pcvolkmer/onkostar-plugin-dnpm
1
0
Fork 0
mirror of https://github.com/pcvolkmer/onkostar-plugin-dnpm.git synced 2025-07-02 01:02:55 +00:00
Code Issues Activity

Merge pull request #57 from CCC-MF/issue_54

Browse Source 
Übernahme des ECOG-Status aus anderen Therapieformularen
This commit is contained in:
Paul-Christian Volkmer
2023-10-10 13:03:55 +02:00
committed by GitHub
parent c1ccac5c16 9c503d2244
commit 1b27a9c290
10 changed files with 353 additions and 78 deletions
Download Patch File Download Diff File Expand all files Collapse all files

3
src/main/java/DNPM/analyzer/DNPMHelper.java
View File

@ -1,5 +1,6 @@
package DNPM.analyzer;
import DNPM.dto.EcogStatusWithDate;
import DNPM.VerweisVon;
import DNPM.security.DelegatingDataBasedPermissionEvaluator;
import DNPM.security.IllegalSecuredObjectAccessException;
@ -237,7 +238,7 @@ public class DNPMHelper extends BackendService {
}
public List<SystemtherapieService.EcogStatusWithDate> getEcogStatus(final Map<String, Object> input) {
public List<EcogStatusWithDate> getEcogStatus(final Map<String, Object> input) {
var pid = AnalyzerUtils.getRequiredId(input, "PatientId");
if (pid.isEmpty()) {
logger.error("Kein Parameter 'PatientId' angegeben, gebe leere Liste zurück");

35
src/main/java/DNPM/analyzer/SystemtherapieAnalyzer.java → src/main/java/DNPM/analyzer/TherapieMitEcogAnalyzer.java
View File

@ -1,5 +1,7 @@
package DNPM.analyzer;
import DNPM.dto.EcogStatusWithDate;
import DNPM.services.strahlentherapie.StrahlentherapieService;
import DNPM.services.systemtherapie.SystemtherapieService;
import de.itc.onkostar.api.Disease;
import de.itc.onkostar.api.IOnkostarApi;
@ -20,28 +22,31 @@ import java.util.stream.Collectors;
/**
* Diese Klasse implementiert ein Plugin, welches Aktionen nach Bearbeitung eines Formulars zur Systemtherapie durchführt.
*
* @since 0.4.0
* @since 0.6.0
*/
@Component
public class SystemtherapieAnalyzer extends Analyzer {
public class TherapieMitEcogAnalyzer extends Analyzer {
private final Logger logger = LoggerFactory.getLogger(this.getClass());
private final IOnkostarApi onkostarApi;
private final StrahlentherapieService strahlentherapieService;
private final SystemtherapieService systemtherapieService;
public SystemtherapieAnalyzer(
public TherapieMitEcogAnalyzer(
final IOnkostarApi onkostarApi,
final StrahlentherapieService strahlentherapieService,
final SystemtherapieService systemtherapieService
) {
this.onkostarApi = onkostarApi;
this.strahlentherapieService = strahlentherapieService;
this.systemtherapieService = systemtherapieService;
}
@Override
public String getDescription() {
return "Aktualisiert verknüpfte Formulare nach Änderungen im Formularen vom Typ Systemtherapie";
return "Aktualisiert verknüpfte Formulare nach Änderungen in Formularen vom Typ Strahlen-/Systemtherapie mit ECOG-Status";
}
/**
@ -55,7 +60,9 @@ public class SystemtherapieAnalyzer extends Analyzer {
@Override
public boolean isRelevantForAnalyzer(Procedure procedure, Disease disease) {
return null != procedure && null != disease && (
procedure.getFormName().equals("OS.Systemische Therapie")
procedure.getFormName().equals("OS.Strahlentherapie")
|| procedure.getFormName().equals("OS.Strahlentherapie.VarianteUKW")
|| procedure.getFormName().equals("OS.Systemische Therapie")
|| procedure.getFormName().equals("OS.Systemische Therapie.VarianteUKW")
);
}
@ -89,12 +96,18 @@ public class SystemtherapieAnalyzer extends Analyzer {
return;
}
var ecogFromCompleted = systemtherapieService.ecogStatus(procedure.getPatient())
var ecog = strahlentherapieService.ecogStatus(procedure.getPatient())
.stream()
.filter(ecogStatusWithDate -> ecogStatusWithDate.getDate().after(disease.getDiagnosisDate()))
.collect(Collectors.toList());
if (ecogFromCompleted.isEmpty()) {
ecog.addAll(systemtherapieService.ecogStatus(procedure.getPatient())
.stream()
.filter(ecogStatusWithDate -> ecogStatusWithDate.getDate().after(disease.getDiagnosisDate()))
.collect(Collectors.toList()));
if (ecog.isEmpty()) {
// Nothing to do
return;
}
@ -104,14 +117,14 @@ public class SystemtherapieAnalyzer extends Analyzer {
.forEach(p -> {
var ufEcog = p.getValue("ECOGVerlauf");
if (null != ufEcog && ufEcog.getValue() instanceof List) {
updateExistingEcogVerlauf(p, ecogFromCompleted, ufEcog);
updateExistingEcogVerlauf(p, ecog, ufEcog);
} else {
newEcogverlauf(p, ecogFromCompleted);
newEcogverlauf(p, ecog);
}
});
}
private void updateExistingEcogVerlauf(Procedure p, List<SystemtherapieService.EcogStatusWithDate> ecogFromCompleted, Item ufEcog) {
private void updateExistingEcogVerlauf(Procedure p, List<EcogStatusWithDate> ecogFromCompleted, Item ufEcog) {
var shouldSave = false;
var existingDates = ufEcog.<List<Map<String, String>>>getValue().stream()
.map(v -> v.get("Datum"))
@ -136,7 +149,7 @@ public class SystemtherapieAnalyzer extends Analyzer {
}
}
private void newEcogverlauf(Procedure p, List<SystemtherapieService.EcogStatusWithDate> ecogFromCompleted) {
private void newEcogverlauf(Procedure p, List<EcogStatusWithDate> ecogFromCompleted) {
p.setValue("ECOGVerlauf", new Item("ECOGVerlauf", List.of()));
for (var ecog : ecogFromCompleted) {
var newSubProcedure = new Procedure(onkostarApi);

68
src/main/java/DNPM/dto/EcogStatusWithDate.java Normal file
View File

@ -0,0 +1,68 @@
/*
* MIT License
*
* 2023 Comprehensive Cancer Center Mainfranken
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in all
* copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
*/
package DNPM.dto;
import org.springframework.util.Assert;
import java.util.Date;
/**
* Datenklasse zum Abbilden des ECOG-Status und Datum
*/
public class EcogStatusWithDate {
private Date date;
private String status;
public EcogStatusWithDate(Date date, String status) {
Assert.notNull(date, "Date cannot be null");
Assert.hasText(status, "Status cannot be empty String");
Assert.isTrue(isValidEcogCode(status), "Not a valid ADT.LeistungszustandECOG code");
this.date = date;
this.status = status;
}
private boolean isValidEcogCode(String status) {
switch (status) {
case "0":
case "1":
case "2":
case "3":
case "4":
case "5":
case "U":
return true;
default:
return false;
}
}
public Date getDate() {
return date;
}
public String getStatus() {
return status;
}
}

30
src/main/java/DNPM/services/TherapieMitEcogService.java Normal file
View File

@ -0,0 +1,30 @@
package DNPM.services;
import DNPM.dto.EcogStatusWithDate;
import de.itc.onkostar.api.Patient;
import java.util.List;
import java.util.Optional;
/**
* Schnittstelle zum Ermitteln von ECOG-Statusinformationen
*
* @since 0.6.0
*/
public interface TherapieMitEcogService {
/**
* Ermittelt den letzten bekannten ECOG-Status aus allen Therapieformularen des Patienten
* @param patient Der zu verwendende Patient
* @return Der ECOG-Status als String oder leeres Optional
*/
Optional<String> latestEcogStatus(Patient patient);
/**
* Ermittelt jeden bekannten ECOG-Status aus allen Therapieformularen des Patienten
* @param patient Der zu verwendende Patient
* @return Eine Liste mit Datum und ECOG-Status als String
*/
List<EcogStatusWithDate> ecogStatus(Patient patient);
}

74
src/main/java/DNPM/services/strahlentherapie/DefaultStrahlentherapieService.java Normal file
View File

@ -0,0 +1,74 @@
package DNPM.services.strahlentherapie;
import DNPM.dto.EcogStatusWithDate;
import DNPM.services.SettingsService;
import de.itc.onkostar.api.IOnkostarApi;
import de.itc.onkostar.api.Patient;
import de.itc.onkostar.api.Procedure;
import java.util.Comparator;
import java.util.List;
import java.util.Objects;
import java.util.Optional;
import java.util.stream.Collectors;
/**
* Standardimplementierung des StrahlentherapieServices
*
* @since 0.6.0
*/
public class DefaultStrahlentherapieService implements StrahlentherapieService {
private static final String ECOG_FIELD = "ECOGvorTherapie";
private final IOnkostarApi onkostarApi;
private final SettingsService settingsService;
public DefaultStrahlentherapieService(final IOnkostarApi onkostarApi, final SettingsService settingsService) {
this.onkostarApi = onkostarApi;
this.settingsService = settingsService;
}
/**
* Ermittelt den letzten bekannten ECOG-Status aus allen Systemtherapieformularen des Patienten
*
* @param patient Der zu verwendende Patient
* @return Der ECOG-Status als String oder leeres Optional
*/
@Override
public Optional<String> latestEcogStatus(Patient patient) {
return ecogStatus(patient).stream()
.max(Comparator.comparing(EcogStatusWithDate::getDate))
.map(EcogStatusWithDate::getStatus);
}
/**
* Ermittelt jeden bekannten ECOG-Status aus allen Systemtherapieformularen des Patienten
*
* @param patient Der zu verwendende Patient
* @return Eine Liste mit Datum und ECOG-Status als String
*/
@Override
public List<EcogStatusWithDate> ecogStatus(Patient patient) {
return patient.getDiseases().stream()
.flatMap(disease -> onkostarApi.getProceduresForDiseaseByForm(disease.getId(), getFormName()).stream())
.filter(procedure -> null != procedure.getStartDate())
.sorted(Comparator.comparing(Procedure::getStartDate))
.map(procedure -> {
try {
return new EcogStatusWithDate(procedure.getStartDate(), procedure.getValue(ECOG_FIELD).getString());
} catch (IllegalArgumentException e) {
return null;
}
})
.filter(Objects::nonNull)
.collect(Collectors.toList());
}
private String getFormName() {
return settingsService
.getSetting("strahlentherapieform")
.orElse("OS.Strahlentherapie");
}
}

10
src/main/java/DNPM/services/strahlentherapie/StrahlentherapieService.java Normal file
View File

@ -0,0 +1,10 @@
package DNPM.services.strahlentherapie;
import DNPM.services.TherapieMitEcogService;
/**
* Service für Systemtherapieformulare
*
* @since 0.6.0
*/
public interface StrahlentherapieService extends TherapieMitEcogService {}

1
src/main/java/DNPM/services/systemtherapie/DefaultSystemtherapieService.java
View File

@ -1,5 +1,6 @@
package DNPM.services.systemtherapie;
import DNPM.dto.EcogStatusWithDate;
import DNPM.services.SettingsService;
import de.itc.onkostar.api.IOnkostarApi;
import de.itc.onkostar.api.Patient;

60
src/main/java/DNPM/services/systemtherapie/SystemtherapieService.java
View File

@ -1,20 +1,17 @@
package DNPM.services.systemtherapie;
import de.itc.onkostar.api.Patient;
import DNPM.services.TherapieMitEcogService;
import de.itc.onkostar.api.Procedure;
import org.springframework.util.Assert;
import java.util.Date;
import java.util.List;
import java.util.Map;
import java.util.Optional;
/**
* Service für Systemtherapieformulare
*
* @since 0.2.0
*/
public interface SystemtherapieService {
public interface SystemtherapieService extends TherapieMitEcogService {
/**
* Ermittelt eine Zusammenfassung der systemischen Therapien für eine Erkrankung
* @param diseaseId Die ID der Erkrankung
@ -29,57 +26,4 @@ public interface SystemtherapieService {
*/
ProzedurToProzedurwerteMapper prozedurToProzedurwerteMapper(Procedure procedure);
/**
* Ermittelt den letzten bekannten ECOG-Status aus allen Systemtherapieformularen des Patienten
* @param patient Der zu verwendende Patient
* @return Der ECOG-Status als String oder leeres Optional
*/
Optional<String> latestEcogStatus(Patient patient);
/**
* Ermittelt jeden bekannten ECOG-Status aus allen Systemtherapieformularen des Patienten
* @param patient Der zu verwendende Patient
* @return Eine Liste mit Datum und ECOG-Status als String
*/
List<EcogStatusWithDate> ecogStatus(Patient patient);
/**
* Datenklasse zum Abbilden des ECOG-Status und Datum
*/
class EcogStatusWithDate {
private Date date;
private String status;
public EcogStatusWithDate(Date date, String status) {
Assert.notNull(date, "Date cannot be null");
Assert.hasText(status, "Status cannot be empty String");
Assert.isTrue(isValidEcogCode(status), "Not a valid ADT.LeistungszustandECOG code");
this.date = date;
this.status = status;
}
private boolean isValidEcogCode(String status) {
switch (status) {
case "0":
case "1":
case "2":
case "3":
case "4":
case "5":
case "U":
return true;
default:
return false;
}
}
public Date getDate() {
return date;
}
public String getStatus() {
return status;
}
}
}

44
src/test/java/DNPM/analyzer/SystemtherapieAnalyzerTest.java → src/test/java/DNPM/analyzer/TherapieMitEcogAnalyzerTest.java
View File

@ -1,5 +1,7 @@
package DNPM.analyzer;
import DNPM.dto.EcogStatusWithDate;
import DNPM.services.strahlentherapie.StrahlentherapieService;
import DNPM.services.systemtherapie.SystemtherapieService;
import de.itc.onkostar.api.*;
import org.junit.jupiter.api.BeforeEach;
@ -19,13 +21,15 @@ import static org.mockito.ArgumentMatchers.anyInt;
import static org.mockito.Mockito.*;
@ExtendWith(MockitoExtension.class)
class SystemtherapieAnalyzerTest {
class TherapieMitEcogAnalyzerTest {
private IOnkostarApi onkostarApi;
private StrahlentherapieService strahlentherapieService;
private SystemtherapieService systemtherapieService;
private SystemtherapieAnalyzer systemtherapieAnalyzer;
private TherapieMitEcogAnalyzer therapieMitEcogAnalyzer;
private Disease dummyDisease(int id, Date diagnosisDate) {
var disease = new Disease(onkostarApi);
@ -41,11 +45,13 @@ class SystemtherapieAnalyzerTest {
@BeforeEach
void setUp(
@Mock IOnkostarApi onkostarApi,
@Mock StrahlentherapieService strahlentherapieService,
@Mock SystemtherapieService systemtherapieService
) {
this.onkostarApi = onkostarApi;
this.strahlentherapieService = strahlentherapieService;
this.systemtherapieService = systemtherapieService;
this.systemtherapieAnalyzer = new SystemtherapieAnalyzer(onkostarApi, systemtherapieService);
this.therapieMitEcogAnalyzer = new TherapieMitEcogAnalyzer(onkostarApi, strahlentherapieService, systemtherapieService);
}
@Test
@ -54,7 +60,7 @@ class SystemtherapieAnalyzerTest {
final var ecogDate = daysPassed(1);
final var procedureDate = daysPassed(1);
doAnswer(invocationOnMock -> List.of(new SystemtherapieService.EcogStatusWithDate(ecogDate, "0")))
doAnswer(invocationOnMock -> List.of(new EcogStatusWithDate(ecogDate, "0")))
.when(systemtherapieService).ecogStatus(any(Patient.class));
var patient = new Patient(onkostarApi);
@ -72,7 +78,7 @@ class SystemtherapieAnalyzerTest {
doAnswer(invocationOnMock -> List.of(procedure)).when(onkostarApi).getProceduresForDiseaseByForm(anyInt(), anyString());
systemtherapieAnalyzer.analyze(procedure, dummyDisease(10, diagnosisDate));
therapieMitEcogAnalyzer.analyze(procedure, dummyDisease(10, diagnosisDate));
var idCaptor = ArgumentCaptor.forClass(Integer.class);
var formNameCaptor = ArgumentCaptor.forClass(String.class);
@ -102,7 +108,7 @@ class SystemtherapieAnalyzerTest {
procedure.setPatient(patient);
procedure.setValue("ECOGvorTherapie", new Item("ECOGvorTherapie", 1));
systemtherapieAnalyzer.analyze(procedure, dummyDisease(10, diagnosisDate));
therapieMitEcogAnalyzer.analyze(procedure, dummyDisease(10, diagnosisDate));
verify(onkostarApi, times(0)).getProceduresForDiseaseByForm(anyInt(), anyString());
verify(onkostarApi, times(0)).saveProcedure(any(Procedure.class), anyBoolean());
@ -114,7 +120,7 @@ class SystemtherapieAnalyzerTest {
final var ecogDate = daysPassed(28);
final var procedureDate = daysPassed(1);
doAnswer(invocationOnMock -> List.of(new SystemtherapieService.EcogStatusWithDate(ecogDate, "0")))
doAnswer(invocationOnMock -> List.of(new EcogStatusWithDate(ecogDate, "0")))
.when(systemtherapieService).ecogStatus(any(Patient.class));
var patient = new Patient(onkostarApi);
@ -128,10 +134,32 @@ class SystemtherapieAnalyzerTest {
procedure.setPatient(patient);
procedure.setValue("ECOGvorTherapie", new Item("ECOGvorTherapie", 1));
systemtherapieAnalyzer.analyze(procedure, dummyDisease(10, diagnosisDate));
therapieMitEcogAnalyzer.analyze(procedure, dummyDisease(10, diagnosisDate));
verify(onkostarApi, times(0)).getProceduresForDiseaseByForm(anyInt(), anyString());
verify(onkostarApi, times(0)).saveProcedure(any(Procedure.class), anyBoolean());
}
@Test
void shouldRequestEcogFromStrahlentherapieAndSystemtherapie() {
final var diagnosisDate = daysPassed(7);
final var procedureDate = daysPassed(1);
var patient = new Patient(onkostarApi);
patient.setId(1);
var procedure = new Procedure(onkostarApi);
procedure.setId(1000);
procedure.setStartDate(procedureDate);
procedure.setEditState(ProcedureEditStateType.COMPLETED);
procedure.setPatientId(1);
procedure.setPatient(patient);
procedure.setValue("ECOGvorTherapie", new Item("ECOGvorTherapie", 1));
therapieMitEcogAnalyzer.analyze(procedure, dummyDisease(10, diagnosisDate));
verify(strahlentherapieService, times(1)).ecogStatus(any());
verify(systemtherapieService, times(1)).ecogStatus(any());
}
}

106
src/test/java/DNPM/services/strahlentherapie/DefaultStrahlentherapieServiceTest.java Normal file
View File

@ -0,0 +1,106 @@
package DNPM.services.strahlentherapie;
import DNPM.services.SettingsService;
import de.itc.onkostar.api.*;
import org.assertj.core.util.Lists;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.ArgumentCaptor;
import org.mockito.Mock;
import org.mockito.junit.jupiter.MockitoExtension;
import java.time.Instant;
import java.util.ArrayList;
import java.util.Date;
import java.util.List;
import java.util.Optional;
import static org.assertj.core.api.Assertions.assertThat;
import static org.mockito.ArgumentMatchers.anyInt;
import static org.mockito.ArgumentMatchers.anyString;
import static org.mockito.Mockito.*;
@ExtendWith(MockitoExtension.class)
class DefaultStrahlentherapieServiceTest {
private IOnkostarApi onkostarApi;
private SettingsService settingsService;
private DefaultStrahlentherapieService service;
@BeforeEach
void setup(@Mock IOnkostarApi onkostarApi, @Mock SettingsService settingsService) {
this.onkostarApi = onkostarApi;
this.settingsService = settingsService;
this.service = new DefaultStrahlentherapieService(onkostarApi, settingsService);
}
@Test
void testShouldRequestProceduresWithDefaultFormName() {
when(this.settingsService.getSetting(anyString())).thenReturn(Optional.empty());
doAnswer(invocationOnMock -> {
var procedure = new Procedure(onkostarApi);
procedure.setId(1);
procedure.setFormName("OS.Strahlentherapie");
procedure.setStartDate(Date.from(Instant.parse("2023-07-01T06:00:00Z")));
procedure.setEditState(ProcedureEditStateType.COMPLETED);
procedure.setValue("ECOGvorTherapie", new Item("ECOGvorTherapie", 1));
return Lists.list(procedure);
}).when(this.onkostarApi).getProceduresForDiseaseByForm(anyInt(), anyString());
doAnswer(invocationOnMock -> {
var disease = new Disease(onkostarApi);
disease.setId(1);
disease.setPatientId(123);
return Lists.list(disease);
}).when(this.onkostarApi).getDiseasesByPatientId(anyInt());
var patient = new Patient(onkostarApi);
patient.setId(123);
service.ecogStatus(patient);
var argumentCaptor = ArgumentCaptor.forClass(String.class);
verify(onkostarApi, times(1)).getProceduresForDiseaseByForm(anyInt(), argumentCaptor.capture());
assertThat(argumentCaptor.getValue()).isEqualTo("OS.Strahlentherapie");
}
@Test
void testShouldReturnListOfEcogStatusWithDate() {
doAnswer(invocationOnMock -> {
var disease = new Disease(onkostarApi);
disease.setId(1);
return List.of(disease);
}).when(this.onkostarApi).getDiseasesByPatientId(anyInt());
doAnswer(invocationOnMock -> {
var procedure1 = new Procedure(onkostarApi);
procedure1.setId(1);
procedure1.setFormName("OS.Strahlentherapie");
procedure1.setStartDate(Date.from(Instant.parse("2023-07-01T06:00:00Z")));
procedure1.setEditState(ProcedureEditStateType.COMPLETED);
procedure1.setValue("ECOGvorTherapie", new Item("ECOGvorTherapie", 1));
var procedure2 = new Procedure(onkostarApi);
procedure2.setId(2);
procedure2.setFormName("OS.Strahlentherapie");
procedure2.setStartDate(Date.from(Instant.parse("2023-07-12T06:00:00Z")));
procedure2.setEditState(ProcedureEditStateType.COMPLETED);
procedure2.setValue("ECOGvorTherapie", new Item("ECOGvorTherapie", 2));
return List.of(procedure1, procedure2);
}).when(this.onkostarApi).getProceduresForDiseaseByForm(anyInt(), anyString());
var patient = new Patient(onkostarApi);
patient.setId(1);
var actual = service.ecogStatus(patient);
assertThat(actual)
.isNotNull()
.isExactlyInstanceOf(ArrayList.class)
.hasSize(2);
}
}