Merge pull request #30 from CCC-MF/issue_28

Ermitteln stützender molekularer Alterationen zu einem Formular "OS.Molekulargenetik"

3 files changed, 198 insertions, 0 deletions

diff --git a/src/test/java/DNPM/analyzer/EinzelempfehlungAnalyzerTest.java b/src/test/java/DNPM/analyzer/EinzelempfehlungAnalyzerTest.java
new file mode 100644
index 0000000..337ffdb
--- /dev/null
+++ b/src/test/java/DNPM/analyzer/EinzelempfehlungAnalyzerTest.java
@@ -0,0 +1,46 @@
+package DNPM.analyzer;
+
+import DNPM.security.DelegatingDataBasedPermissionEvaluator;
+import DNPM.services.molekulargenetik.MolekulargenetikFormService;
+import de.itc.onkostar.api.IOnkostarApi;
+import de.itc.onkostar.api.Procedure;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
+import org.mockito.Mock;
+import org.mockito.junit.jupiter.MockitoExtension;
+
+import java.util.Map;
+
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.Mockito.*;
+
+@ExtendWith(MockitoExtension.class)
+class EinzelempfehlungAnalyzerTest {
+
+    private IOnkostarApi onkostarApi;
+
+    private MolekulargenetikFormService molekulargenetikFormService;
+
+    private EinzelempfehlungAnalyzer analyzer;
+
+    @BeforeEach
+    void setup(
+            @Mock IOnkostarApi onkostarApi,
+            @Mock MolekulargenetikFormService molekulargenetikFormService,
+            @Mock DelegatingDataBasedPermissionEvaluator permissionEvaluator
+    ) {
+        this.onkostarApi = onkostarApi;
+        this.molekulargenetikFormService = molekulargenetikFormService;
+        this.analyzer = new EinzelempfehlungAnalyzer(onkostarApi, molekulargenetikFormService, permissionEvaluator);
+    }
+
+    @Test
+    void testShouldRequestVariantsFromMolekulargenetikFormService() {
+        doAnswer(invocationOnMock -> new Procedure(this.onkostarApi)).when(onkostarApi).getProcedure(anyInt());
+
+        analyzer.getVariants(Map.of("id", 123));
+        verify(molekulargenetikFormService, times(1)).getVariants(any(Procedure.class));
+    }
+
+}
diff --git a/src/test/java/DNPM/dto/VariantTest.java b/src/test/java/DNPM/dto/VariantTest.java
new file mode 100644
index 0000000..3242852
--- /dev/null
+++ b/src/test/java/DNPM/dto/VariantTest.java
@@ -0,0 +1,103 @@
+package DNPM.dto;
+
+import de.itc.onkostar.api.Item;
+import de.itc.onkostar.api.Procedure;
+import org.junit.jupiter.api.Test;
+
+import static org.assertj.core.api.Assertions.assertThat;
+
+public class VariantTest {
+
+    @Test
+    void testShouldMapVariantFromProcedureForSimpleVariant() {
+        var procedure = new Procedure(null);
+        procedure.setId(12345);
+        procedure.setFormName("OS.Molekulargenetische Untersuchung");
+
+        procedure.setValue("Ergebnis", new Item("Ergebnis", "P"));
+        procedure.setValue("Untersucht", new Item("Untersucht", "BRAF"));
+        procedure.setValue("ExonInt", new Item("ExonInt", 123));
+        procedure.setValue("Pathogenitaetsklasse", new Item("Pathogenitaetsklasse", "2"));
+
+        var actual = Variant.fromProcedure(procedure);
+
+        assertThat(actual).isPresent();
+        assertThat(actual.get().getId()).isEqualTo(12345);
+        assertThat(actual.get().getErgebnis()).isEqualTo("Einfache Variante (Mutation)");
+        assertThat(actual.get().getGen()).isEqualTo("BRAF");
+        assertThat(actual.get().getExon()).isEqualTo("123");
+        assertThat(actual.get().getPathogenitaetsklasse()).isEqualTo("2");
+    }
+
+    @Test
+    void testShouldMapVariantFromProcedureForCopyNumberVariation() {
+        var procedure = new Procedure(null);
+        procedure.setId(12345);
+        procedure.setFormName("OS.Molekulargenetische Untersuchung");
+
+        procedure.setValue("Ergebnis", new Item("Ergebnis", "CNV"));
+        procedure.setValue("Untersucht", new Item("Untersucht", "BRAF"));
+        procedure.setValue("ExonInt", new Item("ExonInt", 123));
+        procedure.setValue("Pathogenitaetsklasse", new Item("Pathogenitaetsklasse", "2"));
+
+        var actual = Variant.fromProcedure(procedure);
+
+        assertThat(actual).isPresent();
+        assertThat(actual.get().getId()).isEqualTo(12345);
+        assertThat(actual.get().getErgebnis()).isEqualTo("Copy Number Variation (CNV)");
+        assertThat(actual.get().getGen()).isEqualTo("BRAF");
+        assertThat(actual.get().getExon()).isEqualTo("123");
+        assertThat(actual.get().getPathogenitaetsklasse()).isEqualTo("2");
+    }
+
+    @Test
+    void testShouldMapVariantFromProcedureForFusion() {
+        var procedure = new Procedure(null);
+        procedure.setId(12345);
+        procedure.setFormName("OS.Molekulargenetische Untersuchung");
+
+        procedure.setValue("Ergebnis", new Item("Ergebnis", "F"));
+        procedure.setValue("Untersucht", new Item("Untersucht", "BRAF"));
+        procedure.setValue("ExonInt", new Item("ExonInt", 123));
+        procedure.setValue("Pathogenitaetsklasse", new Item("Pathogenitaetsklasse", "2"));
+
+        var actual = Variant.fromProcedure(procedure);
+
+        assertThat(actual).isPresent();
+        assertThat(actual.get().getId()).isEqualTo(12345);
+        assertThat(actual.get().getErgebnis()).isEqualTo("Fusion (Translokation Inversion Insertion)");
+        assertThat(actual.get().getGen()).isEqualTo("BRAF");
+        assertThat(actual.get().getExon()).isEqualTo("123");
+        assertThat(actual.get().getPathogenitaetsklasse()).isEqualTo("2");
+    }
+
+    @Test
+    void testShouldNotMapVariantFromProcedureForUnknownVariant() {
+        var procedure = new Procedure(null);
+        procedure.setId(12345);
+        procedure.setFormName("OS.Molekulargenetische Untersuchung");
+
+        procedure.setValue("Ergebnis", new Item("Ergebnis", "X"));
+        procedure.setValue("Untersucht", new Item("Untersucht", "BRAF"));
+        procedure.setValue("ExonInt", new Item("ExonInt", 123));
+        procedure.setValue("Pathogenitaetsklasse", new Item("Pathogenitaetsklasse", "2"));
+
+        var actual = Variant.fromProcedure(procedure);
+
+        assertThat(actual).isEmpty();
+    }
+
+    @Test
+    void testShouldNotMapVariantFromUnknownProcedureForm() {
+        var procedure = new Procedure(null);
+        procedure.setId(12345);
+        procedure.setFormName("ABC.Irgendwas");
+
+        procedure.setValue("Testfeld", new Item("Testfeld", "T"));
+
+        var actual = Variant.fromProcedure(procedure);
+
+        assertThat(actual).isEmpty();
+    }
+
+}
diff --git a/src/test/java/DNPM/services/molekulargenetik/OsMolekluargenetikFormServiceTest.java b/src/test/java/DNPM/services/molekulargenetik/OsMolekluargenetikFormServiceTest.java
new file mode 100644
index 0000000..4e11341
--- /dev/null
+++ b/src/test/java/DNPM/services/molekulargenetik/OsMolekluargenetikFormServiceTest.java
@@ -0,0 +1,49 @@
+package DNPM.services.molekulargenetik;
+
+import de.itc.onkostar.api.Item;
+import de.itc.onkostar.api.Procedure;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+
+import static org.assertj.core.api.Assertions.assertThat;
+
+public class OsMolekluargenetikFormServiceTest {
+
+    private OsMolekulargenetikFormService service;
+
+    @BeforeEach
+    void setup() {
+        this.service = new OsMolekulargenetikFormService();
+    }
+
+    @Test
+    void testShouldReturnVariants() {
+
+        var procedure = new Procedure(null);
+        procedure.setId(123);
+        procedure.setFormName("OS.Molekulargenetik");
+
+        var subProcedure1 = new Procedure(null);
+        subProcedure1.setId(1123);
+        subProcedure1.setFormName("OS.Molekulargenetische Untersuchung");
+        subProcedure1.setValue("Ergebnis", new Item("Ergebnis", "P"));
+        subProcedure1.setValue("Untersucht", new Item("Untersucht", "BRAF"));
+        subProcedure1.setValue("ExonInt", new Item("ExonInt", 123));
+        subProcedure1.setValue("Pathogenitaetsklasse", new Item("Pathogenitaetsklasse", "2"));
+        procedure.addSubProcedure("MolekulargenetischeUntersuchung", subProcedure1);
+
+        var subProcedure2 = new Procedure(null);
+        subProcedure2.setId(2123);
+        subProcedure2.setFormName("OS.Molekulargenetische Untersuchung");
+        subProcedure2.setValue("Ergebnis", new Item("Ergebnis", "CNV"));
+        subProcedure2.setValue("Untersucht", new Item("Untersucht", "BRAF"));
+        subProcedure2.setValue("ExonInt", new Item("ExonInt", 123));
+        subProcedure2.setValue("Pathogenitaetsklasse", new Item("Pathogenitaetsklasse", "2"));
+        procedure.addSubProcedure("MolekulargenetischeUntersuchung", subProcedure2);
+
+        var actual = service.getVariants(procedure);
+
+        assertThat(actual).hasSize(2);
+    }
+
+}