#1 initial migration from NIEHS

.gitignore

@@ -0,0 +1,33 @@
+**/.classpath
+.DS_Store
+**/nb-configuration.xml
+**/.springBeans
+**/testing.properties
+**/*.eml
+**/Scripts
+.idea
+*.iml
+.project
+.idea
+.metadata
+.DS_Store
+Servers
+.settings
+.classpath
+mvn-repo
+bin
+*.war
+*.log
+*/nbactions.xml
+*.eml
+nbactions.xml
+testing.properties
+*/test-output
+JargonVersion.java
+**/${test.option.mount.basedir}
+**/*.*~
+*.*~
+.dbeaver*
+test.*.properties
+**/target
+target

README.md

@@ -1,2 +1,86 @@
-# notification-service
+# Notification Service(WIP)
 A pluggable Spring Boot RESTful web service to enable Notification system in Metalnx.
+
+## Overview
+This server was generated by the [swagger-codegen](https://github.com/swagger-api/swagger-codegen) project.  
+Refer: [OpenAPI-Spec](https://github.com/swagger-api/swagger-core)
+
+The underlying library integrating swagger to SpringBoot is [springfox](https://github.com/springfox/springfox)  
+
+Start your server as an simple java application  
+
+You can view the api documentation in swagger-ui by pointing to  
+http://localhost:8888/swagger-ui.html
+
+Change default port value in application.properties
+
+
+## Database schema migration and setup
+Database schema should be configured using [flywaydb](https://flywaydb.org/). This project includes code that supports database migrations across versions.
+
+Reference [docs](https://flywaydb.org/documentation/)
+
+We'll use the Maven plugin in our own processes and documentation, but there are other options as well.
+
+>**N.B.:**
+User and password information needs to be kept secure. There are maven plugin configuration [options](https://flywaydb.org/documentation/maven/).
+
+1. Set up the database (we will use postgres in the spirit of the iRODS install)
+```bash
+$ (sudo) su - postgres
+postgres$ psql
+psql> CREATE USER irodsext WITH PASSWORD 'password';
+psql> CREATE DATABASE "notification";
+psql> GRANT ALL PRIVILEGES ON DATABASE "notifications" TO irodsext;
+psql> ALTER USER irodsext WITH SUPERUSER;
+psql>Alter user irodsext with SUPERUSER;
+```
+
+> need to add superuser role to use uuid-ossp
+
+1. Setting up Maven profile
+```bash
+vi ~/.m2/settings.xml
+```
+```xml
+<profile>
+	<id>flyway-local</id>
+	<properties>
+		<flyway.jdbc.url>jdbc:postgresql://<address>:<port>/<metalnx-db-name></flyway.jdbc.url>
+		<flyway.db.user>irodsext</flyway.db.user>
+		<flyway.db.password>password</flyway.db.password>
+		<flyway.db.schema>public</flyway.db.schema>
+	</properties>
+</profile>
+```
+1. Clean database (**Warning** destructive! clears your database)
+```bash
+mvn flyway:clean
+```
+1. Migration, this is the first command to run from 0 on a clean database
+```bash
+mvn flyway:migrate
+```
+
+  For future migration use benchmark
+  ```bash
+  mvn flyway:benchmark
+  ```
+  > Looks at existing database to set to initial version. This is not for new databases.
+
+## Initial database table: "notification"
+
+|attribute_name|datatype|comment|
+|---|---|---|
+| id(PK) | BIGINT | auto generated sequence |
+| notification_id | uuid | using uuid-ossp module functions to generate universally unique identifiers (UUIDs) |
+| sender_id | VARCHAR | notification sender's userId extracted from JWT |
+| recipient_id | VARCHAR | notification recipient's userId | 
+| subject | TEXT | notification subject |
+| message | TEXT | notification message | 
+| seen | BOOLEAN | boolean for user's seen/unseen notification status | 
+| deleted | BOOLEAN | boolean for deleted notification, notification will not be deleted from postgres db |
+| date_created | TIMESTAMP | timestamp auto-generated by postgres db | 
+| severity_level | INTEGER | severity level of notification an integer value between 1 and 5 |
+| notification_type | VARCHAR | type of notification options are workflow, permission, system |
+| data_location_url | TEXT | notification associated logical location of data  |

pom.xml

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+<project xmlns="http://maven.apache.org/POM/4.0.0"
+	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+	<groupId>gov.nih.niehs.notification</groupId>
+	<artifactId>notification-service</artifactId>
+	<packaging>jar</packaging>
+	<name>Notification Service</name>
+	<version>1.0.0</version>
+	<properties>
+		<java.version>1.7</java.version>
+		<maven.compiler.source>${java.version}</maven.compiler.source>
+		<maven.compiler.target>${java.version}</maven.compiler.target>
+		<springfox-version>2.9.2</springfox-version>
+	</properties>
+	<parent>
+		<groupId>org.springframework.boot</groupId>
+		<artifactId>spring-boot-starter-parent</artifactId>
+		<version>1.5.22.RELEASE</version>
+	</parent>
+	<build>
+		<sourceDirectory>src/main/java</sourceDirectory>
+		<plugins>
+			<plugin>
+				<groupId>org.springframework.boot</groupId>
+				<artifactId>spring-boot-maven-plugin</artifactId>
+				<executions>
+					<execution>
+						<goals>
+							<goal>repackage</goal>
+						</goals>
+					</execution>
+				</executions>
+			</plugin>
+			<plugin>
+				<groupId>org.flywaydb</groupId>
+				<artifactId>flyway-maven-plugin</artifactId>
+				<version>4.2.0</version>
+				<configuration>
+					<url>${flyway.jdbc.url}</url>
+					<user>${flyway.db.user}</user>
+					<password>${flyway.db.password}</password>
+					<schemas>
+						<schema>${flyway.db.schema}</schema>
+					</schemas>
+					<locations>
+						<location>classpath:migrations</location>
+					</locations>
+				</configuration>
+			</plugin>
+		</plugins>
+	</build>
+	<dependencies>
+		<dependency>
+			<groupId>org.springframework.boot</groupId>
+			<artifactId>spring-boot-starter-data-jpa</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.springframework.boot</groupId>
+			<artifactId>spring-boot-starter-web</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.springframework.boot</groupId>
+			<artifactId>spring-boot-starter-tomcat</artifactId>
+		</dependency>
+
+		<dependency>
+			<groupId>org.springframework.security</groupId>
+			<artifactId>spring-security-web</artifactId>
+			<exclusions>
+				<exclusion>
+					<groupId>org.slf4j</groupId>
+					<artifactId>log4j-over-slf4j</artifactId>
+				</exclusion>
+			</exclusions>
+		</dependency>
+		<dependency>
+			<groupId>org.springframework.security</groupId>
+			<artifactId>spring-security-config</artifactId>
+			<exclusions>
+				<exclusion>
+					<groupId>org.slf4j</groupId>
+					<artifactId>log4j-over-slf4j</artifactId>
+				</exclusion>
+			</exclusions>
+		</dependency>
+
+		<dependency>
+			<groupId>io.jsonwebtoken</groupId>
+			<artifactId>jjwt</artifactId>
+			<version>0.9.0</version>
+		</dependency>
+
+		<!-- postgresql dependencies -->
+		<dependency>
+			<groupId>org.postgresql</groupId>
+			<artifactId>postgresql</artifactId>
+		</dependency>
+
+		<!--SpringFox dependencies -->
+		<dependency>
+			<groupId>io.springfox</groupId>
+			<artifactId>springfox-swagger2</artifactId>
+			<version>${springfox-version}</version>
+		</dependency>
+		<dependency>
+			<groupId>io.springfox</groupId>
+			<artifactId>springfox-swagger-ui</artifactId>
+			<version>${springfox-version}</version>
+		</dependency>
+
+		<dependency>
+			<groupId>com.github.joschi.jackson</groupId>
+			<artifactId>jackson-datatype-threetenbp</artifactId>
+			<version>2.6.4</version>
+		</dependency>
+		<!-- Bean Validation API support -->
+		<dependency>
+			<groupId>javax.validation</groupId>
+			<artifactId>validation-api</artifactId>
+		</dependency>
+		<!-- https://mvnrepository.com/artifact/javax.xml.bind/jaxb-api -->
+		<dependency>
+			<groupId>javax.xml.bind</groupId>
+			<artifactId>jaxb-api</artifactId>
+			<version>2.3.1</version>
+		</dependency>
+
+		<dependency>
+			<groupId>org.springframework.boot</groupId>
+			<artifactId>spring-boot-starter-test</artifactId>
+			<scope>test</scope>
+		</dependency>
+	</dependencies>
+</project>

src/main/java/gov/nih/niehs/notification/RFC3339DateFormat.java

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+package gov.nih.niehs.notification;
+
+import com.fasterxml.jackson.databind.util.ISO8601DateFormat;
+import com.fasterxml.jackson.databind.util.ISO8601Utils;
+
+import java.text.FieldPosition;
+import java.util.Date;
+
+
+public class RFC3339DateFormat extends ISO8601DateFormat {
+
+  private static final long serialVersionUID = 1L;
+
+  // Same as ISO8601DateFormat but serializing milliseconds.
+  @Override
+  public StringBuffer format(Date date, StringBuffer toAppendTo, FieldPosition fieldPosition) {
+    String value = ISO8601Utils.format(date, true);
+    toAppendTo.append(value);
+    return toAppendTo;
+  }
+
+}

src/main/java/gov/nih/niehs/notification/Swagger2SpringBoot.java

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+package gov.nih.niehs.notification;
+
+import org.springframework.boot.CommandLineRunner;
+import org.springframework.boot.ExitCodeGenerator;
+import org.springframework.boot.SpringApplication;
+import org.springframework.boot.autoconfigure.SpringBootApplication;
+import org.springframework.context.annotation.ComponentScan;
+
+import springfox.documentation.swagger2.annotations.EnableSwagger2;
+
+@SpringBootApplication
+@EnableSwagger2
+@ComponentScan(basePackages = { "gov.nih.niehs.notification", "gov.nih.niehs.notification.api" , "gov.nih.niehs.notification.configuration"})
+public class Swagger2SpringBoot implements CommandLineRunner {
+
+    @Override
+    public void run(String... arg0) throws Exception {
+        if (arg0.length > 0 && arg0[0].equals("exitcode")) {
+            throw new ExitException();
+        }
+    }
+
+    public static void main(String[] args) throws Exception {
+        new SpringApplication(Swagger2SpringBoot.class).run(args);
+    }
+
+    class ExitException extends RuntimeException implements ExitCodeGenerator {
+        private static final long serialVersionUID = 1L;
+
+        @Override
+        public int getExitCode() {
+            return 10;
+        }
+
+    }
+}

src/main/java/gov/nih/niehs/notification/api/ApiException.java

@@ -0,0 +1,11 @@
+package gov.nih.niehs.notification.api;
+
+
+public class ApiException extends Exception {
+	private int code;
+
+	public ApiException(int code, String msg) {
+		super(msg);
+		this.code = code;
+	}
+}

src/main/java/gov/nih/niehs/notification/api/ApiOriginFilter.java

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+package gov.nih.niehs.notification.api;
+
+import java.io.IOException;
+
+import javax.servlet.*;
+import javax.servlet.http.HttpServletResponse;
+
+public class ApiOriginFilter implements javax.servlet.Filter {
+    @Override
+    public void doFilter(ServletRequest request, ServletResponse response,
+            FilterChain chain) throws IOException, ServletException {
+        HttpServletResponse res = (HttpServletResponse) response;
+        res.addHeader("Access-Control-Allow-Origin", "*");
+        res.addHeader("Access-Control-Allow-Methods", "GET, POST, DELETE, PUT");
+        res.addHeader("Access-Control-Allow-Headers", "Content-Type");
+        chain.doFilter(request, response);
+    }
+
+    @Override
+    public void destroy() {
+    }
+
+    @Override
+    public void init(FilterConfig filterConfig) throws ServletException {
+    }
+}