Clean up mongo query and fix aggregation

service/src/db/dbOperations.ts

@@ -20,7 +20,7 @@ export async function findResourcesWithQuery<T extends fhir4.FhirResource[]>(
   resourceType: FhirResourceType
 ) {
   const collection = Connection.db.collection(resourceType);
-  const projection = { 'data._id': 0, 'data._dataRequirements': 0 };
+  const projection = { _id: 0, _dataRequirements: 0 };
   const pagination: any = query.skip ? [{ $skip: query.skip }, { $limit: query.limit }] : [];
   query._dataRequirements = { $exists: false };
   query._summary = { $exists: false };
@@ -31,13 +31,13 @@ export async function findResourcesWithQuery<T extends fhir4.FhirResource[]>(
   return collection
     .aggregate<{ metadata: { total: number }[]; data: T }>([
       { $match: query },
+      { $project: projection },
       {
         $facet: {
           metadata: [{ $count: 'total' }],
           data: pagination
         }
-      },
-      { $project: projection }
+      }
     ])
     .toArray();
 }
@@ -46,7 +46,7 @@ export async function findResourcesWithQuery<T extends fhir4.FhirResource[]>(
  * searches the database and returns an array objects that contain metadata and each respective resource of the given type that match the given query
  * but the resources only include the elements specified by the _elements parameter
  */
-export async function findResourceElementsWithQuery<T extends fhir4.FhirResource>(
+export async function findResourceElementsWithQuery<T extends fhir4.FhirResource[]>(
   query: Filter<any>,
   resourceType: FhirResourceType
 ) {
@@ -57,7 +57,7 @@ export async function findResourceElementsWithQuery<T extends fhir4.FhirResource
     resourceType === 'Library' ? { status: 1, resourceType: 1, type: 1 } : { status: 1, resourceType: 1 };
 
   (query._elements as string[]).forEach(elem => {
-    projection[elem] = 1;
+    projection[`${elem}`] = 1;
   });
   projection['_id'] = 0;
 
@@ -72,13 +72,13 @@ export async function findResourceElementsWithQuery<T extends fhir4.FhirResource
   return collection
     .aggregate<{ metadata: { total: number }[]; data: T }>([
       { $match: query },
+      { $project: projection },
       {
         $facet: {
           metadata: [{ $count: 'total' }],
           data: pagination
         }
-      },
-      { $project: projection }
+      }
     ])
     .toArray();
 }
@@ -93,6 +93,8 @@ export async function findResourceCountWithQuery(query: Filter<any>, resourceTyp
   query._dataRequirements = { $exists: false };
   query._summary = { $exists: false };
   query._elements = { $exists: false };
+  query.limit = { $exists: false };
+  query.skip = { $exists: false };
   return collection.countDocuments(query);
 }
 

service/src/services/LibraryService.ts

@@ -61,8 +61,8 @@ export class LibraryService implements Service<fhir4.Library> {
     // then return a searchset bundle that includes only those elements
     // on those resource entries
     else if (parsedQuery._elements) {
-      const result = await findResourceElementsWithQuery<fhir4.Library>(mongoQuery, 'Library');
-      const entries = result.map(r => r.data);
+      const result = await findResourceElementsWithQuery<fhir4.Library[]>(mongoQuery, 'Library');
+      const entries = result[0].data;
       // add the SUBSETTED tag to the resources returned by the _elements parameter
       entries.map(e => {
         if (e.meta) {

service/src/services/MeasureService.ts

@@ -62,8 +62,8 @@ export class MeasureService implements Service<fhir4.Measure> {
     // then return a searchset bundle that includes only those elements
     // on those resource entries
     else if (parsedQuery._elements) {
-      const result = await findResourceElementsWithQuery<fhir4.Measure>(mongoQuery, 'Measure');
-      const entries = result.map(r => r.data);
+      const result = await findResourceElementsWithQuery<fhir4.Measure[]>(mongoQuery, 'Measure');
+      const entries = result[0].data;
       // add the SUBSETTED tag to the resources returned by the _elements parameter
       entries.map(e => {
         if (e.meta) {

service/src/util/queryUtils.ts

@@ -8,43 +8,38 @@ const STRING_TYPE_PARAMS = ['name', 'title', 'description', 'version'];
  * a usable mongo query
  */
 export function getMongoQueryFromRequest(query: RequestQuery): Filter<any> {
-  const pageSize = (query['_count'] && parseInt(query['_count'] as string)) || 100; // set a base limit of 100
-  if (!query['page']) query['page'] = '1'; // default to first page
-
-  //TODO: Handle potential for query value to be array
-  return Object.keys(query).reduce((mf: Filter<any>, key: string) => {
+  const pageSize = parseInt((query['_count'] || '50') as string); //default to limit 50
+  const filter: Filter<any> = { limit: pageSize, skip: (parseInt((query['page'] || '1') as string) - 1) * pageSize }; //default to first page
+  Object.keys(query).forEach((key: string) => {
+    //TODO: Handle potential for query value to be array
     if (!query[key] || Array.isArray(query[key])) {
       throw new NotImplementedError(
         `Retrieved undefined or multiple arguments for query param: ${key}. Multiple arguments for the same query param and undefined arguments are not supported.`
       );
     } else if (STRING_TYPE_PARAMS.includes(key)) {
       // For string arguments in query they may match just the start of a string and are case insensitive
-      mf[key] = { $regex: `^${query[key]}`, $options: 'i' };
+      filter[key] = { $regex: `^${query[key]}`, $options: 'i' };
     } else if (key === 'identifier') {
       // Identifier can check against the identifier.system, identifier.value, or both on a resource
       const iden = query.identifier as string;
       const splitIden = iden.split('|');
       if (splitIden.length === 1) {
-        mf['identifier.value'] = splitIden[0];
+        filter['identifier.value'] = splitIden[0];
       } else if (splitIden[0] === '') {
-        mf['identifier.value'] = splitIden[1];
+        filter['identifier.value'] = splitIden[1];
       } else if (splitIden[1] === '') {
-        mf['identifier.system'] = splitIden[0];
+        filter['identifier.system'] = splitIden[0];
       } else {
-        mf['identifier.system'] = splitIden[0];
-        mf['identifier.value'] = splitIden[1];
+        filter['identifier.system'] = splitIden[0];
+        filter['identifier.value'] = splitIden[1];
       }
     } else if (key === '_elements') {
       const elements = query[key] as string;
-      mf[key] = elements.split(',');
-    } else if (key === '_count') {
-      mf['limit'] = pageSize;
-    } else if (key === 'page') {
-      mf['skip'] = (parseInt((query[key] || '1') as string) - 1) * pageSize; //default to first page
-    } else {
-      // Otherwise no parsing necessary
-      mf[key] = query[key];
+      filter[key] = elements.split(',');
+    } else if (key !== '_count' && key !== 'page') {
+      // Skip _count and page, otherwise no parsing necessary
+      filter[key] = query[key];
     }
-    return mf;
-  }, {});
+  });
+  return filter;
 }

service/test/services/LibraryService.test.ts

@@ -434,7 +434,7 @@ describe('LibraryService', () => {
         .then(response => {
           expect(response.body.issue[0].code).toEqual('invalid');
           expect(response.body.issue[0].details.text).toEqual(
-            'Multiple resources found in collection: Library, with identifier: http://example.com/libraryWithSameSystem| and page: 1. /Library/$cqfm.package operation must specify a single Library'
+            'Multiple resources found in collection: Library, with identifier: http://example.com/libraryWithSameSystem|. /Library/$cqfm.package operation must specify a single Library'
           );
         });
     });
@@ -496,7 +496,7 @@ describe('LibraryService', () => {
         .then(response => {
           expect(response.body.issue[0].code).toEqual('not-found');
           expect(response.body.issue[0].details.text).toEqual(
-            'No resource found in collection: Library, with id: testLibraryWithDeps and url: http://example.com/invalid and page: 1'
+            'No resource found in collection: Library, with id: testLibraryWithDeps and url: http://example.com/invalid'
           );
         });
     });
@@ -516,7 +516,7 @@ describe('LibraryService', () => {
         .then(response => {
           expect(response.body.issue[0].code).toEqual('not-found');
           expect(response.body.issue[0].details.text).toEqual(
-            'No resource found in collection: Library, with id: invalid and url: http://example.com/invalid and page: 1'
+            'No resource found in collection: Library, with id: invalid and url: http://example.com/invalid'
           );
         });
     });

service/test/services/MeasureService.test.ts

@@ -437,7 +437,7 @@ describe('MeasureService', () => {
         .then(response => {
           expect(response.body.issue[0].code).toEqual('not-found');
           expect(response.body.issue[0].details.text).toEqual(
-            'No resource found in collection: Measure, with id: testWithUrl and url: http://example.com/invalid and page: 1'
+            'No resource found in collection: Measure, with id: testWithUrl and url: http://example.com/invalid'
           );
         });
     });
@@ -499,7 +499,7 @@ describe('MeasureService', () => {
         .then(response => {
           expect(response.body.issue[0].code).toEqual('not-found');
           expect(response.body.issue[0].details.text).toEqual(
-            'No resource found in collection: Measure, with id: invalid and url: http://example.com/invalid and page: 1'
+            'No resource found in collection: Measure, with id: invalid and url: http://example.com/invalid'
           );
         });
     });

service/test/util/queryUtils.test.ts

@@ -8,16 +8,17 @@ const QUERY_WITH_SYSTEM_AND_CODE_IDEN = { url: 'http://example.com', identifier:
 const QUERY_WITH_STRING_PARAM = { url: 'http://example.com', version: 'test' };
 const QUERY_WITH_MULTIPLE_STRING_PARAM = { url: 'http://example.com', version: ['test', '...anotherTest?'] };
 
-const EXPECTED_QUERY_WITH_NO_IDEN = { skip: 0, url: 'http://example.com' };
-const EXPECTED_QUERY_WITH_CODE_IDEN = { skip: 0,  url: 'http://example.com', 'identifier.value': 'testCode' };
-const EXPECTED_QUERY_WITH_SYSTEM_IDEN = { skip: 0, url: 'http://example.com', 'identifier.system': 'testSystem' };
+const EXPECTED_QUERY_WITH_NO_IDEN = { limit: 50, skip: 0, url: 'http://example.com' };
+const EXPECTED_QUERY_WITH_CODE_IDEN = { limit: 50, skip: 0,  url: 'http://example.com', 'identifier.value': 'testCode' };
+const EXPECTED_QUERY_WITH_SYSTEM_IDEN = { limit: 50, skip: 0, url: 'http://example.com', 'identifier.system': 'testSystem' };
 const EXPECTED_QUERY_WITH_SYSTEM_AND_CODE_IDEN = {
+  limit: 50, 
   skip: 0, 
   url: 'http://example.com',
   'identifier.system': 'testSystem',
   'identifier.value': 'testCode'
 };
-const EXPECTED_QUERY_WITH_STRING_PARAM = { skip: 0, url: 'http://example.com', version: { $regex: '^test', $options: 'i' } };
+const EXPECTED_QUERY_WITH_STRING_PARAM = { limit: 50, skip: 0, url: 'http://example.com', version: { $regex: '^test', $options: 'i' } };
 
 describe('getMongoQueryFromRequest', () => {
   it('correctly parses a query with no identifier field', () => {