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15153: update FHIRConvert to create empty report/lineages for items with no next action #15224
15153: update FHIRConvert to create empty report/lineages for items with no next action #15224
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…ith no next action
…itoring-azure-events
…items with no next action
Dependency Review✅ No vulnerabilities or license issues or OpenSSF Scorecard issues found.OpenSSF Scorecard
Scanned Manifest Files |
Test Results1 275 tests - 5 1 271 ✅ - 5 7m 28s ⏱️ -15s Results for commit 53afdbb. ± Comparison against base commit 93a1c3d. This pull request removes 5 tests.
♻️ This comment has been updated with latest results. |
Integration Test Results 63 files 63 suites 29m 16s ⏱️ Results for commit 53afdbb. ♻️ This comment has been updated with latest results. |
…itoring-azure-events
prime-router/src/test/kotlin/fhirengine/azure/FHIRConverterIntegrationTests.kt
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@@ -727,679 +721,6 @@ class FhirFunctionIntegrationTests() { | |||
} | |||
} | |||
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@Test | |||
fun `test successfully processes a convert message for a bulk (ndjson) FHIR message`() { |
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Are the test cases being deleted here covered somewhere else now?
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Yep, these are covered in FhirConverterIntegrationTests
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@mkalish replied to the comments, so lgtm once the agreed updates are made
…items with no next action
prime-router/src/main/kotlin/fhirengine/engine/FHIRConverter.kt
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Co-authored-by: Angela DeGolier <[email protected]>
I'm getting 10 reports, 9 report lineages/item lineages, and 4 with none as a next action |
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Changes look good! Here are my test results:
submitted this curl (the one given had TWO valid messages instead of 1. The only way I could think to get receive to accept the message but convert to reject it is to use the RadxMars topic and have validation fail)
curl --location 'http://localhost:7071/api/reports' \
--header 'client: ignore.ignore-mars-otc' \
--header 'Content-Type: application/hl7-v2' \
--header 'x-functions-key: 09xifjf....444s' \
--header 'Authorization: Bearer dummy' \
--data 'MSH|^~\&|MMTC.PROD^2.16.840.1.113883.3.8589.4.2.106.1^ISO|CAREEVOLUTION^00Z0000024^CLIA|AIMS.INTEGRATION.PRD^2.16.840.1.114222.4.3.15.1^ISO|AIMS.PLATFORM^2.16.840.1.114222.4.1.217446^ISO|20240403205305+0000||ORU^R01^ORU_R01|20240403205305_dba7572cc6334f1ea0744c5f235c823e|P|2.5.1|||NE|NE|||||PHLabReport-NoAck^ELR251R1_Rcvr_Prof^2.16.840.1.113883.9.11^ISO
SFT|CAREEVOLUTION|2022|MMTC.PROD|16498||20240402
PID|1||8be6fa3710374dcebe0174e0fd5a1a7c^^^MMTC.PROD&2.16.840.1.113883.3.8589.4.2.106.1&ISO^PI||^^^^^^~^^^^^^||||||^^^^02139^USA||^^^^^111^1111111
ORC|RE||^MMTC.PROD^2.16.840.1.113883.3.8589.4.2.106.1^ISO|||||||||^^||^^^^^^|||||||SA.OTCSelfReport|^^^^02139^^^^|^^^^^^
OBR|1||^MMTC.PROD^2.16.840.1.113883.3.8589.4.2.106.1^ISO|94558-4^SARS-CoV-2 (COVID-19) Ag [Presence] in Respiratory specimen by Rapid immunoassay^LN^^^^2.71|||20240403120000|||||||||^^|^^^^^^|||||20240403120000|||F
OBX|1|CWE|94558-4^SARS-CoV-2 (COVID-19) Ag [Presence] in Respiratory specimen by Rapid immunoassay^LN^^^^2.71||260373001^Detected^SCT^^^^20200901||||||F||||00Z0000042||BinaxNOW COVID-19 Antigen Self Test_Abbott Diagnostics Scarborough, Inc._EUA^^99ELR^^^^Vunknown||20240403120000||||SA.OTCSelfReport^^^^^&2.16.840.1.113883.3.8589.4.1.152&ISO^XX^^^00Z0000042|
NTE|1|L|Note
OBX|2|NM|35659-2^Age at specimen collection^LN^^^^2.71||24|a^year^UCUM^^^^2.1|||||F||||00Z0000042||||||||SA.OTCSelfReport^^^^^&2.16.840.1.113883.3.8589.4.1.152&ISO^XX^^^00Z0000042||||||QST
SPM|1|^dba7572cc6334f1ea0744c5f235c823e&MMTC.PROD&2.16.840.1.113883.3.8589.4.2.106.1&ISO||697989009^Anterior nares swab^SCT^^^^20200901|||||||||||||20240403120000-0400|20240403120000-0400
MSH|^~\&|MMTC.PROD^2.16.840.1.113883.3.8589.4.2.106.1^ISO|CAREEVOLUTION^00Z0000024^CLIA|AIMS.INTEGRATION.PRD^2.16.840.1.114222.4.3.15.1^ISO|AIMS.PLATFORM^2.16.840.1.114222.4.1.217446^ISO|20240403205305+0000||ORU^R01^ORU_R01|20240403205305_dba7572cc6334f1ea0744c5f235c823e|P|2.5.1|||INVALID|NE|||||PHLabReport-NoAck^ELR251R1_Rcvr_Prof^2.16.840.1.113883.9.11^ISO
SFT|CAREEVOLUTION|2022|MMTC.PROD|16498||20240402
PID|1||8be6fa3710374dcebe0174e0fd5a1a7c^^^MMTC.PROD&2.16.840.1.113883.3.8589.4.2.106.1&ISO^PI||^^^^^^~^^^^^^||||||^^ROCINANTE^IG^02139^USA||^^^^^111^1111111
ORC|RE||^MMTC.PROD^2.16.840.1.113883.3.8589.4.2.106.1^ISO|||||||||^^||^^^^^^|||||||SA.OTCSelfReport|^^^IG^12345^USA|^^^^^^
OBR|1||^MMTC.PROD^2.16.840.1.113883.3.8589.4.2.106.1^ISO|94558-4^SARS-CoV-2 (COVID-19) Ag [Presence] in Respiratory specimen by Rapid immunoassay^LN^^^^2.71|||20240403120000-0400|||||||||^^|^^^^^^|||||20240403120000-0400|||F
OBX|1|CWE|94558-4^SARS-CoV-2 (COVID-19) Ag [Presence] in Respiratory specimen by Rapid immunoassay^LN^^^^2.71||260373001^Detected^SCT^^^^20200901||||||F||||00Z0000042||BinaxNOW COVID-19 Antigen Self Test_Abbott Diagnostics Scarborough, Inc._EUA^^99ELR^^^^Vunknown||20240403120000-0400||||SA.OTCSelfReport^^^^^&2.16.840.1.113883.3.8589.4.1.152&ISO^XX^^^00Z0000042|
NTE|1|L|Note
OBX|2|NM|35659-2^Age at specimen collection^LN^^^^2.71||24|a^year^UCUM^^^^2.1|||||F||||00Z0000042||||||||SA.OTCSelfReport^^^^^&2.16.840.1.113883.3.8589.4.1.152&ISO^XX^^^00Z0000042||||||QST
SPM|1|^dba7572cc6334f1ea0744c5f235c823e&MMTC.PROD&2.16.840.1.113883.3.8589.4.2.106.1&ISO||697989009^Anterior nares swab^SCT^^^^20200901|||||||||||||20240403120000-0400|20240403120000-0400'
Then query the DB:
SELECT report_file.created_at, report_id, action_name, next_action FROM report_file
JOIN action ON report_file.action_id = action.action_id ORDER BY report_file.created_at
SELECT * FROM report_lineage
…itoring-azure-events
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Got the same result with the curl Arnej provided.
…itoring-azure-events
…itoring-azure-events
Quality Gate passedIssues Measures |
…ith no next action (#15224) * 15153: update FHIRConvert to create empty report/lineages for items with no next action * fixup! 15153: update FHIRConvert to create empty report/lineages for items with no next action * fixup! 15153: update FHIRConvert to create empty report/lineages for items with no next action * Delete duplicated FHIR Converter integration tests * fixup! 15153: update FHIRConvert to create empty report/lineages for items with no next action * Update prime-router/src/main/kotlin/fhirengine/engine/FHIRConverter.kt Co-authored-by: Angela DeGolier <[email protected]> --------- Co-authored-by: Angela DeGolier <[email protected]>
…ith no next action (#15224) * 15153: update FHIRConvert to create empty report/lineages for items with no next action * fixup! 15153: update FHIRConvert to create empty report/lineages for items with no next action * fixup! 15153: update FHIRConvert to create empty report/lineages for items with no next action * Delete duplicated FHIR Converter integration tests * fixup! 15153: update FHIRConvert to create empty report/lineages for items with no next action * Update prime-router/src/main/kotlin/fhirengine/engine/FHIRConverter.kt Co-authored-by: Angela DeGolier <[email protected]> --------- Co-authored-by: Angela DeGolier <[email protected]>
This PR update the convert step to create a report/item lineage even when the item is not going to be processed further. This allows the submitted index to be accurately tracked in downstream steps.
This is some pre-work required to be able to track all properties for the report and item events
Test Steps:
none
Changes
none
Checklist
Testing
./prime test
or./gradlew testSmoke
against local Docker ReportStream container?npm run lint:write
?Process
Linked Issues
To Be Done
Specific Security-related subjects a reviewer should pay specific attention to