Expose draft operation (#103)

* Expose operation * Update service/src/requestSchemas.ts Co-authored-by: hossenlopp <[email protected]> --------- Co-authored-by: hossenlopp <[email protected]>
projecttacoma · Jul 8, 2024 · f876096 · f876096
1 parent 299f778
commit f876096
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Showing 15 changed files with 702 additions and 41 deletions.
diff --git a/service/.env.test b/service/.env.test
@@ -1,2 +1,3 @@
 VSAC_API_KEY="example-api-key"
-AUTHORING=true
+AUTHORING=true
+DATABASE_URL='mongodb://localhost:27017/measure-repository?replicaSet=rs0'
diff --git a/service/jest-mongodb-config.js b/service/jest-mongodb-config.js
@@ -1,12 +1,14 @@
 module.exports = {
   mongodbMemoryServerOptions: {
     binary: {
-      verison: '6.0.1',
+      version: '6.0.1',
       skipMD5: true
     },
     autoStart: false,
-    instance: {}
-  },
-
-  useSharedDBForAllJestWorkers: false
+    instance: {},
+    replSet: {
+      count: 3,
+      storageEngine: 'wiredTiger'
+    }
+  }
 };
diff --git a/service/package.json b/service/package.json
@@ -22,7 +22,7 @@
     "dev:watch": "nodemon ./src/index.ts",
     "dev:clean": "npm run db:reset && npm run dev",
     "start": "node ./dist/index.js",
-    "test": "jest",
+    "test": "jest --runInBand --silent",
     "test:watch": "jest --watch"
   },
   "devDependencies": {
@@ -57,4 +57,4 @@
     "uuid": "^9.0.0",
     "zod": "^3.20.2"
   }
-}
+}
diff --git a/service/src/config/serverConfig.ts b/service/src/config/serverConfig.ts
@@ -85,6 +85,30 @@ export const serverConfig: ServerConfig = {
           route: '/:id/$data-requirements',
           method: 'POST',
           reference: 'http://hl7.org/fhir/us/cqfmeasures/OperationDefinition/Measure-data-requirements'
+        },
+        {
+          name: 'draft',
+          route: '/$draft',
+          method: 'GET',
+          reference: 'https://hl7.org/fhir/uv/crmi/STU1/OperationDefinition-crmi-draft.html'
+        },
+        {
+          name: 'draft',
+          route: '/$draft',
+          method: 'POST',
+          reference: 'https://hl7.org/fhir/uv/crmi/STU1/OperationDefinition-crmi-draft.html'
+        },
+        {
+          name: 'draft',
+          route: '/:id/$draft',
+          method: 'GET',
+          reference: 'https://hl7.org/fhir/uv/crmi/STU1/OperationDefinition-crmi-draft.html'
+        },
+        {
+          name: 'draft',
+          route: '/:id/$draft',
+          method: 'POST',
+          reference: 'https://hl7.org/fhir/uv/crmi/STU1/OperationDefinition-crmi-draft.html'
         }
       ]
     },
@@ -139,6 +163,30 @@ export const serverConfig: ServerConfig = {
           route: '/:id/$data-requirements',
           method: 'POST',
           reference: 'http://hl7.org/fhir/us/cqfmeasures/OperationDefinition/Library-data-requirements'
+        },
+        {
+          name: 'draft',
+          route: '/$draft',
+          method: 'GET',
+          reference: 'https://hl7.org/fhir/uv/crmi/STU1/OperationDefinition-crmi-draft.html'
+        },
+        {
+          name: 'draft',
+          route: '/$draft',
+          method: 'POST',
+          reference: 'https://hl7.org/fhir/uv/crmi/STU1/OperationDefinition-crmi-draft.html'
+        },
+        {
+          name: 'draft',
+          route: '/:id/$draft',
+          method: 'GET',
+          reference: 'https://hl7.org/fhir/uv/crmi/STU1/OperationDefinition-crmi-draft.html'
+        },
+        {
+          name: 'draft',
+          route: '/:id/$draft',
+          method: 'POST',
+          reference: 'https://hl7.org/fhir/uv/crmi/STU1/OperationDefinition-crmi-draft.html'
         }
       ]
     }

diff --git a/service/src/db/dbOperations.ts b/service/src/db/dbOperations.ts
@@ -1,6 +1,7 @@
 import { FhirResourceType, loggers } from '@projecttacoma/node-fhir-server-core';
 import { Filter } from 'mongodb';
 import { Connection } from './Connection';
+import { ArtifactResourceType, FhirArtifact } from '../types/service-types';
 
 const logger = loggers.get('default');
 
@@ -12,6 +13,18 @@ export async function findResourceById<T extends fhir4.FhirResource>(id: string,
   return collection.findOne<T>({ id: id }, { projection: { _id: 0, _dataRequirements: 0 } });
 }
 
+/**
+ * Retrieves the artifact of the given type with the given url and version
+ */
+export async function findArtifactByUrlAndVersion<T extends FhirArtifact>(
+  url: string,
+  version: string,
+  resourceType: ArtifactResourceType
+) {
+  const collection = Connection.db.collection(resourceType);
+  return collection.findOne<T>({ url, version }, { projection: { _id: 0 } });
+}
+
 /**
  * searches the database and returns an array of all resources of the given type that match the given query
  */
@@ -112,3 +125,29 @@ export async function deleteResource(id: string, resourceType: string) {
   }
   return { id, deleted: false };
 }
+
+/**
+ * Drafts an active parent artifact and all of its children (if applicable) in a batch
+ */
+export async function batchDraft(drafts: FhirArtifact[]) {
+  let error = null;
+  const results: FhirArtifact[] = [];
+  const draftSession = Connection.connection?.startSession();
+  try {
+    await draftSession?.withTransaction(async () => {
+      for (const draft of drafts) {
+        const collection = await Connection.db.collection(draft.resourceType);
+        await collection.insertOne(draft as any, { session: draftSession });
+        results.push(draft);
+      }
+    });
+    console.log('Batch draft transaction committed.');
+  } catch (err) {
+    console.log('Batch draft transaction failed: ' + err);
+    error = err;
+  } finally {
+    await draftSession?.endSession();
+  }
+  if (error) throw error;
+  return results;
+}
diff --git a/service/src/requestSchemas.ts b/service/src/requestSchemas.ts
@@ -3,6 +3,7 @@ import { z } from 'zod';
 import { BadRequestError, NotImplementedError } from './util/errorUtils';
 
 const DATE_REGEX = /([0-9]([0-9]([0-9][1-9]|[1-9]0)|[1-9]00)|[1-9]000)(-(0[1-9]|1[0-2])(-(0[1-9]|[1-2][0-9]|3[0-1]))?)/;
+const VERSION_REGEX = /^\d+\.\d+\.\d+(\.\d+|)$/;
 
 // Operation Definition: http://hl7.org/fhir/us/cqfmeasures/STU4/OperationDefinition-cqfm-package.html
 const UNSUPPORTED_PACKAGE_ARGS = [
@@ -52,6 +53,8 @@ const UNSUPPORTED_LIBRARY_SEARCH_ARGS = [...UNSUPPORTED_CORE_SEARCH_ARGS, 'conte
 
 const hasIdentifyingInfo = (args: Record<string, any>) => args.id || args.url || args.identifier;
 
+const idAndVersion = (args: Record<string, any>) => args.id && args.version;
+
 /**
  * Returns a function that checks if any unsupported params are present, then runs the
  * other passed in functions in sequence. Each catchFunction is expected to check for
@@ -90,6 +93,20 @@ export function catchMissingIdentifyingInfo(val: Record<string, any>, ctx: z.Ref
   }
 }
 
+/**
+ * Checks that id and version are included. Adds an issue to the ctx
+ * that triggers a BadRequest to be thrown if not.
+ */
+export function catchMissingIdAndVersion(val: Record<string, any>, ctx: z.RefinementCtx) {
+  if (!idAndVersion(val)) {
+    ctx.addIssue({
+      code: z.ZodIssueCode.custom,
+      params: { serverErrorCode: constants.ISSUE.CODE.REQUIRED },
+      message: 'Must provide id and version'
+    });
+  }
+}
+
 /**
  * For searches, checks that the version only appears in combination with a url. Adds an
  * issue to the ctx that triggers a BadRequest to be thrown if url is not specified when version
@@ -110,6 +127,12 @@ const stringToBool = z
   .transform(x => (typeof x === 'boolean' ? x : x === 'true'));
 const stringToNumber = z.coerce.number();
 const checkDate = z.string().regex(DATE_REGEX, 'Invalid FHIR date');
+const checkVersion = z.string().regex(VERSION_REGEX, 'Invalid Semantic Version');
+
+export const DraftArgs = z
+  .object({ id: z.string(), version: checkVersion })
+  .strict()
+  .superRefine(catchInvalidParams([hasIdentifyingInfo, catchMissingIdAndVersion]));
 
 export const IdentifyingParameters = z
   .object({

diff --git a/service/src/services/LibraryService.ts b/service/src/services/LibraryService.ts
@@ -1,5 +1,6 @@
 import { loggers, RequestArgs, RequestCtx } from '@projecttacoma/node-fhir-server-core';
 import {
+  batchDraft,
   createResource,
   deleteResource,
   findDataRequirementsWithQuery,
@@ -9,9 +10,20 @@ import {
   findResourcesWithQuery,
   updateResource
 } from '../db/dbOperations';
-import { LibrarySearchArgs, LibraryDataRequirementsArgs, PackageArgs, parseRequestSchema } from '../requestSchemas';
+import {
+  LibrarySearchArgs,
+  LibraryDataRequirementsArgs,
+  PackageArgs,
+  parseRequestSchema,
+  DraftArgs
+} from '../requestSchemas';
 import { Service } from '../types/service';
-import { createLibraryPackageBundle, createSearchsetBundle, createSummarySearchsetBundle } from '../util/bundleUtils';
+import {
+  createBatchResponseBundle,
+  createLibraryPackageBundle,
+  createSearchsetBundle,
+  createSummarySearchsetBundle
+} from '../util/bundleUtils';
 import { BadRequestError, ResourceNotFoundError } from '../util/errorUtils';
 import { getMongoQueryFromRequest } from '../util/queryUtils';
 import {
@@ -22,13 +34,17 @@ import {
   checkExpectedResourceType,
   checkFieldsForCreate,
   checkFieldsForUpdate,
-  checkFieldsForDelete
+  checkFieldsForDelete,
+  checkExistingArtifact,
+  checkIsOwned,
+  checkDraft
 } from '../util/inputUtils';
 import { v4 as uuidv4 } from 'uuid';
 import { Calculator } from 'fqm-execution';
 const logger = loggers.get('default');
 import { Filter } from 'mongodb';
-import { FhirLibraryWithDR } from '../types/service-types';
+import { CRMILibrary, FhirLibraryWithDR } from '../types/service-types';
+import { getChildren, modifyResourcesForDraft } from '../util/serviceUtils';
 
 /*
  * Implementation of a service for the `Library` resource
@@ -144,6 +160,54 @@ export class LibraryService implements Service<fhir4.Library> {
     return deleteResource(args.id, 'Library');
   }
 
+  /**
+   * result of sending a POST or GET request to:
+   * {BASE_URL}/4_0_1/Library/$draft or {BASE_URL}/4_0_1/Library/[id]/$draft
+   * drafts a new version of an existing Library artifact in active status,
+   * as well as for all resource it is composed of
+   * requires id and version parameters
+   */
+  async draft(args: RequestArgs, { req }: RequestCtx) {
+    logger.info(`${req.method} ${req.path}`);
+
+    // checks that the authoring environment variable is true
+    checkDraft();
+
+    if (req.method === 'POST') {
+      const contentType: string | undefined = req.headers['content-type'];
+      checkContentTypeHeader(contentType);
+    }
+
+    const params = gatherParams(req.query, args.resource);
+    validateParamIdSource(req.params.id, params.id);
+
+    const query = extractIdentificationForQuery(args, params);
+
+    const parsedParams = parseRequestSchema({ ...params, ...query }, DraftArgs);
+
+    const activeLibrary = await findResourceById<CRMILibrary>(parsedParams.id, 'Library');
+    if (!activeLibrary) {
+      throw new ResourceNotFoundError(`No resource found in collection: Library, with id: ${args.id}`);
+    }
+    checkIsOwned(activeLibrary, 'Child artifacts cannot be directly drafted');
+
+    await checkExistingArtifact(activeLibrary.url, parsedParams.version, 'Library');
+
+    // recursively get any child artifacts from the artifact if they exist
+    const children = activeLibrary.relatedArtifact ? await getChildren(activeLibrary.relatedArtifact) : [];
+
+    const draftArtifacts = await modifyResourcesForDraft(
+      [activeLibrary, ...(await Promise.all(children))],
+      params.version
+    );
+
+    // now we want to batch insert the parent Library artifact and any of its children
+    const newDrafts = await batchDraft(draftArtifacts);
+
+    // we want to return a Bundle containing the created artifacts
+    return createBatchResponseBundle(newDrafts);
+  }
+
   /**
    * result of sending a POST or GET request to:
    * {BASE_URL}/4_0_1/Library/$cqfm.package or {BASE_URL}/4_0_1/Library/:id/$cqfm.package