Examples with Dataset org.obiba.mica.dataset.domain.Dataset used on opensource projects

Example 1 with Dataset

use of org.obiba.mica.dataset.domain.Dataset in project mica2 by obiba.

the class VariableSetService method createOpalViews.

/**
 * Get a list of opal view dto for backup restore purposes
 *
 * @param variables The source variables set
 * @return a list of opal views grouped by project and entity type
 */
private List<Magma.ViewDto> createOpalViews(List<DatasetVariable> variables, MicaConfig.OpalViewsGrouping opalViewsGrouping) {
    List<Magma.ViewDto> views = new ArrayList<>();
    List<Dataset> datasets = publishedDatasetService.findByIds(variables.stream().map(DatasetVariable::getDatasetId).distinct().collect(Collectors.toList()));
    Map<String, List<String>> opalTableFullNameMap = datasets.stream().collect(Collectors.toMap(Dataset::getId, this::toOpalTableFullName));
    switch(opalViewsGrouping) {
        case PROJECT_TABLE:
            Map<String, List<DatasetVariable>> variablesGroupedByProjectTable = Maps.newHashMap();
            variables.forEach(variable -> {
                List<String> projectTables = opalTableFullNameMap.get(variable.getDatasetId());
                projectTables.forEach(projectTable -> {
                    if (!variablesGroupedByProjectTable.containsKey(projectTable))
                        variablesGroupedByProjectTable.put(projectTable, Lists.newArrayList());
                    variablesGroupedByProjectTable.get(projectTable).add(variable);
                });
            });
            for (Entry<String, List<DatasetVariable>> entry : variablesGroupedByProjectTable.entrySet()) {
                views.add(createViewDto(entry.getValue(), entry.getKey()));
            }
            break;
        case PROJECT_ENTITY_TYPE:
            Map<String, List<DatasetVariable>> variablesGroupedByProjectEntityType = Maps.newHashMap();
            variables.forEach(variable -> {
                List<String> projectTables = opalTableFullNameMap.get(variable.getDatasetId());
                projectTables.forEach(projectTable -> {
                    String projectEntityType = projectTable.split("\\.")[0] + "." + variable.getEntityType();
                    if (!variablesGroupedByProjectEntityType.containsKey(projectEntityType))
                        variablesGroupedByProjectEntityType.put(projectEntityType, Lists.newArrayList());
                    Optional<DatasetVariable> varOpt = variablesGroupedByProjectEntityType.get(projectEntityType).stream().filter(var -> var.getName().equals(variable.getName())).findFirst();
                    if (!varOpt.isPresent())
                        variablesGroupedByProjectEntityType.get(projectEntityType).add(variable);
                });
            });
            for (Entry<String, List<DatasetVariable>> entry : variablesGroupedByProjectEntityType.entrySet()) {
                views.add(createViewDto(entry.getValue(), entry.getKey(), opalTableFullNameMap));
            }
            break;
        case ENTITY_TYPE:
            Map<String, List<DatasetVariable>> variablesGroupedByEntityType = variables.stream().collect(Collectors.groupingBy(DatasetVariable::getEntityType));
            for (Entry<String, List<DatasetVariable>> entry : variablesGroupedByEntityType.entrySet()) {
                views.add(createViewDto(entry.getValue(), entry.getKey(), opalTableFullNameMap));
            }
            break;
    }
    return views;
}

Example 2 with Dataset

use of org.obiba.mica.dataset.domain.Dataset in project mica2 by obiba.

the class DatasetDtos method fromDto.

@NotNull
public Dataset fromDto(Mica.DatasetDtoOrBuilder dto) {
    Dataset dataset = dto.hasExtension(Mica.HarmonizedDatasetDto.type) ? fromDto(dto.getExtension(Mica.HarmonizedDatasetDto.type)) : dto.hasExtension(Mica.CollectedDatasetDto.type) ? fromDto(dto.getExtension(Mica.CollectedDatasetDto.type)) : new StudyDataset();
    if (dto.hasId())
        dataset.setId(dto.getId());
    dataset.setAcronym(localizedStringDtos.fromDto(dto.getAcronymList()));
    dataset.setName(localizedStringDtos.fromDto(dto.getNameList()));
    dataset.setDescription(localizedStringDtos.fromDto(dto.getDescriptionList()));
    dataset.setEntityType(dto.getEntityType());
    dataset.setPublished(dto.getPublished());
    if (dto.getAttributesCount() > 0) {
        dto.getAttributesList().forEach(attributeDto -> dataset.addAttribute(attributeDtos.fromDto(attributeDto)));
    }
    if (dto.hasContent()) {
        dataset.setModel(JSONUtils.toMap(dto.getContent()));
    }
    return dataset;
}

Example 3 with Dataset

use of org.obiba.mica.dataset.domain.Dataset in project mica2 by obiba.

the class DatasetController method dataset.

@GetMapping("/dataset/{id:.+}")
public ModelAndView dataset(@PathVariable String id, @RequestParam(value = "draft", required = false) String shareKey) {
    Map<String, Object> params = newParameters();
    Dataset dataset = getDataset(id, shareKey);
    params.put("dataset", dataset);
    params.put("type", (dataset instanceof StudyDataset) ? "Collected" : "Harmonized");
    params.put("draft", !Strings.isNullOrEmpty(shareKey));
    if (dataset instanceof StudyDataset) {
        addStudyTableParameters(params, ((StudyDataset) dataset).getStudyTable());
    } else {
        HarmonizationDataset harmoDataset = (HarmonizationDataset) dataset;
        addHarmonizationTableParameters(params, harmoDataset.getHarmonizationTable());
        Map<String, BaseStudy> allStudies = Maps.newHashMap();
        List<BaseStudyTable> allTables = Lists.newArrayList();
        List<Map<String, Object>> studyTables = Lists.newArrayList();
        List<String> ids = Lists.newArrayList();
        for (StudyTable sTable : harmoDataset.getStudyTables()) {
            Map<String, Object> p = new HashMap<>();
            if (addStudyTableParameters(p, sTable, ids))
                allTables.add(sTable);
            if (!p.isEmpty()) {
                studyTables.add(p);
                allStudies.put(sTable.getStudyId(), (BaseStudy) p.get("study"));
            }
        }
        params.put("studyTables", studyTables);
        List<Map<String, Object>> harmonizationTables = Lists.newArrayList();
        ids.clear();
        for (HarmonizationStudyTable hTable : harmoDataset.getHarmonizationTables()) {
            Map<String, Object> p = new HashMap<>();
            if (addHarmonizationTableParameters(p, hTable, ids))
                allTables.add(hTable);
            if (!p.isEmpty()) {
                harmonizationTables.add(p);
                allStudies.put(hTable.getStudyId(), (BaseStudy) p.get("study"));
            }
        }
        params.put("harmonizationTables", harmonizationTables);
        params.put("allTables", allTables);
        params.put("allStudies", allStudies);
    }
    params.put("showDatasetContingencyLink", showDatasetContingencyLink());
    return new ModelAndView("dataset", params);
}

Example 4 with Dataset

use of org.obiba.mica.dataset.domain.Dataset in project mica2 by obiba.

the class DatasetAnalysisController method crosstab.

@GetMapping("/dataset-crosstab/{id:.+}")
public ModelAndView crosstab(HttpServletRequest request, @PathVariable String id, @RequestParam(value = "var1", required = false) String var1, @RequestParam(value = "var2", required = false) String var2) {
    // check if service is available
    if (!micaConfigService.getConfig().isContingencyEnabled()) {
        return new ModelAndView("redirect:/dataset/" + id);
    }
    Subject subject = SecurityUtils.getSubject();
    String contextPath = micaConfigService.getContextPath();
    if (!subject.isAuthenticated() && (micaConfigService.getConfig().isVariableSummaryRequiresAuthentication() || subjectAclService.hasDatasetContingencyPermissions())) {
        String query = "";
        if (!Strings.isNullOrEmpty(var1))
            query = "var1=" + var1;
        if (!Strings.isNullOrEmpty(var2))
            query = (Strings.isNullOrEmpty(query) ? "" : query + "&") + "var2=" + var2;
        String redirect = encode(contextPath + "/dataset-crosstab/" + id + (Strings.isNullOrEmpty(query) ? "" : "?") + query);
        return new ModelAndView("redirect:/signin?redirect=" + redirect);
    }
    // check if user is permitted
    if (!subjectAclService.isDatasetContingencyPermitted()) {
        return new ModelAndView("redirect:/dataset/" + id);
    }
    ModelAndView mv = new ModelAndView("dataset-crosstab");
    Dataset dataset = getDataset(id);
    mv.getModelMap().addAttribute("dataset", dataset);
    String type = (dataset instanceof StudyDataset) ? "Collected" : "Harmonized";
    String variableType = (dataset instanceof StudyDataset) ? "Collected" : "Dataschema";
    mv.getModelMap().addAttribute("type", type);
    if (!Strings.isNullOrEmpty(var1)) {
        mv.getModelMap().addAttribute("var1", var1);
        DatasetVariable variable1 = getDatasetVariable(id + ":" + var1 + ":" + variableType, var1);
        mv.getModelMap().addAttribute("variable1", getDatasetVariableJSON(variable1));
    }
    if (!Strings.isNullOrEmpty(var2)) {
        mv.getModelMap().addAttribute("var2", var2);
        DatasetVariable variable2 = getDatasetVariable(id + ":" + var2 + ":" + variableType, var2);
        mv.getModelMap().addAttribute("variable2", getDatasetVariableJSON(variable2));
    }
    return mv;
}

Example 5 with Dataset

use of org.obiba.mica.dataset.domain.Dataset in project mica2 by obiba.

the class DraftHarmonizedDatasetResource method update.

@PUT
@Timed
public Response update(Mica.DatasetDto datasetDto, @Context UriInfo uriInfo, @Nullable @QueryParam("comment") String comment) {
    checkPermission("/draft/harmonized-dataset", "EDIT");
    if (!datasetDto.hasId() || !datasetDto.getId().equals(id))
        throw new IllegalArgumentException("Not the expected dataset id");
    Dataset dataset = dtos.fromDto(datasetDto);
    if (!(dataset instanceof HarmonizationDataset))
        throw new IllegalArgumentException("An harmonization dataset is expected");
    datasetService.save((HarmonizationDataset) dataset, comment);
    return Response.noContent().build();
}