Examples with StudyConfig org.obiba.mica.micaConfig.domain.StudyConfig used on opensource projects

Example 1 with StudyConfig

use of org.obiba.mica.micaConfig.domain.StudyConfig in project mica2 by obiba.

the class EntityConfigKeyTranslationService method getCompleteConfigTranslationMap.

public RegexHashMap getCompleteConfigTranslationMap(String serviceTypename, String locale) {
    RegexHashMap translationMap = new RegexHashMap();
    Translator translator = JsonTranslator.buildSafeTranslator(() -> micaConfigService.getTranslations(locale, false));
    beanFieldToTranslationKeyMap.forEach((key, translationKey) -> translationMap.put(key, translator.translate(translationKey)));
    switch(serviceTypename) {
        case "individual-study":
            Optional<StudyConfig> optionalIndividualStudySchemaForm = individualStudyConfigService.findComplete();
            Optional<PopulationConfig> optionalPopulationSchemaForm = populationConfigService.findComplete();
            Optional<DataCollectionEventConfig> optionalDataCollectionEventSchemaForm = dataCollectionEventConfigService.findComplete();
            if (optionalIndividualStudySchemaForm.isPresent()) {
                StudyConfig individualStudySchemaForm = optionalIndividualStudySchemaForm.get();
                translateSchemaForm(translator, individualStudySchemaForm);
                translationMap.putAll(getTranslationMap(individualStudySchemaForm, ""));
            }
            if (optionalPopulationSchemaForm.isPresent()) {
                PopulationConfig populationSchemaForm = optionalPopulationSchemaForm.get();
                translateSchemaForm(translator, populationSchemaForm);
                translationMap.putAll(getTranslationMap(populationSchemaForm, "^populations\\[\\d+\\]\\."));
            }
            if (optionalDataCollectionEventSchemaForm.isPresent()) {
                DataCollectionEventConfig dataCollectionEventSchemaForm = optionalDataCollectionEventSchemaForm.get();
                translateSchemaForm(translator, dataCollectionEventSchemaForm);
                translationMap.putAll(getTranslationMap(dataCollectionEventSchemaForm, "^populations\\[\\d+\\]\\.dataCollectionEvents\\[\\d+\\]\\."));
            }
            break;
        case "harmonization-study":
            Optional<HarmonizationStudyConfig> optionalHarmonizationStudySchemaForm = harmonizationStudyConfigService.findComplete();
            Optional<HarmonizationPopulationConfig> optionalHarmonizationPopulationSchemaForm = harmonizationPopulationConfigService.findComplete();
            if (optionalHarmonizationStudySchemaForm.isPresent()) {
                HarmonizationStudyConfig harmonizationStudySchemaForm = optionalHarmonizationStudySchemaForm.get();
                translateSchemaForm(translator, harmonizationStudySchemaForm);
                translationMap.putAll(getTranslationMap(harmonizationStudySchemaForm, ""));
            }
            if (optionalHarmonizationPopulationSchemaForm.isPresent()) {
                HarmonizationPopulationConfig harmonizationPopulationSchemaForm = optionalHarmonizationPopulationSchemaForm.get();
                translateSchemaForm(translator, harmonizationPopulationSchemaForm);
                translationMap.putAll(getTranslationMap(harmonizationPopulationSchemaForm, "^populations\\[\\d+\\]\\."));
            }
            break;
        case "network":
            Optional<NetworkConfig> optionalNetworkSchemaForm = networkConfigService.findComplete();
            if (optionalNetworkSchemaForm.isPresent()) {
                NetworkConfig networkSchemaForm = optionalNetworkSchemaForm.get();
                translateSchemaForm(translator, networkSchemaForm);
                translationMap.putAll(getTranslationMap(networkSchemaForm, ""));
            }
            break;
        case "collected-dataset":
            Optional<StudyDatasetConfig> optionalStudyDatasetSchemaForm = studyDatasetConfigService.findComplete();
            if (optionalStudyDatasetSchemaForm.isPresent()) {
                StudyDatasetConfig studyDatasetSchemaForm = optionalStudyDatasetSchemaForm.get();
                translateSchemaForm(translator, studyDatasetSchemaForm);
                translationMap.putAll(getTranslationMap(studyDatasetSchemaForm, ""));
            }
            break;
        case "harmonized-dataset":
            Optional<HarmonizationDatasetConfig> optionalHarmonizationDatasetSchemaForm = harmonizationDatasetConfigService.findComplete();
            if (optionalHarmonizationDatasetSchemaForm.isPresent()) {
                HarmonizationDatasetConfig harmonizationDatasetSchemaForm = optionalHarmonizationDatasetSchemaForm.get();
                translateSchemaForm(translator, harmonizationDatasetSchemaForm);
                translationMap.putAll(getTranslationMap(harmonizationDatasetSchemaForm, ""));
            }
            break;
        case "project":
            Optional<ProjectConfig> optionalProjectSchemaForm = projectConfigService.findComplete();
            if (optionalProjectSchemaForm.isPresent()) {
                ProjectConfig projectSchemaForm = optionalProjectSchemaForm.get();
                translateSchemaForm(translator, projectSchemaForm);
                translationMap.putAll(getTranslationMap(projectSchemaForm, ""));
            }
            break;
        default:
            break;
    }
    return translationMap;
}

Example 2 with StudyConfig

use of org.obiba.mica.micaConfig.domain.StudyConfig in project mica2 by obiba.

the class Mica220Upgrade method updateBioSamplesAttributes.

private void updateBioSamplesAttributes() throws IOException {
    List<StudyConfig> studyConfigs = studyConfigRepository.findAll();
    if (studyConfigs.size() != 1)
        return;
    StudyConfig studyConfig = studyConfigs.get(0);
    JsonNode schemaNode = new ObjectMapper().readTree(studyConfig.getSchema());
    if (!propertyExistsInSchema(schemaNode))
        return;
    JsonNode definitionNode = new ObjectMapper().readTree(studyConfig.getDefinition());
    if (!replacePropertyInDefinition(definitionNode))
        return;
    replacePropertyInSchema(schemaNode);
    studyConfig.setSchema(new ObjectMapper().writer().writeValueAsString(schemaNode));
    studyConfig.setDefinition(new ObjectMapper().writer().writeValueAsString(definitionNode));
    studyConfigRepository.save(studyConfig);
    updateAttributeNameInStudies();
}