added observationCategory in FHIRProperties

bzkf · Dec 9, 2024 · 1311da1 · 1311da1
1 parent 82a5107
commit 1311da1
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Showing 28 changed files with 436 additions and 16 deletions.
diff --git a/src/main/java/org/miracum/streams/ume/obdstofhir/FhirProperties.java b/src/main/java/org/miracum/streams/ume/obdstofhir/FhirProperties.java
@@ -86,6 +86,7 @@ public static class FhirSystems {
     private String atcBfarm;
     private String atcWho;
     private String observationHistologieId;
+    private String observationCategory;
   }
 
   @Data

diff --git a/...ain/java/org/miracum/streams/ume/obdstofhir/mapper/mii/LymphknotenuntersuchungMapper.java b/...ain/java/org/miracum/streams/ume/obdstofhir/mapper/mii/LymphknotenuntersuchungMapper.java
@@ -112,8 +112,7 @@ public List<Observation> map(
       // Category
       var laboratory =
           new CodeableConcept(
-              new Coding(
-                  fhirProperties.getSystems().getObservationCategorySystem(), "laboratory", ""));
+              new Coding(fhirProperties.getSystems().getObservationCategory(), "laboratory", ""));
       List<CodeableConcept> list = new ArrayList<>();
       list.add(laboratory);
       obs_befallen.setCategory(list);

diff --git a/src/main/resources/application.yml b/src/main/resources/application.yml
@@ -74,6 +74,7 @@ fhir:
     mii-cs-therapie-grund-ende: "https://www.medizininformatik-initiative.de/fhir/ext/modul-onko/CodeSystem/mii-cs-therapie-grund-ende"
     atcBfarm: "http://fhir.de/CodeSystem/bfarm/atc"
     atcWho: "http://www.whocc.no/atc"
+    observationCategory: "http://terminology.hl7.org/CodeSystem/observation-category"
   profiles:
     histologie: "http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Observation-Histologie"
     grading: "http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Observation-Grading"

diff --git a/...java/org/miracum/streams/ume/obdstofhir/mapper/mii/LymphknotenuntersuchungMapperTest.java b/...java/org/miracum/streams/ume/obdstofhir/mapper/mii/LymphknotenuntersuchungMapperTest.java
@@ -32,8 +32,7 @@ static void beforeAll(@Autowired FhirProperties fhirProps) {
 
   @ParameterizedTest
   @CsvSource({"Testpatient_1.xml", "Testpatient_2.xml", "Testpatient_3.xml"})
-  void map_withGivenObds_shouldCreateValidObservation(String sourceFile)
-      throws IOException {
+  void map_withGivenObds_shouldCreateValidObservation(String sourceFile) throws IOException {
     final var resource = this.getClass().getClassLoader().getResource("obds3/" + sourceFile);
     assertThat(resource).isNotNull();
 

diff --git a/...venObds_shouldCreateValidMedicationStatement.Testpatient_1.xml.index_0.approved.fhir.json b/...venObds_shouldCreateValidMedicationStatement.Testpatient_1.xml.index_0.approved.fhir.json
@@ -0,0 +1,35 @@
+{
+  "resourceType": "Observation",
+  "meta": {
+    "profile": [ "https://www.medizininformatik-initiative.de/fhir/ext/modul-onko/StructureDefinition/mii-pr-onko-anzahl-befallene-lymphknoten" ]
+  },
+  "identifier": [ {
+    "system": "https://bzkf.github.io/obds-to-fhir/identifiers/observation-histologie-id",
+    "value": "521_befallen"
+  } ],
+  "status": "final",
+  "category": [ {
+    "coding": [ {
+      "system": "http://hl7.org/fhir/observation-category",
+      "code": "laboratory"
+    } ]
+  } ],
+  "code": {
+    "coding": [ {
+      "system": "http://loinc.org",
+      "code": "21893-3"
+    }, {
+      "system": "http://snomed.info/sct",
+      "code": "443527007"
+    } ]
+  },
+  "subject": {
+    "reference": "Patient/any"
+  },
+  "effectiveDateTime": "2020-03-05",
+  "valueQuantity": {
+    "value": 2,
+    "system": "http://unitsofmeasure.org",
+    "code": "1"
+  }
+}
diff --git a/...venObds_shouldCreateValidMedicationStatement.Testpatient_1.xml.index_1.approved.fhir.json b/...venObds_shouldCreateValidMedicationStatement.Testpatient_1.xml.index_1.approved.fhir.json
@@ -0,0 +1,35 @@
+{
+  "resourceType": "Observation",
+  "meta": {
+    "profile": [ "https://www.medizininformatik-initiative.de/fhir/ext/modul-onko/StructureDefinition/mii-pr-onko-anzahl-untersuchte-lymphknoten" ]
+  },
+  "identifier": [ {
+    "system": "https://bzkf.github.io/obds-to-fhir/identifiers/observation-histologie-id",
+    "value": "521_untersucht"
+  } ],
+  "status": "final",
+  "category": [ {
+    "coding": [ {
+      "system": "http://hl7.org/fhir/observation-category",
+      "code": "laboratory"
+    } ]
+  } ],
+  "code": {
+    "coding": [ {
+      "system": "http://loinc.org",
+      "code": "21894-1"
+    }, {
+      "system": "http://snomed.info/sct",
+      "code": "444025001"
+    } ]
+  },
+  "subject": {
+    "reference": "Patient/any"
+  },
+  "effectiveDateTime": "2020-03-05",
+  "valueQuantity": {
+    "value": 10,
+    "system": "http://unitsofmeasure.org",
+    "code": "1"
+  }
+}
diff --git a/...enObds_shouldCreateValidMedicationStatement.Testpatient_1.xml.index_10.approved.fhir.json b/...enObds_shouldCreateValidMedicationStatement.Testpatient_1.xml.index_10.approved.fhir.json
@@ -0,0 +1,35 @@
+{
+  "resourceType": "Observation",
+  "meta": {
+    "profile": [ "https://www.medizininformatik-initiative.de/fhir/ext/modul-onko/StructureDefinition/mii-pr-onko-anzahl-befallene-sentinel-lymphknoten" ]
+  },
+  "identifier": [ {
+    "system": "https://bzkf.github.io/obds-to-fhir/identifiers/observation-histologie-id",
+    "value": "523_befallen_sentinel"
+  } ],
+  "status": "final",
+  "category": [ {
+    "coding": [ {
+      "system": "http://hl7.org/fhir/observation-category",
+      "code": "laboratory"
+    } ]
+  } ],
+  "code": {
+    "coding": [ {
+      "system": "http://loinc.org",
+      "code": "92832-5"
+    }, {
+      "system": "http://snomed.info/sct",
+      "code": "1264491009"
+    } ]
+  },
+  "subject": {
+    "reference": "Patient/any"
+  },
+  "effectiveDateTime": "2021-06-01",
+  "valueQuantity": {
+    "value": 1,
+    "system": "http://unitsofmeasure.org",
+    "code": "1"
+  }
+}
diff --git a/...enObds_shouldCreateValidMedicationStatement.Testpatient_1.xml.index_11.approved.fhir.json b/...enObds_shouldCreateValidMedicationStatement.Testpatient_1.xml.index_11.approved.fhir.json
@@ -0,0 +1,35 @@
+{
+  "resourceType": "Observation",
+  "meta": {
+    "profile": [ "https://www.medizininformatik-initiative.de/fhir/ext/modul-onko/StructureDefinition/mii-pr-onko-anzahl-untersuchte-sentinel-lymphknoten" ]
+  },
+  "identifier": [ {
+    "system": "https://bzkf.github.io/obds-to-fhir/identifiers/observation-histologie-id",
+    "value": "523_untersucht_sentinel"
+  } ],
+  "status": "final",
+  "category": [ {
+    "coding": [ {
+      "system": "http://hl7.org/fhir/observation-category",
+      "code": "laboratory"
+    } ]
+  } ],
+  "code": {
+    "coding": [ {
+      "system": "http://loinc.org",
+      "code": "85347-3"
+    }, {
+      "system": "http://snomed.info/sct",
+      "code": "444411008"
+    } ]
+  },
+  "subject": {
+    "reference": "Patient/any"
+  },
+  "effectiveDateTime": "2021-06-01",
+  "valueQuantity": {
+    "value": 1,
+    "system": "http://unitsofmeasure.org",
+    "code": "1"
+  }
+}
diff --git a/...venObds_shouldCreateValidMedicationStatement.Testpatient_1.xml.index_2.approved.fhir.json b/...venObds_shouldCreateValidMedicationStatement.Testpatient_1.xml.index_2.approved.fhir.json
@@ -0,0 +1,35 @@
+{
+  "resourceType": "Observation",
+  "meta": {
+    "profile": [ "https://www.medizininformatik-initiative.de/fhir/ext/modul-onko/StructureDefinition/mii-pr-onko-anzahl-befallene-sentinel-lymphknoten" ]
+  },
+  "identifier": [ {
+    "system": "https://bzkf.github.io/obds-to-fhir/identifiers/observation-histologie-id",
+    "value": "521_befallen_sentinel"
+  } ],
+  "status": "final",
+  "category": [ {
+    "coding": [ {
+      "system": "http://hl7.org/fhir/observation-category",
+      "code": "laboratory"
+    } ]
+  } ],
+  "code": {
+    "coding": [ {
+      "system": "http://loinc.org",
+      "code": "92832-5"
+    }, {
+      "system": "http://snomed.info/sct",
+      "code": "1264491009"
+    } ]
+  },
+  "subject": {
+    "reference": "Patient/any"
+  },
+  "effectiveDateTime": "2020-03-05",
+  "valueQuantity": {
+    "value": 1,
+    "system": "http://unitsofmeasure.org",
+    "code": "1"
+  }
+}
diff --git a/...venObds_shouldCreateValidMedicationStatement.Testpatient_1.xml.index_3.approved.fhir.json b/...venObds_shouldCreateValidMedicationStatement.Testpatient_1.xml.index_3.approved.fhir.json
@@ -0,0 +1,35 @@
+{
+  "resourceType": "Observation",
+  "meta": {
+    "profile": [ "https://www.medizininformatik-initiative.de/fhir/ext/modul-onko/StructureDefinition/mii-pr-onko-anzahl-untersuchte-sentinel-lymphknoten" ]
+  },
+  "identifier": [ {
+    "system": "https://bzkf.github.io/obds-to-fhir/identifiers/observation-histologie-id",
+    "value": "521_untersucht_sentinel"
+  } ],
+  "status": "final",
+  "category": [ {
+    "coding": [ {
+      "system": "http://hl7.org/fhir/observation-category",
+      "code": "laboratory"
+    } ]
+  } ],
+  "code": {
+    "coding": [ {
+      "system": "http://loinc.org",
+      "code": "85347-3"
+    }, {
+      "system": "http://snomed.info/sct",
+      "code": "444411008"
+    } ]
+  },
+  "subject": {
+    "reference": "Patient/any"
+  },
+  "effectiveDateTime": "2020-03-05",
+  "valueQuantity": {
+    "value": 2,
+    "system": "http://unitsofmeasure.org",
+    "code": "1"
+  }
+}
diff --git a/...venObds_shouldCreateValidMedicationStatement.Testpatient_1.xml.index_4.approved.fhir.json b/...venObds_shouldCreateValidMedicationStatement.Testpatient_1.xml.index_4.approved.fhir.json
@@ -0,0 +1,35 @@
+{
+  "resourceType": "Observation",
+  "meta": {
+    "profile": [ "https://www.medizininformatik-initiative.de/fhir/ext/modul-onko/StructureDefinition/mii-pr-onko-anzahl-befallene-lymphknoten" ]
+  },
+  "identifier": [ {
+    "system": "https://bzkf.github.io/obds-to-fhir/identifiers/observation-histologie-id",
+    "value": "522_befallen"
+  } ],
+  "status": "final",
+  "category": [ {
+    "coding": [ {
+      "system": "http://hl7.org/fhir/observation-category",
+      "code": "laboratory"
+    } ]
+  } ],
+  "code": {
+    "coding": [ {
+      "system": "http://loinc.org",
+      "code": "21893-3"
+    }, {
+      "system": "http://snomed.info/sct",
+      "code": "443527007"
+    } ]
+  },
+  "subject": {
+    "reference": "Patient/any"
+  },
+  "effectiveDateTime": "2020-03-05",
+  "valueQuantity": {
+    "value": 2,
+    "system": "http://unitsofmeasure.org",
+    "code": "1"
+  }
+}
diff --git a/...venObds_shouldCreateValidMedicationStatement.Testpatient_1.xml.index_5.approved.fhir.json b/...venObds_shouldCreateValidMedicationStatement.Testpatient_1.xml.index_5.approved.fhir.json
@@ -0,0 +1,35 @@
+{
+  "resourceType": "Observation",
+  "meta": {
+    "profile": [ "https://www.medizininformatik-initiative.de/fhir/ext/modul-onko/StructureDefinition/mii-pr-onko-anzahl-untersuchte-lymphknoten" ]
+  },
+  "identifier": [ {
+    "system": "https://bzkf.github.io/obds-to-fhir/identifiers/observation-histologie-id",
+    "value": "522_untersucht"
+  } ],
+  "status": "final",
+  "category": [ {
+    "coding": [ {
+      "system": "http://hl7.org/fhir/observation-category",
+      "code": "laboratory"
+    } ]
+  } ],
+  "code": {
+    "coding": [ {
+      "system": "http://loinc.org",
+      "code": "21894-1"
+    }, {
+      "system": "http://snomed.info/sct",
+      "code": "444025001"
+    } ]
+  },
+  "subject": {
+    "reference": "Patient/any"
+  },
+  "effectiveDateTime": "2020-03-05",
+  "valueQuantity": {
+    "value": 10,
+    "system": "http://unitsofmeasure.org",
+    "code": "1"
+  }
+}
diff --git a/...venObds_shouldCreateValidMedicationStatement.Testpatient_1.xml.index_6.approved.fhir.json b/...venObds_shouldCreateValidMedicationStatement.Testpatient_1.xml.index_6.approved.fhir.json
@@ -0,0 +1,35 @@
+{
+  "resourceType": "Observation",
+  "meta": {
+    "profile": [ "https://www.medizininformatik-initiative.de/fhir/ext/modul-onko/StructureDefinition/mii-pr-onko-anzahl-befallene-sentinel-lymphknoten" ]
+  },
+  "identifier": [ {
+    "system": "https://bzkf.github.io/obds-to-fhir/identifiers/observation-histologie-id",
+    "value": "522_befallen_sentinel"
+  } ],
+  "status": "final",
+  "category": [ {
+    "coding": [ {
+      "system": "http://hl7.org/fhir/observation-category",
+      "code": "laboratory"
+    } ]
+  } ],
+  "code": {
+    "coding": [ {
+      "system": "http://loinc.org",
+      "code": "92832-5"
+    }, {
+      "system": "http://snomed.info/sct",
+      "code": "1264491009"
+    } ]
+  },
+  "subject": {
+    "reference": "Patient/any"
+  },
+  "effectiveDateTime": "2020-03-05",
+  "valueQuantity": {
+    "value": 1,
+    "system": "http://unitsofmeasure.org",
+    "code": "1"
+  }
+}