Merge pull request #1187 from ericenns/hotfix/correct-rest-api-date-f…

…ields

Hotfix/correct rest api date fields

CHANGELOG.md

@@ -1,6 +1,10 @@
 Changes
 =======
 
+22.01 to 22.05
+--------------
+* [REST]: Corrected behaviour of date fields in REST API to return epoch instead of textual string. (22.01.1)
+
 21.09 to 22.01
 --------------
 * [REST]: Fixed bug where analysis output file bytes were being included in responses when only JSON should have been sent. (21.09.1)

UPGRADING.md

@@ -7,6 +7,12 @@ upgrading IRIDA that cannot be automated.
 21.09 to 22.01
 --------------
 * This upgrade converted the project from bare Spring to Spring Boot, which deprecated a number of properties relating to database connection and setup. These deprecated properties are mentioned in [/etc/irida/irida.conf](https://phac-nml.github.io/irida-documentation/administrator/web/#core-configuration).
+* Due to an update in Spring you will need to revoke tokens for all OAuth clients, you can perform this through the UI or with the following sql:
+```sql
+USE IRIDA_DB_NAME;
+truncate oauth_access_token;
+truncate oauth_refresh_token;
+```
 
 21.09.1 to 21.09.2
 ------------------

pom.xml

@@ -1,16 +1,15 @@
-<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">
+<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>
 	<parent>
 		<groupId>org.springframework.boot</groupId>
 		<artifactId>spring-boot-starter-parent</artifactId>
 		<version>2.6.3</version>
-		<relativePath/>
+		<relativePath />
 	</parent>
 	<groupId>ca.corefacility.bioinformatics</groupId>
 	<artifactId>irida</artifactId>
 	<packaging>war</packaging>
-	<version>22.01</version>
+	<version>22.01.1</version>
 	<name>irida</name>
 	<url>http://www.irida.ca</url>
 
@@ -953,7 +952,9 @@
 		<profile>
 			<id>ui_testing</id>
 			<properties>
-				<include.tags><![CDATA[IntegrationTest & UI]]></include.tags>
+				<include.tags>
+					<![CDATA[IntegrationTest & UI]]>
+				</include.tags>
 				<tomcat.skip>true</tomcat.skip>
 				<exclude.test.listeners>
 					ca.corefacility.bioinformatics.irida.junit5.listeners.UnitTestListener,
@@ -963,7 +964,9 @@
 		<profile>
 			<id>service_testing</id>
 			<properties>
-				<include.tags><![CDATA[IntegrationTest & Service]]></include.tags>
+				<include.tags>
+					<![CDATA[IntegrationTest & Service]]>
+				</include.tags>
 				<tomcat.skip>true</tomcat.skip>
 				<exclude.test.listeners>
 					ca.corefacility.bioinformatics.irida.junit5.listeners.UnitTestListener,
@@ -974,7 +977,9 @@
 		<profile>
 			<id>rest_testing</id>
 			<properties>
-				<include.tags><![CDATA[IntegrationTest & Rest]]></include.tags>
+				<include.tags>
+					<![CDATA[IntegrationTest & Rest]]>
+				</include.tags>
 				<tomcat.skip>true</tomcat.skip>
 				<exclude.test.listeners>
 					ca.corefacility.bioinformatics.irida.junit5.listeners.UnitTestListener,
@@ -985,7 +990,9 @@
 		<profile>
 			<id>galaxy_testing</id>
 			<properties>
-				<include.tags><![CDATA[IntegrationTest & Galaxy & !Pipeline]]></include.tags>
+				<include.tags>
+					<![CDATA[IntegrationTest & Galaxy & !Pipeline]]>
+				</include.tags>
 				<tomcat.skip>true</tomcat.skip>
 				<exclude.test.listeners>
 					ca.corefacility.bioinformatics.irida.junit5.listeners.UnitTestListener,
@@ -996,7 +1003,9 @@
 		<profile>
 			<id>galaxy_pipeline_testing</id>
 			<properties>
-				<include.tags><![CDATA[IntegrationTest & Galaxy & Pipeline]]></include.tags>
+				<include.tags>
+					<![CDATA[IntegrationTest & Galaxy & Pipeline]]>
+				</include.tags>
 				<tomcat.skip>true</tomcat.skip>
 				<exclude.test.listeners>
 					ca.corefacility.bioinformatics.irida.junit5.listeners.UnitTestListener,
@@ -1015,4 +1024,4 @@
 			</properties>
 		</profile>
 	</profiles>
-</project>
+</project>

src/main/java/ca/corefacility/bioinformatics/irida/config/web/IridaRestApiWebConfig.java

@@ -1,8 +1,8 @@
 package ca.corefacility.bioinformatics.irida.config.web;
 
 import java.nio.file.Path;
-import java.text.SimpleDateFormat;
 import java.util.ArrayList;
+import java.util.Date;
 import java.util.List;
 import java.util.Map;
 
@@ -22,6 +22,7 @@
 import org.springframework.web.servlet.view.json.MappingJackson2JsonView;
 
 import ca.corefacility.bioinformatics.irida.web.controller.api.json.PathJson;
+import ca.corefacility.bioinformatics.irida.web.controller.api.json.TimestampJson;
 import ca.corefacility.bioinformatics.irida.web.spring.view.*;
 
 import com.fasterxml.jackson.databind.module.SimpleModule;
@@ -79,14 +80,18 @@ private List<View> defaultViews() {
 		// add support for serializing Path data
 		SimpleModule module = new SimpleModule();
 		module.addSerializer(Path.class, new PathJson.PathSerializer());
-		jsonView.getObjectMapper()
-				.registerModule(module);
-
-		// java.util.date fields (i.e. createdDate, modifiedDate, etc) are stored in the database with
-		// seconds precision, but are generated at higher precision. To combat this, previously the entity
-		// was re-read from the database. Now we are just formatting the date with 0s for milliseconds
+		jsonView.getObjectMapper().registerModule(module);
+
+		// java.util.date fields (i.e. createdDate, modifiedDate, etc) are
+		// stored in the database with
+		// seconds precision, but are generated at higher precision. To combat
+		// this, previously the entity
+		// was re-read from the database. Now we are just formatting the date
+		// with 0s for milliseconds
 		// portion.
-		jsonView.getObjectMapper().setDateFormat(new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss.'000Z'"));
+		SimpleModule timestampModule = new SimpleModule();
+		timestampModule.addSerializer(Date.class, new TimestampJson.TimestampSerializer());
+		jsonView.getObjectMapper().registerModule(timestampModule);
 
 		views.add(jsonView);
 
@@ -103,8 +108,6 @@ public void configureContentNegotiation(ContentNegotiationConfigurer configurer)
 		Map<String, MediaType> mediaTypes = ImmutableMap.of("json", MediaType.APPLICATION_JSON, "fasta",
 				MediaType.valueOf("application/fasta"), "fastq", MediaType.valueOf("application/fastq"), "gbk",
 				MediaType.valueOf("application/genbank"));
-		configurer.ignoreAcceptHeader(false)
-				.defaultContentType(MediaType.APPLICATION_JSON)
-				.mediaTypes(mediaTypes);
+		configurer.ignoreAcceptHeader(false).defaultContentType(MediaType.APPLICATION_JSON).mediaTypes(mediaTypes);
 	}
 }

src/main/java/ca/corefacility/bioinformatics/irida/web/controller/api/json/TimestampJson.java

@@ -0,0 +1,38 @@
+package ca.corefacility.bioinformatics.irida.web.controller.api.json;
+
+import java.io.IOException;
+import java.util.Calendar;
+import java.util.Date;
+
+import com.fasterxml.jackson.core.JsonGenerator;
+import com.fasterxml.jackson.databind.SerializerProvider;
+import com.fasterxml.jackson.databind.ser.std.StdSerializer;
+
+import org.apache.commons.lang3.time.DateUtils;
+
+/**
+ * Serialization class for java Date objects. We use DATETIME types for storing
+ * our timestamps in mysql. DATETIME only stores at seconds precision by
+ * default. In the REST api when we create an object the timestamps will have
+ * milliseconds precision but on subsequent fetchs the timestamps will only have
+ * seconds precision. This enforces the timestamp fields to only ever have
+ * seconds precision.
+ */
+public class TimestampJson {
+
+	/**
+	 * Default serializer for {@link Date} objects.
+	 */
+	public static class TimestampSerializer extends StdSerializer<Date> {
+
+		public TimestampSerializer() {
+			super(Date.class);
+		}
+
+		@Override
+		public void serialize(Date value, JsonGenerator gen, SerializerProvider provider) throws IOException {
+			gen.writeNumber(DateUtils.truncate(value, Calendar.SECOND).getTime());
+		}
+
+	}
+}