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 --- src/main/java/ATCCodes/AgentCode.java | 15 +++ src/main/java/ATCCodes/AtcCode.java | 51 ++++++++++ src/main/java/ATCCodes/AtcCodesPlugin.java | 110 +++++++++++++++++++++ src/main/java/ATCCodes/CodeSystem.java | 12 +++ src/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 ++++++++++++++ 11 files changed, 516 insertions(+) create mode 100644 src/main/java/ATCCodes/AgentCode.java create mode 100644 src/main/java/ATCCodes/AtcCode.java create mode 100644 src/main/java/ATCCodes/AtcCodesPlugin.java create mode 100644 src/main/java/ATCCodes/CodeSystem.java create mode 100644 src/main/java/ATCCodes/FileParsingException.java create mode 100644 src/main/java/ATCCodes/UnregisteredCode.java create mode 100644 src/main/java/ATCCodes/services/AgentCodeService.java create mode 100644 src/main/java/ATCCodes/services/CsvAtcCodeService.java create mode 100644 src/main/java/ATCCodes/services/FileBasedAgentCodeService.java create mode 100644 src/main/java/ATCCodes/services/OnkostarAgentCodeService.java create mode 100644 src/main/java/ATCCodes/services/WhoAtcCodeService.java (limited to 'src/main/java/ATCCodes') diff --git a/src/main/java/ATCCodes/AgentCode.java b/src/main/java/ATCCodes/AgentCode.java new file mode 100644 index 0000000..04d6065 --- /dev/null +++ b/src/main/java/ATCCodes/AgentCode.java @@ -0,0 +1,15 @@ +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/src/main/java/ATCCodes/AtcCode.java b/src/main/java/ATCCodes/AtcCode.java new file mode 100644 index 0000000..e8bf9f1 --- /dev/null +++ b/src/main/java/ATCCodes/AtcCode.java @@ -0,0 +1,51 @@ +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/src/main/java/ATCCodes/AtcCodesPlugin.java b/src/main/java/ATCCodes/AtcCodesPlugin.java new file mode 100644 index 0000000..d0077ae --- /dev/null +++ b/src/main/java/ATCCodes/AtcCodesPlugin.java @@ -0,0 +1,110 @@ +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/src/main/java/ATCCodes/CodeSystem.java b/src/main/java/ATCCodes/CodeSystem.java new file mode 100644 index 0000000..ea20f49 --- /dev/null +++ b/src/main/java/ATCCodes/CodeSystem.java @@ -0,0 +1,12 @@ +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 new file mode 100644 index 0000000..b009578 --- /dev/null +++ b/src/main/java/ATCCodes/FileParsingException.java @@ -0,0 +1,14 @@ +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 new file mode 100644 index 0000000..345b057 --- /dev/null +++ b/src/main/java/ATCCodes/UnregisteredCode.java @@ -0,0 +1,51 @@ +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 new file mode 100644 index 0000000..8057008 --- /dev/null +++ b/src/main/java/ATCCodes/services/AgentCodeService.java @@ -0,0 +1,23 @@ +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 new file mode 100644 index 0000000..fa834e7 --- /dev/null +++ b/src/main/java/ATCCodes/services/CsvAtcCodeService.java @@ -0,0 +1,51 @@ +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 new file mode 100644 index 0000000..17ba389 --- /dev/null +++ b/src/main/java/ATCCodes/services/FileBasedAgentCodeService.java @@ -0,0 +1,63 @@ +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 new file mode 100644 index 0000000..f29f074 --- /dev/null +++ b/src/main/java/ATCCodes/services/OnkostarAgentCodeService.java @@ -0,0 +1,54 @@ +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/src/main/java/ATCCodes/services/WhoAtcCodeService.java b/src/main/java/ATCCodes/services/WhoAtcCodeService.java new file mode 100644 index 0000000..5bb9b11 --- /dev/null +++ b/src/main/java/ATCCodes/services/WhoAtcCodeService.java @@ -0,0 +1,72 @@ +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 -- cgit v1.2.3