diff options
| author | Paul-Christian Volkmer | 2024-09-21 22:10:24 +0200 |
|---|---|---|
| committer | Paul-Christian Volkmer | 2024-09-21 22:10:24 +0200 |
| commit | cc27edc544cec1b892e7c224aec9e6e42342aa39 (patch) | |
| tree | 3036b92f84a707d769782d63c2b018166623abf5 /src/main/java/dev/dnpm/analyzer | |
| parent | 93215825f5c8aec0912d562b544f370cffe9cda7 (diff) | |
refactor: use package name following Java guidelines
Diffstat (limited to 'src/main/java/dev/dnpm/analyzer')
| -rw-r--r-- | src/main/java/dev/dnpm/analyzer/Analyzer.java | 12 | ||||
| -rw-r--r-- | src/main/java/dev/dnpm/analyzer/AnalyzerUtils.java | 145 | ||||
| -rw-r--r-- | src/main/java/dev/dnpm/analyzer/BackendService.java | 25 | ||||
| -rw-r--r-- | src/main/java/dev/dnpm/analyzer/ConsentManager.java | 63 | ||||
| -rw-r--r-- | src/main/java/dev/dnpm/analyzer/DNPMHelper.java | 260 | ||||
| -rw-r--r-- | src/main/java/dev/dnpm/analyzer/EinzelempfehlungAnalyzer.java | 134 | ||||
| -rw-r--r-- | src/main/java/dev/dnpm/analyzer/FollowUpAnalyzer.java | 103 | ||||
| -rw-r--r-- | src/main/java/dev/dnpm/analyzer/IPluginPart.java | 19 | ||||
| -rw-r--r-- | src/main/java/dev/dnpm/analyzer/Merkmalskatalog.java | 97 | ||||
| -rw-r--r-- | src/main/java/dev/dnpm/analyzer/TherapieMitEcogAnalyzer.java | 168 | ||||
| -rw-r--r-- | src/main/java/dev/dnpm/analyzer/TherapieplanAnalyzer.java | 127 |
11 files changed, 1153 insertions, 0 deletions
diff --git a/src/main/java/dev/dnpm/analyzer/Analyzer.java b/src/main/java/dev/dnpm/analyzer/Analyzer.java new file mode 100644 index 0000000..7868f32 --- /dev/null +++ b/src/main/java/dev/dnpm/analyzer/Analyzer.java @@ -0,0 +1,12 @@ +package dev.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/dev/dnpm/analyzer/AnalyzerUtils.java b/src/main/java/dev/dnpm/analyzer/AnalyzerUtils.java new file mode 100644 index 0000000..937cc74 --- /dev/null +++ b/src/main/java/dev/dnpm/analyzer/AnalyzerUtils.java @@ -0,0 +1,145 @@ +package dev.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/dev/dnpm/analyzer/BackendService.java b/src/main/java/dev/dnpm/analyzer/BackendService.java new file mode 100644 index 0000000..c5fca5c --- /dev/null +++ b/src/main/java/dev/dnpm/analyzer/BackendService.java @@ -0,0 +1,25 @@ +package dev.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/dev/dnpm/analyzer/ConsentManager.java b/src/main/java/dev/dnpm/analyzer/ConsentManager.java new file mode 100644 index 0000000..601399d --- /dev/null +++ b/src/main/java/dev/dnpm/analyzer/ConsentManager.java @@ -0,0 +1,63 @@ +package dev.dnpm.analyzer; + +import dev.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/dev/dnpm/analyzer/DNPMHelper.java b/src/main/java/dev/dnpm/analyzer/DNPMHelper.java new file mode 100644 index 0000000..211b3bd --- /dev/null +++ b/src/main/java/dev/dnpm/analyzer/DNPMHelper.java @@ -0,0 +1,260 @@ +package dev.dnpm.analyzer; + +import dev.dnpm.dto.EcogStatusWithDate; +import dev.dnpm.VerweisVon; +import dev.dnpm.security.DelegatingDataBasedPermissionEvaluator; +import dev.dnpm.security.IllegalSecuredObjectAccessException; +import dev.dnpm.security.PermissionType; +import dev.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/dev/dnpm/analyzer/EinzelempfehlungAnalyzer.java b/src/main/java/dev/dnpm/analyzer/EinzelempfehlungAnalyzer.java new file mode 100644 index 0000000..4a6bfdf --- /dev/null +++ b/src/main/java/dev/dnpm/analyzer/EinzelempfehlungAnalyzer.java @@ -0,0 +1,134 @@ +package dev.dnpm.analyzer; + +import dev.dnpm.dto.Studie; +import dev.dnpm.dto.Variant; +import dev.dnpm.security.PermissionType; +import dev.dnpm.security.PersonPoolBasedPermissionEvaluator; +import dev.dnpm.services.StudienService; +import dev.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/dev/dnpm/analyzer/FollowUpAnalyzer.java b/src/main/java/dev/dnpm/analyzer/FollowUpAnalyzer.java new file mode 100644 index 0000000..1e1bbb9 --- /dev/null +++ b/src/main/java/dev/dnpm/analyzer/FollowUpAnalyzer.java @@ -0,0 +1,103 @@ +package dev.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/dev/dnpm/analyzer/IPluginPart.java b/src/main/java/dev/dnpm/analyzer/IPluginPart.java new file mode 100644 index 0000000..23940fa --- /dev/null +++ b/src/main/java/dev/dnpm/analyzer/IPluginPart.java @@ -0,0 +1,19 @@ +package dev.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/dev/dnpm/analyzer/Merkmalskatalog.java b/src/main/java/dev/dnpm/analyzer/Merkmalskatalog.java new file mode 100644 index 0000000..76892f3 --- /dev/null +++ b/src/main/java/dev/dnpm/analyzer/Merkmalskatalog.java @@ -0,0 +1,97 @@ +package dev.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/dev/dnpm/analyzer/TherapieMitEcogAnalyzer.java b/src/main/java/dev/dnpm/analyzer/TherapieMitEcogAnalyzer.java new file mode 100644 index 0000000..8afa7d8 --- /dev/null +++ b/src/main/java/dev/dnpm/analyzer/TherapieMitEcogAnalyzer.java @@ -0,0 +1,168 @@ +package dev.dnpm.analyzer; + +import dev.dnpm.dto.EcogStatusWithDate; +import dev.dnpm.services.strahlentherapie.StrahlentherapieService; +import dev.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/dev/dnpm/analyzer/TherapieplanAnalyzer.java b/src/main/java/dev/dnpm/analyzer/TherapieplanAnalyzer.java new file mode 100644 index 0000000..a623a99 --- /dev/null +++ b/src/main/java/dev/dnpm/analyzer/TherapieplanAnalyzer.java @@ -0,0 +1,127 @@ +package dev.dnpm.analyzer; + +import dev.dnpm.security.DelegatingDataBasedPermissionEvaluator; +import dev.dnpm.security.PermissionType; +import dev.dnpm.services.mtb.MtbService; +import dev.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 ""; + } + +} |
