diff options
Diffstat (limited to 'src/main/java/DNPM')
61 files changed, 0 insertions, 3611 deletions
diff --git a/src/main/java/DNPM/VerweisVon.java b/src/main/java/DNPM/VerweisVon.java deleted file mode 100644 index afb6824..0000000 --- a/src/main/java/DNPM/VerweisVon.java +++ /dev/null @@ -1,54 +0,0 @@ -package DNPM; - -import java.text.SimpleDateFormat; -import java.util.Date; - -public class VerweisVon { - private int procedure_id; - private int data_form_id; - private String data_catalogue; - private String data_catalogue_entry; - private String formname; - private Date datum; - - public VerweisVon() { - } - - @SuppressWarnings("unused") - public int getProcedure_id() { return this.procedure_id; } - public int getData_form_id() { return this.data_form_id; } - public String getData_catalogue_name() { return this.data_catalogue; } - public String getData_catalogue_entry_name() { return this.data_catalogue_entry; } - public String getFormname() { return this.formname; } - public Date getDate() { return this.datum; } - public String getTable() { - return "dk_" + this.data_catalogue.toLowerCase().replaceAll("[^a-zA-Z0-9]", "_"); - } - public String getField() { - return this.data_catalogue_entry.toLowerCase(); - } - public String getSQL() { - return "SELECT " + this.getField() + " AS value FROM " + this.getTable() + " WHERE id = " + this.getProcedure_id(); - } - private String getDatumAsString() { - SimpleDateFormat DATE_FORMAT = new SimpleDateFormat("dd.MM.yyyy"); - String Datum = null; - if (this.getDate() != null) { - Datum = DATE_FORMAT.format(this.getDate()); - } - return Datum; - } - public String getVerbundenesFormular() { - String FName = "Formular " + this.getFormname(); - if (this.getDatumAsString() != null ) { FName += " vom " + this.getDatumAsString(); } - return FName; - } - - @SuppressWarnings("unused") - public void setProcedure_id(int procedure_id) {this.procedure_id = procedure_id; } - public void setData_form_id(int data_form_id) {this.data_form_id = data_form_id; } - public void setData_catalogue_name(String data_catalogue_name) {this.data_catalogue = data_catalogue_name; } - public void setData_catalogue_entry_name(String data_catalogue_entry) {this.data_catalogue_entry = data_catalogue_entry; } - public void setDate(Date datum) { this.datum = datum; } - public void setFormname(String formname) { this.formname = formname; } -} diff --git a/src/main/java/DNPM/analyzer/Analyzer.java b/src/main/java/DNPM/analyzer/Analyzer.java deleted file mode 100644 index fd2fdec..0000000 --- a/src/main/java/DNPM/analyzer/Analyzer.java +++ /dev/null @@ -1,12 +0,0 @@ -package DNPM.analyzer; - -import de.itc.onkostar.api.analysis.OnkostarPluginType; - -public abstract class Analyzer implements IPluginPart { - - @Override - public final OnkostarPluginType getType() { - return OnkostarPluginType.ANALYZER; - } - -} diff --git a/src/main/java/DNPM/analyzer/AnalyzerUtils.java b/src/main/java/DNPM/analyzer/AnalyzerUtils.java deleted file mode 100644 index dfa4c0d..0000000 --- a/src/main/java/DNPM/analyzer/AnalyzerUtils.java +++ /dev/null @@ -1,145 +0,0 @@ -package DNPM.analyzer; - -import java.util.Map; -import java.util.Optional; - -/** - * Klasse mit Hilfsfunktionen für Analyzer - * - * @since 0.1.0 - */ -public class AnalyzerUtils { - - private AnalyzerUtils() {} - - /** - * Prüft, ob in InputMap einen Eintrag mit key <code>key</code> und Typ <code>type</code> - * gefunden wurde. - * - * @param input InputMap - * @param key Key des Werts - * @param type Typ des Werts - * @return <code>true</code>>, wenn ein Wert von dem Typ gefunden wurde - */ - public static boolean requiredValuePresent(final Map<String, Object> input, final String key, final Class<?> type) { - var value = input.get(key); - - if (null == value) { - return false; - } - - return type.isInstance(value); - } - - /** - * Übergibt ein Optional mit Wert, wenn in InputMap ein Eintrag mit key <code>key</code> und Typ <code>type</code> - * gefunden wurde. Anderenfalls ein leeres Optional - * - * <p><b>Beispiel</b> - * <pre> - * var id = AnalyzerUtils.getRequiredValue(input, "id", Integer.class); - * if (id.isEmpty()) { - * logger.error("Keine ID angegeben!"); - * return false; - * } - * - * var idNummer = id.get(); - * ... - * </pre> - * - * @param input InputMap - * @param key Key des Werts - * @param type Typ des Werts - * @return Optional mit entsprechendem Wert oder leeres Optional - */ - public static <T> Optional<T> getRequiredValue(final Map<String, Object> input, final String key, final Class<T> type) { - if (! requiredValuePresent(input, key, type)) { - return Optional.empty(); - } - - @SuppressWarnings("unchecked") - var result = Optional.of((T)input.get(key)); - - return result; - } - - /** - * Prüft, ob ein Wert in der InputMap als Zeichenkette dem angegebenen RegExp entspricht - * - * @param input InputMap - * @param key Key des Werts - * @param regexp Der zu prüfende reguläre Ausdruck - * @return <code>true</code>>, wenn ein Wert gefunden wurde, der dem RegExp entspricht - */ - public static boolean requiredValueMatches(final Map<String, Object> input, final String key, final String regexp) { - var value = input.get(key); - - if (null == value) { - return false; - } - - return value.toString().matches(regexp); - } - - /** - * Übergibt ein Optional mit dem Wert als Zeichenkette, wenn er dem angegebenen RegExp entspricht. - * Hierzu wird die Methode <code>toString()</code> auf den Wert angewendet. - * - * @param input InputMap - * @param key Key des Werts - * @param regexp Der zu prüfende reguläre Ausdruck - * @return Optional mit entsprechendem Wert als Zeichenkette oder leeres Optional - */ - public static Optional<String> getRequiredValueMatching(final Map<String, Object> input, final String key, final String regexp) { - if (! requiredValueMatches(input, key, regexp)) { - return Optional.empty(); - } - - return Optional.of(input.get(key).toString()); - } - - /** - * Prüft, ob ein Wert in der InputMap eine ID ist und damit eine Zahl größer Null ist. - * - * @param input InputMap - * @param key Key des Werts - * @return <code>true</code>>, wenn ein Wert gefunden wurde, der dem RegExp entspricht - */ - public static boolean requiredValueIsId(final Map<String, Object> input, final String key) { - return requiredValuePresent(input, key, Integer.class) && Integer.parseInt(input.get(key).toString()) > 0; - } - - /** - * Übergibt ein Optional, wenn der Wert eine ID ist und damit eine Zahl größer Null ist. - * <p><b>Beispiel</b> - * <pre> - * var id = AnalyzerUtils.getRequiredId(input, "id"); - * if (id.isEmpty()) { - * logger.error("Keine gültige ID angegeben!"); - * return false; - * } - * - * // Ist hier immer größer als Null - * var idNummer = id.get(); - * ... - * </pre> - * - * @param input InputMap - * @param key Key des Werts - * @return Optional mit entsprechendem Wert oder leeres Optional - */ - public static Optional<Integer> getRequiredId(final Map<String, Object> input, final String key) { - if (! requiredValuePresent(input, key, Integer.class)) { - return Optional.empty(); - } - - var id = (int)input.get(key); - - if (id > 0) { - return Optional.of(id); - } - - return Optional.empty(); - } - -} diff --git a/src/main/java/DNPM/analyzer/BackendService.java b/src/main/java/DNPM/analyzer/BackendService.java deleted file mode 100644 index 84895dd..0000000 --- a/src/main/java/DNPM/analyzer/BackendService.java +++ /dev/null @@ -1,25 +0,0 @@ -package DNPM.analyzer; - -import de.itc.onkostar.api.Disease; -import de.itc.onkostar.api.Procedure; -import de.itc.onkostar.api.analysis.OnkostarPluginType; - -public abstract class BackendService implements IPluginPart { - - @Override - public final OnkostarPluginType getType() { - return OnkostarPluginType.BACKEND_SERVICE; - } - - /** - * Ein Backend-Service verwendet die Methode nicht, daher wird hier eine final Stub-Implementierung - * verwendet, die ein Überschreiben verhindert. - * @param procedure - * @param disease - */ - @Override - public final void analyze(Procedure procedure, Disease disease) { - // No op - } - -} diff --git a/src/main/java/DNPM/analyzer/ConsentManager.java b/src/main/java/DNPM/analyzer/ConsentManager.java deleted file mode 100644 index 6051bc0..0000000 --- a/src/main/java/DNPM/analyzer/ConsentManager.java +++ /dev/null @@ -1,63 +0,0 @@ -package DNPM.analyzer; - -import DNPM.services.consent.ConsentManagerServiceFactory; -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 org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -public class ConsentManager extends Analyzer { - - private final Logger logger = LoggerFactory.getLogger(this.getClass()); - - private final IOnkostarApi onkostarApi; - - private final ConsentManagerServiceFactory consentManagerServiceFactory; - - public ConsentManager( - final IOnkostarApi onkostarApi, - final ConsentManagerServiceFactory consentManagerServiceFactory - ) { - this.onkostarApi = onkostarApi; - this.consentManagerServiceFactory = consentManagerServiceFactory; - } - - @Override - public String getDescription() { - return "Aktualisiert Consent Daten in verknüpften Formularen"; - } - - @Override - public AnalyzerRequirement getRequirement() { - return AnalyzerRequirement.PROCEDURE; - } - - @Override - public boolean isRelevantForAnalyzer(Procedure prozedur, Disease erkrankung) { - return prozedur.getFormName().equals(onkostarApi.getGlobalSetting("consentform")); - } - - @Override - public boolean isRelevantForDeletedProcedure() { - // TODO is relevant for deleted procedure = true - return false; - } - - @Override - public boolean isSynchronous() { - return true; - } - - @Override - public void analyze(Procedure prozedur, Disease erkrankung) { - var consentManagerService = consentManagerServiceFactory.currentUsableInstance(); - if (! consentManagerService.canApply(prozedur)) { - logger.error("Fehler im ConsentManagement: Kann Prozedur mit Formularnamen '{}' nicht anwenden", prozedur.getFormName()); - return; - } - consentManagerService.applyConsent(prozedur); - } - -} diff --git a/src/main/java/DNPM/analyzer/DNPMHelper.java b/src/main/java/DNPM/analyzer/DNPMHelper.java deleted file mode 100644 index bb21fa0..0000000 --- a/src/main/java/DNPM/analyzer/DNPMHelper.java +++ /dev/null @@ -1,260 +0,0 @@ -package DNPM.analyzer; - -import DNPM.dto.EcogStatusWithDate; -import DNPM.VerweisVon; -import DNPM.security.DelegatingDataBasedPermissionEvaluator; -import DNPM.security.IllegalSecuredObjectAccessException; -import DNPM.security.PermissionType; -import DNPM.services.systemtherapie.SystemtherapieService; -import com.fasterxml.jackson.core.JsonProcessingException; -import com.fasterxml.jackson.databind.ObjectMapper; -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 org.hibernate.SQLQuery; -import org.hibernate.Session; -import org.hibernate.SessionFactory; -import org.hibernate.transform.Transformers; -import org.hibernate.type.StandardBasicTypes; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; -import org.springframework.security.core.context.SecurityContextHolder; - -import java.util.ArrayList; -import java.util.HashMap; -import java.util.List; -import java.util.Map; - -public class DNPMHelper extends BackendService { - - private static final Logger logger = LoggerFactory.getLogger(DNPMHelper.class); - - private final IOnkostarApi onkostarApi; - - private final SystemtherapieService systemtherapieService; - - private final DelegatingDataBasedPermissionEvaluator delegatingDataBasedPermissionEvaluator; - - public DNPMHelper( - final IOnkostarApi onkostarApi, - final SystemtherapieService systemtherapieService, - final DelegatingDataBasedPermissionEvaluator permissionEvaluator - ) { - this.onkostarApi = onkostarApi; - this.systemtherapieService = systemtherapieService; - this.delegatingDataBasedPermissionEvaluator = permissionEvaluator; - } - - @Override - public String getDescription() { - return "Methoden für DNPM-Formulare"; - } - - @Override - public boolean isRelevantForDeletedProcedure() { - return false; - } - - @Override - public boolean isSynchronous() { - return true; - } - - @Override - public AnalyzerRequirement getRequirement() { - return AnalyzerRequirement.PROCEDURE; - } - - @Override - public boolean isRelevantForAnalyzer(Procedure entry, Disease currentDisease) { - // Plugin enthält nur Methoden für Formulare und soll nicht ausgeführt werden - return false; - } - - @SuppressWarnings("unchecked") - public List<Map<String, String>> getVerweise(final Map<String, Object> input) { - var procedureId = AnalyzerUtils.getRequiredId(input, "ProcedureId"); - var patientId = AnalyzerUtils.getRequiredId(input, "PatientId"); - - if (procedureId.isEmpty() || patientId.isEmpty()) { - return null; - } - - var verbundeneFormulare = new ArrayList<Map<String, String>>(); - - try { - SessionFactory sessionFactory = onkostarApi.getSessionFactory(); - Session session = sessionFactory.getCurrentSession(); - - String sql = "SELECT prozedur.id AS procedure_id, prozedur.data_form_id, data_catalogue.name AS data_catalogue, data_catalogue_entry.name AS data_catalogue_entry, data_form.description AS formname, prozedur.beginndatum AS datum " + - "FROM prozedur " + - "LEFT JOIN data_form_data_catalogue ON data_form_data_catalogue.data_form_id = prozedur.data_form_id " + - "LEFT JOIN data_catalogue_entry ON data_catalogue_entry.data_catalogue_id = data_form_data_catalogue.data_catalogue_id " + - "LEFT JOIN data_catalogue ON data_catalogue.id = data_catalogue_entry.data_catalogue_id " + - "LEFT JOIN data_form ON data_form.id = prozedur.data_form_id " + - "WHERE patient_id = " + patientId.get() + " " + - "AND geloescht = 0 " + - "AND data_catalogue_entry.type = 'formReference' " + - "GROUP BY prozedur.id, prozedur.data_form_id, data_catalogue.name, data_catalogue_entry.name"; - - SQLQuery query = session.createSQLQuery(sql) - .addScalar("procedure_id", StandardBasicTypes.INTEGER) - .addScalar("data_form_id", StandardBasicTypes.INTEGER) - .addScalar("data_catalogue", StandardBasicTypes.STRING) - .addScalar("data_catalogue_entry", StandardBasicTypes.STRING) - .addScalar("formname", StandardBasicTypes.STRING) - .addScalar("datum", StandardBasicTypes.DATE); - - query.setResultTransformer(Transformers.aliasToBean(VerweisVon.class)); - List<VerweisVon> result = query.list(); - try { - int value = 0; - for (VerweisVon verweisVon : result) { - sql = verweisVon.getSQL(); - query = session.createSQLQuery(sql) - .addScalar("value", StandardBasicTypes.INTEGER); - if (query.uniqueResult() != null) { - value = (Integer) query.uniqueResult(); - } - if (value == procedureId.get()) { - verbundeneFormulare.add(Map.of("formular", verweisVon.getVerbundenesFormular())); - value = 0; - } - } - } catch (Exception e) { - logger.warn("Fehler beim Hinzufügen eines Formularverweises", e); - } - } catch (Exception e) { - logger.error("Fehler beim Ermitteln der Formularverweise", e); - return null; - } - return verbundeneFormulare; - } - - public List<Map<String, String>> getSystemischeTherapienFromDiagnose(final Map<String, Object> input) { - var diagnoseId = AnalyzerUtils.getRequiredId(input, "DiagnoseId"); - if (diagnoseId.isEmpty()) { - logger.error("Kein Parameter 'DiagnoseId' angegeben, gebe 'null' zurück"); - return null; - } - - return systemtherapieService.getSystemischeTherapienFromDiagnose(diagnoseId.get()); - } - - public String getProzedurenFromDiagnose(final Map<String, Object> input) { - // Prozedur, Feldname, Wert - var dataForm = AnalyzerUtils.getRequiredValue(input, "dataForm", String.class); - var diagnoseId = AnalyzerUtils.getRequiredId(input, "DiagnoseId"); - var patientId = AnalyzerUtils.getRequiredId(input, "PatientId"); - - if (dataForm.isEmpty() || diagnoseId.isEmpty() || patientId.isEmpty()) { - return ""; - } - - var formulare = new ArrayList<Map<String, Object>>(); - List<Procedure> prozeduren = onkostarApi.getProceduresByPatientId(patientId.get()); - for (Procedure Prozedur : prozeduren) { - // Formular gehört zur aktuellen Diagnose und hat den angegebenen Namen - if (Prozedur.getDiseaseIds().contains(diagnoseId.get()) && Prozedur.getFormName().contains(dataForm.get())) { - // alle Werte auslesen - // System.out.println(WerteListe.getKey() + ": " + WerteListe.getValue()); - formulare.add(Map.of( - "Formular", Prozedur.getFormName(), - "Felder", new HashMap<>(Prozedur.getAllValues()) - )); - } - } - try { - ObjectMapper objectMapper = new ObjectMapper(); - return objectMapper.writeValueAsString(formulare); - } catch (JsonProcessingException e) { - logger.error("Kann Formulare nicht in JSON mappen", e); - } - return ""; - } - - public Object getEmpfehlung(final Map<String, Object> input) { - var procedureID = AnalyzerUtils.getRequiredId(input, "ProcedureID"); - - if (procedureID.isEmpty()) { - logger.error("Kein Parameter 'ProcedureID' angegeben, gebe 'null' zurück"); - return null; - } - - try { - SessionFactory sessionFactory = onkostarApi.getSessionFactory(); - Session session = sessionFactory.getCurrentSession(); - var sql = "SELECT prozedur.id, genname, geneid, geneidlink, empfehlung, beginndatum FROM prozedur " - + "LEFT JOIN dk_mtb_einzelempfehlung em ON em.id = prozedur.id " - + "JOIN data_form df ON prozedur.data_form_id = df.id AND df.name = 'MR.MTB_Einzelempfehlung' " - + "WHERE prozedur.hauptprozedur_id = " + procedureID.get() + " AND prozedur.geloescht = 0 " - + "ORDER BY beginndatum"; - - SQLQuery query = session.createSQLQuery(sql) - .addScalar("id", StandardBasicTypes.STRING) - .addScalar("genname", StandardBasicTypes.STRING) - .addScalar("geneid", StandardBasicTypes.STRING) - .addScalar("geneidlink", StandardBasicTypes.STRING) - .addScalar("empfehlung", StandardBasicTypes.STRING) - .addScalar("beginndatum", StandardBasicTypes.STRING); - - @SuppressWarnings("unchecked") - List<String[]> rows = query.list(); - return rows; - } catch (Exception e) { - logger.error("Fehler bei Abfrage von Empfehlungen", e); - return null; - } - } - - public Object updateEmpfehlungPrio(final Map<String, Object> input) { - // Auslesen und Prüfen der Parameter aus 'input' - var rid = AnalyzerUtils.getRequiredId(input, "rid"); - if (rid.isEmpty()) { - logger.error("Kein Parameter 'rid' angegeben, gebe 'false' zurück"); - return false; - } - - var strDate = AnalyzerUtils.getRequiredValueMatching(input, "bd", "[\\d]{4}-[\\d]{2}-[\\d]{2}"); - if (strDate.isEmpty()) { - logger.error("Kein oder ungültiger Parameter 'bd' angegeben, gebe 'false' zurück"); - return false; - } - - //String strD = strDate.toString(); - //String CompareDate = strD.substring(1, 11); - //DateFormat simpleDateFormat=new SimpleDateFormat("yyyy-MM-dd"); - - try { - String sql = "UPDATE prozedur SET beginndatum = '" + strDate.get() + "' WHERE id = '" + rid.get() + "' "; - SQLQuery result = onkostarApi.getSessionFactory().getCurrentSession().createSQLQuery(sql); - result.executeUpdate(); - return true; - } catch (Exception e) { - return "Achtung: Ein Fehler ist aufgetreten, Änderung konnte nicht gespeichert werden!"; - //return null; - } - - } - - 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"); - return List.of(); - } - - var patient = onkostarApi.getPatient(pid.get()); - if (null == patient) { - logger.error("Patient nicht gefunden, gebe leere Liste zurück"); - return List.of(); - } - - if (delegatingDataBasedPermissionEvaluator.hasPermission(SecurityContextHolder.getContext().getAuthentication(), patient, PermissionType.READ)) { - return systemtherapieService.ecogStatus(patient); - } - - throw new IllegalSecuredObjectAccessException("Kein Zugriff auf diesen Patienten"); - } -}
\ No newline at end of file diff --git a/src/main/java/DNPM/analyzer/EinzelempfehlungAnalyzer.java b/src/main/java/DNPM/analyzer/EinzelempfehlungAnalyzer.java deleted file mode 100644 index 1724272..0000000 --- a/src/main/java/DNPM/analyzer/EinzelempfehlungAnalyzer.java +++ /dev/null @@ -1,134 +0,0 @@ -package DNPM.analyzer; - -import DNPM.dto.Studie; -import DNPM.dto.Variant; -import DNPM.security.PermissionType; -import DNPM.security.PersonPoolBasedPermissionEvaluator; -import DNPM.services.StudienService; -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 org.slf4j.Logger; -import org.slf4j.LoggerFactory; -import org.springframework.security.core.context.SecurityContextHolder; -import org.springframework.stereotype.Component; - -import java.util.List; -import java.util.Map; - -/** - * Diese Klasse implementiert ein Plugin, welches Funktionen für DNPM UF Einzelempfehlung bereitstellt. - * - * @since 0.2.0 - */ -@Component -public class EinzelempfehlungAnalyzer extends BackendService { - - private final static Logger logger = LoggerFactory.getLogger(EinzelempfehlungAnalyzer.class); - - private final IOnkostarApi onkostarApi; - - private final MolekulargenetikFormService molekulargenetikFormService; - - private final StudienService studienService; - - private final PersonPoolBasedPermissionEvaluator permissionEvaluator; - - public EinzelempfehlungAnalyzer( - final IOnkostarApi onkostarApi, - final StudienService studienService, - final MolekulargenetikFormService molekulargenetikFormService, - final PersonPoolBasedPermissionEvaluator permissionEvaluator - ) { - this.onkostarApi = onkostarApi; - this.studienService = studienService; - this.molekulargenetikFormService = molekulargenetikFormService; - this.permissionEvaluator = permissionEvaluator; - } - - @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; - } - - 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(); - } - - if (permissionEvaluator.hasPermission(SecurityContextHolder.getContext().getAuthentication(), procedure, PermissionType.READ)) { - return molekulargenetikFormService.getVariants(procedure); - } else { - logger.error("Security: No permission to access procedure '{}'", procedure.getId()); - return List.of(); - } - } - - /** - * Übergibt alle Studien, deren (Kurz-)Beschreibung oder NCT-Nummer den übergebenen Eingabewert <code>q</code> enthält - * - * <p>Wurde der Eingabewert nicht angegeben oder ist leer, werden alle Studien übergeben. - * - * <p>Beispiel zur Nutzung in einem Formularscript - * <pre> - * executePluginMethod( - * 'TherapieplanAnalyzer', - * 'getStudien', - * { q: 'NCT-12', inactive: true }, - * (response) => console.log(response), - * false - * ); - * </pre> - * - * @param input Map mit Eingabewerten - * @return Liste mit Studien - */ - public List<Studie> getStudien(Map<String, Object> input) { - var query = AnalyzerUtils.getRequiredValue(input, "q", String.class); - var inactive = AnalyzerUtils.getRequiredValue(input, "inactive", Boolean.class).orElse(false); - - if (query.isEmpty() || query.get().isBlank()) { - if (inactive) { - return studienService.findAll(); - } - return studienService.findActive(); - } - if (inactive) { - return studienService.findByQuery(query.get()); - } - return studienService.findActiveByQuery(query.get()); - } - -} diff --git a/src/main/java/DNPM/analyzer/FollowUpAnalyzer.java b/src/main/java/DNPM/analyzer/FollowUpAnalyzer.java deleted file mode 100644 index 07b5fa0..0000000 --- a/src/main/java/DNPM/analyzer/FollowUpAnalyzer.java +++ /dev/null @@ -1,103 +0,0 @@ -package DNPM.analyzer; - -import de.itc.onkostar.api.Disease; -import de.itc.onkostar.api.IOnkostarApi; -import de.itc.onkostar.api.Item; -import de.itc.onkostar.api.Procedure; -import de.itc.onkostar.api.analysis.AnalyseTriggerEvent; -import de.itc.onkostar.api.analysis.AnalyzerRequirement; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; -import org.springframework.stereotype.Component; - -import java.util.Set; - -/** - * Diese Klasse implementiert ein Plugin, welches Aktionen nach Bearbeitung eines FollowUps durchführt. - * - * @since 0.0.2 - */ -@Component -public class FollowUpAnalyzer extends Analyzer { - - private final Logger logger = LoggerFactory.getLogger(this.getClass()); - - private final IOnkostarApi onkostarApi; - - public FollowUpAnalyzer(IOnkostarApi onkostarApi) { - this.onkostarApi = onkostarApi; - } - - @Override - public String getDescription() { - return "Aktualisiert verknüpfte Formulare nach Änderungen im FollowUp-Formular"; - } - - /** - * @deprecated - */ - @Override - public boolean isRelevantForDeletedProcedure() { - return false; - } - - @Override - public boolean isRelevantForAnalyzer(Procedure procedure, Disease disease) { - return null != procedure && procedure.getFormName().equals("DNPM FollowUp"); - } - - @Override - public boolean isSynchronous() { - return false; - } - - @Override - public AnalyzerRequirement getRequirement() { - return AnalyzerRequirement.PROCEDURE; - } - - @Override - public Set<AnalyseTriggerEvent> getTriggerEvents() { - return Set.of( - AnalyseTriggerEvent.EDIT_SAVE, - AnalyseTriggerEvent.EDIT_LOCK, - AnalyseTriggerEvent.REORG - ); - } - - @Override - public void analyze(Procedure procedure, Disease disease) { - backlinkToEinzelempfehlung(procedure); - } - - /** - * Verlinke aktuelles FollowUp in angegebener Einzelempfehlung - * - * @param procedure Das FollowUp - */ - private void backlinkToEinzelempfehlung(Procedure procedure) { - if (null == procedure.getValue("LinkTherapieempfehlung")) { - return; - } - - var referencedProcedureId = procedure.getValue("LinkTherapieempfehlung"); - if (null == referencedProcedureId || referencedProcedureId.getInt() == 0) { - // Alles gut, es ist keine Einzelempfehlung angegeben - return; - } - - var referencedProcedure = onkostarApi.getProcedure(referencedProcedureId.getInt()); - if (null == referencedProcedure) { - logger.error("Referenzierte Einzelempfehlung wurde nicht gefunden: {}", referencedProcedureId); - return; - } - - referencedProcedure.setValue("refdnpmfollowup", new Item("ref_dnpm_followup", procedure.getId())); - - try { - onkostarApi.saveProcedure(referencedProcedure); - } catch (Exception e) { - logger.error("FollowUp konnte nicht mit Einzelempfehlung verknüpft werden", e); - } - } -} diff --git a/src/main/java/DNPM/analyzer/IPluginPart.java b/src/main/java/DNPM/analyzer/IPluginPart.java deleted file mode 100644 index 31e9fff..0000000 --- a/src/main/java/DNPM/analyzer/IPluginPart.java +++ /dev/null @@ -1,19 +0,0 @@ -package DNPM.analyzer; - -import de.itc.onkostar.api.analysis.IProcedureAnalyzer; - -public interface IPluginPart extends IProcedureAnalyzer { - - default String getVersion() { - return "0.4.0"; - } - - default String getName() { - return "DNPM Plugin"; - } - - default String getDescription() { - return String.format("Plugin-Bestandteil '%s'", this.getClass().getSimpleName()); - } - -} diff --git a/src/main/java/DNPM/analyzer/Merkmalskatalog.java b/src/main/java/DNPM/analyzer/Merkmalskatalog.java deleted file mode 100644 index 275fccd..0000000 --- a/src/main/java/DNPM/analyzer/Merkmalskatalog.java +++ /dev/null @@ -1,97 +0,0 @@ -package DNPM.analyzer; - -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 org.hibernate.SQLQuery; -import org.hibernate.Session; -import org.hibernate.SessionFactory; -import org.hibernate.type.StandardBasicTypes; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import java.util.List; -import java.util.Map; - -public class Merkmalskatalog extends BackendService { - - private final Logger logger = LoggerFactory.getLogger(this.getClass()); - - private final IOnkostarApi onkostarApi; - - public Merkmalskatalog(final IOnkostarApi onkostarApi) { - this.onkostarApi = onkostarApi; - } - - @Override - public String getDescription() { - return "Methoden für Merkmalskataloge"; - } - - @Override - public boolean isRelevantForDeletedProcedure() { - return false; - } - - @Override - public boolean isSynchronous() { - return true; - } - - @Override - public AnalyzerRequirement getRequirement() { - return AnalyzerRequirement.PROCEDURE; - } - - @Override - public boolean isRelevantForAnalyzer(Procedure procedure, Disease currentDisease) { - return false; - } - - public List<String[]> getMerkmalskatalog(final Map<String, Object> input) { - var merkmalskatalog = AnalyzerUtils.getRequiredValue(input, "Merkmalskatalog", String.class); - var spalten = AnalyzerUtils.getRequiredValue(input, "Spalten", String.class); - - if (merkmalskatalog.isEmpty()) { - logger.error("Kein Merkmalskatalog angegeben!"); - return null; - } - - if (spalten.isEmpty()) { - logger.error("Keine Spalten angegeben!"); - return null; - } - - String[] spaltenArray = spalten.get().split("\\s*,\\s*"); - - try { - SQLQuery query = getSqlQuery(merkmalskatalog.get()); - - for (String s : spaltenArray) { - query.addScalar(s, StandardBasicTypes.STRING); - } - - @SuppressWarnings("unchecked") - List<String[]> rows = query.list(); - return rows; - } catch (Exception e) { - logger.error("Fehler bei der Ausführung von getMerkmalskatalog()", e); - return null; - } - } - - private SQLQuery getSqlQuery(String merkmalskatalog) { - SessionFactory sessionFactory = onkostarApi.getSessionFactory(); - Session session = sessionFactory.getCurrentSession(); - - String sql = "SELECT p.id, p.code, p.shortdesc, p.description, p.note, p.synonyms " - + "FROM property_catalogue " - + "LEFT JOIN property_catalogue_version ON property_catalogue_version.datacatalog_id = property_catalogue.id " - + "LEFT JOIN property_catalogue_version_entry p ON p.property_version_id = property_catalogue_version.id " - + "WHERE name = '" + merkmalskatalog + "' AND aktiv = 1 " - + "ORDER BY position ASC"; - - return session.createSQLQuery(sql); - } -} diff --git a/src/main/java/DNPM/analyzer/TherapieMitEcogAnalyzer.java b/src/main/java/DNPM/analyzer/TherapieMitEcogAnalyzer.java deleted file mode 100644 index 46841e1..0000000 --- a/src/main/java/DNPM/analyzer/TherapieMitEcogAnalyzer.java +++ /dev/null @@ -1,168 +0,0 @@ -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; -import de.itc.onkostar.api.Item; -import de.itc.onkostar.api.Procedure; -import de.itc.onkostar.api.analysis.AnalyseTriggerEvent; -import de.itc.onkostar.api.analysis.AnalyzerRequirement; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; -import org.springframework.stereotype.Component; - -import java.text.SimpleDateFormat; -import java.util.List; -import java.util.Map; -import java.util.Set; -import java.util.stream.Collectors; - -/** - * Diese Klasse implementiert ein Plugin, welches Aktionen nach Bearbeitung eines Formulars zur Systemtherapie durchführt. - * - * @since 0.6.0 - */ -@Component -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 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 in Formularen vom Typ Strahlen-/Systemtherapie mit ECOG-Status"; - } - - /** - * @deprecated - */ - @Override - public boolean isRelevantForDeletedProcedure() { - return true; - } - - @Override - public boolean isRelevantForAnalyzer(Procedure procedure, Disease disease) { - return null != procedure && null != disease && ( - procedure.getFormName().equals("OS.Strahlentherapie") - || procedure.getFormName().equals("OS.Strahlentherapie.VarianteUKW") - || procedure.getFormName().equals("OS.Systemische Therapie") - || procedure.getFormName().equals("OS.Systemische Therapie.VarianteUKW") - ); - } - - @Override - public boolean isSynchronous() { - return false; - } - - @Override - public AnalyzerRequirement getRequirement() { - return AnalyzerRequirement.PROCEDURE; - } - - @Override - public Set<AnalyseTriggerEvent> getTriggerEvents() { - return Set.of( - AnalyseTriggerEvent.EDIT_SAVE, - AnalyseTriggerEvent.EDIT_LOCK, - AnalyseTriggerEvent.REORG - ); - } - - @Override - public void analyze(Procedure procedure, Disease disease) { - var date = procedure.getStartDate(); - var status = procedure.getValue("ECOGvorTherapie"); - - if (null == date || null == status) { - // Ignore - return; - } - - var ecog = strahlentherapieService.ecogStatus(procedure.getPatient()) - .stream() - .filter(ecogStatusWithDate -> ecogStatusWithDate.getDate().after(disease.getDiagnosisDate())) - .collect(Collectors.toList()); - - ecog.addAll(systemtherapieService.ecogStatus(procedure.getPatient()) - .stream() - .filter(ecogStatusWithDate -> ecogStatusWithDate.getDate().after(disease.getDiagnosisDate())) - .collect(Collectors.toList())); - - - if (ecog.isEmpty()) { - // Nothing to do - return; - } - - procedure.getPatient().getDiseases().stream() - .flatMap(d -> onkostarApi.getProceduresForDiseaseByForm(d.getId(), "DNPM Klinik/Anamnese").stream()) - .forEach(p -> { - var ufEcog = p.getValue("ECOGVerlauf"); - if (null != ufEcog && ufEcog.getValue() instanceof List) { - updateExistingEcogVerlauf(p, ecog, ufEcog); - } else { - newEcogverlauf(p, ecog); - } - }); - } - - 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")) - .collect(Collectors.toList()); - for (var ecog : ecogFromCompleted) { - var formattedDate = new SimpleDateFormat("yyyy-MM-dd").format(ecog.getDate()); - if (!existingDates.contains(formattedDate)) { - var newSubProcedure = new Procedure(onkostarApi); - newSubProcedure.setStartDate(ecog.getDate()); - newSubProcedure.setValue("Datum", new Item("Datum", ecog.getDate())); - newSubProcedure.setValue("ECOG", new Item("ECOG", ecog.getStatus())); - p.addSubProcedure("ECOGVerlauf", newSubProcedure); - shouldSave = true; - } - } - if (shouldSave) { - try { - onkostarApi.saveProcedure(p, true); - } catch (Exception e) { - logger.error("Cannot update ECOG for procedure '{}'", p.getId()); - } - } - } - - 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); - newSubProcedure.setStartDate(ecog.getDate()); - newSubProcedure.setValue("Datum", new Item("Datum", ecog.getDate())); - newSubProcedure.setValue("ECOG", new Item("ECOG", ecog.getStatus())); - p.addSubProcedure("ECOGVerlauf", newSubProcedure); - } - try { - onkostarApi.saveProcedure(p, true); - } catch (Exception e) { - logger.error("Create update ECOG for procedure '{}'", p.getId()); - } - } - -} diff --git a/src/main/java/DNPM/analyzer/TherapieplanAnalyzer.java b/src/main/java/DNPM/analyzer/TherapieplanAnalyzer.java deleted file mode 100644 index 932cafb..0000000 --- a/src/main/java/DNPM/analyzer/TherapieplanAnalyzer.java +++ /dev/null @@ -1,127 +0,0 @@ -package DNPM.analyzer; - -import DNPM.security.DelegatingDataBasedPermissionEvaluator; -import DNPM.security.PermissionType; -import DNPM.services.mtb.MtbService; -import DNPM.services.therapieplan.TherapieplanServiceFactory; -import de.itc.onkostar.api.Disease; -import de.itc.onkostar.api.Procedure; -import de.itc.onkostar.api.analysis.AnalyseTriggerEvent; -import de.itc.onkostar.api.analysis.AnalyzerRequirement; -import org.springframework.security.core.context.SecurityContextHolder; -import org.springframework.stereotype.Component; - -import java.util.Map; -import java.util.Set; - -/** - * Diese Klasse implementiert ein Plugin, welches Aktionen nach Bearbeitung eines Therapieplans durchführt. - * - * @since 0.0.2 - */ -@Component -public class TherapieplanAnalyzer extends Analyzer { - - private final TherapieplanServiceFactory therapieplanServiceFactory; - - private final MtbService mtbService; - - private final DelegatingDataBasedPermissionEvaluator permissionEvaluator; - - public TherapieplanAnalyzer( - final TherapieplanServiceFactory therapieplanServiceFactory, - final MtbService mtbService, - final DelegatingDataBasedPermissionEvaluator permissionEvaluator - ) { - this.therapieplanServiceFactory = therapieplanServiceFactory; - this.mtbService = mtbService; - this.permissionEvaluator = permissionEvaluator; - } - - @Override - public String getDescription() { - return "Aktualisiert Unterformulare nach Änderungen im Therapieplan-Formular"; - } - - /** - * @deprecated - */ - @Override - public boolean isRelevantForDeletedProcedure() { - return false; - } - - @Override - public boolean isRelevantForAnalyzer(Procedure procedure, Disease disease) { - return null != procedure && procedure.getFormName().equals("DNPM Therapieplan"); - } - - @Override - public boolean isSynchronous() { - return false; - } - - @Override - public AnalyzerRequirement getRequirement() { - return AnalyzerRequirement.PROCEDURE; - } - - @Override - public Set<AnalyseTriggerEvent> getTriggerEvents() { - return Set.of( - AnalyseTriggerEvent.EDIT_SAVE, - AnalyseTriggerEvent.EDIT_LOCK, - AnalyseTriggerEvent.REORG - ); - } - - @Override - public void analyze(Procedure procedure, Disease disease) { - therapieplanServiceFactory.currentUsableInstance().updateRequiredMtbEntries(procedure); - } - - /** - * Übergibt den Text der referenzierten MTBs für den Protokollauszug - * - * <p>Wurde der Eingabewert <code>id</code> nicht übergeben, wird ein leerer String zurück gegeben. - * - * <p>Beispiel zur Nutzung in einem Formularscript - * <pre> - * executePluginMethod( - * 'TherapieplanAnalyzer', - * 'getProtokollauszug', - * { id: 12345 }, - * (response) => console.log(response), - * false - * ); - * </pre> - * - * @param input Map mit Eingabewerten - * @return Zeichenkette mit Protokollauszug - */ - public String getProtokollauszug(Map<String, Object> input) { - var procedureId = AnalyzerUtils.getRequiredId(input, "id"); - - if (procedureId.isEmpty()) { - return ""; - } - - if ( - permissionEvaluator.hasPermission( - SecurityContextHolder.getContext().getAuthentication(), - procedureId.get(), - Procedure.class.getSimpleName(), - PermissionType.READ - ) - ) { - return mtbService.getProtocol( - therapieplanServiceFactory - .currentUsableInstance() - .findReferencedMtbs(procedureId.get()) - ); - } - - return ""; - } - -} diff --git a/src/main/java/DNPM/config/PluginConfiguration.java b/src/main/java/DNPM/config/PluginConfiguration.java deleted file mode 100644 index 5fcf309..0000000 --- a/src/main/java/DNPM/config/PluginConfiguration.java +++ /dev/null @@ -1,88 +0,0 @@ -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.strahlentherapie.DefaultStrahlentherapieService; -import DNPM.services.strahlentherapie.StrahlentherapieService; -import DNPM.services.systemtherapie.DefaultSystemtherapieService; -import DNPM.services.systemtherapie.SystemtherapieService; -import DNPM.services.therapieplan.TherapieplanServiceFactory; -import de.itc.onkostar.api.IOnkostarApi; -import org.springframework.context.annotation.Bean; -import org.springframework.context.annotation.ComponentScan; -import org.springframework.context.annotation.Configuration; -import org.springframework.data.jpa.repository.config.EnableJpaRepositories; - -import javax.sql.DataSource; - -/** - * Dynamische Konfiguration des Plugins basierend auf Onkostar-Einstellungen - * - * @since 0.0.2 - */ -@Configuration -@ComponentScan(basePackages = { "DNPM.analyzer", "DNPM.security" }) -@EnableJpaRepositories(basePackages = "DNPM.database") -public class PluginConfiguration { - - @Bean - public FormService formService(final DataSource dataSource) { - return new DefaultFormService(dataSource); - } - - @Bean - public StudienService studienService(final DataSource dataSource) { - return new DefaultStudienService(dataSource); - } - - @Bean - public SettingsService settingsService(final SettingsRepository settingsRepository) { - return new SettingsService(settingsRepository); - } - - @Bean - public MtbService mtbService(final IOnkostarApi onkostarApi) { - return new DefaultMtbService(onkostarApi); - } - - @Bean - public SystemtherapieService systemtherapieService( - final IOnkostarApi onkostarApi, - final SettingsService settingsService - ) { - return new DefaultSystemtherapieService(onkostarApi, settingsService); - } - - @Bean - public StrahlentherapieService strahlentherapieService( - final IOnkostarApi onkostarApi, - final SettingsService settingsService - ) { - return new DefaultStrahlentherapieService(onkostarApi, settingsService); - } - - @Bean - public ConsentManagerServiceFactory consentManagerServiceFactory(final IOnkostarApi onkostarApi) { - return new ConsentManagerServiceFactory(onkostarApi); - } - - @Bean - public TherapieplanServiceFactory therapieplanServiceFactory( - final IOnkostarApi onkostarApi, - final SettingsService settingsService, - final FormService formService - ) { - return new TherapieplanServiceFactory(onkostarApi, settingsService, formService); - } - - @Bean - public MolekulargenetikFormService molekulargenetikFormService() { - return new OsMolekulargenetikFormService(); - } - -} diff --git a/src/main/java/DNPM/database/ReadOnlyRepository.java b/src/main/java/DNPM/database/ReadOnlyRepository.java deleted file mode 100644 index 3f8509d..0000000 --- a/src/main/java/DNPM/database/ReadOnlyRepository.java +++ /dev/null @@ -1,22 +0,0 @@ -package DNPM.database; - -import org.springframework.data.repository.NoRepositoryBean; -import org.springframework.data.repository.Repository; - -import java.io.Serializable; -import java.util.List; - -/** - * Basis-Repository for ReadOnly Spring-Data-JPA Repositories - * <p>Entity-Klassen müssen in Package <code>de.itc.db.dnpm</code> liegen - * @param <T> Typ des Entities - * @param <ID> Typ der ID - */ -@NoRepositoryBean -public interface ReadOnlyRepository<T, ID extends Serializable> extends Repository<T, ID> { - - T findById(ID id); - - List<T> findAll(); - -} diff --git a/src/main/java/DNPM/database/SettingsRepository.java b/src/main/java/DNPM/database/SettingsRepository.java deleted file mode 100644 index 9a6e331..0000000 --- a/src/main/java/DNPM/database/SettingsRepository.java +++ /dev/null @@ -1,14 +0,0 @@ -package DNPM.database; - -import de.itc.db.dnpm.Setting; -import org.springframework.stereotype.Repository; - -/** - * Spring Data JPA Repository zum Lesen von Einstellungen - */ -@Repository("dnpmSettingRepository") -public interface SettingsRepository extends ReadOnlyRepository<Setting, Long> { - - Setting findByName(String name); - -} diff --git a/src/main/java/DNPM/dto/EcogStatusWithDate.java b/src/main/java/DNPM/dto/EcogStatusWithDate.java deleted file mode 100644 index a1ec575..0000000 --- a/src/main/java/DNPM/dto/EcogStatusWithDate.java +++ /dev/null @@ -1,44 +0,0 @@ -package DNPM.dto; - -import org.springframework.util.Assert; - -import java.util.Date; - -/** - * Datenklasse zum Abbilden des ECOG-Status und Datum - */ -public class EcogStatusWithDate { - private final Date date; - private final 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; - } -} diff --git a/src/main/java/DNPM/dto/Studie.java b/src/main/java/DNPM/dto/Studie.java deleted file mode 100644 index 59d3cfe..0000000 --- a/src/main/java/DNPM/dto/Studie.java +++ /dev/null @@ -1,74 +0,0 @@ -package DNPM.dto; - -public class Studie { - private final String kategorieName; - private final String code; - private final String studiennummer; - private final String shortDesc; - private final String description; - private final int version; - - private final boolean active; - - public Studie(final String kategorieName, final int version, final String code, final String studiennummer, final String shortDesc, final String description, final boolean active) { - this.kategorieName = kategorieName; - this.version = version; - this.code = code; - this.studiennummer = studiennummer; - this.shortDesc = shortDesc; - this.description = description; - this.active = active; - } - - public String getKategorieName() { - return kategorieName; - } - - public int getVersion() { - return version; - } - - public String getCode() { - return code; - } - - public String getStudiennummer() { - return studiennummer; - } - - public String getShortDesc() { - return shortDesc; - } - - public String getDescription() { - return description; - } - - public boolean isActive() { - return active; - } - - public Type getType() { - if (this.hasNctNumber()) { - return Type.NCT; - } else if (this.hasEudraCtNumber()) { - return Type.EUDRA_CT; - } else { - return Type.UNKNOWN; - } - } - - private boolean hasNctNumber() { - return null != studiennummer && studiennummer.toLowerCase().startsWith("nct"); - } - - private boolean hasEudraCtNumber() { - return null != studiennummer && studiennummer.matches("\\d{4}-\\d{6}-\\d{2}"); - } - - public enum Type { - NCT, - EUDRA_CT, - UNKNOWN - } -} diff --git a/src/main/java/DNPM/dto/Variant.java b/src/main/java/DNPM/dto/Variant.java deleted file mode 100644 index d3fab9e..0000000 --- a/src/main/java/DNPM/dto/Variant.java +++ /dev/null @@ -1,110 +0,0 @@ -package DNPM.dto; - -import de.itc.onkostar.api.Procedure; - -import java.util.Optional; - -/** - * Ein Auszug der Variante aus dem NGS-Bericht zur Übertragung an das Frontend zur Auswahl der stützenden molekularen Alteration - * - * @since 0.2.0 - */ -public class Variant { - private final Integer id; - - private final String ergebnis; - - private final String gen; - - private final String exon; - - private final String pathogenitaetsklasse; - - private Variant( - final int id, - final String ergebnis, - final String gen, - final String exon, - final String pathogenitaetsklasse - ) { - this.id = id; - this.ergebnis = ergebnis; - this.gen = gen; - this.exon = exon; - this.pathogenitaetsklasse = pathogenitaetsklasse; - } - - public Integer getId() { - return id; - } - - public String getErgebnis() { - return ergebnis; - } - - public String getGen() { - return gen; - } - - public String getExon() { - return exon; - } - - public String getPathogenitaetsklasse() { - return pathogenitaetsklasse; - } - - /** - * Erstellt ein Optional einer Variante aus einer Prozedur - * @param procedure Die zu verwendende Prozedur - * @return Das Optional, wenn die Prozedur verwendet werden kann, ansonsten ein leeres Optional - */ - 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(), - "Einfache Variante (Mutation)", - gene.getString().isBlank() ? "-" : gene.getString(), - null == exon || exon.getString().isBlank() ? "-" : exon.getString(), - null == pathogenitaetsklasse || pathogenitaetsklasse.getString().isBlank() ? "-" : pathogenitaetsklasse.getString() - ) - ); - } else if (ergebnis.getString().equals("CNV")) { - return Optional.of( - new Variant( - procedure.getId(), - "Copy Number Variation (CNV)", - gene.getString().isBlank() ? "-" : gene.getString(), - null == exon || exon.getString().isBlank() ? "-" : exon.getString(), - null == pathogenitaetsklasse || pathogenitaetsklasse.getString().isBlank() ? "-" : pathogenitaetsklasse.getString() - ) - ); - } else if (ergebnis.getString().equals("F")) { - return Optional.of( - new Variant( - procedure.getId(), - "Fusion (Translokation Inversion Insertion)", - gene.getString().isBlank() ? "-" : gene.getString(), - null == exon || exon.getString().isBlank() ? "-" : exon.getString(), - null == pathogenitaetsklasse || pathogenitaetsklasse.getString().isBlank() ? "-" : pathogenitaetsklasse.getString() - ) - ); - } else { - return Optional.empty(); - } - } -} diff --git a/src/main/java/DNPM/exceptions/FormException.java b/src/main/java/DNPM/exceptions/FormException.java deleted file mode 100644 index 4d0d6dd..0000000 --- a/src/main/java/DNPM/exceptions/FormException.java +++ /dev/null @@ -1,9 +0,0 @@ -package DNPM.exceptions; - -public class FormException extends RuntimeException { - - public FormException(String message) { - super(message); - } - -} diff --git a/src/main/java/DNPM/security/AbstractDelegatedPermissionEvaluator.java b/src/main/java/DNPM/security/AbstractDelegatedPermissionEvaluator.java deleted file mode 100644 index 60e7ad2..0000000 --- a/src/main/java/DNPM/security/AbstractDelegatedPermissionEvaluator.java +++ /dev/null @@ -1,23 +0,0 @@ -package DNPM.security; - -import de.itc.onkostar.api.IOnkostarApi; -import de.itc.onkostar.api.Patient; -import de.itc.onkostar.api.Procedure; -import org.springframework.security.access.PermissionEvaluator; - -public abstract class AbstractDelegatedPermissionEvaluator implements PermissionEvaluator { - - protected static final String PATIENT = Patient.class.getSimpleName(); - - protected static final String PROCEDURE = Procedure.class.getSimpleName(); - - protected final IOnkostarApi onkostarApi; - - protected final SecurityService securityService; - - protected AbstractDelegatedPermissionEvaluator(final IOnkostarApi onkostarApi, final SecurityService securityService) { - this.onkostarApi = onkostarApi; - this.securityService = securityService; - } - -} diff --git a/src/main/java/DNPM/security/DelegatingDataBasedPermissionEvaluator.java b/src/main/java/DNPM/security/DelegatingDataBasedPermissionEvaluator.java deleted file mode 100644 index d8ca92e..0000000 --- a/src/main/java/DNPM/security/DelegatingDataBasedPermissionEvaluator.java +++ /dev/null @@ -1,56 +0,0 @@ -package DNPM.security; - -import org.springframework.security.access.PermissionEvaluator; -import org.springframework.security.core.Authentication; -import org.springframework.stereotype.Component; - -import java.io.Serializable; -import java.util.List; - -/** - * PermissionEvaluator zur Gesamtprüfung der Zugriffsberechtigung. - * Die konkrete Berechtigungsprüfung wird an die nachgelagerten PermissionEvaluatoren delegiert, - * welche jeweils einzeln dem Zugriff zustimmen müssen. - */ -@Component -public class DelegatingDataBasedPermissionEvaluator implements PermissionEvaluator { - - private final List<AbstractDelegatedPermissionEvaluator> permissionEvaluators; - - public DelegatingDataBasedPermissionEvaluator(final List<AbstractDelegatedPermissionEvaluator> permissionEvaluators) { - this.permissionEvaluators = permissionEvaluators; - } - - /** - * Auswertung der Zugriffsberechtigung für authentifizierten Benutzer auf Zielobjekt mit angeforderter Berechtigung. - * Hierbei wird die Berechtigungsprüfung an alle nachgelagerten PermissionEvaluatoren delegiert. - * Alle müssen dem Zugriff zustimmen. - * - * @param authentication Das Authentication Objekt - * @param targetObject Das Zielobjekt - * @param permissionType Die angeforderte Berechtigung - * @return Gibt <code>true</code> zurück, wenn der Benutzer die Berechtigung hat - */ - @Override - public boolean hasPermission(Authentication authentication, Object targetObject, Object permissionType) { - return permissionEvaluators.stream() - .allMatch(permissionEvaluator -> permissionEvaluator.hasPermission(authentication, targetObject, permissionType)); - } - - /** - * Auswertung anhand der ID und des Namens des Zielobjekts. - * Hierbei wird die Berechtigungsprüfung an alle nachgelagerten PermissionEvaluatoren delegiert. - * Alle müssen dem Zugriff zustimmen. - * - * @param authentication Authentication-Object - * @param targetId ID des Objekts - * @param targetType Name der Zielobjektklasse - * @param permissionType Die angeforderte Berechtigung - * @return Gibt <code>true</code> zurück, wenn der Benutzer die Berechtigung hat - */ - @Override - public boolean hasPermission(Authentication authentication, Serializable targetId, String targetType, Object permissionType) { - return permissionEvaluators.stream() - .allMatch(permissionEvaluator -> permissionEvaluator.hasPermission(authentication, targetId, targetType, permissionType)); - } -} diff --git a/src/main/java/DNPM/security/FormBasedPermissionEvaluator.java b/src/main/java/DNPM/security/FormBasedPermissionEvaluator.java deleted file mode 100644 index 912a19c..0000000 --- a/src/main/java/DNPM/security/FormBasedPermissionEvaluator.java +++ /dev/null @@ -1,59 +0,0 @@ -package DNPM.security; - -import de.itc.onkostar.api.IOnkostarApi; -import de.itc.onkostar.api.Procedure; -import org.springframework.security.core.Authentication; -import org.springframework.stereotype.Component; - -import java.io.Serializable; - -/** - * Permission-Evaluator zur Auswertung der Berechtigung auf Objekte aufgrund der Formularberechtigung - */ -@Component -public class FormBasedPermissionEvaluator extends AbstractDelegatedPermissionEvaluator { - - public FormBasedPermissionEvaluator(final IOnkostarApi onkostarApi, final SecurityService securityService) { - super(onkostarApi, securityService); - } - - /** - * Auswertung der Zugriffsberechtigung für authentifizierten Benutzer auf Zielobjekt mit angeforderter Berechtigung. - * Zugriff auf Objekte vom Typ "Patient" wird immer gewährt. - * - * @param authentication Das Authentication Objekt - * @param targetObject Das Zielobjekt - * @param permissionType Die angeforderte Berechtigung - * @return Gibt <code>true</code> zurück, wenn der Benutzer die Berechtigung hat - */ - @Override - public boolean hasPermission(Authentication authentication, Object targetObject, Object permissionType) { - if (permissionType instanceof PermissionType && targetObject instanceof Procedure) { - return this.securityService.getFormNamesForPermission(authentication, (PermissionType)permissionType) - .contains(((Procedure)targetObject).getFormName()); - } - return true; - } - - /** - * Auswertung anhand der ID und des Namens des Zielobjekts. - * Zugriff auf Objekte vom Typ "Patient" wird immer gewährt. - * - * @param authentication Authentication-Object - * @param targetId ID des Objekts - * @param targetType Name der Zielobjektklasse - * @param permissionType Die angeforderte Berechtigung - * @return Gibt <code>true</code> zurück, wenn der Benutzer die Berechtigung hat - */ - @Override - public boolean hasPermission(Authentication authentication, Serializable targetId, String targetType, Object permissionType) { - if (permissionType instanceof PermissionType && targetId instanceof Integer && PROCEDURE.equals(targetType)) { - var procedure = this.onkostarApi.getProcedure((int)targetId); - if (null != procedure) { - return this.securityService.getFormNamesForPermission(authentication, (PermissionType) permissionType).contains(procedure.getFormName()); - } - } - return true; - } - -} diff --git a/src/main/java/DNPM/security/FormBasedSecurityAspects.java b/src/main/java/DNPM/security/FormBasedSecurityAspects.java deleted file mode 100644 index 306c062..0000000 --- a/src/main/java/DNPM/security/FormBasedSecurityAspects.java +++ /dev/null @@ -1,51 +0,0 @@ -package DNPM.security; - -import de.itc.onkostar.api.Procedure; -import org.aspectj.lang.JoinPoint; -import org.aspectj.lang.annotation.AfterReturning; -import org.aspectj.lang.annotation.Aspect; -import org.aspectj.lang.annotation.Before; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; -import org.springframework.security.core.context.SecurityContextHolder; - -import java.util.Arrays; - -// TODO Disabled for now - check bytecode reported incompatibility for older OS installations -//@Component -@Aspect -public class FormBasedSecurityAspects { - - private final Logger logger = LoggerFactory.getLogger(this.getClass()); - - private final FormBasedPermissionEvaluator permissionEvaluator; - - public FormBasedSecurityAspects( - final FormBasedPermissionEvaluator permissionEvaluator - ) { - this.permissionEvaluator = permissionEvaluator; - } - - @AfterReturning(value = "@annotation(FormSecuredResult)", returning = "procedure") - public void afterProcedureFormBased(Procedure procedure) { - if ( - null != procedure - && ! permissionEvaluator.hasPermission(SecurityContextHolder.getContext().getAuthentication(), procedure, PermissionType.READ_WRITE) - ) { - logger.warn("Rückgabe von Prozedur blockiert: {}", procedure.getId()); - throw new IllegalSecuredObjectAccessException(); - } - } - - @Before(value = "@annotation(FormSecured)") - public void beforeProcedureFormBased(JoinPoint jp) { - Arrays.stream(jp.getArgs()) - .filter(arg -> arg instanceof Procedure) - .forEach(procedure -> { - if (! permissionEvaluator.hasPermission(SecurityContextHolder.getContext().getAuthentication(), procedure, PermissionType.READ_WRITE)) { - logger.warn("Zugriff auf Prozedur blockiert: {}", ((Procedure)procedure).getId()); - throw new IllegalSecuredObjectAccessException(); - } - }); - } -} diff --git a/src/main/java/DNPM/security/FormSecured.java b/src/main/java/DNPM/security/FormSecured.java deleted file mode 100644 index 2e12667..0000000 --- a/src/main/java/DNPM/security/FormSecured.java +++ /dev/null @@ -1,14 +0,0 @@ -package DNPM.security; - -import java.lang.annotation.ElementType; -import java.lang.annotation.Retention; -import java.lang.annotation.RetentionPolicy; -import java.lang.annotation.Target; - -@Retention(RetentionPolicy.RUNTIME) -@Target(ElementType.METHOD) -public @interface FormSecured { - - PermissionType value() default PermissionType.READ_WRITE; - -} diff --git a/src/main/java/DNPM/security/FormSecuredResult.java b/src/main/java/DNPM/security/FormSecuredResult.java deleted file mode 100644 index ccfbd24..0000000 --- a/src/main/java/DNPM/security/FormSecuredResult.java +++ /dev/null @@ -1,14 +0,0 @@ -package DNPM.security; - -import java.lang.annotation.ElementType; -import java.lang.annotation.Retention; -import java.lang.annotation.RetentionPolicy; -import java.lang.annotation.Target; - -@Retention(RetentionPolicy.RUNTIME) -@Target(ElementType.METHOD) -public @interface FormSecuredResult { - - PermissionType value() default PermissionType.READ_WRITE; - -} diff --git a/src/main/java/DNPM/security/IllegalSecuredObjectAccessException.java b/src/main/java/DNPM/security/IllegalSecuredObjectAccessException.java deleted file mode 100644 index 542b604..0000000 --- a/src/main/java/DNPM/security/IllegalSecuredObjectAccessException.java +++ /dev/null @@ -1,13 +0,0 @@ -package DNPM.security; - -public class IllegalSecuredObjectAccessException extends RuntimeException { - - public IllegalSecuredObjectAccessException() { - super(); - } - - public IllegalSecuredObjectAccessException(String message) { - super(message); - } - -} diff --git a/src/main/java/DNPM/security/PermissionType.java b/src/main/java/DNPM/security/PermissionType.java deleted file mode 100644 index 1539aea..0000000 --- a/src/main/java/DNPM/security/PermissionType.java +++ /dev/null @@ -1,6 +0,0 @@ -package DNPM.security; - -public enum PermissionType { - READ, - READ_WRITE -} diff --git a/src/main/java/DNPM/security/PersonPoolBasedPermissionEvaluator.java b/src/main/java/DNPM/security/PersonPoolBasedPermissionEvaluator.java deleted file mode 100644 index e3ba16e..0000000 --- a/src/main/java/DNPM/security/PersonPoolBasedPermissionEvaluator.java +++ /dev/null @@ -1,81 +0,0 @@ -package DNPM.security; - -import de.itc.onkostar.api.IOnkostarApi; -import de.itc.onkostar.api.Patient; -import de.itc.onkostar.api.Procedure; -import org.springframework.security.core.Authentication; -import org.springframework.stereotype.Component; - -import java.io.Serializable; - -/** - * Permission-Evaluator zur Auswertung der Berechtigung auf Objekte aufgrund der Personenstammberechtigung - */ -@Component -public class PersonPoolBasedPermissionEvaluator extends AbstractDelegatedPermissionEvaluator { - - public PersonPoolBasedPermissionEvaluator(final IOnkostarApi onkostarApi, final SecurityService securityService) { - super(onkostarApi, securityService); - } - - /** - * Auswertung der Zugriffsberechtigung für authentifizierten Benutzer auf Zielobjekt mit angeforderter Berechtigung. - * @param authentication Das Authentication Objekt - * @param targetObject Das Zielobjekt - * @param permissionType Die angeforderte Berechtigung - * @return Gibt <code>true</code> zurück, wenn der Benutzer die Berechtigung hat - */ - @Override - public boolean hasPermission(Authentication authentication, Object targetObject, Object permissionType) { - if (permissionType instanceof PermissionType) { - if (targetObject instanceof Patient) { - return this.securityService.getPersonPoolIdsForPermission(authentication, (PermissionType)permissionType) - .contains(((Patient)targetObject).getPersonPoolCode()); - } else if (targetObject instanceof Procedure) { - return this.securityService.getPersonPoolIdsForPermission(authentication, (PermissionType)permissionType) - .contains(((Procedure)targetObject).getPatient().getPersonPoolCode()); - } - } - return false; - } - - /** - * Auswertung anhand der ID und des Namens des Zielobjekts. - * @param authentication Authentication-Object - * @param targetId ID des Objekts - * @param targetType Name der Zielobjektklasse - * @param permissionType Die angeforderte Berechtigung - * @return Gibt <code>true</code> zurück, wenn der Benutzer die Berechtigung hat - */ - @Override - public boolean hasPermission(Authentication authentication, Serializable targetId, String targetType, Object permissionType) { - if (targetId instanceof Integer && permissionType instanceof PermissionType) { - var personPoolCode = getPersonPoolCode((int)targetId, targetType); - if (null != personPoolCode) { - return this.securityService.getPersonPoolIdsForPermission(authentication, (PermissionType) permissionType).contains(personPoolCode); - } - } - return false; - } - - private String getPersonPoolCode(int id, String type) { - Patient patient = null; - - if (PATIENT.equals(type)) { - patient = onkostarApi.getPatient(id); - } else if (PROCEDURE.equals(type)) { - var procedure = onkostarApi.getProcedure(id); - if (null != procedure) { - patient = procedure.getPatient(); - } - } - - if (null != patient) { - return patient.getPersonPoolCode(); - } - - return null; - } - - -} diff --git a/src/main/java/DNPM/security/PersonPoolBasedSecurityAspects.java b/src/main/java/DNPM/security/PersonPoolBasedSecurityAspects.java deleted file mode 100644 index 37c313f..0000000 --- a/src/main/java/DNPM/security/PersonPoolBasedSecurityAspects.java +++ /dev/null @@ -1,74 +0,0 @@ -package DNPM.security; - -import de.itc.onkostar.api.Patient; -import de.itc.onkostar.api.Procedure; -import org.aspectj.lang.JoinPoint; -import org.aspectj.lang.annotation.AfterReturning; -import org.aspectj.lang.annotation.Aspect; -import org.aspectj.lang.annotation.Before; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; -import org.springframework.security.core.context.SecurityContextHolder; -import org.springframework.stereotype.Component; - -import java.util.Arrays; - -@Component -@Aspect -public class PersonPoolBasedSecurityAspects { - - private final Logger logger = LoggerFactory.getLogger(this.getClass()); - - private final PersonPoolBasedPermissionEvaluator permissionEvaluator; - - public PersonPoolBasedSecurityAspects(PersonPoolBasedPermissionEvaluator permissionEvaluator) { - this.permissionEvaluator = permissionEvaluator; - } - - @AfterReturning(value = "@annotation(PersonPoolSecuredResult) ", returning = "patient") - public void afterPatient(Patient patient) { - if ( - null != patient - && ! permissionEvaluator.hasPermission(SecurityContextHolder.getContext().getAuthentication(), patient, PermissionType.READ_WRITE) - ) { - logger.warn("Rückgabe von Patient blockiert: {}", patient.getId()); - throw new IllegalSecuredObjectAccessException(); - } - } - - @AfterReturning(value = "@annotation(PersonPoolSecuredResult)", returning = "procedure") - public void afterProcedure(Procedure procedure) { - if ( - null != procedure - && ! permissionEvaluator.hasPermission(SecurityContextHolder.getContext().getAuthentication(), procedure, PermissionType.READ_WRITE) - ) { - logger.warn("Rückgabe von Prozedur blockiert: {}", procedure.getId()); - throw new IllegalSecuredObjectAccessException(); - } - } - - @Before(value = "@annotation(PersonPoolSecured)") - public void beforePatient(JoinPoint jp) { - Arrays.stream(jp.getArgs()) - .filter(arg -> arg instanceof Patient) - .forEach(patient -> { - if (! permissionEvaluator.hasPermission(SecurityContextHolder.getContext().getAuthentication(), patient, PermissionType.READ_WRITE)) { - logger.warn("Zugriff auf Patient blockiert: {}", ((Patient)patient).getId()); - throw new IllegalSecuredObjectAccessException(); - } - }); - } - - @Before(value = "@annotation(PersonPoolSecured)") - public void beforeProcedure(JoinPoint jp) { - Arrays.stream(jp.getArgs()) - .filter(arg -> arg instanceof Procedure) - .forEach(procedure -> { - if (! permissionEvaluator.hasPermission(SecurityContextHolder.getContext().getAuthentication(), procedure, PermissionType.READ_WRITE)) { - logger.warn("Zugriff auf Prozedur blockiert: {}", ((Procedure)procedure).getId()); - throw new IllegalSecuredObjectAccessException(); - } - }); - } - -} diff --git a/src/main/java/DNPM/security/PersonPoolSecured.java b/src/main/java/DNPM/security/PersonPoolSecured.java deleted file mode 100644 index cac0f78..0000000 --- a/src/main/java/DNPM/security/PersonPoolSecured.java +++ /dev/null @@ -1,14 +0,0 @@ -package DNPM.security; - -import java.lang.annotation.ElementType; -import java.lang.annotation.Retention; -import java.lang.annotation.RetentionPolicy; -import java.lang.annotation.Target; - -@Retention(RetentionPolicy.RUNTIME) -@Target(ElementType.METHOD) -public @interface PersonPoolSecured { - - PermissionType value() default PermissionType.READ_WRITE; - -} diff --git a/src/main/java/DNPM/security/PersonPoolSecuredResult.java b/src/main/java/DNPM/security/PersonPoolSecuredResult.java deleted file mode 100644 index 0ca8edf..0000000 --- a/src/main/java/DNPM/security/PersonPoolSecuredResult.java +++ /dev/null @@ -1,14 +0,0 @@ -package DNPM.security; - -import java.lang.annotation.ElementType; -import java.lang.annotation.Retention; -import java.lang.annotation.RetentionPolicy; -import java.lang.annotation.Target; - -@Retention(RetentionPolicy.RUNTIME) -@Target(ElementType.METHOD) -public @interface PersonPoolSecuredResult { - - PermissionType value() default PermissionType.READ_WRITE; - -} diff --git a/src/main/java/DNPM/security/SecurityService.java b/src/main/java/DNPM/security/SecurityService.java deleted file mode 100644 index 479701f..0000000 --- a/src/main/java/DNPM/security/SecurityService.java +++ /dev/null @@ -1,60 +0,0 @@ -package DNPM.security; - -import org.springframework.jdbc.core.JdbcTemplate; -import org.springframework.security.core.Authentication; -import org.springframework.security.core.userdetails.UserDetails; -import org.springframework.stereotype.Service; - -import javax.sql.DataSource; -import java.util.List; - -/** - * Service mit Methoden zum Feststellen von sicherheitsrelevanten Informationen eines Benutzers - */ -@Service -public class SecurityService { - - private final JdbcTemplate jdbcTemplate; - - public SecurityService(final DataSource dataSource) { - this.jdbcTemplate = new JdbcTemplate(dataSource); - } - - List<String> getPersonPoolIdsForPermission(Authentication authentication, PermissionType permissionType) { - var sql = "SELECT p.kennung FROM personenstamm_zugriff " + - " JOIN usergroup u ON personenstamm_zugriff.benutzergruppe_id = u.id " + - " JOIN akteur_usergroup au ON u.id = au.usergroup_id " + - " JOIN akteur a ON au.akteur_id = a.id " + - " JOIN personenstamm p on personenstamm_zugriff.personenstamm_id = p.id " + - " WHERE a.login = ? AND a.aktiv AND a.anmelden_moeglich "; - - if (PermissionType.READ_WRITE == permissionType) { - sql += " AND personenstamm_zugriff.bearbeiten "; - } - - var userDetails = (UserDetails)authentication.getPrincipal(); - - return jdbcTemplate - .query(sql, new Object[]{userDetails.getUsername()}, (rs, rowNum) -> rs.getString("kennung")); - } - - List<String> getFormNamesForPermission(Authentication authentication, PermissionType permissionType) { - - var sql = "SELECT df.name FROM formular_usergroup_zugriff " + - " JOIN data_form df ON formular_usergroup_zugriff.formular_id = df.id " + - " JOIN usergroup u ON formular_usergroup_zugriff.usergroup_id = u.id " + - " JOIN akteur_usergroup au ON u.id = au.usergroup_id " + - " JOIN akteur a on au.akteur_id = a.id " + - " WHERE a.login = ? AND a.aktiv AND a.anmelden_moeglich "; - - if (PermissionType.READ_WRITE == permissionType) { - sql += " AND formular_usergroup_zugriff.bearbeiten "; - } - - var userDetails = (UserDetails)authentication.getPrincipal(); - - return jdbcTemplate - .query(sql, new Object[]{userDetails.getUsername()}, (rs, rowNum) -> rs.getString("name")); - } - -} diff --git a/src/main/java/DNPM/services/DefaultFormService.java b/src/main/java/DNPM/services/DefaultFormService.java deleted file mode 100644 index 9feaeb2..0000000 --- a/src/main/java/DNPM/services/DefaultFormService.java +++ /dev/null @@ -1,37 +0,0 @@ -package DNPM.services; - -import DNPM.exceptions.FormException; -import org.springframework.jdbc.core.JdbcTemplate; - -import javax.sql.DataSource; -import java.util.List; - -/** - * Standardimplementierung zum Ermitteln von Unter- und Hauptformularen - * - * @since 0.0.2 - */ -public class DefaultFormService implements FormService { - - private final JdbcTemplate jdbcTemplate; - - public DefaultFormService(final DataSource dataSource) { - this.jdbcTemplate = new JdbcTemplate(dataSource); - } - - @Override - public int getMainFormProcedureId(int procedureId) throws FormException { - var sql = "SELECT hauptprozedur_id FROM prozedur WHERE id = ?"; - try { - return jdbcTemplate.queryForObject(sql, (resultSet, i) -> resultSet.getInt("hauptprozedur_id"), procedureId); - } catch (Exception e) { - throw new FormException(String.format("No main form found for subform with ID '%d'", procedureId)); - } - } - - @Override - public List<Integer> getSubFormProcedureIds(int procedureId) { - var sql = "SELECT id FROM prozedur WHERE hauptprozedur_id = ?"; - return jdbcTemplate.queryForList(sql, Integer.class, procedureId); - } -} diff --git a/src/main/java/DNPM/services/DefaultStudienService.java b/src/main/java/DNPM/services/DefaultStudienService.java deleted file mode 100644 index e172cc8..0000000 --- a/src/main/java/DNPM/services/DefaultStudienService.java +++ /dev/null @@ -1,78 +0,0 @@ -package DNPM.services; - -import DNPM.dto.Studie; -import org.springframework.jdbc.core.JdbcTemplate; - -import javax.sql.DataSource; -import java.util.List; -import java.util.stream.Collectors; - -/** - * Standardimplementierung zum Ermitteln von Studien - * - * @since 0.0.2 - */ -public class DefaultStudienService implements StudienService { - - private final JdbcTemplate jdbcTemplate; - - public DefaultStudienService(final DataSource dataSource) { - this.jdbcTemplate = new JdbcTemplate(dataSource); - } - - @Override - public List<Studie> findAll() { - var sql = "SELECT pcc.name, pcv.version_number, TRIM(studie.studien_nummer) AS studien_nummer, studie.startdatum, studie.endedatum, pcve.code, pcve.shortdesc, pcve.description, studie.aktiv FROM studie " - + "LEFT JOIN category_entry ce ON ce.version_entry_id = studie.property_version_entry " - + "LEFT JOIN property_catalogue_category pcc ON pcc.id = ce.category_id " - + "JOIN property_catalogue_version_entry pcve ON pcve.id = studie.property_version_entry " - + "JOIN property_catalogue_version pcv ON pcv.id = pcve.property_version_id " - + "JOIN property_catalogue pc ON pc.id = pcv.datacatalog_id " - + "WHERE pc.name = 'OS.Studien'" - + "ORDER BY TRIM(studie.studien_nummer)"; - - return this.jdbcTemplate.query(sql, (resultSet, i) -> new Studie( - resultSet.getString("name"), - resultSet.getInt("version_number"), - resultSet.getString("code"), - resultSet.getString("studien_nummer"), - resultSet.getString("shortdesc"), - resultSet.getString("description"), - resultSet.getBoolean("aktiv") - )); - } - - @Override - public List<Studie> findByQuery(String query) { - var sql = "SELECT pcc.name, pcv.version_number, TRIM(studie.studien_nummer) AS studien_nummer, studie.startdatum, studie.endedatum, pcve.code, pcve.shortdesc, pcve.description, studie.aktiv FROM studie " - + "LEFT JOIN category_entry ce ON ce.version_entry_id = studie.property_version_entry " - + "LEFT JOIN property_catalogue_category pcc ON pcc.id = ce.category_id " - + "JOIN property_catalogue_version_entry pcve ON pcve.id = studie.property_version_entry " - + "JOIN property_catalogue_version pcv ON pcv.id = pcve.property_version_id " - + "JOIN property_catalogue pc ON pc.id = pcv.datacatalog_id " - + "WHERE pc.name = 'OS.Studien' AND (pcve.shortdesc LIKE ? OR pcve.description LIKE ? OR studie.studien_nummer LIKE ?)" - + "ORDER BY TRIM(studie.studien_nummer)"; - - var like = String.format("%%%s%%", query); - - return this.jdbcTemplate.query(sql, new Object[]{like, like, like}, (resultSet, i) -> new Studie( - resultSet.getString("name"), - resultSet.getInt("version_number"), - resultSet.getString("code"), - resultSet.getString("studien_nummer"), - resultSet.getString("shortdesc"), - resultSet.getString("description"), - resultSet.getBoolean("aktiv") - )); - } - - @Override - public List<Studie> findActive() { - return findAll().stream().filter(Studie::isActive).collect(Collectors.toList()); - } - - @Override - public List<Studie> findActiveByQuery(String query) { - return findByQuery(query).stream().filter(Studie::isActive).collect(Collectors.toList()); - } -} diff --git a/src/main/java/DNPM/services/FormService.java b/src/main/java/DNPM/services/FormService.java deleted file mode 100644 index f10d6c3..0000000 --- a/src/main/java/DNPM/services/FormService.java +++ /dev/null @@ -1,51 +0,0 @@ -package DNPM.services; - -import DNPM.exceptions.FormException; -import de.itc.onkostar.api.Procedure; -import de.itc.onkostar.api.constants.JaNeinUnbekannt; - -import java.util.List; - -public interface FormService { - - /** - * Diese Methode übergibt die Prozedur-ID des zugehörigen Hauptformulars zu einem Unterformular - * Siehe auch: <a href="https://github.com/CCC-MF/onkostar-plugin-forminfo/blob/master/src/main/java/de/ukw/ccc/onkostar/forminfo/services/FormInfoService.java">FormInfoService.java</a> - * - * @param procedureId Die Prozedur-ID des Unterformulars - * @return Die Prozedur-ID des zugehörigen Hauptformulars - * @throws FormException Wird geworfen, wenn ein Fehler auftrat - */ - int getMainFormProcedureId(int procedureId) throws FormException; - - /** - * Diese Methode übergibt die Prozedur-IDs von Unterformularen zu einem Formular - * Siehe auch: <a href="https://github.com/CCC-MF/onkostar-plugin-forminfo/blob/master/src/main/java/de/ukw/ccc/onkostar/forminfo/services/FormInfoService.java">FormInfoService.java</a> - * - * @param procedureId Die Prozedur-ID des Formulars - * @return Eine Liste mit Prozedur-IDs der Unterformulare - */ - List<Integer> getSubFormProcedureIds(int procedureId); - - /** - * Prüft, ob ein Formularfeld in der Prozedur einen Wert hat oder null ist - * @param procedure Die zu prüfende Prozedur - * @param fieldName Der Formularfeldname - * @return Gibt <code>true</code> zurück, wenn das Feld einen Wert hat - */ - static boolean hasValue(final Procedure procedure, final String fieldName) { - return null != procedure.getValue(fieldName); - } - - /** - * Prüft, ob ein Formularfeld mit Ja/Nein/Unbekannt den Wert Ja hat - * @param procedure Die zu prüfende Prozedur - * @param fieldName Der Formularfeldname - * @return Gibt <code>true</code> zurück, wenn das Feld den Wert "Ja" hat - */ - static boolean isYes(final Procedure procedure, final String fieldName) { - return hasValue(procedure, fieldName) - && procedure.getValue(fieldName).getString().equals(JaNeinUnbekannt.JA.getCode()); - } - -} diff --git a/src/main/java/DNPM/services/SettingsService.java b/src/main/java/DNPM/services/SettingsService.java deleted file mode 100644 index 7459d4e..0000000 --- a/src/main/java/DNPM/services/SettingsService.java +++ /dev/null @@ -1,47 +0,0 @@ -package DNPM.services; - -import DNPM.database.SettingsRepository; - -import java.util.Optional; - -/** - * Implementiert den Dienst zur Ermittlung von Systemeinstellungen - */ -public class SettingsService { - - private final SettingsRepository settingsRepository; - - public SettingsService(final SettingsRepository settingsRepository) { - this.settingsRepository = settingsRepository; - } - - /** - * Übergibt ein <code>Optional</code> für die Einstellung mit angegebenen Namen - * @param name Name der Einstellung - * @return Optional mit Wert der Einstellung oder ein leeres Optional, wenn Einstellung nicht gefunden - */ - public Optional<String> getSetting(String name) { - var sid = settingsRepository.findByName(name); - if (null == sid) { - return Optional.empty(); - } - return Optional.of(sid.getValue()); - } - - /** - * Übergibt die SID als <code>Optional</code> - * @return Optional mit Wert der SID - */ - public Optional<String> getSID() { - return getSetting("SID"); - } - - /** - * Übergibt die Einstellung für <code>mehrere_mtb_in_mtbepisode</code> - * @return Übergibt <code>true</code>, wenn <code>mehrere_mtb_in_mtbepisode</code> auf "Ja" gesetzt ist. - */ - public boolean multipleMtbsInMtbEpisode() { - var setting = getSetting("mehrere_mtb_in_mtbepisode"); - return setting.isPresent() && setting.get().equals("true"); - } -} diff --git a/src/main/java/DNPM/services/StudienService.java b/src/main/java/DNPM/services/StudienService.java deleted file mode 100644 index c82947d..0000000 --- a/src/main/java/DNPM/services/StudienService.java +++ /dev/null @@ -1,39 +0,0 @@ -package DNPM.services; - -import DNPM.dto.Studie; - -import java.util.List; - -public interface StudienService { - - /** - * Übergibt eine Liste mit allen Studien - * - * @return Liste mit allen Studien - */ - List<Studie> findAll(); - - /** - * Übergibt eine Liste mit Studien, deren (Kurz-)Beschreibung oder Studiennummer den übergebenen Wert enthalten - * - * @param query Wert der enthalten sein muss - * @return Gefilterte Liste mit Studien - */ - List<Studie> findByQuery(String query); - - /** - * Übergibt eine Liste mit aktiven Studien - * - * @return Liste mit aktiven Studien - */ - List<Studie> findActive(); - - /** - * Übergibt eine Liste mit aktiven Studien, deren (Kurz-)Beschreibung oder Studiennummer den übergebenen Wert enthalten - * - * @param query Wert der enthalten sein muss - * @return Gefilterte Liste mit aktiven Studien - */ - List<Studie> findActiveByQuery(String query); - -} diff --git a/src/main/java/DNPM/services/TherapieMitEcogService.java b/src/main/java/DNPM/services/TherapieMitEcogService.java deleted file mode 100644 index e8cbae4..0000000 --- a/src/main/java/DNPM/services/TherapieMitEcogService.java +++ /dev/null @@ -1,30 +0,0 @@ -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); - -} diff --git a/src/main/java/DNPM/services/consent/ConsentManagerService.java b/src/main/java/DNPM/services/consent/ConsentManagerService.java deleted file mode 100644 index c05ad6b..0000000 --- a/src/main/java/DNPM/services/consent/ConsentManagerService.java +++ /dev/null @@ -1,27 +0,0 @@ -package DNPM.services.consent; - -import de.itc.onkostar.api.Procedure; - -/** - * Schnittstelle für die Anwendung von Consent-Änderungen - * - * @since 0.2.0 - */ -public interface ConsentManagerService { - - /** - * Wende Consent an, wenn dieses Consent-Formular gespeichert wird - * @param procedure Prozedur des Consent-Formulars - */ - void applyConsent(Procedure procedure); - - /** - * Optionale Prüfung, ob die angegebene Prozedur angewendet werden kann. - * @param procedure Anzuwendende Prozedur - * @return Gibt <code>true</code> zurück, wenn die Prozedur angewendet werden kann. - */ - default boolean canApply(Procedure procedure) { - return null != procedure; - } - -} diff --git a/src/main/java/DNPM/services/consent/ConsentManagerServiceFactory.java b/src/main/java/DNPM/services/consent/ConsentManagerServiceFactory.java deleted file mode 100644 index 0ec7a15..0000000 --- a/src/main/java/DNPM/services/consent/ConsentManagerServiceFactory.java +++ /dev/null @@ -1,28 +0,0 @@ -package DNPM.services.consent; - -import de.itc.onkostar.api.IOnkostarApi; - -public class ConsentManagerServiceFactory { - - private final IOnkostarApi onkostarApi; - - public ConsentManagerServiceFactory( - final IOnkostarApi onkostarApi - ) { - this.onkostarApi = onkostarApi; - } - - public ConsentManagerService currentUsableInstance() { - var consentFormName = onkostarApi.getGlobalSetting("consentform"); - - switch (consentFormName) { - case "Excel-Formular": - return new UkwConsentManagerService(this.onkostarApi); - case "MR.Consent": - return new MrConsentManagerService(this.onkostarApi); - default: - return procedure -> {}; - } - } - -} diff --git a/src/main/java/DNPM/services/consent/MrConsentManagerService.java b/src/main/java/DNPM/services/consent/MrConsentManagerService.java deleted file mode 100644 index 20ee4db..0000000 --- a/src/main/java/DNPM/services/consent/MrConsentManagerService.java +++ /dev/null @@ -1,126 +0,0 @@ -package DNPM.services.consent; - -import DNPM.VerweisVon; -import de.itc.onkostar.api.IOnkostarApi; -import de.itc.onkostar.api.Item; -import de.itc.onkostar.api.Procedure; -import org.hibernate.SQLQuery; -import org.hibernate.Session; -import org.hibernate.SessionFactory; -import org.hibernate.transform.Transformers; -import org.hibernate.type.StandardBasicTypes; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import java.util.List; -import java.util.Map; - -/** - * Detailimplementierung für das Formular `MR.Consent` - * - * @since 0.2.0 - */ -public class MrConsentManagerService implements ConsentManagerService { - - private final Logger logger = LoggerFactory.getLogger(this.getClass()); - - private final IOnkostarApi onkostarApi; - - public MrConsentManagerService(final IOnkostarApi onkostarApi) { - this.onkostarApi = onkostarApi; - } - - @Override - public boolean canApply(Procedure procedure) { - return null != procedure && procedure.getFormName().equals("MR.Consent"); - } - - /** - * Wende Consent an, wenn dieses Consent-Formular gespeichert wird - * - * @param procedure Prozedur des Consent-Formulars - */ - @Override - public void applyConsent(Procedure procedure) { - int value = 0; - try { - SessionFactory sessionFactory = onkostarApi.getSessionFactory(); - Session session = sessionFactory.getCurrentSession(); - // geänderte Werte checken - String sql1 = "select id, max(timestamp) AS datum from aenderungsprotokoll where entity_id = '" + procedure.getId() + "'"; - SQLQuery query1 = session.createSQLQuery(sql1) - .addScalar("id", StandardBasicTypes.INTEGER) - .addScalar("datum", StandardBasicTypes.TIMESTAMP); - logger.info("Wert-Check: {}", query1.uniqueResult()); - - String sql = "SELECT prozedur.id AS procedure_id, prozedur.data_form_id, data_catalogue.name AS data_catalogue, data_catalogue_entry.name AS data_catalogue_entry, data_form.description AS formname, prozedur.beginndatum AS datum " + - "FROM prozedur " + - "LEFT JOIN data_form_data_catalogue ON data_form_data_catalogue.data_form_id = prozedur.data_form_id " + - "LEFT JOIN data_catalogue_entry ON data_catalogue_entry.data_catalogue_id = data_form_data_catalogue.data_catalogue_id " + - "LEFT JOIN data_catalogue ON data_catalogue.id = data_catalogue_entry.data_catalogue_id " + - "LEFT JOIN data_form ON data_form.id = prozedur.data_form_id " + - "WHERE patient_id = " + procedure.getPatientId() + " " + - "AND geloescht = 0 " + - "AND data_catalogue_entry.type = 'formReference' " + - "GROUP BY prozedur.id, prozedur.data_form_id, data_catalogue.name, data_catalogue_entry.name"; - - SQLQuery query = session.createSQLQuery(sql) - .addScalar("procedure_id", StandardBasicTypes.INTEGER) - .addScalar("data_form_id", StandardBasicTypes.INTEGER) - .addScalar("data_catalogue", StandardBasicTypes.STRING) - .addScalar("data_catalogue_entry", StandardBasicTypes.STRING) - .addScalar("formname", StandardBasicTypes.STRING) - .addScalar("datum", StandardBasicTypes.DATE); - - query.setResultTransformer(Transformers.aliasToBean(VerweisVon.class)); - - @SuppressWarnings("unchecked") - List<VerweisVon> result = query.list(); - - for (VerweisVon verweisVon : result) { - sql = verweisVon.getSQL(); - query = session.createSQLQuery(sql) - .addScalar("value", StandardBasicTypes.INTEGER); - if (query.uniqueResult() != null) { - value = (Integer) query.uniqueResult(); - } - if (value == procedure.getId()) { - saveReferencedProcedure(procedure, verweisVon); - value = 0; - } - } - } catch (RuntimeException e) { - logger.error("Sonstiger Fehler bei der Ausführung von analyze()", e); - } - } - - private void saveReferencedProcedure(Procedure prozedur, VerweisVon verweisVon) { - Procedure andereprozedur = onkostarApi.getProcedure(verweisVon.getProcedure_id()); - try { - Map<String, Item> felder = prozedur.getAllValues(); - for (Map.Entry<String, Item> feld : felder.entrySet()) { - if (feld.getKey().startsWith("Consent")) { - if (feld.getKey().equals("ConsentStatusEinwilligungDNPM")) { - switch (feld.getValue().getValue().toString()) { - case "z": - andereprozedur.setValue(feld.getKey(), new Item(feld.getKey(), "active")); - break; - case "a": - case "w": - andereprozedur.setValue(feld.getKey(), new Item(feld.getKey(), "rejected")); - break; - default: - break; - } - } else { - andereprozedur.setValue(feld.getKey(), prozedur.getValue(feld.getKey())); - } - } - } - onkostarApi.saveProcedure(andereprozedur); - } catch (Exception e) { - logger.error("Kann Prozedur nicht speichern", e); - } - } - -} diff --git a/src/main/java/DNPM/services/consent/UkwConsentManagerService.java b/src/main/java/DNPM/services/consent/UkwConsentManagerService.java deleted file mode 100644 index c539e5a..0000000 --- a/src/main/java/DNPM/services/consent/UkwConsentManagerService.java +++ /dev/null @@ -1,72 +0,0 @@ -package DNPM.services.consent; - -import de.itc.onkostar.api.IOnkostarApi; -import de.itc.onkostar.api.Item; -import de.itc.onkostar.api.Procedure; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import java.util.Comparator; - -/** - * Detailimplementierung für das Formular `Excel-Formular` - * - * @since 0.2.0 - */ -public class UkwConsentManagerService implements ConsentManagerService { - - private final Logger logger = LoggerFactory.getLogger(this.getClass()); - - private final IOnkostarApi onkostarApi; - - public UkwConsentManagerService(final IOnkostarApi onkostarApi) { - this.onkostarApi = onkostarApi; - } - - @Override - public boolean canApply(Procedure procedure) { - return null != procedure && procedure.getFormName().equals("Excel-Formular"); - } - - /** - * Wende Consent an, wenn dieses Consent-Formular gespeichert wird - * - * @param procedure Prozedur des Consent-Formulars - */ - @Override - public void applyConsent(Procedure procedure) { - var refdnpmklinikanamnese = procedure.getValue("refdnpmklinikanamnese").getInt(); - var dnpmKlinikAnamnese = this.onkostarApi.getProcedure(refdnpmklinikanamnese); - - if (null == dnpmKlinikAnamnese) { - return; - } - - var consents = procedure.getSubProceduresMap().get("ufdnpmconsent"); - - if (null == consents) { - return; - } - - consents.stream() - .max(Comparator.comparing(Procedure::getStartDate)) - .ifPresent(lastConsent -> { - var date = lastConsent.getStartDate(); - var status = lastConsent.getValue("status"); - if (null == date || null == status || status.getString().isBlank()) { - logger.warn("Kein DNPM-Einwilligungstatus angegeben"); - return; - } - - dnpmKlinikAnamnese.setValue("ConsentStatusEinwilligungDNPM", new Item("Einwilligung", status.getString())); - dnpmKlinikAnamnese.setValue("ConsentDatumEinwilligungDNPM", new Item("DatumEinwilligung", date)); - - try { - onkostarApi.saveProcedure(dnpmKlinikAnamnese, false); - } catch (Exception e) { - logger.error("Kann DNPM-Einwilligungstatus nicht aktualisieren", e); - } - }); - } - -} diff --git a/src/main/java/DNPM/services/molekulargenetik/MolekulargenetikFormService.java b/src/main/java/DNPM/services/molekulargenetik/MolekulargenetikFormService.java deleted file mode 100644 index 60cfaf2..0000000 --- a/src/main/java/DNPM/services/molekulargenetik/MolekulargenetikFormService.java +++ /dev/null @@ -1,20 +0,0 @@ -package DNPM.services.molekulargenetik; - -import DNPM.dto.Variant; -import de.itc.onkostar.api.Procedure; - -import java.util.List; - -/** - * Schnittstellenbeschreibung für Methoden zum Formular "OS.Molekulargenetik" - */ -public interface MolekulargenetikFormService { - - /** - * Ermittelt alle (unterstützten) Varianten zur Prozedur eines Formulars "OS.Molekulargenetik" - * @param procedure Die Prozedur zum Formular "OS.Molekulargenetik" - * @return Die unterstützten Varianten oder eine leere Liste, wenn keine Varianten gefunden wurden. - */ - List<Variant> getVariants(Procedure procedure); - -} diff --git a/src/main/java/DNPM/services/molekulargenetik/OsMolekulargenetikFormService.java b/src/main/java/DNPM/services/molekulargenetik/OsMolekulargenetikFormService.java deleted file mode 100644 index 3bc6000..0000000 --- a/src/main/java/DNPM/services/molekulargenetik/OsMolekulargenetikFormService.java +++ /dev/null @@ -1,45 +0,0 @@ -package DNPM.services.molekulargenetik; - -import DNPM.dto.Variant; -import de.itc.onkostar.api.Procedure; - -import java.util.List; -import java.util.Optional; -import java.util.stream.Collectors; - -public class OsMolekulargenetikFormService implements MolekulargenetikFormService { - - /** - * Ermittelt alle (unterstützten) Varianten zur Prozedur eines Formulars "OS.Molekulargenetik" (oder Variante) - * Unterstützte Varianten sind: - * <uL> - * <li>Einfache Variante - * <li>CNV - * <li>Fusion - * @param procedure Die Prozedur zum Formular "OS.Molekulargenetik" (oder Variante) - * @return Die unterstützten Varianten oder eine leere Liste, wenn keine Varianten gefunden wurden. - */ - @Override - public List<Variant> getVariants(Procedure procedure) { - if (! procedureWithUsableFormVariant(procedure)) { - 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()); - - } - - private boolean procedureWithUsableFormVariant(Procedure procedure) { - return "OS.Molekulargenetik".equals(procedure.getFormName()) - || "UKER.Molekulargenetik".equals(procedure.getFormName()); - } -} diff --git a/src/main/java/DNPM/services/mtb/DefaultMtbService.java b/src/main/java/DNPM/services/mtb/DefaultMtbService.java deleted file mode 100644 index e14e1d7..0000000 --- a/src/main/java/DNPM/services/mtb/DefaultMtbService.java +++ /dev/null @@ -1,70 +0,0 @@ -package DNPM.services.mtb; - -import de.itc.onkostar.api.IOnkostarApi; -import de.itc.onkostar.api.Procedure; - -import java.util.Comparator; -import java.util.List; -import java.util.Optional; -import java.util.stream.Collectors; -import java.util.stream.Stream; - -/** - * Standardimplementierung des MtbService - * - * @since 0.0.2 - */ -public class DefaultMtbService implements MtbService { - - private final IOnkostarApi onkostarApi; - - public DefaultMtbService(final IOnkostarApi onkostarApi) { - this.onkostarApi = onkostarApi; - } - - /** - * Zusammenfassung der Prozeduren. - * Dabei werden alle Prozeduren sortiert, mit ermitteltem Mapper in {@link Optional} eines {@link String}s - * gewandelt und, wenn dies erfolgreich war, die Zeichenkette extrahiert. - * Im Anschluss wird die Abfolge der Zeichenketten mit den einzelnen Prozedur-Zusammenfassungen in eine - * einzige Zusammenfassung zusammengefügt. - * @param procedures Prozeduren, die zusammen gefasst werden sollen - * @return Text mit Zusammenfassung aller übergebenen Prozeduren - */ - @Override - public String getProtocol(List<Procedure> procedures) { - return this.sortedDistinctProcedureProtocolList(procedures.stream()) - .collect(Collectors.joining("\n\n")); - } - - private Stream<String> sortedDistinctProcedureProtocolList(Stream<Procedure> procedures) { - return procedures - .sorted(Comparator.comparing(Procedure::getStartDate)) - .map(this::selectAndApplyMapper) - .filter(Optional::isPresent) - .map(Optional::get) - .distinct(); - } - - /** - * Übergibt anzuwendenden Mapper für eine Prozedur. - * Wurde keine Implementierung festgelegt, wird ein Mapper zurückgegeben, der eine - * Prozedur in ein leeres {@link Optional} zurück gibt, übergeben. - * @param procedure Prozedur, für die ein Mapper ermittelt werden soll - * @return Mapper für diese Prozedur - */ - @Override - public ProcedureToProtocolMapper procedureToProtocolMapper(Procedure procedure) { - switch (procedure.getFormName()) { - case "OS.Tumorkonferenz": - return new OsTumorkonferenzToProtocolMapper(); - case "OS.Tumorkonferenz.VarianteUKW": - return new OsTumorkonferenzVarianteUkwToProtocolMapper(); - case "MR.MTB_Anmeldung": - return new MrMtbAnmeldungToProtocolMapper(this.onkostarApi); - default: - return p -> Optional.empty(); - } - } - -} diff --git a/src/main/java/DNPM/services/mtb/MrMtbAnmeldungToProtocolMapper.java b/src/main/java/DNPM/services/mtb/MrMtbAnmeldungToProtocolMapper.java deleted file mode 100644 index bf22f47..0000000 --- a/src/main/java/DNPM/services/mtb/MrMtbAnmeldungToProtocolMapper.java +++ /dev/null @@ -1,63 +0,0 @@ -package DNPM.services.mtb; - -import de.itc.onkostar.api.IOnkostarApi; -import de.itc.onkostar.api.Procedure; - -import java.util.ArrayList; -import java.util.Comparator; -import java.util.Optional; - -public class MrMtbAnmeldungToProtocolMapper implements ProcedureToProtocolMapper { - - private final IOnkostarApi onkostarApi; - - public MrMtbAnmeldungToProtocolMapper(final IOnkostarApi onkostarApi) { - this.onkostarApi = onkostarApi; - } - - /** - * Wandelt eine Prozedur mit Formularnamen "MR.MTB_Anmeldung" in ein {@link Optional} mit einer - * Zeichenkette oder im Fehlerfall in ein leeres Optional um. - * - * @param procedure Die Prozedur, für die eine Zusammenfassung ermittelt werden soll. - * @return Das {@link Optional} mit, im Erfolgsfall, der Zusammenfassung für die Prozedur. - */ - @Override - public Optional<String> apply(Procedure procedure) { - if ((!procedure.getFormName().equals("MR.MTB_Anmeldung"))) { - throw new AssertionError("Procedure is not of form type 'MR.MTB_Anmeldung'"); - } - - var resultParts = new ArrayList<String>(); - - var fragestellung = procedure.getValue("Fragestellung"); - if (null != fragestellung && !fragestellung.getString().isBlank()) { - resultParts.add(String.format("Fragestellung:%n%s", fragestellung.getString())); - } - - var refEmpfehlung = procedure.getValue("Empfehlung"); - if (null != refEmpfehlung && refEmpfehlung.getInt() > 0) { - var empfehlungsProzedur = onkostarApi.getProcedure(refEmpfehlung.getInt()); - var refEinzelempfehlungen = onkostarApi.getSubprocedures(empfehlungsProzedur.getId()); - - if (null != refEinzelempfehlungen) { - refEinzelempfehlungen.stream() - .sorted(Comparator.comparingInt(proc -> proc.getValue("Prioritaet").getInt())) - .forEach(proc -> { - if (proc.getFormName().equals("MR.MTB_Einzelempfehlung")) { - var empfehlung = proc.getValue("Empfehlung"); - if (null != empfehlung && !empfehlung.getString().isBlank()) { - resultParts.add(String.format("Empfehlung:%n%s", empfehlung.getString())); - } - } - }); - } - } - - if (resultParts.isEmpty()) { - return Optional.empty(); - } - - return Optional.of(String.join("\n\n", resultParts)); - } -} diff --git a/src/main/java/DNPM/services/mtb/MtbService.java b/src/main/java/DNPM/services/mtb/MtbService.java deleted file mode 100644 index 19a6c3a..0000000 --- a/src/main/java/DNPM/services/mtb/MtbService.java +++ /dev/null @@ -1,31 +0,0 @@ -package DNPM.services.mtb; - -import de.itc.onkostar.api.Procedure; - -import java.util.List; -import java.util.Optional; - -public interface MtbService { - /** - * Zusammenfassung der Prozeduren - * @param procedures Prozeduren, die zusammen gefasst werden sollen - * @return Text mit Zusammenfassung der Prozeduren - */ - String getProtocol(List<Procedure> procedures); - - /** - * Übergibt anzuwendenden Mapper für eine Prozedur - * @param procedure Prozedur, für die ein Mapper ermittelt werden soll - * @return Mapper für diese Prozedur - */ - ProcedureToProtocolMapper procedureToProtocolMapper(Procedure procedure); - - /** - * Select mapper using method {@link #procedureToProtocolMapper(Procedure)} and apply procedure - * @param procedure The Procedure to select mapper for and apply - * @return {@link Optional} with protocol or empty {@link Optional} - */ - default Optional<String> selectAndApplyMapper(Procedure procedure) { - return this.procedureToProtocolMapper(procedure).apply(procedure); - } -} diff --git a/src/main/java/DNPM/services/mtb/OsTumorkonferenzToProtocolMapper.java b/src/main/java/DNPM/services/mtb/OsTumorkonferenzToProtocolMapper.java deleted file mode 100644 index dc3d326..0000000 --- a/src/main/java/DNPM/services/mtb/OsTumorkonferenzToProtocolMapper.java +++ /dev/null @@ -1,43 +0,0 @@ -package DNPM.services.mtb; - -import de.itc.onkostar.api.Procedure; - -import java.util.Optional; - - -/** - * Mapper zum Ermitteln des Protokollauszugs für Formular "OS.Tumorkonferenz" - * - * @since 0.0.2 - */ -public class OsTumorkonferenzToProtocolMapper implements ProcedureToProtocolMapper { - - /** - * Wandelt eine Prozedur mit Formularnamen "OS.Tumorkonferenz" in ein {@link Optional} mit einer - * Zeichenkette oder im Fehlerfall in ein leeres Optional um. - * @param procedure Die Prozedur, für die eine Zusammenfassung ermittelt werden soll. - * @return Das {@link Optional} mit, im Erfolgsfall, der Zusammenfassung für die Prozedur. - */ - @Override - public Optional<String> apply(Procedure procedure) { - if ((!procedure.getFormName().equals("OS.Tumorkonferenz"))) { - throw new AssertionError("Procedure is not of form type 'OS.Tumorkonferenz'"); - } - - var fragestellung = procedure.getValue("Fragestellung"); - var empfehlung = procedure.getValue("Empfehlung"); - - if ( - null != fragestellung && !fragestellung.getString().isBlank() - && null != empfehlung && !empfehlung.getString().isBlank() - ) { - return Optional.of(String.format("Fragestellung:%n%s%n%nEmpfehlung:%n%s", fragestellung.getString(), empfehlung.getString())); - } else if (null != fragestellung && !fragestellung.getString().isBlank()) { - return Optional.of(fragestellung.getString()); - } else if (null != empfehlung && !empfehlung.getString().isBlank()) { - return Optional.of(empfehlung.getString()); - } - - return Optional.empty(); - } -} diff --git a/src/main/java/DNPM/services/mtb/OsTumorkonferenzVarianteUkwToProtocolMapper.java b/src/main/java/DNPM/services/mtb/OsTumorkonferenzVarianteUkwToProtocolMapper.java deleted file mode 100644 index e2edd2e..0000000 --- a/src/main/java/DNPM/services/mtb/OsTumorkonferenzVarianteUkwToProtocolMapper.java +++ /dev/null @@ -1,42 +0,0 @@ -package DNPM.services.mtb; - -import de.itc.onkostar.api.Procedure; - -import java.util.Optional; - -/** - * Mapper zum Ermitteln des Protokollauszugs für Formular "OS.Tumorkonferenz.VarianteUKW" - * - * @since 0.0.2 - */ -public class OsTumorkonferenzVarianteUkwToProtocolMapper implements ProcedureToProtocolMapper { - - /** - * Wandelt eine Prozedur mit Formularnamen "OS.Tumorkonferenz.VarianteUKW" in ein {@link Optional} mit einer - * Zeichenkette oder im Fehlerfall in ein leeres Optional um. - * @param procedure Die Prozedur, für die eine Zusammenfassung ermittelt werden soll. - * @return Das {@link Optional} mit, im Erfolgsfall, der Zusammenfassung für die Prozedur. - */ - @Override - public Optional<String> apply(Procedure procedure) { - if ((!procedure.getFormName().equals("OS.Tumorkonferenz.VarianteUKW"))) { - throw new AssertionError("Procedure is not of form type 'OS.Tumorkonferenz.VarianteUKW'"); - } - - - var fragestellung = procedure.getValue("Fragestellung"); - var empfehlung = procedure.getValue("Empfehlung"); - - if ( - null != fragestellung && !fragestellung.getString().isBlank() - && null != empfehlung && !empfehlung.getString().isBlank() - ) { - return Optional.of(String.format("Fragestellung:%n%s%n%nEmpfehlung:%n%s", fragestellung.getString().trim(), empfehlung.getString().trim())); - } else if (null != fragestellung && !fragestellung.getString().isBlank()) { - return Optional.of(fragestellung.getString().trim()); - } else if (null != empfehlung && !empfehlung.getString().isBlank()) { - return Optional.of(empfehlung.getString().trim()); - } - return Optional.empty(); - } -} diff --git a/src/main/java/DNPM/services/mtb/ProcedureToProtocolMapper.java b/src/main/java/DNPM/services/mtb/ProcedureToProtocolMapper.java deleted file mode 100644 index d4e0e4c..0000000 --- a/src/main/java/DNPM/services/mtb/ProcedureToProtocolMapper.java +++ /dev/null @@ -1,9 +0,0 @@ -package DNPM.services.mtb; - -import de.itc.onkostar.api.Procedure; - -import java.util.Optional; -import java.util.function.Function; - -@FunctionalInterface -public interface ProcedureToProtocolMapper extends Function<Procedure, Optional<String>> {} diff --git a/src/main/java/DNPM/services/strahlentherapie/DefaultStrahlentherapieService.java b/src/main/java/DNPM/services/strahlentherapie/DefaultStrahlentherapieService.java deleted file mode 100644 index a318a81..0000000 --- a/src/main/java/DNPM/services/strahlentherapie/DefaultStrahlentherapieService.java +++ /dev/null @@ -1,74 +0,0 @@ -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"); - } -} diff --git a/src/main/java/DNPM/services/strahlentherapie/StrahlentherapieService.java b/src/main/java/DNPM/services/strahlentherapie/StrahlentherapieService.java deleted file mode 100644 index a8de923..0000000 --- a/src/main/java/DNPM/services/strahlentherapie/StrahlentherapieService.java +++ /dev/null @@ -1,10 +0,0 @@ -package DNPM.services.strahlentherapie; - -import DNPM.services.TherapieMitEcogService; - -/** - * Service für Systemtherapieformulare - * - * @since 0.6.0 - */ -public interface StrahlentherapieService extends TherapieMitEcogService {} diff --git a/src/main/java/DNPM/services/systemtherapie/DefaultSystemtherapieService.java b/src/main/java/DNPM/services/systemtherapie/DefaultSystemtherapieService.java deleted file mode 100644 index 578613f..0000000 --- a/src/main/java/DNPM/services/systemtherapie/DefaultSystemtherapieService.java +++ /dev/null @@ -1,98 +0,0 @@ -package DNPM.services.systemtherapie; - -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.*; -import java.util.stream.Collectors; - -/** - * Standardimplementierung des Systemtherapieservices - * - * @since 0.2.0 - */ -public class DefaultSystemtherapieService implements SystemtherapieService { - - private static final String ECOG_FIELD = "ECOGvorTherapie"; - - private final IOnkostarApi onkostarApi; - - private final SettingsService settingsService; - - public DefaultSystemtherapieService(final IOnkostarApi onkostarApi, final SettingsService settingsService) { - this.onkostarApi = onkostarApi; - this.settingsService = settingsService; - } - - /** - * Ermittelt eine Zusammenfassung der systemischen Therapien für eine Erkrankung - * - * @param diseaseId Die ID der Erkrankung - * @return Zusammenfassung der systemischen Therapien - */ - @Override - public List<Map<String, String>> getSystemischeTherapienFromDiagnose(int diseaseId) { - List<Map<String, String>> result = new ArrayList<>(); - for (Procedure prozedur : onkostarApi.getProceduresForDiseaseByForm(diseaseId, getFormName())) { - prozedurToProzedurwerteMapper(prozedur).apply(prozedur).ifPresent(result::add); - } - return result; - } - - /** - * Übergibt aktuell immer den Mapper für das Formular "OS.Systemische Therapie", - * da beide bekannte Varianten damit gemappt werden können. - * - * @param procedure Die Prozedur für die ein Mapper erstellt werden soll - * @return Der Mapper für die Prozedur - */ - @Override - public ProzedurToProzedurwerteMapper prozedurToProzedurwerteMapper(Procedure procedure) { - return new OsSystemischeTherapieToProzedurwerteMapper(); - } - - /** - * 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("systemtherapieform") - .orElse("OS.Systemische Therapie"); - } -} diff --git a/src/main/java/DNPM/services/systemtherapie/OsSystemischeTherapieToProzedurwerteMapper.java b/src/main/java/DNPM/services/systemtherapie/OsSystemischeTherapieToProzedurwerteMapper.java deleted file mode 100644 index f78dde9..0000000 --- a/src/main/java/DNPM/services/systemtherapie/OsSystemischeTherapieToProzedurwerteMapper.java +++ /dev/null @@ -1,90 +0,0 @@ -package DNPM.services.systemtherapie; - -import com.fasterxml.jackson.core.JsonProcessingException; -import com.fasterxml.jackson.databind.ObjectMapper; -import de.itc.onkostar.api.Item; -import de.itc.onkostar.api.Procedure; -import de.ukw.ccc.onkostar.atccodes.AtcCode; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import java.util.*; - -/** - * Implementierung zum Mappen des Formulars "OS.Systemische Therapie" auf die Prozedurwerte - * - * @since 0.2.0 - */ -public class OsSystemischeTherapieToProzedurwerteMapper implements ProzedurToProzedurwerteMapper { - - private static final Logger logger = LoggerFactory.getLogger(OsSystemischeTherapieToProzedurwerteMapper.class); - - @Override - public Optional<Map<String, String>> apply(Procedure procedure) { - try { - return Optional.of(getProzedurwerte(procedure)); - } catch (Exception e) { - logger.error("Fehler beim Mappen der Prozedur auf Prozedurwerte", e); - return Optional.empty(); - } - } - - private static Map<String, String> getProzedurwerte(Procedure prozedur) { - List<String> wirkstoffListe = new ArrayList<>(); - // SubstanzenCodesListe enthält die Liste der SubstanzenCodes - List<Map<String, String>> substanzenCodesListe = new ArrayList<>(); - - // alle Werte der Prozedur auslesen - Map<String, Item> alleWerte = prozedur.getAllValues(); - // Prozedurwerte enthält nur die interessanten Werte - Map<String, String> prozedurwerte = new HashMap<>(); - // alle Werte durchgehen und die interessanten übernehmen - if (alleWerte.containsKey("Beendigung")) { - prozedurwerte.put("Beendigung", alleWerte.get("Beendigung").getValue()); - } - if (alleWerte.containsKey("Ergebnis")) { - prozedurwerte.put("Ergebnis", alleWerte.get("Ergebnis").getValue()); - } - if (alleWerte.containsKey("Beginn")) { - prozedurwerte.put("Beginn", alleWerte.get("Beginn").getString()); - } - if (alleWerte.containsKey("Ende")) { - prozedurwerte.put("Ende", alleWerte.get("Ende").getString()); - } - if (alleWerte.containsKey("SubstanzenList")) { - List<Map<String, String>> substanzList = alleWerte.get("SubstanzenList").getValue(); - for (var substanz : substanzList) { - var substanzCodes = getSubstanzCode(substanz); - substanzenCodesListe.add(substanzCodes); - wirkstoffListe.add(substanzCodes.get("substance")); - } - } - - prozedurwerte.put("Wirkstoffe", String.join(", ", wirkstoffListe)); - try { - ObjectMapper mapper = new ObjectMapper(); - prozedurwerte.put("WirkstoffCodes", mapper.writeValueAsString(substanzenCodesListe)); - } catch (JsonProcessingException e) { - logger.error("Kann 'WirkstoffCodes' nicht in JSON-String mappen", e); - } - - return prozedurwerte; - } - - private static Map<String, String> getSubstanzCode(Map<String, String> substanz) { - Map<String, String> substanzCode = new HashMap<>(); - if (substanz.containsKey("Substanz")) { - if (AtcCode.isAtcCode(substanz.get("Substanz"))) { - substanzCode.put("system", "ATC"); - } else { - substanzCode.put("system", "other"); - } - substanzCode.put("code", substanz.get("Substanz")); - - } - if (substanz.containsKey("Substanz_shortDescription")) { - substanzCode.put("substance", substanz.get("Substanz_shortDescription")); - } - return substanzCode; - } -} diff --git a/src/main/java/DNPM/services/systemtherapie/ProzedurToProzedurwerteMapper.java b/src/main/java/DNPM/services/systemtherapie/ProzedurToProzedurwerteMapper.java deleted file mode 100644 index f205554..0000000 --- a/src/main/java/DNPM/services/systemtherapie/ProzedurToProzedurwerteMapper.java +++ /dev/null @@ -1,14 +0,0 @@ -package DNPM.services.systemtherapie; - -import de.itc.onkostar.api.Procedure; - -import java.util.Map; -import java.util.Optional; -import java.util.function.Function; - -/** - * Mapper um ein Systemtherapieformular in eine Optional-Map mit Prozedurwerten umzuwandeln - * - * @since 0.2.0 - */ -public interface ProzedurToProzedurwerteMapper extends Function<Procedure, Optional<Map<String, String>>> {} diff --git a/src/main/java/DNPM/services/systemtherapie/SystemtherapieService.java b/src/main/java/DNPM/services/systemtherapie/SystemtherapieService.java deleted file mode 100644 index a7ac1bd..0000000 --- a/src/main/java/DNPM/services/systemtherapie/SystemtherapieService.java +++ /dev/null @@ -1,29 +0,0 @@ -package DNPM.services.systemtherapie; - -import DNPM.services.TherapieMitEcogService; -import de.itc.onkostar.api.Procedure; - -import java.util.List; -import java.util.Map; - -/** - * Service für Systemtherapieformulare - * - * @since 0.2.0 - */ -public interface SystemtherapieService extends TherapieMitEcogService { - /** - * Ermittelt eine Zusammenfassung der systemischen Therapien für eine Erkrankung - * @param diseaseId Die ID der Erkrankung - * @return Die Zusammenfassung der systemischen Therapien - */ - List<Map<String, String>> getSystemischeTherapienFromDiagnose(int diseaseId); - - /** - * Erstellt den Mapper for die Prozedur - * @param procedure Die Prozedur für die ein Mapper erstellt werden soll - * @return Der erstellte ProzedurToProzedurwerteMapper - */ - ProzedurToProzedurwerteMapper prozedurToProzedurwerteMapper(Procedure procedure); - -} diff --git a/src/main/java/DNPM/services/therapieplan/AbstractTherapieplanService.java b/src/main/java/DNPM/services/therapieplan/AbstractTherapieplanService.java deleted file mode 100644 index 1cdba18..0000000 --- a/src/main/java/DNPM/services/therapieplan/AbstractTherapieplanService.java +++ /dev/null @@ -1,42 +0,0 @@ -package DNPM.services.therapieplan; - -import DNPM.services.FormService; -import de.itc.onkostar.api.IOnkostarApi; -import de.itc.onkostar.api.Procedure; - -import java.util.List; -import java.util.stream.Collectors; - -public abstract class AbstractTherapieplanService implements TherapieplanService { - - protected final IOnkostarApi onkostarApi; - - protected final FormService formService; - - protected AbstractTherapieplanService(final IOnkostarApi onkostarApi, final FormService formService) { - this.onkostarApi = onkostarApi; - this.formService = formService; - } - - @Override - public List<Procedure> findReferencedFollowUpsForSubform(Procedure procedure) { - if (null == procedure || !"DNPM UF Einzelempfehlung".equals(procedure.getFormName())) { - return List.of(); - } - - return procedure.getDiseaseIds().stream() - .flatMap(diseaseId -> onkostarApi.getProceduresForDiseaseByForm(diseaseId, "DNPM FollowUp").stream()) - .filter(p -> p.getValue("LinkTherapieempfehlung").getInt() == procedure.getId()) - .collect(Collectors.toList()); - } - - @Override - public List<Procedure> findReferencedFollowUpsForSubform(int procedureId) { - var procedure = this.onkostarApi.getProcedure(procedureId); - if (null == procedure || !"DNPM UF Einzelempfehlung".equals(procedure.getFormName())) { - return List.of(); - } - return findReferencedFollowUpsForSubform(procedure); - } - -} diff --git a/src/main/java/DNPM/services/therapieplan/DefaultTherapieplanService.java b/src/main/java/DNPM/services/therapieplan/DefaultTherapieplanService.java deleted file mode 100644 index 5338baa..0000000 --- a/src/main/java/DNPM/services/therapieplan/DefaultTherapieplanService.java +++ /dev/null @@ -1,196 +0,0 @@ -package DNPM.services.therapieplan; - -import DNPM.services.FormService; -import de.itc.onkostar.api.IOnkostarApi; -import de.itc.onkostar.api.Item; -import de.itc.onkostar.api.Procedure; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -import java.util.Date; -import java.util.List; -import java.util.Objects; - -import static DNPM.services.FormService.hasValue; -import static DNPM.services.FormService.isYes; - -public class DefaultTherapieplanService extends AbstractTherapieplanService { - - public static final String FORMFIELD_REFERSTEMTB = "referstemtb"; - public static final String FORMFIELD_HUMANGENBERATUNG = "humangenberatung"; - public static final String FORMFIELD_REEVALUATION = "reevaluation"; - public static final String FORMFIELD_DATUM = "datum"; - public static final String FORMFIELD_REFTKHUMANGENBER = "reftkhumangenber"; - public static final String FORMFIELD_DATUMTKHUMANGENBER = "datumtkhumangenber"; - public static final String FORMFIELD_REFTKREEVALUATION = "reftkreevaluation"; - public static final String FORMFIELD_DATUMTKREEVALUATION = "datumtkreevaluation"; - public static final String FORMFIELD_MTB = "mtb"; - public static final String FORMFIELD_UFEEDATUM = "ufeedatum"; - public static final String FORMFIELD_REFTUMORKONFERENZ = "reftumorkonferenz"; - public static final String FORMFIELD_UFRBDATUM = "ufrbdatum"; - - public static final String DATAFIELD_REF_TK_HUMANGENBER = "ref_tk_humangenber"; - public static final String DATAFIELD_DATUM_TK_HUMANGENBER = "datum_tk_humangenber"; - public static final String DATAFIELD_DATUM = "datum"; - - private final Logger logger = LoggerFactory.getLogger(this.getClass()); - - public DefaultTherapieplanService(final IOnkostarApi onkostarApi, final FormService formService) { - super(onkostarApi, formService); - } - - /** - * Verlinke MTB und Übernahme Datum aus Hauptformular in weiteren Bereichen - * "Humangenetische Beratung" und "Reevaluation" und Unterformularen, wenn erforderlich. - * - * @param procedure Die Prozedur mit Hauptformular - */ - @Override - public void updateRequiredMtbEntries(Procedure procedure) { - this.updateMtbInSections(procedure); - this.updateMtbInSubforms(procedure); - } - - /** - * Finde verlinkte MTBs in Hauptformular und Unterformularen - * - * @param procedure Die Prozedur mit Hauptformular - * @return Liste mit verlinkten MTBs - */ - @Override - public List<Procedure> findReferencedMtbs(Procedure procedure) { - if (!hasValue(procedure, FORMFIELD_REFERSTEMTB)) { - return List.of(); - } - - var mtbProcedure = this.onkostarApi.getProcedure(procedure.getValue(FORMFIELD_REFERSTEMTB).getInt()); - if (null == mtbProcedure) { - return List.of(); - } - return List.of(mtbProcedure); - } - - /** - * Finde verlinkte MTBs in Hauptformular und Unterformularen - * - * @param procedureId ID der Prozedur mit Hauptformular - * @return Liste mit verlinkten MTBs - */ - @Override - public List<Procedure> findReferencedMtbs(int procedureId) { - var procedure = this.onkostarApi.getProcedure(procedureId); - if (null == procedure) { - return List.of(); - } - return findReferencedMtbs(procedure); - } - - private void updateMtbInSections(Procedure procedure) { - if (!isYes(procedure, FORMFIELD_HUMANGENBERATUNG) && !isYes(procedure, FORMFIELD_REEVALUATION)) { - return; - } - - var mtbReference = procedure.getValue(FORMFIELD_REFERSTEMTB).getInt(); - var mtbDate = procedure.getValue(FORMFIELD_DATUM).getDate(); - var noUpdateRequired = true; - - if ( - isYes(procedure, FORMFIELD_HUMANGENBERATUNG) && ( - !hasValue(procedure, FORMFIELD_REFTKHUMANGENBER) - || mtbReference != procedure.getValue(FORMFIELD_REFTKHUMANGENBER).getInt() - ) - ) { - procedure.setValue(FORMFIELD_REFTKHUMANGENBER, new Item(DATAFIELD_REF_TK_HUMANGENBER, mtbReference)); - noUpdateRequired = false; - } - - if ( - isYes(procedure, FORMFIELD_HUMANGENBERATUNG) && ( - !hasValue(procedure, FORMFIELD_DATUMTKHUMANGENBER) - || !mtbDate.equals(procedure.getValue(FORMFIELD_DATUMTKHUMANGENBER).getDate()) - ) - ) { - procedure.setValue(FORMFIELD_DATUMTKHUMANGENBER, new Item(DATAFIELD_DATUM_TK_HUMANGENBER, mtbDate)); - noUpdateRequired = false; - } - - if ( - isYes(procedure, FORMFIELD_REEVALUATION) && ( - !hasValue(procedure, FORMFIELD_REFTKREEVALUATION) - || mtbReference != procedure.getValue(FORMFIELD_REFTKREEVALUATION).getInt() - ) - ) { - procedure.setValue(FORMFIELD_REFTKREEVALUATION, new Item("ref_tk_reevaluation", mtbReference)); - noUpdateRequired = false; - } - - if ( - isYes(procedure, FORMFIELD_REEVALUATION) && ( - !hasValue(procedure, FORMFIELD_DATUMTKREEVALUATION) - || !mtbDate.equals(procedure.getValue(FORMFIELD_DATUMTKREEVALUATION).getDate()) - ) - ) { - procedure.setValue(FORMFIELD_DATUMTKREEVALUATION, new Item("datum_tk_reevaluation", mtbDate)); - noUpdateRequired = false; - } - - if (noUpdateRequired) { - return; - } - - try { - onkostarApi.saveProcedure(procedure, false); - } catch (Exception e) { - logger.error("Formular 'DNPM Therapieplan' konnte nicht aktualisiert werden", e); - } - } - - private void updateMtbInSubforms(Procedure procedure) { - if ( - !hasValue(procedure, FORMFIELD_REFERSTEMTB) || !hasValue(procedure, FORMFIELD_DATUM) - ) { - return; - } - - var mtbReference = procedure.getValue(FORMFIELD_REFERSTEMTB).getInt(); - var mtbDate = procedure.getValue(FORMFIELD_DATUM).getDate(); - - formService.getSubFormProcedureIds(procedure.getId()).stream() - .map(onkostarApi::getProcedure) - .filter(Objects::nonNull) - .forEach(subform -> { - if (isUsableEinzelempfehlung(subform, mtbReference, mtbDate)) { - subform.setValue(FORMFIELD_MTB, new Item("ref_tumorkonferenz", mtbReference)); - subform.setValue(FORMFIELD_UFEEDATUM, new Item(DATAFIELD_DATUM, mtbDate)); - - try { - onkostarApi.saveProcedure(subform, false); - } catch (Exception e) { - logger.error("Formular 'DNPM UF Einzelempfehlung' konnte nicht aktualisiert werden", e); - } - } - - - if (isUsableRebiopsie(subform, mtbReference, mtbDate)) { - subform.setValue(FORMFIELD_REFTUMORKONFERENZ, new Item("ref_tumorkonferenz", mtbReference)); - subform.setValue(FORMFIELD_UFRBDATUM, new Item(DATAFIELD_DATUM, mtbDate)); - - try { - onkostarApi.saveProcedure(subform, false); - } catch (Exception e) { - logger.error("Formular 'DNPM UF Rebiopsie' konnte nicht aktualisiert werden", e); - } - } - - }); - } - - private static boolean isUsableRebiopsie(Procedure subform, int mtbReference, Date mtbDate) { - return subform.getFormName().equals("DNPM UF Rebiopsie") && mtbReference != subform.getValue(FORMFIELD_REFTUMORKONFERENZ).getInt() && !mtbDate.equals(subform.getValue(FORMFIELD_UFRBDATUM).getDate()); - } - - private static boolean isUsableEinzelempfehlung(Procedure subform, int mtbReference, Date mtbDate) { - return subform.getFormName().equals("DNPM UF Einzelempfehlung") && mtbReference != subform.getValue(FORMFIELD_MTB).getInt() && !mtbDate.equals(subform.getValue(FORMFIELD_UFEEDATUM).getDate()); - } - -} diff --git a/src/main/java/DNPM/services/therapieplan/MultipleMtbTherapieplanService.java b/src/main/java/DNPM/services/therapieplan/MultipleMtbTherapieplanService.java deleted file mode 100644 index 1627cb4..0000000 --- a/src/main/java/DNPM/services/therapieplan/MultipleMtbTherapieplanService.java +++ /dev/null @@ -1,71 +0,0 @@ -package DNPM.services.therapieplan; - -import DNPM.services.FormService; -import de.itc.onkostar.api.IOnkostarApi; -import de.itc.onkostar.api.Procedure; - -import java.util.ArrayList; -import java.util.Comparator; -import java.util.List; -import java.util.Objects; -import java.util.stream.Collectors; - -import static DNPM.services.FormService.hasValue; -import static DNPM.services.FormService.isYes; - -public class MultipleMtbTherapieplanService extends AbstractTherapieplanService { - - public MultipleMtbTherapieplanService(final IOnkostarApi onkostarApi, final FormService formService) { - super(onkostarApi, formService); - } - - @Override - public void updateRequiredMtbEntries(Procedure procedure) { - // No action required - } - - @Override - public List<Procedure> findReferencedMtbs(Procedure procedure) { - var procedureIds = new ArrayList<Integer>(); - - var mtbReference = procedure.getValue("referstemtb").getInt(); - procedureIds.add(mtbReference); - - if (isYes(procedure, "humangenberatung") && hasValue(procedure, "reftkhumangenber")) { - procedureIds.add(procedure.getValue("reftkhumangenber").getInt()); - } - - if (isYes(procedure, "reevaluation") && hasValue(procedure, "reftkreevaluation")) { - procedureIds.add(procedure.getValue("reftkreevaluation").getInt()); - } - - formService.getSubFormProcedureIds(procedure.getId()).stream() - .map(onkostarApi::getProcedure) - .filter(Objects::nonNull) - .forEach(subform -> { - if (subform.getFormName().equals("DNPM UF Einzelempfehlung")) { - procedureIds.add(subform.getValue("mtb").getInt()); - } - - if (subform.getFormName().equals("DNPM UF Rebiopsie")) { - procedureIds.add(subform.getValue("reftumorkonferenz").getInt()); - } - }); - - return procedureIds.stream() - .distinct() - .map(onkostarApi::getProcedure) - .filter(Objects::nonNull) - .sorted(Comparator.comparing(Procedure::getStartDate)) - .collect(Collectors.toList()); - } - - @Override - public List<Procedure> findReferencedMtbs(int procedureId) { - var procedure = this.onkostarApi.getProcedure(procedureId); - if (null == procedure) { - return List.of(); - } - return findReferencedMtbs(procedure); - } -} diff --git a/src/main/java/DNPM/services/therapieplan/TherapieplanService.java b/src/main/java/DNPM/services/therapieplan/TherapieplanService.java deleted file mode 100644 index 957d15c..0000000 --- a/src/main/java/DNPM/services/therapieplan/TherapieplanService.java +++ /dev/null @@ -1,49 +0,0 @@ -package DNPM.services.therapieplan; - -import de.itc.onkostar.api.Procedure; - -import java.util.List; - -public interface TherapieplanService { - - /** - * Verlinke MTB und Übernahme Datum aus Hauptformular in weiteren Bereichen - * "Humangenetische Beratung" und "Reevaluation" und Unterformularen, wenn erforderlich. - * - * @param procedure Die Prozedur mit Hauptformular - */ - void updateRequiredMtbEntries(Procedure procedure); - - /** - * Finde verlinkte MTBs in Hauptformular und Unterformularen - * - * @param procedure Die Prozedur mit Hauptformular - * @return Liste mit verlinkten MTBs - */ - List<Procedure> findReferencedMtbs(Procedure procedure); - - /** - * Finde verlinkte MTBs in Hauptformular und Unterformularen - * - * @param procedureId ID der Prozedur mit Hauptformular - * @return Liste mit verlinkten MTBs - */ - List<Procedure> findReferencedMtbs(int procedureId); - - /** - * Finde verlinkte FollowUps für DNPM UF Einzelempfehlung - * - * @param procedure Die DNPM UF Einzelempfehlung Prozedur - * @return Liste mit verlinkten FollowUps - */ - List<Procedure> findReferencedFollowUpsForSubform(Procedure procedure); - - /** - * Finde verlinkte FollowUps für DNPM UF Einzelempfehlung - * - * @param procedureId ID der Prozedur - * @return Liste mit verlinkten FollowUps - */ - List<Procedure> findReferencedFollowUpsForSubform(int procedureId); - -} diff --git a/src/main/java/DNPM/services/therapieplan/TherapieplanServiceFactory.java b/src/main/java/DNPM/services/therapieplan/TherapieplanServiceFactory.java deleted file mode 100644 index c109198..0000000 --- a/src/main/java/DNPM/services/therapieplan/TherapieplanServiceFactory.java +++ /dev/null @@ -1,33 +0,0 @@ -package DNPM.services.therapieplan; - -import DNPM.services.FormService; -import DNPM.services.SettingsService; -import de.itc.onkostar.api.IOnkostarApi; - -public class TherapieplanServiceFactory { - - private final IOnkostarApi onkostarApi; - - private final SettingsService settingsService; - - private final FormService formService; - - public TherapieplanServiceFactory( - final IOnkostarApi onkostarApi, - final SettingsService settingsService, - final FormService formService - ) { - this.onkostarApi = onkostarApi; - this.settingsService = settingsService; - this.formService = formService; - } - - public TherapieplanService currentUsableInstance() { - if (settingsService.multipleMtbsInMtbEpisode()) { - return new MultipleMtbTherapieplanService(onkostarApi, formService); - } - - return new DefaultTherapieplanService(onkostarApi, formService); - } - -} |