Merge pull request #1451 from phac-nml/hotfix/ncbi-upload-template

Fix NCBI Export
phac-nml · Jan 24, 2023 · 773d014 · 773d014
2 parents 9e2c02a + 8046499
commit 773d014
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,6 +1,9 @@
 
 # Changelog
 
+## [22.09.7] - Unreleased
+* [UI]: Fixed bugs on NCBI Export page preventing the NCBI `submission.xml` file from being properly written. See [PR 1451](https://github.com/phac-nml/irida/pull/1451)
+
 ## [22.09.6] - 2022/12/21
 * [UI]: Fixed bug on NCBI Export page preventing the export from occuring. See [PR 1439](https://github.com/phac-nml/irida/pull/1439)
 

diff --git a/build.gradle.kts b/build.gradle.kts
@@ -14,7 +14,7 @@ plugins {
 }
 
 group = "ca.corefacility.bioinformatics"
-version = "22.09.6"
+version = "22.09.7"
 description = "irida"
 
 java {

diff --git a/src/main/java/ca/corefacility/bioinformatics/irida/ria/web/services/UINcbiService.java b/src/main/java/ca/corefacility/bioinformatics/irida/ria/web/services/UINcbiService.java
@@ -14,14 +14,13 @@
 import ca.corefacility.bioinformatics.irida.model.export.NcbiBioSampleFiles;
 import ca.corefacility.bioinformatics.irida.model.project.Project;
 import ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFilePair;
-import ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject;
 import ca.corefacility.bioinformatics.irida.model.sequenceFile.SingleEndSequenceFile;
 import ca.corefacility.bioinformatics.irida.model.user.User;
 import ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.NcbiExportSubmissionTableModel;
 import ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiBioSampleModel;
 import ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiExportSubmissionAdminTableModel;
-import ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionRequest;
 import ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionModel;
+import ca.corefacility.bioinformatics.irida.ria.web.models.export.NcbiSubmissionRequest;
 import ca.corefacility.bioinformatics.irida.ria.web.models.tables.TableRequest;
 import ca.corefacility.bioinformatics.irida.ria.web.models.tables.TableResponse;
 import ca.corefacility.bioinformatics.irida.service.ProjectService;
@@ -89,22 +88,8 @@ public TableResponse<NcbiExportSubmissionAdminTableModel> getNCBIExportsForAdmin
 	 */
 	public NcbiSubmissionModel getExportDetails(Long exportId) {
 		NcbiExportSubmission submission = ncbiService.read(exportId);
-		Project project = projectService.read(submission.getProject()
-				.getId());
 
-		List<NcbiBioSampleModel> bioSamples = submission.getBioSampleFiles()
-				.stream()
-				.map(bioSampleFile -> {
-					List<SequencingObject> pairs = bioSampleFile.getPairs()
-							.stream()
-							.peek(pair -> uiSampleService.enhanceQcEntries(pair, project))
-							.collect(Collectors.toList());
-					List<SequencingObject> singles = bioSampleFile.getFiles()
-							.stream()
-							.peek(single -> uiSampleService.enhanceQcEntries(single, project))
-							.collect(Collectors.toList());
-					return new NcbiBioSampleModel(bioSampleFile);
-				})
+		List<NcbiBioSampleModel> bioSamples = submission.getBioSampleFiles().stream().map(NcbiBioSampleModel::new)
 				.collect(Collectors.toList());
 
 		return new NcbiSubmissionModel(submission, bioSamples);

diff --git a/src/main/resources/ca/corefacility/bioinformatics/irida/export/ncbi.xml b/src/main/resources/ca/corefacility/bioinformatics/irida/export/ncbi.xml
@@ -1,7 +1,8 @@
 <?xml version='1.0' encoding='utf-8'?>
 
 <Submission schema_version="2.0" xmlns:th="http://www.thymeleaf.org"
-	xmlns:layout="http://www.ultraq.net.nz/thymeleaf/layout" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xmlns:layout="http://www.ultraq.net.nz/thymeleaf/layout"
+	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
 	xsi:noNamespaceSchemaLocation="http://www.ncbi.nlm.nih.gov/viewvc/v1/trunk/submit/public-docs/common/submission.xsd?view=co">
 	<Description>
 		<Organization role="owner" type="institute">
@@ -17,13 +18,12 @@
 	</Description>
 
 	<Action th:each="sample : ${submission.bioSampleFiles}">
-		<!--/*-->
-		IRIDA sequence files may either be plaintext (.fastq) or gzip compressed (.fastq.gz)
-		NCBI requires that uploaded files should have the appropriate file extension.
-		Determine if the IRIDA sequence file is compressed by looking for .gz extension
-		and add the appropriate extension to the uploaded files.
-		<!--*/-->
-		<AddFiles target_db="SRA" th:each="file : ${sample.files}">
+		<!--/*--> IRIDA sequence files may either be
+		plaintext (.fastq) or gzip compressed (.fastq.gz) NCBI requires that uploaded files should
+		have the appropriate file extension. Determine if the IRIDA sequence file is compressed by
+		looking for .gz extension and add the appropriate extension to the uploaded files. <!--*/-->
+		<AddFiles
+			target_db="SRA" th:each="file : ${sample.files}">
 			<th:block th:if="${file.getFiles().toString().endsWith(&quot;.gz&quot;)}">
 				<File th:attr="file_path=${file.getId() + '.fastq.gz'}">
 					<DataType>generic-data</DataType>
@@ -34,13 +34,15 @@
 					<DataType>generic-data</DataType>
 				</File>
 			</th:block>
-			<Attribute name="instrument_model" th:text="${sample.instrumentModel.value}">_Model_</Attribute>
+			<Attribute name="instrument_model" th:text="${sample.instrumentModel.model}">_Model_</Attribute>
 			<Attribute name="library_name" th:text="${sample.libraryName}">_name_</Attribute>
 			<Attribute name="library_strategy" th:text="${sample.libraryStrategy.value}">_Strategy_</Attribute>
 			<Attribute name="library_source" th:text="${sample.librarySource.value}">_Source_</Attribute>
-			<Attribute name="library_selection" th:text="${sample.librarySelection.value}">_Selection_</Attribute>
+			<Attribute name="library_selection" th:text="${sample.librarySelection.value}">
+		_Selection_</Attribute>
 			<Attribute name="library_layout">SINGLE</Attribute>
-			<Attribute name="library_construction_protocol" th:text="${sample.libraryConstructionProtocol}">_Protocol_</Attribute>
+			<Attribute name="library_construction_protocol"
+				th:text="${sample.libraryConstructionProtocol}">_Protocol_</Attribute>
 			<AttributeRefId name="BioProject">
 				<RefId>
 					<PrimaryId db="BioProject" th:text="${submission.bioProjectId}">_Project_</PrimaryId>
@@ -56,8 +58,10 @@
 					th:text="${sample.id}">_spuid_</SPUID>
 			</Identifier>
 		</AddFiles>
-		<AddFiles target_db="SRA" th:each="pair : ${sample.pairs}" th:with="forward=${pair.getForwardSequenceFile()}, reverse=${pair.getReverseSequenceFile()}">
-            <th:block th:if="${forward.getFile().toString().endsWith(&quot;.gz&quot;)}">
+		<AddFiles
+			target_db="SRA" th:each="pair : ${sample.pairs}"
+			th:with="forward=${pair.getForwardSequenceFile()}, reverse=${pair.getReverseSequenceFile()}">
+			<th:block th:if="${forward.getFile().toString().endsWith(&quot;.gz&quot;)}">
 				<File th:attr="file_path=${forward.getId() + '.fastq.gz'}">
 					<DataType>generic-data</DataType>
 				</File>
@@ -67,7 +71,7 @@
 					<DataType>generic-data</DataType>
 				</File>
 			</th:block>
-			<th:block th:if="${reverse.getFile().toString().endsWith(&quot;.gz&quot;)}" >
+			<th:block th:if="${reverse.getFile().toString().endsWith(&quot;.gz&quot;)}">
 				<File th:attr="file_path=${reverse.getId() + '.fastq.gz'}">
 					<DataType>generic-data</DataType>
 				</File>
@@ -77,13 +81,15 @@
 					<DataType>generic-data</DataType>
 				</File>
 			</th:block>
-			<Attribute name="instrument_model" th:text="${sample.instrumentModel.value}">_Model_</Attribute>
+			<Attribute name="instrument_model" th:text="${sample.instrumentModel.model}">_Model_</Attribute>
 			<Attribute name="library_name" th:text="${sample.libraryName}">_name_</Attribute>
 			<Attribute name="library_strategy" th:text="${sample.libraryStrategy.value}">_Strategy_</Attribute>
 			<Attribute name="library_source" th:text="${sample.librarySource.value}">_Source_</Attribute>
-			<Attribute name="library_selection" th:text="${sample.librarySelection.value}">_Selection_</Attribute>
+			<Attribute name="library_selection" th:text="${sample.librarySelection.value}">
+		_Selection_</Attribute>
 			<Attribute name="library_layout">PAIRED</Attribute>
-			<Attribute name="library_construction_protocol" th:text="${sample.libraryConstructionProtocol}">_Protocol_</Attribute>
+			<Attribute name="library_construction_protocol"
+				th:text="${sample.libraryConstructionProtocol}">_Protocol_</Attribute>
 			<AttributeRefId name="BioProject">
 				<RefId>
 					<PrimaryId db="BioProject" th:text="${submission.bioProjectId}">_Project_</PrimaryId>
@@ -100,4 +106,4 @@
 			</Identifier>
 		</AddFiles>
 	</Action>
-</Submission>
+</Submission>
diff --git a/src/main/webapp/resources/js/components/ncbi/details/utils.tsx b/src/main/webapp/resources/js/components/ncbi/details/utils.tsx
@@ -17,8 +17,14 @@ import ExportUploadStateTag from "../ExportUploadStateTag";
 export const formatNcbiSubmissionDetails = (
   submission: Omit<NcbiSubmission, "bioSamples">
 ): BasicListItem[] => {
+  const LOCALE = window.TL?.LANGUAGE_TAG || "en";
   const releaseDate = submission.releaseDate
-    ? formatInternationalizedDateTime(submission.releaseDate)
+    ? new Date(submission.releaseDate).toLocaleDateString(LOCALE, {
+        month: "short",
+        year: "numeric",
+        day: "numeric",
+        timeZone: "UTC", // ignoring timezone
+      })
     : i18n("NcbiExportDetailsView.not-released");
 
   return [

diff --git a/src/main/webapp/resources/js/pages/projects/ncbi/create/CreateNcbiExport.tsx b/src/main/webapp/resources/js/pages/projects/ncbi/create/CreateNcbiExport.tsx
@@ -219,7 +219,7 @@ function CreateNcbiExport(): JSX.Element {
             pairs?: number[];
             singles?: number[];
             bioSample: string;
-            libraryName: { value: string };
+            libraryName: string;
             libraryStrategy: { value: string };
             librarySource: { value: string };
             libraryConstructionProtocol: { value: string };
@@ -234,7 +234,7 @@ function CreateNcbiExport(): JSX.Element {
           bioProject,
           namespace,
           organization,
-          releaseDate: releaseDate.unix(),
+          releaseDate: releaseDate.endOf("day").valueOf(),
           samples: Object.values(_samples).map(
             ({
               pairs = [],
@@ -251,7 +251,7 @@ function CreateNcbiExport(): JSX.Element {
                 singles,
                 pairs,
                 bioSample,
-                libraryName: libraryName.value,
+                libraryName,
                 libraryStrategy: libraryStrategy.value,
                 librarySource: librarySource.value,
                 libraryConstructionProtocol: libraryConstructionProtocol.value,

diff --git a/...a/ca/corefacility/bioinformatics/irida/ria/integration/pages/projects/NcbiExportPage.java b/...a/ca/corefacility/bioinformatics/irida/ria/integration/pages/projects/NcbiExportPage.java
@@ -4,6 +4,7 @@
 import java.util.List;
 
 import org.openqa.selenium.By;
+import org.openqa.selenium.Keys;
 import org.openqa.selenium.WebDriver;
 import org.openqa.selenium.WebElement;
 import org.openqa.selenium.support.FindBy;
@@ -30,6 +31,9 @@ public class NcbiExportPage extends AbstractPage {
 	@FindBy(xpath = "//*[@id=\"namespace\"]")
 	private WebElement namespaceInput;
 
+	@FindBy(xpath = "//*[@id=\"releaseDate\"]")
+	private WebElement releaseDateInput;
+
 	@FindBy(className = "t-defaults-panel")
 	private WebElement defaultsPanel;
 
@@ -73,6 +77,12 @@ public void enterNamespace(String value) {
 		namespaceInput.sendKeys(value);
 	}
 
+	public void setReleaseDateInput(String value) {
+		releaseDateInput.sendKeys(Keys.chord(Keys.CONTROL, "a"));
+		releaseDateInput.sendKeys(value);
+		releaseDateInput.sendKeys(Keys.ENTER);
+	}
+
 	public void toggleDefaultsPanel() {
 		defaultsPanel.click();
 	}

diff --git a/...efacility/bioinformatics/irida/ria/integration/pages/projects/NcbiExportsListingPage.java b/...efacility/bioinformatics/irida/ria/integration/pages/projects/NcbiExportsListingPage.java
@@ -1,11 +1,15 @@
 package ca.corefacility.bioinformatics.irida.ria.integration.pages.projects;
 
+import java.time.Duration;
 import java.util.List;
 
+import org.openqa.selenium.By;
 import org.openqa.selenium.WebDriver;
 import org.openqa.selenium.WebElement;
 import org.openqa.selenium.support.FindBy;
 import org.openqa.selenium.support.PageFactory;
+import org.openqa.selenium.support.ui.ExpectedConditions;
+import org.openqa.selenium.support.ui.WebDriverWait;
 
 import ca.corefacility.bioinformatics.irida.ria.integration.pages.AbstractPage;
 
@@ -25,4 +29,11 @@ public static NcbiExportsListingPage goTo(WebDriver driver) {
 	public int getNumberOfBioSampleIdsDisplayed() {
 		return biodamplesIds.size();
 	}
+
+	public void gotoSubmissionPage(String bioprojectId) {
+		WebElement link = driver.findElement(By.xpath("//table/tbody//a[text() = '" + bioprojectId + "']"));
+		link.click();
+		WebDriverWait wait = new WebDriverWait(driver, Duration.ofSeconds(5));
+		wait.until(ExpectedConditions.urlMatches("/projects/\\d+/export/\\d+"));
+	}
 }
diff --git a/.../java/ca/corefacility/bioinformatics/irida/ria/integration/projects/NcbiExportPageIT.java b/.../java/ca/corefacility/bioinformatics/irida/ria/integration/projects/NcbiExportPageIT.java
@@ -4,7 +4,9 @@
 
 import ca.corefacility.bioinformatics.irida.ria.integration.AbstractIridaUIITChromeDriver;
 import ca.corefacility.bioinformatics.irida.ria.integration.pages.LoginPage;
+import ca.corefacility.bioinformatics.irida.ria.integration.pages.projects.ExportDetailsPage;
 import ca.corefacility.bioinformatics.irida.ria.integration.pages.projects.NcbiExportPage;
+import ca.corefacility.bioinformatics.irida.ria.integration.pages.projects.NcbiExportsListingPage;
 import ca.corefacility.bioinformatics.irida.ria.integration.pages.projects.ProjectSamplesPage;
 
 import com.github.springtestdbunit.annotation.DatabaseSetup;
@@ -22,6 +24,7 @@ void testCreateNcbiSubmission() throws Exception {
 		String SAMPLE_3 = "sample3";
 		String BIOPROJECT = "BIOPROJECT-1";
 		String NAMESPACE = "NAMESPACE-FOOBAR";
+		String RELEASE_DATE = "2030-06-15";
 		String ORGANIZATION = "ORGANIZATION-FOOBAR";
 		String PROTOCOL = "AMAZING_PROTOCOL";
 		String DEFAULT_PROTOCOL = "DEFAULT_PROTOCOL";
@@ -40,6 +43,7 @@ void testCreateNcbiSubmission() throws Exception {
 		page.enterBioProject(BIOPROJECT);
 		page.enterNamespace(NAMESPACE);
 		page.enterOrganization(ORGANIZATION);
+		page.setReleaseDateInput(RELEASE_DATE);
 
 		// Test default sample settings.
 		page.toggleDefaultsPanel();
@@ -84,5 +88,16 @@ void testCreateNcbiSubmission() throws Exception {
 		assertTrue(page.isSuccessAlertDisplayed(), "Success notification should be displayed");
 		assertTrue(page.isUserRedirectedToProjectSamplesPage(PROJECT_ID),
 				"User should be redirected within 5 seconds of submission");
+
+		// Make sure all fields submitted successfully
+		NcbiExportsListingPage listingPage = NcbiExportsListingPage.goTo(driver());
+		listingPage.gotoSubmissionPage(BIOPROJECT);
+
+		ExportDetailsPage detailsPage = ExportDetailsPage.initPage(driver());
+		assertEquals(BIOPROJECT, detailsPage.getBioproject());
+		assertEquals(NAMESPACE, detailsPage.getNamespace());
+
+		assertEquals(ORGANIZATION, detailsPage.getOrganization());
+		assertTrue(detailsPage.getReleaseDate().equals("Jun 15, 2030"));
 	}
 }