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

11 files changed, 516 insertions, 0 deletions

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<AgentCode> {
+    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<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());
+    }
+}
\ 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<AgentCode> 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<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;
+    }
+
+}
\ 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<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());
+    }
+
+}
\ 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<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"))
+        );
+    }
+}
\ 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<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;
+    }
+}
\ No newline at end of file