User DAO Mongoose Migration

[AustinSMueller]

No description provided.

[Copilot]

Pull request overview

This PR migrates user data access in the backend from direct/native collection usage (and prior Prisma patterns) to a Mongoose-backed UserDAO, updating service code paths and tests accordingly.

Changes:

• Reworked UserDAO to extend a new MongooseGenericDAO using a new Mongoose User model.
• Updated UserService (and some other services) to query via userDAO methods (findById, findFirst, findMany, update, updateMany, aggregate) and added findByID/findByIDs helpers.
• Updated a broad set of unit tests to mock userDAO instead of userCollection / aggregation pipelines.

Reviewed changes

Copilot reviewed 40 out of 40 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
apps/backend/services/user.js	Switches user operations to UserDAO + adds helper methods; updates several query/update paths.
apps/backend/dao/user.js	Converts UserDAO from Prisma/collection usage to Mongoose via MongooseGenericDAO.
apps/backend/mongoose/models/user.js	Adds Mongoose User schema/model aligned to existing document shape (incl. updateAt).
apps/backend/services/organization-service.js	Drops native userCollection dependency; uses UserDAO for user org updates.
apps/backend/services/application.js	Replaces direct user collection queries with userService.findByID/findByIDs and updates user lookups.
apps/backend/services/approved-studies.js	Removes native userCollection dependency; uses UserDAO for submitter lookup.
apps/backend/services/submission.js	Updates user queries to use _id-based filters with userDAO.
apps/backend/routers/graphql-router.js	Updates service constructors to match new signatures (no user collection injection).
apps/backend/app.js	Updates service wiring for organization/approved-studies/user services (no user collection injection).
apps/backend/test/dao/dao.user.test.js	Replaces Prisma-based DAO tests with Mongoose model mock coverage for UserDAO.
apps/backend/test/graphql-queries/batch-job.test.js	Adjusts UserService construction to new constructor signature.
apps/backend/test/services/user.updateUserInstitution.test.js	Updates tests to mock userDAO.updateMany and new error-handling behavior.
apps/backend/test/services/user.updateUserInfo.approvedStudyStatus.test.js	Updates tests to assert userDAO.update usage; adds rejection test for UPDATE_FAILED.
apps/backend/test/services/user.updateMyUser.test.js	Updates test scaffolding to use userDAO.findById/update semantics.
apps/backend/test/services/user.requestAccess.test.js	Uses userDAO.getUsersByNotifications mocking instead of user collection.
apps/backend/test/services/user.reopenOwner.test.js	Updates UserService constructor call signature.
apps/backend/test/services/user.listUsers.test.js	Replaces aggregation expectations with userDAO.findMany expectations.
apps/backend/test/services/user.listActiveDCPs.test.js	Updates constructor + DAO mocking to findMany.
apps/backend/test/services/user.listActiveCurators.test.js	Updates constructor + DAO mocking to findMany.
apps/backend/test/services/user.isUserPrimaryContact.test.js	Updates constructor + DAO mocking to findMany.
apps/backend/test/services/user.grantToken.test.js	Updates tests to assert userDAO.update usage and UPDATE_FAILED behavior.
apps/backend/test/services/user.getUsersByIDs.test.js	Updates construction comments/signature for UserService.
apps/backend/test/services/user.getUser.test.js	Switches from mocked implementation to real getUser bound to instance; updates mocks to userDAO.findFirst.
apps/backend/test/services/user.getFedLeads.test.js	Replaces aggregation with userDAO.findMany expectations.
apps/backend/test/services/user.getDCPs.test.js	Replaces aggregation with userDAO.findMany expectations.
apps/backend/test/services/user.getCollaboratorsByStudyID.test.js	Replaces aggregation pipeline usage with userDAO.findMany expectations.
apps/backend/test/services/user.getAdminPBACUsers.test.js	Replaces aggregation with userDAO.findMany expectations.
apps/backend/test/services/user.getAdmin.test.js	Replaces aggregation with userDAO.findMany expectations.
apps/backend/test/services/user.disableInactiveUsers.test.js	Updates to userDAO.updateMany returning {count} and userDAO.findMany for post-update fetch.
apps/backend/test/services/user.checkForInactiveUsers.test.js	Updates aggregation execution to userDAO.aggregate instead of native collection.
apps/backend/test/services/submission.editSubmissionCollaborators.test.js	Updates user lookup filter from {id: ...} to {_id: ...}.
apps/backend/test/services/data-submission.test.js	Updates user lookup filter from {id: ...} to {_id: ...}.
apps/backend/test/services/organization.service.test.js	Updates Organization constructor signature and asserts userDAO.updateUserOrg integration.
apps/backend/test/services/approved-studies.test.js	Updates ApprovedStudiesService constructor signature (no user collection).
apps/backend/test/services/approved-studies-notification-error-handling.test.js	Updates ApprovedStudiesService constructor signature (no user collection).
apps/backend/test/services/application.test.js	Refactors mocked userService interface away from userCollection to findByID/findByIDs.
apps/backend/test/services/application.remindApplicationSubmission.test.js	Refactors mocked userService interface away from userCollection to findByID/findByIDs.
apps/backend/test/services/application.deleteInactiveApplications.test.js	Refactors mocked userService interface away from userCollection.aggregate to findByIDs.

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