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⬆️ Upmerge release/2023.2.x to release/2023.3.x #447

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merged 3 commits into from
Aug 17, 2023
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⬆️ Upmerge release/2023.2.x to release/2023.3.x #447

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439a3fd
ACAS-699: Accept projects list to filter /api/experiments/protocolCod…
brianbolt Aug 15, 2023
f94a2db
Throw TooManyResultsException instead
brianbolt Aug 17, 2023
40a0dc8
Merge pull request #446 from mcneilco/ACAS-699
brianbolt Aug 17, 2023
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18 changes: 9 additions & 9 deletions src/main/java/com/labsynch/labseer/api/ApiExperimentController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -44,6 +44,7 @@
import com.labsynch.labseer.dto.TsvLoaderResponseDTO;
import com.labsynch.labseer.exceptions.ErrorMessage;
import com.labsynch.labseer.exceptions.NotFoundException;
import com.labsynch.labseer.exceptions.TooManyResultsException;
import com.labsynch.labseer.exceptions.UniqueNameException;
import com.labsynch.labseer.service.AnalysisGroupService;
import com.labsynch.labseer.service.AnalysisGroupValueService;
Expand Down Expand Up @@ -1634,20 +1635,19 @@ public ResponseEntity<java.lang.String> jsonFindExperimentByNameGet(@RequestPara
@RequestMapping(value = "/protocol/{codeName}", method = RequestMethod.GET, headers = "Accept=application/json")
@ResponseBody
public ResponseEntity<java.lang.String> jsonFindExperimentsByProtocolCodeName(
@PathVariable("codeName") String codeName, @RequestParam(value = "with", required = false) String with) {
@PathVariable("codeName") String codeName, @RequestParam(value = "projects", required = false) List<String> projects, @RequestParam(value = "with", required = false) String with) {
HttpHeaders headers = new HttpHeaders();
headers.add("Content-Type", "application/json; charset=utf-8");
List<Protocol> protocols = Protocol.findProtocolsByCodeNameEqualsAndIgnoredNot(codeName, true).getResultList();
if (protocols.size() == 1) {
try {
Collection<Experiment> experiments = experimentService.findExperimentsByProtocolCodeName(codeName, projects);
return new ResponseEntity<String>(
Experiment.toJsonArrayStub(Experiment.findExperimentsByProtocol(protocols.get(0)).getResultList()),
Experiment.toJsonArrayStub(experiments),
headers, HttpStatus.OK);
} else if (protocols.size() > 1) {
logger.error("ERROR: multiple protocols found with the same code name");
return new ResponseEntity<String>("[ ]", headers, HttpStatus.CONFLICT);
} else {
logger.warn("WARN: no protocols found with the query code name");
} catch (NoResultException e) {
return new ResponseEntity<String>("[ ]", headers, HttpStatus.NOT_FOUND);

} catch (TooManyResultsException e) {
return new ResponseEntity<String>("[ ]", headers, HttpStatus.CONFLICT);
}
}

Expand Down
4 changes: 4 additions & 0 deletions src/main/java/com/labsynch/labseer/service/ExperimentService.java
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Expand Up @@ -51,6 +51,10 @@ public Collection<JSTreeNodeDTO> getExperimentNodesByProtocolTree(
public Collection<Experiment> findExperimentsByMetadataJson(
List<StringCollectionDTO> metaDataList);


public Collection<Experiment> findExperimentsByProtocolCodeName(String query, List<String> projects)
throws TooManyResultsException;

public Collection<Experiment> findExperimentsByGenericMetaDataSearch(String query, String userName, Boolean includeDeleted)
throws TooManyResultsException;

Expand Down
39 changes: 39 additions & 0 deletions src/main/java/com/labsynch/labseer/service/ExperimentServiceImpl.java
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Expand Up @@ -1118,6 +1118,45 @@ public Collection<Experiment> findExperimentsByGenericMetaDataSearch(String quer

}

public Collection<Experiment> findExperimentsByProtocolCodeName(String codeName, List<String> projects)
throws TooManyResultsException, NoResultException {
List<Protocol> protocols = Protocol.findProtocolsByCodeNameEqualsAndIgnoredNot(codeName, true).getResultList();

if (protocols.size() > 1) {
logger.error("ERROR: multiple protocols found with the same code name");
throw new TooManyResultsException("ERROR: multiple protocols found with the same code name");
} else if (protocols.size() < 1) {
logger.warn("WARN: no protocols found with the query code name");
throw new NoResultException("WARN: no protocols found with the query code name");
}

Collection<Experiment> rawResults = Experiment.findExperimentsByProtocol(protocols.get(0)).getResultList();
if (propertiesUtilService.getRestrictExperiments()) {
projects.add("unassigned");
Collection<Experiment> results = new HashSet<Experiment>();
for (Experiment rawResult : rawResults) {
String experimentProject = null;
for (ExperimentState state : rawResult.getLsStates()) {
if (!state.isIgnored() && !state.isDeleted()) {
for (ExperimentValue value : state.getLsValues()) {
if (value.getLsKind().equals("project") && !value.getDeleted() && !value.getIgnored()) {
experimentProject = value.getCodeValue();
break;
}
}
}
}
if (projects.contains(experimentProject)) {
results.add(rawResult);
}
}
return results;
} else {
return rawResults;
}

}

@Override
public Collection<Experiment> findExperimentsByGenericMetaDataSearch(String queryString, List<String> projects, Boolean includeDeleted)
throws TooManyResultsException {
Expand Down
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