Merge pull request #1313 from ericenns/hotfix/22.05.2

Hotfix/22.05.2

CHANGELOG.md

@@ -1,6 +1,12 @@
 
 # Changelog
 
+## [22.05.2] - 2022/06/10
+* [Developer/UI]: Fix flaky UI Integration tests. See [PR 1313](https://github.com/phac-nml/irida/pull/1313)
+* [Developer]: Update war build to decrease size and remove executable ability. See [PR 1313](https://github.com/phac-nml/irida/pull/1313)
+* [Developer/UI]: Fixed bug where context path was not set for login and password reset components. See [PR 1313](https://github.com/phac-nml/irida/pull/1313)
+* [Developer]: Fixed bug where duplicate project_subscriptions were added for users who had direct project membership with email subscriptions and were also a member of the project through group membership. See [PR 1313](https://github.com/phac-nml/irida/pull/1313)
+
 ## [22.05.1] - 2022/06/01
 * [UI]: Fixed bug where samples could not be removed from share page. See [PR 1296](https://github.com/phac-nml/irida/pull/1296) for more.
 * [Developer]: Fixed bug where project_subscriptions were added for groups without projects. See [PR 1296](https://github.com/phac-nml/irida/pull/1296) for more.
@@ -80,6 +86,7 @@
 
 ## [...previous](https://github.com/phac-nml/irida/blob/21.09.2/CHANGELOG.md)
 
+[22.05.2]: https://github.com/phac-nml/irida/compare/22.05.1...22.05.2
 [22.05.1]: https://github.com/phac-nml/irida/compare/22.05...22.05.1
 [22.05]: https://github.com/phac-nml/irida/compare/22.03.1...22.05
 [22.03.1]: https://github.com/phac-nml/irida/compare/22.03...22.03.1

pom.xml

@@ -9,7 +9,7 @@
   <groupId>ca.corefacility.bioinformatics</groupId>
   <artifactId>irida</artifactId>
   <packaging>war</packaging>
-  <version>22.05.1</version>
+  <version>22.05.2</version>
   <name>irida</name>
   <url>http://www.irida.ca</url>
 
@@ -542,6 +542,15 @@
           <jvmArguments>${failsafeArgLine}</jvmArguments>
         </configuration>
         <executions>
+          <execution>
+            <id>repackage</id>
+            <goals>
+              <goal>repackage</goal>
+            </goals>
+            <configuration>
+              <skip>true</skip>
+            </configuration>
+          </execution>
           <execution>
             <id>pre-integration-test</id>
             <goals>
@@ -749,10 +758,18 @@
         <configuration>
           <failOnMissingWebXml>false</failOnMissingWebXml>
           <packagingExcludes>
+						node/,
 						node_modules/,
 						.yarn/,
 						resources/css/,
-						resources/js/
+						resources/js/,
+            webpack*,
+            .yarn*,
+            package.json,
+            styles.js,
+            entries.js,
+            .eslintr.js,
+            postcss.config.js
 </packagingExcludes>
           <attachClasses>true</attachClasses>
         </configuration>
@@ -1027,4 +1044,4 @@
       </properties>
     </profile>
   </profiles>
-</project>
+</project>

src/main/resources/ca/corefacility/bioinformatics/irida/database/changesets/22.05/user-account-project-subscription.xml

@@ -1,69 +1,64 @@
 <?xml version="1.0" encoding="UTF-8"?>
 
-<databaseChangeLog xmlns="http://www.liquibase.org/xml/ns/dbchangelog"
-                   xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-                   xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog
+<databaseChangeLog xmlns="http://www.liquibase.org/xml/ns/dbchangelog" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog
          http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-4.3.xsd">
 
     <changeSet id="user-account-project-subscription" author="katherine">
         <validCheckSum>8:e75125f4b2af1759f21078bafe3b8ed9</validCheckSum>
+        <validCheckSum>8:4b751d31b04454a4763d8dca46ef4857</validCheckSum>
         <createTable tableName="project_subscription">
             <column name="id" type="bigint(20)" autoIncrement="true">
-                <constraints primaryKey="true" nullable="false"/>
+                <constraints primaryKey="true" nullable="false" />
             </column>
             <column name="project_id" type="bigint(20)">
-                <constraints foreignKeyName="FK_PROJECT_SUBSCRIPTION_PROJECT"
-                             referencedColumnNames="id" referencedTableName="project" nullable="false"/>
+                <constraints foreignKeyName="FK_PROJECT_SUBSCRIPTION_PROJECT" referencedColumnNames="id" referencedTableName="project" nullable="false" />
             </column>
             <column name="user_id" type="bigint(20)">
-                <constraints foreignKeyName="FK_PROJECT_SUBSCRIPTION_USER"
-                             referencedColumnNames="id" referencedTableName="user" nullable="false"/>
+                <constraints foreignKeyName="FK_PROJECT_SUBSCRIPTION_USER" referencedColumnNames="id" referencedTableName="user" nullable="false" />
             </column>
-            <column name="email_subscription" type="bit(1)" >
-                <constraints nullable="false"/>
+            <column name="email_subscription" type="bit(1)">
+                <constraints nullable="false" />
             </column>
             <column name="created_date" type="datetime">
-                <constraints nullable="false"/>
+                <constraints nullable="false" />
             </column>
         </createTable>
 
-        <addUniqueConstraint columnNames="project_id, user_id"
-                             constraintName="UK_PROJECT_SUBSCRIPTION_PROJECT_USER" tableName="project_subscription"/>
+        <addUniqueConstraint columnNames="project_id, user_id" constraintName="UK_PROJECT_SUBSCRIPTION_PROJECT_USER" tableName="project_subscription" />
 
         <createTable tableName="project_subscription_AUD">
             <column name="id" type="bigint(20)" autoIncrement="true">
-                <constraints primaryKey="true" nullable="false"/>
+                <constraints primaryKey="true" nullable="false" />
             </column>
             <column name="REV" type="int(11)">
-                <constraints primaryKey="true" nullable="false"
-                             foreignKeyName="FK_PROJECT_SUBSCRIPTION_REVISION" referencedColumnNames="id"
-                             referencedTableName="Revisions"/>
+                <constraints primaryKey="true" nullable="false" foreignKeyName="FK_PROJECT_SUBSCRIPTION_REVISION" referencedColumnNames="id" referencedTableName="Revisions" />
             </column>
-            <column name="REVTYPE" type="tinyint(4)"/>
+            <column name="REVTYPE" type="tinyint(4)" />
             <column name="project_id" type="bigint(20)">
-                <constraints nullable="false"/>
+                <constraints nullable="false" />
             </column>
             <column name="user_id" type="bigint(20)">
-                <constraints nullable="false"/>
+                <constraints nullable="false" />
             </column>
             <column name="email_subscription" type="bit(1)">
-                <constraints nullable="false"/>
+                <constraints nullable="false" />
             </column>
             <column name="created_date" type="datetime">
-                <constraints nullable="false"/>
+                <constraints nullable="false" />
             </column>
         </createTable>
 
         <sql>
             INSERT INTO project_subscription (project_id, user_id, email_subscription, created_date)
-            SELECT project_id, user_id, IF(email_subscription=b'1', 1, 0), now() FROM project_user
+            SELECT project_id, user_id, MAX(email_subscription), MIN(created_date) FROM
+            (SELECT project_id, user_id, IF(email_subscription=b'1', 1, 0) as email_subscription, now() as created_date FROM project_user
             UNION
-            SELECT p.project_id, m.user_id, 0, now() from user_group_member m INNER JOIN user_group_project p ON
-            m.group_id = p.user_group_id;
+            SELECT p.project_id, m.user_id, 0 as email_subscription, now() as created_date from user_group_member m INNER JOIN user_group_project p ON
+            m.group_id = p.user_group_id) t group by project_id, user_id;
         </sql>
 
-        <dropColumn tableName="project_user" columnName="email_subscription"/>
-        <dropColumn tableName="project_user_AUD" columnName="email_subscription"/>
+        <dropColumn tableName="project_user" columnName="email_subscription" />
+        <dropColumn tableName="project_user_AUD" columnName="email_subscription" />
 
     </changeSet>
 </databaseChangeLog>

src/main/webapp/pages/password/password_reset.html

@@ -22,6 +22,10 @@
       window.PAGE = {
         passwordReset: /*[[${passwordReset}]]*/ "0",
       };
+
+      window.TL = {
+        _BASE_URL: /*[[@{/}]]*/ '/',
+      }
     </script>
   </head>
   <body>

src/main/webapp/resources/js/apis/password-reset.js

@@ -1,15 +1,15 @@
 import { createApi, fetchBaseQuery } from "@reduxjs/toolkit/query/react";
 import { setBaseUrl } from "../utilities/url-utilities";
 
-const BASE_URL = setBaseUrl(`ajax/password_reset`);
+const BASE_URL = setBaseUrl(`/ajax/password_reset`);
 
 /**
  * Redux API for password resets.
  */
 export const passwordResetApi = createApi({
   reducerPath: `passwordResetApi`,
   baseQuery: fetchBaseQuery({
-    baseUrl: setBaseUrl(BASE_URL),
+    baseUrl: BASE_URL,
   }),
   tagTypes: ["PasswordReset"],
   endpoints: (build) => ({

src/main/webapp/resources/js/pages/LoginPage.jsx

@@ -12,6 +12,14 @@ import store from "./store";
 import { ForgotPassword } from "./password/ForgotPassword";
 import { ActivateAccount } from "./password/ActivateAccount";
 
+/*
+WEBPACK PUBLIC PATH:
+Webpack does not know what the servlet context path is.  To fix this, webpack exposed
+the variable `__webpack_public_path__`
+See: https://webpack.js.org/guides/public-path/#on-the-fly
+ */
+__webpack_public_path__ = setBaseUrl(`/dist/`);
+
 const { Item } = Form;
 
 /**
@@ -99,7 +107,7 @@ function LoginForm({ updateDisplayLoginPage, updatePageType }) {
                   history.pushState(
                     "forgot",
                     "Forgot Password",
-                    "/forgot_password"
+                    setBaseUrl("/forgot_password")
                   );
                 }}
                 style={{ padding: 0, marginLeft: 15 }}
@@ -116,7 +124,7 @@ function LoginForm({ updateDisplayLoginPage, updatePageType }) {
                   history.pushState(
                     "activate",
                     "Activate Account",
-                    "/activate_account"
+                    setBaseUrl("/activate_account")
                   );
                 }}
                 style={{ padding: 0, marginLeft: 25 }}
@@ -180,7 +188,7 @@ function LoginPage() {
                     history.pushState(
                       "forgot",
                       "Forgot Password",
-                      "/forgot_password"
+                      setBaseUrl("/forgot_password")
                     );
                   }}
                 >

src/main/webapp/resources/js/pages/password/PasswordReset.jsx

@@ -14,6 +14,14 @@ import store from "../store";
 import { Provider } from "react-redux";
 import { validatePassword } from "../../utilities/validation-utilities";
 
+/*
+WEBPACK PUBLIC PATH:
+Webpack does not know what the servlet context path is.  To fix this, webpack exposed
+the variable `__webpack_public_path__`
+See: https://webpack.js.org/guides/public-path/#on-the-fly
+ */
+__webpack_public_path__ = setBaseUrl(`/dist/`);
+
 const { Item } = Form;
 const passwordExpired =
   new URLSearchParams(window.location.search).get("expired") || false;

src/main/webapp/resources/js/pages/projects/samples/index.js

@@ -13,6 +13,15 @@ import {
 } from "../../../apis/projects/associated-projects";
 import samplesReducer from "../redux/samplesSlice";
 import { projectApi } from "../../../apis/projects/project";
+import { setBaseUrl } from "../../../utilities/url-utilities";
+
+/*
+WEBPACK PUBLIC PATH:
+Webpack does not know what the servlet context path is.  To fix this, webpack exposed
+the variable `__webpack_public_path__`
+See: https://webpack.js.org/guides/public-path/#on-the-fly
+ */
+__webpack_public_path__ = setBaseUrl(`/dist/`);
 
 /**
  * Redux store for project samples

src/main/webapp/resources/js/pages/user/index.js

@@ -18,6 +18,14 @@ const UserSecurityPage = React.lazy(() =>
   import("./components/UserSecurityPage")
 );
 
+/*
+WEBPACK PUBLIC PATH:
+Webpack does not know what the servlet context path is.  To fix this, webpack exposed
+the variable `__webpack_public_path__`
+See: https://webpack.js.org/guides/public-path/#on-the-fly
+ */
+__webpack_public_path__ = setBaseUrl(`/dist/`);
+
 /**
  * React component that displays the user pages.
  * @returns {*}

src/test/java/ca/corefacility/bioinformatics/irida/ria/integration/AbstractIridaUIITChromeDriver.java

@@ -8,8 +8,6 @@
 import java.util.List;
 
 import org.junit.jupiter.api.AfterAll;
-import org.junit.jupiter.api.AfterEach;
-import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Tag;
 import org.junit.jupiter.api.extension.ExtensionContext;
 import org.junit.jupiter.api.extension.RegisterExtension;
@@ -47,8 +45,8 @@
 @Tag("IntegrationTest")
 @Tag("UI")
 @ActiveProfiles("it")
-@SpringBootTest(classes = { IridaApplication.class,
-		IridaApiTestFilesystemConfig.class }, webEnvironment = WebEnvironment.RANDOM_PORT)
+@SpringBootTest(classes = { IridaApplication.class, IridaApiTestFilesystemConfig.class },
+		webEnvironment = WebEnvironment.RANDOM_PORT)
 @Import(IridaIntegrationTestUriConfig.class)
 @TestExecutionListeners({ DependencyInjectionTestExecutionListener.class, DbUnitTestExecutionListener.class })
 @DatabaseTearDown("classpath:/ca/corefacility/bioinformatics/irida/test/integration/TableReset.xml")
@@ -67,26 +65,6 @@ public class AbstractIridaUIITChromeDriver {
 	@RegisterExtension
 	public ScreenshotOnFailureWatcher watcher = new ScreenshotOnFailureWatcher();
 
-	/**
-	 * Code to execute before *each* test.
-	 */
-	@BeforeEach
-	public void setUpTest() throws IOException {
-		// logout before everything else.
-		LoginPage.logout(driver());
-	}
-
-	/**
-	 * Code to execute after *each* test.
-	 */
-	@AfterEach
-	public void tearDown() {
-		// NOTE: DO **NOT** log out in this method. This method happens because
-		// the @After method happens immediately after test failure, but before
-		// the @Rule TestWatcher checks the outcome of the test. We want to take
-		// a screenshot of the application state **before** logging out.
-	}
-
 	/**
 	 * Code to execute *once* after the class is finished.
 	 */
@@ -119,18 +97,12 @@ public static WebDriver driver() {
 	}
 
 	/**
-	 * Method to use on any page to check to ensure that internationalization
-	 * messages are being automatically loaded onto the page.
+	 * Method to use on any page to check to ensure that internationalization messages are being automatically loaded
+	 * onto the page.
 	 *
-	 * @param page
-	 *            - the instance of {@link AbstractPage} to check for
-	 *            internationalization.
-	 * @param entries
-	 *            - a {@link List} of bundle names. This will correspond to the
-	 *            loaded webpack bundles.
-	 * @param header
-	 *            - Expected text for the main heading on the page. Needs to
-	 *            have class name `t-main-heading`
+	 * @param page    - the instance of {@link AbstractPage} to check for internationalization.
+	 * @param entries - a {@link List} of bundle names. This will correspond to the loaded webpack bundles.
+	 * @param header  - Expected text for the main heading on the page. Needs to have class name `t-main-heading`
 	 */
 	public void checkTranslations(AbstractPage page, List<String> entries, String header) {
 		// Always check for app :)
@@ -167,6 +139,22 @@ public void testFailed(ExtensionContext context, Throwable t) {
 			} catch (final IOException e) {
 				logger.error("Unable to write screenshot out.", e);
 			}
+			testFinished();
+		}
+
+		/**
+		 * {@inheritDoc}}
+		 */
+		@Override
+		public void testSuccessful(ExtensionContext context) {
+			testFinished();
+		}
+
+		/**
+		 * Logout after test has finished executing
+		 */
+		private void testFinished() {
+			LoginPage.logout(driver());
 		}
 	}
 }