T2d 262 verify

Jenkinsfile

@@ -6,14 +6,16 @@ pipeline {
   }
   environment {
     stagingPostgresDbUrl = credentials('STAGINGPROPERTYREGISTRYDBURL')
-    fallBackPostgresDbUrl = credentials('STAGINGPROPERTYREGISTRYDBURL')
-    productionPostgresDbUrl = credentials('STAGINGPROPERTYREGISTRYDBURL')
+    fallBackPostgresDbUrl = credentials('PRODUCTIONPROPERTYREGISTRYDBURL')
+    productionPostgresDbUrl = credentials('PRODUCTIONPROPERTYREGISTRYDBURL')
     postgresDBUserName = credentials('POSTGRESDBUSERNAME')
     postgresDBPassword = credentials('POSTGRESDBPASSWORD')
     tomcatCredentials = credentials('TOMCATCREDENTIALS')
     stagingHost = credentials('STAGINGHOST')
     fallbackHost = credentials('FALLBACKHOST')
     productionHost = credentials('PRODUCTIONHOST')
+    smtpHost = credentials('SMTPHOST')
+    ampt2dEmailId = credentials('AMPT2DEMAILID')
   }
   parameters {
     booleanParam(name: 'DeployToStaging' , defaultValue: false , description: '')
@@ -22,7 +24,7 @@ pipeline {
   stages {
     stage('Default Build pointing to Staging DB') {
       steps {
-        sh "mvn clean package -DskipTests -DbuildDirectory=staging/target -Dampt2d-property-registry-db.url=${stagingPostgresDbUrl} -Dampt2d-property-registry-db.username=${postgresDBUserName} -Dampt2d-property-registry-db.password=${postgresDBPassword}"
+        sh "mvn clean package -DskipTests -DbuildDirectory=staging/target -Dampt2d-property-registry-db.url=${stagingPostgresDbUrl} -Dampt2d-property-registry-db.username=${postgresDBUserName} -Dampt2d-property-registry-db.password=${postgresDBPassword} -Dsmtp-host=${smtpHost} -Damp-t2d-email-id=${ampt2dEmailId}"
       }
     }
     stage('Build For FallBack And Production') {
@@ -33,9 +35,9 @@ pipeline {
       }
       steps {
         echo 'Build pointing to FallBack DB'
-        sh "mvn clean package -DskipTests -DbuildDirectory=fallback/target -Dampt2d-property-registry-db.url=${fallBackPostgresDbUrl} -Dampt2d-property-registry-db.username=${postgresDBUserName} -Dampt2d-property-registry-db.password=${postgresDBPassword}"
+        sh "mvn clean package -DskipTests -DbuildDirectory=fallback/target -Dampt2d-property-registry-db.url=${fallBackPostgresDbUrl} -Dampt2d-property-registry-db.username=${postgresDBUserName} -Dampt2d-property-registry-db.password=${postgresDBPassword} -Dsmtp-host=${smtpHost} -Damp-t2d-email-id=${ampt2dEmailId}"
         echo 'Build pointing to Production DB'
-        sh "mvn clean package -DskipTests -DbuildDirectory=production/target -Dampt2d-property-registry-db.url=${productionPostgresDbUrl} -Dampt2d-property-registry-db.username=${postgresDBUserName} -Dampt2d-property-registry-db.password=${postgresDBPassword}"
+        sh "mvn clean package -DskipTests -DbuildDirectory=production/target -Dampt2d-property-registry-db.url=${productionPostgresDbUrl} -Dampt2d-property-registry-db.username=${postgresDBUserName} -Dampt2d-property-registry-db.password=${postgresDBPassword} -Dsmtp-host=${smtpHost} -Damp-t2d-email-id=${ampt2dEmailId}"
       }
     }
     stage('Deploy To Staging') {
@@ -46,7 +48,7 @@ pipeline {
       }
       steps {
         echo 'Deploying to Staging'
-        sh "curl --upload-file staging/target/amp-t2d-property-registry-*.war 'http://'${tomcatCredentials}'@'${stagingHost}':8080/manager/text/deploy?path=/registry&update=true' | grep 'OK - Deployed application at context path '"
+        sh "curl --upload-file staging/target/amp-t2d-property-registry-*.war 'http://'${tomcatCredentials}'@'${stagingHost}':8080/manager/text/deploy?path=/dev/registry&update=true' | grep 'OK - Deployed application at context path '"
       }
     }
     stage('Deploy To FallBack And Production') {

pom.xml

@@ -31,6 +31,10 @@
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-starter-web</artifactId>
         </dependency>
+        <dependency>
+            <groupId>org.springframework.boot</groupId>
+            <artifactId>spring-boot-starter-mail</artifactId>
+        </dependency>
         <dependency>
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-starter-data-jpa</artifactId>
@@ -68,7 +72,7 @@
         <dependency>
             <groupId>com.h2database</groupId>
             <artifactId>h2</artifactId>
-            <scope>test</scope>
+            <!--<scope>test</scope>
         </dependency>
         <dependency>
             <groupId>org.postgresql</groupId>
@@ -78,7 +82,7 @@
         <dependency>
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-starter-tomcat</artifactId>
-            <scope>provided</scope>
+            <scope>provided</scope>-->
         </dependency>
         <!-- documentation -->
         <dependency>

src/main/java/uk/ac/ebi/ampt2d/registry/PropertyRegistryServiceApplication.java

@@ -23,14 +23,14 @@
 import org.springframework.boot.web.support.SpringBootServletInitializer;
 
 @SpringBootApplication
-public class PropertyRegistryServiceApplication extends SpringBootServletInitializer {
+public class PropertyRegistryServiceApplication {//extends SpringBootServletInitializer {
 
     public static void main(String[] args) throws Exception {
         SpringApplication.run(PropertyRegistryServiceApplication.class, args);
     }
 
-    @Override
-    protected SpringApplicationBuilder configure(SpringApplicationBuilder application) {
-        return application.sources(PropertyRegistryServiceApplication.class);
-    }
+//    @Override
+//    protected SpringApplicationBuilder configure(SpringApplicationBuilder application) {
+//        return application.sources(PropertyRegistryServiceApplication.class);
+//    }
 }

src/main/java/uk/ac/ebi/ampt2d/registry/entities/EntityEventListener.java

@@ -0,0 +1,54 @@
+/*
+ *
+ * Copyright 2018 EMBL - European Bioinformatics Institute
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+package uk.ac.ebi.ampt2d.registry.entities;
+
+import uk.ac.ebi.ampt2d.registry.util.BeanUtil;
+import uk.ac.ebi.ampt2d.registry.service.mail.MailService;
+
+import javax.persistence.PostPersist;
+import javax.persistence.PostRemove;
+import javax.persistence.PostUpdate;
+
+public class EntityEventListener {
+
+    private enum Event {
+        CREATED,
+        UPDATED,
+        REMOVED
+    }
+
+    @PostPersist
+    public void onPersistEntity(IdentifiableEntity entity) {
+        sendNotification(entity, Event.CREATED);
+    }
+
+    @PostUpdate
+    public void onUpdateEntity(IdentifiableEntity entity) {
+        sendNotification(entity, Event.UPDATED);
+    }
+
+    @PostRemove
+    public void onRemoveEntity(IdentifiableEntity entity) {
+        sendNotification(entity, Event.REMOVED);
+    }
+
+    private void sendNotification(IdentifiableEntity entity, Event event) {
+        BeanUtil.getBean(MailService.class).send(entity.getClass().getSimpleName() + " " + entity.getId() + " " + event);
+    }
+
+}

src/main/java/uk/ac/ebi/ampt2d/registry/entities/IdentifiableEntity.java

@@ -0,0 +1,24 @@
+/*
+ *
+ * Copyright 2018 EMBL - European Bioinformatics Institute
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+package uk.ac.ebi.ampt2d.registry.entities;
+
+public interface IdentifiableEntity<ENTITY_ID> {
+
+    ENTITY_ID getId();
+
+}

src/main/java/uk/ac/ebi/ampt2d/registry/entities/Phenotype.java

@@ -34,8 +34,8 @@
 import java.time.ZonedDateTime;
 
 @Entity
-@EntityListeners(AuditingEntityListener.class)
-public class Phenotype {
+@EntityListeners({AuditingEntityListener.class, EntityEventListener.class})
+public class Phenotype implements IdentifiableEntity<String> {
 
     public enum Group {
 
@@ -68,4 +68,8 @@ public enum Group {
 
     @LastModifiedDate
     private ZonedDateTime lastModifiedDate;
+
+    public String getId() {
+        return id;
+    }
 }

src/main/java/uk/ac/ebi/ampt2d/registry/entities/Property.java

@@ -35,8 +35,8 @@
 import java.time.ZonedDateTime;
 
 @Entity
-@EntityListeners(AuditingEntityListener.class)
-public class Property {
+@EntityListeners({AuditingEntityListener.class, EntityEventListener.class})
+public class Property implements IdentifiableEntity<String> {
 
     public enum Type {
 
@@ -102,4 +102,7 @@ public enum Meaning {
     @LastModifiedDate
     private ZonedDateTime lastModifiedDate;
 
+    public String getId() {
+        return id;
+    }
 }

src/main/java/uk/ac/ebi/ampt2d/registry/entities/User.java

@@ -24,7 +24,7 @@
 import javax.persistence.Enumerated;
 import javax.persistence.Id;
 
-@Entity
+@Entity(name = "users")
 public class User {
 
     public enum Role {

src/main/java/uk/ac/ebi/ampt2d/registry/exceptionhandling/ExceptionHandlers.java

@@ -0,0 +1,48 @@
+/*
+ *
+ * Copyright 2018 EMBL - European Bioinformatics Institute
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+package uk.ac.ebi.ampt2d.registry.exceptionhandling;
+
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.http.HttpStatus;
+import org.springframework.http.ResponseEntity;
+import org.springframework.mail.MailSendException;
+import org.springframework.transaction.TransactionSystemException;
+import org.springframework.web.bind.annotation.ControllerAdvice;
+import org.springframework.web.bind.annotation.ExceptionHandler;
+
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
+@ControllerAdvice
+public class ExceptionHandlers {
+
+    private static final Logger exceptionLogger = Logger.getLogger(ExceptionHandlers.class.getSimpleName());
+
+    @Value("${mail.from}")
+    private String mailFrom;
+
+    @ExceptionHandler(value = TransactionSystemException.class)
+    public ResponseEntity<String> handleMailSendException(TransactionSystemException ex) {
+        if (ex.getOriginalException().getCause().getClass().equals(MailSendException.class)) {
+            exceptionLogger.log(Level.SEVERE, ex.getOriginalException().getCause().getMessage());
+            return new ResponseEntity("An automated email could not be sent, please contact " + mailFrom,
+                    HttpStatus.INTERNAL_SERVER_ERROR);
+        }
+        throw ex;
+    }
+}

src/main/java/uk/ac/ebi/ampt2d/registry/service/mail/MailService.java

@@ -0,0 +1,54 @@
+/*
+ *
+ * Copyright 2018 EMBL - European Bioinformatics Institute
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+package uk.ac.ebi.ampt2d.registry.service.mail;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.mail.SimpleMailMessage;
+import org.springframework.mail.javamail.JavaMailSender;
+import org.springframework.stereotype.Service;
+
+@Service
+public class MailService {
+
+    @Autowired
+    private JavaMailSender javaMailSender;
+
+    @Value("${mail.notify:false}")
+    private Boolean nofify;
+
+    @Value("${mail.to}")
+    private String to;
+
+    @Value("${mail.from}")
+    private String from;
+
+    @Value("${mail.subject}")
+    private String subject;
+
+    public void send(String text) {
+        if (nofify == true) {
+            SimpleMailMessage message = new SimpleMailMessage();
+            message.setTo(to);
+            message.setFrom(from);
+            message.setSubject(subject);
+            message.setText(text);
+            javaMailSender.send(message);
+        }
+    }
+}

src/main/java/uk/ac/ebi/ampt2d/registry/util/BeanUtil.java

@@ -0,0 +1,38 @@
+/*
+ *
+ * Copyright 2018 EMBL - European Bioinformatics Institute
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+package uk.ac.ebi.ampt2d.registry.util;
+
+import org.springframework.beans.BeansException;
+import org.springframework.context.ApplicationContext;
+import org.springframework.context.ApplicationContextAware;
+import org.springframework.stereotype.Service;
+
+@Service
+public class BeanUtil implements ApplicationContextAware {
+
+    private static ApplicationContext context;
+
+    @Override
+    public void setApplicationContext(ApplicationContext applicationContext) throws BeansException {
+        context = applicationContext;
+    }
+
+    public static <T> T getBean(Class<T> beanClass) {
+        return context.getBean(beanClass);
+    }
+}