Examples with Network org.obiba.mica.network.domain.Network used on opensource projects

Example 16 with Network

use of org.obiba.mica.network.domain.Network in project mica2 by obiba.

the class Mica2Upgrade method migrateNetworks.

private void migrateNetworks() {
    List<Network> networksWithoutModel = networkRepository.findWithoutModel();
    if (!networksWithoutModel.isEmpty()) {
        logger.info("Migrating networks from 1.x to 2.x: START");
        for (Network networkWithoutModel : networksWithoutModel) {
            networkWithoutModel.getModel();
            networkRepository.save(networkWithoutModel);
        }
        logger.info("Migrating networks: END");
    }
}

Example 17 with Network

use of org.obiba.mica.network.domain.Network in project mica2 by obiba.

the class NetworkService method delete.

/**
 * Delete a {@link Network}.
 *
 * @param id
 * @throws NoSuchNetworkException
 */
public void delete(@NotNull String id) throws NoSuchNetworkException {
    Network network = findById(id);
    checkConstraints(network);
    networkRepository.deleteWithReferences(network);
    if (network.getLogo() != null)
        fileStoreService.delete(network.getLogo().getId());
    fileSystemService.delete(FileUtils.getEntityPath(network));
    networkStateRepository.delete(id);
    gitService.deleteGitRepository(network);
    eventBus.post(new NetworkDeletedEvent(network));
}

Example 18 with Network

use of org.obiba.mica.network.domain.Network in project mica2 by obiba.

the class StudyPackageImportServiceImpl method importZip.

@Override
public void importZip(InputStream inputStream, boolean publish) throws IOException {
    final StudyPackage studyPackage = new StudyPackage(inputStream);
    if (studyPackage.study != null) {
        Map<String, ByteSource> dict = studyPackage.attachments.entrySet().stream().collect(Collectors.toMap(Map.Entry::getKey, Map.Entry::getValue));
        Optional.ofNullable(studyPackage.study.getLogo()).ifPresent(a -> saveAttachmentTempFile(dict, a));
        Set<String> attachmentIds = Sets.newHashSet();
        studyPackage.studyAttachments.forEach(a -> {
            if (attachmentIds.contains(a.getId())) {
                String origId = a.getId();
                a.setId(new ObjectId().toString());
                saveAttachmentTempFile(dict, a, origId);
            } else {
                saveAttachmentTempFile(dict, a);
                attachmentIds.add(a.getId());
            }
        });
        importStudy(studyPackage.study, studyPackage.studyAttachments, publish);
        for (Network net : studyPackage.networks) {
            importNetwork(net, publish, studyPackage);
        }
        studyPackage.datasets.forEach(ds -> importDataset(ds, publish));
    }
}

Example 19 with Network

use of org.obiba.mica.network.domain.Network in project mica2 by obiba.

the class VariableQuery method processHits.

@Override
protected void processHits(MicaSearch.QueryResultDto.Builder builder, Searcher.DocumentResults results, QueryScope scope, CountStatsData counts) throws IOException {
    MicaSearch.DatasetVariableResultDto.Builder resBuilder = MicaSearch.DatasetVariableResultDto.newBuilder();
    Map<String, BaseStudy> studyMap = Maps.newHashMap();
    Map<String, Network> networkMap = Maps.newHashMap();
    for (Searcher.DocumentResult result : results.getDocuments()) {
        if (result.hasSource()) {
            DatasetVariable.IdResolver resolver = DatasetVariable.IdResolver.from(result.getId());
            DatasetVariable variable = objectMapper.readValue(result.getSourceInputStream(), DatasetVariable.class);
            resBuilder.addSummaries(processHit(resolver, variable, studyMap, networkMap));
        }
    }
    builder.setExtension(MicaSearch.DatasetVariableResultDto.result, resBuilder.build());
}