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/src/main/java/ATCCodes/CodeSystem.java b/src/main/java/ATCCodes/CodeSystem.java
deleted file mode 100644
index ea20f49..0000000
--- a/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/src/main/java/ATCCodes/FileParsingException.java b/src/main/java/ATCCodes/FileParsingException.java
deleted file mode 100644
index b009578..0000000
--- a/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/src/main/java/ATCCodes/UnregisteredCode.java b/src/main/java/ATCCodes/UnregisteredCode.java
deleted file mode 100644
index 345b057..0000000
--- a/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/src/main/java/ATCCodes/services/AgentCodeService.java b/src/main/java/ATCCodes/services/AgentCodeService.java
deleted file mode 100644
index 8057008..0000000
--- a/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/src/main/java/ATCCodes/services/CsvAtcCodeService.java b/src/main/java/ATCCodes/services/CsvAtcCodeService.java
deleted file mode 100644
index fa834e7..0000000
--- a/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/src/main/java/ATCCodes/services/FileBasedAgentCodeService.java b/src/main/java/ATCCodes/services/FileBasedAgentCodeService.java
deleted file mode 100644
index 17ba389..0000000
--- a/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/src/main/java/ATCCodes/services/OnkostarAgentCodeService.java b/src/main/java/ATCCodes/services/OnkostarAgentCodeService.java
deleted file mode 100644
index e0c75f4..0000000
--- a/src/main/java/ATCCodes/services/OnkostarAgentCodeService.java
+++ /dev/null
@@ -1,61 +0,0 @@
-package ATCCodes.services;
-
-import ATCCodes.AgentCode;
-import ATCCodes.AtcCode;
-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) -> {
- var code = resultSet.getString("code");
- var shortdesc = resultSet.getString("shortdesc");
- if (AtcCode.isAtcCode(code)) {
- return new AtcCode(code, shortdesc);
- }
- return new UnregisteredCode(code, shortdesc);
- }
- );
- }
-}
\ No newline at end of file
diff --git a/src/main/java/ATCCodes/services/WhoAtcCodeService.java b/src/main/java/ATCCodes/services/WhoAtcCodeService.java
deleted file mode 100644
index 5bb9b11..0000000
--- a/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/src/main/java/DNPM/services/systemtherapie/OsSystemischeTherapieToProzedurwerteMapper.java b/src/main/java/DNPM/services/systemtherapie/OsSystemischeTherapieToProzedurwerteMapper.java
index eb6371b..0ee17b5 100644
--- a/src/main/java/DNPM/services/systemtherapie/OsSystemischeTherapieToProzedurwerteMapper.java
+++ b/src/main/java/DNPM/services/systemtherapie/OsSystemischeTherapieToProzedurwerteMapper.java
@@ -1,10 +1,10 @@
package DNPM.services.systemtherapie;
-import ATCCodes.AtcCode;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import de.itc.onkostar.api.Item;
import de.itc.onkostar.api.Procedure;
+import de.ukw.ccc.onkostar.atccodes.AtcCode;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
diff --git a/src/main/resources/de/itc/onkostar/library/moduleContext.xml b/src/main/resources/de/itc/onkostar/library/moduleContext.xml
index 6bce989..7a78f8c 100644
--- a/src/main/resources/de/itc/onkostar/library/moduleContext.xml
+++ b/src/main/resources/de/itc/onkostar/library/moduleContext.xml
@@ -26,4 +26,5 @@
+
\ No newline at end of file
diff --git a/src/test/java/ATCCodes/AtcCodeTest.java b/src/test/java/ATCCodes/AtcCodeTest.java
deleted file mode 100644
index f2a7262..0000000
--- a/src/test/java/ATCCodes/AtcCodeTest.java
+++ /dev/null
@@ -1,28 +0,0 @@
-package ATCCodes;
-
-import org.junit.jupiter.api.Test;
-
-import static org.junit.jupiter.api.Assertions.assertFalse;
-import static org.junit.jupiter.api.Assertions.assertTrue;
-
-class AtcCodeTest {
-
- @Test
- void testShouldDetectAtcCodeScheme() {
- assertTrue(AtcCode.isAtcCode("L01"));
- assertTrue(AtcCode.isAtcCode("L01A"));
- assertTrue(AtcCode.isAtcCode("L01AA"));
- assertTrue(AtcCode.isAtcCode("L01AA01"));
- }
-
- @Test
- void testShouldDetectInvalidAtcCodeScheme() {
- assertFalse(AtcCode.isAtcCode(null));
- assertFalse(AtcCode.isAtcCode(" "));
- assertFalse(AtcCode.isAtcCode("irgendwas"));
- assertFalse(AtcCode.isAtcCode("L00AA"));
- assertFalse(AtcCode.isAtcCode("Z01AA"));
- assertFalse(AtcCode.isAtcCode("L01AA0"));
- }
-
-}