Ejemplo n.º 1
0
 private void writeOptionalTagWithTextNode(
     XMLStreamWriter theEventWriter, String theTagName, InstantDt theInstantDt)
     throws XMLStreamException {
   if (theInstantDt.getValue() != null) {
     theEventWriter.writeStartElement(theTagName);
     theEventWriter.writeCharacters(theInstantDt.getValueAsString());
     theEventWriter.writeEndElement();
   }
 }
Ejemplo n.º 2
0
  private void encodeResourceToXmlStreamWriter(
      IBaseResource theResource,
      XMLStreamWriter theEventWriter,
      boolean theContainedResource,
      String theResourceId)
      throws XMLStreamException {
    if (!theContainedResource) {
      super.containResourcesForEncoding(theResource);
    }

    RuntimeResourceDefinition resDef = myContext.getResourceDefinition(theResource);
    if (resDef == null) {
      throw new ConfigurationException("Unknown resource type: " + theResource.getClass());
    }

    theEventWriter.writeStartElement(resDef.getName());
    theEventWriter.writeDefaultNamespace(FHIR_NS);

    if (theResource instanceof IAnyResource) {

      // HL7.org Structures
      encodeCompositeElementToStreamWriter(
          theResource, theResource, theEventWriter, resDef, theContainedResource);

    } else {

      if (myContext.getVersion().getVersion().isNewerThan(FhirVersionEnum.DSTU1)) {

        // DSTU2+

        IResource resource = (IResource) theResource;
        writeOptionalTagWithValue(theEventWriter, "id", theResourceId);

        InstantDt updated =
            (InstantDt) resource.getResourceMetadata().get(ResourceMetadataKeyEnum.UPDATED);
        IdDt resourceId = resource.getId();
        String versionIdPart = resourceId.getVersionIdPart();
        if (isBlank(versionIdPart)) {
          versionIdPart = ResourceMetadataKeyEnum.VERSION.get(resource);
        }
        List<BaseCodingDt> securityLabels =
            extractMetadataListNotNull(resource, ResourceMetadataKeyEnum.SECURITY_LABELS);
        List<IdDt> profiles =
            extractMetadataListNotNull(resource, ResourceMetadataKeyEnum.PROFILES);
        TagList tags = ResourceMetadataKeyEnum.TAG_LIST.get(resource);
        if (ElementUtil.isEmpty(versionIdPart, updated, securityLabels, profiles) == false) {
          theEventWriter.writeStartElement("meta");
          writeOptionalTagWithValue(theEventWriter, "versionId", versionIdPart);
          if (updated != null) {
            writeOptionalTagWithValue(theEventWriter, "lastUpdated", updated.getValueAsString());
          }

          for (IdDt profile : profiles) {
            theEventWriter.writeStartElement("profile");
            theEventWriter.writeAttribute("value", profile.getValue());
            theEventWriter.writeEndElement();
          }
          for (BaseCodingDt securityLabel : securityLabels) {
            theEventWriter.writeStartElement("security");
            BaseRuntimeElementCompositeDefinition<?> def =
                (BaseRuntimeElementCompositeDefinition<?>)
                    myContext.getElementDefinition(securityLabel.getClass());
            encodeCompositeElementChildrenToStreamWriter(
                resource, securityLabel, theEventWriter, def.getChildren(), theContainedResource);
            theEventWriter.writeEndElement();
          }
          if (tags != null) {
            for (Tag tag : tags) {
              theEventWriter.writeStartElement("tag");
              writeOptionalTagWithValue(theEventWriter, "system", tag.getScheme());
              writeOptionalTagWithValue(theEventWriter, "code", tag.getTerm());
              writeOptionalTagWithValue(theEventWriter, "display", tag.getLabel());
              theEventWriter.writeEndElement();
            }
          }
          theEventWriter.writeEndElement();
        }

        if (theResource instanceof IBaseBinary) {
          IBaseBinary bin = (IBaseBinary) theResource;
          writeOptionalTagWithValue(theEventWriter, "contentType", bin.getContentType());
          writeOptionalTagWithValue(theEventWriter, "content", bin.getContentAsBase64());
        } else {
          encodeResourceToStreamWriterInDstu2Format(
              resDef, theResource, theResource, theEventWriter, resDef, theContainedResource);
        }

      } else {

        // DSTU1
        if (theResourceId != null && theContainedResource) {
          theEventWriter.writeAttribute("id", theResourceId);
        }

        if (theResource instanceof IBaseBinary) {
          IBaseBinary bin = (IBaseBinary) theResource;
          if (bin.getContentType() != null) {
            theEventWriter.writeAttribute("contentType", bin.getContentType());
          }
          theEventWriter.writeCharacters(bin.getContentAsBase64());
        } else {
          encodeCompositeElementToStreamWriter(
              theResource, theResource, theEventWriter, resDef, theContainedResource);
        }
      }
    }

    theEventWriter.writeEndElement();
  }
Ejemplo n.º 3
0
  private void encodeBundleToWriterDstu2(Bundle theBundle, XMLStreamWriter theEventWriter)
      throws XMLStreamException {
    theEventWriter.writeStartElement("Bundle");
    theEventWriter.writeDefaultNamespace(FHIR_NS);

    writeOptionalTagWithValue(theEventWriter, "id", theBundle.getId().getIdPart());

    InstantDt updated =
        (InstantDt) theBundle.getResourceMetadata().get(ResourceMetadataKeyEnum.UPDATED);
    IdDt bundleId = theBundle.getId();
    if (bundleId != null && isNotBlank(bundleId.getVersionIdPart())
        || (updated != null && !updated.isEmpty())) {
      theEventWriter.writeStartElement("meta");
      writeOptionalTagWithValue(theEventWriter, "versionId", bundleId.getVersionIdPart());
      if (updated != null) {
        writeOptionalTagWithValue(theEventWriter, "lastUpdated", updated.getValueAsString());
      }
      theEventWriter.writeEndElement();
    }

    String bundleBaseUrl = theBundle.getLinkBase().getValue();

    writeOptionalTagWithValue(theEventWriter, "type", theBundle.getType().getValue());
    writeOptionalTagWithValue(theEventWriter, "base", bundleBaseUrl);
    writeOptionalTagWithValue(
        theEventWriter, "total", theBundle.getTotalResults().getValueAsString());

    writeBundleResourceLink(theEventWriter, "first", theBundle.getLinkFirst());
    writeBundleResourceLink(theEventWriter, "previous", theBundle.getLinkPrevious());
    writeBundleResourceLink(theEventWriter, "next", theBundle.getLinkNext());
    writeBundleResourceLink(theEventWriter, "last", theBundle.getLinkLast());
    writeBundleResourceLink(theEventWriter, "self", theBundle.getLinkSelf());

    for (BundleEntry nextEntry : theBundle.getEntries()) {
      theEventWriter.writeStartElement("entry");

      boolean deleted = false;
      if (nextEntry.getDeletedAt() != null && nextEntry.getDeletedAt().isEmpty() == false) {
        deleted = true;
      }

      writeOptionalTagWithValue(
          theEventWriter, "base", determineResourceBaseUrl(bundleBaseUrl, nextEntry));

      IResource resource = nextEntry.getResource();
      if (resource != null && !resource.isEmpty() && !deleted) {
        theEventWriter.writeStartElement("resource");
        encodeResourceToXmlStreamWriter(resource, theEventWriter, false);
        theEventWriter.writeEndElement(); // content
      } else {
        ourLog.debug("Bundle entry contains null resource");
      }

      if (nextEntry.getSearchMode().isEmpty() == false || nextEntry.getScore().isEmpty() == false) {
        theEventWriter.writeStartElement("search");
        writeOptionalTagWithValue(
            theEventWriter, "mode", nextEntry.getSearchMode().getValueAsString());
        writeOptionalTagWithValue(theEventWriter, "score", nextEntry.getScore().getValueAsString());
        theEventWriter.writeEndElement();
        // IResource nextResource = nextEntry.getResource();
      }

      if (nextEntry.getTransactionMethod().isEmpty() == false
          || nextEntry.getLinkSearch().isEmpty() == false) {
        theEventWriter.writeStartElement("transaction");
        writeOptionalTagWithValue(
            theEventWriter, "method", nextEntry.getTransactionMethod().getValue());
        writeOptionalTagWithValue(theEventWriter, "url", nextEntry.getLinkSearch().getValue());
        theEventWriter.writeEndElement();
      }

      if (deleted) {
        theEventWriter.writeStartElement("deleted");
        writeOptionalTagWithValue(theEventWriter, "type", nextEntry.getId().getResourceType());
        writeOptionalTagWithValue(theEventWriter, "id", nextEntry.getId().getIdPart());
        writeOptionalTagWithValue(
            theEventWriter, "versionId", nextEntry.getId().getVersionIdPart());
        writeOptionalTagWithValue(
            theEventWriter, "instant", nextEntry.getDeletedAt().getValueAsString());
        theEventWriter.writeEndElement();
      }

      theEventWriter.writeEndElement(); // entry
    }

    theEventWriter.writeEndElement();
    theEventWriter.close();
  }
Ejemplo n.º 4
0
  @Transactional(propagation = Propagation.REQUIRED)
  @Override
  public List<IResource> transaction(
      RequestDetails theRequestDetails, List<IResource> theResources) {
    ourLog.info("Beginning transaction with {} resources", theResources.size());

    // Notify interceptors
    ActionRequestDetails requestDetails = new ActionRequestDetails(null, null);
    notifyInterceptors(RestOperationTypeEnum.TRANSACTION, requestDetails);

    long start = System.currentTimeMillis();

    Set<IdDt> allIds = new HashSet<IdDt>();

    for (int i = 0; i < theResources.size(); i++) {
      IResource res = theResources.get(i);
      if (res.getId().hasIdPart()
          && !res.getId().hasResourceType()
          && !isPlaceholder(res.getId())) {
        res.setId(new IdDt(toResourceName(res.getClass()), res.getId().getIdPart()));
      }

      /*
       * Ensure that the bundle doesn't have any duplicates, since this causes all kinds of weirdness
       */
      if (isPlaceholder(res.getId())) {
        if (!allIds.add(res.getId())) {
          throw new InvalidRequestException(
              "Transaction bundle contains multiple resources with ID: " + res.getId());
        }
      } else if (res.getId().hasResourceType() && res.getId().hasIdPart()) {
        IdDt nextId = res.getId().toUnqualifiedVersionless();
        if (!allIds.add(nextId)) {
          throw new InvalidRequestException(
              "Transaction bundle contains multiple resources with ID: " + nextId);
        }
      }
    }

    FhirTerser terser = getContext().newTerser();

    int creations = 0;
    int updates = 0;

    Map<IdDt, IdDt> idConversions = new HashMap<IdDt, IdDt>();

    List<ResourceTable> persistedResources = new ArrayList<ResourceTable>();

    List<IResource> retVal = new ArrayList<IResource>();
    OperationOutcome oo = new OperationOutcome();
    retVal.add(oo);

    Date updateTime = new Date();
    for (int resourceIdx = 0; resourceIdx < theResources.size(); resourceIdx++) {
      IResource nextResource = theResources.get(resourceIdx);

      IdDt nextId = nextResource.getId();
      if (nextId == null) {
        nextId = new IdDt();
      }

      String resourceName = toResourceName(nextResource);
      BundleEntryTransactionMethodEnum nextResouceOperationIn =
          ResourceMetadataKeyEnum.ENTRY_TRANSACTION_METHOD.get(nextResource);
      if (nextResouceOperationIn == null
          && hasValue(ResourceMetadataKeyEnum.DELETED_AT.get(nextResource))) {
        nextResouceOperationIn = BundleEntryTransactionMethodEnum.DELETE;
      }

      String matchUrl = ResourceMetadataKeyEnum.LINK_SEARCH.get(nextResource);
      Set<Long> candidateMatches = null;
      if (StringUtils.isNotBlank(matchUrl)) {
        candidateMatches = processMatchUrl(matchUrl, nextResource.getClass());
      }

      ResourceTable entity;
      if (nextResouceOperationIn == BundleEntryTransactionMethodEnum.POST) {
        entity = null;
      } else if (nextResouceOperationIn == BundleEntryTransactionMethodEnum.PUT
          || nextResouceOperationIn == BundleEntryTransactionMethodEnum.DELETE) {
        if (candidateMatches == null || candidateMatches.size() == 0) {
          if (nextId == null || StringUtils.isBlank(nextId.getIdPart())) {
            throw new InvalidRequestException(
                getContext()
                    .getLocalizer()
                    .getMessage(
                        BaseHapiFhirSystemDao.class,
                        "transactionOperationFailedNoId",
                        nextResouceOperationIn.name()));
          }
          entity = tryToLoadEntity(nextId);
          if (entity == null) {
            if (nextResouceOperationIn == BundleEntryTransactionMethodEnum.PUT) {
              ourLog.debug(
                  "Attempting to UPDATE resource with unknown ID '{}', will CREATE instead",
                  nextId);
            } else if (candidateMatches == null) {
              throw new InvalidRequestException(
                  getContext()
                      .getLocalizer()
                      .getMessage(
                          BaseHapiFhirSystemDao.class,
                          "transactionOperationFailedUnknownId",
                          nextResouceOperationIn.name(),
                          nextId));
            } else {
              ourLog.debug("Resource with match URL [{}] already exists, will be NOOP", matchUrl);
              persistedResources.add(null);
              retVal.add(nextResource);
              continue;
            }
          }
        } else if (candidateMatches.size() == 1) {
          entity = loadFirstEntityFromCandidateMatches(candidateMatches);
        } else {
          throw new InvalidRequestException(
              getContext()
                  .getLocalizer()
                  .getMessage(
                      BaseHapiFhirSystemDao.class,
                      "transactionOperationWithMultipleMatchFailure",
                      nextResouceOperationIn.name(),
                      matchUrl,
                      candidateMatches.size()));
        }
      } else if (nextId.isEmpty() || isPlaceholder(nextId)) {
        entity = null;
      } else {
        entity = tryToLoadEntity(nextId);
      }

      BundleEntryTransactionMethodEnum nextResouceOperationOut;
      if (entity == null) {
        nextResouceOperationOut = BundleEntryTransactionMethodEnum.POST;
        entity = toEntity(nextResource);
        entity.setUpdated(updateTime);
        entity.setPublished(updateTime);
        if (nextId.isEmpty() == false && "cid:".equals(nextId.getBaseUrl())) {
          ourLog.debug(
              "Resource in transaction has ID[{}], will replace with server assigned ID",
              nextId.getIdPart());
        } else if (nextResouceOperationIn == BundleEntryTransactionMethodEnum.POST) {
          if (nextId.isEmpty() == false) {
            ourLog.debug(
                "Resource in transaction has ID[{}] but is marked for CREATE, will ignore ID",
                nextId.getIdPart());
          }
          if (candidateMatches != null) {
            if (candidateMatches.size() == 1) {
              ourLog.debug("Resource with match URL [{}] already exists, will be NOOP", matchUrl);
              BaseHasResource existingEntity =
                  loadFirstEntityFromCandidateMatches(candidateMatches);
              IResource existing = (IResource) toResource(existingEntity, false);
              persistedResources.add(null);
              retVal.add(existing);
              continue;
            }
            if (candidateMatches.size() > 1) {
              throw new InvalidRequestException(
                  getContext()
                      .getLocalizer()
                      .getMessage(
                          BaseHapiFhirSystemDao.class,
                          "transactionOperationWithMultipleMatchFailure",
                          BundleEntryTransactionMethodEnum.POST.name(),
                          matchUrl,
                          candidateMatches.size()));
            }
          }
        } else {
          createForcedIdIfNeeded(entity, nextId);
        }
        myEntityManager.persist(entity);
        if (entity.getForcedId() != null) {
          myEntityManager.persist(entity.getForcedId());
        }
        creations++;
        ourLog.info(
            "Resource Type[{}] with ID[{}] does not exist, creating it", resourceName, nextId);
      } else {
        nextResouceOperationOut = nextResouceOperationIn;
        if (nextResouceOperationOut == null) {
          nextResouceOperationOut = BundleEntryTransactionMethodEnum.PUT;
        }
        updates++;
        ourLog.info("Resource Type[{}] with ID[{}] exists, updating it", resourceName, nextId);
      }

      persistedResources.add(entity);
      retVal.add(nextResource);
      ResourceMetadataKeyEnum.ENTRY_TRANSACTION_METHOD.put(nextResource, nextResouceOperationOut);
    }

    ourLog.info("Flushing transaction to database");
    myEntityManager.flush();

    for (int i = 0; i < persistedResources.size(); i++) {
      ResourceTable entity = persistedResources.get(i);

      String resourceName = toResourceName(theResources.get(i));
      IdDt nextId = theResources.get(i).getId();

      IdDt newId;

      if (entity == null) {
        newId = retVal.get(i + 1).getId().toUnqualifiedVersionless();
      } else {
        newId = entity.getIdDt().toUnqualifiedVersionless();
      }

      if (nextId == null || nextId.isEmpty()) {
        ourLog.info(
            "Transaction resource (with no preexisting ID) has been assigned new ID[{}]",
            nextId,
            newId);
      } else {
        if (nextId.toUnqualifiedVersionless().equals(newId)) {
          ourLog.info("Transaction resource ID[{}] is being updated", newId);
        } else {
          if (isPlaceholder(nextId)) {
            // nextId = new IdDt(resourceName, nextId.getIdPart());
            ourLog.info("Transaction resource ID[{}] has been assigned new ID[{}]", nextId, newId);
            idConversions.put(nextId, newId);
            idConversions.put(new IdDt(resourceName + "/" + nextId.getValue()), newId);
          }
        }
      }
    }

    for (IResource nextResource : theResources) {
      List<BaseResourceReferenceDt> allRefs =
          terser.getAllPopulatedChildElementsOfType(nextResource, BaseResourceReferenceDt.class);
      for (BaseResourceReferenceDt nextRef : allRefs) {
        IdDt nextId = nextRef.getReference();
        if (idConversions.containsKey(nextId)) {
          IdDt newId = idConversions.get(nextId);
          ourLog.info(" * Replacing resource ref {} with {}", nextId, newId);
          nextRef.setReference(newId);
        } else {
          ourLog.debug(" * Reference [{}] does not exist in bundle", nextId);
        }
      }
    }

    ourLog.info("Re-flushing updated resource references and extracting search criteria");

    for (int i = 0; i < theResources.size(); i++) {
      IResource resource = theResources.get(i);
      ResourceTable table = persistedResources.get(i);
      if (table == null) {
        continue;
      }

      InstantDt deletedInstantOrNull = ResourceMetadataKeyEnum.DELETED_AT.get(resource);
      Date deletedTimestampOrNull =
          deletedInstantOrNull != null ? deletedInstantOrNull.getValue() : null;
      if (deletedInstantOrNull == null
          && ResourceMetadataKeyEnum.ENTRY_TRANSACTION_METHOD.get(resource)
              == BundleEntryTransactionMethodEnum.DELETE) {
        deletedTimestampOrNull = updateTime;
        ResourceMetadataKeyEnum.DELETED_AT.put(resource, new InstantDt(deletedTimestampOrNull));
      }

      updateEntity(resource, table, table.getId() != null, deletedTimestampOrNull, updateTime);
    }

    long delay = System.currentTimeMillis() - start;
    ourLog.info(
        "Transaction completed in {}ms with {} creations and {} updates",
        new Object[] {delay, creations, updates});

    oo.addIssue()
        .setSeverity(IssueSeverityEnum.INFORMATION)
        .setDetails(
            "Transaction completed in "
                + delay
                + "ms with "
                + creations
                + " creations and "
                + updates
                + " updates");

    return retVal;
  }