Merge pull request #6 from CCC-MF/issue_5

Issue #5: Vorschlag für den Aufbau des Projekts

11 files changed, 0 insertions, 516 deletions

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<AgentCode> {
-    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<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/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<AgentCode> 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<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/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<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/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<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/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<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