test: finalized snapshot testing implementation

bzkf · Nov 8, 2023 · bf30551 · bf30551
1 parent 10fd5ec
commit bf30551
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Showing 17 changed files with 2,296 additions and 134 deletions.
diff --git a/.gitignore b/.gitignore
@@ -57,3 +57,5 @@ bin
 # ignored since it isn't automatically refreshed by renovate
 # (we're also pinning the dependency versions anyways)
 fhirpkg.lock.json
+
+*.received.fhir.json
diff --git a/README.md b/README.md
@@ -4,7 +4,33 @@ This project contains a Kafka Stream processor that creates FHIR resources from
 
 ## Used FHIR profiles
 
-See [package.json](package.json) for a list of used profiles and their versions.
+See [package.json](package.json) for a list of used packages and their versions.
+
+## Observations
+
+- Histologie (<https://simplifier.net/oncology/histologie>)
+- Grading (<https://simplifier.net/oncology/grading>)
+- TNMc (<https://simplifier.net/oncology/tnmc>)
+- TNMp (<https://simplifier.net/oncology/tnmp>)
+- Fernmetastasen (<https://simplifier.net/oncology/fernmetastasen-duplicate-2>)
+- Tod Ursache (<https://simplifier.net/oncology/todursache>)
+
+## Condition
+
+- Primärdiagnose (<https://simplifier.net/oncology/primaerdiagnose>)
+
+## Procedure
+
+- Operation (<https://simplifier.net/oncology/operation>)
+- Strahlentherapie (<https://simplifier.net/oncology/strahlentherapie>)
+
+## MedicationStatement
+
+- Systemtherapie (<https://simplifier.net/oncology/systemtherapie>)
+
+## Patient
+
+- Patient (<https://simplifier.net/medizininformatikinitiative-modulperson>)
 
 ## Dev
 

diff --git a/src/main/resources/application.yml b/src/main/resources/application.yml
@@ -18,7 +18,7 @@ fhir:
     observationId: "https://fhir.diz.uk-erlangen.de/identifiers/onkostar-xml-observation-id"
     procedureId: "https://fhir.diz.uk-erlangen.de/identifiers/onkostar-xml-procedure-id"
     medicationStatementId: "https://fhir.diz.uk-erlangen.de/identifiers/onkostar-xml-medication-statement-id"
-    observationCategorySystem: "http://terminology.hl7.org/CodeSystem/observation-category"
+    observationCategorySystem: "http://hl7.org/fhir/observation-category"
     loinc: "http://loinc.org"
     idco3Morphologie: "urn:oid:2.16.840.1.113883.6.43.1"
     gradingDktk: "http://dktk.dkfz.de/fhir/onco/core/CodeSystem/GradingCS"

diff --git a/src/test/java/org/miracum/streams/ume/obdstofhir/processor/ObdsConditionProcessorTest.java b/src/test/java/org/miracum/streams/ume/obdstofhir/processor/ObdsConditionProcessorTest.java
@@ -2,30 +2,24 @@
 
 import static org.assertj.core.api.Assertions.assertThat;
 
-import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.util.BundleUtil;
-import java.io.File;
 import java.io.IOException;
-import java.nio.file.Files;
 import java.util.*;
 import java.util.stream.Stream;
-import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.tuple.Pair;
+import org.approvaltests.Approvals;
 import org.hl7.fhir.r4.model.Condition;
 import org.junit.jupiter.params.ParameterizedTest;
 import org.junit.jupiter.params.provider.Arguments;
 import org.junit.jupiter.params.provider.MethodSource;
 import org.miracum.streams.ume.obdstofhir.FhirProperties;
 import org.miracum.streams.ume.obdstofhir.mapper.*;
-import org.miracum.streams.ume.obdstofhir.model.MeldungExport;
-import org.miracum.streams.ume.obdstofhir.model.MeldungExportList;
 import org.miracum.streams.ume.obdstofhir.model.Tupel;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.boot.context.properties.EnableConfigurationProperties;
 import org.springframework.boot.test.context.SpringBootTest;
-import org.springframework.util.ResourceUtils;
 
 @SpringBootTest(
     classes = {
@@ -48,7 +42,6 @@ public class ObdsConditionProcessorTest extends ObdsProcessorTest {
   private final ObdsProcedureMapper onkoProcedureMapper;
   private final ObdsPatientMapper onkoPatientMapper;
   private final ObdsConditionMapper onkoConditionMapper;
-  private final FhirContext ctx = FhirContext.forR4();
 
   @Autowired
   public ObdsConditionProcessorTest(
@@ -123,31 +116,7 @@ void mapCondition_withGivenAdtXml(
       String expectedOnsetDate)
       throws IOException {
 
-    MeldungExportList meldungExportList = new MeldungExportList();
-
-    int payloadId = 1;
-
-    for (var xmlTupel : xmlFileNames) {
-      File xmlFile = ResourceUtils.getFile("classpath:" + xmlTupel.getFirst());
-      String xmlContent = new String(Files.readAllBytes(xmlFile.toPath()));
-
-      var meldungsId = StringUtils.substringBetween(xmlContent, "Meldung_ID=\"", "\" Melder_ID");
-      var melderId = StringUtils.substringBetween(xmlContent, "Melder_ID=\"", "\">");
-      var patId = StringUtils.substringBetween(xmlContent, "Patient_ID=\"", "\">");
-
-      Map<String, Object> payloadOnkoRessource = new HashMap<>();
-      payloadOnkoRessource.put("ID", payloadId);
-      payloadOnkoRessource.put("REFERENZ_NUMMER", patId);
-      payloadOnkoRessource.put("LKR_MELDUNG", Integer.parseInt(meldungsId.replace(melderId, "")));
-      payloadOnkoRessource.put("VERSIONSNUMMER", xmlTupel.getSecond());
-      payloadOnkoRessource.put("XML_DATEN", xmlContent);
-
-      MeldungExport meldungExport = new MeldungExport();
-      meldungExport.getPayload(payloadOnkoRessource);
-      meldungExportList.addElement(meldungExport);
-
-      payloadId++;
-    }
+    var meldungExportList = buildMeldungExportList(xmlFileNames);
 
     ObdsProcessor onkoProcessor =
         new ObdsProcessor(
@@ -192,7 +161,13 @@ void mapCondition_withGivenAdtXml(
       assertThat(conditionList.get(0).getOnsetDateTimeType().getValueAsString())
           .isEqualTo(expectedOnsetDate);
 
-      // assertThat(isValid(resultBundle)).isTrue();
+      var fhirJson = fhirParser.encodeResourceToString(resultBundle);
+      Approvals.verify(
+          fhirJson,
+          Approvals.NAMES
+              .withParameters(xmlFileNames.stream().map(t -> t.getFirst()).toArray(String[]::new))
+              .forFile()
+              .withExtension(".fhir.json"));
     }
   }
 }
diff --git a/...va/org/miracum/streams/ume/obdstofhir/processor/ObdsMedicationStatementProcessorTest.java b/...va/org/miracum/streams/ume/obdstofhir/processor/ObdsMedicationStatementProcessorTest.java
@@ -4,28 +4,23 @@
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.util.BundleUtil;
-import java.io.File;
 import java.io.IOException;
-import java.nio.file.Files;
 import java.util.*;
 import java.util.stream.Stream;
-import org.apache.commons.lang3.StringUtils;
+import org.approvaltests.Approvals;
 import org.hl7.fhir.r4.model.CodeableConcept;
 import org.hl7.fhir.r4.model.MedicationStatement;
 import org.junit.jupiter.params.ParameterizedTest;
 import org.junit.jupiter.params.provider.Arguments;
 import org.junit.jupiter.params.provider.MethodSource;
 import org.miracum.streams.ume.obdstofhir.FhirProperties;
 import org.miracum.streams.ume.obdstofhir.mapper.*;
-import org.miracum.streams.ume.obdstofhir.model.MeldungExport;
-import org.miracum.streams.ume.obdstofhir.model.MeldungExportList;
 import org.miracum.streams.ume.obdstofhir.model.Tupel;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.boot.context.properties.EnableConfigurationProperties;
 import org.springframework.boot.test.context.SpringBootTest;
-import org.springframework.util.ResourceUtils;
 
 @SpringBootTest(
     classes = {
@@ -101,31 +96,7 @@ void mapMedicationStatement_withGivenAdtXml(
       String expectedIntention)
       throws IOException {
 
-    MeldungExportList meldungExportList = new MeldungExportList();
-
-    int payloadId = 1;
-
-    for (var xmlTupel : xmlFileNames) {
-      File xmlFile = ResourceUtils.getFile("classpath:" + xmlTupel.getFirst());
-      String xmlContent = new String(Files.readAllBytes(xmlFile.toPath()));
-
-      var meldungsId = StringUtils.substringBetween(xmlContent, "Meldung_ID=\"", "\" Melder_ID");
-      var melderId = StringUtils.substringBetween(xmlContent, "Melder_ID=\"", "\">");
-      var patId = StringUtils.substringBetween(xmlContent, "Patient_ID=\"", "\">");
-
-      Map<String, Object> payloadOnkoRessource = new HashMap<>();
-      payloadOnkoRessource.put("ID", payloadId);
-      payloadOnkoRessource.put("REFERENZ_NUMMER", patId);
-      payloadOnkoRessource.put("LKR_MELDUNG", Integer.parseInt(meldungsId.replace(melderId, "")));
-      payloadOnkoRessource.put("VERSIONSNUMMER", xmlTupel.getSecond());
-      payloadOnkoRessource.put("XML_DATEN", xmlContent);
-
-      MeldungExport meldungExport = new MeldungExport();
-      meldungExport.getPayload(payloadOnkoRessource);
-      meldungExportList.addElement(meldungExport);
-
-      payloadId++;
-    }
+    var meldungExportList = buildMeldungExportList(xmlFileNames);
 
     ObdsProcessor medicationStatementProcessor =
         new ObdsProcessor(
@@ -186,7 +157,13 @@ void mapMedicationStatement_withGivenAdtXml(
       String finalPartOfId = partOfId;
       assertThat(partOfReferences).allSatisfy(ref -> ref.equals(finalPartOfId));
 
-      // assertThat(isValid(resultBundle)).isTrue();
+      var fhirJson = fhirParser.encodeResourceToString(resultBundle);
+      Approvals.verify(
+          fhirJson,
+          Approvals.NAMES
+              .withParameters(xmlFileNames.stream().map(t -> t.getFirst()).toArray(String[]::new))
+              .forFile()
+              .withExtension(".fhir.json"));
     }
   }
 }
diff --git a/src/test/java/org/miracum/streams/ume/obdstofhir/processor/ObdsObservationProcessorTest.java b/src/test/java/org/miracum/streams/ume/obdstofhir/processor/ObdsObservationProcessorTest.java
@@ -2,30 +2,24 @@
 
 import static org.assertj.core.api.Assertions.assertThat;
 
-import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.util.BundleUtil;
-import java.io.File;
 import java.io.IOException;
-import java.nio.file.Files;
 import java.util.*;
 import java.util.stream.Stream;
-import org.apache.commons.lang3.StringUtils;
+import org.approvaltests.Approvals;
 import org.hl7.fhir.r4.model.CodeableConcept;
 import org.hl7.fhir.r4.model.Observation;
 import org.junit.jupiter.params.ParameterizedTest;
 import org.junit.jupiter.params.provider.Arguments;
 import org.junit.jupiter.params.provider.MethodSource;
 import org.miracum.streams.ume.obdstofhir.FhirProperties;
 import org.miracum.streams.ume.obdstofhir.mapper.*;
-import org.miracum.streams.ume.obdstofhir.model.MeldungExport;
-import org.miracum.streams.ume.obdstofhir.model.MeldungExportList;
 import org.miracum.streams.ume.obdstofhir.model.Tupel;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.boot.context.properties.EnableConfigurationProperties;
 import org.springframework.boot.test.context.SpringBootTest;
-import org.springframework.util.ResourceUtils;
 
 @SpringBootTest(
     classes = {
@@ -48,7 +42,6 @@ public class ObdsObservationProcessorTest extends ObdsProcessorTest {
   private final ObdsProcedureMapper onkoProcedureMapper;
   private final ObdsPatientMapper onkoPatientMapper;
   private final ObdsConditionMapper onkoConditionMapper;
-  private final FhirContext ctx = FhirContext.forR4();
 
   @Autowired
   public ObdsObservationProcessorTest(
@@ -110,31 +103,7 @@ void mapObservation_withGivenAdtXml(
       String expectedDeathDate)
       throws IOException {
 
-    MeldungExportList meldungExportList = new MeldungExportList();
-
-    int payloadId = 1;
-
-    for (var xmlTupel : xmlFileNames) {
-      File xmlFile = ResourceUtils.getFile("classpath:" + xmlTupel.getFirst());
-      String xmlContent = new String(Files.readAllBytes(xmlFile.toPath()));
-
-      var meldungsId = StringUtils.substringBetween(xmlContent, "Meldung_ID=\"", "\" Melder_ID");
-      var melderId = StringUtils.substringBetween(xmlContent, "Melder_ID=\"", "\">");
-      var patId = StringUtils.substringBetween(xmlContent, "Patient_ID=\"", "\">");
-
-      Map<String, Object> payloadOnkoRessource = new HashMap<>();
-      payloadOnkoRessource.put("ID", payloadId);
-      payloadOnkoRessource.put("REFERENZ_NUMMER", patId);
-      payloadOnkoRessource.put("LKR_MELDUNG", Integer.parseInt(meldungsId.replace(melderId, "")));
-      payloadOnkoRessource.put("VERSIONSNUMMER", xmlTupel.getSecond());
-      payloadOnkoRessource.put("XML_DATEN", xmlContent);
-
-      MeldungExport meldungExport = new MeldungExport();
-      meldungExport.getPayload(payloadOnkoRessource);
-      meldungExportList.addElement(meldungExport);
-
-      payloadId++;
-    }
+    var meldungExportList = buildMeldungExportList(xmlFileNames);
 
     ObdsProcessor observationProcessor =
         new ObdsProcessor(
@@ -226,7 +195,13 @@ void mapObservation_withGivenAdtXml(
       }
       assertThat(fenMetaCount).isEqualTo(expectedFernMetaCount);
 
-      // assertThat(isValid(resultBundle)).isTrue();
+      var fhirJson = fhirParser.encodeResourceToString(resultBundle);
+      Approvals.verify(
+          fhirJson,
+          Approvals.NAMES
+              .withParameters(xmlFileNames.stream().map(t -> t.getFirst()).toArray(String[]::new))
+              .forFile()
+              .withExtension(".fhir.json"));
     }
   }
 }