feat(dr): rebasing

Refs: #1379

packages/api/src/command/connected-user/get-connected-user.ts

@@ -2,7 +2,7 @@ import { Op } from "sequelize";
 import NotFoundError from "../../errors/not-found";
 import { ConnectedUser } from "../../models/connected-user";
 import { ProviderOptions } from "../../shared/constants";
-import { AtLeastOne } from "../../shared/types";
+import { AtLeastOne } from "@metriport/shared";
 import { capture } from "../../shared/notifications";
 
 export const getConnectedUser = async ({

packages/api/src/command/medical/admin/upload-doc.ts

@@ -6,7 +6,7 @@ import { createDocReferenceContent, getFHIRDocRef } from "../../../external/fhir
 import { metriportDataSourceExtension } from "../../../external/fhir/shared/extensions/metriport";
 import { Config } from "../../../shared/config";
 import { capture } from "../../../shared/notifications";
-import { randomInt } from "../../../shared/numbers";
+import { randomInt } from "@metriport/shared/common/numbers";
 import { getPatientOrFail } from "../patient/get-patient";
 import { cloneDeep } from "lodash";
 

packages/api/src/command/medical/document/__tests__/document-query_calculateAndUpdateDocQuery.test.ts

@@ -5,7 +5,7 @@ import {
  ConvertResult,
  DocumentQueryProgress,
  DocumentQueryStatus,
-} from "../../../../domain/medical/document-query";
+} from "@metriport/core/domain/medical/document-query";
 import { makeDocumentQueryProgress } from "../../../../domain/medical/__tests__/document-query";
 import { makePatient, makePatientData } from "../../../../domain/medical/__tests__/patient";
 import { PatientModel } from "../../../../models/medical/patient";

packages/api/src/command/medical/document/check-doc-queries-notification.ts

@@ -1,5 +1,5 @@
 import { uniqBy } from "lodash";
-import { Patient } from "../../../domain/medical/patient";
+import { Patient } from "@metriport/core/domain/medical/patient";
 import { MAPIWebhookType } from "../../../domain/webhook";
 import {
  GroupedValidationResult,

packages/api/src/command/medical/document/check-doc-queries-shared.ts

@@ -1,4 +1,4 @@
-import { Progress } from "../../../domain/medical/document-query";
+import { Progress } from "@metriport/core/domain/medical/document-query";
 
 export type MainProgressProps = keyof Pick<Progress, "total" | "status">;
 

packages/api/src/command/medical/document/check-doc-queries.ts

@@ -8,8 +8,8 @@ import {
  DocumentQueryProgress,
  DocumentQueryStatus,
  Progress,
-} from "../../../domain/medical/document-query";
-import { Patient, PatientCreate, PatientData } from "../../../domain/medical/patient";
+} from "@metriport/core/domain/medical/document-query";
+import { Patient, PatientCreate, PatientData } from "@metriport/core/domain/medical/patient";
 import { PatientModel } from "../../../models/medical/patient";
 import { executeOnDBTx } from "../../../models/transaction-wrapper";
 import { capture } from "../../../shared/notifications";

packages/api/src/command/medical/document/document-query-storage-info.ts

@@ -1,7 +1,7 @@
 import { DocumentReferenceContent } from "@medplum/fhirtypes";
 import { Document } from "@metriport/commonwell-sdk";
 import { S3Utils } from "@metriport/core/external/aws/s3";
-import { Patient } from "../../../domain/medical/patient";
+import { Patient } from "@metriport/core/domain/medical/patient";
 import {
  DocumentWithMetriportId,
  getFileExtension,

packages/api/src/command/medical/document/document-query.ts

@@ -6,8 +6,8 @@ import {
  DocumentQueryProgress,
  DocumentQueryStatus,
  Progress,
-} from "../../../domain/medical/document-query";
-import { Patient } from "../../../domain/medical/patient";
+} from "@metriport/core/domain/medical/document-query";
+import { Patient } from "@metriport/core/domain/medical/patient";
 import { validateOptionalFacilityId } from "../../../domain/medical/patient-facility";
 import { queryAndProcessDocuments as getDocumentsFromCW } from "../../../external/commonwell/document/document-query";
 import { PatientModel } from "../../../models/medical/patient";

packages/api/src/command/medical/document/document-reconvert.ts

@@ -9,15 +9,15 @@ import dayjs from "dayjs";
 import duration from "dayjs/plugin/duration";
 import { groupBy } from "lodash";
 import { DocRefMapping } from "../../../domain/medical/docref-mapping";
-import { Patient } from "../../../domain/medical/patient";
+import { Patient } from "@metriport/core/domain/medical/patient";
 import { convertCDAToFHIR } from "../../../external/fhir-converter/converter";
 import { getDocuments as getDocumentsFromFHIRServer } from "../../../external/fhir/document/get-documents";
 import { countResources } from "../../../external/fhir/patient/count-resources";
 import { downloadedFromHIEs } from "../../../external/fhir/shared";
 import { getMetriportContent } from "../../../external/fhir/shared/extensions/metriport";
 import { Config } from "../../../shared/config";
 import { errorToString } from "../../../shared/log";
-import { formatNumber } from "../../../shared/numbers";
+import { formatNumber } from "@metriport/shared/common/numbers";
 import { getDocRefMappings } from "../docref-mapping/get-docref-mapping";
 import { deleteConsolidated as deleteConsolidatedOnFHIRServer } from "../patient/consolidated-delete";
 import { getPatientOrFail } from "../patient/get-patient";

packages/api/src/command/medical/document/document-status.ts

@@ -1,5 +1,5 @@
-import { DocumentQueryProgress, isProcessing } from "../../../domain/medical/document-query";
-import { Patient } from "../../../domain/medical/patient";
+import { DocumentQueryProgress, isProcessing } from "@metriport/core/domain/medical/document-query";
+import { Patient } from "@metriport/core/domain/medical/patient";
 
 export function areDocumentsProcessing(patient: Patient): boolean;
 export function areDocumentsProcessing(progress: DocumentQueryProgress | undefined): boolean;

packages/api/src/command/medical/document/start-bulk-get-doc-url.ts

@@ -2,10 +2,10 @@ import {
  BulkGetDocumentsUrlProgress,
  isBulkGetDocUrlProcessing,
  BulkGetDocUrlStatus,
-} from "../../../domain/medical/bulk-get-document-url";
+} from "@metriport/core/domain/medical/bulk-get-document-url";
 import { Util } from "../../../shared/util";
 import { getPatientOrFail } from "../patient/get-patient";
-import { Patient } from "../../../domain/medical/patient";
+import { Patient } from "@metriport/core/domain/medical/patient";
 import { uuidv7 } from "@metriport/core/util/uuid-v7";
 import { storeBulkGetDocumentUrlQueryInit } from "../patient/bulk-get-doc-url-progress";
 import { makeLambdaClient } from "../../../external/aws/lambda";

packages/api/src/command/medical/patient/__tests__/append-doc-query-progress.test.ts

@@ -1,7 +1,7 @@
 /* eslint-disable @typescript-eslint/no-empty-function */
 import { faker } from "@faker-js/faker";
-import { DocumentQueryProgress } from "../../../../domain/medical/document-query";
-import { Patient } from "../../../../domain/medical/patient";
+import { DocumentQueryProgress } from "@metriport/core/domain/medical/document-query";
+import { Patient } from "@metriport/core/domain/medical/patient";
 import { makeProgress } from "../../../../domain/medical/__tests__/document-query";
 import { makePatient, makePatientData } from "../../../../domain/medical/__tests__/patient";
 import { PatientModel } from "../../../../models/medical/patient";

packages/api/src/command/medical/patient/append-consolidated-query-progress.ts

@@ -1,5 +1,5 @@
-import { Patient } from "../../../domain/medical/patient";
-import { QueryProgress } from "../../../domain/medical/query-status";
+import { Patient } from "@metriport/core/domain/medical/patient";
+import { QueryProgress } from "@metriport/core/domain/medical/query-status";
 import { PatientModel } from "../../../models/medical/patient";
 import { executeOnDBTx } from "../../../models/transaction-wrapper";
 import { getPatientOrFail } from "./get-patient";

packages/api/src/command/medical/patient/append-doc-query-progress.ts

@@ -1,5 +1,5 @@
-import { getStatusFromProgress, Progress } from "../../../domain/medical/document-query";
-import { Patient } from "../../../domain/medical/patient";
+import { getStatusFromProgress, Progress } from "@metriport/core/domain/medical/document-query";
+import { Patient } from "@metriport/core/domain/medical/patient";
 import { PatientModel } from "../../../models/medical/patient";
 import { executeOnDBTx } from "../../../models/transaction-wrapper";
 import { getPatientOrFail } from "./get-patient";

packages/api/src/command/medical/patient/bulk-get-doc-url-progress.ts

@@ -1,8 +1,8 @@
 import {
  BulkGetDocUrlStatus,
  BulkGetDocumentsUrlProgress,
-} from "../../../domain/medical/bulk-get-document-url";
-import { Patient } from "../../../domain/medical/patient";
+} from "@metriport/core/domain/medical/bulk-get-document-url";
+import { Patient } from "@metriport/core/domain/medical/patient";
 import { PatientModel } from "../../../models/medical/patient";
 import { executeOnDBTx } from "../../../models/transaction-wrapper";
 import { BaseUpdateCmdWithCustomer } from "../base-update-command";

packages/api/src/command/medical/patient/consolidated-delete.ts

@@ -1,14 +1,23 @@
 import { OperationOutcomeError } from "@medplum/core";
-import { OperationOutcomeIssue } from "@medplum/fhirtypes";
+import { BundleEntry, Resource } from "@medplum/fhirtypes";
 import { ResourceTypeForConsolidation } from "@metriport/api-sdk";
-import { flatten } from "lodash";
-import { Patient } from "../../../domain/medical/patient";
+import { FhirClient } from "@metriport/core/external/fhir/api/api";
+import { logDuration } from "@metriport/shared/common/duration";
+import dayjs from "dayjs";
+import duration from "dayjs/plugin/duration";
+import { chunk, flatten } from "lodash";
+import { Patient } from "@metriport/core/domain/medical/patient";
 import { makeFhirApi } from "../../../external/fhir/api/api-factory";
+import { getDetailFromOutcomeError } from "../../../external/fhir/shared";
 import { capture } from "../../../shared/notifications";
 import { Util } from "../../../shared/util";
 import { getConsolidatedPatientData } from "./consolidated-get";
 
+dayjs.extend(duration);
+
+const MAX_ITEMS_PER_BATCH = 100;
 const SUCCESS_CODE = `SUCCESSFUL_DELETE`;
+
 export type DeleteConsolidatedFilters = {
  resources?: ResourceTypeForConsolidation[];
  docIds: string[];
@@ -28,37 +37,46 @@ export async function deleteConsolidated(params: DeleteConsolidatedParams): Prom
  const { log } = Util.out(`deleteConsolidated - cxId ${patient.cxId}, patientId ${patient.id}`);
  const fhir = makeFhirApi(patient.cxId);
 
- const getResourcesToDelete = async () => {
- try {
- const bundle = await getConsolidatedPatientData({
- patient,
- documentIds: docIds,
- resources,
- });
- const resourcesFromFHIRServer = bundle.entry;
- if (!resourcesFromFHIRServer || resourcesFromFHIRServer.length <= 0) {
- log(`No resources to delete`);
- return;
- }
+ const resourcesToDelete = await getResourcesToDelete(patient, docIds, resources, log);
+ if (!resourcesToDelete || resourcesToDelete.length <= 0) return;
 
- const resourcesToDelete = resourcesFromFHIRServer.filter(r => {
- const resource = r.resource;
- if (!resource) return false;
- // TODO make this dynamic, get a list of resources to exclude
- return resource.resourceType !== "DocumentReference";
- });
- return resourcesToDelete;
- } catch (error) {
- const msg = `Failed to get consolidated FHIR resources`;
- log(`${msg}: ${JSON.stringify(params)}`);
- throw error;
- }
- };
+ await deleteResources(resourcesToDelete, patient, fhir, dryRun, log);
+}
 
- const resourcesToDelete = await getResourcesToDelete();
- if (!resourcesToDelete || resourcesToDelete.length <= 0) return;
+async function getResourcesToDelete(
+ patient: Pick<Patient, "id" | "cxId">,
+ documentIds: string[],
+ resources: ResourceTypeForConsolidation[] | undefined,
+ log: typeof console.log
+): Promise<BundleEntry<Resource>[]> {
+ const bundle = await getConsolidatedPatientData({
+ patient,
+ documentIds,
+ resources,
+ });
+ const resourcesFromFHIRServer = bundle.entry;
+ if (!resourcesFromFHIRServer || resourcesFromFHIRServer.length <= 0) {
+ log(`No resources to delete`);
+ return [];
+ }
+
+ const resourcesToDelete = resourcesFromFHIRServer.filter(r => {
+ const resource = r.resource;
+ if (!resource) return false;
+ // TODO make this dynamic, get a list of resources to exclude
+ return resource.resourceType !== "DocumentReference";
+ });
+ return resourcesToDelete;
+}
 
- const entries = resourcesToDelete.flatMap(r => {
+async function deleteResources(
+ resourcesToDelete: BundleEntry<Resource>[],
+ patient: Pick<Patient, "id" | "cxId">,
+ fhir: FhirClient,
+ dryRun: boolean,
+ log: typeof console.log
+): Promise<void> {
+ const entriesForFHIRBundle = resourcesToDelete.flatMap(r => {
  const resource = r.resource;
  if (!resource || !resource.id || !resource.resourceType) return [];
  return {
@@ -70,17 +88,34 @@ export async function deleteConsolidated(params: DeleteConsolidatedParams): Prom
  });
 
  if (dryRun) {
- log(`[DRY-RUN] Would delete ${entries.length} resources from FHIR server`);
+ log(`[DRY-RUN] Would delete ${entriesForFHIRBundle.length} resources from FHIR server`);
  return;
  }
 
+ const chunks = chunk(entriesForFHIRBundle, MAX_ITEMS_PER_BATCH);
+ for (const [i, chunk] of chunks.entries()) {
+ log(`Deleting chunk ${i + 1}/${chunks.length}...`);
+ await deleteChunk(chunk, patient.id, fhir, log);
+ }
+}
+
+async function deleteChunk(
+ entries: BundleEntry<Resource>[],
+ patientId: string,
+ fhir: FhirClient,
+ log: typeof console.log
+): Promise<void> {
  try {
  log(`Deleting ${entries.length} resources from FHIR server...`);
- const resp = await fhir.executeBatch({
- resourceType: "Bundle",
- type: "transaction",
- entry: entries,
- });
+ const resp = await logDuration(
+ () =>
+ fhir.executeBatch({
+ resourceType: "Bundle",
+ type: "transaction",
+ entry: entries,
+ }),
+ { log, withMinutes: true }
+ );
  const issues = resp.entry?.flatMap(e => {
  return e.response?.outcome?.issue?.flatMap(i => {
  return i.details?.coding?.map(c => {
@@ -99,35 +134,25 @@ export async function deleteConsolidated(params: DeleteConsolidatedParams): Prom
  capture.error(msg, {
  extra: {
  context: `deleteConsolidated.graceful-fail`,
- patientId: patient.id,
+ patientId: patientId,
  issues: issuesFlattened,
  },
  });
  }
  } catch (error) {
- const detailMsg = error instanceof OperationOutcomeError ? getMessage(error) : String(error);
+ const detailMsg =
+ error instanceof OperationOutcomeError ? getDetailFromOutcomeError(error) : String(error);
  const msg = `Failed to delete FHIR resources`;
  log(`${msg} - ${detailMsg} - ${JSON.stringify(error)}`);
  capture.error(msg, {
  extra: {
  context: `deleteConsolidated.catch`,
- patientId: patient.id,
+ patientId: patientId,
  detailMsg,
+ entries,
  error,
  },
  });
  throw error;
  }
 }
-
-function getMessage(err: OperationOutcomeError): string {
- return err.outcome.issue ? err.outcome.issue.map(issueToString).join(",") : "";
-}
-
-function issueToString(issue: OperationOutcomeIssue): string {
- return (
- issue.details?.text ??
- (issue.diagnostics ? issue.diagnostics.slice(0, 100) + "..." : null) ??
- JSON.stringify(issue)
- );
-}

packages/api/src/command/medical/patient/consolidated-get.ts

@@ -10,8 +10,8 @@ import {
 import { ResourceTypeForConsolidation } from "@metriport/api-sdk";
 import { ConsolidationConversionType } from "@metriport/core/domain/conversion/fhir-to-medical-record";
 import { emptyFunction } from "@metriport/shared";
-import { Patient } from "../../../domain/medical/patient";
-import { QueryProgress } from "../../../domain/medical/query-status";
+import { Patient } from "@metriport/core/domain/medical/patient";
+import { QueryProgress } from "@metriport/core/domain/medical/query-status";
 import { makeFhirApi } from "../../../external/fhir/api/api-factory";
 import {
  fullDateQueryForResource,

packages/api/src/command/medical/patient/consolidated-webhook.ts

@@ -1,5 +1,5 @@
 import { Bundle, Resource } from "@medplum/fhirtypes";
-import { Patient } from "../../../domain/medical/patient";
+import { Patient } from "@metriport/core/domain/medical/patient";
 import { Product } from "../../../domain/product";
 import { errorToString } from "../../../shared/log";
 import { capture } from "../../../shared/notifications";

packages/api/src/command/medical/patient/convert-fhir-bundle.ts

@@ -9,7 +9,7 @@ import { getLambdaResultPayload, makeLambdaClient } from "@metriport/core/extern
 import { makeS3Client } from "@metriport/core/external/aws/s3";
 import dayjs from "dayjs";
 import duration from "dayjs/plugin/duration";
-import { Patient } from "../../../domain/medical/patient";
+import { Patient } from "@metriport/core/domain/medical/patient";
 import { makeFhirApi } from "../../../external/fhir/api/api-factory";
 import { Config } from "../../../shared/config";
 import { createS3FileName } from "../../../shared/external";

packages/api/src/command/medical/patient/create-patient.ts

@@ -1,5 +1,5 @@
 import { uuidv7 } from "@metriport/core/util/uuid-v7";
-import { Patient, PatientCreate, PatientData } from "../../../domain/medical/patient";
+import { Patient, PatientCreate, PatientData } from "@metriport/core/domain/medical/patient";
 import { processAsyncError } from "../../../errors";
 import cwCommands from "../../../external/commonwell";
 import cqCommands from "../../../external/carequality";