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feat: implement op mapping #155

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@jasminziegler jasminziegler commented Nov 2, 2024 •
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@jasminziegler jasminziegler marked this pull request as draft November 2, 2024 14:27
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github-actions bot commented Nov 2, 2024 •
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@chgl chgl changed the base branch from master to beta November 2, 2024 14:48
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github-advanced-security bot found potential problems Dec 6, 2024
View reviewed changes
src/main/java/org/miracum/streams/ume/obdstofhir/mapper/mii/OperationMapper.java Fixed Show fixed Hide fixed
src/main/java/org/miracum/streams/ume/obdstofhir/mapper/mii/OperationMapper.java Fixed Show fixed Hide fixed
src/test/java/org/miracum/streams/ume/obdstofhir/mapper/mii/OperationMapperTest.java

var fhirParser = FhirContext.forR4().newJsonParser().setPrettyPrint(true);

LOG.info("Number of OPS codes: {}", opMeldung);

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Code scanning / CodeQL

Use of default toString() Note test

Default toString(): Meldung inherits toString() from Object, and so is not suitable for printing.
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Code Coverage Report

Overall Project 68.11% -0.16% 🍏
Files changed 91.29% 🍏

File Coverage
OperationMapper.java 91.29% -8.71% 🍏

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jasminziegler commented Dec 12, 2024 •
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one validation error persists.
error: Instance count for 'Procedure.code.coding:ops' is 0, which is not within the specified cardinality of 1..1
Firstly, we thought this is because I had multiple OPS Codings in Procedure.code, but the issue persists after I changed the mapper so it creates one seperate procedure resource per OPS Code.
Secondly, we thought it's caused by the missing category, but after adding the category, the error still persists.

Any ideas?
@MarcelErpi @chgl @pcvolkmer

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Trivy image scan report

ghcr.io/bzkf/obds-to-fhir:pr-155 (debian 12.7)

No Vulnerabilities found

No Misconfigurations found

Java

14 known vulnerabilities found (CRITICAL: 0 HIGH: 8 MEDIUM: 6 LOW: 0)

Show detailed table of vulnerabilities
Package ID Severity Installed Version Fixed Version
ca.uhn.hapi.fhir:org.hl7.fhir.r4 CVE-2024-45294 HIGH 6.3.11 6.3.23
ca.uhn.hapi.fhir:org.hl7.fhir.r4 CVE-2024-51132 HIGH 6.3.11 6.4.0
ca.uhn.hapi.fhir:org.hl7.fhir.r4 CVE-2024-52007 HIGH 6.3.11 6.4.0
ca.uhn.hapi.fhir:org.hl7.fhir.utilities CVE-2024-45294 HIGH 6.3.11 6.3.23
ca.uhn.hapi.fhir:org.hl7.fhir.utilities CVE-2024-51132 HIGH 6.3.11 6.4.0
ca.uhn.hapi.fhir:org.hl7.fhir.utilities CVE-2024-52007 HIGH 6.3.11 6.4.0
commons-io:commons-io CVE-2024-47554 HIGH 2.11.0 2.14.0
org.springframework:spring-beans CVE-2024-38827 MEDIUM 6.1.11 6.1.14
org.springframework:spring-context CVE-2024-38820 MEDIUM 6.1.11 6.1.14
org.springframework:spring-context CVE-2024-38827 MEDIUM 6.1.11 6.1.14
org.springframework:spring-core CVE-2024-38827 MEDIUM 6.1.11 6.1.14
org.springframework:spring-expression CVE-2024-38827 MEDIUM 6.1.11 6.1.14
org.springframework:spring-web CVE-2024-38809 MEDIUM 6.1.11 5.3.38, 6.0.23, 6.1.12
org.springframework:spring-webmvc CVE-2024-38816 HIGH 6.1.11 6.1.13

No Misconfigurations found

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pcvolkmer commented Dec 12, 2024 •
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Any ideas? @MarcelErpi @chgl @pcvolkmer

The example (https://simplifier.net/guide/mii-ig-modul-onkologie-2024-de/miiigmodulonkologie/technischeimplementierung/fhir-profile/operation/operation-procedure.page.md?version=current) shows the version value starting with “OPS” followed by the year. However, the description only states that the value should be the (plain) year with 4 digits.

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chgl commented Dec 12, 2024

https://github.com/medizininformatik-initiative/kerndatensatzmodul-onkologie/actions/runs/11856173496/job/33041925911#step:3:565

Die offiziellen Ressourcen aus dem IG failen ebenfalls die Validierung. - also gut möglich dass es nicht auf unserer Seite ein problem ist. Ich Guck spätestens im Januar mal drauf.

Aber das mit der Version ist auch ein guter Punkt mMn ist es nur das Jahr anzuheben korrekt, vermutlich wird es nicht explizit validiert. Müsste man nochmal im kds Prozedur Profil nachsehen.

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Das Beispiel oben von simplifier.net wird auch nicht korrekt validiert:

warning: Cannot resolve reference CarePlan/example
error: Instance count for 'Procedure.code.coding:ops' is 0, which is not within the specified cardinality of 1..1
warning: Cannot resolve reference Patient/example
warning: Cannot resolve reference Encounter/example
error: Instance failed constraint proc-mii-1 "Falls die Prozedur per OPS kodiert wird, MUSS eine SNOMED-CT kodierte Category abgebildet werden"
Result: INVALID

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@jasminziegler @pcvolkmer @chgl