Spring Boot 2.7.3

CHANGELOG.md

@@ -25,6 +25,7 @@
 * [Developer]: Added description and metadata to create & update project sample endpoints. See [PR 1359](https://github.com/phac-nml/irida/pull/1359)
 * [UI]: Fix issue where year is displayed incorrectly when the last day of the week for the date is in another year. See [PR 1364](https://github.com/phac-nml/irida/pull/1364)
 * [Developer]: Fix issue where large downloads silent failed due to async request timeout. See [PR 1368](https://github.com/phac-nml/irida/pull/1368)
+* [Developer]: Update to Spring Boot 2.7.3 and update various other dependencies. See [PR 1369](https://github.com/phac-nml/irida/pull/1369)
 
 ## [22.05.5] - 2022/06/28
 * [UI]: Fixed bug preventing export of project samples table due to invalid url. [PR 1331](https://github.com/phac-nml/irida/pull/1331)

build.gradle.kts

@@ -122,7 +122,7 @@ dependencies {
     implementation("org.springframework.boot:spring-boot-starter-validation")
     implementation("org.springframework.boot:spring-boot-starter-security")
     implementation("org.springframework.security:spring-security-oauth2-authorization-server:0.3.1")
-    implementation("org.springframework.security:spring-security-oauth2-resource-server:5.7.2")
+    implementation("org.springframework.security:spring-security-oauth2-resource-server:5.7.3")
     implementation("org.apache.oltu.oauth2:org.apache.oltu.oauth2.client:1.0.0") {
         exclude(group = "org.slf4j")
     }
@@ -136,11 +136,11 @@ dependencies {
         exclude(group = "commons-logging", module = "commons-logging")
     }
     implementation("commons-net:commons-net:3.8.0")
-    implementation("org.apache.jena:jena-tdb:4.3.2") {
+    implementation("org.apache.jena:jena-tdb:4.6.1") {
         exclude(group = "xml-apis")
         exclude(group = "org.slf4j")
     }
-    implementation("org.apache.jena:jena-text:4.3.2") {
+    implementation("org.apache.jena:jena-text:4.6.1") {
         exclude(group = "xml-apis")
         exclude(group = "org.slf4j")
         exclude(group = "log4j")
@@ -163,15 +163,15 @@ dependencies {
     implementation("org.apache.logging.log4j:log4j-api")
     implementation("org.apache.logging.log4j:log4j-to-slf4j")
     implementation("com.google.guava:guava:31.0.1-jre")
-    implementation("commons-cli:commons-cli:1.2")
+    implementation("commons-cli:commons-cli:1.5.0")
     implementation("org.aspectj:aspectjweaver")
-    implementation("org.apache.commons:commons-csv:1.8")
+    implementation("org.apache.commons:commons-csv:1.9.0")
     implementation("com.sksamuel.diff:diff:1.1.11")
     implementation("org.pf4j:pf4j:2.4.0")
     implementation("org.biojava:biojava3-core:3.0")
     implementation("com.google.code.gson:gson")
     implementation("com.github.pjfanning:excel-streaming-reader:3.6.1")
-    implementation("org.springdoc:springdoc-openapi-webmvc-core:1.5.6") {
+    implementation("org.springdoc:springdoc-openapi-webmvc-core:1.6.11") {
         exclude(group = "jakarta.xml.bind", module = "jakarta.xml.bind-api")
         exclude(group = "jakarta.validation", module = "jakarta.validation-api")
     }
@@ -206,12 +206,12 @@ dependencies {
     testImplementation("io.rest-assured:rest-assured")
     testImplementation("io.rest-assured:json-path")
     testImplementation("com.github.springtestdbunit:spring-test-dbunit:1.3.0")
-    testImplementation("org.dbunit:dbunit:2.7.2") {
+    testImplementation("org.dbunit:dbunit:2.7.3") {
         exclude(group = "org.slf4j")
     }
-    testImplementation("org.seleniumhq.selenium:selenium-support:3.141.59")
-    testImplementation("org.seleniumhq.selenium:selenium-chrome-driver:3.141.59")
-    testImplementation("org.mockftpserver:MockFtpServer:2.6")
+    testImplementation("org.seleniumhq.selenium:selenium-support:4.4.0")
+    testImplementation("org.seleniumhq.selenium:selenium-chrome-driver:4.4.0")
+    testImplementation("org.mockftpserver:MockFtpServer:3.0.0")
 }
 
 tasks.register<Zip>("packageDistribution") {

settings.gradle.kts

@@ -7,7 +7,7 @@ pluginManagement {
         id("com.github.node-gradle.node") version "3.4.0"
         id("io.spring.dependency-management") version "1.0.11.RELEASE"
         id("org.gradle.test-retry") version "1.4.0"
-        id("org.springframework.boot") version "2.6.6"
+        id("org.springframework.boot") version "2.7.3"
         id("org.springdoc.openapi-gradle-plugin") version "1.3.4"
     }
 }

src/main/java/ca/corefacility/bioinformatics/irida/config/security/IridaOauthSecurityConfig.java

@@ -49,7 +49,7 @@
 import org.springframework.security.oauth2.server.resource.authentication.JwtGrantedAuthoritiesConverter;
 import org.springframework.security.web.SecurityFilterChain;
 import org.springframework.security.web.authentication.LoginUrlAuthenticationEntryPoint;
-import org.springframework.security.web.context.SecurityContextPersistenceFilter;
+import org.springframework.security.web.context.SecurityContextHolderFilter;
 import org.springframework.security.web.util.matcher.AntPathRequestMatcher;
 import org.springframework.security.web.util.matcher.RequestMatcher;
 import org.springframework.util.ResourceUtils;
@@ -116,7 +116,7 @@ public SecurityFilterChain resourceServerSecurityFilterChain(HttpSecurity http)
 			// user filter into the filter chain after that.
 			http.antMatcher("/api/**")
 					.addFilterAfter(new UnauthenticatedAnonymousAuthenticationFilter("anonymousTokenAuthProvider"),
-							SecurityContextPersistenceFilter.class);
+							SecurityContextHolderFilter.class);
 
 			return http.build();
 		}

src/main/java/ca/corefacility/bioinformatics/irida/model/sequenceFile/Fast5Object.java

@@ -7,6 +7,7 @@
 import javax.persistence.*;
 import javax.validation.constraints.NotNull;
 
+import org.apache.commons.io.FilenameUtils;
 import org.hibernate.envers.Audited;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -16,7 +17,6 @@
 
 import com.fasterxml.jackson.annotation.JsonIgnore;
 import com.google.common.collect.ImmutableSet;
-import liquibase.util.file.FilenameUtils;
 
 /**
  * {@link SequencingObject} implementation for storing .fast5 files.
@@ -57,8 +57,7 @@ public Set<SequenceFile> getFiles() {
 	}
 
 	/**
-	 * Throws {@link UnsupportedOperationException} because you should not be
-	 * able to update a file.
+	 * Throws {@link UnsupportedOperationException} because you should not be able to update a file.
 	 */
 	@JsonIgnore
 	@Override
@@ -68,15 +67,13 @@ public void setModifiedDate(Date modifiedDate) {
 
 	@Override
 	public String getLabel() {
-		return file.getFileName()
-				.toString();
+		return file.getFileName().toString();
 	}
 
 	public SequenceFile getFile() {
 		return file;
 	}
 
-
 	public Fast5Type getFast5Type() {
 		return fast5Type;
 	}

src/main/java/ca/corefacility/bioinformatics/irida/repositories/joins/project/ProjectSampleJoinRepository.java

@@ -104,6 +104,6 @@ public interface ProjectSampleJoinRepository
 	 * @param sampleIds {@link Sample} ids
 	 * @return A List of {@link Tuple}s with first entry as the sample id and second entry as the coverage
 	 */
-	@Query("SELECT ps.sample.id, ROUND(SUM(qc.totalBases)/ps.project.genomeSize) FROM ProjectSampleJoin ps join SampleSequencingObjectJoin sso on sso.sample = ps.sample join CoverageQCEntry qc on qc.sequencingObject = sso.sequencingObject where ps.project=?1 and ps.sample.id in ?2 group by ps.sample.id")
+	@Query("SELECT ps.sample.id, ROUND(SUM(qc.totalBases)/ps.project.genomeSize) FROM ProjectSampleJoin ps join SampleSequencingObjectJoin sso on sso.sample = ps.sample join CoverageQCEntry qc on qc.sequencingObject = sso.sequencingObject where ps.project=?1 and ps.sample.id in ?2 group by ps.sample.id, ps.project.genomeSize")
 	public List<Tuple> calculateCoverageForSamplesInProject(Project project, List<Long> sampleIds);
 }

src/main/java/ca/corefacility/bioinformatics/irida/ria/web/components/datatables/DataTablesExportToFile.java

@@ -7,13 +7,13 @@
 
 import javax.servlet.http.HttpServletResponse;
 
+import org.apache.commons.csv.CSVFormat;
+import org.apache.commons.csv.CSVPrinter;
 import org.apache.poi.ss.usermodel.Cell;
 import org.apache.poi.ss.usermodel.Row;
 import org.apache.poi.xssf.usermodel.XSSFSheet;
 import org.apache.poi.xssf.usermodel.XSSFWorkbook;
 
-import liquibase.util.csv.CSVWriter;
-
 /**
  * Used to export datatables to either excel or csv formatted files.
  */
@@ -22,19 +22,12 @@ public class DataTablesExportToFile {
 	/**
 	 * Write data within datatable to an excel formatted file.
 	 * 
-	 * @param type
-	 *            {@link DataTablesExportTypes} type of file to create (either
-	 *            excel or csv)
-	 * @param response
-	 *            {@link HttpServletResponse}
-	 * @param filename
-	 *            {@link String} name of the file to download.
-	 * @param models
-	 *            Data to download in the table
-	 * @param headers
-	 *            for the table
-	 * @throws IOException
-	 *             thrown if file cannot be written
+	 * @param type     {@link DataTablesExportTypes} type of file to create (either excel or csv)
+	 * @param response {@link HttpServletResponse}
+	 * @param filename {@link String} name of the file to download.
+	 * @param models   Data to download in the table
+	 * @param headers  for the table
+	 * @throws IOException thrown if file cannot be written
 	 */
 	public static void writeFile(DataTablesExportTypes type, HttpServletResponse response, String filename,
 			List<? extends DataTablesExportable> models, List<String> headers) throws IOException {
@@ -50,16 +43,11 @@ public static void writeFile(DataTablesExportTypes type, HttpServletResponse res
 	/**
 	 * Write data within datatable to an excel formatted file.
 	 * 
-	 * @param response
-	 *            {@link HttpServletResponse}
-	 * @param filename
-	 *            {@link String} name of the file to download.
-	 * @param models
-	 *            Data to download in the table
-	 * @param headers
-	 *            for the table
-	 * @throws IOException
-	 *             thrown if file cannot be written
+	 * @param response {@link HttpServletResponse}
+	 * @param filename {@link String} name of the file to download.
+	 * @param models   Data to download in the table
+	 * @param headers  for the table
+	 * @throws IOException thrown if file cannot be written
 	 */
 	private static void writeToExcel(HttpServletResponse response, String filename,
 			List<? extends DataTablesExportable> models, List<String> headers) throws IOException {
@@ -95,16 +83,11 @@ private static void writeToExcel(HttpServletResponse response, String filename,
 	/**
 	 * Write data within datatable to a csv formatted file.
 	 * 
-	 * @param response
-	 *            {@link HttpServletResponse}
-	 * @param filename
-	 *            {@link String} name of the file to download.
-	 * @param models
-	 *            Data to download in the table
-	 * @param headers
-	 *            for the table
-	 * @throws IOException
-	 *             thrown if file cannot be written
+	 * @param response {@link HttpServletResponse}
+	 * @param filename {@link String} name of the file to download.
+	 * @param models   Data to download in the table
+	 * @param headers  for the table
+	 * @throws IOException thrown if file cannot be written
 	 */
 	private static void writeToCSV(HttpServletResponse response, String filename,
 			List<? extends DataTablesExportable> models, List<String> headers) throws IOException {
@@ -117,9 +100,9 @@ private static void writeToCSV(HttpServletResponse response, String filename,
 		response.setHeader("Content-Disposition", "attachment; filename=\"" + filename + ".csv\"");
 		response.setContentType("text/csv");
 		OutputStreamWriter outputStreamWriter = new OutputStreamWriter(response.getOutputStream());
-		CSVWriter csvWriter = new CSVWriter(outputStreamWriter, ',');
-		csvWriter.writeAll(results);
-		csvWriter.flush();
-		csvWriter.close();
+		CSVPrinter printer = CSVFormat.DEFAULT.print(outputStreamWriter);
+		printer.printRecords(results);
+		printer.flush();
+		outputStreamWriter.close();
 	}
 }

src/main/java/ca/corefacility/bioinformatics/irida/ria/web/services/UISampleService.java

@@ -13,6 +13,8 @@
 import javax.servlet.http.HttpServletResponse;
 import javax.validation.ConstraintViolationException;
 
+import org.apache.commons.csv.CSVFormat;
+import org.apache.commons.csv.CSVPrinter;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.poi.ss.usermodel.Cell;
 import org.apache.poi.ss.usermodel.CellStyle;
@@ -72,7 +74,6 @@
 
 import com.google.common.base.Strings;
 import com.google.common.collect.ImmutableList;
-import liquibase.util.csv.CSVWriter;
 
 /**
  * UI Service for samples
@@ -714,9 +715,9 @@ private void writeToCSV(HttpServletResponse response, String filename, List<Proj
 		response.setHeader("Content-Disposition", "attachment; filename=\"" + filename + ".csv\"");
 		response.setContentType("text/csv");
 		OutputStreamWriter outputStreamWriter = new OutputStreamWriter(response.getOutputStream());
-		CSVWriter csvWriter = new CSVWriter(outputStreamWriter, ',');
-		csvWriter.writeAll(results);
-		csvWriter.flush();
-		csvWriter.close();
+		CSVPrinter printer = CSVFormat.DEFAULT.print(outputStreamWriter);
+		printer.printRecords(results);
+		printer.flush();
+		outputStreamWriter.close();
 	}
 }

src/main/java/ca/corefacility/bioinformatics/irida/ria/web/utilities/ExceptionUtilities.java

@@ -36,10 +36,10 @@ public static void throwConstraintViolationException(TransactionSystemException
 		if (exception.getRootCause() instanceof ConstraintViolationException) {
 			constraintViolationException = (ConstraintViolationException) exception.getRootCause();
 			Set<ConstraintViolation<?>> constraintViolationSet = constraintViolationException.getConstraintViolations();
-			for (ConstraintViolation constraintViolation : constraintViolationSet) {
+			for (ConstraintViolation<?> constraintViolation : constraintViolationSet) {
 				// The constraintViolation.getMessage() returns the i18n key in this case
-				constraintViolationMessage +=
-						messageSource.getMessage(constraintViolation.getMessage(), new Object[] {}, locale) + "\n";
+				constraintViolationMessage += messageSource.getMessage(constraintViolation.getMessage(),
+						new Object[] {}, locale) + "\n";
 			}
 		}
 		throw new UIConstraintViolationException(constraintViolationMessage);

src/test/java/ca/corefacility/bioinformatics/irida/junit5/listeners/IntegrationUITestListener.java

@@ -1,10 +1,8 @@
 package ca.corefacility.bioinformatics.irida.junit5.listeners;
 
-import static org.junit.jupiter.api.Assertions.fail;
-
 import java.net.MalformedURLException;
 import java.net.URL;
-import java.util.concurrent.TimeUnit;
+import java.time.Duration;
 
 import org.junit.platform.launcher.TestExecutionListener;
 import org.junit.platform.launcher.TestPlan;
@@ -15,8 +13,10 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import static org.junit.jupiter.api.Assertions.fail;
+
 public class IntegrationUITestListener implements TestExecutionListener {
-	
+
 	private static final Logger logger = LoggerFactory.getLogger(IntegrationUITestListener.class);
 	public static final int DRIVER_TIMEOUT_IN_SECONDS = 3;
 
@@ -89,7 +89,7 @@ public static void startWebDriver() {
 			driver = new ChromeDriver(options);
 		}
 
-		driver.manage().timeouts().implicitlyWait(DRIVER_TIMEOUT_IN_SECONDS, TimeUnit.SECONDS);
+		driver.manage().timeouts().implicitlyWait(Duration.ofSeconds(DRIVER_TIMEOUT_IN_SECONDS));
 	}
 
 	public static void stopWebDriver() {

src/test/java/ca/corefacility/bioinformatics/irida/ria/integration/Select2Utility.java

@@ -1,5 +1,7 @@
 package ca.corefacility.bioinformatics.irida.ria.integration;
 
+import java.time.Duration;
+
 import org.openqa.selenium.By;
 import org.openqa.selenium.WebDriver;
 import org.openqa.selenium.WebElement;
@@ -19,14 +21,15 @@ public void openSelect2Input() {
 	}
 
 	public void searchByText(String text) {
-		WebDriverWait wait = new WebDriverWait(driver, 10L);
+		WebDriverWait wait = new WebDriverWait(driver, Duration.ofSeconds(10L));
 		WebElement input = wait.until(ExpectedConditions.elementToBeClickable(By.cssSelector("a.select2-choice")));
 		input.sendKeys(text);
 	}
 
 	public void selectDefaultMatch() {
-		WebDriverWait wait = new WebDriverWait(driver, 10L);
-		WebElement match = wait.until(ExpectedConditions.visibilityOf(driver.findElement(By.className("select2-match"))));
+		WebDriverWait wait = new WebDriverWait(driver, Duration.ofSeconds(10L));
+		WebElement match = wait
+				.until(ExpectedConditions.visibilityOf(driver.findElement(By.className("select2-match"))));
 		match.click();
 	}
 }

src/test/java/ca/corefacility/bioinformatics/irida/ria/integration/components/AddMemberButton.java

@@ -1,5 +1,6 @@
 package ca.corefacility.bioinformatics.irida.ria.integration.components;
 
+import java.time.Duration;
 import java.util.List;
 
 import org.openqa.selenium.By;
@@ -28,7 +29,7 @@ public class AddMemberButton {
 	private static WebDriverWait wait;
 
 	public static AddMemberButton getAddMemberButton(WebDriver driver) {
-		wait = new WebDriverWait(driver, 3);
+		wait = new WebDriverWait(driver, Duration.ofSeconds(3L));
 		return PageFactory.initElements(driver, AddMemberButton.class);
 	}
 

src/test/java/ca/corefacility/bioinformatics/irida/ria/integration/components/Announcements.java

@@ -1,5 +1,6 @@
 package ca.corefacility.bioinformatics.irida.ria.integration.components;
 
+import java.time.Duration;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
@@ -14,8 +15,7 @@
 import org.openqa.selenium.support.ui.WebDriverWait;
 
 /**
- * Used to test the state of the React AnnouncementsModal component.
- * This component can be found at login.
+ * Used to test the state of the React AnnouncementsModal component. This component can be found at login.
  */
 public class Announcements {
 	private static final String RATIO_REGULAR_EXPRESSION = "Read: (\\d+) / (\\d+)";
@@ -48,7 +48,7 @@ public class Announcements {
 	private static Actions actions;
 
 	public static Announcements goTo(WebDriver driver) {
-		wait = new WebDriverWait(driver, 5);
+		wait = new WebDriverWait(driver, Duration.ofSeconds(5L));
 		actions = new Actions(driver);
 		return PageFactory.initElements(driver, Announcements.class);
 	}