Issue #28: Initiale Implementierung zur Ermittlung der NGS-Befund-Varianten

src/main/java/DNPM/analyzer/EinzelempfehlungAnalyzer.java

@@ -0,0 +1,104 @@
+package DNPM.analyzer;
+
+import DNPM.dto.Variant;
+import DNPM.security.DelegatingDataBasedPermissionEvaluator;
+import DNPM.services.molekulargenetik.MolekulargenetikFormService;
+import de.itc.onkostar.api.Disease;
+import de.itc.onkostar.api.IOnkostarApi;
+import de.itc.onkostar.api.Procedure;
+import de.itc.onkostar.api.analysis.AnalyzerRequirement;
+import de.itc.onkostar.api.analysis.IProcedureAnalyzer;
+import de.itc.onkostar.api.analysis.OnkostarPluginType;
+import org.springframework.stereotype.Component;
+
+import java.util.List;
+import java.util.Map;
+
+/**
+ * Diese Klasse implementiert ein Plugin, welches Funktionen für DNPM UF Einzelempfehlung bereit stellt.
+ *
+ * @since 0.2.0
+ */
+@Component
+public class EinzelempfehlungAnalyzer implements IProcedureAnalyzer {
+
+    private final IOnkostarApi onkostarApi;
+
+    private final MolekulargenetikFormService molekulargenetikFormService;
+
+    private final DelegatingDataBasedPermissionEvaluator permissionEvaluator;
+
+    public EinzelempfehlungAnalyzer(
+            final IOnkostarApi onkostarApi,
+            final MolekulargenetikFormService molekulargenetikFormService,
+            final DelegatingDataBasedPermissionEvaluator permissionEvaluator
+    ) {
+        this.onkostarApi = onkostarApi;
+        this.molekulargenetikFormService = molekulargenetikFormService;
+        this.permissionEvaluator = permissionEvaluator;
+    }
+
+    @Override
+    public OnkostarPluginType getType() {
+        return OnkostarPluginType.BACKEND_SERVICE;
+    }
+
+    @Override
+    public String getVersion() {
+        return "0.1.0";
+    }
+
+    @Override
+    public String getName() {
+        return "DNPM Einzelempfehlung Backend Service";
+    }
+
+    @Override
+    public String getDescription() {
+        return "Stellt Funktionen zur Nutzung im Therapieplan-Unterformular für Einzelempfehlungen bereit";
+    }
+
+    /**
+     * @deprecated
+     */
+    @Override
+    public boolean isRelevantForDeletedProcedure() {
+        return false;
+    }
+
+    @Override
+    public boolean isRelevantForAnalyzer(Procedure procedure, Disease disease) {
+        return false;
+    }
+
+    @Override
+    public boolean isSynchronous() {
+        return false;
+    }
+
+    @Override
+    public AnalyzerRequirement getRequirement() {
+        return AnalyzerRequirement.PROCEDURE;
+    }
+
+    @Override
+    public void analyze(Procedure procedure, Disease disease) {
+        // No op
+    }
+
+    public List<Variant> getVariants(Map<String, Object> input) {
+        var procedureId = AnalyzerUtils.getRequiredId(input, "id");
+
+        if (procedureId.isEmpty()) {
+            return List.of();
+        }
+
+        var procedure = onkostarApi.getProcedure(procedureId.get());
+        if (null == procedure) {
+            return List.of();
+        }
+
+        return molekulargenetikFormService.getVariants(procedure);
+    }
+
+}

src/main/java/DNPM/config/PluginConfiguration.java

@@ -3,6 +3,8 @@ package DNPM.config;
 import DNPM.database.SettingsRepository;
 import DNPM.services.*;
 import DNPM.services.consent.ConsentManagerServiceFactory;
+import DNPM.services.molekulargenetik.MolekulargenetikFormService;
+import DNPM.services.molekulargenetik.OsMolekulargenetikFormService;
 import DNPM.services.mtb.DefaultMtbService;
 import DNPM.services.mtb.MtbService;
 import DNPM.services.systemtherapie.DefaultSystemtherapieService;
@@ -68,4 +70,9 @@ public class PluginConfiguration {
         return new TherapieplanServiceFactory(onkostarApi, settingsService, formService);
     }
 
+    @Bean
+    public MolekulargenetikFormService molekulargenetikFormService() {
+        return new OsMolekulargenetikFormService();
+    }
+
 }

src/main/java/DNPM/dto/Variant.java

@@ -0,0 +1,67 @@
+package DNPM.dto;
+
+import de.itc.onkostar.api.Procedure;
+
+import java.util.Optional;
+
+public class Variant {
+    private final Integer id;
+
+    private final String shortDescription;
+
+    private Variant(
+            final int id,
+            final String shortDescription
+    ) {
+        this.id = id;
+        this.shortDescription = shortDescription.trim();
+    }
+
+    public Integer getId() {
+        return id;
+    }
+
+    public String getShortDescription() {
+        return shortDescription;
+    }
+
+    public static Optional<Variant> fromProcedure(Procedure procedure) {
+        if (! "OS.Molekulargenetische Untersuchung".equals(procedure.getFormName())) {
+            return Optional.empty();
+        }
+
+        var ergebnis = procedure.getValue("Ergebnis");
+        var gene = procedure.getValue("Untersucht");
+        var exon = procedure.getValue("ExonInt");
+        var pathogenitaetsklasse = procedure.getValue("Pathogenitaetsklasse");
+
+        if (null == gene) {
+            return Optional.empty();
+        }
+
+        if (ergebnis.getString().equals("P")) {
+            return Optional.of(
+                    new Variant(
+                            procedure.getId(),
+                            String.format("Einfache Variante: %s, %s, %s", gene.getString(), exon.getString(), pathogenitaetsklasse.getString())
+                    )
+            );
+        } else if (ergebnis.getString().equals("CNV")) {
+            return Optional.of(
+                    new Variant(
+                            procedure.getId(),
+                            String.format("Copy Number Variation: %s, %s, %s", gene.getString(), exon.getString(), pathogenitaetsklasse.getString())
+                    )
+            );
+        } else if (ergebnis.getString().equals("F")) {
+            return Optional.of(
+                    new Variant(
+                            procedure.getId(),
+                            String.format("Fusion: %s, %s, %s", gene.getString(), exon.getString(), pathogenitaetsklasse.getString())
+                    )
+            );
+        } else {
+            return Optional.empty();
+        }
+    }
+}

src/main/java/DNPM/services/molekulargenetik/MolekulargenetikFormService.java

@@ -0,0 +1,12 @@
+package DNPM.services.molekulargenetik;
+
+import DNPM.dto.Variant;
+import de.itc.onkostar.api.Procedure;
+
+import java.util.List;
+
+public interface MolekulargenetikFormService {
+
+    List<Variant> getVariants(Procedure procedure);
+
+}

src/main/java/DNPM/services/molekulargenetik/OsMolekulargenetikFormService.java

@@ -0,0 +1,34 @@
+package DNPM.services.molekulargenetik;
+
+import DNPM.dto.Variant;
+import DNPM.security.FormSecured;
+import DNPM.security.PersonPoolSecured;
+import de.itc.onkostar.api.Procedure;
+
+import java.util.List;
+import java.util.Optional;
+import java.util.stream.Collectors;
+
+public class OsMolekulargenetikFormService implements MolekulargenetikFormService {
+
+    @Override
+    @FormSecured
+    @PersonPoolSecured
+    public List<Variant> getVariants(Procedure procedure) {
+        if (! "OS.Molekulargenetik".equals(procedure.getFormName())) {
+            return List.of();
+        }
+
+        var subforms = procedure.getSubProceduresMap().get("MolekulargenetischeUntersuchung");
+        if (null == subforms) {
+            return List.of();
+        }
+
+        return subforms.stream()
+                .map(Variant::fromProcedure)
+                .filter(Optional::isPresent)
+                .map(Optional::get)
+                .collect(Collectors.toList());
+
+    }
+}