Merge pull request #1439 from phac-nml/hotfix-ncbi-export

HOTFIX: Fixed issue with export file and instrument model using the NCBI Exporter

CHANGELOG.md

@@ -1,6 +1,9 @@
 
 # Changelog
 
+## Unreleased
+* [UI]: Fixed bug on NCBI Export page preventing the export from occuring. See [PR 1439](https://github.com/phac-nml/irida/pull/1439)
+
 ## [22.09.5] - 2022/12/14
 * [Developer/UI]: Fixed bug preventing a manager of a user group from adding new members when this manager is a collaborator on one of these users projects. Also, fixed issue with a user group member added with an owner role for a group was set with a member role. See [PR 1431](https://github.com/phac-nml/irida/pull/1431)
 * [Developer/UI]: Updated synchronize new remote project page to display http errors when setting the url manually and an error is encountered. See [PR 1433](https://github.com/phac-nml/irida/pull/1433)

src/main/webapp/resources/js/pages/projects/ncbi/create/CreateNcbiExport.tsx

@@ -7,22 +7,22 @@ import {
   Form,
   Input,
   Layout,
-  notification,
   PageHeader,
   Row,
   Space,
+  notification,
 } from "antd";
 import type { RangePickerProps } from "antd/es/date-picker";
 import { LabeledValue } from "antd/lib/select";
 import moment from "moment";
 import React from "react";
 import { useLoaderData, useNavigate, useParams } from "react-router-dom";
 import {
+  NcbiSubmissionBioSample,
+  NcbiSubmissionRequest,
   getNCBISelections,
   getNCBISources,
   getNCBIStrategies,
-  NcbiSubmissionBioSample,
-  NcbiSubmissionRequest,
   submitNcbiSubmissionRequest,
 } from "../../../../apis/export/ncbi";
 import { SequencingFiles } from "../../../../apis/projects/samples";
@@ -85,12 +85,12 @@ export interface UpdateDefaultValues {
   (field: DefaultModifiableField, value: string | string[]): void;
 }
 
-enum CreateStatus {
-  REJECTED,
-  RESOLVED,
-  PENDING,
-  IDLE,
-}
+const CreateStatus = {
+  REJECTED: 0,
+  RESOLVED: 1,
+  PENDING: 2,
+  IDLE: 3,
+} as const;
 
 /**
  * React router loader
@@ -133,7 +133,7 @@ function CreateNcbiExport(): JSX.Element {
   );
   const [formSamples, setFormSamples] = React.useState<FormSamples>({});
   const [invalid, setInvalid] = React.useState<SampleRecord[]>([]);
-  const [createStatus, setCreateStatus] = React.useState<CreateStatus>(
+  const [createStatus, setCreateStatus] = React.useState<number>(
     CreateStatus.IDLE
   );
 
@@ -216,17 +216,15 @@ function CreateNcbiExport(): JSX.Element {
         releaseDate: moment.Moment;
         samples: {
           string: {
-            files: {
-              pairs?: number[];
-              singles?: number[];
-            };
+            pairs?: number[];
+            singles?: number[];
             bioSample: string;
-            libraryName: string;
-            libraryStrategy: string;
-            librarySource: string;
-            libraryConstructionProtocol: string;
-            instrumentModel: [string, string];
-            librarySelection: string;
+            libraryName: { value: string };
+            libraryStrategy: { value: string };
+            librarySource: { value: string };
+            libraryConstructionProtocol: { value: string };
+            instrumentModel: { value: [string, string] };
+            librarySelection: { value: string };
           };
         };
       }) => {
@@ -239,15 +237,26 @@ function CreateNcbiExport(): JSX.Element {
           releaseDate: releaseDate.unix(),
           samples: Object.values(_samples).map(
             ({
-              files = { pairs: [], singles: [] },
+              pairs = [],
+              singles = [],
+              bioSample,
+              libraryName,
+              libraryStrategy,
+              librarySource,
+              libraryConstructionProtocol,
               instrumentModel,
-              ...rest
+              librarySelection,
             }): NcbiSubmissionBioSample => {
               return {
-                ...rest,
-                instrumentModel: instrumentModel[1],
-                singles: files.singles ? files.singles : [],
-                pairs: files.pairs ? files.pairs : [],
+                singles,
+                pairs,
+                bioSample,
+                libraryName: libraryName.value,
+                libraryStrategy: libraryStrategy.value,
+                librarySource: librarySource.value,
+                libraryConstructionProtocol: libraryConstructionProtocol.value,
+                instrumentModel: instrumentModel.value[1],
+                librarySelection: librarySelection.value,
               };
             }
           ),

src/main/webapp/resources/js/pages/projects/ncbi/create/CreateNcbiSampleDetails.tsx

@@ -133,6 +133,36 @@ export default function CreateNcbiSampleDetails({
     value: file.id,
   }));
 
+  async function filesValidator(
+    singlesFiles = [],
+    pairsFiles = []
+  ): Promise<string> {
+    if (singlesFiles.length > 0 || pairsFiles.length > 0) {
+      return Promise.resolve("");
+    }
+    return Promise.reject(
+      new Error("Must select at least one file of any type.")
+    );
+  }
+
+  function validateFiles({ getFieldValue, associatedField }) {
+    return {
+      validator(_, value) {
+        const otherFiles = getFieldValue([
+          "samples",
+          sample.name,
+          associatedField,
+        ]);
+        if (otherFiles.length > 0 || value.length > 0) {
+          return Promise.resolve("");
+        }
+        return Promise.reject(
+          new Error("Must select at least one file of any type.")
+        );
+      },
+    };
+  }
+
   return (
     <Row gutter={[16, 16]}>
       <Col md={12} xs={24}>
@@ -249,11 +279,19 @@ export default function CreateNcbiSampleDetails({
             label={i18n("CreateNcbiExport.singles")}
             valuePropName="checked"
             className="t-samples-singles"
+            rules={[
+              ({ getFieldValue }) =>
+                validateFiles({ getFieldValue, associatedField: "pairs" }),
+            ]}
           >
             <Checkbox.Group
               style={{ width: `100%` }}
               options={singles}
-              onChange={onChange}
+              onChange={function () {
+                form
+                  .validateFields([["samples", sample.name, "pairs"]])
+                  .then(onChange);
+              }}
             />
           </Form.Item>
         </Col>
@@ -264,11 +302,19 @@ export default function CreateNcbiSampleDetails({
             name={["samples", sample.name, "pairs"]}
             label={i18n("CreateNcbiExport.pairs")}
             valuePropName="checked"
+            rules={[
+              ({ getFieldValue }) =>
+                validateFiles({ getFieldValue, associatedField: "singles" }),
+            ]}
           >
             <Checkbox.Group
               style={{ width: `100%` }}
               options={pairs}
-              onChange={onChange}
+              onChange={function () {
+                form
+                  .validateFields([["samples", sample.name, "singles"]])
+                  .then(onChange);
+              }}
             />
           </Form.Item>
         </Col>

src/test/java/ca/corefacility/bioinformatics/irida/ria/integration/pages/projects/NcbiExportPage.java

@@ -80,8 +80,8 @@ public void toggleDefaultsPanel() {
 	public void setDefaultStrategySelect(String strategy) {
 		defaultStrategySelect.click();
 		WebDriverWait wait = new WebDriverWait(driver, Duration.ofSeconds(1));
-		List<WebElement> selectOptions = wait
-				.until(ExpectedConditions.presenceOfAllElementsLocatedBy(By.className("ant-select-item")));
+		List<WebElement> selectOptions = wait.until(
+				ExpectedConditions.presenceOfAllElementsLocatedBy(By.className("ant-select-item")));
 		for (WebElement option : selectOptions) {
 			if (option.getAttribute("title").equals(strategy)) {
 				option.click();
@@ -120,8 +120,8 @@ public void setSelectForSampleFieldValue(String field, String value) {
 		WebElement select = driver.findElement(By.className("t-sample-" + field));
 		select.click();
 		WebDriverWait wait = new WebDriverWait(driver, Duration.ofSeconds(1));
-		List<WebElement> selectOptions = wait
-				.until(ExpectedConditions.presenceOfAllElementsLocatedBy(By.className("ant-select-item")));
+		List<WebElement> selectOptions = wait.until(
+				ExpectedConditions.presenceOfAllElementsLocatedBy(By.className("ant-select-item")));
 		for (WebElement option : selectOptions) {
 			if (option.getAttribute("title").equals(value)) {
 				option.click();
@@ -134,8 +134,8 @@ public void setCascaderForSampleField(String field, String firstValue, String se
 		WebElement cascader = driver.findElement(By.className("t-sample-" + field));
 		cascader.click();
 		WebDriverWait wait = new WebDriverWait(driver, Duration.ofSeconds(1));
-		List<WebElement> cascaderMenus = wait
-				.until(ExpectedConditions.presenceOfAllElementsLocatedBy(By.className("ant-cascader-menu")));
+		List<WebElement> cascaderMenus = wait.until(
+				ExpectedConditions.presenceOfAllElementsLocatedBy(By.className("ant-cascader-menu")));
 		for (WebElement option : cascaderMenus.get(0).findElements(By.className("ant-cascader-menu-item"))) {
 			if (option.getText().equals(firstValue)) {
 				option.click();
@@ -182,10 +182,12 @@ public void selectSingleEndSequenceFile(String filename) {
 	}
 
 	public boolean areFormErrorsPresent() {
-		waitForTime(250);
+		waitForTime(500);
+		WebDriverWait wait = new WebDriverWait(driver, Duration.ofSeconds(5));
 		try {
-			List<WebElement> errors = driver.findElements(By.className("ant-form-item-explain-error"));
-			return errors != null && errors.size() > 0;
+			List<WebElement> errors = wait.until(
+					ExpectedConditions.visibilityOfAllElementsLocatedBy(By.className("ant-form-item-explain-error")));
+			return errors.size() > 0;
 		} catch (Exception e) {
 			return false;
 		}
@@ -196,6 +198,11 @@ public void submitExportForm() {
 	}
 
 	public boolean isSuccessAlertDisplayed() {
-		return driver.findElements(By.cssSelector(".ant-alert.ant-alert-success")).size() == 0;
+		return driver.findElements(By.cssSelector(".ant-alert.ant-alert-success")).size() == 1;
+	}
+
+	public boolean isUserRedirectedToProjectSamplesPage(int projectId) {
+		WebDriverWait wait = new WebDriverWait(driver, Duration.ofSeconds(5));
+		return wait.until(ExpectedConditions.urlMatches("/projects/" + projectId));
 	}
 }

src/test/java/ca/corefacility/bioinformatics/irida/ria/integration/projects/NcbiExportPageIT.java

@@ -27,7 +27,8 @@ void testCreateNcbiSubmission() throws Exception {
 		String DEFAULT_PROTOCOL = "DEFAULT_PROTOCOL";
 
 		LoginPage.loginAsManager(driver());
-		ProjectSamplesPage samplesPage = ProjectSamplesPage.goToPage(driver(), 1);
+		int PROJECT_ID = 1;
+		ProjectSamplesPage samplesPage = ProjectSamplesPage.goToPage(driver(), PROJECT_ID);
 		samplesPage.selectSampleByName(SAMPLE_1);
 		samplesPage.selectSampleByName(SAMPLE_2);
 		samplesPage.selectSampleByName(SAMPLE_3);
@@ -81,6 +82,7 @@ void testCreateNcbiSubmission() throws Exception {
 
 		page.submitExportForm();
 		assertTrue(page.isSuccessAlertDisplayed(), "Success notification should be displayed");
-
+		assertTrue(page.isUserRedirectedToProjectSamplesPage(PROJECT_ID),
+				"User should be redirected within 5 seconds of submission");
 	}
 }