Spring Boot 2 upgrade

PR notes Use pipe delimiter in application properties so that they can be parametrized for both Travis and Gitlab Replace Fongo with real MongoDB tests because Fongo is not supported in Spring Boot 2.1 - see [here](fakemongo/fongo#357) Update Travis and Gitlab scripts to include Mongo installations Update POMs to support "|" delimiters so that EVA mongo host for tests can be parametrized for both Travis and Gitlab javax.validation API dependency need no longer be explicitly pulled in since Spring Boot 2 contains it Upgrade jackson-databind version to 2.9.7 to work with Spring Boot 2 JPA repository query methods should be marked with "Query" annotation
sundarvenkata-EBI · May 20, 2020 · 7dcbd65 · 7dcbd65
1 parent a271299
commit 7dcbd65
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diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -12,8 +12,11 @@ variables:
 test:
     stage: test
     image: maven:3.6.1-jdk-8-alpine
+    services:
+        - mongo:4.0.18
     script:
-        - mvn clean test --projects 'eva-lib,eva-server'
+        # Gitlab exposes services under their own hostnames. So test host should be "mongo" instead of "localhost".
+        - mvn clean test --projects 'eva-lib,eva-server' -Deva.mongo.host.test=mongo
     only:
         - master
         - tags

diff --git a/.travis.yml b/.travis.yml
@@ -1,16 +1,18 @@
 sudo: false
-
-language: java
-
-jdk:
-  - openjdk8
-
-env:
-  - OPENCGA_HOME=$TRAVIS_BUILD_DIR/opencga/opencga-app/build
-
-install:
-  - mvn install -DskipTests=true -Dmaven.javadoc.skip=true -B -V -PTravis
-
-script:
-  - mvn test -s .travis.settings.xml -PTravis
-
+matrix:
+  include:
+    - language: "java"
+      jdk: "openjdk8"
+      env:
+        - OPENCGA_HOME=$TRAVIS_BUILD_DIR/opencga/opencga-app/build
+        - MONGODB_VERSION=4.0.18
+      install:
+        - wget http://fastdl.mongodb.org/linux/mongodb-linux-x86_64-$MONGODB_VERSION.tgz
+        - tar xfz mongodb-linux-x86_64-$MONGODB_VERSION.tgz
+        - export PATH=`pwd`/mongodb-linux-x86_64-$MONGODB_VERSION/bin:$PATH
+        - mkdir -p data/db
+        - mongod --dbpath=data/db &
+        - mongod --version
+        - mvn install -DskipTests=true -Dmaven.javadoc.skip=true -B -V -PTravis
+      script:
+        - mvn test -s .travis.settings.xml -PTravis
diff --git a/dbsnp-import/pom.xml b/dbsnp-import/pom.xml
@@ -64,12 +64,6 @@
             <artifactId>hsqldb</artifactId>
            <!-- <scope>test</scope>-->
         </dependency>
-        <dependency>
-            <groupId>com.github.fakemongo</groupId>
-            <artifactId>fongo</artifactId>
-            <version>2.0.12</version>
-            <scope>test</scope>
-        </dependency>
     </dependencies>
 
     <build>

diff --git a/dbsnp-import/src/main/java/uk/ac/ebi/eva/server/Application.java b/dbsnp-import/src/main/java/uk/ac/ebi/eva/server/Application.java
@@ -19,7 +19,7 @@
 import org.springframework.boot.SpringApplication;
 import org.springframework.boot.autoconfigure.SpringBootApplication;
 import org.springframework.boot.builder.SpringApplicationBuilder;
-import org.springframework.boot.web.support.SpringBootServletInitializer;
+import org.springframework.boot.web.servlet.support.SpringBootServletInitializer;
 
 @SpringBootApplication
 public class Application extends SpringBootServletInitializer {

diff --git a/dbsnp-import/src/main/resources/application.properties b/dbsnp-import/src/main/resources/application.properties
@@ -1,10 +1,13 @@
 spring.datasource.driver-class-name=org.postgresql.Driver
-spring.datasource.url=@eva.evapro.jdbc.url@?currentSchema=@eva.evapro.dbsnp-progress.schema@
-spring.datasource.username=@eva.evapro.user@
-spring.datasource.password=@eva.evapro.password@
+spring.datasource.url=|eva.evapro.jdbc.url|?currentSchema=|eva.evapro.dbsnp-progress.schema|
+spring.datasource.username=|eva.evapro.user|
+spring.datasource.password=|eva.evapro.password|
 
 spring.jpa.generate-ddl=false
 spring.data.rest.base-path=/v1/
 
 management.endpoints.web.exposure.include=info,health
 management.info.git.mode=full
+
+# See https://github.com/spring-projects/spring-boot/wiki/Spring-Boot-2.1-Release-Notes#bean-overriding
+spring.main.allow-bean-definition-overriding=true
diff --git a/...-import/src/test/java/uk/ac/ebi/eva/server/repositories/ProgressReportRepositoryTest.java b/...-import/src/test/java/uk/ac/ebi/eva/server/repositories/ProgressReportRepositoryTest.java
@@ -28,10 +28,11 @@
 import java.util.Calendar;
 import java.util.Date;
 import java.util.HashSet;
+import java.util.Optional;
 import java.util.Set;
 
 import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
 
 @RunWith(SpringRunner.class)
 @DataJpaTest
@@ -47,13 +48,14 @@ public void testCountRecords() {
 
     @Test
     public void testFindById() {
-        ProgressReport report = progressReportRepository.findOne(new ProgressReportPK("fruitfly_7227",
-                                                                                      "GCA_000001215.4"));
+        Optional<ProgressReport> report = progressReportRepository.findById(new ProgressReportPK("fruitfly_7227",
+                                                                                                 "GCA_000001215.4"));
+        assertTrue(report.isPresent());
         ProgressReport expected = new ProgressReport("fruitfly_7227", 7227, "Drosophila melanogaster", "Fruit fly",
                                                      "GCA_000001215.4", 149, true, false, false, Status.pending,
                                                      Status.pending, Status.pending, null, null, null, 0L, 0L, 0L, 0L,
                                                      0L, 0L);
-        assertEquals(expected, report);
+        assertEquals(expected, report.get());
     }
 
     @Test
@@ -70,24 +72,25 @@ public void testFindMultipleAssemblies() {
 
     @Test
     public void testVariantWithEvidenceImportFields() {
-        ProgressReport report = progressReportRepository.findOne(new ProgressReportPK("arabidopsis_3702",
-                                                                                      "GCA_000001735.1"));
-        assertEquals(Status.done, report.getVariantsWithEvidenceImported());
+        Optional<ProgressReport> report = progressReportRepository.findById(new ProgressReportPK("arabidopsis_3702",
+                                                                                                 "GCA_000001735.1"));
+        assertTrue(report.isPresent());
+        assertEquals(Status.done, report.get().getVariantsWithEvidenceImported());
         Calendar cal = Calendar.getInstance();
         cal.set(2018, Calendar.MAY, 30, 0, 0, 0);
         cal.set(Calendar.MILLISECOND, 0);
         Date date = cal.getTime();
-        assertEquals(date.getTime(), report.getVariantsWithEvidenceImportedDate().getTime());
+        assertEquals(date.getTime(), report.get().getVariantsWithEvidenceImportedDate().getTime());
     }
 
     @Test
     public void testVariantWithoutGenbankAccession() {
         String databaseName = "orangutan_9600";
         String genbankAssemblyAccession = "";
-        ProgressReport report = progressReportRepository.findOne(new ProgressReportPK(databaseName,
-                                                                                      genbankAssemblyAccession));
-        assertNotNull(report);
-        assertEquals(genbankAssemblyAccession, report.getGenbankAssemblyAccession());
-        assertEquals(databaseName, report.getDatabaseName());
+        Optional<ProgressReport> report = progressReportRepository.findById(new ProgressReportPK(databaseName,
+                                                                                                 genbankAssemblyAccession));
+        assertTrue(report.isPresent());
+        assertEquals(genbankAssemblyAccession, report.get().getGenbankAssemblyAccession());
+        assertEquals(databaseName, report.get().getDatabaseName());
     }
 }
diff --git a/dbsnp-import/src/test/resources/application.properties b/dbsnp-import/src/test/resources/application.properties
@@ -9,3 +9,6 @@ spring.datasource.generate-unique-name=true
 
 spring.jpa.generate-ddl=true
 spring.jpa.show-sql=true
+
+# See https://github.com/spring-projects/spring-boot/wiki/Spring-Boot-2.1-Release-Notes#bean-overriding
+spring.main.allow-bean-definition-overriding=true
diff --git a/dgva-server/src/main/java/uk/ac/ebi/dgva/server/Application.java b/dgva-server/src/main/java/uk/ac/ebi/dgva/server/Application.java
@@ -19,7 +19,7 @@
 import org.springframework.boot.SpringApplication;
 import org.springframework.boot.autoconfigure.SpringBootApplication;
 import org.springframework.boot.builder.SpringApplicationBuilder;
-import org.springframework.boot.web.support.SpringBootServletInitializer;
+import org.springframework.boot.web.servlet.support.SpringBootServletInitializer;
 
 @SpringBootApplication
 public class Application extends SpringBootServletInitializer {

diff --git a/dgva-server/src/main/resources/application.properties b/dgva-server/src/main/resources/application.properties
@@ -15,3 +15,6 @@ springfox.documentation.swagger.v2.path=/webservices/api
 
 management.endpoints.web.exposure.include=info,health
 management.info.git.mode=full
+
+# See https://github.com/spring-projects/spring-boot/wiki/Spring-Boot-2.1-Release-Notes#bean-overriding
+spring.main.allow-bean-definition-overriding=true
diff --git a/dgva-server/src/test/resources/application.properties b/dgva-server/src/test/resources/application.properties
@@ -11,3 +11,6 @@ spring.jpa.show-sql=true
 
 logging.level.com.bytestree.restful=DEBUG
 logging.level.org.springframework.web.client.RestTemplate=DEBUG
+
+# See https://github.com/spring-projects/spring-boot/wiki/Spring-Boot-2.1-Release-Notes#bean-overriding
+spring.main.allow-bean-definition-overriding=true
diff --git a/eva-lib/pom.xml b/eva-lib/pom.xml
@@ -13,6 +13,7 @@
 
     <properties>
         <compileSource>1.8</compileSource>
+        <eva.mongo.host.test>localhost</eva.mongo.host.test>
     </properties>
 
     <dependencies>
@@ -32,24 +33,13 @@
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-starter-data-jpa</artifactId>
         </dependency>
-        <dependency>
-            <groupId>com.github.fakemongo</groupId>
-            <artifactId>fongo</artifactId>
-            <scope>test</scope>
-        </dependency>
         <dependency>
             <groupId>com.lordofthejars</groupId>
             <artifactId>nosqlunit-core</artifactId>
         </dependency>
         <dependency>
             <groupId>com.lordofthejars</groupId>
             <artifactId>nosqlunit-mongodb</artifactId>
-            <exclusions>
-                <exclusion>
-                    <groupId>com.github.fakemongo</groupId>
-                    <artifactId>fongo</artifactId>
-                </exclusion>
-            </exclusions>
         </dependency>
         <dependency>
             <groupId>com.h2database</groupId>
@@ -60,10 +50,6 @@
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-starter-validation</artifactId>
         </dependency>
-        <dependency>
-            <groupId>javax.validation</groupId>
-            <artifactId>validation-api</artifactId>
-        </dependency>
         <dependency>
             <groupId>com.fasterxml.jackson.core</groupId>
             <artifactId>jackson-databind</artifactId>
@@ -77,6 +63,19 @@
 
     <build>
         <finalName>${project.artifactId}-${project.version}-${git.commit.id.abbrev}</finalName>
+        <testResources>
+            <testResource>
+                <directory>src/test/resources/properties</directory>
+                <filtering>true</filtering>
+            </testResource>
+            <testResource>
+                <directory>src/test/resources/</directory>
+                <filtering>false</filtering>
+                <excludes>
+                    <exclude>src/test/resources/properties/*</exclude>
+                </excludes>
+            </testResource>
+        </testResources>
     </build>
 
 </project>
diff --git a/eva-lib/src/main/java/uk/ac/ebi/eva/lib/MongoConfiguration.java b/eva-lib/src/main/java/uk/ac/ebi/eva/lib/MongoConfiguration.java
@@ -15,6 +15,13 @@
  */
 package uk.ac.ebi.eva.lib;
 
+import com.mongodb.AuthenticationMechanism;
+import com.mongodb.MongoClient;
+import com.mongodb.MongoClientOptions;
+import com.mongodb.MongoCredential;
+import com.mongodb.ReadPreference;
+import com.mongodb.ServerAddress;
+
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.ApplicationContext;
 import org.springframework.context.annotation.Bean;
@@ -29,8 +36,13 @@
 import org.springframework.data.mongodb.repository.config.EnableMongoRepositories;
 
 import uk.ac.ebi.eva.lib.configuration.DbCollectionsProperties;
+import uk.ac.ebi.eva.lib.configuration.SpringDataMongoDbProperties;
 
 import java.io.IOException;
+import java.net.UnknownHostException;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
 
 @Configuration
 @Import(DbCollectionsProperties.class)
@@ -47,6 +59,9 @@ public class MongoConfiguration {
     @Autowired
     private DbCollectionsProperties dbCollectionsProperties;
 
+    @Autowired
+    private SpringDataMongoDbProperties springDataMongoDbProperties;
+
     @Bean
     public String mongoCollectionsVariants() {
         return dbCollectionsProperties.getVariants();
@@ -91,4 +106,57 @@ public MappingMongoConverter mappingMongoConverter() throws IOException {
         return mongoConverter;
     }
 
+    /**
+     * Get a MongoClient using the configuration (credentials) in a given Properties.
+     *
+     * @param springDataMongoDbProperties can have the next values:
+     *                   - eva.mongo.auth.db authentication database
+     *                   - eva.mongo.host comma-separated strings of colon-separated host and port strings: host_1:port_1,host_2:port_2
+     *                   - eva.mongo.user
+     *                   - eva.mongo.passwd
+     *                   - eva.mongo.read-preference string, "secondaryPreferred" if unspecified. one of:
+     *                          [primary, primaryPreferred, secondary, secondaryPreferred, nearest]
+     * @return MongoClient with given credentials
+     * @throws UnknownHostException
+     */
+    public static MongoClient getMongoClient(SpringDataMongoDbProperties springDataMongoDbProperties) throws UnknownHostException {
+
+        String[] hosts = springDataMongoDbProperties.getHost().split(",");
+        List<ServerAddress> servers = new ArrayList<>();
+
+        // Get the list of hosts (optionally including the port number)
+        for (String host : hosts) {
+            String[] params = host.split(":");
+            if (params.length > 1) {
+                servers.add(new ServerAddress(params[0], Integer.parseInt(params[1])));
+            } else {
+                servers.add(new ServerAddress(params[0], 27017));
+            }
+        }
+
+        String readPreference = springDataMongoDbProperties.getReadPreference();
+        readPreference = readPreference == null || readPreference.isEmpty()? "secondaryPreferred" : readPreference;
+
+        MongoClientOptions options = MongoClientOptions.builder()
+                                                       .readPreference(ReadPreference.valueOf(readPreference))
+                                                       .build();
+
+        List<MongoCredential> mongoCredentialList = new ArrayList<>();
+        String authenticationDb = springDataMongoDbProperties.getAuthenticationDatabase();
+        if (authenticationDb != null && !authenticationDb.isEmpty()) {
+            MongoCredential mongoCredential = MongoCredential.createCredential(
+                    springDataMongoDbProperties.getUsername(),
+                    authenticationDb,
+                    springDataMongoDbProperties.getPassword().toCharArray());
+            String authenticationMechanism = springDataMongoDbProperties.getAuthenticationMechanism();
+            if (authenticationMechanism == null) {
+                return new MongoClient(servers, options);
+            }
+            mongoCredential = mongoCredential.withMechanism(
+                    AuthenticationMechanism.fromMechanismName(authenticationMechanism));
+            mongoCredentialList = Collections.singletonList(mongoCredential);
+        }
+
+        return new MongoClient(servers, mongoCredentialList, options);
+    }
 }
diff --git a/eva-lib/src/main/java/uk/ac/ebi/eva/lib/configuration/SpringDataMongoDbProperties.java b/eva-lib/src/main/java/uk/ac/ebi/eva/lib/configuration/SpringDataMongoDbProperties.java
@@ -24,21 +24,33 @@
 @Component
 public class SpringDataMongoDbProperties {
 
+    private String database;
+
     @Size(min = 1)
     private String host;
 
     private String authenticationDatabase;
 
+    private String authenticationMechanism;
+
     private String username;
 
     private String password;
 
     private String readPreference;
 
+    public String getDatabase() {
+        return database;
+    }
+
     public String getHost() {
         return host;
     }
 
+    public void setDatabase(String database) {
+        this.database = database;
+    }
+
     public void setHost(String host) {
         this.host = host;
     }
@@ -51,6 +63,14 @@ public void setAuthenticationDatabase(String authenticationDatabase) {
         this.authenticationDatabase = authenticationDatabase;
     }
 
+    public String getAuthenticationMechanism() {
+        return authenticationMechanism;
+    }
+
+    public void setAuthenticationMechanism(String authenticationMechanism) {
+        this.authenticationMechanism = authenticationMechanism;
+    }
+
     public String getUsername() {
         return username;
     }