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integrate openehrmapper
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@nr23730
nr23730 committed Feb 23, 2024
1 parent b75189e commit a4dd39f
Showing 1 changed file with 138 additions and 48 deletions.
186 changes: 138 additions & 48 deletions src/main/java/de/uksh/medic/etl/OpenEhrObds.java
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Original file line number Diff line number Diff line change
Expand Up @@ -8,26 +8,32 @@
import de.uksh.medic.etl.jobs.mdr.centraxx.CxxMdrConvert;
import de.uksh.medic.etl.jobs.mdr.centraxx.CxxMdrItemSet;
import de.uksh.medic.etl.jobs.mdr.centraxx.CxxMdrLogin;
import de.uksh.medic.etl.model.FhirAttributes;
import de.uksh.medic.etl.model.MappingAttributes;
import de.uksh.medic.etl.model.mdr.centraxx.CxxItemSet;
import de.uksh.medic.etl.model.mdr.centraxx.RelationConvert;
import de.uksh.medic.etl.openehrmapper.EHRParser;
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.BufferedWriter;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileWriter;
import java.io.IOException;
import java.io.InputStream;
import java.net.URISyntaxException;
import java.util.*;
import java.util.Map.Entry;
import java.util.stream.Collectors;
import javax.xml.parsers.ParserConfigurationException;
import javax.xml.xpath.XPathExpressionException;
import org.tinylog.Logger;
import org.xml.sax.SAXException;

public final class OpenEhrObds {

private static final Map<String, Map<String, FhirAttributes>> ATTRIBUTE_CACHE = new HashMap<>();
private static final Map<String, Map<String, MappingAttributes>> FHIR_ATTRIBUTES = new HashMap<>();

private OpenEhrObds() {
}
Expand All @@ -48,14 +54,17 @@ public static void main(String[] args) throws IOException {
}

Settings.getMapping().values().forEach(m -> {
if (m.getSource() == null) {
return;
}
CxxItemSet is = CxxMdrItemSet.get(Settings.getCxxmdr(), m.getTarget());
is.getItems().forEach(it -> {
try {
if (!ATTRIBUTE_CACHE.containsKey(m.getTarget())) {
ATTRIBUTE_CACHE.put(m.getTarget(), new HashMap<>());
if (!FHIR_ATTRIBUTES.containsKey(m.getTarget())) {
FHIR_ATTRIBUTES.put(m.getTarget(), new HashMap<>());
}
ATTRIBUTE_CACHE.getOrDefault(m.getTarget(), new HashMap<>()).put(it.getId(),
CxxMdrAttributes.getAttributes(Settings.getCxxmdr(), m.getTarget(), it.getId()));
FHIR_ATTRIBUTES.getOrDefault(m.getTarget(), new HashMap<>()).put(it.getId(),
CxxMdrAttributes.getAttributes(Settings.getCxxmdr(), m.getTarget(), "fhir", it.getId()));
} catch (URISyntaxException e) {
// TODO Auto-generated catch block
e.printStackTrace();
Expand All @@ -67,69 +76,150 @@ public static void main(String[] args) throws IOException {

// ToDo: Replace with Kafka consumer

File f = new File("file_1705482057-clean.xml");
File f = new File("tod.xml");

Map<String, Object> m = new LinkedHashMap<>();
walkXmlTree(xmlMapper.readValue(f, new TypeReference<LinkedHashMap<String, Object>>() {
}).entrySet(), 1, "");
}).entrySet(), 1, "", m);

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)));
@SuppressWarnings({ "unchecked" })
public static void walkXmlTree(Set<Map.Entry<String, Object>> xmlSet, int depth, String path,
Map<String, Object> resMap) {

try {
RelationConvert res = CxxMdrConvert.convert(Settings.getCxxmdr(), conv);
if (depth > Settings.getDepthLimit()) {
return;
}
if (Settings.getMapping().containsKey(path) && Settings.getMapping().get(path).getSource() != null) {

res.getValues().entrySet().forEach(e -> {
queryFhirTs(m, e);
});
Mapping m = Settings.getMapping().get(path);

System.out.println(res);
} catch (JsonProcessingException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
Map<String, Object> mapped = convertMdr(xmlSet, m);
mapped.entrySet().forEach(e -> queryFhirTs(m, e));
Map<String, Object> result = formatMap((Map<String, Object>) mapped);

buildOpenEhrComposition(result);

xmlSet.forEach(entry -> {
String newPath = path + "/" + entry.getKey();
int newDepth = depth + 1;
resMap.putAll(result);

switch (entry.getValue()) {
case Map h -> {
walkXmlTree(h.entrySet(), newDepth, newPath);
}

xmlSet.forEach(entry -> {
String newPath = path + "/" + entry.getKey();
int newDepth = depth + 1;

switch (entry.getValue()) {
case @SuppressWarnings("rawtypes") Map h -> {
if (Settings.getMapping().containsKey(newPath)
&& Settings.getMapping().get(newPath).getSplit()) {
Map<String, Object> m = new LinkedHashMap<>();
System.out.println(entry.getKey());
walkXmlTree(h.entrySet(), newDepth, newPath, m);
resMap.put(newPath, List.of(m));
} else {
walkXmlTree(h.entrySet(), newDepth, newPath, resMap);
}
case List a -> a.forEach(b -> walkXmlTree(((Map) b).entrySet(), newDepth, newPath));
default -> {
}
case @SuppressWarnings("rawtypes") List a -> {

if (Settings.getMapping().containsKey(newPath)
&& Settings.getMapping().get(newPath).getSplit()) {
List<Map<String, Object>> l = new ArrayList<>();
a.forEach(b -> {
Map<String, Object> m = new LinkedHashMap<>();
l.add(m);
System.out.println(entry.getKey());
walkXmlTree(((Map<String, Object>) b).entrySet(), newDepth, newPath, m);
});
resMap.put(newPath, l);
} else {
a.forEach(b -> {
System.out.println(entry.getKey());
walkXmlTree(((Map<String, Object>) b).entrySet(), newDepth, newPath, resMap);
});
}
}
});
}

default -> {
}
}
});

}

@SuppressWarnings("unchecked")
private static void queryFhirTs(Mapping m, Map.Entry<String, Object> e) {
FhirAttributes fa = ATTRIBUTE_CACHE.get(m.getTarget()).getOrDefault(e.getKey(), null);
if (fa != null) {
if (fa.getVersion() != null) {
e.setValue(FhirResolver.lookUp(fa.getSystem(), fa.getVersion(), (String) e.getValue()));
MappingAttributes fa = FHIR_ATTRIBUTES.get(m.getTarget()).get(e.getKey());
if (fa != null && fa.getSystem() != null) {
String code = switch (e.getValue()) {
case String c -> c;
case Map map -> ((Map<String, String>) map).get("code");
default -> null;
};
if (fa.getConceptMap() == null) {
String version = switch (e.getValue()) {
case String c -> fa.getVersion();
case Map map -> ((Map<String, String>) map).get("version");
default -> null;
};
e.setValue(FhirResolver.lookUp(fa.getSystem(), version, code));
} else if (fa.getConceptMap() != null) {
e.setValue(FhirResolver.conceptMap(fa.getConceptMap(), fa.getId(), fa.getSource(),
fa.getTarget(), (String) e.getValue()).getCode());
fa.getTarget(), code));
}
}
}

private static Map<String, Object> formatMap(Map<String, Object> input) {
Map<String, Object> out = new LinkedHashMap<>();
for (Entry<String, Object> e : input.entrySet()) {
ArrayList<String> al = new ArrayList<>();
al.addAll(Arrays.asList(e.getKey().split("/")));
splitMap(e.getValue(), al, out);
}
return out;
}

@SuppressWarnings({ "unchecked" })
private static void splitMap(Object value, List<String> key, Map<String, Object> out) {
if (key.size() > 1) {
String k = key.removeFirst();
Map<String, Object> m = (Map<String, Object>) out.getOrDefault(k,
new LinkedHashMap<>());
out.put(k, m);
splitMap(value, key, m);
} else if (key.size() == 1) {
out.put(key.removeFirst(), value);
}
}

private static Map<String, Object> convertMdr(Set<Map.Entry<String, Object>> xmlSet, Mapping m) {
RelationConvert conv = new RelationConvert();
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 {
return CxxMdrConvert.convert(Settings.getCxxmdr(), conv).getValues();
} catch (JsonProcessingException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
return null;
}

private static void buildOpenEhrComposition(Map<String, Object> data) {
EHRParser ep = new EHRParser();
try (BufferedWriter writer = new BufferedWriter(new FileWriter("output.json"))) {
writer.write(ep.build(data));
} catch (XPathExpressionException | IOException | ParserConfigurationException | SAXException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}

}

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