From 7b60c021ad4d520c608d552087c28ab61c6c1ad7 Mon Sep 17 00:00:00 2001 From: Katherine Thiessen Date: Wed, 2 Nov 2022 13:23:07 -0500 Subject: [PATCH 1/4] fixing bug preventing managers from sharing project samples --- .../service/impl/sample/SampleServiceImpl.java | 13 ++++++------- .../irida/ria/web/projects/ProjectSamplesPage.xml | 0 ...ojectSamplesView.xml => ProjectShareSamples.xml} | 4 ++-- 3 files changed, 8 insertions(+), 9 deletions(-) create mode 100644 src/test/resources/ca/corefacility/bioinformatics/irida/ria/web/projects/ProjectSamplesPage.xml rename src/test/resources/ca/corefacility/bioinformatics/irida/ria/web/projects/{ProjectSamplesView.xml => ProjectShareSamples.xml} (98%) diff --git a/src/main/java/ca/corefacility/bioinformatics/irida/service/impl/sample/SampleServiceImpl.java b/src/main/java/ca/corefacility/bioinformatics/irida/service/impl/sample/SampleServiceImpl.java index c64b15d85f6..69dcdeed60c 100644 --- a/src/main/java/ca/corefacility/bioinformatics/irida/service/impl/sample/SampleServiceImpl.java +++ b/src/main/java/ca/corefacility/bioinformatics/irida/service/impl/sample/SampleServiceImpl.java @@ -345,7 +345,7 @@ public Sample getSampleBySampleName(Project project, String sampleName) { */ @Override @Transactional(readOnly = true) - @PreAuthorize("hasAnyRole('ROLE_ADMIN', 'ROLE_SEQUENCER') or hasPermission(#project, 'canReadProject')") + @PreAuthorize("hasAnyRole('ROLE_ADMIN', 'ROLE_SEQUENCER') or hasPermission(#projectIds, 'canReadProject')") public Map> getSampleIdsBySampleNameForProjects(List projectIds, List sampleNames) { return sampleRepository.getSampleIdsBySampleNameInProjects(projectIds, sampleNames) @@ -673,8 +673,9 @@ public List getQCEntriesForSample(Sample sample) { public Map> getQCEntriesForSamples(List samples) { return qcEntryRepository.getQCEntriesForSamples(samples) .stream() - .collect(Collectors.groupingBy(sampleQCEntryTuple -> (Long) sampleQCEntryTuple.get(0), Collectors - .mapping(sampleQCEntryTuple -> (QCEntry) sampleQCEntryTuple.get(1), Collectors.toList()))); + .collect(Collectors.groupingBy(sampleQCEntryTuple -> (Long) sampleQCEntryTuple.get(0), + Collectors.mapping(sampleQCEntryTuple -> (QCEntry) sampleQCEntryTuple.get(1), + Collectors.toList()))); } /** @@ -835,9 +836,7 @@ public List getSamplesCreatedGrouped(Date createdDate, Statist public Map getCoverageForSamplesInProject(Project project, List sampleIds) { return psjRepository.calculateCoverageForSamplesInProject(project, sampleIds) .stream() - .collect(HashMap::new, - (sampleCoverageMap, sampleCoverageTuple) -> sampleCoverageMap - .put((Long) sampleCoverageTuple.get(0), (Long) sampleCoverageTuple.get(1)), - Map::putAll); + .collect(HashMap::new, (sampleCoverageMap, sampleCoverageTuple) -> sampleCoverageMap.put( + (Long) sampleCoverageTuple.get(0), (Long) sampleCoverageTuple.get(1)), Map::putAll); } } diff --git a/src/test/resources/ca/corefacility/bioinformatics/irida/ria/web/projects/ProjectSamplesPage.xml b/src/test/resources/ca/corefacility/bioinformatics/irida/ria/web/projects/ProjectSamplesPage.xml new file mode 100644 index 00000000000..e69de29bb2d diff --git a/src/test/resources/ca/corefacility/bioinformatics/irida/ria/web/projects/ProjectSamplesView.xml b/src/test/resources/ca/corefacility/bioinformatics/irida/ria/web/projects/ProjectShareSamples.xml similarity index 98% rename from src/test/resources/ca/corefacility/bioinformatics/irida/ria/web/projects/ProjectSamplesView.xml rename to src/test/resources/ca/corefacility/bioinformatics/irida/ria/web/projects/ProjectShareSamples.xml index 9002f9e289d..fb97d888d14 100644 --- a/src/test/resources/ca/corefacility/bioinformatics/irida/ria/web/projects/ProjectSamplesView.xml +++ b/src/test/resources/ca/corefacility/bioinformatics/irida/ria/web/projects/ProjectShareSamples.xml @@ -1,6 +1,6 @@ - + @@ -26,7 +26,7 @@ - + From cd824a2dbd4685dde22df8ae94f90ba7ac4eee56 Mon Sep 17 00:00:00 2001 From: Katherine Thiessen Date: Wed, 2 Nov 2022 13:24:42 -0500 Subject: [PATCH 2/4] fixing seleniums tests to actually use a manager --- .../projects/ProjectSamplesPageIT.java | 2 +- .../projects/ProjectShareSamplesIT.java | 2 +- .../ria/web/projects/ProjectSamplesPage.xml | 123 ++++++++++++++++++ 3 files changed, 125 insertions(+), 2 deletions(-) diff --git a/src/test/java/ca/corefacility/bioinformatics/irida/ria/integration/projects/ProjectSamplesPageIT.java b/src/test/java/ca/corefacility/bioinformatics/irida/ria/integration/projects/ProjectSamplesPageIT.java index a7df60c973a..24a59c51744 100644 --- a/src/test/java/ca/corefacility/bioinformatics/irida/ria/integration/projects/ProjectSamplesPageIT.java +++ b/src/test/java/ca/corefacility/bioinformatics/irida/ria/integration/projects/ProjectSamplesPageIT.java @@ -19,7 +19,7 @@ * Integration test to ensure that the Project Details Page. *

*/ -@DatabaseSetup("/ca/corefacility/bioinformatics/irida/ria/web/projects/ProjectSamplesView.xml") +@DatabaseSetup("/ca/corefacility/bioinformatics/irida/ria/web/projects/ProjectSamplesPage.xml") public class ProjectSamplesPageIT extends AbstractIridaUIITChromeDriver { String FIRST_SAMPLE_NAME = "sample55422r"; String SECOND_SAMPLE_NAME = "sample-5-fg-22"; diff --git a/src/test/java/ca/corefacility/bioinformatics/irida/ria/integration/projects/ProjectShareSamplesIT.java b/src/test/java/ca/corefacility/bioinformatics/irida/ria/integration/projects/ProjectShareSamplesIT.java index b9273d1da63..723e12eb1bc 100644 --- a/src/test/java/ca/corefacility/bioinformatics/irida/ria/integration/projects/ProjectShareSamplesIT.java +++ b/src/test/java/ca/corefacility/bioinformatics/irida/ria/integration/projects/ProjectShareSamplesIT.java @@ -12,7 +12,7 @@ import static org.assertj.core.api.Assertions.assertThat; import static org.junit.jupiter.api.Assertions.*; -@DatabaseSetup("/ca/corefacility/bioinformatics/irida/ria/web/projects/ProjectSamplesView.xml") +@DatabaseSetup("/ca/corefacility/bioinformatics/irida/ria/web/projects/ProjectShareSamples.xml") public class ProjectShareSamplesIT extends AbstractIridaUIITChromeDriver { private ShareSamplesPage shareSamplesPage = ShareSamplesPage.initPage(driver()); diff --git a/src/test/resources/ca/corefacility/bioinformatics/irida/ria/web/projects/ProjectSamplesPage.xml b/src/test/resources/ca/corefacility/bioinformatics/irida/ria/web/projects/ProjectSamplesPage.xml index e69de29bb2d..735668ebddf 100644 --- a/src/test/resources/ca/corefacility/bioinformatics/irida/ria/web/projects/ProjectSamplesPage.xml +++ b/src/test/resources/ca/corefacility/bioinformatics/irida/ria/web/projects/ProjectSamplesPage.xml @@ -0,0 +1,123 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file From 91dbcf19ba67d990ea720d1a1167480722b6a591 Mon Sep 17 00:00:00 2001 From: Katherine Thiessen Date: Wed, 2 Nov 2022 13:25:08 -0500 Subject: [PATCH 3/4] updating change log --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 52af82abd15..537f02e034a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,7 @@ ## [22.09.2] * [UI]: Fixed bug causing associated project samples to be added to the cart with the wrong project identifier. See [PR 1395](https://github.com/phac-nml/irida/pull/1395) +* [UI]: Fixed bug preventing managers from sharing project samples. See [PR 1398](https://github.com/phac-nml/irida/pull/1398) ## [22.09.1] - 2022/10/21 * [UI]: Fixed when sharing or exporting sample on the project sample page, and other minor bugs. See [PR 1382](https://github.com/phac-nml/irida/pull/1382) From d41037e90b005f2082aa0a0673ca5bc6f4030d8c Mon Sep 17 00:00:00 2001 From: Katherine Thiessen Date: Wed, 2 Nov 2022 13:55:28 -0500 Subject: [PATCH 4/4] updating change log --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 537f02e034a..b250668677f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ ## [22.09.2] * [UI]: Fixed bug causing associated project samples to be added to the cart with the wrong project identifier. See [PR 1395](https://github.com/phac-nml/irida/pull/1395) -* [UI]: Fixed bug preventing managers from sharing project samples. See [PR 1398](https://github.com/phac-nml/irida/pull/1398) +* [Developer/UI]: Fixed bug preventing managers from sharing project samples. See [PR 1398](https://github.com/phac-nml/irida/pull/1398) ## [22.09.1] - 2022/10/21 * [UI]: Fixed when sharing or exporting sample on the project sample page, and other minor bugs. See [PR 1382](https://github.com/phac-nml/irida/pull/1382)