From 4b121482f1a8323ea23858e8118934be5d9aa54c Mon Sep 17 00:00:00 2001 From: Paul-Christian Volkmer Date: Fri, 10 Mar 2023 09:24:12 +0100 Subject: Issue #5: Vorschlag für den Aufbau des Projekts * Maven-Projekt direkt im Hauptverzeichnis * Anpassung der Maven-POM-Datei - nicht benötigte Abhängigkeiten entfernt * Gitignore-Datei angelegt --- DNPMPlugins/src/main/java/ATCCodes/AgentCode.java | 15 - DNPMPlugins/src/main/java/ATCCodes/AtcCode.java | 51 ---- .../src/main/java/ATCCodes/AtcCodesPlugin.java | 110 ------- DNPMPlugins/src/main/java/ATCCodes/CodeSystem.java | 12 - .../main/java/ATCCodes/FileParsingException.java | 14 - .../src/main/java/ATCCodes/UnregisteredCode.java | 51 ---- .../java/ATCCodes/services/AgentCodeService.java | 23 -- .../java/ATCCodes/services/CsvAtcCodeService.java | 51 ---- .../services/FileBasedAgentCodeService.java | 63 ----- .../services/OnkostarAgentCodeService.java | 54 ---- .../java/ATCCodes/services/WhoAtcCodeService.java | 72 ----- DNPMPlugins/src/main/java/DNPM/ConsentManager.java | 151 ---------- DNPMPlugins/src/main/java/DNPM/DNPMHelper.java | 315 --------------------- .../src/main/java/DNPM/Merkmalskatalog.java | 98 ------- DNPMPlugins/src/main/java/DNPM/VerweisVon.java | 54 ---- DNPMPlugins/src/main/java/DNPM/logger.java | 7 - 16 files changed, 1141 deletions(-) delete mode 100644 DNPMPlugins/src/main/java/ATCCodes/AgentCode.java delete mode 100644 DNPMPlugins/src/main/java/ATCCodes/AtcCode.java delete mode 100644 DNPMPlugins/src/main/java/ATCCodes/AtcCodesPlugin.java delete mode 100644 DNPMPlugins/src/main/java/ATCCodes/CodeSystem.java delete mode 100644 DNPMPlugins/src/main/java/ATCCodes/FileParsingException.java delete mode 100644 DNPMPlugins/src/main/java/ATCCodes/UnregisteredCode.java delete mode 100644 DNPMPlugins/src/main/java/ATCCodes/services/AgentCodeService.java delete mode 100644 DNPMPlugins/src/main/java/ATCCodes/services/CsvAtcCodeService.java delete mode 100644 DNPMPlugins/src/main/java/ATCCodes/services/FileBasedAgentCodeService.java delete mode 100644 DNPMPlugins/src/main/java/ATCCodes/services/OnkostarAgentCodeService.java delete mode 100644 DNPMPlugins/src/main/java/ATCCodes/services/WhoAtcCodeService.java delete mode 100644 DNPMPlugins/src/main/java/DNPM/ConsentManager.java delete mode 100644 DNPMPlugins/src/main/java/DNPM/DNPMHelper.java delete mode 100644 DNPMPlugins/src/main/java/DNPM/Merkmalskatalog.java delete mode 100644 DNPMPlugins/src/main/java/DNPM/VerweisVon.java delete mode 100644 DNPMPlugins/src/main/java/DNPM/logger.java (limited to 'DNPMPlugins/src/main/java') diff --git a/DNPMPlugins/src/main/java/ATCCodes/AgentCode.java b/DNPMPlugins/src/main/java/ATCCodes/AgentCode.java deleted file mode 100644 index 04d6065..0000000 --- a/DNPMPlugins/src/main/java/ATCCodes/AgentCode.java +++ /dev/null @@ -1,15 +0,0 @@ -package ATCCodes; - -/** - * Common Agent Code definition - * - * @author Paul-Christian Volkmer - * @since 0.1.0 - */ -public interface AgentCode extends Comparable { - String getCode(); - - String getName(); - - CodeSystem getSystem(); -} \ No newline at end of file diff --git a/DNPMPlugins/src/main/java/ATCCodes/AtcCode.java b/DNPMPlugins/src/main/java/ATCCodes/AtcCode.java deleted file mode 100644 index e8bf9f1..0000000 --- a/DNPMPlugins/src/main/java/ATCCodes/AtcCode.java +++ /dev/null @@ -1,51 +0,0 @@ -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()); - } -} \ No newline at end of file diff --git a/DNPMPlugins/src/main/java/ATCCodes/AtcCodesPlugin.java b/DNPMPlugins/src/main/java/ATCCodes/AtcCodesPlugin.java deleted file mode 100644 index d0077ae..0000000 --- a/DNPMPlugins/src/main/java/ATCCodes/AtcCodesPlugin.java +++ /dev/null @@ -1,110 +0,0 @@ -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 agentCodeServices; - - public AtcCodesPlugin(List 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: - * - * 
-     *      executePluginMethod(
-     *          'AtcCodesPlugin',
-     *          'query',
-     *          { q: '', size: 10 },
-     *          function (result) {console.log(result);},
-     *          false
-     *      );
-     *
- * - * @param input The data Map - * @return The result list filtered by input - */ - public List query(final Map 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(); - for (var agentCodeService : this.agentCodeServices) { - result.addAll(agentCodeService.findAgentCodes(query, size)); - } - return result.stream().distinct().sorted().collect(Collectors.toList()); - } -} \ No newline at end of file diff --git a/DNPMPlugins/src/main/java/ATCCodes/CodeSystem.java b/DNPMPlugins/src/main/java/ATCCodes/CodeSystem.java deleted file mode 100644 index ea20f49..0000000 --- a/DNPMPlugins/src/main/java/ATCCodes/CodeSystem.java +++ /dev/null @@ -1,12 +0,0 @@ -package ATCCodes; - -/** - * This enum provides usable coding systems - * - * @author Paul-Christion Volkmer - * @since 0.1.0 - */ -public enum CodeSystem { - ATC, - UNREGISTERED -} \ No newline at end of file diff --git a/DNPMPlugins/src/main/java/ATCCodes/FileParsingException.java b/DNPMPlugins/src/main/java/ATCCodes/FileParsingException.java deleted file mode 100644 index b009578..0000000 --- a/DNPMPlugins/src/main/java/ATCCodes/FileParsingException.java +++ /dev/null @@ -1,14 +0,0 @@ -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); - } -} \ No newline at end of file diff --git a/DNPMPlugins/src/main/java/ATCCodes/UnregisteredCode.java b/DNPMPlugins/src/main/java/ATCCodes/UnregisteredCode.java deleted file mode 100644 index 345b057..0000000 --- a/DNPMPlugins/src/main/java/ATCCodes/UnregisteredCode.java +++ /dev/null @@ -1,51 +0,0 @@ -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()); - } -} \ No newline at end of file diff --git a/DNPMPlugins/src/main/java/ATCCodes/services/AgentCodeService.java b/DNPMPlugins/src/main/java/ATCCodes/services/AgentCodeService.java deleted file mode 100644 index 8057008..0000000 --- a/DNPMPlugins/src/main/java/ATCCodes/services/AgentCodeService.java +++ /dev/null @@ -1,23 +0,0 @@ -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 findAgentCodes(String query, int size); -} \ No newline at end of file diff --git a/DNPMPlugins/src/main/java/ATCCodes/services/CsvAtcCodeService.java b/DNPMPlugins/src/main/java/ATCCodes/services/CsvAtcCodeService.java deleted file mode 100644 index fa834e7..0000000 --- a/DNPMPlugins/src/main/java/ATCCodes/services/CsvAtcCodeService.java +++ /dev/null @@ -1,51 +0,0 @@ -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 parseFile(final ResourceLoader resourceLoader) { - var result = new ArrayList(); - 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; - } - -} \ No newline at end of file diff --git a/DNPMPlugins/src/main/java/ATCCodes/services/FileBasedAgentCodeService.java b/DNPMPlugins/src/main/java/ATCCodes/services/FileBasedAgentCodeService.java deleted file mode 100644 index 17ba389..0000000 --- a/DNPMPlugins/src/main/java/ATCCodes/services/FileBasedAgentCodeService.java +++ /dev/null @@ -1,63 +0,0 @@ -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 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 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 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()); - } - -} \ No newline at end of file diff --git a/DNPMPlugins/src/main/java/ATCCodes/services/OnkostarAgentCodeService.java b/DNPMPlugins/src/main/java/ATCCodes/services/OnkostarAgentCodeService.java deleted file mode 100644 index f29f074..0000000 --- a/DNPMPlugins/src/main/java/ATCCodes/services/OnkostarAgentCodeService.java +++ /dev/null @@ -1,54 +0,0 @@ -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 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")) - ); - } -} \ No newline at end of file diff --git a/DNPMPlugins/src/main/java/ATCCodes/services/WhoAtcCodeService.java b/DNPMPlugins/src/main/java/ATCCodes/services/WhoAtcCodeService.java deleted file mode 100644 index 5bb9b11..0000000 --- a/DNPMPlugins/src/main/java/ATCCodes/services/WhoAtcCodeService.java +++ /dev/null @@ -1,72 +0,0 @@ -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 parseFile(final ResourceLoader resourceLoader) { - var result = new ArrayList(); - 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 rows; - } - - private static class XmlRow { - @XmlAttribute(name = "ATCCode") - public String code; - - @XmlAttribute(name = "Name") - public String name; - } -} \ No newline at end of file diff --git a/DNPMPlugins/src/main/java/DNPM/ConsentManager.java b/DNPMPlugins/src/main/java/DNPM/ConsentManager.java deleted file mode 100644 index d6b9994..0000000 --- a/DNPMPlugins/src/main/java/DNPM/ConsentManager.java +++ /dev/null @@ -1,151 +0,0 @@ -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 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 Felder = Prozedur.getAllValues(); - for (Map.Entry 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()); - } - } - -} diff --git a/DNPMPlugins/src/main/java/DNPM/DNPMHelper.java b/DNPMPlugins/src/main/java/DNPM/DNPMHelper.java deleted file mode 100644 index 408c262..0000000 --- a/DNPMPlugins/src/main/java/DNPM/DNPMHelper.java +++ /dev/null @@ -1,315 +0,0 @@ -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 input) { - int ProcedureId = (int) input.get("ProcedureId"); - int PatientId = (int) input.get("PatientId"); - int value = 0; - List> VerbundeneFormulare = new ArrayList>(); - - 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 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 input) { - int DiagnoseId = (int) input.get("DiagnoseId"); - - String jsonStr = ""; - List Rueckgabewerte = new ArrayList(); - List 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> SubstanzenCodesListe = new ArrayList>(); - - // alle Werte der Prozedur auslesen - Map alleWerte = Prozedur.getAllValues(); - // Prozedurwerte enthält nur die interessanten Werte - Map Prozedurwerte = new HashMap<>(); - // alle Werte durchgehen und die interessanten übernehmen - for (Map.Entry 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>> Subformular = new ArrayList<>(); - Subformular = WerteListe.getValue().getValue(); - // Werte aus Subformular verarbeiten - for (Map> SubformularWerte: Subformular) { - - // SubstanzenCodes enthält den Code und den Namen einer Substanz - Map SubstanzenCodes = new HashMap(); - // 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 input) { - String dataForm = (String) input.get("dataForm"); - int DiagnoseId = (int) input.get("DiagnoseId"); - int PatientId = (int) input.get("PatientId"); - // Prozedur, Feldname, Wert - - List Formulare = new ArrayList(); - String jsonStr = ""; - List 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 Werte = Prozedur.getAllValues(); - Map Values = new HashMap<>(); - for (Map.Entry WerteListe: Werte.entrySet()) { - Values.put(WerteListe.getKey(), WerteListe.getValue()); -// System.out.println(WerteListe.getKey() + ": " + WerteListe.getValue()); - } - Map 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 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 rows = query.list(); - return rows; - } catch (Exception e) { - return null; - } - } catch (Exception e) { - return null; - } - } - - public Object updateEmpfehlungPrio(final Map 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; - } - - } -} \ No newline at end of file diff --git a/DNPMPlugins/src/main/java/DNPM/Merkmalskatalog.java b/DNPMPlugins/src/main/java/DNPM/Merkmalskatalog.java deleted file mode 100644 index 8160156..0000000 --- a/DNPMPlugins/src/main/java/DNPM/Merkmalskatalog.java +++ /dev/null @@ -1,98 +0,0 @@ -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 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 rows = query.list(); - return rows; - } catch (Exception e) { - return null; - } - } catch (Exception e) { - return null; - } - } -} diff --git a/DNPMPlugins/src/main/java/DNPM/VerweisVon.java b/DNPMPlugins/src/main/java/DNPM/VerweisVon.java deleted file mode 100644 index afb6824..0000000 --- a/DNPMPlugins/src/main/java/DNPM/VerweisVon.java +++ /dev/null @@ -1,54 +0,0 @@ -package DNPM; - -import java.text.SimpleDateFormat; -import java.util.Date; - -public class VerweisVon { - private int procedure_id; - private int data_form_id; - private String data_catalogue; - private String data_catalogue_entry; - private String formname; - private Date datum; - - public VerweisVon() { - } - - @SuppressWarnings("unused") - public int getProcedure_id() { return this.procedure_id; } - public int getData_form_id() { return this.data_form_id; } - public String getData_catalogue_name() { return this.data_catalogue; } - public String getData_catalogue_entry_name() { return this.data_catalogue_entry; } - public String getFormname() { return this.formname; } - public Date getDate() { return this.datum; } - public String getTable() { - return "dk_" + this.data_catalogue.toLowerCase().replaceAll("[^a-zA-Z0-9]", "_"); - } - public String getField() { - return this.data_catalogue_entry.toLowerCase(); - } - public String getSQL() { - return "SELECT " + this.getField() + " AS value FROM " + this.getTable() + " WHERE id = " + this.getProcedure_id(); - } - private String getDatumAsString() { - SimpleDateFormat DATE_FORMAT = new SimpleDateFormat("dd.MM.yyyy"); - String Datum = null; - if (this.getDate() != null) { - Datum = DATE_FORMAT.format(this.getDate()); - } - return Datum; - } - public String getVerbundenesFormular() { - String FName = "Formular " + this.getFormname(); - if (this.getDatumAsString() != null ) { FName += " vom " + this.getDatumAsString(); } - return FName; - } - - @SuppressWarnings("unused") - public void setProcedure_id(int procedure_id) {this.procedure_id = procedure_id; } - public void setData_form_id(int data_form_id) {this.data_form_id = data_form_id; } - public void setData_catalogue_name(String data_catalogue_name) {this.data_catalogue = data_catalogue_name; } - public void setData_catalogue_entry_name(String data_catalogue_entry) {this.data_catalogue_entry = data_catalogue_entry; } - public void setDate(Date datum) { this.datum = datum; } - public void setFormname(String formname) { this.formname = formname; } -} diff --git a/DNPMPlugins/src/main/java/DNPM/logger.java b/DNPMPlugins/src/main/java/DNPM/logger.java deleted file mode 100644 index 15dadb6..0000000 --- a/DNPMPlugins/src/main/java/DNPM/logger.java +++ /dev/null @@ -1,7 +0,0 @@ -package DNPM; - -public class logger { - public static void error (String messagetext) { - System.out.println(messagetext); - } -} -- cgit v1.2.3