Create Patient Service and Implement CRUD operations

[cgolemme]

Summary

This PR adds endpoints to the bulk-export-server to handle operations related to Patients. Adds operations to create, get, update and delete patients on the server. This PR also adds Group delete endpoint. [host]/Patient and [host]/Group now correctly return a searchset as per fhir spec, https://hl7.org/fhir/R4/http.html#search.

JIRA Issue

New behavior

bulk-export-server now has CRUD operations for Patients

• GET : [host]/Patient
• GET : [host]/Patient/[patientId]
• POST : [host]/Patient
• PUT : [host]/Patient/[patientID]
• DELETE : [host]/Patient/[patientID]

Now has new delete operation for Group

• DELETE : [host]/Group/[groupID]

Endpoints that find multiple Patients or Groups from the server, GET : [host]/Patient and GET : [host]/Group, now return a searchset object instead of a json list of fhir Patient or Group objects.

Code changes

• .eslintrc.json and .prettierignore were changed to add ecqm-content-r4-2021 to the excluded folders because they were causing warnings with eslint and prettier.
• src/server/app.js was changed to add the new patient endpoints and new group endpoint to the server.
• src/services/group.service.js: updated some comments to be more specific, wrapped the /Group get endpoint in a search set object, added new function for DELETE endpoint.
• src/services/patient.service.js was created to implement functions that will interact with the database to fulfill the CRUD operations requested when a user accesses the endpoints for Patients.
• test/fixtures/updatedTestPatient.json was created to test the PUT endpoint.
• test/services/patient.service.test.js are tests for the patient.service.js operations that follows closely from the group.service.test.js file.
• src/util/bundleUtils.js: created to generate the searchset bundle object that wraps the response from the server for the /Patient and /Group endpoints.
• src/util/mongo.controller.js: added a default projection to filter out mongo-generated ids from the server's responses to all operations.
• test/services/group.service.test.js: changed /Group test to interact with new searchset response from server

Testing guidance

• run npm run check
• Check that prettier and eslint cause no errors
• Check that all the tests pass
• Test endpoints on Insomnia

[github-actions]

Coverage report

St.❔	Category	Percentage	Covered / Total
🟡	Statements	76.59% (+1.7% 🔼)	543/709
🟡	Branches	62.58% (+0.94% 🔼)	189/302
🟡	Functions	75.44% (+2.8% 🔼)	86/114
🟡	Lines	76.9% (+1.71% 🔼)	536/697

Show new covered files 🐣

St.❔	File	Statements	Branches	Functions	Lines
🟢	... / patient.service.js	96.55%	87.5%	100%	96.55%

Test suite run success

89 tests passing in 8 suites.

Report generated by 🧪jest coverage report action from 957a8ab

[elsaperelli]

Lgtm!

The only thing I would change in the future (not a big deal for this one at all) but just make sure that you include in the testing guidance to try out the new endpoints in Insomnia! (This should be kinda obvious but good to add)

[hossenlopp]

The listing of all patients is returning a JSON Array this should be a searchset Bundle instead. See https://hl7.org/fhir/R4/http.html#search for more info.

Additionally we should have the internal mongo _ids projected out of the responses.

[cgolemme]

I made the requested changes. One potentially weird thing that I did was call const found = await findResourceById(request.params.groupId, 'Group'); in the group and patient delete functions in order to correctly return the 404 that we want because there is nowhere in the call stack of removeReasource that could throw an error the resource to remove is not found.

[elsaperelli]

Just one small comment but otherwise almost good to go!

[elsaperelli]

Lgtm! Way to be flexible!!