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person to FHIR patient #4842

Merged
merged 56 commits into from
Dec 20, 2022
Merged

person to FHIR patient #4842

merged 56 commits into from
Dec 20, 2022

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BobanL
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@BobanL BobanL commented Dec 12, 2022 •
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BACKEND PULL REQUEST

Related Issue

Changes Proposed

  • A new toFhir method was added to convert our models into FHIR models.

Additional Information

  • We are using the Hapi FHIR structures library as recommended.
  • For Race we are using local race (as recommended by report stream), tribal affilation we are using us-core, and ethnicity we are using us-core
  • Update wiremock dependency to fix an issue with running TestResultUploadServiceTest locally since I was experiencing this java.lang.IllegalStateException: No Server ALPNProcessors!

Testing

  • View response from toFhir and ensure that it looks like it has everything it would need. There may need to be additional changes in the future when we begin testing the full bundle with report stream.

@BobanL
add fhir structure dependency
a4e5c3f
@BobanL
WIP patient
85a378e
@BobanL
write lock for fhir
0814e4a
@BobanL
add to fhir method
411520e
@BobanL
add to fhir method with mobile support
bcc32a8
@BobanL
add landline support
521bd73
@BobanL
add invalid test and reformat
d1f528a
@BobanL
rename assert function and make it static
344a4ba
@BobanL
add toFhir method
6148456
@BobanL
add a null test to street toFhir
c164331
@BobanL
use assertThat instead of assertEquals
e03eaad
@BobanL
add basic test for person toFhir
f237181
@BobanL
add null check to toFhir method
ced62f9
@BobanL
add additional gender checks
b506371
@BobanL
remove comments
6a1833e
@BobanL
delete unused method
a70a6ba
@BobanL
refactor to chain methods
eefd82c
@BobanL
rename method toFhir method to match other places
e8f1c86
@BobanL
refactor test to check identifier alone.
b3458dc
@BobanL
refactor toFhir to own methods.
943b447
@BobanL
add race extension
8bb602b
@BobanL
add additional race extension tests
1cf43d2
@BobanL
refactor tests
e0b5134
@BobanL
fix word
4b7103f
@BobanL
fix
35e3856
@BobanL
refactor to replace filter with get extension by url
0fbce0c
@BobanL
add ethnicity extension
16c1acb
@BobanL
add tribal affiliation extension
cf23833
@BobanL
do a full comparison of a patient object
00fa282
@BobanL
add json ignore on all person methods
d699105
DanielSass
DanielSass previously approved these changes Dec 14, 2022
View reviewed changes
@BobanL BobanL marked this pull request as draft December 15, 2022 02:20
@BobanL BobanL changed the title person to FHIR patient [changes in progress] person to FHIR patient Dec 15, 2022
@BobanL
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BobanL commented Dec 15, 2022

Working on a refactor of this to move much of the fhir conversition out of the db models and into it's own file.

@sonarcloud
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sonarcloud bot commented Dec 19, 2022

Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

98.6% 98.6% Coverage
0.0% 0.0% Duplication

@BobanL BobanL changed the title [changes in progress] person to FHIR patient person to FHIR patient Dec 19, 2022
@BobanL BobanL marked this pull request as ready for review December 19, 2022 13:35
@BobanL
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BobanL commented Dec 19, 2022

This is now ready for a review @zdeveloper @DanielSass! The last changes now introduced a new converter where you can simply pass primitives into it to convert values so that it can be re-used in any other part of the code where we may not have the db models.

zdeveloper
zdeveloper reviewed Dec 20, 2022
View reviewed changes
backend/src/main/java/gov/cdc/usds/simplereport/api/converter/FhirConstants.java
throw new IllegalStateException("Utility class");
}

public static final String NULL_CODE_SYSTEM =
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I recommend adding _URL to the name to keep it consistent with the others

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So the reason why these don't have _URL at the end is because the are used as the system and the _URL are added to the URL, but if that's confusing I can totally change it to describe what the contents of that variable is like recommended.

zdeveloper
zdeveloper approved these changes Dec 20, 2022
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LGTM! thanks for your work on this

@BobanL BobanL merged commit 96aeaeb into main Dec 20, 2022
@BobanL BobanL deleted the boban/eventToFHIR branch December 20, 2022 19:50
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@DanielSass DanielSass DanielSass approved these changes

@zdeveloper zdeveloper zdeveloper approved these changes

@emmastephenson emmastephenson Awaiting requested review from emmastephenson

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Create FHIR Patient using person
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@BobanL @zdeveloper @DanielSass