Updates for validation

[lmd59]

Summary

Update the qpp_qicore.yaml file to pass qicore validation

New behavior

Generated synthea files pass validation (with a few potential exceptions).

Code changes

• Adds or updates flexporter instructions for DeviceRequest, AdverseEvent, and Task

Testing guidance

1. Create large set of patients using qpp mapping file from Add QPP profiles to flexporter mapping file #52
   a. Use the randomcode_updates branch or main if Flexporter - Update randomCode fn to take output type as an optional second param synthetichealth/synthea#1527 has been merged
   b. Follow additional instructions from the bulk PR above
   c. Set exporter.fhir.us_core_version = 3.1.1 in the synthea.properties file
   d. Use -p to specify the number of patients, i.e. ./run_synthea -fm ../../bulk-export-server/synthea/qpp_qicore.yaml -p 10

2. Use HAPI FHIR validator to validate the patients.
   a. Use https://github.com/hapifhir/org.hl7.fhir.validator-wrapper/releases/latest/download/validator_cli.jar
   b. Run with java -jar validator_cli.jar synthea/output/fhir/ -ig http://hl7.org/fhir/us/qicore/ImplementationGuide/hl7.fhir.us.qicore%7C4.1.1 -extension any -display-issues-are-warnings -sct us

Most issues are solved by the settings above, but some remaining issues that don’t effect calculation may include:
i. "Unknown code 'X9999-"* from the loinc code set

[github-actions]

Coverage report

St.❔	Category	Percentage	Covered / Total
🟡	Statements	75.63%	574/759
🟡	Branches	63.19%	206/326
🟡	Functions	75.83%	91/120
🟡	Lines	75.87%	566/746

Test suite run success

95 tests passing in 8 suites.

Report generated by 🧪jest coverage report action from 52c586b

[elsaperelli]

One question:

1. When I ran the validator, it looks like I got errors with .recorded attributes on Procedure and Immunization resources? Is this expected?

Two suggestions:

1. I think the -ig parameter in the PR description is wrong- I think it should be -ig hl7.fhir.us.qicore#4.1.1. Not a huge deal, but I mention this because maybe some super quick validator instructions could be added to the synthea/README.md here! Not totally necessary but may be useful info in the future.

2. IF you end up adding something brief to the README, I would add the -html-output parameter. This is something I found in the Validator docs here and made my life a lot easier. I actually think you probably used this input, it just wasn't reflected in the description.

[elsaperelli]

One question:

1. When I ran the validator, it looks like I got errors with .recorded attributes on Procedure and Immunization resources? Is this expected?

Two suggestions:

1. I think the -ig parameter in the PR description is wrong- I think it should be -ig hl7.fhir.us.qicore#4.1.1. Not a huge deal, but I mention this because maybe some super quick validator instructions could be added to the synthea/README.md here! Not totally necessary but may be useful info in the future.
2. IF you end up adding something brief to the README, I would add the -html-output parameter. This is something I found in the Validator docs here and made my life a lot easier. I actually think you probably used this input, it just wasn't reflected in the description.

Update:

1. No longer get that error! I needed to run the following command: java -jar validator_cli.jar synthea/output/fhir/ -ig http://hl7.org/fhir/us/qicore/ImplementationGuide/hl7.fhir.us.qicore%7C4.1.1 -extension any -display-issues-are-warnings -sct us -html-output output.html -version 4.0.1 (Need the http url, not hl7.fhir.us.qicore#4.1.1 AND -version 4.0.1)
2. I would still add something to the README so that we can keep track of the -ig, -version, -html-output, and clear-tx-cache inputs.

[elsaperelli]

Besides a suggestion to add a bit of information to the README, this is looking good to me!!

[elsaperelli]

Thanks for adding that stuff to the README! I think future us will thank now us 😄 Lgtm!