Merge branch 'master' into development

CHANGELOG.md

@@ -3,6 +3,14 @@
 
 ## [Unreleased]
 
+## [22.09.2] - 2022/11/04
+* [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 the removal of locked samples within a project. See [PR 1396](https://github.com/phac-nml/irida/pull/1396)
+* [Developer/UI]: Fixed bug preventing managers from sharing project samples. See [PR 1398](https://github.com/phac-nml/irida/pull/1398)
+* [UI]: Fixed bug where a sample added to the cart from the sample detail viewer still had a `Add to Cart` button if the viewer was closed and relaunched. See [PR 1397](https://github.com/phac-nml/irida/pull/1397)
+* [Galaxy]: Fixed missing "deferred" state found in the Galaxy API but not in the IRIDA API for getting status of Galaxy histories. See [PR 1402](https://github.com/phac-nml/irida/pull/1402).
+* [UI]: Fixed a bug that allowed the sharing and moving of locked samples. See [PR 1403](https://github.com/phac-nml/irida/pull/1403)
+
 ## [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)
 
@@ -135,8 +143,9 @@
 
 ## [...previous](https://github.com/phac-nml/irida/blob/21.09.2/CHANGELOG.md)
 
-[Unreleased]: https://github.com/phac-nml/irida/compare/22.09.1...HEAD
+[Unreleased]: https://github.com/phac-nml/irida/compare/22.09.2...HEAD
 
+[22.09.2]: https://github.com/phac-nml/irida/compare/22.09.1...22.09.2
 [22.09.1]: https://github.com/phac-nml/irida/compare/22.09...22.09.1
 [22.09]: https://github.com/phac-nml/irida/compare/22.05.5...22.09
 [22.05.5]: https://github.com/phac-nml/irida/compare/22.05.4...22.05.5

doc/_includes/tutorials/common/ncbi-export.md

@@ -29,7 +29,7 @@ Default values for all samples can be set by clicking on the "Default Sample Set
 
 Once all fields and files are selected for a sample, the label will change from "MISSING DATA" to "VALID" indicating that the sample is ready for submission. All samples must be valid before submitting.
 
-![Default Sample Settings]({{ site.baseurl}}/images/tutorials/common/ncbi-export/ncbi-export-sample-validation.png)
+![Sample Validation]({{ site.baseurl}}/images/tutorials/common/ncbi-export/ncbi-export-sample-validation.png)
 
 After entering this metadata you can select which files should be uploaded from each sample.  Only files selected with checkboxes will be uploaded to NCBI.
 

src/main/java/ca/corefacility/bioinformatics/irida/model/workflow/execution/galaxy/GalaxyWorkflowState.java

@@ -8,8 +8,8 @@
 /**
  * Defines the state of a workflow.
  * Based off of states defined within Galaxy.
- * @see <a href="https://bitbucket.org/galaxy/galaxy-dist/src/097bbb3b7d3246faaa5188a1fc2a79b01630025c/lib/galaxy/model/__init__.py#cl-1316">Galaxy Dataset Model</a>
- * @see <a href="https://bitbucket.org/galaxy/galaxy-dist/src/097bbb3b7d3246faaa5188a1fc2a79b01630025c/lib/galaxy/web/base/controller.py#cl-429">Galaxy API</a>
+ * @see <a href="https://github.com/galaxyproject/galaxy/blob/21375c6b821b85863a6c95f4ed1ebd6a217495f1/lib/galaxy/model/__init__.py#L3410-L3427">Galaxy Dataset Model</a>
+ * @see <a href="https://github.com/galaxyproject/galaxy/blob/21375c6b821b85863a6c95f4ed1ebd6a217495f1/lib/galaxy/webapps/galaxy/api/histories.py#L181-L192">Galaxy API show_history</a>
  * @see <a href="https://github.com/jmchilton/blend4j/blob/c5e3f157d402950a843d4e395e1daf889945d587/src/main/java/com/github/jmchilton/blend4j/galaxy/beans/HistoryDetails.java">HistoryDetails in blend4j</a>
  *
  */
@@ -30,6 +30,7 @@ public enum GalaxyWorkflowState {
 	PAUSED("paused"),
 	SETTING_METADATA("setting_metadata"),
 	FAILED_METADATA("failed_metadata"),
+	DEFERRED("deferred"),
 	RESUBMITTED("resubmitted");
 
 	private static Map<String, GalaxyWorkflowState> stateMap = new HashMap<>();
@@ -66,4 +67,4 @@ public static GalaxyWorkflowState stringToState(String stateString) {
 	public String toString() {
 		return stateString;
 	}
-}
+}

src/main/java/ca/corefacility/bioinformatics/irida/ria/web/ajax/projects/ProjectSamplesAjaxController.java

@@ -1,17 +1,5 @@
 package ca.corefacility.bioinformatics.irida.ria.web.ajax.projects;
 
-import java.io.IOException;
-import java.util.List;
-import java.util.Locale;
-
-import javax.servlet.http.HttpServletResponse;
-
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.HttpStatus;
-import org.springframework.http.ResponseEntity;
-import org.springframework.web.bind.annotation.*;
-import org.springframework.web.servlet.mvc.method.annotation.StreamingResponseBody;
-
 import ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.CreateSampleRequest;
 import ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.SampleFilesResponse;
 import ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.SampleNameValidationResponse;
@@ -32,6 +20,16 @@
 import ca.corefacility.bioinformatics.irida.ria.web.samples.dto.ShareSamplesRequest;
 import ca.corefacility.bioinformatics.irida.ria.web.services.UIProjectSampleService;
 import ca.corefacility.bioinformatics.irida.ria.web.services.UISampleService;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.HttpStatus;
+import org.springframework.http.ResponseEntity;
+import org.springframework.web.bind.annotation.*;
+import org.springframework.web.servlet.mvc.method.annotation.StreamingResponseBody;
+
+import javax.servlet.http.HttpServletResponse;
+import java.io.IOException;
+import java.util.List;
+import java.util.Locale;
 
 /**
  * AJAX Controller for handling asynchronous requests for project samples.
@@ -148,8 +146,8 @@ public ResponseEntity<AjaxResponse> mergeSamples(@PathVariable Long projectId, @
 	@DeleteMapping("/remove")
 	public ResponseEntity<AjaxResponse> removeSamplesFromProject(@PathVariable long projectId,
 			@RequestBody RemoveSamplesRequest request) {
-		String result = uiSampleService.removeSamplesFromProject(projectId, request.getSampleIds());
-		return ResponseEntity.ok(new AjaxSuccessResponse(result));
+		uiSampleService.removeSamplesFromProject(projectId, request.getSampleIds());
+		return ResponseEntity.ok(new AjaxSuccessResponse(""));
 	}
 
 	/**

src/main/java/ca/corefacility/bioinformatics/irida/ria/web/services/UISampleService.java

@@ -1,80 +1,22 @@
 package ca.corefacility.bioinformatics.irida.ria.web.services;
 
-import java.io.IOException;
-
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.text.SimpleDateFormat;
-import java.time.Instant;
-
-import java.io.OutputStreamWriter;
-import java.nio.file.attribute.BasicFileAttributes;
-
-import java.util.*;
-import java.util.stream.Collectors;
-import java.util.zip.ZipEntry;
-import java.util.zip.ZipOutputStream;
-
-import javax.servlet.http.HttpServletResponse;
-import javax.validation.ConstraintViolationException;
-
 import ca.corefacility.bioinformatics.irida.exceptions.ConcatenateException;
 import ca.corefacility.bioinformatics.irida.exceptions.EntityNotFoundException;
+import ca.corefacility.bioinformatics.irida.model.assembly.GenomeAssembly;
 import ca.corefacility.bioinformatics.irida.model.assembly.UploadedAssembly;
 import ca.corefacility.bioinformatics.irida.model.enums.ProjectMetadataRole;
-import ca.corefacility.bioinformatics.irida.model.sample.MetadataTemplateField;
-import ca.corefacility.bioinformatics.irida.model.sample.metadata.MetadataRestriction;
-import ca.corefacility.bioinformatics.irida.model.sequenceFile.*;
-import ca.corefacility.bioinformatics.irida.repositories.sample.MetadataEntryRepository;
-import ca.corefacility.bioinformatics.irida.repositories.sample.MetadataRestrictionRepository;
-import ca.corefacility.bioinformatics.irida.ria.web.samples.SamplePairer;
-import ca.corefacility.bioinformatics.irida.ria.web.samples.dto.*;
-import ca.corefacility.bioinformatics.irida.service.sample.MetadataTemplateService;
-
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.context.MessageSource;
-
-import org.springframework.security.core.Authentication;
-import org.springframework.security.core.context.SecurityContextHolder;
-import org.springframework.stereotype.Component;
-import org.springframework.web.multipart.MultipartFile;
-import org.springframework.web.multipart.MultipartHttpServletRequest;
-
-import org.apache.commons.csv.CSVFormat;
-import org.apache.commons.csv.CSVPrinter;
-
-import org.apache.commons.lang3.StringUtils;
-import org.apache.poi.ss.usermodel.Cell;
-import org.apache.poi.ss.usermodel.CellStyle;
-import org.apache.poi.ss.usermodel.CreationHelper;
-import org.apache.poi.ss.usermodel.Row;
-import org.apache.poi.ss.util.DateFormatConverter;
-import org.apache.poi.xssf.usermodel.XSSFSheet;
-import org.apache.poi.xssf.usermodel.XSSFWorkbook;
-import org.springframework.data.domain.Page;
-import org.springframework.transaction.annotation.Transactional;
-import org.springframework.web.servlet.mvc.method.annotation.StreamingResponseBody;
-
-import ca.corefacility.bioinformatics.irida.model.assembly.GenomeAssembly;
-
 import ca.corefacility.bioinformatics.irida.model.joins.impl.ProjectSampleJoin;
 import ca.corefacility.bioinformatics.irida.model.joins.impl.SampleGenomeAssemblyJoin;
 import ca.corefacility.bioinformatics.irida.model.project.Project;
+import ca.corefacility.bioinformatics.irida.model.sample.MetadataTemplateField;
 import ca.corefacility.bioinformatics.irida.model.sample.QCEntry;
 import ca.corefacility.bioinformatics.irida.model.sample.Sample;
 import ca.corefacility.bioinformatics.irida.model.sample.SampleSequencingObjectJoin;
 import ca.corefacility.bioinformatics.irida.model.sample.metadata.MetadataEntry;
-import ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleGenomeAssemblyFileModel;
-import ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleSequencingObjectFileModel;
-import ca.corefacility.bioinformatics.irida.model.sequenceFile.Fast5Object;
-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.ria.web.samples.dto.SampleDetails;
-import ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleFiles;
-import ca.corefacility.bioinformatics.irida.ria.web.samples.dto.ShareMetadataRestriction;
-import ca.corefacility.bioinformatics.irida.ria.web.samples.dto.ShareSamplesRequest;
-
+import ca.corefacility.bioinformatics.irida.model.sample.metadata.MetadataRestriction;
+import ca.corefacility.bioinformatics.irida.model.sequenceFile.*;
+import ca.corefacility.bioinformatics.irida.repositories.sample.MetadataEntryRepository;
+import ca.corefacility.bioinformatics.irida.repositories.sample.MetadataRestrictionRepository;
 import ca.corefacility.bioinformatics.irida.repositories.specification.ProjectSampleJoinSpecification;
 import ca.corefacility.bioinformatics.irida.repositories.specification.SearchCriteria;
 import ca.corefacility.bioinformatics.irida.repositories.specification.SearchOperation;
@@ -92,19 +34,51 @@
 import ca.corefacility.bioinformatics.irida.ria.web.projects.dto.samples.ProjectSamplesFilter;
 import ca.corefacility.bioinformatics.irida.ria.web.projects.dto.samples.SampleObject;
 import ca.corefacility.bioinformatics.irida.ria.web.projects.error.SampleMergeException;
-
+import ca.corefacility.bioinformatics.irida.ria.web.samples.SamplePairer;
+import ca.corefacility.bioinformatics.irida.ria.web.samples.dto.*;
 import ca.corefacility.bioinformatics.irida.security.permissions.sample.UpdateSamplePermission;
 import ca.corefacility.bioinformatics.irida.service.GenomeAssemblyService;
 import ca.corefacility.bioinformatics.irida.service.ProjectService;
 import ca.corefacility.bioinformatics.irida.service.SequencingObjectService;
-
+import ca.corefacility.bioinformatics.irida.service.sample.MetadataTemplateService;
 import ca.corefacility.bioinformatics.irida.service.sample.SampleService;
-
 import com.google.common.base.Strings;
-
+import com.google.common.collect.ImmutableList;
 import com.google.common.collect.Lists;
+import org.apache.commons.csv.CSVFormat;
+import org.apache.commons.csv.CSVPrinter;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.poi.ss.usermodel.Cell;
+import org.apache.poi.ss.usermodel.CellStyle;
+import org.apache.poi.ss.usermodel.CreationHelper;
+import org.apache.poi.ss.usermodel.Row;
+import org.apache.poi.ss.util.DateFormatConverter;
+import org.apache.poi.xssf.usermodel.XSSFSheet;
+import org.apache.poi.xssf.usermodel.XSSFWorkbook;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.MessageSource;
+import org.springframework.data.domain.Page;
+import org.springframework.security.core.Authentication;
+import org.springframework.security.core.context.SecurityContextHolder;
+import org.springframework.stereotype.Component;
+import org.springframework.transaction.annotation.Transactional;
+import org.springframework.web.multipart.MultipartFile;
+import org.springframework.web.multipart.MultipartHttpServletRequest;
+import org.springframework.web.servlet.mvc.method.annotation.StreamingResponseBody;
 
-import com.google.common.collect.ImmutableList;
+import javax.servlet.http.HttpServletResponse;
+import javax.validation.ConstraintViolationException;
+import java.io.IOException;
+import java.io.OutputStreamWriter;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.attribute.BasicFileAttributes;
+import java.text.SimpleDateFormat;
+import java.time.Instant;
+import java.util.*;
+import java.util.stream.Collectors;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipOutputStream;
 
 /**
  * UI Service for samples
@@ -1215,12 +1189,10 @@ private SequenceFile createSequenceFile(MultipartFile file) throws IOException {
 	 *
 	 * @param projectId identifier for the project
 	 * @param sampleIds list of sampleIds to remove
-	 * @return result of the removal of samples
 	 */
-	public String removeSamplesFromProject(Long projectId, List<Long> sampleIds) {
+	public void removeSamplesFromProject(Long projectId, List<Long> sampleIds) {
 		Project project = projectService.read(projectId);
 		projectService.removeSamplesFromProject(project, sampleService.readMultiple(sampleIds));
-		return "FOOBAR";
 	}
 
 	/**

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<String, List<Long>> getSampleIdsBySampleNameForProjects(List<Long> projectIds,
 			List<String> sampleNames) {
 		return sampleRepository.getSampleIdsBySampleNameInProjects(projectIds, sampleNames)
@@ -673,8 +673,9 @@ public List<QCEntry> getQCEntriesForSample(Sample sample) {
 	public Map<Long, List<QCEntry>> getQCEntriesForSamples(List<Sample> 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<GenericStatModel> getSamplesCreatedGrouped(Date createdDate, Statist
 	public Map<Long, Long> getCoverageForSamplesInProject(Project project, List<Long> 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);
 	}
 }

src/main/resources/i18n/messages.properties

@@ -364,9 +364,8 @@ ShareSamples.title=Share Samples with Another Project
 ShareSamples.projects=Select a project to share samples with
 ShareSamples.ready=These samples are ready to copy
 ShareSamples.exists=Samples that exist in the target project and will not be copied
-ShareSamples.avatar.unlocked=This sample is modifiable in this project.
-ShareSamples.avatar.locked=This sample is not modifiable in this project.
 ShareSamples.remove=Remove
+ShareSamples.locked=The follow samples are locked and cannot be shared
 ShareSamplesList.title=Review samples to share
 ShareSamples.no-samples.message=All samples exist in the target project
 ShareSamples.no-samples.description=Since these samples exists, there is no reason to re-share them.
@@ -2872,6 +2871,8 @@ SampleMenu.excel=Export to Excel
 SampleMenu.csv=Export to CSV
 SampleMenu.fileFilter=Filter by File
 SampleMenu.fileFilter.clear=Clear File Filter: {0}
+SampleMenu.share-all-locked=All samples are locked and cannot be shared.
+SampleMenu.share-some-locked={0} samples are locked and cannot be shared:
 SampleIcon.locked=You do not have ownership of this sample and cannot modify it.
 SamplesTable.Column.sampleName=Name
 SamplesTable.Column.quality=QC

src/main/webapp/resources/js/apis/cart/cart.ts

@@ -122,7 +122,7 @@ export const {
   useRemoveSampleMutation,
 } = cartApi;
 
-const updateCart = (data: CartUpdated) => {
+export const updateCart = (data: CartUpdated) => {
   data.notifications.forEach((n) => notification[n.type](n));
   cartUpdated(data.count);
   return data.count;