fix: update year formatting from week year to calendar year

CHANGELOG.md

@@ -23,6 +23,7 @@
 * [Developer/UI]: Increased speed of Project Samples table export and added estimated coverage to Project Samples table and exports. See [PR 1360](https://github.com/phac-nml/irida/pull/1360)
 * [Workflow]: Start the Galaxy Data Library timeout when an upload begins rather than when it is first queued up. See [PR 1337](https://github.com/phac-nml/irida/pull/1337)
 * [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)
 
 ## [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)

doc/developer/rest/index.md

@@ -635,7 +635,7 @@ An individual sample contains the metadata associated with an isolate. The sampl
 | `sampleName` | The name used to refer to the sample by the user. This is often the same as `sequencerSampleId`, but *may* be different. | Required. Must be at least 3 characters long. Must not contain any of the following characters: `? ( ) [ ] / \ = + < > : ; " , * ^ | & ' . |` (note: this blocklist of characters is defined by the set of invalid characters on the Windows file system)|
 | `description` | A plain-text description of the sample. | Not required. |
 | `strain` | The microbial or eukaryotic strain name. | Not required. Must be at least 3 characters long. |
-| `collectionDate` | The date that the sample was collected. | Not required. Must be a valid date in the format of "YYYY-MM-DD" (e.g,. "2019-01-25" for January 25, 2019). |
+| `collectionDate` | The date that the sample was collected. | Not required. Must be a valid date in the format of "yyyy-MM-DD" (e.g,. "2019-01-25" for January 25, 2019). |
 | `collectedBy` | The person (or organization) that collected the sample. | Not required. Must be at least 3 characters long. |
 | `latitude` | The latitude of the location where the sample was collected. | Not required. Must be a valid latitude (must match the pattern `^-?(\d){1,2}(\.\d+)?$` and the first number group must be in the range `[-90, 90]`). |
 | `longitude` | The longitude of the location where the sample was collected. | Not required. Must be a valid longitude (must match the pattern `-?(\d){1,3}(\.\d+)?$` and the first number group must be in the range `[-180, 180]`). |

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

@@ -1,10 +1,10 @@
 package ca.corefacility.bioinformatics.irida.web.controller.api.json;
 
 import java.io.IOException;
-import java.util.Date;
 import java.text.DateFormat;
 import java.text.ParseException;
 import java.text.SimpleDateFormat;
+import java.util.Date;
 
 import com.fasterxml.jackson.core.JsonGenerator;
 import com.fasterxml.jackson.core.JsonParser;
@@ -20,8 +20,9 @@
 public class DateJson {
 
 	private static final DateFormat DATE_FORMAT = new SimpleDateFormat("yyyy-MM-dd");
+
 	/**
-	 * Custom JSON serializer to format date as YYYY-MM-DD.
+	 * Custom JSON serializer to format date as yyyy-MM-DD.
 	 */
 	public static class DateSerializer extends StdSerializer<Date> {
 
@@ -41,7 +42,7 @@ public void serialize(Date value, JsonGenerator gen, SerializerProvider provider
 	}
 
 	/**
-	 * Custom JSON deserializer date from format YYYY-MM-DD.
+	 * Custom JSON deserializer date from format yyyy-MM-DD.
 	 */
 	public static class DateDeserializer extends StdDeserializer<Date> {
 

src/main/resources/i18n/messages.properties

@@ -3,8 +3,8 @@ generic.unknown=unknown
 generic.percent-complete={0}% Complete
 generic.irida.website=IRIDA Website
 generic.irida.contact=Contact Us
-generic.dateformat=MMM dd, YYYY
-generic.datetimeformat=MMM dd, YYYY, h:m:s a
+generic.dateformat=MMM dd, yyyy
+generic.datetimeformat=MMM dd, yyyy, h:m:s a
 generic.ajax-unexpected-error=Unexpected error has occurred.
 
 pipeline=Pipeline
@@ -1020,7 +1020,7 @@ project.sample.filter.date.month=Previous Month
 project.sample.filter.date.months3=Previous 3 Months
 project.sample.filter.date.months6=Previous 6 Months
 project.sample.filter.date.year=Previous Year
-project.sample.filter.date.format=MMMM DD, YYYY
+project.sample.filter.date.format=MMMM DD, yyyy
 project.sample.filter.apply=Apply Filters
 project.sample.filterByFile=Filter & Select by File
 project.sample.ClearFilterByFile=Clear File Filter
@@ -1536,10 +1536,10 @@ location.latitude=Latitude
 location.longitude=Longitude
 
 # LOCALE
-locale.date.short=dd MMM YYYY
+locale.date.short=dd MMM yyyy
 datepicker.short=dd MMM yyyy
-locale.date.long=dd MMM, YYYY - h:mm a
-date.iso-8601=YYYYMMdd
+locale.date.long=dd MMM, yyyy - h:mm a
+date.iso-8601=yyyyMMdd
 
 # ANALYSIS
 analysis.page.admin.title=All Analyses

src/main/webapp/pages/projects/export/ncbi.html

@@ -46,7 +46,7 @@ <h2 th:text="${project.label}">_project id_</h2>
             </div>
             <div class="form-group col-md-6">
               <label for="release_date" th:text="#{project.export.release_date.title}">_Release Date_</label>
-              <input type="date" id="release_date" class="form-control" th:value="${#calendars.format(#dates.createToday(),'YYYY-MM-dd')}">
+              <input type="date" id="release_date" class="form-control" th:value="${#calendars.format(#dates.createToday(),'yyyy-MM-dd')}">
               <p class="help-block" th:text="#{project.export.release_date.description}">_When data will be released_</p>
             </div>
           </div>

src/main/webapp/pages/samples/sample_files.html

@@ -229,7 +229,7 @@ <h2 th:text="#{sample.files.fast5}">FAST5 Files</h2>
 					<td>
 						<div class="td_info pull-right">
 							<div class="td_info--value"
-								 th:text="${#dates.format(file.createdDate, dateFormat)}"></div>
+								 th:text="${#dates.format(file.getCreatedDate(), dateFormat)}"></div>
 							<div class="small text-muted pull-right td_info--desc"
 								 th:text="#{samples.files.createdDate}">Created Date</div>
 						</div>

src/main/webapp/pages/templates/_sequenceFile.html

@@ -42,7 +42,7 @@
 	</td>
 	<td>
 		<div class="td_info pull-right">
-			<div class="td_info--value"
+			<div class="td_info--value created-date"
 			     th:text="${#dates.format(file.getCreatedDate(), dateFormat)}"></div>
 			<div class="small text-muted pull-right td_info--desc"
 			     th:text="#{samples.files.createdDate}">Created Date

src/main/webapp/resources/js/pages/projects/linelist/components/Table/Table.jsx

@@ -203,7 +203,7 @@ export class TableComponent extends React.Component {
    * @returns {string}
    */
   generateFileName = (ext) => {
-    // YYYY-MM-dd-project-X-<metadata template name>.csv
+    // yyyy-MM-dd-project-X-<metadata template name>.csv
     const fullDate = new Date();
     const date = `${fullDate.getFullYear()}-${
       fullDate.getMonth() + 1

src/main/webapp/resources/js/utilities/date-utilities.js

@@ -44,7 +44,7 @@ export function fromNow({ date }) {
 /**
  * Format unix timestamp as human readable string.
  * @param  {(string | number)} date unix timestamp
- * @param {String} format defaults to "lll" which is mmm dd, YYYY h:mm AM
+ * @param {String} format defaults to "lll" which is mmm dd, yyyy h:mm AM
  * @return {string} formatted date
  */
 export function formatDate({ date, format }) {

src/test/java/ca/corefacility/bioinformatics/irida/ria/integration/pages/samples/SampleFilesPage.java

@@ -17,7 +17,6 @@
  * <p>
  * Page Object to represent the sample sequence files page.
  * </p>
- *
  */
 public class SampleFilesPage extends AbstractPage {
 	public static final String RELATIVE_URL = "samples/{id}/sequenceFiles";
@@ -38,43 +37,50 @@ public String getSequenceFileName() {
 		return driver.findElements(By.className("file-name")).get(0).getText();
 	}
 
+	public String getSequenceFileCreatedDate(String sequenceFileName) {
+		WebElement createdDateDiv = driver
+				.findElement(By.xpath("//tr[contains(@class, 'sequence-file-row')]/td/a[text()='" + sequenceFileName
+						+ "']/../../td/div/div[contains(@class, 'created-date')]"));
+		return createdDateDiv.getText();
+	}
+
 	public int getSequenceFileCount() {
 		return driver.findElements(By.className("sequence-file-row")).size();
 	}
-	
+
 	public int getAssemblyFileCount() {
 		return driver.findElements(By.className("assembly_row")).size();
 	}
-	
-	public String getSampleName(){
+
+	public String getSampleName() {
 		return driver.findElement(By.id("sample-name")).getText();
 	}
-	
+
 	public int getQcEntryCount() {
 		return driver.findElements(By.className("qc-item")).size();
 	}
-	
-	public void deleteFirstSequenceFile(){
+
+	public void deleteFirstSequenceFile() {
 		WebElement removeButton = driver.findElements(By.className("remove-file")).iterator().next();
 		removeButton.click();
-		WebElement confirmRemoveButton = (new WebDriverWait(driver, 10)).until(ExpectedConditions.elementToBeClickable(By
-				.id("remove-file-confirm")));
+		WebElement confirmRemoveButton = (new WebDriverWait(driver, 10))
+				.until(ExpectedConditions.elementToBeClickable(By.id("remove-file-confirm")));
 		confirmRemoveButton.click();
 	}
-	
-	public void deleteFirstSequenceFilePair(){
+
+	public void deleteFirstSequenceFilePair() {
 		WebElement removeButton = driver.findElements(By.className("remove-pair")).iterator().next();
 		removeButton.click();
-		WebElement confirmRemoveButton = (new WebDriverWait(driver, 10)).until(ExpectedConditions.elementToBeClickable(By
-				.id("remove-file-confirm")));
+		WebElement confirmRemoveButton = (new WebDriverWait(driver, 10))
+				.until(ExpectedConditions.elementToBeClickable(By.id("remove-file-confirm")));
 		confirmRemoveButton.click();
 	}
-	
-	public void deleteFirstAssemblyFile(){
+
+	public void deleteFirstAssemblyFile() {
 		WebElement removeButton = driver.findElements(By.className("remove-assembly")).iterator().next();
 		removeButton.click();
-		WebElement confirmRemoveButton = (new WebDriverWait(driver, 10)).until(ExpectedConditions.elementToBeClickable(By
-				.id("remove-file-confirm")));
+		WebElement confirmRemoveButton = (new WebDriverWait(driver, 10))
+				.until(ExpectedConditions.elementToBeClickable(By.id("remove-file-confirm")));
 		confirmRemoveButton.click();
 	}
 

src/test/java/ca/corefacility/bioinformatics/irida/ria/integration/samples/SampleFilesPageIT.java

@@ -18,8 +18,9 @@
 import static org.junit.jupiter.api.Assertions.assertTrue;
 
 /**
- * <p> Integration test to ensure that the Sample Details Page. </p>
- *
+ * <p>
+ * Integration test to ensure that the Sample Details Page.
+ * </p>
  */
 @DatabaseSetup("/ca/corefacility/bioinformatics/irida/ria/web/samples/SamplePagesIT.xml")
 public class SampleFilesPageIT extends AbstractIridaUIITChromeDriver {
@@ -32,12 +33,8 @@ public class SampleFilesPageIT extends AbstractIridaUIITChromeDriver {
 	private SampleFilesPage page;
 
 	private final List<Map<String, String>> BREADCRUMBS = ImmutableList.of(
-			ImmutableMap.of(
-					"href", "/samples",
-					"text", "Samples"
-			),
-			ImmutableMap.of("href", "/samples/" + SAMPLE_ID, "text", "sample1")
-	);
+			ImmutableMap.of("href", "/samples", "text", "Samples"),
+			ImmutableMap.of("href", "/samples/" + SAMPLE_ID, "text", "sample1"));
 
 	@BeforeEach
 	public void setUpTest() {
@@ -54,38 +51,40 @@ public void testPageSetup() {
 		assertEquals(4, page.getSequenceFileCount(), "Displays the correct number of sequence files");
 		assertEquals(2, page.getAssemblyFileCount(), "Displays the correct number of assemblies");
 		assertEquals(1, page.getQcEntryCount(), "should be 1 qc entry");
-		
+
 		page.checkBreadCrumbs(BREADCRUMBS);
 	}
-	
+
 	@Test
 	public void testDeleteFile() {
 		page.gotoPage(SAMPLE_ID);
-		
+
 		page.deleteFirstSequenceFile();
 		assertTrue(page.isDeleteConfirmationMessageDisplayed(),
 				"Should display a confirmation message that the file was deleted");
 		assertEquals(3, page.getSequenceFileCount(), "Displays the correct number of sequence files");
 	}
 
 	@Test
-	public void testDeletePair(){
+	public void testDeletePair() {
 		page.gotoPage(SAMPLE_ID);
-		
+
 		page.deleteFirstSequenceFilePair();
-		assertTrue(page.isDeleteConfirmationMessageDisplayed(), "Should display a confirmation message that the file was deleted");
+		assertTrue(page.isDeleteConfirmationMessageDisplayed(),
+				"Should display a confirmation message that the file was deleted");
 		assertEquals(2, page.getSequenceFileCount(), "Displays the correct number of sequence files");
 	}
-	
+
 	@Test
 	public void testDeleteAssembly() {
 		page.gotoPage(SAMPLE_ID);
-		
+
 		page.deleteFirstAssemblyFile();
 		assertTrue(page.isDeleteConfirmationMessageDisplayed(),
 				"Should display a confirmation message that the file was deleted");
 		assertEquals(1, page.getAssemblyFileCount(), "Displays the correct number of assemblies");
-		assertEquals(4, page.getSequenceFileCount(), "Should not have deleted sequence files (displays correct number of sequence files)");
+		assertEquals(4, page.getSequenceFileCount(),
+				"Should not have deleted sequence files (displays correct number of sequence files)");
 	}
 
 	@Test
@@ -98,7 +97,8 @@ public void testSequenceFilesUploads() {
 		page.gotoPage(SAMPLE_ID);
 		// Test wrong file format
 		page.uploadSequenceFile(FASTA_FILE);
-		assertTrue(page.isFileTypeWarningDisplayed(), "Should display a warning if the wrong file type is being uploaded.");
+		assertTrue(page.isFileTypeWarningDisplayed(),
+				"Should display a warning if the wrong file type is being uploaded.");
 	}
 
 	@Test
@@ -110,9 +110,10 @@ public void testAssemblyUploads() {
 		assertEquals(3, page.getAssemblyFileCount(), "Displays the correct number of assemblies displayed");
 		// Test wrong file format
 		page.uploadAssemblyFile(FASTQ_FILE);
-		assertTrue(page.isFileTypeWarningDisplayed(), "Should display a warning if the wrong file type is being uploaded.");
+		assertTrue(page.isFileTypeWarningDisplayed(),
+				"Should display a warning if the wrong file type is being uploaded.");
 	}
-	
+
 	@Test
 	public void testAccessMultiProjectSamplePage() {
 		LoginPage.logout(driver());
@@ -121,4 +122,11 @@ public void testAccessMultiProjectSamplePage() {
 		page.gotoPage(5L);
 		assertTrue(page.getPageTitle().contains("sample5"), "Page Title contains the sample label");
 	}
+
+	@Test
+	public void testCorrectYear() {
+		page.gotoPage(SAMPLE_ID);
+		assertEquals("31 Dec 2013", page.getSequenceFileCreatedDate("03-3333_S1_L001_R1_001.fastq"),
+				"Year should be 2013");
+	}
 }

src/test/resources/ca/corefacility/bioinformatics/irida/ria/web/samples/SamplePagesIT.xml

@@ -104,12 +104,12 @@
 		file_path="src/test/resources/files/sequence-files/02-2222_S1_L001_R1_001.fastq" />
 	<sequence_file id="3" created_date="2013-07-18 14:20:19.0"
 		file_path="src/test/resources/files/sequence-files/02-2222_S1_L001_R2_001.fastq" />
-	<sequence_file id="4" created_date="2013-07-18 14:20:19.0"
+	<sequence_file id="4" created_date="2013-12-31 14:20:19.0"
 		file_path="src/test/resources/files/sequence-files/03-3333_S1_L001_R1_001.fastq" />
 
 	<sequencing_object id="1" created_date="2013-07-18 14:20:19.0" />
 	<sequencing_object id="2" created_date="2013-07-18 14:20:19.0" />
-	<sequencing_object id="3" created_date="2013-07-18 14:20:19.0" />
+	<sequencing_object id="3" created_date="2013-12-31 14:20:19.0" />
 
 	<sequence_file_pair id="1" />
 	<sequence_file_pair_files pair_id="1"
@@ -127,7 +127,7 @@
 		created_date="2013-07-18 14:20:19.0" sample_id="1"
 		sequencingobject_id="2" />
 	<sample_sequencingobject id="3"
-		created_date="2013-07-18 14:20:19.0" sample_id="1"
+		created_date="2013-12-31 14:20:19.0" sample_id="1"
 		sequencingobject_id="3" />
 
 	<analysis_submission id="1" name="my analysis"