fix: add some filters and cleanups

src/main/java/dev/pcvolkmer/onco/datamapper/ResultSet.java

@@ -131,6 +131,8 @@ public class ResultSet {
             return null;
         } else if (raw instanceof Integer) {
             return ((Integer) raw).longValue();
+        } else if (raw instanceof Double) {
+            return ((Double) raw).longValue();
         } else if (raw instanceof Long) {
             return ((Long) raw);
         }

src/main/java/dev/pcvolkmer/onco/datamapper/datacatalogues/AbstractDataCatalogue.java

@@ -54,7 +54,7 @@ public abstract class AbstractDataCatalogue implements DataCatalogue {
     public ResultSet getById(int id) {
         var result = this.jdbcTemplate.queryForList(
                 String.format(
-                        "SELECT patient.patienten_id, %s.*, prozedur.* FROM %s JOIN prozedur ON (prozedur.id = %s.id) JOIN patient ON (patient.id = prozedur.patient_id) WHERE geloescht = 0 AND prozedur.id = ?",
+                        "SELECT patient.patienten_id, %s.*, prozedur.patient_id, prozedur.hauptprozedur_id FROM %s JOIN prozedur ON (prozedur.id = %s.id) JOIN patient ON (patient.id = prozedur.patient_id) WHERE geloescht = 0 AND prozedur.id = ?",
                         getTableName(),
                         getTableName(),
                         getTableName()

src/main/java/dev/pcvolkmer/onco/datamapper/datacatalogues/AbstractSubformDataCatalogue.java

@@ -51,7 +51,7 @@ public abstract class AbstractSubformDataCatalogue extends AbstractDataCatalogue
     public List<ResultSet> getAllByParentId(int id) {
         return this.jdbcTemplate.queryForList(
                         String.format(
-                                "SELECT patient.patienten_id, %s.*, prozedur.* FROM %s JOIN prozedur ON (prozedur.id = %s.id) JOIN patient ON (patient.id = prozedur.patient_id) WHERE geloescht = 0 AND hauptprozedur_id = ?",
+                                "SELECT patient.patienten_id, %s.*, prozedur.patient_id, prozedur.hauptprozedur_id FROM %s JOIN prozedur ON (prozedur.id = %s.id) JOIN patient ON (patient.id = prozedur.patient_id) WHERE geloescht = 0 AND hauptprozedur_id = ?",
                                 getTableName(),
                                 getTableName(),
                                 getTableName()

src/main/java/dev/pcvolkmer/onco/datamapper/mapper/AbstractEinzelempfehlungDataMapper.java

@@ -212,4 +212,23 @@ public abstract class AbstractEinzelempfehlungDataMapper<T> extends AbstractSubf
 
         return resultBuilder.build();
     }
+
+    protected RecommendationPriorityCoding getRecommendationPriorityCoding(int value) {
+        var resultBuilder = RecommendationPriorityCoding.builder()
+                .system("dnpm-dip/recommendation/priority")
+                .display(String.format("%d", value));
+        switch (value) {
+            case 1:
+                resultBuilder.code(RecommendationPriorityCodingCode.CODE_1);
+            case 2:
+                resultBuilder.code(RecommendationPriorityCodingCode.CODE_3);
+            case 3:
+                resultBuilder.code(RecommendationPriorityCodingCode.CODE_3);
+            case 4:
+            default:
+                resultBuilder.code(RecommendationPriorityCodingCode.CODE_4);
+        }
+
+        return resultBuilder.build();
+    }
 }

src/main/java/dev/pcvolkmer/onco/datamapper/mapper/EinzelempfehlungProzedurDataMapper.java

@@ -20,10 +20,7 @@
 
 package dev.pcvolkmer.onco.datamapper.mapper;
 
-import dev.pcvolkmer.mv64e.mtb.MtbProcedureRecommendationCategoryCoding;
+import dev.pcvolkmer.mv64e.mtb.*;
-import dev.pcvolkmer.mv64e.mtb.MtbProcedureRecommendationCategoryCodingCode;
-import dev.pcvolkmer.mv64e.mtb.ProcedureRecommendation;
-import dev.pcvolkmer.mv64e.mtb.Reference;
 import dev.pcvolkmer.onco.datamapper.ResultSet;
 import dev.pcvolkmer.onco.datamapper.datacatalogues.EinzelempfehlungCatalogue;
 
@@ -49,6 +46,7 @@ public class EinzelempfehlungProzedurDataMapper extends AbstractEinzelempfehlung
         var resultBuilder = ProcedureRecommendation.builder()
                 .id(resultSet.getString("id"))
                 .patient(resultSet.getPatientReference())
+                .priority(getRecommendationPriorityCoding(resultSet.getInteger("prio")))
                 // TODO Fix id?
                 .reason(Reference.builder().id(resultSet.getString("id")).build())
                 .issuedOn(resultSet.getDate("datum"))

src/main/java/dev/pcvolkmer/onco/datamapper/mapper/EinzelempfehlungStudieDataMapper.java

@@ -45,15 +45,10 @@ public class EinzelempfehlungStudieDataMapper extends AbstractEinzelempfehlungDa
         var resultBuilder = MtbStudyEnrollmentRecommendation.builder()
                 .id(resultSet.getString("id"))
                 .patient(resultSet.getPatientReference())
+                .priority(getRecommendationPriorityCoding(resultSet.getInteger("prio")))
                 // TODO Fix id?
                 .reason(Reference.builder().id(resultSet.getString("id")).build())
                 .issuedOn(resultSet.getDate("datum"))
-                .priority(
-                        getRecommendationPriorityCoding(
-                                resultSet.getString("evidenzlevel"),
-                                resultSet.getInteger("evidenzlevel_propcat_version")
-                        )
-                )
                 .medication(JsonToMedicationMapper.map(resultSet.getString("wirkstoffe_json")))
                 .levelOfEvidence(getLevelOfEvidence(resultSet))
                 .study(JsonToStudyMapper.map(resultSet.getString("studien_alle_json")));

src/main/java/dev/pcvolkmer/onco/datamapper/mapper/EinzelempfehlungWirkstoffDataMapper.java

@@ -53,15 +53,10 @@ public class EinzelempfehlungWirkstoffDataMapper extends AbstractEinzelempfehlun
         var resultBuilder = MtbMedicationRecommendation.builder()
                 .id(resultSet.getString("id"))
                 .patient(resultSet.getPatientReference())
+                .priority(getRecommendationPriorityCoding(resultSet.getInteger("prio")))
                 // TODO Fix id?
                 .reason(Reference.builder().id(resultSet.getString("id")).build())
                 .issuedOn(resultSet.getDate("datum"))
-                .priority(
-                        getRecommendationPriorityCoding(
-                                resultSet.getString("evidenzlevel"),
-                                resultSet.getInteger("evidenzlevel_propcat_version")
-                        )
-                )
                 .medication(JsonToMedicationMapper.map(resultSet.getString("wirkstoffe_json")))
                 .levelOfEvidence(getLevelOfEvidence(resultSet));
 

src/main/java/dev/pcvolkmer/onco/datamapper/mapper/KpaDiagnosisDataMapper.java

@@ -22,6 +22,7 @@ package dev.pcvolkmer.onco.datamapper.mapper;
 
 import dev.pcvolkmer.mv64e.mtb.*;
 import dev.pcvolkmer.onco.datamapper.PropertyCatalogue;
+import dev.pcvolkmer.onco.datamapper.ResultSet;
 import dev.pcvolkmer.onco.datamapper.datacatalogues.KpaCatalogue;
 import dev.pcvolkmer.onco.datamapper.datacatalogues.TumorausbreitungCatalogue;
 import dev.pcvolkmer.onco.datamapper.datacatalogues.TumorgradingCatalogue;
@@ -79,7 +80,9 @@ public class KpaDiagnosisDataMapper implements DataMapper<MtbDiagnosis> {
                                 .version(propertyCatalogue.getByCodeAndVersion(data.getString("icd10"), data.getInteger("icd10_propcat_version")).getVersionDescription())
                                 .build()
                 )
-                .topography(Coding.builder().code(data.getString("icdo3localisation")).build())
+                .recordedOn(data.getDate("datumerstdiagnose"))
+                .topography(Coding.builder().code(data.getString("icdo3lokalisation")).build())
+                .type(getType(data))
                 // Nicht in Onkostar erfasst
                 //.germlineCodes()
                 .guidelineTreatmentStatus(
@@ -168,4 +171,29 @@ public class KpaDiagnosisDataMapper implements DataMapper<MtbDiagnosis> {
 
         return Staging.builder().history(all).build();
     }
+
+    private Type getType(final ResultSet resultSet) {
+        var diagnosisCoding = MtbDiagnosisCoding.builder();
+        var code = resultSet.getString("diagnosetyp");
+        if (code == null || !Arrays.stream(ValueCode.values()).map(ValueCode::toValue).collect(Collectors.toSet()).contains(code)) {
+            return null;
+        }
+
+        try {
+            diagnosisCoding.code(ValueCode.forValue(code));
+        } catch (IOException e) {
+            throw new IllegalStateException("No valid code found");
+        }
+
+        return Type.builder()
+                .history(
+                        List.of(
+                                History.builder()
+                                        .date(resultSet.getDate("datumerstdiagnose"))
+                                        .value(diagnosisCoding.build())
+                                        .build()
+                        )
+                )
+                .build();
+    }
 }

src/main/java/dev/pcvolkmer/onco/datamapper/mapper/KpaHistologieDataMapper.java

@@ -93,8 +93,8 @@ public class KpaHistologieDataMapper extends AbstractSubformDataMapper<Histology
                                                     .patient(resultSet.getPatientReference())
                                                     .specimen(Reference.builder().id(osMolGen.getId().toString()).type("Specimen").build())
                                                     .value(resultSet.getLong("tumorzellgehalt"))
-                                                    // Nicht in OS.Molekulargenetik
+                                                    // TODO: Nicht in OS.Molekulargenetik
-                                                    //.method()
+                                                    .method(TumorCellContentMethodCoding.builder().code(TumorCellContentMethodCodingCode.HISTOLOGIC).build())
                                                     .build()
                                     )
                                     .tumorMorphology(

src/main/java/dev/pcvolkmer/onco/datamapper/mapper/KpaMolekulargenetikDataMapper.java

@@ -96,18 +96,20 @@ public class KpaMolekulargenetikDataMapper implements DataMapper<SomaticNgsRepor
 
         var resultBuilder = NgsReportResults.builder();
 
-        // TODO: Aktuell nicht eingebunden, da Fehler, wenn nicht bioinformatisch gemäß: https://ibmi-ut.atlassian.net/wiki/spaces/DAM/pages/698777783/ Zeile 144!
+        // TODO: Aktuell problematisch, wenn nicht bioinformatisch gemäß: https://ibmi-ut.atlassian.net/wiki/spaces/DAM/pages/698777783/ Zeile 144!
         //  In Würzburg immer histologisch!
-        /*if (null != resultSet.getLong("tumorzellgehalt")) {
+        if (null != resultSet.getLong("tumorzellgehalt")) {
             resultBuilder.tumorCellContent(
                     TumorCellContent.builder()
                             .id(resultSet.getId().toString())
                             .patient(resultSet.getPatientReference())
                             .specimen(Reference.builder().id(resultSet.getString("einsendenummer")).type("Specimen").build())
                             .value(resultSet.getLong("tumorzellgehalt"))
+                            // TODO: Missing in OS.Molekulargenetik
+                            .method(TumorCellContentMethodCoding.builder().code(TumorCellContentMethodCodingCode.HISTOLOGIC).build())
                             .build()
             );
-        }*/
+        }
 
         resultBuilder.simpleVariants(
                 subforms.stream()
@@ -123,6 +125,7 @@ public class KpaMolekulargenetikDataMapper implements DataMapper<SomaticNgsRepor
                                     .id(subform.getString("id"))
                                     .patient(subform.getPatientReference())
                                     .gene(GeneUtils.toCoding(geneOptional.get()))
+                                    .transcriptId(TranscriptId.builder().value(geneOptional.get().getEnsemblId()).system(TranscriptIdSystem.ENSEMBL_ORG).build())
                                     .exonId(subform.getString("exon"))
                                     .dnaChange(subform.getString("cdnanomenklatur"))
                                     .proteinChange(subform.getString("proteinebenenomenklatur"));
@@ -133,10 +136,19 @@ public class KpaMolekulargenetikDataMapper implements DataMapper<SomaticNgsRepor
                             if (null != subform.getLong("evreaddepth")) {
                                 snvBuilder.readDepth(subform.getLong("evreaddepth"));
                             }
+                            if (null != subform.getString("evaltnucleotide")) {
+                                snvBuilder.altAllele(subform.getString("evaltnucleotide"));
+                            }
+                            if (null != subform.getString("evrefnucleotide")) {
+                                snvBuilder.altAllele(subform.getString("evrefnucleotide"));
+                            }
+
                             geneOptional.get().getSingleChromosomeInPropertyForm().ifPresent(snvBuilder::chromosome);
 
                             return snvBuilder.build();
                         })
+                        // TODO: Filter missing position, altAllele, refAllele
+                        .filter(snv -> snv.getPosition() != null && snv.getAltAllele() != null && snv.getRefAllele() != null)
                         .collect(Collectors.toList())
         );
 

src/main/java/dev/pcvolkmer/onco/datamapper/mapper/KpaProzedurDataMapper.java

@@ -28,6 +28,7 @@ import dev.pcvolkmer.onco.datamapper.ResultSet;
 import dev.pcvolkmer.onco.datamapper.datacatalogues.ProzedurCatalogue;
 
 import java.util.List;
+import java.util.stream.Collectors;
 
 /**
  * Mapper class to load and map prozedur data from database table 'dk_dnpm_uf_prozedur'
@@ -53,6 +54,12 @@ public class KpaProzedurDataMapper extends AbstractKpaTherapieverlaufDataMapper<
         return this.map(data);
     }
 
+    // TODO: Fix for DNPM:DIP verification that does not accept procedures without reason.id
+    @Override
+    public List<OncoProcedure> getByParentId(final int id) {
+        return super.getByParentId(id).stream().filter(p -> p.getReason() != null && p.getReason().getId() != null).collect(Collectors.toList());
+    }
+
     @Override
     protected OncoProcedure map(final ResultSet resultSet) {
         var diseases = catalogue.getDiseases(resultSet.getId());