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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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346 changes: 173 additions & 173 deletions examples/Test/Automated/003_CA_ORU_R01_CDPH_produced.hl7
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6 changes: 3 additions & 3 deletions examples/Test/Automated/004_CA_ORU_R01_leading_zeroes.hl7
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@@ -1,6 +1,6 @@
MSH|^~\&|SISGDSP|SISGDSP|SISHIERECEIVER^11903029^L,M,N|^automated-staging-test-receiver-id^L,M,N|20240226034304||ORU^R01^ORU_R01|004|N|2.5.1
MSH|^~\&|SISGDSP|SISGDSP|SISHIERECEIVER^11903029^L,M,N|^automated-staging-test-receiver-id^L,M,N|20240226034304||ORU^R01^ORU_R01|004|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||54079-9^Galactosemia newborn screening panel|||202402131546|||||||||^JOHNSON^KATHRYN||||||20240226034304|||F
OBX|1|NM|42906-8^Galactose 1 phosphate uridyl transferase^LN|1|05.100|enzyme units|>50|N|||F|||20240226034304
OBR|1|7181233072^FormNumber||54089-8^NB Screen Panel Patient AHIC|||202402131546|||||||||^JOHNSON^KATHRYN||||||20240226034304|||F
OBX|1|NM|42906-8^Galactose 1 phosphate uridyl transferase^LN|1|05.100|enzyme units|>50|N|||F|||20240226034304
6 changes: 3 additions & 3 deletions examples/Test/Automated/005_CA_ORU_R01_no_leading_zeroes.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|005|N|2.5.1
MSH|^~\&|SISGDSP|SISGDSP|SISHIERECEIVER^11903029^L,M,N|^automated-staging-test-receiver-id^L,M,N|20240226034304||ORU^R01^ORU_R01|005|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||54079-9^Galactosemia newborn screening panel|||202402131546|||||||||^JOHNSON^KATHRYN||||||20240226034304|||F
OBX|1|NM|42906-8^Galactose 1 phosphate uridyl transferase^LN|1|0.6500|enzyme units|>50|N|||F|||20240226034304
OBR|1|7181233072^FormNumber||54089-8^NB Screen Panel Patient AHIC|||202402131546|||||||||^JOHNSON^KATHRYN||||||20240226034304|||F
OBX|1|NM|42906-8^Galactose 1 phosphate uridyl transferase^LN|1|0.6500|enzyme units|>50|N|||F|||20240226034304
7 changes: 7 additions & 0 deletions examples/Test/Automated/006_CA_ORU_R01_LOINC.hl7
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@@ -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||||||||||
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"
]
}
]
}