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Fix for metadata uploader overwriting existing data #1489

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merged 7 commits into from
May 9, 2023
Merged

Fix for metadata uploader overwriting existing data #1489

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1861823
switching the methods that create/update metadata
ksierks Apr 26, 2023
b5e0a5d
enhancing tests
ksierks Apr 26, 2023
aff3ec4
updating to only use mergeSampleMetadata
ksierks Apr 26, 2023
21121af
updating changelog
ksierks Apr 26, 2023
d70b26b
fixing changelog
ksierks Apr 27, 2023
8911b5d
adding a better test
ksierks May 1, 2023
36ee360
adding project samples to ProjectSampleMetadataView.xml
ksierks May 2, 2023
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8 changes: 5 additions & 3 deletions CHANGELOG.md
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@@ -1,13 +1,14 @@

# Changelog
## [23.01.3]
* [Developer]: Fixed issue with metadata uploader removing exiting data. See [PR 1489](https://github.com/phac-nml/irida/pull/1489)

## [23.01.2]
## [23.01.2] - 2023/04/17
* [UI]: Fixed bug that caused all metadata fields to be removed when single field was removed from a template. See [PR 1482](https://github.com/phac-nml/irida/pull/1482)
* [Developer]: Fixed bug which allowed duplicated entries in the user_group_project table which prevented the user group from being removed. Fixed bug which was preventing analyses with `html` file outputs from completing. See [PR 1483](https://github.com/phac-nml/irida/pull/1483)
* [Developer]: Fixed flaky PipelinesPhylogenomicsPageIT test. See [PR 1482](https://github.com/phac-nml/irida/pull/1482)
* [REST]: Fixed issues with syncing between newer IRIDA (>22.09) and older IRIDA (<=20.09) by disabling requests for `application/xml` for some of the REST requests and only requesting data as `application/json`. See [PR 1484](https://github.com/phac-nml/irida/pull/1484).


## [23.01.1] - 2023/03/21
* [UI]: Fixed issue where template order was not applied when applying a linelist template. See [PR 1479](https://github.com/phac-nml/irida/pull/1479)
* [UI]: Added select all to associated projects filter on project > samples page. See [PR 1479](https://github.com/phac-nml/irida/pull/1479)
Expand Down Expand Up @@ -187,8 +188,9 @@

## [...previous](https://github.com/phac-nml/irida/blob/21.09.2/CHANGELOG.md)

[Unreleased]: https://github.com/phac-nml/irida/compare/23.01.2...HEAD
[Unreleased]: https://github.com/phac-nml/irida/compare/23.01.3...HEAD

[23.01.3]: https://github.com/phac-nml/irida/compare/23.01.2...23.01.3
[23.01.2]: https://github.com/phac-nml/irida/compare/23.01.1...23.01.2
[23.01.1]: https://github.com/phac-nml/irida/compare/23.01...23.01.1
[23.01]: https://github.com/phac-nml/irida/compare/22.09.7...23.01
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2 changes: 1 addition & 1 deletion build.gradle.kts
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Expand Up @@ -14,7 +14,7 @@ plugins {
}

group = "ca.corefacility.bioinformatics"
version = "23.01.2"
version = "23.01.3"
description = "irida"

java {
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2 changes: 1 addition & 1 deletion ...in/java/ca/corefacility/bioinformatics/irida/ria/web/services/UIProjectSampleService.java
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Expand Up @@ -208,7 +208,7 @@ public Sample updateSample(UpdateSampleRequest request)
}
if (request.getMetadata() != null) {
Set<MetadataEntry> metadataEntrySet = createMetadata(request.getMetadata());
sampleService.updateSampleMetadata(sample, metadataEntrySet);
sampleService.mergeSampleMetadata(sample, metadataEntrySet);
}
return sampleService.update(sample);

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24 changes: 24 additions & 0 deletions ...lity/bioinformatics/irida/ria/integration/projects/ProjectSampleMetadataImportPageIT.java
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Expand Up @@ -9,6 +9,7 @@
import org.junit.jupiter.api.Test;

import ca.corefacility.bioinformatics.irida.ria.integration.AbstractIridaUIITChromeDriver;
import ca.corefacility.bioinformatics.irida.ria.integration.components.SampleDetailsViewer;
import ca.corefacility.bioinformatics.irida.ria.integration.pages.LoginPage;
import ca.corefacility.bioinformatics.irida.ria.integration.pages.ProjectMembersPage;
import ca.corefacility.bioinformatics.irida.ria.integration.pages.projects.ProjectDeletePage;
Expand All @@ -30,6 +31,8 @@ public class ProjectSampleMetadataImportPageIT extends AbstractIridaUIITChromeDr
private static final String EMPTY_AND_DUPLICATE_HEADERS_FILE_PATH = "src/test/resources/files/metadata-upload/empty_and_duplicate_headers.xlsx";
private static final String DUPLICATE_HEADERS_FILE_PATH = "src/test/resources/files/metadata-upload/duplicate_headers.xlsx";
private static final String SAMPLE_NAME_COLUMN = "NLEP #";

private static final String SAMPLE_NAME = "sample1";
private static final Long PROJECT_ID = 1L;

@BeforeEach
Expand Down Expand Up @@ -189,4 +192,25 @@ public void testFailedUploadByRemovingPrivileges() {
page.clickUploadButton();
assertTrue(page.isErrorNotificationDisplayed(), "Error notification did not display");
}

@Test
public void testUploadDoesNotOverwriteExistingSampleMetadata() {
ProjectSampleMetadataImportPage page = ProjectSampleMetadataImportPage.goToPage(driver());
page.uploadMetadataFile(GOOD_FILE_PATH);
page.selectSampleNameColumn(SAMPLE_NAME_COLUMN);
page.goToReviewPage();
page.goToCompletePage();
assertTrue(page.isSuccessDisplayed(), "Successful upload did not happen");
ProjectSamplesPage samplePage = ProjectSamplesPage.goToPage(driver(), PROJECT_ID);
samplePage.clickSampleName(SAMPLE_NAME);
SampleDetailsViewer sampleDetailsViewer = SampleDetailsViewer.getSampleDetails(driver());
sampleDetailsViewer.clickMetadataTabLink();
assertTrue(sampleDetailsViewer.addNewMetadataButtonVisible());
sampleDetailsViewer.getNumberOfMetadataEntries();
assertEquals(10, sampleDetailsViewer.getNumberOfMetadataEntries(),
"Should have the proper number of metadata entries");
assertEquals("Sneezing", sampleDetailsViewer.getValueForMetadataField("symptom"),
"Should have existing metadata");
assertEquals("AB", sampleDetailsViewer.getValueForMetadataField("Province"), "Should have uploaded metadata");
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}
}
25 changes: 17 additions & 8 deletions ...a/corefacility/bioinformatics/irida/ria/unit/web/services/UIProjectSampleServiceTest.java
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Expand Up @@ -25,11 +25,17 @@

import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.mockito.ArgumentMatchers.any;
import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.when;
import static org.mockito.Mockito.*;

public class UIProjectSampleServiceTest {
private UIProjectSampleService service;
private ProjectService projectService;
private SampleService sampleService;
private MetadataTemplateService metadataTemplateService;
private MessageSource messageSource;

private Sample sample;
private Join<Project, Sample> join;

// DATA
private final Long PROJECT_1_ID = 1L;
Expand All @@ -44,20 +50,20 @@ public class UIProjectSampleServiceTest {

@BeforeEach
public void setUp() {
ProjectService projectService = mock(ProjectService.class);
SampleService sampleService = mock(SampleService.class);
MetadataTemplateService metadataTemplateService = mock(MetadataTemplateService.class);
MessageSource messageSource = mock(MessageSource.class);
projectService = mock(ProjectService.class);
sampleService = mock(SampleService.class);
metadataTemplateService = mock(MetadataTemplateService.class);
messageSource = mock(MessageSource.class);

service = new UIProjectSampleService(projectService, sampleService, metadataTemplateService, messageSource);

when(projectService.read(PROJECT_1_ID)).thenReturn(PROJECT_1);
when(sampleService.read(SAMPLE_1_ID)).thenReturn(SAMPLE_1);
when(sampleService.getSampleBySampleName(PROJECT_1, GOOD_NAME)).thenThrow(
new EntityNotFoundException("Sample not found"));
Sample sample = new Sample(GOOD_NAME);
sample = new Sample(GOOD_NAME);
sample.setId(SAMPLE_1_ID);
Join<Project, Sample> join = new ProjectSampleJoin(PROJECT_1, sample, true);
join = new ProjectSampleJoin(PROJECT_1, sample, true);
when(projectService.addSampleToProject(any(Project.class), any(Sample.class), any(Boolean.class))).thenReturn(
join);
when(projectService.addSampleToProjectWithoutEvent(any(Project.class), any(Sample.class),
Expand Down Expand Up @@ -135,6 +141,7 @@ public void testCreateSampleWithMetadata() {
.stream()
.filter(response -> ((SampleResponse) response.getValue()).isError())
.count();
verify(sampleService, times(1)).mergeSampleMetadata(any(), any());
assertEquals(0, errorCount, "Sample should be created");
}

Expand All @@ -149,6 +156,8 @@ public void testUpdateSampleWithMetadata() {
.stream()
.filter(response -> ((SampleErrorResponse) response.getValue()).isError())
.count();
verify(sampleService, times(1)).mergeSampleMetadata(any(), any());
assertEquals(0, errorCount, "Sample should be updated");
}

}
41 changes: 4 additions & 37 deletions ...urces/ca/corefacility/bioinformatics/irida/ria/web/projects/ProjectSampleMetadataView.xml
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Expand Up @@ -31,47 +31,14 @@
<sample id="1" createdDate="2013-07-01 14:00:19.0" modifiedDate="2015-07-01 14:00:19.0" description="description1" sampleName="sample1" organism="E. coli" />
<sample id="2" createdDate="2013-07-02 14:01:19.0" modifiedDate="2015-07-02 14:00:19.0" description="description2" sampleName="sample2" organism="E. coli" />
<sample id="3" createdDate="2013-07-03 14:02:19.0" modifiedDate="2015-07-02 14:00:19.0" description="description3" sampleName="sample3" organism="E. coli" />
<sample id="4" createdDate="2013-07-04 14:03:19.0" modifiedDate="2015-07-03 14:00:19.0" description="description4" sampleName="sample4" organism="Listeria" />
<sample id="5" createdDate="2013-07-06 14:05:19.0" modifiedDate="2015-07-06 14:00:19.0" description="description5" sampleName="sample523423" />
<sample id="6" createdDate="2013-07-07 14:06:19.0" modifiedDate="2015-07-07 14:00:19.0" description="description5" sampleName="sample534534" />
<sample id="7" createdDate="2013-07-08 14:07:19.0" modifiedDate="2015-07-08 14:00:19.0" description="description5" sampleName="sample589789" />
<sample id="8" createdDate="2013-07-09 14:08:19.0" modifiedDate="2015-07-09 14:00:19.0" description="description5" sampleName="sample52342" />
<sample id="9" createdDate="2013-07-10 14:09:19.0" modifiedDate="2015-07-10 14:00:19.0" description="description5" sampleName="sample565" />
<sample id="10" createdDate="2013-07-11 14:10:19.0" modifiedDate="2015-07-11 14:00:19.0" description="description5" sampleName="sample6735" />
<sample id="11" createdDate="2013-07-12 14:11:19.0" modifiedDate="2015-07-12 14:00:19.0" description="description5" sampleName="sample3452345" />
<sample id="12" createdDate="2013-07-13 14:12:19.0" modifiedDate="2015-07-13 14:00:19.0" description="description5" sampleName="sample3643225" />
<sample id="13" createdDate="2013-07-14 14:13:19.0" modifiedDate="2015-07-14 14:00:19.0" description="description5" sampleName="sample64565" />
<sample id="14" createdDate="2013-07-15 14:14:19.0" modifiedDate="2015-07-15 14:00:19.0" description="description5" sampleName="sample57567" />
<sample id="15" createdDate="2013-07-16 14:15:19.0" modifiedDate="2015-07-16 14:00:19.0" description="description5" sampleName="sample55422r" />
<sample id="16" createdDate="2013-07-17 14:16:19.0" modifiedDate="2015-07-17 14:00:19.0" description="description5" sampleName="sample5dt5" />
<sample id="17" createdDate="2013-07-18 14:17:19.0" modifiedDate="2015-07-18 14:00:19.0" description="description5" sampleName="sample5ddfg4" />
<sample id="18" createdDate="2013-07-19 14:18:19.0" modifiedDate="2015-07-19 14:00:19.0" description="description5" sampleName="sample554sg5" />
<sample id="19" createdDate="2013-07-20 14:19:19.0" modifiedDate="2015-07-20 14:00:19.0" description="description5" sampleName="sample5fdgr" />
<sample id="20" createdDate="2013-07-21 14:20:19.0" modifiedDate="2015-07-22 14:00:19.0" description="description5" sampleName="sample5fg44" />
<sample id="21" createdDate="2013-07-22 14:20:19.0" modifiedDate="2015-07-22 14:00:19.0" description="description22" sampleName="sample5fg22" />

<metadata_field id="1" label="symptom" type="text" DTYPE="MetadataTemplateField"/>

<metadata_entry id="1" value="Sneezing" type="text" sample_id="1" field_id="1"/>

<project_sample id="1" project_id="1" sample_id="1" createdDate="2013-07-10 14:21:19.0" />
<project_sample id="2" project_id="1" sample_id="2" createdDate="2013-07-12 14:22:19.0" />
<project_sample id="3" project_id="1" sample_id="3" createdDate="2013-07-14 14:23:19.0" />
<project_sample id="4" project_id="1" sample_id="4" createdDate="2013-07-16 14:24:19.0" />
<project_sample id="5" project_id="1" sample_id="5" createdDate="2013-07-18 14:26:19.0" />
<project_sample id="6" project_id="1" sample_id="6" createdDate="2013-07-18 14:27:19.0" />
<project_sample id="7" project_id="1" sample_id="7" createdDate="2013-07-18 14:28:19.0" />
<project_sample id="8" project_id="1" sample_id="8" createdDate="2013-07-18 14:29:19.0" />
<project_sample id="9" project_id="1" sample_id="9" createdDate="2013-07-18 14:31:19.0" />
<project_sample id="10" project_id="1" sample_id="10" createdDate="2013-07-18 14:32:19.0" />
<project_sample id="11" project_id="1" sample_id="11" createdDate="2013-07-18 14:33:19.0" />
<project_sample id="12" project_id="1" sample_id="12" createdDate="2013-07-18 14:34:19.0" />
<project_sample id="13" project_id="1" sample_id="13" createdDate="2013-07-18 14:35:19.0" />
<project_sample id="14" project_id="1" sample_id="14" createdDate="2013-07-18 14:36:19.0" />
<project_sample id="15" project_id="1" sample_id="15" createdDate="2013-07-18 14:37:19.0" />
<project_sample id="16" project_id="1" sample_id="16" createdDate="2013-07-18 14:38:19.0" />
<project_sample id="17" project_id="1" sample_id="17" createdDate="2013-07-18 14:39:19.0" />
<project_sample id="18" project_id="1" sample_id="18" createdDate="2013-07-18 14:40:19.0" />
<project_sample id="19" project_id="1" sample_id="19" createdDate="2013-07-18 14:41:19.0" />
<project_sample id="20" project_id="1" sample_id="20" createdDate="2013-07-18 14:42:19.0" />
<project_sample id="21" project_id="6" sample_id="20" createdDate="2013-07-18 14:42:19.0" />
<project_sample id="22" project_id="3" sample_id="20" createdDate="2013-07-18 14:42:19.0" />

<sequence_file id="1" created_date="2013-07-18 14:20:19.0" file_path="src/test/resources/files/test_file.fastq" />
<sequence_file id="2" created_date="2013-07-18 14:20:19.0" file_path="/sequenceFile2" />
Expand Down