add workarounds until fixed kds mikrobiologie packages are released

Author: schwzr

codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/ValueSetExpansionClientWithModifiers.java

@@ -11,20 +11,22 @@
 import org.hl7.fhir.r4.model.ValueSet;
 import org.springframework.beans.factory.InitializingBean;
 
+import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.validation.value_set.KdsMikrobiologieBugFixer;
 import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.validation.value_set.MissingEntriesIncluder;
 import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.validation.value_set.ValueSetModifier;
 import jakarta.ws.rs.WebApplicationException;
 
 public class ValueSetExpansionClientWithModifiers implements ValueSetExpansionClient, InitializingBean
 {
 	public static final ValueSetModifier MISSING_ENTRIES_INCLUDER = new MissingEntriesIncluder();
+	public static final KdsMikrobiologieBugFixer KDS_MIKROBIOLOGIE_BUG_FIXER = new KdsMikrobiologieBugFixer();
 
 	private final ValueSetExpansionClient delegate;
 	private final List<ValueSetModifier> valueSetModifiers = new ArrayList<>();
 
 	public ValueSetExpansionClientWithModifiers(ValueSetExpansionClient delegate)
 	{
-		this(delegate, Arrays.asList(MISSING_ENTRIES_INCLUDER));
+		this(delegate, Arrays.asList(KDS_MIKROBIOLOGIE_BUG_FIXER, MISSING_ENTRIES_INCLUDER));
 	}
 
 	public ValueSetExpansionClientWithModifiers(ValueSetExpansionClient delegate,

codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/value_set/KdsMikrobiologieBugFixer.java

@@ -0,0 +1,36 @@
+package de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.validation.value_set;
+
+import java.util.Map;
+
+import org.hl7.fhir.r4.model.ValueSet;
+
+import ca.uhn.fhir.context.FhirContext;
+
+public class KdsMikrobiologieBugFixer implements ValueSetModifier
+{
+
+	private final Map<String, String> fixedValueSets = Map.of(
+			"https://www.medizininformatik-initiative.de/fhir/modul-mikrobio/ValueSet/mii-vs-mikrobio-empfindlichkeit-phenotyp-loinc",
+			"mii-vs-mikrobio-empfindlichkeit-phenotyp-loinc.json",
+			"https://www.medizininformatik-initiative.de/fhir/modul-mikrobio/ValueSet/mii-vs-mikrobio-empfindlichkeit-genotyp-loinc",
+			"mii-vs-mikrobio-empfindlichkeit.json",
+			"https://www.medizininformatik-initiative.de/fhir/modul-mikrobio/ValueSet/mii-vs-mikrobio-mre-klasse-snomedct",
+			"mii-vs-mikrobio-mre-klasse-snomedct.json");
+
+	@Override
+	public ValueSet modifyPreExpansion(ValueSet vs)
+	{
+
+		if (vs.getUrl() != null && vs.getVersion() != null && vs.getVersion().equals("2024.0.0"))
+		{
+			String fileName = fixedValueSets.get(vs.getUrl());
+			if (fileName != null)
+			{
+				return (ValueSet) FhirContext.forR4().newJsonParser()
+						.parseResource(getClass().getResourceAsStream("/bugfix/fhir/ValueSet/" + fileName));
+			}
+		}
+
+		return vs;
+	}
+}