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Merge pull request #1457 from phac-nml/fix-sample-modified-date-delet…
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…e-metadata

Fix for updating sample modified date when metadata is deleted
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@ericenns
ericenns authored Feb 2, 2023
2 parents b45b01a + 5556c62 commit 3c22445
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Showing 5 changed files with 95 additions and 108 deletions.
1 change: 1 addition & 0 deletions CHANGELOG.md
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* [UI]: Fixed bug where the `User` column was named `User Group` on the admin User Groups page. [See PR 1450](https://github.com/phac-nml/irida/pull/1450)
* [Developer]: Replaced Apache OLTU with Nimbusds for performing OAuth2 authentication flow during syncing and Galaxy exporting. See [PR 1432](https://github.com/phac-nml/irida/pull/1432)
* [Developer/UI]: Performance enhancements to the metadata uploader. See [PR 1445](https://github.com/phac-nml/irida/pull/1445).
* [Developer/UI]: Fix for updating sample modified date when metadata is deleted. See [PR 1457](https://github.com/phac-nml/irida/pull/1457).

## [22.09.7] - 2022/01/24
* [UI]: Fixed bugs on NCBI Export page preventing the NCBI `submission.xml` file from being properly written. See [PR 1451](https://github.com/phac-nml/irida/pull/1451)
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58 changes: 23 additions & 35 deletions ...main/java/ca/corefacility/bioinformatics/irida/ria/web/samples/SamplesAjaxController.java
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Expand Up @@ -2,18 +2,14 @@

import java.io.IOException;
import java.security.Principal;
import java.util.*;
import java.util.List;
import java.util.Locale;
import java.util.Set;

import javax.servlet.http.HttpServletResponse;
import javax.validation.ConstraintViolation;
import javax.validation.ConstraintViolationException;

import ca.corefacility.bioinformatics.irida.exceptions.ConcatenateException;
import ca.corefacility.bioinformatics.irida.exceptions.EntityExistsException;
import ca.corefacility.bioinformatics.irida.exceptions.EntityNotFoundException;
import ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject;
import ca.corefacility.bioinformatics.irida.ria.web.samples.dto.*;

import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.HttpStatus;
import org.springframework.http.MediaType;
Expand All @@ -22,16 +18,17 @@
import org.springframework.web.multipart.MultipartFile;
import org.springframework.web.multipart.MultipartHttpServletRequest;

import ca.corefacility.bioinformatics.irida.exceptions.ConcatenateException;
import ca.corefacility.bioinformatics.irida.exceptions.EntityExistsException;
import ca.corefacility.bioinformatics.irida.exceptions.EntityNotFoundException;
import ca.corefacility.bioinformatics.irida.model.sample.Sample;
import ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFile;

import ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject;
import ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ajax.AjaxErrorResponse;
import ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ajax.AjaxResponse;
import ca.corefacility.bioinformatics.irida.ria.web.ajax.dto.ajax.AjaxSuccessResponse;
import ca.corefacility.bioinformatics.irida.ria.web.samples.dto.*;
import ca.corefacility.bioinformatics.irida.ria.web.services.UIAnalysesService;

import ca.corefacility.bioinformatics.irida.ria.web.samples.dto.SampleDetails;

import ca.corefacility.bioinformatics.irida.ria.web.services.UISampleService;

/**
Expand Down Expand Up @@ -62,8 +59,7 @@ public ResponseEntity<List<SampleSequencingObjectFileModel>> uploadSequenceFiles
try {
return ResponseEntity.ok(uiSampleService.uploadSequenceFiles(sampleId, request));
} catch (IOException e) {
return ResponseEntity.status(HttpStatus.INTERNAL_SERVER_ERROR)
.body(null);
return ResponseEntity.status(HttpStatus.INTERNAL_SERVER_ERROR).body(null);
}
}

Expand All @@ -80,8 +76,7 @@ public ResponseEntity<List<SampleSequencingObjectFileModel>> uploadFast5Files(@P
try {
return ResponseEntity.ok(uiSampleService.uploadFast5Files(sampleId, request));
} catch (IOException e) {
return ResponseEntity.status(HttpStatus.INTERNAL_SERVER_ERROR)
.body(null);
return ResponseEntity.status(HttpStatus.INTERNAL_SERVER_ERROR).body(null);
}
}

Expand All @@ -98,8 +93,7 @@ public ResponseEntity<List<SampleGenomeAssemblyFileModel>> uploadAssemblies(@Pat
try {
return ResponseEntity.ok(uiSampleService.uploadAssemblies(sampleId, request));
} catch (IOException e) {
return ResponseEntity.status(HttpStatus.INTERNAL_SERVER_ERROR)
.body(null);
return ResponseEntity.status(HttpStatus.INTERNAL_SERVER_ERROR).body(null);
}
}

Expand Down Expand Up @@ -145,8 +139,7 @@ public ResponseEntity<AjaxResponse> updateSampleDetails(@PathVariable Long id,
for (ConstraintViolation a : e.getConstraintViolations()) {
constraintViolations += a.getMessage() + "\n";
}
return ResponseEntity.status(HttpStatus.BAD_REQUEST)
.body(new AjaxErrorResponse(constraintViolations));
return ResponseEntity.status(HttpStatus.BAD_REQUEST).body(new AjaxErrorResponse(constraintViolations));
}
}

Expand All @@ -165,17 +158,16 @@ public ResponseEntity<AjaxResponse> updateDefaultSequencingObjectForSample(@Path
return ResponseEntity.ok(new AjaxSuccessResponse(
uiSampleService.updateDefaultSequencingObjectForSample(id, sequencingObjectId, locale)));
} catch (EntityNotFoundException e) {
return ResponseEntity.status(HttpStatus.BAD_REQUEST)
.body(new AjaxErrorResponse(e.getMessage()));
return ResponseEntity.status(HttpStatus.BAD_REQUEST).body(new AjaxErrorResponse(e.getMessage()));
}
}

/**
* Update the default genome assembly for the sample
*
* @param id {@link Long} identifier for the sample
* @param id {@link Long} identifier for the sample
* @param genomeAssemblyId The genome assembly identifier
* @param locale {@link Locale} for the currently logged in user
* @param locale {@link Locale} for the currently logged in user
* @return {@link ResponseEntity} explaining to the user the results of the update.
*/
@PutMapping(value = "/{id}/default-genome-assembly")
Expand All @@ -185,8 +177,7 @@ public ResponseEntity<AjaxResponse> updateDefaultGenomeAssemblyForSample(@PathVa
return ResponseEntity.ok(new AjaxSuccessResponse(
uiSampleService.updateDefaultGenomeAssemblyForSample(id, genomeAssemblyId, locale)));
} catch (EntityNotFoundException e) {
return ResponseEntity.status(HttpStatus.BAD_REQUEST)
.body(new AjaxErrorResponse(e.getMessage()));
return ResponseEntity.status(HttpStatus.BAD_REQUEST).body(new AjaxErrorResponse(e.getMessage()));
}
}

Expand All @@ -204,8 +195,7 @@ public ResponseEntity<List<SampleAnalyses>> getSampleAnalyses(@PathVariable Long
try {
return ResponseEntity.ok(uiAnalysesService.getSampleAnalyses(sampleId, principal, locale));
} catch (Exception e) {
return ResponseEntity.status(HttpStatus.BAD_REQUEST)
.body(null);
return ResponseEntity.status(HttpStatus.BAD_REQUEST).body(null);
}
}

Expand All @@ -227,16 +217,17 @@ public ResponseEntity<AddSampleMetadataResponse> addSampleMetadata(@PathVariable
* Remove metadata field and entry from {@link Sample}
*
* @param projectId The project identifier
* @param metadataFieldId The metadata field id
* @param sampleId The sample identifier
* @param metadataFieldId The metadata field id
* @param metadataEntryId The metadata entry identifier
* @param locale {@link Locale} for the currently logged in user
* @return {@link ResponseEntity} explaining to the user the results of the deletion.
*/
@DeleteMapping(value = "/metadata")
public ResponseEntity<AjaxResponse> removeSampleMetadata(@RequestParam Long projectId,
public ResponseEntity<AjaxResponse> removeSampleMetadata(@RequestParam Long projectId, @RequestParam Long sampleId,
@RequestParam Long metadataFieldId, @RequestParam Long metadataEntryId, Locale locale) {
return ResponseEntity.ok(new AjaxSuccessResponse(
uiSampleService.removeSampleMetadata(projectId, metadataFieldId, metadataEntryId, locale)));
uiSampleService.removeSampleMetadata(projectId, sampleId, metadataFieldId, metadataEntryId, locale)));
}

/**
Expand All @@ -254,8 +245,7 @@ public ResponseEntity<AjaxResponse> updateSampleMetadata(@PathVariable Long id,
return ResponseEntity.ok(new AjaxSuccessResponse(
uiSampleService.updateSampleMetadata(id, updateSampleMetadataRequest, locale)));
} catch (EntityExistsException e) {
return ResponseEntity.status(HttpStatus.BAD_REQUEST)
.body(new AjaxErrorResponse(e.getMessage()));
return ResponseEntity.status(HttpStatus.BAD_REQUEST).body(new AjaxErrorResponse(e.getMessage()));
}
}

Expand All @@ -273,7 +263,6 @@ public ResponseEntity<AjaxResponse> getFilesForSample(@PathVariable Long id,
}

/**
* Get updated sample sequencing objects for given sequencing object ids
*
* @param id Identifier for a sample
Expand Down Expand Up @@ -341,8 +330,7 @@ public ResponseEntity<List<SampleSequencingObjectFileModel>> concatenateSequence
return ResponseEntity.ok(uiSampleService.concatenateSequenceFiles(sampleId, sequenceObjectIds, newFileName,
removeOriginals));
} catch (ConcatenateException e) {
return ResponseEntity.status(HttpStatus.BAD_REQUEST)
.body(null);
return ResponseEntity.status(HttpStatus.BAD_REQUEST).body(null);
}
}

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