Merge pull request #1377 from deepsidhu85/fix-analysis-share

Fixed analysis results manage results

CHANGELOG.md

@@ -28,6 +28,7 @@
 * [Developer]: Update to Spring Boot 2.7.3 and update various other dependencies. See [PR 1369](https://github.com/phac-nml/irida/pull/1369)
 * [Developer]: Fixed issue with disabled user accounts requesting a password reset. See [PR 1373](https://github.com/phac-nml/irida/pull/1373)
 * [Developer/UI]: Updated sample details view to use Ant Design and moved into a modal which can be launched from anywhere the sample name is listed. See [PR 1370](https://github.com/phac-nml/irida/pull/1370)
+* [UI]: Updated analysis results manage results page to not allow a project collaborator to view the save results back to a sample section. See [PR 1377](https://github.com/phac-nml/irida/pull/1377)
 
 ## [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)

src/main/java/ca/corefacility/bioinformatics/irida/ria/web/analysis/AnalysisAjaxController.java

@@ -51,6 +51,7 @@
 import ca.corefacility.bioinformatics.irida.ria.web.dto.ResponseDetails;
 import ca.corefacility.bioinformatics.irida.ria.web.utilities.DateUtilities;
 import ca.corefacility.bioinformatics.irida.security.permissions.analysis.UpdateAnalysisSubmissionPermission;
+import ca.corefacility.bioinformatics.irida.security.permissions.sample.UpdateSamplePermission;
 import ca.corefacility.bioinformatics.irida.service.*;
 import ca.corefacility.bioinformatics.irida.service.sample.MetadataTemplateService;
 import ca.corefacility.bioinformatics.irida.service.sample.SampleService;
@@ -93,14 +94,16 @@ public class AnalysisAjaxController {
 	private AnalysisTypesService analysisTypesService;
 	private EmailController emailController;
 
+	private UpdateSamplePermission updateSamplePermission;
+
 	@Autowired
 	public AnalysisAjaxController(AnalysisSubmissionService analysisSubmissionService,
 			IridaWorkflowsService iridaWorkflowsService, UserService userService, SampleService sampleService,
 			ProjectService projectService, UpdateAnalysisSubmissionPermission updateAnalysisPermission,
 			MetadataTemplateService metadataTemplateService, SequencingObjectService sequencingObjectService,
 			AnalysisSubmissionSampleProcessor analysisSubmissionSampleProcessor, MessageSource messageSource,
 			ExecutionManagerConfig configFile, AnalysisAudit analysisAudit, AnalysisTypesService analysisTypesService,
-			EmailController emailController) {
+			EmailController emailController, UpdateSamplePermission updateSamplePermission) {
 
 		this.analysisSubmissionService = analysisSubmissionService;
 		this.workflowsService = iridaWorkflowsService;
@@ -116,6 +119,7 @@ public AnalysisAjaxController(AnalysisSubmissionService analysisSubmissionServic
 		this.analysisAudit = analysisAudit;
 		this.analysisTypesService = analysisTypesService;
 		this.emailController = emailController;
+		this.updateSamplePermission = updateSamplePermission;
 	}
 
 	/**
@@ -212,11 +216,15 @@ public AnalysisDetails ajaxGetDataForDetailsTab(@PathVariable Long submissionId,
 
 		response.setStatus(HttpServletResponse.SC_OK);
 
+		Collection<Sample> samples = sampleService.getSamplesForAnalysisSubmission(submission);
+
+		boolean canModifySample = updateSamplePermission.isAllowed(authentication, samples);
+
 		// details is a DTO (Data Transfer Object)
 		return new AnalysisDetails(analysisDescription, workflowName, version, priority, duration,
 				submission.getCreatedDate(), priorities, emailPipelineResultCompleted, emailPipelineResultError,
 				canShareToSamples, updateAnalysisPermission.isAllowed(authentication, submission),
-				submission.getUpdateSamples());
+				submission.getUpdateSamples(), canModifySample);
 	}
 
 	/**

src/main/java/ca/corefacility/bioinformatics/irida/ria/web/analysis/dto/AnalysisDetails.java

@@ -22,12 +22,14 @@ public class AnalysisDetails {
 	private boolean updatePermission;
 	private boolean updateSamples;
 
+	private boolean allowedToModifySample;
+
 	public AnalysisDetails() {
 	}
 
 	public AnalysisDetails(String analysisDescription, String workflowName, String version, String priority, Long duration,
 			Date createdDate, AnalysisSubmission.Priority[] priorities, boolean emailPipelineResultCompleted, boolean emailPipelineResultError,
-			boolean canShareToSamples, boolean updatePermission, boolean updateSamples) {
+			boolean canShareToSamples, boolean updatePermission, boolean updateSamples, boolean allowedToModifySample) {
 		this.analysisDescription=analysisDescription;
 		this.workflowName = workflowName;
 		this.version = version;
@@ -40,6 +42,7 @@ public AnalysisDetails(String analysisDescription, String workflowName, String v
 		this.canShareToSamples = canShareToSamples;
 		this.updatePermission = updatePermission;
 		this.updateSamples = updateSamples;
+		this.allowedToModifySample = allowedToModifySample;
 	}
 
 	public String getAnalysisDescription() {
@@ -137,4 +140,12 @@ public boolean isUpdateSamples() {
 	public void setUpdateSamples(boolean updateSamples) {
 		this.updateSamples = updateSamples;
 	}
+
+	public boolean isAllowedToModifySample() {
+		return allowedToModifySample;
+	}
+
+	public void setAllowedToModifySample(boolean allowedToModifySample) {
+		this.allowedToModifySample = allowedToModifySample;
+	}
 }

src/main/webapp/resources/js/contexts/AnalysisDetailsContext.js

@@ -67,9 +67,10 @@ const initialContext = {
   createdDate: null,
   priority: null,
   priorities: [],
-  canShareToSamples: false,
-  updatePermission: false,
-  updateSamples: false,
+  canShareToSamples: false, // submission has ability to save results back to samples
+  updatePermission: false, // user can update the submission details/parameters
+  updateSamples: false, // Update samples from results on completion
+  allowedToModifySample: false, // User can modify sample
 };
 
 const AnalysisDetailsContext = React.createContext(initialContext);

src/main/webapp/resources/js/pages/analysis/components/settings/AnalysisShare.jsx

@@ -158,8 +158,12 @@ export default function AnalysisShare() {
       ) : null}
 
       {analysisDetailsContext.canShareToSamples &&
+      analysisDetailsContext.allowedToModifySample &&
       analysisContext.isCompleted ? (
-        <section style={{ marginTop: SPACE_MD }}>
+        <section
+          style={{ marginTop: SPACE_MD }}
+          className="t-save-results-to-samples"
+        >
           <Title level={4}>{i18n("AnalysisShare.saveResults")}</Title>
           {renderSaveToRelatedSamples()}
         </section>

src/test/java/ca/corefacility/bioinformatics/irida/ria/integration/analysis/AnalysisDetailsPageIT.java

@@ -254,6 +254,22 @@ public void testSharedProjects() {
 		assertTrue(page.hasSharedWithProjects(), "Analysis shared with projects");
 	}
 
+	@Test
+	public void testSaveResultBackToSamplesProjectManager() {
+		LoginPage.loginAsManager(driver());
+		AnalysisDetailsPage page = AnalysisDetailsPage.initPage(driver(), 11L, "settings/share");
+		assertTrue(page.compareTabTitle("Manage Results"), "Page title should equal");
+		assertTrue(page.saveToSamplesVisible(), "Save results back to sample should be visible to a project manager");
+	}
+
+	@Test
+	public void testSaveResultBackToSamplesProjectUser() {
+		LoginPage.loginAsUser(driver());
+		AnalysisDetailsPage page = AnalysisDetailsPage.initPage(driver(), 11L, "settings/share");
+		assertTrue(page.compareTabTitle("Manage Results"), "Page title should equal");
+		assertFalse(page.saveToSamplesVisible(), "Save results back to sample should not be visible to a project user");
+	}
+
 	@Test
 	public void testSistrOutput() throws IOException {
 		fileUtilities.copyFileToDirectory(outputFileBaseDirectory,

src/test/java/ca/corefacility/bioinformatics/irida/ria/integration/pages/analysis/AnalysisDetailsPage.java

@@ -108,6 +108,7 @@ public class AnalysisDetailsPage extends AbstractPage {
 	@FindBy(className = "ant-menu-title-content")
 	private List<WebElement> menuItems;
 
+
 	public AnalysisDetailsPage(WebDriver driver) {
 		super(driver);
 	}
@@ -527,4 +528,12 @@ public boolean galaxyHistoryIdVisible() {
 		}
 		return false;
 	}
+
+	public boolean saveToSamplesVisible() {
+		try {
+			return driver.findElement(By.className("t-save-results-to-samples")).isDisplayed();
+		} catch (Exception e) {
+			return false;
+		}
+	}
 }

src/test/java/ca/corefacility/bioinformatics/irida/ria/unit/web/analysis/AnalysisAjaxControllerTest.java

@@ -30,6 +30,7 @@
 import ca.corefacility.bioinformatics.irida.ria.web.analysis.dto.*;
 import ca.corefacility.bioinformatics.irida.ria.web.analysis.auditing.AnalysisAudit;
 import ca.corefacility.bioinformatics.irida.security.permissions.analysis.UpdateAnalysisSubmissionPermission;
+import ca.corefacility.bioinformatics.irida.security.permissions.sample.UpdateSamplePermission;
 import ca.corefacility.bioinformatics.irida.service.*;
 import ca.corefacility.bioinformatics.irida.service.sample.MetadataTemplateService;
 import ca.corefacility.bioinformatics.irida.service.sample.SampleService;
@@ -66,6 +67,8 @@ public class AnalysisAjaxControllerTest {
 	private AnalysisTypesService analysisTypesServiceMock;
 	private EmailController emailControllerMock;
 
+	private UpdateSamplePermission updateSamplePermission;
+
 	/**
 	 * Analysis Output File key names from
 	 * {@link TestDataFactory#constructAnalysis()}
@@ -89,11 +92,12 @@ public void init() {
 		httpServletResponseMock = mock(HttpServletResponse.class);
 		analysisTypesServiceMock = mock(AnalysisTypesService.class);
 		emailControllerMock = mock(EmailController.class);
+		updateSamplePermission = mock(UpdateSamplePermission.class);
 
 		analysisAjaxController = new AnalysisAjaxController(analysisSubmissionServiceMock, iridaWorkflowsServiceMock,
 				userServiceMock, sampleService, projectServiceMock, updatePermission, metadataTemplateService,
 				sequencingObjectService, analysisSubmissionSampleProcessor, messageSourceMock, configFileMock,
-				analysisAuditMock, analysisTypesServiceMock, emailControllerMock);
+				analysisAuditMock, analysisTypesServiceMock, emailControllerMock, updateSamplePermission);
 
 	}
 

src/test/resources/ca/corefacility/bioinformatics/irida/ria/web/analysis/AnalysisAdminView.xml

@@ -54,6 +54,11 @@
           credentialsNonExpired="true" locale="en" />
 
 
+    <project_user id="1" project_id="1" user_id="1"
+                  projectRole="PROJECT_OWNER" metadataRole="LEVEL_4" createdDate="2013-07-18 14:20:19.0"/>
+    <project_user id="2" project_id="1" user_id="2"
+                  projectRole="PROJECT_USER" metadataRole="LEVEL_4" createdDate="2013-07-18 14:20:19.0"/>
+
 	<sequencing_object id="1" created_date="2014-07-30 08:24:34"
 		sequencing_run_id="1" />
     <sequencing_object id="2" created_date="2014-08-01 08:24:34"
@@ -199,5 +204,6 @@
     <analysis_submission_sequencing_object analysis_submission_id="14" sequencing_object_id="1" />
 
     <project_analysis_submission id="1" project_id="1" analysis_submission_id="4" created_date="2013-07-18 14:20:19.0"/>
+    <project_analysis_submission id="2" project_id="1" analysis_submission_id="11" created_date="2013-07-18 14:20:19.0"/>
 
 </dataset>