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E2e/1452/map local and loinc codes #1515

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merged 8 commits into from
Nov 1, 2024
Merged

E2e/1452/map local and loinc codes #1515

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c1c4243
skeleton
jorg3lopez Oct 24, 2024
90328a8
Add LOINC and PLT tests
jbiskie Oct 24, 2024
91faa6d
Renumber tests
jbiskie Oct 31, 2024
da92294
Merge remote-tracking branch 'origin/main' into e2e/1452/map-local-an…
jbiskie Oct 31, 2024
6a415ad
Adding pipes to end of MSH segments
jbiskie Nov 1, 2024
c6a6bed
Added more delimeters after HL7 version number to try fix the issue p…
basiliskus Nov 1, 2024
9407c9f
Fixed typo
basiliskus Nov 1, 2024
52c9d65
Updated OBR-4.1 expectation for UCSD
basiliskus Nov 1, 2024
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7 changes: 7 additions & 0 deletions examples/Test/Automated/006_CA_ORU_R01_LOINC.hl7
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Original file line number Diff line number Diff line change
@@ -0,0 +1,7 @@
MSH|^~\&|SISGDSP|SISGDSP|SISHIERECEIVER^11903029^L,M,N|^automated-staging-test-receiver-id^L,M,N|20240226034304||ORU^R01^ORU_R01|006|N|2.5.1
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I tried running the assertions on these files but for some reason the Hapi library is not able to parse them. It triggers an error when trying to parse the 2.5.1 version number: ca.uhn.hl7v2.HL7Exception: The HL7 version 2.5.1\nPID is not recognized. I also noticed the files Gilmore added are not getting parsed either. Could you try adding a | after 2.5.1? That may fix it

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I updated the 4 files. Could you try them again? *Also, what's your process for running the assertions?

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I run the Automated Staging Test - Submit Messages github workflow on the branch to send the new files to RS staging. You can then check they are delivered to the RS blob storage account cdctiautomatedstg (you need to log in to your -SU account to be able to check this). After making sure they are in the storage account, you can then run and debug the AutomatedTest test in TI. To be able to run it, you need to set the AZURE_STORAGE_CONNECTION_STRING for the cdctiautomatedstg account. I can give that to you. Otherwise, you can also run the Automated Staging Test - Run integration tests workflow, but you won't be able to debug there

PID|1||80008836^^^&NPI^MR||CDPHSIX^BOY MOMSIX^^^^^B|||M||2106-3^White||||||||||||2186-5^Not Hispanic or Latino||N|1
NK1|1|CDPHSIX|MTH^Mother|132 ST^^SAN DIEGO^CA^92126^USA
ORC|RE|7181233072^FormNumber||189430284^HospOrdNumber||||||||^ROSEN^REBECCA|||||||||UCSD JACOBS MEDICAL CENTER^^^^^^^^^R797| 2961DR YLLUT^^SAN DIEGO^CA^99999-9999
OBR|1|7181233072^FormNumber||54089-8^NB Screen Panel Patient AHIC|||202402131546|||||||||^JOHNSON^KATHRYN||||||20240226034304|||F
OBR|2|7181233072^FormNumber||57128-1^Newborn Screening Report summary panel|||202402131546|||||||||^JOHNSON^KATHRYN||||||20240226034304|||F
OBX|1|CE|^^^99717-32^Adrenoleukodystrophy deficiency newborn screening interpretation^L|1|LA18592-8^In range^LN|||N|||F|||20240226034304
7 changes: 7 additions & 0 deletions examples/Test/Automated/007_CA_ORU_R01_PLT.hl7
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MSH|^~\&|SISGDSP|SISGDSP|SISHIERECEIVER^11903029^L,M,N|^automated-staging-test-receiver-id^L,M,N|20240226034304||ORU^R01^ORU_R01|007|N|2.5.1
PID|1||80008836^^^&NPI^MR||CDPHSIX^BOY MOMSIX^^^^^B|||M||2106-3^White||||||||||||2186-5^Not Hispanic or Latino||N|1
NK1|1|CDPHSIX|MTH^Mother|132 ST^^SAN DIEGO^CA^92126^USA
ORC|RE|7181233072^FormNumber||189430284^HospOrdNumber||||||||^ROSEN^REBECCA|||||||||UCSD JACOBS MEDICAL CENTER^^^^^^^^^R797| 2961DR YLLUT^^SAN DIEGO^CA^99999-9999
OBR|1|7181233072^FormNumber||54089-8^NB Screen Panel Patient AHIC|||202402131546|||||||||^JOHNSON^KATHRYN||||||20240226034304|||F
OBR|2|7181233072^FormNumber||57128-1^Newborn Screening Report summary panel|||202402131546|||||||||^JOHNSON^KATHRYN||||||20240226034304|||F
OBX|1|TX|^^^99717-60^SMN1 Homozygous Deletion Analysis^L|1|Exon 7 Absent||Exon 7 Present|A|||F|||20240226034304
28 changes: 28 additions & 0 deletions rs-e2e/src/main/resources/assertion_definitions.json
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Expand Up @@ -54,6 +54,34 @@
"rules": [
"OBX-5 = '0.6500'"
]
},
{
"name": "UCSD ORU LOINC replacement",
"conditions": [
"MSH-10 = '006'"
],
"rules": [
"OBX-3.1 = '85269-9'",
"OBX-3.2 = 'X-linked Adrenoleukodystrophy (X- ALD) newborn screen interpretation'",
"OBX-3.3 = 'LN'",
"OBX-3.4 = input.OBX-3.4",
"OBX-3.5 = input.OBX-3.5",
"OBX-3.6 = input.OBX-3.6"
]
},
{
"name": "UCSD ORU PLT replacement",
"conditions": [
"MSH-10 = '007'"
],
"rules": [
"OBX-3.1 = 'PLT3293",
"OBX-3.2 = 'SMN1 exon 7 deletion analysis in DBS by Sequencing'",
"OBX-3.3 = 'PLT'",
"OBX-3.4 = input.OBX-3.4",
"OBX-3.5 = input.OBX-3.5",
"OBX-3.6 = input.OBX-3.6"
]
}
]
}