25036)
+APP_HOME=$( cd "${APP_HOME:-./}" > /dev/null && pwd -P ) || exit
 
 # Use the maximum available, or set MAX_FD != -1 to use that value.
 MAX_FD=maximum
@@ -133,22 +131,29 @@ location of your Java installation."
     fi
 else
     JAVACMD=java
-    which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+    if ! command -v java >/dev/null 2>&1
+    then
+        die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
 
 Please set the JAVA_HOME variable in your environment to match the
 location of your Java installation."
+    fi
 fi
 
 # Increase the maximum file descriptors if we can.
 if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then
     case $MAX_FD in #(
       max*)
+        # In POSIX sh, ulimit -H is undefined. That's why the result is checked to see if it worked.
+        # shellcheck disable=SC2039,SC3045
         MAX_FD=$( ulimit -H -n ) ||
             warn "Could not query maximum file descriptor limit"
     esac
     case $MAX_FD in  #(
       '' | soft) :;; #(
       *)
+        # In POSIX sh, ulimit -n is undefined. That's why the result is checked to see if it worked.
+        # shellcheck disable=SC2039,SC3045
         ulimit -n "$MAX_FD" ||
             warn "Could not set maximum file descriptor limit to $MAX_FD"
     esac
@@ -193,11 +198,15 @@ if "$cygwin" || "$msys" ; then
     done
 fi
 
-# Collect all arguments for the java command;
-#   * $DEFAULT_JVM_OPTS, $JAVA_OPTS, and $GRADLE_OPTS can contain fragments of
-#     shell script including quotes and variable substitutions, so put them in
-#     double quotes to make sure that they get re-expanded; and
-#   * put everything else in single quotes, so that it's not re-expanded.
+
+# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
+
+# Collect all arguments for the java command:
+#   * DEFAULT_JVM_OPTS, JAVA_OPTS, JAVA_OPTS, and optsEnvironmentVar are not allowed to contain shell fragments,
+#     and any embedded shellness will be escaped.
+#   * For example: A user cannot expect ${Hostname} to be expanded, as it is an environment variable and will be
+#     treated as '${Hostname}' itself on the command line.
 
 set -- \
         "-Dorg.gradle.appname=$APP_BASE_NAME" \

apps/openchallenges/organization-service/gradlew.bat

@@ -0,0 +1,92 @@
+@rem
+@rem Copyright 2015 the original author or authors.
+@rem
+@rem Licensed under the Apache License, Version 2.0 (the "License");
+@rem you may not use this file except in compliance with the License.
+@rem You may obtain a copy of the License at
+@rem
+@rem      https://www.apache.org/licenses/LICENSE-2.0
+@rem
+@rem Unless required by applicable law or agreed to in writing, software
+@rem distributed under the License is distributed on an "AS IS" BASIS,
+@rem WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+@rem See the License for the specific language governing permissions and
+@rem limitations under the License.
+@rem
+
+@if "%DEBUG%"=="" @echo off
+@rem ##########################################################################
+@rem
+@rem  Gradle startup script for Windows
+@rem
+@rem ##########################################################################
+
+@rem Set local scope for the variables with windows NT shell
+if "%OS%"=="Windows_NT" setlocal
+
+set DIRNAME=%~dp0
+if "%DIRNAME%"=="" set DIRNAME=.
+@rem This is normally unused
+set APP_BASE_NAME=%~n0
+set APP_HOME=%DIRNAME%
+
+@rem Resolve any "." and ".." in APP_HOME to make it shorter.
+for %%i in ("%APP_HOME%") do set APP_HOME=%%~fi
+
+@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+set DEFAULT_JVM_OPTS="-Xmx64m" "-Xms64m"
+
+@rem Find java.exe
+if defined JAVA_HOME goto findJavaFromJavaHome
+
+set JAVA_EXE=java.exe
+%JAVA_EXE% -version >NUL 2>&1
+if %ERRORLEVEL% equ 0 goto execute
+
+echo.
+echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+echo.
+echo Please set the JAVA_HOME variable in your environment to match the
+echo location of your Java installation.
+
+goto fail
+
+:findJavaFromJavaHome
+set JAVA_HOME=%JAVA_HOME:"=%
+set JAVA_EXE=%JAVA_HOME%/bin/java.exe
+
+if exist "%JAVA_EXE%" goto execute
+
+echo.
+echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
+echo.
+echo Please set the JAVA_HOME variable in your environment to match the
+echo location of your Java installation.
+
+goto fail
+
+:execute
+@rem Setup the command line
+
+set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
+
+
+@rem Execute Gradle
+"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %*
+
+:end
+@rem End local scope for the variables with windows NT shell
+if %ERRORLEVEL% equ 0 goto mainEnd
+
+:fail
+rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of
+rem the _cmd.exe /c_ return code!
+set EXIT_CODE=%ERRORLEVEL%
+if %EXIT_CODE% equ 0 set EXIT_CODE=1
+if not ""=="%GRADLE_EXIT_CONSOLE%" exit %EXIT_CODE%
+exit /b %EXIT_CODE%
+
+:mainEnd
+if "%OS%"=="Windows_NT" endlocal
+
+:omega

apps/openchallenges/organization-service/src/main/java/org/sagebionetworks/openchallenges/organization/service/configuration/HibernateSearchIndexBuild.java

@@ -6,12 +6,16 @@
 import org.hibernate.search.mapper.orm.Search;
 import org.hibernate.search.mapper.orm.massindexing.MassIndexer;
 import org.hibernate.search.mapper.orm.session.SearchSession;
+import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty;
 import org.springframework.boot.context.event.ApplicationReadyEvent;
 import org.springframework.context.ApplicationListener;
 import org.springframework.context.annotation.Configuration;
 
 @Slf4j
 @Configuration
+@ConditionalOnProperty(
+    value = "spring.jpa.properties.hibernate.search.enabled",
+    havingValue = "true")
 public class HibernateSearchIndexBuild implements ApplicationListener<ApplicationReadyEvent> {
 
   private final EntityManager entityManager;

apps/openchallenges/organization-service/src/test/java/org/sagebionetworks/openchallenges/organization/service/OpenApiGeneratorApplicationTests.java → apps/openchallenges/organization-service/src/test/java/org/sagebionetworks/openchallenges/organization/service/OrganizationServiceApplicationTests.java

@@ -4,7 +4,7 @@
 import org.springframework.boot.test.context.SpringBootTest;
 
 @SpringBootTest
-class OpenApiGeneratorApplicationTests {
+class OrganizationServiceApplicationTests {
 
   @Test
   void contextLoads() {}

apps/openchallenges/organization-service/src/test/resources/application.yml

@@ -0,0 +1,27 @@
+openchallenges-organization-service:
+  welcome-message: 'Welcome to the organization service (test)'
+
+spring:
+  application:
+    name: openchallenges-organization-service
+  profiles:
+    active: test
+  cloud:
+    config:
+      enabled: false
+    discovery:
+      enabled: false
+  datasource:
+    url: jdbc:h2:mem:challenge
+    username: openchallenges
+    password: changeme
+  flyway:
+    enabled: false
+  jpa:
+    properties:
+      hibernate:
+        search:
+          enabled: false
+  autoconfigure:
+    # Stop hibernate search from sniffing the nodes of a non-existent local elastic search server
+    exclude: org.springframework.boot.autoconfigure.elasticsearch.ElasticsearchRestClientAutoConfiguration

apps/openchallenges/organization-service/src/test/resources/mockito-extensions/org.mockito.plugins.MockMaker

@@ -0,0 +1 @@
+mock-maker-inline