By patient

[lmd59]

Summary

Support option for exporting files by patient (rather than by type)

New behavior

POST or GET requests sent to either the Patient or Group (but not System) $export endpoint may include a parameter _bySubject with value Patient which causes an export kickoff that will create files with resources grouped by patient. Each file is named based on the patient id, and the resulting stored bulk export status has a byPatient flag set to true. This may be used in combination with the patient parameter to create files for specified patients.

Code changes

• Update readme
• Update exportWorker to pass bySubject option through job data
• Update export service to handle _bySubject validation and pass it to the job and bulk export request.
• Update exportToNDJSON to create byPatient ndjson files with subject headers and to take in job data as options rather than individual parameters
• Update mongo controller to create bulk export request with byPatient flag
• Update tests for new functionality as well as fix some testing issues with not clearing tmp files in the exportToNDJson test file.
• Update: Update bulkstatus service to add appropriate inputDetails to the import manifest for the kickoff import endpoint

Testing guidance

• npm run check
• npm run start
• Test the _bySubject=Patient parameter with the typical kickoff/status/file-fetch $export workflow. Try some other parameter combinations. Attached Insomnia package has a couple of requests as a jumping off point.
  _bySubject-Insomnia.json

Update: Also test kickoff import as described here: #47 . Test with deqm-test-server branch here: projecttacoma/deqm-test-server#156

Note: There are a couple of TODO questions left that aren't really to do with this task but are potentially small things we might want to spruce up in other parts of the code. Interested in opinions on whether we want to address those things as well either in this PR or maybe a future general code cleanup task.

[github-actions]

Coverage report

St.❔	Category	Percentage	Covered / Total
🟡	Statements	75.59% (+1.24% 🔼)	573/758
🟡	Branches	63.19% (+2.22% 🔼)	206/326
🟡	Functions	75.63% (+1.49% 🔼)	90/119
🟡	Lines	75.87% (+1.25% 🔼)	566/746

Show files with reduced coverage 🔻

St.❔	File	Statements	Branches	Functions	Lines
🟡	... / bulkstatus.service.js	61.76% (-1.87% 🔻)	59.38% (-3.96% 🔻)	66.67%	61.76% (-1.87% 🔻)

Test suite run success

95 tests passing in 8 suites.

Report generated by 🧪jest coverage report action from 28e5af2

[elsaperelli]

Woo great functionality! Just some small comments :)

[elsaperelli]

Yeah good call, looks like we can remove it and the one below but I would do some quick testing to be sure

[lmd59]

Updated this and did some testing across POST/GET for _type and _elements

[elsaperelli]

Lgtm!