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Issue #5: Vorschlag für den Aufbau des Projekts

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* Maven-Projekt direkt im Hauptverzeichnis
* Anpassung der Maven-POM-Datei - nicht benötigte Abhängigkeiten entfernt
* Gitignore-Datei angelegt
This commit is contained in:
Paul-Christian Volkmer
2023-03-10 09:24:12 +01:00
parent 9d66c42460
commit 4b121482f1
22 changed files with 93 additions and 167 deletions
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151
src/main/java/DNPM/ConsentManager.java Normal file
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package DNPM;
import java.util.List;
import java.util.Map;
import org.hibernate.SQLQuery;
import org.hibernate.Session;
import org.hibernate.SessionFactory;
import org.hibernate.transform.Transformers;
import org.hibernate.type.StandardBasicTypes;
import org.springframework.beans.factory.annotation.Autowired;
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.AnalyzerRequirement;
import de.itc.onkostar.api.analysis.IProcedureAnalyzer;
import de.itc.onkostar.api.analysis.OnkostarPluginType;
public class ConsentManager implements IProcedureAnalyzer {
@Autowired
private IOnkostarApi onkostarApi;
@Override
public String getDescription() {
return "Aktualisiert Consent Daten in verknüpften Formularen";
}
@Override
public String getName() {
return "Consent Manager";
}
@Override
public AnalyzerRequirement getRequirement() {
return AnalyzerRequirement.PROCEDURE;
}
@Override
public OnkostarPluginType getType() {
return OnkostarPluginType.ANALYZER;
}
@Override
public String getVersion() {
return "1";
}
@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) {
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 = '" + Prozedur.getId() + "'";
SQLQuery query1 = session.createSQLQuery(sql1)
.addScalar("id", StandardBasicTypes.INTEGER)
.addScalar("datum", StandardBasicTypes.TIMESTAMP);
System.out.println(query1.uniqueResult().toString());
try {
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 = " + Prozedur.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));
List<VerweisVon> result = query.list();
try {
for (VerweisVon var : result) {
sql = var.getSQL();
query = session.createSQLQuery(sql)
.addScalar("value", StandardBasicTypes.INTEGER);
if (query.uniqueResult() != null) {
value = (Integer)query.uniqueResult();
}
if (value == Prozedur.getId()) {
Procedure andereprozedur = onkostarApi.getProcedure(var.getProcedure_id());
try {
Map<String, Item> Felder = Prozedur.getAllValues();
for (Map.Entry<String, Item> Feld: Felder.entrySet()) {
if (Feld.getKey().length() > 6 && Feld.getKey().substring(0, 7).equals("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":
andereprozedur.setValue(Feld.getKey(), new Item(Feld.getKey(), "rejected"));
break;
case "w":
andereprozedur.setValue(Feld.getKey(), new Item(Feld.getKey(), "rejected"));
break;
}
} else {
andereprozedur.setValue(Feld.getKey(), Prozedur.getValue(Feld.getKey()));
}
}
}
onkostarApi.saveProcedure(andereprozedur);
} catch (Exception e) {
e.printStackTrace();
}
value = 0;
}
}
} catch (Exception e) {
e.printStackTrace();
}
} catch (Exception e) {
System.out.println(e.getMessage());
}
} catch (Exception e) {
System.out.println(e.getMessage());
}
}
}

315
src/main/java/DNPM/DNPMHelper.java Normal file
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package DNPM;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.hibernate.SQLQuery;
import org.hibernate.Session;
import org.hibernate.SessionFactory;
import org.hibernate.transform.Transformers;
import org.hibernate.type.StandardBasicTypes;
import org.springframework.beans.factory.annotation.Autowired;
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.Item;
import de.itc.onkostar.api.Procedure;
import de.itc.onkostar.api.analysis.AnalyzerRequirement;
import de.itc.onkostar.api.analysis.IProcedureAnalyzer;
import de.itc.onkostar.api.analysis.OnkostarPluginType;
public class DNPMHelper implements IProcedureAnalyzer{
// Laden der API
@Autowired
private IOnkostarApi onkostarApi;
@Override
public OnkostarPluginType getType() {
// Typ des Plugins
// Für das Interface IProcedureAnalyzer gültig sind ANALYZER und BACKEND_SERVICE
return OnkostarPluginType.BACKEND_SERVICE;
}
@Override
public String getVersion() {
return "1";
}
@Override
public String getName() {
return "UMR DNPM";
}
@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;
}
@Override
public void analyze(Procedure entry, Disease currentDisease) {
// wird nicht benötigt, da dass Plugin nicht ausgeführt wird
}
@SuppressWarnings("unchecked")
public Object getVerweise(final Map<String, Object> input) {
int ProcedureId = (int) input.get("ProcedureId");
int PatientId = (int) input.get("PatientId");
int value = 0;
List<Map<String, String>> VerbundeneFormulare = new ArrayList<Map<String, String>>();
try {
SessionFactory sessionFactory = onkostarApi.getSessionFactory();
Session session = sessionFactory.getCurrentSession();
try {
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 + " " +
"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 {
for (VerweisVon var : result) {
sql = var.getSQL();
query = session.createSQLQuery(sql)
.addScalar("value", StandardBasicTypes.INTEGER);
if (query.uniqueResult() != null) {
value = (Integer)query.uniqueResult();
}
if (value == ProcedureId) {
VerbundeneFormulare.add(Map.of("formular", var.getVerbundenesFormular()));
value = 0;
}
}
} catch (Exception e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
} catch (Exception e) {
return null;
}
} catch (Exception e) {
return null;
}
return VerbundeneFormulare;
}
public Object getSystemischeTherapienFromDiagnose(final Map<String, Object> input) {
int DiagnoseId = (int) input.get("DiagnoseId");
String jsonStr = "";
List<Object> Rueckgabewerte = new ArrayList<Object>();
List<Procedure> Prozeduren = onkostarApi.getProceduresForDiseaseByForm(DiagnoseId, "OS.Systemische Therapie");
// für jede Prozedur
for (Procedure Prozedur : Prozeduren) {
String Beginn = new String();
String Ende = new String();
String Wirkstoffe = new String();
String Beendigung = new String();
String Ergebnis = new String();
// SubstanzenCodesListe enthält die Liste der SubstanzenCodes
List<Map<String, String>> SubstanzenCodesListe = new ArrayList<Map<String, String>>();
// alle Werte der Prozedur auslesen
Map<String, Item> alleWerte = Prozedur.getAllValues();
// Prozedurwerte enthält nur die interessanten Werte
Map<String, Object> Prozedurwerte = new HashMap<>();
// alle Werte durchgehen und die interessanten übernehmen
for (Map.Entry<String, Item> WerteListe : alleWerte.entrySet()) {
// Datum des Hauptformulars merken
if (WerteListe.getKey().equals("Beendigung")) {
Beendigung = WerteListe.getValue().getValue();
}
if (WerteListe.getKey().equals("Ergebnis")) {
Ergebnis = WerteListe.getValue().getValue();
}
if (WerteListe.getKey().equals("Beginn")) {
Beginn = WerteListe.getValue().getString();// + "," + WerteListe.getValue().getDateAccuracy();
}
if (WerteListe.getKey().equals("Ende")) {
Ende = WerteListe.getValue().getString();// + "," + WerteListe.getValue().getDateAccuracy();
}
// im Subformular (SubstanzenList) Substanzen auslesen
if (WerteListe.getKey().equals("SubstanzenList")) {
int Index = -1;
// SubstanzenCodesListe enthält die Liste der SubstanzenCodes eines Subformulars
ArrayList<Map<String, Map<String, String>>> Subformular = new ArrayList<>();
Subformular = WerteListe.getValue().getValue();
// Werte aus Subformular verarbeiten
for (Map<String, Map<String, String>> SubformularWerte: Subformular) {
// SubstanzenCodes enthält den Code und den Namen einer Substanz
Map<String, String> SubstanzenCodes = new HashMap<String, String>();
// Index des Codes (Substanz)
Index = Arrays.asList((SubformularWerte.keySet().toArray())).indexOf("Substanz");
if (SubformularWerte.values().toArray()[Index].toString().matches("[A-V]0[1-9][A-Z]{2}[0-9]{0,2}")) {
SubstanzenCodes.put("system", "ATC");
} else {
SubstanzenCodes.put("system", "other");
}
SubstanzenCodes.put("code", (String) SubformularWerte.values().toArray()[Index]);
// Index der Substanz (Substanz_shortDescription)
Index = Arrays.asList((SubformularWerte.keySet().toArray())).indexOf("Substanz_shortDescription");
SubstanzenCodes.put("substance", (String) SubformularWerte.values().toArray()[Index]);
SubstanzenCodesListe.add(SubstanzenCodes);
Wirkstoffe = Wirkstoffe + (String) SubformularWerte.values().toArray()[Index] + ", ";
}
}
}
ObjectMapper Obj = new ObjectMapper();
try {
jsonStr = Obj.writeValueAsString(SubstanzenCodesListe);
} catch (JsonProcessingException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
Prozedurwerte.put("Beginn", Beginn);
Prozedurwerte.put("Ende", Ende);
Prozedurwerte.put("Beendigung", Beendigung);
Prozedurwerte.put("Ergebnis", Ergebnis);
Prozedurwerte.put("Wirkstoffe", Wirkstoffe.substring(0, Wirkstoffe.length()-2));
Prozedurwerte.put("WirkstoffCodes", jsonStr);
Rueckgabewerte.add(Prozedurwerte);
}
return Rueckgabewerte;
}
public Object getProzedurenFromDiagnose(final Map<String, Object> input) {
String dataForm = (String) input.get("dataForm");
int DiagnoseId = (int) input.get("DiagnoseId");
int PatientId = (int) input.get("PatientId");
// Prozedur, Feldname, Wert
List<Object> Formulare = new ArrayList<Object>();
String jsonStr = "";
List<Procedure> Prozeduren = onkostarApi.getProceduresByPatientId(PatientId);
for (Procedure Prozedur: Prozeduren ) {
// Formular gehört zur aktuellen Diagnose und hat den angegebenen Namen
if (Prozedur.getDiseaseIds().contains(DiagnoseId) && Prozedur.getFormName().contains(dataForm)) {
// alle Werte auslesen
Map<String, Item> Werte = Prozedur.getAllValues();
Map<String, Object> Values = new HashMap<>();
for (Map.Entry<String, Item> WerteListe: Werte.entrySet()) {
Values.put(WerteListe.getKey(), WerteListe.getValue());
// System.out.println(WerteListe.getKey() + ": " + WerteListe.getValue());
}
Map<String, Object> Formular = new HashMap<>();
Formular.put("Formular", Prozedur.getFormName());
Formular.put("Felder", Values);
Formulare.add(Formular);
}
}
ObjectMapper Obj = new ObjectMapper();
try {
jsonStr = Obj.writeValueAsString(Formulare);
} catch (JsonProcessingException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
return jsonStr;
}
public Object getEmpfehlung(final Map<String, Object> input) {
// Auslesen der Parameter aus 'input'
int ProcedureID = (int) input.get("ProcedureID");
String sql;
try {
SessionFactory sessionFactory = onkostarApi.getSessionFactory();
Session session = sessionFactory.getCurrentSession();
try {
sql = "SELECT * FROM prozedur "
+ "LEFT JOIN dk_mtb_einzelempfehlung em ON em.id = prozedur.id "
+ "WHERE prozedur.hauptprozedur_id = " + ProcedureID + " AND prozedur.geloescht = 0 AND prozedur.data_form_id = 489 "
+ "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) {
return null;
}
} catch (Exception e) {
return null;
}
}
public Object updateEmpfehlungPrio(final Map<String, Object> input) {
// Auslesen der Parameter aus 'input'
//int rid = (int) input.get("rid");
Object rid = input.get("rid");
Object strDate = input.get("bd");
SQLQuery result = null;
//String strD = strDate.toString();
//String CompareDate = strD.substring(1, 11);
//DateFormat simpleDateFormat=new SimpleDateFormat("yyyy-MM-dd");
String sql;
try {
sql = "UPDATE prozedur SET beginndatum = '"+ strDate +"' WHERE id = '"+ rid +"' ";
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;
}
}
}

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src/main/java/DNPM/Merkmalskatalog.java Normal file
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package DNPM;
import java.util.List;
import java.util.Map;
import org.hibernate.SQLQuery;
import org.hibernate.Session;
import org.hibernate.SessionFactory;
import org.hibernate.type.StandardBasicTypes;
import org.springframework.beans.factory.annotation.Autowired;
import de.itc.onkostar.api.Disease;
import de.itc.onkostar.api.IOnkostarApi;
import de.itc.onkostar.api.Procedure;
import de.itc.onkostar.api.analysis.AnalyzerRequirement;
import de.itc.onkostar.api.analysis.IProcedureAnalyzer;
import de.itc.onkostar.api.analysis.OnkostarPluginType;
public class Merkmalskatalog implements IProcedureAnalyzer{
@Autowired
private IOnkostarApi onkostarApi;
@Override
public OnkostarPluginType getType() {
return OnkostarPluginType.BACKEND_SERVICE;
}
@Override
public String getVersion() {
return "1";
}
@Override
public String getName() {
return "UMR Merkmalskatalog";
}
@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;
}
@Override
public void analyze(Procedure procedurea, Disease disease) {}
public Object getMerkmalskatalog(final Map<String, Object> input) {
String Merkmalskatalog = (String) input.get("Merkmalskatalog");
String Spalten = (String) input.get("Spalten");
String[] SpaltenArray = Spalten.split("\\s*,\\s*");
String sql;
try {
SessionFactory sessionFactory = onkostarApi.getSessionFactory();
Session session = sessionFactory.getCurrentSession();
try {
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";
SQLQuery query = session.createSQLQuery(sql);
for (int i = 0; i < SpaltenArray.length; i++) {
query.addScalar(SpaltenArray[i], StandardBasicTypes.STRING);
}
@SuppressWarnings("unchecked")
List<String[]> rows = query.list();
return rows;
} catch (Exception e) {
return null;
}
} catch (Exception e) {
return null;
}
}
}

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src/main/java/DNPM/VerweisVon.java Normal file
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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; }
}

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src/main/java/DNPM/logger.java Normal file
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package DNPM;
public class logger {
public static void error (String messagetext) {
System.out.println(messagetext);
}
}