Examples with NoSuchEntityException org.obiba.mica.NoSuchEntityException used on opensource projects

Example 1 with NoSuchEntityException

use of org.obiba.mica.NoSuchEntityException in project mica2 by obiba.

the class NetworkDtos method asDtoBuilderInternal.

private Mica.NetworkDto.Builder asDtoBuilderInternal(@NotNull Network network, boolean asDraft, boolean forListing) {
    Mica.NetworkDto.Builder builder = Mica.NetworkDto.newBuilder();
    if (network.hasModel())
        builder.setContent(JSONUtils.toJSON(network.getModel()));
    // 
    builder.setId(network.getId()).addAllName(// 
    localizedStringDtos.asDto(network.getName())).addAllDescription(// 
    localizedStringDtos.asDto(network.getDescription())).addAllAcronym(localizedStringDtos.asDto(network.getAcronym()));
    NetworkState networkState = networkService.getEntityState(network.getId());
    builder.setPublished(networkState.isPublished());
    if (asDraft) {
        Mica.PermissionsDto permissionsDto = permissionsDtos.asDto(network);
        // 
        builder.setTimestamps(TimestampsDtos.asDto(network)).setPublished(// 
        networkState.isPublished()).setExtension(Mica.EntityStateDto.state, entityStateDtos.asDto(networkState).setPermissions(permissionsDto).build());
        builder.setPermissions(permissionsDto);
    }
    if (network.getLogo() != null) {
        builder.setLogo(attachmentDtos.asDto(network.getLogo()));
    }
    List<BaseStudy> publishedStudies = publishedStudyService.findByIds(network.getStudyIds());
    Set<String> publishedStudyIds = publishedStudies.stream().map(AbstractGitPersistable::getId).collect(Collectors.toSet());
    Sets.SetView<String> unpublishedStudyIds = Sets.difference(ImmutableSet.copyOf(network.getStudyIds().stream().filter(sId -> asDraft && subjectAclService.isPermitted("/draft/individual-study", "VIEW", sId) || subjectAclService.isAccessible("/individual-study", sId)).collect(toList())), publishedStudyIds);
    if (!publishedStudies.isEmpty()) {
        Map<String, Long> datasetVariableCounts = asDraft ? null : datasetVariableService.getCountByStudyIds(Lists.newArrayList(publishedStudyIds));
        publishedStudies.forEach(study -> {
            builder.addStudyIds(study.getId());
            if (!forListing) {
                builder.addStudySummaries(studySummaryDtos.asDtoBuilder(study, true, datasetVariableCounts == null ? 0 : datasetVariableCounts.get(study.getId())));
            }
        });
    }
    unpublishedStudyIds.forEach(studyId -> {
        try {
            if (!forListing)
                builder.addStudySummaries(studySummaryDtos.asDto(studyId));
            builder.addStudyIds(studyId);
        } catch (NoSuchEntityException e) {
            log.warn("Study not found in network {}: {}", network.getId(), studyId);
        // ignore
        }
    });
    network.getNetworkIds().stream().filter(nId -> asDraft && subjectAclService.isPermitted("/draft/network", "VIEW", nId) || subjectAclService.isAccessible("/network", nId)).forEach(nId -> {
        try {
            if (!forListing)
                builder.addNetworkSummaries(networkSummaryDtos.asDtoBuilder(nId, asDraft));
            builder.addNetworkIds(nId);
        } catch (NoSuchEntityException e) {
            log.warn("Network not found in network {}: {}", network.getId(), nId);
        // ignore
        }
    });
    return builder;
}

Example 2 with NoSuchEntityException

use of org.obiba.mica.NoSuchEntityException in project mica2 by obiba.

the class NetworkDtos method asDtoBuilder.

@NotNull
Mica.NetworkDto.Builder asDtoBuilder(@NotNull Network network, boolean asDraft) {
    Mica.NetworkDto.Builder builder = Mica.NetworkDto.newBuilder();
    if (network.hasModel())
        builder.setContent(JSONUtils.toJSON(network.getModel()));
    // 
    builder.setId(network.getId()).addAllName(// 
    localizedStringDtos.asDto(network.getName())).addAllDescription(// 
    localizedStringDtos.asDto(network.getDescription())).addAllAcronym(localizedStringDtos.asDto(network.getAcronym()));
    Mica.PermissionsDto permissionsDto = permissionsDtos.asDto(network);
    NetworkState networkState = networkService.getEntityState(network.getId());
    builder.setPublished(networkState.isPublished());
    if (asDraft) {
        // 
        builder.setTimestamps(TimestampsDtos.asDto(network)).setPublished(// 
        networkState.isPublished()).setExtension(Mica.EntityStateDto.state, entityStateDtos.asDto(networkState).setPermissions(permissionsDto).build());
    }
    builder.setPermissions(permissionsDto);
    List<String> roles = micaConfigService.getConfig().getRoles();
    if (network.getMemberships() != null) {
        List<Mica.MembershipsDto> memberships = network.getMemberships().entrySet().stream().filter(e -> roles.contains(e.getKey())).map(e -> Mica.MembershipsDto.newBuilder().setRole(e.getKey()).addAllMembers(e.getValue().stream().map(m -> personDtos.asDto(m.getPerson(), asDraft)).collect(toList())).build()).collect(toList());
        builder.addAllMemberships(memberships);
    }
    List<BaseStudy> publishedStudies = publishedStudyService.findByIds(network.getStudyIds());
    Set<String> publishedStudyIds = publishedStudies.stream().map(AbstractGitPersistable::getId).collect(Collectors.toSet());
    Sets.SetView<String> unpublishedStudyIds = Sets.difference(ImmutableSet.copyOf(network.getStudyIds().stream().filter(sId -> asDraft && subjectAclService.isPermitted("/draft/individual-study", "VIEW", sId) || subjectAclService.isAccessible("/individual-study", sId)).collect(toList())), publishedStudyIds);
    if (!publishedStudies.isEmpty()) {
        Map<String, Long> datasetVariableCounts = asDraft ? null : datasetVariableService.getCountByStudyIds(Lists.newArrayList(publishedStudyIds));
        publishedStudies.forEach(study -> {
            builder.addStudyIds(study.getId());
            builder.addStudySummaries(studySummaryDtos.asDtoBuilder(study, true, datasetVariableCounts == null ? 0 : datasetVariableCounts.get(study.getId())));
        });
    }
    unpublishedStudyIds.forEach(studyId -> {
        try {
            builder.addStudySummaries(studySummaryDtos.asDto(studyId));
            builder.addStudyIds(studyId);
        } catch (NoSuchEntityException e) {
            log.warn("Study not found in network {}: {}", network.getId(), studyId);
        // ignore
        }
    });
    if (network.getLogo() != null) {
        builder.setLogo(attachmentDtos.asDto(network.getLogo()));
    }
    network.getNetworkIds().stream().filter(nId -> asDraft && subjectAclService.isPermitted("/draft/network", "VIEW", nId) || subjectAclService.isAccessible("/network", nId)).forEach(nId -> {
        try {
            builder.addNetworkSummaries(networkSummaryDtos.asDtoBuilder(nId, asDraft));
            builder.addNetworkIds(nId);
        } catch (NoSuchEntityException e) {
            log.warn("Network not found in network {}: {}", network.getId(), nId);
        // ignore
        }
    });
    return builder;
}

Example 3 with NoSuchEntityException

use of org.obiba.mica.NoSuchEntityException in project mica2 by obiba.

the class DraftFileSystemResource method downloadFile.

@GET
@Path("/file-dl/{path:.*}")
public Response downloadFile(@PathParam("path") String path, @QueryParam("version") String version, @QueryParam("inline") @DefaultValue("false") boolean inline, @QueryParam("key") String shareKey) {
    try {
        Attachment attachment = doGetAttachment(path, version, shareKey);
        String filename = attachment.getName();
        String uriEncodedFilename = UriUtils.encode(filename, "UTF-8");
        if (inline) {
            return Response.ok(fileStoreService.getFile(attachment.getFileReference())).header("Content-Disposition", "inline; filename=\"" + uriEncodedFilename + "\"").type(FileMediaType.type(Files.getFileExtension(filename))).build();
        }
        return Response.ok(fileStoreService.getFile(attachment.getFileReference())).header("Content-Disposition", "attachment; filename=" + uriEncodedFilename).build();
    } catch (NoSuchEntityException | UnsupportedEncodingException e) {
        String name = doZip(path);
        return Response.ok(tempFileService.getInputStreamFromFile(name)).header("Content-Disposition", "attachment; filename=\"" + name + "\"").build();
    }
}

Example 4 with NoSuchEntityException

use of org.obiba.mica.NoSuchEntityException in project mica2 by obiba.

the class PublishedFileSystemResource method downloadFile.

@GET
@Path("/file-dl/{path:.*}")
@Timed
public Response downloadFile(@PathParam("path") String path, @QueryParam("inline") @DefaultValue("false") boolean inline) {
    try {
        Attachment attachment = doGetAttachment(path);
        String filename = attachment.getName();
        String uriEncodedFilename = UriUtils.encode(filename, "UTF-8");
        if (inline) {
            return Response.ok(fileStoreService.getFile(attachment.getFileReference())).header("Content-Disposition", "inline; filename=\"" + uriEncodedFilename + "\"").type(FileMediaType.type(Files.getFileExtension(filename))).build();
        }
        return Response.ok(fileStoreService.getFile(attachment.getFileReference())).header("Content-Disposition", "attachment; filename*=" + uriEncodedFilename).build();
    } catch (NoSuchEntityException | UnsupportedEncodingException e) {
        String name = doZip(path);
        return Response.ok(tempFileService.getInputStreamFromFile(name)).header("Content-Disposition", "attachment; filename=\"" + name + "\"").build();
    }
}

Example 5 with NoSuchEntityException

use of org.obiba.mica.NoSuchEntityException in project mica2 by obiba.

the class NetworkSummaryDtos method asDto.

@NotNull
public Mica.NetworkSummaryDto asDto(@NotNull Network network, boolean asDraft) {
    Mica.NetworkSummaryDto.Builder builder = Mica.NetworkSummaryDto.newBuilder();
    NetworkState networkState = networkService.getEntityState(network.getId());
    builder.setId(network.getId()).addAllAcronym(localizedStringDtos.asDto(network.getAcronym())).addAllName(localizedStringDtos.asDto(network.getName())).setPublished(networkState.isPublished());
    Mica.PermissionsDto permissionsDto = permissionsDtos.asDto(network);
    if (asDraft) {
        // 
        builder.setTimestamps(TimestampsDtos.asDto(network)).setPublished(// 
        networkState.isPublished()).setExtension(Mica.EntityStateDto.networkSummaryState, entityStateDtos.asDto(networkState).setPermissions(permissionsDto).build());
    }
    builder.setPermissions(permissionsDto);
    network.getStudyIds().stream().filter(sId -> asDraft && subjectAclService.isPermitted("/draft/individual-study", "VIEW", sId) || subjectAclService.isAccessible("/individual-study", sId)).forEach(sId -> {
        try {
            builder.addStudyIds(sId);
        } catch (NoSuchEntityException e) {
            log.warn("Study not found in network {}: {}", network.getId(), sId);
        // ignore
        }
    });
    network.getNetworkIds().stream().filter(nId -> asDraft && subjectAclService.isPermitted("/draft/network", "VIEW", nId) || subjectAclService.isAccessible("/network", nId)).forEach(nId -> {
        try {
            builder.addNetworkIds(nId);
        } catch (NoSuchEntityException e) {
            log.warn("Network not found in network {}: {}", network.getId(), nId);
        // ignore
        }
    });
    return builder.build();
}