ohif-viewer/extensions/default/src/DicomWebDataSource/index.js

import { api } from 'dicomweb-client';
import { DicomMetadataStore, IWebApiDataSource, utils, errorHandler, classes } from '@ohif/core';

import {
  mapParams,
  search as qidoSearch,
  seriesInStudy,
  processResults,
  processSeriesResults,
} from './qido.js';
import dcm4cheeReject from './dcm4cheeReject';

import getImageId from './utils/getImageId';
import dcmjs from 'dcmjs';
import { retrieveStudyMetadata, deleteStudyMetadataPromise } from './retrieveStudyMetadata.js';
import StaticWadoClient from './utils/StaticWadoClient';
import getDirectURL from '../utils/getDirectURL';
import { fixBulkDataURI } from './utils/fixBulkDataURI';

const { DicomMetaDictionary, DicomDict } = dcmjs.data;

const { naturalizeDataset, denaturalizeDataset } = DicomMetaDictionary;

const ImplementationClassUID = '2.25.270695996825855179949881587723571202391.2.0.0';
const ImplementationVersionName = 'OHIF-VIEWER-2.0.0';
const EXPLICIT_VR_LITTLE_ENDIAN = '1.2.840.10008.1.2.1';

const metadataProvider = classes.MetadataProvider;

/**
 * Creates a DICOM Web API based on the provided configuration.
 *
 * @param {object} dicomWebConfig - Configuration for the DICOM Web API
 * @param {string} dicomWebConfig.name - Data source name
 * @param {string} dicomWebConfig.wadoUriRoot - Legacy? (potentially unused/replaced)
 * @param {string} dicomWebConfig.qidoRoot - Base URL to use for QIDO requests
 * @param {string} dicomWebConfig.wadoRoot - Base URL to use for WADO requests
 * @param {string} dicomWebConfig.wadoUri - Base URL to use for WADO URI requests
 * @param {boolean} dicomWebConfig.qidoSupportsIncludeField - Whether QIDO supports the "Include" option to request additional fields in response
 * @param {string} dicomWebConfig.imageRendering - wadors | ? (unsure of where/how this is used)
 * @param {string} dicomWebConfig.thumbnailRendering - wadors | ? (unsure of where/how this is used)
 * @param {boolean} dicomWebConfig.supportsReject - Whether the server supports reject calls (i.e. DCM4CHEE)
 * @param {boolean} dicomWebConfig.lazyLoadStudy - "enableStudyLazyLoad"; Request series meta async instead of blocking
 * @param {string|boolean} dicomWebConfig.singlepart - indicates if the retrieves can fetch singlepart. Options are bulkdata, video, image, or boolean true
 * @param {string} dicomWebConfig.requestTransferSyntaxUID - Transfer syntax to request from the server
 * @param {object} dicomWebConfig.acceptHeader - Accept header to use for requests
 * @param {boolean} dicomWebConfig.omitQuotationForMultipartRequest - Whether to omit quotation marks for multipart requests
 * @param {boolean} dicomWebConfig.supportsFuzzyMatching - Whether the server supports fuzzy matching
 * @param {boolean} dicomWebConfig.supportsWildcard - Whether the server supports wildcard matching
 * @param {boolean} dicomWebConfig.supportsNativeDICOMModel - Whether the server supports the native DICOM model
 * @param {boolean} dicomWebConfig.enableStudyLazyLoad - Whether to enable study lazy loading
 * @param {boolean} dicomWebConfig.enableRequestTag - Whether to enable request tag
 * @param {boolean} dicomWebConfig.enableStudyLazyLoad - Whether to enable study lazy loading
 * @param {boolean} dicomWebConfig.bulkDataURI - Whether to enable bulkDataURI
 * @param {function} dicomWebConfig.onConfiguration - Function that is called after the configuration is initialized
 * @param {boolean} dicomWebConfig.staticWado - Whether to use the static WADO client
 * @param {object} userAuthenticationService - User authentication service
 * @param {object} userAuthenticationService.getAuthorizationHeader - Function that returns the authorization header
 * @returns {object} - DICOM Web API object
 */
function createDicomWebApi(dicomWebConfig, servicesManager) {
  const { userAuthenticationService, customizationService } = servicesManager.services;
  let dicomWebConfigCopy,
    qidoConfig,
    wadoConfig,
    qidoDicomWebClient,
    wadoDicomWebClient,
    getAuthrorizationHeader,
    generateWadoHeader;

  const implementation = {
    initialize: ({ params, query }) => {
      if (dicomWebConfig.onConfiguration && typeof dicomWebConfig.onConfiguration === 'function') {
        dicomWebConfig = dicomWebConfig.onConfiguration(dicomWebConfig, {
          params,
          query,
        });
      }

      dicomWebConfigCopy = JSON.parse(JSON.stringify(dicomWebConfig));

      getAuthrorizationHeader = () => {
        const xhrRequestHeaders = {};
        const authHeaders = userAuthenticationService.getAuthorizationHeader();
        if (authHeaders && authHeaders.Authorization) {
          xhrRequestHeaders.Authorization = authHeaders.Authorization;
        }
        return xhrRequestHeaders;
      };

      generateWadoHeader = () => {
        let authorizationHeader = getAuthrorizationHeader();
        //Generate accept header depending on config params
        let formattedAcceptHeader = utils.generateAcceptHeader(
          dicomWebConfig.acceptHeader,
          dicomWebConfig.requestTransferSyntaxUID,
          dicomWebConfig.omitQuotationForMultipartRequest
        );

        return {
          ...authorizationHeader,
          Accept: formattedAcceptHeader,
        };
      };

      qidoConfig = {
        url: dicomWebConfig.qidoRoot,
        staticWado: dicomWebConfig.staticWado,
        singlepart: dicomWebConfig.singlepart,
        headers: userAuthenticationService.getAuthorizationHeader(),
        errorInterceptor: errorHandler.getHTTPErrorHandler(),
      };

      wadoConfig = {
        url: dicomWebConfig.wadoRoot,
        staticWado: dicomWebConfig.staticWado,
        singlepart: dicomWebConfig.singlepart,
        headers: userAuthenticationService.getAuthorizationHeader(),
        errorInterceptor: errorHandler.getHTTPErrorHandler(),
      };

      // TODO -> Two clients sucks, but its better than 1000.
      // TODO -> We'll need to merge auth later.
      qidoDicomWebClient = dicomWebConfig.staticWado
        ? new StaticWadoClient(qidoConfig)
        : new api.DICOMwebClient(qidoConfig);

      wadoDicomWebClient = dicomWebConfig.staticWado
        ? new StaticWadoClient(wadoConfig)
        : new api.DICOMwebClient(wadoConfig);
    },
    query: {
      studies: {
        mapParams: mapParams.bind(),
        search: async function (origParams) {
          qidoDicomWebClient.headers = getAuthrorizationHeader();
          const { studyInstanceUid, seriesInstanceUid, ...mappedParams } =
            mapParams(origParams, {
              supportsFuzzyMatching: dicomWebConfig.supportsFuzzyMatching,
              supportsWildcard: dicomWebConfig.supportsWildcard,
            }) || {};

          const results = await qidoSearch(qidoDicomWebClient, undefined, undefined, mappedParams);

          return processResults(results);
        },
        processResults: processResults.bind(),
      },
      series: {
        // mapParams: mapParams.bind(),
        search: async function (studyInstanceUid) {
          qidoDicomWebClient.headers = getAuthrorizationHeader();
          const results = await seriesInStudy(qidoDicomWebClient, studyInstanceUid);

          return processSeriesResults(results);
        },
        // processResults: processResults.bind(),
      },
      instances: {
        search: (studyInstanceUid, queryParameters) => {
          qidoDicomWebClient.headers = getAuthrorizationHeader();
          return qidoSearch.call(
            undefined,
            qidoDicomWebClient,
            studyInstanceUid,
            null,
            queryParameters
          );
        },
      },
    },
    retrieve: {
      /**
       * Generates a URL that can be used for direct retrieve of the bulkdata
       *
       * @param {object} params
       * @param {string} params.tag is the tag name of the URL to retrieve
       * @param {object} params.instance is the instance object that the tag is in
       * @param {string} params.defaultType is the mime type of the response
       * @param {string} params.singlepart is the type of the part to retrieve
       * @returns an absolute URL to the resource, if the absolute URL can be retrieved as singlepart,
       *    or is already retrieved, or a promise to a URL for such use if a BulkDataURI
       */
      directURL: params => {
        return getDirectURL(
          {
            wadoRoot: dicomWebConfig.wadoRoot,
            singlepart: dicomWebConfig.singlepart,
          },
          params
        );
      },
      bulkDataURI: async ({ StudyInstanceUID, BulkDataURI }) => {
        qidoDicomWebClient.headers = getAuthrorizationHeader();
        const options = {
          multipart: false,
          BulkDataURI,
          StudyInstanceUID,
        };
        return qidoDicomWebClient.retrieveBulkData(options).then(val => {
          const ret = (val && val[0]) || undefined;
          return ret;
        });
      },
      series: {
        metadata: async ({
          StudyInstanceUID,
          filters,
          sortCriteria,
          sortFunction,
          madeInClient = false,
          returnPromises = false,
        } = {}) => {
          if (!StudyInstanceUID) {
            throw new Error('Unable to query for SeriesMetadata without StudyInstanceUID');
          }

          if (dicomWebConfig.enableStudyLazyLoad) {
            return implementation._retrieveSeriesMetadataAsync(
              StudyInstanceUID,
              filters,
              sortCriteria,
              sortFunction,
              madeInClient,
              returnPromises
            );
          }

          return implementation._retrieveSeriesMetadataSync(
            StudyInstanceUID,
            filters,
            sortCriteria,
            sortFunction,
            madeInClient
          );
        },
      },
    },

    store: {
      dicom: async (dataset, request, dicomDict) => {
        wadoDicomWebClient.headers = getAuthrorizationHeader();
        if (dataset instanceof ArrayBuffer) {
          const options = {
            datasets: [dataset],
            request,
          };
          await wadoDicomWebClient.storeInstances(options);
        } else {
          let effectiveDicomDict = dicomDict;

          if (!dicomDict) {
            const meta = {
              FileMetaInformationVersion: dataset._meta?.FileMetaInformationVersion?.Value,
              MediaStorageSOPClassUID: dataset.SOPClassUID,
              MediaStorageSOPInstanceUID: dataset.SOPInstanceUID,
              TransferSyntaxUID: EXPLICIT_VR_LITTLE_ENDIAN,
              ImplementationClassUID,
              ImplementationVersionName,
            };

            const denaturalized = denaturalizeDataset(meta);
            const defaultDicomDict = new DicomDict(denaturalized);
            defaultDicomDict.dict = denaturalizeDataset(dataset);

            effectiveDicomDict = defaultDicomDict;
          }

          const part10Buffer = effectiveDicomDict.write();

          const options = {
            datasets: [part10Buffer],
            request,
          };

          await wadoDicomWebClient.storeInstances(options);
        }
      },
    },

    _retrieveSeriesMetadataSync: async (
      StudyInstanceUID,
      filters,
      sortCriteria,
      sortFunction,
      madeInClient
    ) => {
      const enableStudyLazyLoad = false;
      wadoDicomWebClient.headers = generateWadoHeader();
      // data is all SOPInstanceUIDs
      const data = await retrieveStudyMetadata(
        wadoDicomWebClient,
        StudyInstanceUID,
        enableStudyLazyLoad,
        filters,
        sortCriteria,
        sortFunction,
        dicomWebConfig
      );

      // first naturalize the data
      const naturalizedInstancesMetadata = data.map(naturalizeDataset);

      const seriesSummaryMetadata = {};
      const instancesPerSeries = {};

      naturalizedInstancesMetadata.forEach(instance => {
        if (!seriesSummaryMetadata[instance.SeriesInstanceUID]) {
          seriesSummaryMetadata[instance.SeriesInstanceUID] = {
            StudyInstanceUID: instance.StudyInstanceUID,
            StudyDescription: instance.StudyDescription,
            SeriesInstanceUID: instance.SeriesInstanceUID,
            SeriesDescription: instance.SeriesDescription,
            SeriesNumber: instance.SeriesNumber,
            SeriesTime: instance.SeriesTime,
            SOPClassUID: instance.SOPClassUID,
            ProtocolName: instance.ProtocolName,
            Modality: instance.Modality,
          };
        }

        if (!instancesPerSeries[instance.SeriesInstanceUID]) {
          instancesPerSeries[instance.SeriesInstanceUID] = [];
        }

        const imageId = implementation.getImageIdsForInstance({
          instance,
        });

        instance.imageId = imageId;
        instance.wadoRoot = dicomWebConfig.wadoRoot;
        instance.wadoUri = dicomWebConfig.wadoUri;

        metadataProvider.addImageIdToUIDs(imageId, {
          StudyInstanceUID,
          SeriesInstanceUID: instance.SeriesInstanceUID,
          SOPInstanceUID: instance.SOPInstanceUID,
        });

        instancesPerSeries[instance.SeriesInstanceUID].push(instance);
      });

      // grab all the series metadata
      const seriesMetadata = Object.values(seriesSummaryMetadata);
      DicomMetadataStore.addSeriesMetadata(seriesMetadata, madeInClient);

      Object.keys(instancesPerSeries).forEach(seriesInstanceUID =>
        DicomMetadataStore.addInstances(instancesPerSeries[seriesInstanceUID], madeInClient)
      );

      return seriesSummaryMetadata;
    },

    _retrieveSeriesMetadataAsync: async (
      StudyInstanceUID,
      filters,
      sortCriteria,
      sortFunction,
      madeInClient = false,
      returnPromises = false
    ) => {
      const enableStudyLazyLoad = true;
      wadoDicomWebClient.headers = generateWadoHeader();
      // Get Series
      const { preLoadData: seriesSummaryMetadata, promises: seriesPromises } =
        await retrieveStudyMetadata(
          wadoDicomWebClient,
          StudyInstanceUID,
          enableStudyLazyLoad,
          filters,
          sortCriteria,
          sortFunction,
          dicomWebConfig
        );

      /**
       * naturalizes the dataset, and adds a retrieve bulkdata method
       * to any values containing BulkDataURI.
       * @param {*} instance
       * @returns naturalized dataset, with retrieveBulkData methods
       */
      const addRetrieveBulkData = instance => {
        const naturalized = naturalizeDataset(instance);

        // if we know the server doesn't use bulkDataURI, then don't
        if (!dicomWebConfig.bulkDataURI?.enabled) {
          return naturalized;
        }

        Object.keys(naturalized).forEach(key => {
          const value = naturalized[key];

          // The value.Value will be set with the bulkdata read value
          // in which case it isn't necessary to re-read this.
          if (value && value.BulkDataURI && !value.Value) {
            // Provide a method to fetch bulkdata
            value.retrieveBulkData = (options = {}) => {
              // handle the scenarios where bulkDataURI is relative path
              fixBulkDataURI(value, naturalized, dicomWebConfig);

              const { mediaType } = options;
              const useOptions = {
                // The bulkdata fetches work with either multipart or
                // singlepart, so set multipart to false to let the server
                // decide which type to respond with.
                multipart: false,
                BulkDataURI: value.BulkDataURI,
                // The study instance UID is required if the bulkdata uri
                // is relative - that isn't disallowed by DICOMweb, but
                // isn't well specified in the standard, but is needed in
                // any implementation that stores static copies of the metadata
                StudyInstanceUID: naturalized.StudyInstanceUID,
                mediaTypes: mediaType
                  ? [{ mediaType }, { mediaType: 'application/octet-stream' }]
                  : undefined,
                ...options,
              };
              // Todo: this needs to be from wado dicom web client
              return qidoDicomWebClient.retrieveBulkData(useOptions).then(val => {
                // There are DICOM PDF cases where the first ArrayBuffer in the array is
                // the bulk data and DICOM video cases where the second ArrayBuffer is
                // the bulk data. Here we play it safe and do a find.
                const ret =
                  (val instanceof Array && val.find(arrayBuffer => arrayBuffer?.byteLength)) ||
                  undefined;
                value.Value = ret;
                return ret;
              });
            };
          }
        });
        return naturalized;
      };

      // Async load series, store as retrieved
      function storeInstances(instances) {
        const naturalizedInstances = instances.map(addRetrieveBulkData);

        // Adding instanceMetadata to OHIF MetadataProvider
        naturalizedInstances.forEach(instance => {
          instance.wadoRoot = dicomWebConfig.wadoRoot;
          instance.wadoUri = dicomWebConfig.wadoUri;

          const imageId = implementation.getImageIdsForInstance({
            instance,
          });

          // Adding imageId to each instance
          // Todo: This is not the best way I can think of to let external
          // metadata handlers know about the imageId that is stored in the store
          instance.imageId = imageId;

          // Adding UIDs to metadataProvider
          // Note: storing imageURI in metadataProvider since stack viewports
          // will use the same imageURI
          metadataProvider.addImageIdToUIDs(imageId, {
            StudyInstanceUID,
            SeriesInstanceUID: instance.SeriesInstanceUID,
            SOPInstanceUID: instance.SOPInstanceUID,
          });
        });

        DicomMetadataStore.addInstances(naturalizedInstances, madeInClient);
      }

      function setSuccessFlag() {
        const study = DicomMetadataStore.getStudy(StudyInstanceUID);
        if (!study) {
          return;
        }
        study.isLoaded = true;
      }

      // Google Cloud Healthcare doesn't return StudyInstanceUID, so we need to add
      // it manually here
      seriesSummaryMetadata.forEach(aSeries => {
        aSeries.StudyInstanceUID = StudyInstanceUID;
      });

      DicomMetadataStore.addSeriesMetadata(seriesSummaryMetadata, madeInClient);

      const seriesDeliveredPromises = seriesPromises.map(promise => {
        if (!returnPromises) {
          promise?.start();
        }
        return promise.then(instances => {
          storeInstances(instances);
        });
      });

      if (returnPromises) {
        Promise.all(seriesDeliveredPromises).then(() => setSuccessFlag());
        return seriesPromises;
      } else {
        await Promise.all(seriesDeliveredPromises);
        setSuccessFlag();
      }

      return seriesSummaryMetadata;
    },
    deleteStudyMetadataPromise,
    getImageIdsForDisplaySet(displaySet) {
      const images = displaySet.images;
      const imageIds = [];

      if (!images) {
        return imageIds;
      }

      displaySet.images.forEach(instance => {
        const NumberOfFrames = instance.NumberOfFrames;

        if (NumberOfFrames > 1) {
          for (let frame = 1; frame <= NumberOfFrames; frame++) {
            const imageId = this.getImageIdsForInstance({
              instance,
              frame,
            });
            imageIds.push(imageId);
          }
        } else {
          const imageId = this.getImageIdsForInstance({ instance });
          imageIds.push(imageId);
        }
      });

      return imageIds;
    },
    getImageIdsForInstance({ instance, frame = undefined }) {
      const imageIds = getImageId({
        instance,
        frame,
        config: dicomWebConfig,
      });
      return imageIds;
    },
    getConfig() {
      return dicomWebConfigCopy;
    },
    getStudyInstanceUIDs({ params, query }) {
      const { StudyInstanceUIDs: paramsStudyInstanceUIDs } = params;
      const queryStudyInstanceUIDs = utils.splitComma(query.getAll('StudyInstanceUIDs'));

      const StudyInstanceUIDs =
        (queryStudyInstanceUIDs.length && queryStudyInstanceUIDs) || paramsStudyInstanceUIDs;
      const StudyInstanceUIDsAsArray =
        StudyInstanceUIDs && Array.isArray(StudyInstanceUIDs)
          ? StudyInstanceUIDs
          : [StudyInstanceUIDs];

      return StudyInstanceUIDsAsArray;
    },
  };

  if (dicomWebConfig.supportsReject) {
    implementation.reject = dcm4cheeReject(dicomWebConfig.wadoRoot);
  }

  return IWebApiDataSource.create(implementation);
}

export { createDicomWebApi };