Examples with EntityType org.molgenis.data.meta.model.EntityType used on opensource projects

Example 86 with EntityType

use of org.molgenis.data.meta.model.EntityType in project molgenis by molgenis.

the class RestController method retrieveEntityAttributeInternal.

private Object retrieveEntityAttributeInternal(String entityTypeId, String untypedId, String refAttributeName, EntityCollectionRequest request, Set<String> attributesSet, Map<String, Set<String>> attributeExpandSet) {
    EntityType meta = dataService.getEntityType(entityTypeId);
    if (meta == null) {
        throw new UnknownEntityTypeException(entityTypeId);
    }
    Object id = getTypedValue(untypedId, meta.getIdAttribute());
    // Check if the entity has an attribute with name refAttributeName
    Attribute attr = meta.getAttribute(refAttributeName);
    if (attr == null) {
        throw new UnknownAttributeException(meta, refAttributeName);
    }
    // Get the entity
    Entity entity = dataService.findOneById(entityTypeId, id);
    if (entity == null) {
        throw new UnknownEntityException(entityTypeId + " " + id + " not found");
    }
    String attrHref = Href.concatAttributeHref(RestController.BASE_URI, meta.getId(), entity.getIdValue(), refAttributeName);
    switch(attr.getDataType()) {
        case COMPOUND:
            Map<String, Object> entityHasAttributeMap = new LinkedHashMap<>();
            entityHasAttributeMap.put("href", attrHref);
            @SuppressWarnings("unchecked") Iterable<Attribute> attributeParts = (Iterable<Attribute>) entity.get(refAttributeName);
            for (Attribute attribute : attributeParts) {
                String attrName = attribute.getName();
                entityHasAttributeMap.put(attrName, entity.get(attrName));
            }
            return entityHasAttributeMap;
        case CATEGORICAL_MREF:
        case MREF:
        case ONE_TO_MANY:
            List<Entity> mrefEntities = new ArrayList<>();
            for (Entity e : entity.getEntities((attr.getName()))) mrefEntities.add(e);
            int count = mrefEntities.size();
            int toIndex = request.getStart() + request.getNum();
            mrefEntities = mrefEntities.subList(request.getStart(), toIndex > count ? count : toIndex);
            List<Map<String, Object>> refEntityMaps = new ArrayList<>();
            for (Entity refEntity : mrefEntities) {
                Map<String, Object> refEntityMap = getEntityAsMap(refEntity, attr.getRefEntity(), attributesSet, attributeExpandSet);
                refEntityMaps.add(refEntityMap);
            }
            EntityPager pager = new EntityPager(request.getStart(), request.getNum(), (long) count, mrefEntities);
            return new EntityCollectionResponse(pager, refEntityMaps, attrHref, null, permissionService, dataService);
        case CATEGORICAL:
        case XREF:
            Map<String, Object> entityXrefAttributeMap = getEntityAsMap((Entity) entity.get(refAttributeName), attr.getRefEntity(), attributesSet, attributeExpandSet);
            entityXrefAttributeMap.put("href", attrHref);
            return entityXrefAttributeMap;
        default:
            Map<String, Object> entityAttributeMap = new LinkedHashMap<>();
            entityAttributeMap.put("href", attrHref);
            entityAttributeMap.put(refAttributeName, entity.get(refAttributeName));
            return entityAttributeMap;
    }
}

Example 87 with EntityType

use of org.molgenis.data.meta.model.EntityType in project molgenis by molgenis.

the class RestController method updateInternal.

private void updateInternal(String entityTypeId, String untypedId, Map<String, Object> entityMap) {
    EntityType meta = dataService.getEntityType(entityTypeId);
    if (meta.getIdAttribute() == null) {
        throw new IllegalArgumentException(entityTypeId + " does not have an id attribute");
    }
    Object id = getTypedValue(untypedId, meta.getIdAttribute());
    Entity existing = dataService.findOneById(entityTypeId, id, new Fetch().field(meta.getIdAttribute().getName()));
    if (existing == null) {
        throw new UnknownEntityException("Entity of type " + entityTypeId + " with id " + id + " not found");
    }
    Entity entity = this.restService.toEntity(meta, entityMap);
    dataService.update(entityTypeId, entity);
    restService.updateMappedByEntities(entity, existing);
}

Example 88 with EntityType

use of org.molgenis.data.meta.model.EntityType in project molgenis by molgenis.

the class RestController method retrieveEntity.

/**
 * Same as retrieveEntity (GET) only tunneled through POST.
 */
@PostMapping(value = "/{entityTypeId}/{id:.+}", params = "_method=GET", produces = APPLICATION_JSON_VALUE)
@ResponseBody
public Map<String, Object> retrieveEntity(@PathVariable("entityTypeId") String entityTypeId, @PathVariable("id") String untypedId, @Valid @RequestBody EntityTypeRequest request) {
    Set<String> attributesSet = toAttributeSet(request != null ? request.getAttributes() : null);
    Map<String, Set<String>> attributeExpandSet = toExpandMap(request != null ? request.getExpand() : null);
    EntityType meta = dataService.getEntityType(entityTypeId);
    Object id = getTypedValue(untypedId, meta.getIdAttribute());
    Entity entity = dataService.findOneById(entityTypeId, id);
    if (entity == null) {
        throw new UnknownEntityException(entityTypeId + " " + untypedId + " not found");
    }
    return getEntityAsMap(entity, meta, attributesSet, attributeExpandSet);
}

Example 89 with EntityType

use of org.molgenis.data.meta.model.EntityType in project molgenis by molgenis.

the class RestController method retrieveEntityCollectionInternal.

// Handles a Query
@SuppressWarnings("deprecation")
private EntityCollectionResponse retrieveEntityCollectionInternal(String entityTypeId, EntityCollectionRequest request, Set<String> attributesSet, Map<String, Set<String>> attributeExpandsSet) {
    EntityType meta = dataService.getEntityType(entityTypeId);
    if (meta == null) {
        throw new UnknownEntityTypeException(entityTypeId);
    }
    Repository<Entity> repository = dataService.getRepository(entityTypeId);
    // convert sort
    Sort sort;
    SortV1 sortV1 = request.getSort();
    if (sortV1 != null) {
        sort = new Sort();
        for (SortV1.OrderV1 orderV1 : sortV1) {
            sort.on(orderV1.getProperty(), orderV1.getDirection() == SortV1.DirectionV1.ASC ? Sort.Direction.ASC : Sort.Direction.DESC);
        }
    } else {
        sort = null;
    }
    List<QueryRule> queryRules = request.getQ() == null ? Collections.emptyList() : request.getQ();
    Query<Entity> q = new QueryImpl<>(queryRules).pageSize(request.getNum()).offset(request.getStart()).sort(sort);
    Iterable<Entity> it = () -> dataService.findAll(entityTypeId, q).iterator();
    Long count = repository.count(new QueryImpl<>(q).setOffset(0).setPageSize(0));
    EntityPager pager = new EntityPager(request.getStart(), request.getNum(), count, it);
    List<Map<String, Object>> entities = new ArrayList<>();
    for (Entity entity : it) {
        entities.add(getEntityAsMap(entity, meta, attributesSet, attributeExpandsSet));
    }
    return new EntityCollectionResponse(pager, entities, BASE_URI + "/" + entityTypeId, meta, permissionService, dataService);
}

Example 90 with EntityType

use of org.molgenis.data.meta.model.EntityType in project molgenis by molgenis.

the class RestController method retrieveEntity.

/**
 * Get's an entity by it's id
 * <p>
 * Examples:
 * <p>
 * /api/v1/person/99 Retrieves a person with id 99
 */
@GetMapping(value = "/{entityTypeId}/{id:.+}", produces = APPLICATION_JSON_VALUE)
public Map<String, Object> retrieveEntity(@PathVariable("entityTypeId") String entityTypeId, @PathVariable("id") String untypedId, @RequestParam(value = "attributes", required = false) String[] attributes, @RequestParam(value = "expand", required = false) String[] attributeExpands) {
    Set<String> attributesSet = toAttributeSet(attributes);
    Map<String, Set<String>> attributeExpandSet = toExpandMap(attributeExpands);
    EntityType meta = dataService.getEntityType(entityTypeId);
    if (meta == null) {
        throw new UnknownEntityTypeException(entityTypeId);
    }
    Object id = getTypedValue(untypedId, meta.getIdAttribute());
    Entity entity = dataService.findOneById(entityTypeId, id);
    if (entity == null) {
        throw new UnknownEntityException(entityTypeId + " " + untypedId + " not found");
    }
    return getEntityAsMap(entity, meta, attributesSet, attributeExpandSet);
}