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Busfreak
2023-03-10 00:30:42 +01:00
parent 89153c391e
commit 9d66c42460
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167
DNPMPlugins/pom.xml Normal file
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<project xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>DNPMHelper</groupId>
<artifactId>DNPMHelper</artifactId>
<version>0.0.2</version>
<name>DNPMHelper</name>
<dependencies>
<!-- This is the onkostar-api -->
<dependency>
<groupId>de.itc</groupId>
<artifactId>onkostar-parent</artifactId>
<version>2.11.1.1</version>
<scope>system</scope>
<systemPath>${project.basedir}/libs/onkostar-api-2.11.1.1.jar</systemPath>
</dependency>
<!-- This is the core HAPI library -->
<dependency>
<groupId>ca.uhn.hapi</groupId>
<artifactId>hapi-base</artifactId>
<version>2.2</version>
<scope>system</scope>
<systemPath>${project.basedir}/libs/hapi-base-2.2.jar</systemPath>
</dependency>
<!-- This is the structure JAR for HL7 v2.1 -->
<dependency>
<groupId>ca.uhn.hapi</groupId>
<artifactId>hapi-structures-v23</artifactId>
<version>2.2</version>
<scope>system</scope>
<systemPath>${project.basedir}/libs/hapi-structures-v23-2.2.jar</systemPath>
</dependency>
<dependency>
<groupId>ca.uhn.hapi</groupId>
<artifactId>hapi-structures-v24</artifactId>
<version>2.2</version>
<scope>system</scope>
<systemPath>${project.basedir}/libs/hapi-structures-v24-2.2.jar</systemPath>
</dependency>
<dependency>
<groupId>ca.uhn.hapi</groupId>
<artifactId>hapi-structures-v25</artifactId>
<version>2.2</version>
<scope>system</scope>
<systemPath>${project.basedir}/libs/hapi-structures-v25-2.2.jar</systemPath>
</dependency>
<dependency>
<groupId>ca.uhn.hapi</groupId>
<artifactId>hapi-structures-v26</artifactId>
<version>2.2</version>
<scope>system</scope>
<systemPath>${project.basedir}/libs/hapi-structures-v26-2.2.jar</systemPath>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-beans</artifactId>
<version>4.3.8.RELEASE</version>
<scope>system</scope>
<systemPath>${project.basedir}/libs/spring-beans-4.3.8.RELEASE.jar</systemPath>
</dependency>
<!-- Hibernate -->
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-core</artifactId>
<version>5.1.8.Final</version>
<scope>system</scope>
<systemPath>${project.basedir}/libs/hibernate-core-5.1.8.Final.jar</systemPath>
</dependency>
<!-- zusätzliche Erweiterungen. -->
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
<version>2.10.1</version>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-web</artifactId>
<version>2.2.1.RELEASE</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-tx</artifactId>
<version>3.2.1.RELEASE</version>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-api</artifactId>
<version>2.14.1</version>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-core</artifactId>
<version>2.14.1</version>
</dependency>
<dependency>
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
<version>2.3.0</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-jdbc</artifactId>
<version>5.3.14</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-csv</artifactId>
<version>1.2</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>commons-lang</groupId>
<artifactId>commons-lang</artifactId>
<version>2.6</version>
<scope>provided</scope>
</dependency>
</dependencies>
<!-- Hier wird definiert, wie Maven das Artifakt bauen soll. -->
<!-- Das erste Plugin kopiert die Resourcen in das JAR -->
<!-- Das zweite Plugin kompiliert die Klassen als Java 11 -->
<build>
<plugins>
<plugin>
<artifactId>maven-jar-plugin</artifactId>
<version>2.4</version>
<configuration>
<outputDirectory>C:\Onkostar-System\Onkostar\files\onkostar\plugins</outputDirectory>
</configuration>
<executions>
<execution>
<id>default-jar</id>
<phase>package</phase>
<goals>
<goal>jar</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.8.1</version>
<configuration>
<source>11</source>
<target>11</target>
</configuration>
</plugin>
</plugins>
</build>
<properties>
<maven.compiler.source>11</maven.compiler.source>
<maven.compiler.target>11</maven.compiler.target>
<java.version>11</java.version>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<spring-version>4.3.8.RELEASE</spring-version>
</properties>
</project>

15
DNPMPlugins/src/main/java/ATCCodes/AgentCode.java Normal file
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package ATCCodes;
/**
* Common Agent Code definition
*
* @author Paul-Christian Volkmer
* @since 0.1.0
*/
public interface AgentCode extends Comparable<AgentCode> {
String getCode();
String getName();
CodeSystem getSystem();
}

51
DNPMPlugins/src/main/java/ATCCodes/AtcCode.java Normal file
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package ATCCodes;
import java.util.Objects;
/**
* ATC-Code as used in WHO XML file
*
* @author Paul-Christian Volkmer
* @since 0.1.0
*/
public class AtcCode implements AgentCode {
private final String code;
private final String name;
public AtcCode(String code, String name) {
this.code = code;
this.name = name;
}
public String getCode() {
return code;
}
public String getName() {
return name;
}
public CodeSystem getSystem() {
return CodeSystem.ATC;
}
@Override
public int compareTo(final AgentCode agentCode) {
return this.name.toLowerCase().compareTo(agentCode.getName().toLowerCase());
}
@Override
public boolean equals(final Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
AgentCode otherAgentCode = (AgentCode) o;
return Objects.equals(code.toLowerCase(), otherAgentCode.getCode().toLowerCase())
&& Objects.equals(name.toLowerCase(), otherAgentCode.getName().toLowerCase());
}
@Override
public int hashCode() {
return Objects.hash(code.toLowerCase(), name.toLowerCase());
}
}

110
DNPMPlugins/src/main/java/ATCCodes/AtcCodesPlugin.java Normal file
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package ATCCodes;
import de.itc.onkostar.api.Disease;
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;
import ATCCodes.services.AgentCodeService;
import org.springframework.stereotype.Component;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import java.util.stream.Collectors;
/**
* Plugin implementation
* Provides methods exposed to Onkostar
*
* @author Paul-Christian Volkmer
* @since 0.1.0
*/
@Component
public class AtcCodesPlugin implements IProcedureAnalyzer {
private final List<AgentCodeService> agentCodeServices;
public AtcCodesPlugin(List<AgentCodeService> agentCodeServices) {
this.agentCodeServices = agentCodeServices;
}
@Override
public OnkostarPluginType getType() {
return OnkostarPluginType.BACKEND_SERVICE;
}
@Override
public String getVersion() {
return "0.4.0";
}
@Override
public String getName() {
return "ATC-Codes und Substanzen";
}
@Override
public String getDescription() {
return "ATC-Codes und Substanzen";
}
@Override
public boolean isSynchronous() {
return false;
}
@Override
public AnalyzerRequirement getRequirement() {
return AnalyzerRequirement.PROCEDURE;
}
@Override
public boolean isRelevantForDeletedProcedure() {
return false;
}
@Override
public boolean isRelevantForAnalyzer(final Procedure procedure, final Disease disease) {
return false;
}
@Override
public void analyze(final Procedure procedure, final Disease disease) {
// Nothing to do - should never be called
}
/**
* Return list with ATC codes and agents.
* Usage in script:
*
* <pre>
* executePluginMethod(
* 'AtcCodesPlugin',
* 'query',
* { q: '', size: 10 },
* function (result) {console.log(result);},
* false
* );
* </pre>
*
* @param input The data Map
* @return The result list filtered by input
*/
public List<AgentCode> query(final Map<String, Object> input) {
String query = "";
if (null != input.get("q")) {
query = input.get("q").toString();
}
int size = Integer.parseInt(input.get("size").toString());
if (size == 0) {
size = 10;
}
var result = new ArrayList<AgentCode>();
for (var agentCodeService : this.agentCodeServices) {
result.addAll(agentCodeService.findAgentCodes(query, size));
}
return result.stream().distinct().sorted().collect(Collectors.toList());
}
}

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DNPMPlugins/src/main/java/ATCCodes/CodeSystem.java Normal file
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package ATCCodes;
/**
* This enum provides usable coding systems
*
* @author Paul-Christion Volkmer
* @since 0.1.0
*/
public enum CodeSystem {
ATC,
UNREGISTERED
}

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DNPMPlugins/src/main/java/ATCCodes/FileParsingException.java Normal file
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package ATCCodes;
/**
* Exception to be thrown if any file parsing error occurs
*
* @author Paul-Christian Volkmer
* @since 0.1.0
*/
public class FileParsingException extends RuntimeException {
public FileParsingException(final String msg) {
super(msg);
}
}

51
DNPMPlugins/src/main/java/ATCCodes/UnregisteredCode.java Normal file
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package ATCCodes;
import java.util.Objects;
/**
* Unregistered code as used in Onkostar database
*
* @author Paul-Christian Volkmer
* @since 0.1.0
*/
public class UnregisteredCode implements AgentCode {
private final String code;
private final String name;
public UnregisteredCode(String code, String name) {
this.code = code;
this.name = name;
}
public String getCode() {
return code;
}
public String getName() {
return name;
}
public CodeSystem getSystem() {
return CodeSystem.UNREGISTERED;
}
@Override
public int compareTo(final AgentCode agentCode) {
return this.name.toLowerCase().compareTo(agentCode.getName().toLowerCase());
}
@Override
public boolean equals(final Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
AgentCode otherAgentCode = (AgentCode) o;
return Objects.equals(code.toLowerCase(), otherAgentCode.getCode().toLowerCase())
&& Objects.equals(name.toLowerCase(), otherAgentCode.getName().toLowerCase());
}
@Override
public int hashCode() {
return Objects.hash(code.toLowerCase(), name.toLowerCase());
}
}

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DNPMPlugins/src/main/java/ATCCodes/services/AgentCodeService.java Normal file
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package ATCCodes.services;
import ATCCodes.AgentCode;
import java.util.List;
/**
* Common interface for agent code services
*
* @author Paul-Christian Volkmer
*/
public interface AgentCodeService {
/**
* Queries source for agents with name and code starting with query string.
* If size is zero, all available results will be returned.
*
* @param query The query string
* @param size Maximal amount of responses
* @return A list with agent codes
*/
List<AgentCode> findAgentCodes(String query, int size);
}

51
DNPMPlugins/src/main/java/ATCCodes/services/CsvAtcCodeService.java Normal file
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package ATCCodes.services;
import ATCCodes.AgentCode;
import ATCCodes.AtcCode;
import ATCCodes.FileParsingException;
import org.apache.commons.csv.CSVFormat;
import org.springframework.core.io.ResourceLoader;
import org.springframework.stereotype.Service;
import java.io.IOException;
import java.io.InputStreamReader;
import java.util.ArrayList;
import java.util.List;
/**
* Service to query for agent codes based on WHO xml file
*
* @author Paul-Christian Volkmer
* @since 0.1.0
*/
@Service
public class CsvAtcCodeService extends FileBasedAgentCodeService {
public CsvAtcCodeService(final ResourceLoader resourceLoader) {
super(resourceLoader);
}
protected List<AgentCode> parseFile(final ResourceLoader resourceLoader) {
var result = new ArrayList<AgentCode>();
var filename = getFilePath("atc.csv");
try {
var inputStream = resourceLoader.getResource(filename).getInputStream();
var parser = CSVFormat.RFC4180
.withHeader()
.withSkipHeaderRecord()
.parse(new InputStreamReader(inputStream));
for (var row : parser) {
if (!row.isMapped("CODE") || !row.isMapped("NAME")) {
throw new FileParsingException("No CSV column 'CODE' or 'NAME' found");
}
result.add(new AtcCode(row.get("CODE"), row.get("NAME")));
}
logger.info("Found CSV file for ATC-Codes.");
return result;
} catch (IOException | FileParsingException e) {
logger.warn("Error reading CSV file '{}' for ATC-Codes. Proceeding without data", filename);
}
return result;
}
}

63
DNPMPlugins/src/main/java/ATCCodes/services/FileBasedAgentCodeService.java Normal file
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package ATCCodes.services;
import ATCCodes.AgentCode;
import org.apache.commons.lang.SystemUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.core.io.ResourceLoader;
import java.util.ArrayList;
import java.util.List;
import java.util.stream.Collectors;
/**
* Abstract {@link AgentCodeService} for use with files that will load information into memory
*
* @author Paul-Christian Volkmer
* @since 0.1.0
*/
public abstract class FileBasedAgentCodeService implements AgentCodeService {
protected final Logger logger = LoggerFactory.getLogger(this.getClass());
protected final List<AgentCode> codeList = new ArrayList<>();
FileBasedAgentCodeService(final ResourceLoader resourceLoader) {
this.codeList.addAll(parseFile(resourceLoader));
}
static String getFilePath(final String filename) {
String pluginPathPart = "onkostar/files/onkostar/plugins/onkostar-plugin-atccodes";
if (SystemUtils.IS_OS_WINDOWS) {
return String.format("file:///c:/%s/%s", pluginPathPart, filename);
} else if (SystemUtils.IS_OS_LINUX) {
return String.format("file:///opt/%s/%s", pluginPathPart, filename);
}
return filename;
}
protected abstract List<AgentCode> parseFile(final ResourceLoader resourceLoader);
/**
* Queries source for agents code starting with or name containing query string.
* If size is zero, all available results will be returned.
*
* @param query The query string
* @param size Maximal amount of responses
* @return A list with agent codes
*/
@Override
public List<AgentCode> findAgentCodes(final String query, final int size) {
var resultStream = this.codeList.stream().filter(agentCode ->
agentCode.getCode().toLowerCase().startsWith(query.toLowerCase())
|| agentCode.getName().toLowerCase().contains(query.toLowerCase())
);
if (size > 0) {
return resultStream.limit(size).collect(Collectors.toList());
}
return resultStream.collect(Collectors.toList());
}
}

54
DNPMPlugins/src/main/java/ATCCodes/services/OnkostarAgentCodeService.java Normal file
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package ATCCodes.services;
import ATCCodes.AgentCode;
import ATCCodes.UnregisteredCode;
import org.springframework.jdbc.core.JdbcTemplate;
import org.springframework.stereotype.Service;
import javax.sql.DataSource;
import java.util.List;
/**
* Implementation of {@link AgentCodeService} that uses database to query for unregistered agents
*
* @author Paul-Christian Volkmer
* @since 0.1.0
*/
@Service
public class OnkostarAgentCodeService implements AgentCodeService {
private final JdbcTemplate jdbcTemplate;
public OnkostarAgentCodeService(final DataSource dataSource) {
this.jdbcTemplate = new JdbcTemplate(dataSource);
}
/**
* Queries source for agents code starting with or name containing query string.
* If size is zero, all available results will be returned.
*
* @param query The query string
* @param size Maximal amount of responses
* @return A list with agent codes
*/
@Override
public List<AgentCode> findAgentCodes(final String query, final int size) {
var sql = "SELECT code, shortdesc\n" +
" FROM property_catalogue\n" +
" JOIN property_catalogue_version ON (property_catalogue_version.datacatalog_id = property_catalogue.id)\n" +
" JOIN property_catalogue_version_entry p ON (p.property_version_id = property_catalogue_version.id)\n" +
" WHERE name = 'OS.Substanzen'\n" +
" AND (LOWER(code) LIKE ? OR LOWER(shortdesc) LIKE ? OR LOWER(synonyms) LIKE ?)";
if (size > 0) {
sql = sql + " LIMIT " + size;
}
return jdbcTemplate.query(
sql,
new Object[]{query + "%", "%" + query + "%", "%" + query + "%"},
(resultSet, i) ->
new UnregisteredCode(resultSet.getString("code"), resultSet.getString("shortdesc"))
);
}
}

72
DNPMPlugins/src/main/java/ATCCodes/services/WhoAtcCodeService.java Normal file
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package ATCCodes.services;
import ATCCodes.AgentCode;
import ATCCodes.AtcCode;
import ATCCodes.FileParsingException;
import org.springframework.core.io.ResourceLoader;
import org.springframework.stereotype.Service;
import javax.xml.bind.JAXBContext;
import javax.xml.bind.JAXBException;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlRootElement;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
/**
* Service to query for agent codes based on WHO xml file
*
* @author Paul-Christian Volkmer
* @since 0.1.0
*/
@Service
public class WhoAtcCodeService extends FileBasedAgentCodeService {
public WhoAtcCodeService(final ResourceLoader resourceLoader) {
super(resourceLoader);
}
protected List<AgentCode> parseFile(final ResourceLoader resourceLoader) {
var result = new ArrayList<AgentCode>();
var filename = getFilePath("atc.xml");
try {
var inputStream = resourceLoader.getResource(filename).getInputStream();
var context = JAXBContext.newInstance(XmlResource.class);
var xmlResource = (XmlResource) context.createUnmarshaller().unmarshal(inputStream);
for (var row : xmlResource.data.rows) {
if (null == row.code || null == row.name) {
throw new FileParsingException("No XML attribute 'ATCCode' or 'Name' found");
}
result.add(new AtcCode(row.code, row.name));
}
logger.info("Found WHO XML file for ATC-Codes.");
return result;
} catch (IOException e) {
logger.warn("Error reading WHO XML file '{}' for ATC-Codes. Proceeding without inserting data", filename);
} catch (JAXBException | FileParsingException e) {
logger.warn("Error parsing WHO XML file '{}' for ATC-Codes. Proceeding without inserting data", filename);
}
return result;
}
@XmlRootElement(name = "xml")
private static class XmlResource {
@XmlElement(name = "data", namespace = "urn:schemas-microsoft-com:rowset")
public XmlData data;
}
private static class XmlData {
@XmlElement(name = "row", namespace = "#RowsetSchema")
public List<XmlRow> rows;
}
private static class XmlRow {
@XmlAttribute(name = "ATCCode")
public String code;
@XmlAttribute(name = "Name")
public String name;
}
}

151
DNPMPlugins/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());
}
}
}

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DNPMPlugins/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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DNPMPlugins/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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DNPMPlugins/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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DNPMPlugins/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);
}
}

201
DNPMPlugins/src/main/resources/app/lib/umr/FormUtils.js Normal file
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class FormUtils {
constructor(context) {
this.context = context;
if (!this.context.genericEditForm) {
console.error('Context does not contain "genericEditForm". Please use "new FormUtils(this)" or methods will return undefined values!');
}
}
/**
* Returns field with given name from main form if it exists
* @param fieldName
* @returns {undefined|*}
*/
getMainformField(fieldName) {
if (this.context.genericEditForm) {
const query = '[originalName=' + fieldName + ']';
const fields = this.context.genericEditForm
.query(query)
.filter(e => e.ownerCt.xtype === 'form' || e.ownerCt.xtype === 'panel' && e.ownerCt.title.length !== 0);
if (fields.length > 0) {
return this.context.genericEditForm.down('#' + fields[0].id);
}
console.error('Field with name "' + fieldName + '" not found in main form!');
}
return undefined;
}
/**
* Returns field with given field name found at given index within whole form.
* @param fieldName
* @param index
* @returns {undefined|*}
*/
getFieldAtIndex(fieldName, index) {
if (this.context.genericEditForm) {
const query = '[originalName=' + fieldName + ']';
const fields = this.context.genericEditForm.query(query);
if (fields.length > index) {
return this.context.genericEditForm.down('#' + fields[index].id);
}
console.error('Field with name "' + fieldName + '" and index "' + index + '" not found!');
}
return undefined;
}
/**
* Returns field with given field name found in section with given name.
* @param fieldName
* @param sectionName
* @returns {undefined|*}
*/
getFieldInSection(fieldName, sectionName) {
if (this.genericEditForm) {
const query = '[originalName=' + fieldName + ']';
const fields = this.context.genericEditForm
.query(query)
.filter(e => e.ownerCt.xtype === 'panel' && e.ownerCt.ownerCt.originalName === sectionName);
if (fields.length > 0) {
return this.context.genericEditForm.down('#' + fields[0].id);
}
console.error('Field with name "' + fieldName + '" not found in section with name "' + sectionName + '"!');
}
return undefined;
}
/**
* Returns value of field with given name from main form if it exists.
* @param fieldName
* @returns {undefined|*}
*/
getMainformFieldValue(fieldName) {
let mainformField = this.getMainformField(fieldName);
if (mainformField) {
return mainformField.getValue();
}
return undefined;
}
/**
* Updates field with given name to given new value.
* The field must reside in main form.
* @param fieldName
* @param newValue
* @returns {undefined|*}
*/
setMainformFieldValue(fieldName, newValue) {
let mainformField = this.getMainformField(fieldName);
if (mainformField) {
return mainformField.setValue(newValue);
}
}
/**
* Returns value of field with given name in section with given name if it exists.
* @param fieldName
* @param sectionName
* @returns {undefined|*}
*/
getFieldValueInSection(fieldName, sectionName) {
let sectionField = this.getFieldInSection(fieldName, sectionName);
if (sectionField) {
return sectionField.getValue();
}
return undefined;
}
/**
* Updates field with given name in section with given name new value.
* The field must reside in main form.
* @param fieldName
* @param sectionName
* @param newValue
* @returns {undefined|*}
*/
setFieldValueInSection(fieldName, sectionName, newValue) {
let sectionField = this.getFieldInSection(fieldName, sectionName);
if (sectionField) {
return sectionField.setValue(newValue);
}
}
/**
* Returns value of field with given field name found at given index within whole form.
* @param fieldName
* @param index
* @returns {undefined|*}
*/
getFieldValueAtIndex(fieldName, index) {
let field = this.getFieldAtIndex(fieldName, index);
if (field) {
return field.getValue();
}
return undefined;
}
/**
* Updates value of field with given field name found at given index within whole form.
* @param fieldName
* @param index
* @param newValue
* @returns {undefined|*}
*/
setFieldValueAtIndex(fieldName, index, newValue) {
let field = this.getFieldAtIndex(fieldName, index);
if (field) {
field.setValue(newValue);
}
}
/**
* Returns all values for all fields with given name.
* @param fieldName
* @returns {*|*[]}
*/
getFieldValues(fieldName) {
if (this.context.genericEditForm) {
const query = '[originalName=' + fieldName + ']';
const fields = this.context.genericEditForm.query(query);
return fields.map(f => this.context.genericEditForm.down('#' + f.id).getValue());
}
return undefined;
}
/**
* Counts blocks within given subform field name.
* @param subformFieldName
* @returns {undefined|*|number}
*/
subformBlockCount(subformFieldName) {
if (this.context.genericEditForm) {
const query = '[originalName=' + subformFieldName + ']';
const elements = this.context.genericEditForm.query(query);
if (elements.length === 0) return 0;
return elements
.map(e => e.numberOfBlocks)
.reduce((sum, num) => sum + num);
}
return undefined;
}
/**
* Returns subform field names for given subform name.
* @param subformName
* @returns {undefined|*}
*/
getSubformFieldNames(subformName) {
if (this.context.genericEditForm) {
const query = '[formName=' + subformName + ']';
return Ext.ComponentQuery
.query(query)
.map(e => e.originalName);
}
return undefined;
}
}

20
DNPMPlugins/src/main/resources/de/itc/onkostar/library/moduleContext.xml Normal file
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<?xml version="1.0" encoding="UTF-8"?>
<beans xmlns="http://www.springframework.org/schema/beans"
xmlns:context="http://www.springframework.org/schema/context"
xmlns:mvc="http://www.springframework.org/schema/mvc"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xmlns:tx="http://www.springframework.org/schema/tx"
xsi:schemaLocation="
http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans-3.1.xsd
http://www.springframework.org/schema/context http://www.springframework.org/schema/context/spring-context-3.1.xsd
http://www.springframework.org/schema/mvc http://www.springframework.org/schema/mvc/spring-mvc-3.1.xsd
http://www.springframework.org/schema/tx http://www.springframework.org/schema/tx/spring-tx-3.1.xsd">
<bean id="DNPMHelper" class="DNPM.DNPMHelper" />
<bean id="Merkmalskatalog" class="DNPM.Merkmalskatalog" />
<bean id="ConsentManager" class="DNPM.ConsentManager" />
<context:component-scan base-package="ATCCodes"/>
<mvc:resources mapping="/app/lib/umr/**" location="classpath:/app/lib/umr/" />
</beans>

1
DNPMPlugins/src/main/resources/onkostar-config.properties Normal file
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onkostar-api=2.11.1.1