Examples with IndexChecker uk.ac.bbsrc.tgac.miso.core.util.IndexChecker used on opensource projects

Example 1 with IndexChecker

use of uk.ac.bbsrc.tgac.miso.core.util.IndexChecker in project miso-lims by miso-lims.

the class EditSampleController method setupForm.

@GetMapping(value = "/{sampleId}")
public ModelAndView setupForm(@PathVariable Long sampleId, ModelMap model) throws IOException {
    Sample sample = sampleService.get(sampleId);
    if (sample == null)
        throw new NotFoundException("No sample found for ID " + sampleId.toString());
    model.put("title", "Sample " + sampleId);
    model.put("previousSample", sampleService.getPreviousInProject(sample));
    model.put("nextSample", sampleService.getNextInProject(sample));
    model.put("sampleCategory", LimsUtils.isDetailedSample(sample) ? ((DetailedSample) sample).getSampleClass().getSampleCategory() : "plain");
    List<LibraryDto> libraries = sample.isSaved() ? libraryService.listBySampleId(sample.getId()).stream().map(lib -> Dtos.asDto(lib, false)).collect(Collectors.toList()) : Collections.emptyList();
    model.put("sampleLibraries", libraries);
    Set<Pool> pools = libraries.stream().flatMap(WhineyFunction.flatRethrow(library -> poolService.listByLibraryId(library.getId()))).distinct().collect(Collectors.toSet());
    List<RunDto> runDtos = pools.stream().flatMap(WhineyFunction.flatRethrow(pool -> runService.listByPoolId(pool.getId()))).map(Dtos::asDto).collect(Collectors.toList());
    model.put("samplePools", pools.stream().map(p -> Dtos.asDto(p, false, false, indexChecker)).collect(Collectors.toList()));
    model.put("sampleRuns", runDtos);
    model.put("sampleRelations", getRelations(sample));
    addArrayData(sampleId, model);
    model.put("sampleTransfers", sample.getTransferViews().stream().map(Dtos::asDto).collect(Collectors.toList()));
    model.put("sample", sample);
    SampleDto sampleDto = Dtos.asDto(sample, false, libraries.size());
    setRelatedSlideDtos(sample, sampleDto);
    model.put("sampleDto", !sample.isSaved() ? "null" : mapper.writeValueAsString(sampleDto));
    ObjectNode formConfig = mapper.createObjectNode();
    formConfig.put("detailedSample", isDetailedSampleEnabled());
    MisoWebUtils.addJsonArray(mapper, formConfig, "projects", projectService.list(), Dtos::asDto);
    MisoWebUtils.addJsonArray(mapper, formConfig, Config.SOPS, sopService.listByCategory(SopCategory.SAMPLE), Dtos::asDto);
    model.put("formConfig", mapper.writeValueAsString(formConfig));
    return new ModelAndView("/WEB-INF/pages/editSample.jsp", model);
}

Example 2 with IndexChecker

use of uk.ac.bbsrc.tgac.miso.core.util.IndexChecker in project miso-lims by miso-lims.

the class EditExperimentController method setupForm.

@GetMapping(value = "/{experimentId}")
public ModelAndView setupForm(@PathVariable Long experimentId, ModelMap model) throws IOException {
    Experiment experiment = experimentService.get(experimentId);
    if (experiment == null)
        throw new NotFoundException("No experiment found for ID " + experimentId.toString());
    ObjectMapper mapper = new ObjectMapper();
    ObjectNode consumableConfig = mapper.createObjectNode();
    consumableConfig.put("experimentId", experiment.getId());
    Stream.<// 
    KitDescriptor>concat(// 
    Stream.of(experiment.getLibrary().getKitDescriptor()), // 
    experiment.getRunPartitions().stream().map(// 
    RunPartition::getPartition).flatMap(partition -> Stream.of(partition.getSequencerPartitionContainer().getClusteringKit(), // 
    partition.getSequencerPartitionContainer().getMultiplexingKit()))).filter(// 
    Objects::nonNull).distinct().map(// 
    Dtos::asDto).forEach(consumableConfig.putArray("allowedDescriptors")::addPOJO);
    model.put("experiment", experiment);
    model.put("experimentDto", mapper.writeValueAsString(Dtos.asDto(experiment)));
    model.put("consumables", experiment.getKits().stream().map(Dtos::asDto).collect(Collectors.toList()));
    model.put("consumableConfig", mapper.writeValueAsString(consumableConfig));
    model.put("runPartitions", experiment.getRunPartitions().stream().map(entry -> new ExperimentDto.RunPartitionDto(Dtos.asDto(entry.getRun()), Dtos.asDto(entry.getPartition(), indexChecker))).collect(Collectors.toList()));
    model.put("title", "Edit Experiment");
    return new ModelAndView("/WEB-INF/pages/editExperiment.jsp", model);
}

Example 3 with IndexChecker

use of uk.ac.bbsrc.tgac.miso.core.util.IndexChecker in project miso-lims by miso-lims.

the class RunRestController method getPotentialExperimentExpansions.

@GetMapping("/{runId}/potentialExperimentExpansions")
@ResponseBody
public List<AddRequest> getPotentialExperimentExpansions(@PathVariable long runId) throws IOException {
    Run run = getRun(runId);
    Map<Library, List<Partition>> libraryGroups = getLibraryGroups(run);
    return libraryGroups.entrySet().stream().<AddRequest>flatMap(WhineyFunction.rethrow(// 
    group -> // 
    experimentService.listAllByLibraryId(group.getKey().getId()).stream().filter(experiment -> experiment.getInstrumentModel().getId() == run.getSequencer().getInstrumentModel().getId()).flatMap(experiment -> // 
    group.getValue().stream().filter(partition -> experiment.getRunPartitions().stream().noneMatch(rp -> rp.getPartition().equals(partition))).map(partition -> {
        AddRequest request = new AddRequest();
        request.experiment = Dtos.asDto(experiment);
        request.partition = Dtos.asDto(partition, indexChecker);
        return request;
    })))).collect(Collectors.toList());
}

Example 4 with IndexChecker

use of uk.ac.bbsrc.tgac.miso.core.util.IndexChecker in project miso-lims by miso-lims.

the class RunRestController method getPotentialExperiments.

@GetMapping("/{runId}/potentialExperiments")
@ResponseBody
public List<StudiesForExperiment> getPotentialExperiments(@PathVariable long runId) throws IOException {
    Run run = getRun(runId);
    RunDto runDto = Dtos.asDto(run);
    InstrumentModelDto instrumentModelDto = Dtos.asDto(run.getSequencer().getInstrumentModel());
    Map<Library, List<Partition>> libraryGroups = getLibraryGroups(run);
    return libraryGroups.entrySet().stream().map(group -> new Pair<>(group.getKey(), group.getValue().stream().map(partition -> Dtos.asDto(partition, indexChecker)).map(partitionDto -> new RunPartitionDto(runDto, partitionDto)).collect(Collectors.toList()))).map(group -> {
        StudiesForExperiment result = new StudiesForExperiment();
        result.experiment = new ExperimentDto();
        result.experiment.setLibrary(Dtos.asDto(group.getKey(), false));
        result.experiment.setInstrumentModel(instrumentModelDto);
        result.experiment.setPartitions(group.getValue());
        result.studies = group.getKey().getSample().getProject().getStudies().stream().map(Dtos::asDto).collect(Collectors.toList());
        return result;
    }).collect(Collectors.toList());
}

Example 5 with IndexChecker

use of uk.ac.bbsrc.tgac.miso.core.util.IndexChecker in project miso-lims by miso-lims.

the class EditRunController method setupForm.

public ModelAndView setupForm(Run run, ModelMap model) throws IOException {
    if (run.getId() == Run.UNSAVED_ID) {
        model.put("title", "New Run");
        model.put("multiplexed", false);
        model.put("metrics", "[]");
        model.put("partitionNames", "[]");
    } else {
        model.put("title", "Run " + run.getId());
        model.put("metrics", getSources().filter(Objects::nonNull).map(source -> source.fetchMetrics(run)).filter(metrics -> !isStringBlankOrNull(metrics)).collect(new JsonArrayCollector()));
        if (run.getSequencerPartitionContainers().size() == 1) {
            ObjectMapper mapper = new ObjectMapper();
            model.put("partitionNames", mapper.writeValueAsString(run.getSequencerPartitionContainers().get(0).getPartitions().stream().sorted(Comparator.comparing(Partition::getPartitionNumber)).map(partition -> partition.getPool() == null ? "N/A" : partition.getPool().getAlias()).collect(Collectors.toList())));
        } else {
            model.put("partitionNames", "[]");
        }
        model.put("runReportLinks", externalUriBuilder.getUris(run));
    }
    model.put("runPositions", run.getRunPositions().stream().map(Dtos::asDto).collect(Collectors.toList()));
    model.put("runPartitions", run.getSequencerPartitionContainers().stream().flatMap(container -> container.getPartitions().stream()).map(WhineyFunction.rethrow(partition -> {
        PartitionDto dto = Dtos.asDto(partition, false, indexChecker);
        RunPartition runPartition = runPartitionService.get(run, partition);
        if (runPartition != null) {
            if (runPartition.getQcType() != null) {
                dto.setQcType(runPartition.getQcType().getId());
                dto.setQcNotes(runPartition.getNotes());
            }
            if (runPartition.getPurpose() != null) {
                dto.setRunPurposeId(runPartition.getPurpose().getId());
            }
        } else {
            dto.setQcNotes("");
        }
        return dto;
    })).collect(Collectors.toList()));
    model.put("runAliquots", getRunAliquots(run));
    MisoWebUtils.addIssues(issueTrackerManager, () -> issueTrackerManager.searchIssues(run.getAlias()), model);
    model.put("run", run);
    ObjectMapper mapper = new ObjectMapper();
    ObjectNode partitionConfig = mapper.createObjectNode();
    partitionConfig.put("platformType", run.getPlatformType().name());
    partitionConfig.put("instrumentModelId", run.getSequencer().getInstrumentModel().getId());
    partitionConfig.put("runId", run.getId());
    partitionConfig.put("isFull", run.isFull());
    partitionConfig.put("showContainer", true);
    partitionConfig.put("sequencingParametersId", run.getSequencingParameters() == null ? 0 : run.getSequencingParameters().getId());
    partitionConfig.put("showPool", true);
    model.put("partitionConfig", mapper.writeValueAsString(partitionConfig));
    model.put("experiments", experimentService.listAllByRunId(run.getId()).stream().map(expt -> Dtos.asDto(expt)).collect(Collectors.toList()));
    ObjectNode experimentConfig = mapper.createObjectNode();
    experimentConfig.put("runId", run.getId());
    model.put("experimentConfiguration", mapper.writeValueAsString(experimentConfig));
    model.put("runDto", mapper.writeValueAsString(Dtos.asDto(run)));
    ObjectNode formConfig = mapper.createObjectNode();
    User user = authorizationManager.getCurrentUser();
    formConfig.put("isAdmin", user.isAdmin());
    formConfig.put("isRunReviewer", user.isRunReviewer() || user.isAdmin());
    MisoWebUtils.addJsonArray(mapper, formConfig, "sops", sopService.listByCategory(SopCategory.RUN), Dtos::asDto);
    model.put("formConfig", mapper.writeValueAsString(formConfig));
    return new ModelAndView("/WEB-INF/pages/editRun.jsp", model);
}