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Example 1 with RunService

use of uk.ac.bbsrc.tgac.miso.core.service.RunService in project miso-lims by miso-lims.

the class RunRestController method setPartitionPurposes.

@PutMapping("/{runId}/partition-purposes")
@ResponseStatus(HttpStatus.NO_CONTENT)
public void setPartitionPurposes(@PathVariable long runId, @RequestBody RunPartitionPurposeRequest request) throws IOException {
    Run run = RestUtils.retrieve("Run", runId, runService);
    RunPurpose purpose = RestUtils.retrieve("Run purpose", request.getRunPurposeId(), runPurposeService);
    List<Partition> partitions = run.getSequencerPartitionContainers().stream().flatMap(container -> container.getPartitions().stream()).filter(partition -> request.getPartitionIds().contains(partition.getId())).collect(Collectors.toList());
    for (Partition partition : partitions) {
        RunPartition runPartition = runPartitionService.get(run, partition);
        if (runPartition == null) {
            runPartition = new RunPartition();
            runPartition.setRunId(run.getId());
            runPartition.setPartitionId(partition.getId());
        }
        runPartition.setPurpose(purpose);
        runPartitionService.save(runPartition);
    }
}
Also used : RunPurposeService(uk.ac.bbsrc.tgac.miso.core.service.RunPurposeService) PathVariable(org.springframework.web.bind.annotation.PathVariable) UriComponentsBuilder(org.springframework.web.util.UriComponentsBuilder) RequestParam(org.springframework.web.bind.annotation.RequestParam) SampleTissueProcessing(uk.ac.bbsrc.tgac.miso.core.data.SampleTissueProcessing) PaginationFilter(uk.ac.bbsrc.tgac.miso.core.util.PaginationFilter) DataTablesResponseDto(uk.ac.bbsrc.tgac.miso.dto.DataTablesResponseDto) Autowired(org.springframework.beans.factory.annotation.Autowired) SampleSheet(uk.ac.bbsrc.tgac.miso.core.util.SampleSheet) RunPartition(uk.ac.bbsrc.tgac.miso.core.data.RunPartition) Dtos(uk.ac.bbsrc.tgac.miso.dto.Dtos) RunPartitionDto(uk.ac.bbsrc.tgac.miso.dto.ExperimentDto.RunPartitionDto) PutMapping(org.springframework.web.bind.annotation.PutMapping) Sample(uk.ac.bbsrc.tgac.miso.core.data.Sample) Map(java.util.Map) 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Example 2 with RunService

use of uk.ac.bbsrc.tgac.miso.core.service.RunService in project miso-lims by miso-lims.

the class RunRestController method setQc.

@PostMapping(value = "/{runId}/qc", produces = "application/json")
@ResponseStatus(code = HttpStatus.NO_CONTENT)
public void setQc(@PathVariable Long runId, @RequestBody RunPartitionQCRequest request) throws IOException {
    Run run = RestUtils.retrieve("Run", runId, runService);
    PartitionQCType qcType = partitionQcTypeService.list().stream().filter(qt -> qt.getId() == request.getQcTypeId().longValue()).findAny().orElseThrow(() -> new RestException(String.format("No partition QC type found with ID: %d", request.getQcTypeId()), Status.BAD_REQUEST));
    // 
    run.getSequencerPartitionContainers().stream().flatMap(// 
    container -> container.getPartitions().stream()).filter(// 
    partition -> request.partitionIds.contains(partition.getId())).map(WhineyFunction.rethrow(partition -> {
        RunPartition runPartition = runPartitionService.get(run, partition);
        if (runPartition == null) {
            runPartition = new RunPartition();
            runPartition.setRunId(run.getId());
            runPartition.setPartitionId(partition.getId());
        }
        runPartition.setQcType(qcType);
        runPartition.setNotes(request.notes);
        return runPartition;
    })).forEach(WhineyConsumer.rethrow(runPartitionService::save));
}
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