add xml mapping using treewalker

skfit-uni-luebeck · Feb 21, 2024 · de2b203 · de2b203
1 parent 12452cc
commit de2b203
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Showing 2 changed files with 67 additions and 3 deletions.
diff --git a/pom.xml b/pom.xml
@@ -59,6 +59,11 @@
             <artifactId>jackson-databind</artifactId>
             <version>2.16.1</version>
         </dependency>
+        <dependency>
+            <groupId>com.fasterxml.jackson.dataformat</groupId>
+            <artifactId>jackson-dataformat-xml</artifactId>
+            <version>2.16.1</version>
+        </dependency>
         <dependency>
             <groupId>com.fasterxml.jackson.dataformat</groupId>
             <artifactId>jackson-dataformat-yaml</artifactId>

diff --git a/src/main/java/de/uksh/medic/etl/OpenEhrObds.java b/src/main/java/de/uksh/medic/etl/OpenEhrObds.java
@@ -1,18 +1,29 @@
 package de.uksh.medic.etl;
 
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.core.type.TypeReference;
+import com.fasterxml.jackson.dataformat.xml.XmlMapper;
 import de.uksh.medic.etl.jobs.FhirResolver;
+import de.uksh.medic.etl.jobs.mdr.centraxx.CxxMdrConvert;
 import de.uksh.medic.etl.jobs.mdr.centraxx.CxxMdrLogin;
+import de.uksh.medic.etl.model.mdr.centraxx.RelationConvert;
 import de.uksh.medic.etl.settings.ConfigurationLoader;
 import de.uksh.medic.etl.settings.CxxMdrSettings;
+import de.uksh.medic.etl.settings.Mapping;
 import de.uksh.medic.etl.settings.Settings;
+import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
 import java.io.InputStream;
+import java.util.*;
+import java.util.Map.Entry;
+import java.util.stream.Collectors;
 import org.tinylog.Logger;
 
 public final class OpenEhrObds {
 
-    private OpenEhrObds() {}
+    private OpenEhrObds() {
+    }
 
     public static void main(String[] args) throws IOException {
         InputStream settingsYaml = ClassLoader.getSystemClassLoader().getResourceAsStream("settings.yml");
@@ -23,14 +34,62 @@ public static void main(String[] args) throws IOException {
         ConfigurationLoader configLoader = new ConfigurationLoader();
         configLoader.loadConfiguration(settingsYaml, Settings.class);
 
-        //ToDo: Replace with Kafka consumer
-
         FhirResolver.initalize();
         CxxMdrSettings mdrSettings = Settings.getCxxmdr();
         if (mdrSettings != null) {
             CxxMdrLogin.login(mdrSettings);
         }
 
+        XmlMapper xmlMapper = new XmlMapper();
+
+        // ToDo: Replace with Kafka consumer
+
+        File f = new File("file_1705482057-clean.xml");
+
+        walkXmlTree(xmlMapper.readValue(f, new TypeReference<LinkedHashMap<String, Object>>() {
+        }).entrySet(), 1, "");
+
         Logger.info("OpenEhrObds started!");
     }
+
+    @SuppressWarnings({ "unchecked", "rawtypes" })
+    public static void walkXmlTree(Set<Map.Entry<String, Object>> xmlSet, int depth, String path) {
+        if (depth <= Settings.getDepthLimit()) {
+            if (Settings.getMapping().containsKey(path)) {
+                System.out.println("Mapping " + path);
+
+                RelationConvert conv = new RelationConvert();
+                Mapping m = Settings.getMapping().get(path);
+                conv.setSourceProfileCode(m.getSource());
+                conv.setTargetProfileCode(m.getTarget());
+                conv.setSourceProfileVersion(m.getSourceVersion());
+                conv.setTargetProfileVersion(m.getTargetVersion());
+                conv.setValues(xmlSet.stream()
+                        .collect(Collectors.toMap(Entry::getKey, Entry::getValue)));
+
+                try {
+                    RelationConvert res = CxxMdrConvert.convert(Settings.getCxxmdr(), conv);
+                    System.out.println(res);
+                } catch (JsonProcessingException e) {
+                    // TODO Auto-generated catch block
+                    e.printStackTrace();
+                }
+            }
+
+            xmlSet.forEach(entry -> {
+                String newPath = path + "/" + entry.getKey();
+                int newDepth = depth + 1;
+
+                switch (entry.getValue()) {
+                    case Map h -> {
+                        walkXmlTree(h.entrySet(), newDepth, newPath);
+                    }
+                    case List a -> a.forEach(b -> walkXmlTree(((Map) b).entrySet(), newDepth, newPath));
+                    default -> {
+                    }
+                }
+            });
+        }
+    }
+
 }