Feat upgrade mongo

development-environment/clear-all-data.sh

@@ -15,7 +15,7 @@ print_usage_and_exit () {
 DIR=$(pwd)
 
 # It's fine if these fail as it might be that the databases do not exist at this point
-docker run --rm --network=opencrvs_default mongo:4.4 mongo --host mongo1 --eval "\
+docker run --rm --network=opencrvs_default mongo:5.0 mongo --host mongo1 --eval "\
 db.getSiblingDB('hearth-dev').dropDatabase();\
 db.getSiblingDB('openhim-dev').dropDatabase();\
 db.getSiblingDB('user-mgnt').dropDatabase();\

docker-compose.deps.yml

@@ -10,7 +10,7 @@ volumes:
   metricbeat:
 services:
   mongo1:
-    image: mongo:4.4
+    image: mongo:5.0
     restart: unless-stopped
 
   redis:

packages/events/package.json

@@ -20,7 +20,7 @@
     "@trpc/server": "^11.0.0-rc.532",
     "app-module-path": "^2.2.0",
     "envalid": "^8.0.0",
-    "mongodb": "6.9.0",
+    "mongodb": "6.11.0",
     "superjson": "1.9.0-0",
     "tsconfig-paths": "^3.13.0",
     "zod": "^3.23.8"

packages/metrics/package.json

@@ -34,7 +34,7 @@
     "jsonwebtoken": "^9.0.0",
     "jwt-decode": "^3.0.0",
     "lodash": "^4.17.21",
-    "mongodb": "^4.17.1",
+    "mongodb": "6.11.0",
     "mongoose": "^6.11.3",
     "node-fetch": "^2.6.7",
     "pino": "^7.0.0",

packages/migration/package.json

@@ -33,15 +33,15 @@
     "influx": "^5.0.7",
     "is-svg": "^4.3.2",
     "lodash-es": "^4.17.21",
-    "migrate-mongo": "^10.0.0",
+    "migrate-mongo": "^11.0.0",
     "minio": "^7.0.33",
     "mongoose": "^6.11.3",
     "tsx": "^4.15.7",
     "uuid": "^3.2.1"
   },
   "devDependencies": {
     "@types/fhir": "0.0.30",
-    "mongodb": "^4.17.1",
+    "mongodb": "6.11.0",
     "prettier": "^2.5.0",
     "rimraf": "^5.0.0",
     "typescript": "5.6.3"

packages/migration/src/migrations/application-config/20230518055204-upload-certificate-templates-to-minio.ts

@@ -11,7 +11,7 @@
 import isSvg from 'is-svg'
 import { uploadSvgToMinio } from '../../utils/minio-helper.js'
 import { ICertificateTemplateData } from '../../utils/migration-interfaces.js'
-import { Db, MongoClient } from 'mongodb'
+import { Db, MongoClient, ObjectId } from 'mongodb'
 
 export const up = async (db: Db, client: MongoClient) => {
   const session = client.startSession()
@@ -32,7 +32,7 @@ export const up = async (db: Db, client: MongoClient) => {
           const uri = await uploadSvgToMinio(svgCode)
           await db
             .collection('certificates')
-            .updateOne({ _id }, { $set: { svgCode: uri } })
+            .updateOne({ _id: new ObjectId(_id) }, { $set: { svgCode: uri } })
         } catch (err) {
           console.log(`Saving certificate template failed with error: ${err}`)
         }

packages/migration/src/migrations/hearth/20221017133354-restore-supporting-document.ts

@@ -60,7 +60,7 @@ export const up = async (db: Db, client: MongoClient) => {
           )
           if (hasDocumentSection) {
             await db
-              .collection('Composition')
+              .collection<fhir.Composition>('Composition')
               .updateOne(
                 { id: compositionHistory[correctionIndex].id },
                 { $push: { section: hasDocumentSection } }

packages/migration/src/migrations/hearth/20230127063226-update-practitioner-role.ts

@@ -114,21 +114,23 @@ export const up = async (db: Db, client: MongoClient) => {
                 { $set: { 'code.1.coding.0.code': titleCase(typeCode) } }
               )
           } else {
-            await db.collection('PractitionerRole').updateOne(
-              { id: practitionerRole?.id },
-              {
-                $push: {
-                  code: {
-                    coding: [
-                      {
-                        system: 'http://opencrvs.org/specs/types',
-                        code: JSON.stringify(usersLabels[roleCode])
-                      }
-                    ]
+            await db
+              .collection<fhir.PractitionerRole>('PractitionerRole')
+              .updateOne(
+                { id: practitionerRole?.id },
+                {
+                  $push: {
+                    code: {
+                      coding: [
+                        {
+                          system: 'http://opencrvs.org/specs/types',
+                          code: JSON.stringify(usersLabels[roleCode])
+                        }
+                      ]
+                    }
                   }
                 }
-              }
-            )
+              )
           }
         }
         skip += limit

packages/migration/src/migrations/hearth/20230602090436-update-identifier-with-system.ts

@@ -8,14 +8,12 @@
  *
  * Copyright (C) The OpenCRVS Authors located at https://github.com/opencrvs/opencrvs-core/blob/master/AUTHORS.
  */
-import { Db, MongoClient } from 'mongodb'
-import * as mongoose from 'mongoose'
+import { Db, MongoClient, ObjectId } from 'mongodb'
 
 const USER_MGNT_MONGO_URL =
   process.env.USER_MGNT_MONGO_URL || 'mongodb://localhost/user-mgnt'
 
 export const up = async (db: Db, client: MongoClient) => {
-  const ObjectId = mongoose.Types.ObjectId
   const session = client.startSession()
   const userManagementClient = new MongoClient(USER_MGNT_MONGO_URL)
   const connectedUserManagementClient = await userManagementClient.connect()

packages/migration/src/migrations/hearth/20231024153838-partof-to-address.ts

@@ -9,7 +9,7 @@
  * Copyright (C) The OpenCRVS Authors located at https://github.com/opencrvs/opencrvs-core/blob/master/AUTHORS.
  */
 
-import { Db, MongoClient } from 'mongodb'
+import { Db, MongoClient, ObjectId } from 'mongodb'
 import { isEmpty } from 'lodash-es'
 
 function derivePartOfFromAddress(address: fhir.Address) {
@@ -57,7 +57,7 @@ export const up = async (db: Db, client: MongoClient) => {
     })
 
     patients.updateOne(
-      { _id: patient._id },
+      { _id: new ObjectId(patient._id as string) },
       { $set: { address: updatedAddresses } }
     )
   })
@@ -73,7 +73,7 @@ export const up = async (db: Db, client: MongoClient) => {
 
     if (partOf) {
       locations.updateOne(
-        { _id: location._id },
+        { _id: new ObjectId(location._id as string) },
         { $set: { partOf: { reference: `Location/${partOf}` } } }
       )
     }
@@ -103,7 +103,7 @@ export const down = async (db: Db, client: MongoClient) => {
     })
 
     patients.updateOne(
-      { _id: patient._id },
+      { _id: new ObjectId(patient._id as string) },
       { $set: { address: updatedAddresses } }
     )
   })

packages/migration/src/migrations/user-mgnt/20231106130956-email-mobile-unique-index.ts

@@ -17,7 +17,7 @@ export const up = async (db: Db, client: MongoClient) => {
     await session.withTransaction(async () => {
       console.log('Checking if mobile field already have indices')
       const indexes = Object.keys(
-        (await db.collection('users').stats()).indexSizes
+        (await db.command({ collStats: 'users' })).indexSizes
       )
       const mobileHasIndex = indexes.some(
         (index) => index.split('_')[0] === ('mobile' as const)

packages/migration/src/migrations/user-mgnt/20231117135646-add-bypass-rate-limit-scope.ts

@@ -22,6 +22,6 @@ export const up = async (db: Db, client: MongoClient) => {
 
 export const down = async (db: Db, client: MongoClient) => {
   await db
-    .collection('users')
+    .collection<fhir.Practitioner>('users')
     .updateOne({ username: 'o.admin' }, { $pull: { scope: 'bypassratelimit' } })
 }

packages/migration/src/utils/openhim-helpers.ts

@@ -80,7 +80,7 @@ export async function addRouteToChannel(
   route: Route
 ) {
   await db
-    .collection('channels')
+    .collection<Channel>('channels')
     .updateOne({ name: channelName }, { $push: { routes: route } })
 }
 
@@ -90,7 +90,7 @@ export async function removeRouteFromChannel(
   routeName: string
 ) {
   await db
-    .collection('channels')
+    .collection<Channel>('channels')
     .updateOne(
       { name: channelName },
       { $pull: { routes: { name: routeName } } }

packages/search/package.json

@@ -30,7 +30,7 @@
     "joi": "^17.3.0",
     "jsonwebtoken": "^9.0.0",
     "jwt-decode": "^3.0.0",
-    "mongodb": "4.17.2",
+    "mongodb": "6.11.0",
     "node-fetch": "^2.6.7",
     "pino": "^7.0.0",
     "short-uid": "^0.1.0",

yarn.lock

@@ -5798,7 +5798,7 @@
   dependencies:
     sparse-bitfield "^3.0.3"
 
-"@mongodb-js/saslprep@^1.1.5":
+"@mongodb-js/saslprep@^1.1.5", "@mongodb-js/saslprep@^1.1.9":
   version "1.1.9"
   resolved "https://registry.yarnpkg.com/@mongodb-js/saslprep/-/saslprep-1.1.9.tgz#e974bab8eca9faa88677d4ea4da8d09a52069004"
   integrity sha512-tVkljjeEaAhCqTzajSdgbQ6gE6f3oneVwa3iXR6csiEwXXOFsiC6Uh9iAjAhXPtqa/XMDHWjjeNH/77m/Yq2dw==
@@ -11337,6 +11337,11 @@ bson@^4.7.2:
   dependencies:
     buffer "^5.6.0"
 
+bson@^6.10.0:
+  version "6.10.0"
+  resolved "https://registry.yarnpkg.com/bson/-/bson-6.10.0.tgz#559c767cc8b605c3ab14e5896214c8f2abdd6a12"
+  integrity sha512-ROchNosXMJD2cbQGm84KoP7vOGPO6/bOAW0veMMbzhXLqoZptcaYRVLitwvuhwhjjpU1qP4YZRWLhgETdgqUQw==
+
 bson@^6.7.0:
   version "6.9.0"
   resolved "https://registry.yarnpkg.com/bson/-/bson-6.9.0.tgz#2be50049430dceaa9300402520fe03e4ed5fdfd6"
@@ -19136,10 +19141,10 @@ micromatch@~4.0.8:
     braces "^3.0.3"
     picomatch "^2.3.1"
 
-migrate-mongo@^10.0.0:
-  version "10.0.0"
-  resolved "https://registry.npmjs.org/migrate-mongo/-/migrate-mongo-10.0.0.tgz"
-  integrity sha512-QA/bBKNMq/FmuK3fDbgwfNoW2riiU1wLDWGXv/tGhUItPLGqcciPPmu29SrnYAzRKMOVaGEXxzmrBs1zp5cQ7Q==
+migrate-mongo@^11.0.0:
+  version "11.0.0"
+  resolved "https://registry.yarnpkg.com/migrate-mongo/-/migrate-mongo-11.0.0.tgz#d1b2291624fe8e134a0666ca77ad2fa18f42e337"
+  integrity sha512-GB/gHzUwp/fL1w6ksNGihTyb+cSrm6NbVLlz1OSkQKaLlzAXMwH7iKK2ZS7W5v+I8vXiY2rL58WTUZSAL6QR+A==
   dependencies:
     cli-table3 "^0.6.1"
     commander "^9.1.0"
@@ -19499,7 +19504,7 @@ mongodb-memory-server@^10.1.2:
     mongodb-memory-server-core "10.1.2"
     tslib "^2.7.0"
 
-[email protected], mongodb@^4.17.1:
+[email protected]:
   version "4.17.2"
   resolved "https://registry.yarnpkg.com/mongodb/-/mongodb-4.17.2.tgz#237c0534e36a3449bd74c6bf6d32f87a1ca7200c"
   integrity sha512-mLV7SEiov2LHleRJPMPrK2PMyhXFZt2UQLC4VD4pnth3jMjYKHhtqfwwkkvS/NXuo/Fp3vbhaNcXrIDaLRb9Tg==
@@ -19511,13 +19516,13 @@ [email protected], mongodb@^4.17.1:
     "@aws-sdk/credential-providers" "^3.186.0"
     "@mongodb-js/saslprep" "^1.1.0"
 
-mongodb@6.9.0:
-  version "6.9.0"
-  resolved "https://registry.yarnpkg.com/mongodb/-/mongodb-6.9.0.tgz#743ebfff6b3c14b04ac6e00a55e30d4127d3016d"
-  integrity sha512-UMopBVx1LmEUbW/QE0Hw18u583PEDVQmUmVzzBRH0o/xtE9DBRA5ZYLOjpLIa03i8FXjzvQECJcqoMvCXftTUA==
+mongodb@6.11.0:
+  version "6.11.0"
+  resolved "https://registry.yarnpkg.com/mongodb/-/mongodb-6.11.0.tgz#d09bc055e1e784849279dc41eb2cd1537a0488a0"
+  integrity sha512-yVbPw0qT268YKhG241vAMLaDQAPbRyTgo++odSgGc9kXnzOujQI60Iyj23B9sQQFPSvmNPvMZ3dsFz0aN55KgA==
   dependencies:
-    "@mongodb-js/saslprep" "^1.1.5"
-    bson "^6.7.0"
+    "@mongodb-js/saslprep" "^1.1.9"
+    bson "^6.10.0"
     mongodb-connection-string-url "^3.0.0"
 
 mongodb@^6.9.0: