query fhir ts based on mdr output

src/main/java/de/uksh/medic/etl/OpenEhrObds.java

@@ -4,8 +4,12 @@
 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.CxxMdrAttributes;
 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.mdr.centraxx.CxxItemSet;
 import de.uksh.medic.etl.model.mdr.centraxx.RelationConvert;
 import de.uksh.medic.etl.settings.ConfigurationLoader;
 import de.uksh.medic.etl.settings.CxxMdrSettings;
@@ -15,13 +19,16 @@
 import java.io.FileInputStream;
 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 org.tinylog.Logger;
 
 public final class OpenEhrObds {
 
+    private static final Map<String, Map<String, FhirAttributes>> ATTRIBUTE_CACHE = new HashMap<>();
+
     private OpenEhrObds() {
     }
 
@@ -40,6 +47,22 @@ public static void main(String[] args) throws IOException {
             CxxMdrLogin.login(mdrSettings);
         }
 
+        Settings.getMapping().values().forEach(m -> {
+            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<>());
+                    }
+                    ATTRIBUTE_CACHE.getOrDefault(m.getTarget(), new HashMap<>()).put(it.getId(),
+                            CxxMdrAttributes.getAttributes(Settings.getCxxmdr(), m.getTarget(), it.getId()));
+                } catch (URISyntaxException e) {
+                    // TODO Auto-generated catch block
+                    e.printStackTrace();
+                }
+            });
+        });
+
         XmlMapper xmlMapper = new XmlMapper();
 
         // ToDo: Replace with Kafka consumer
@@ -69,6 +92,11 @@ public static void walkXmlTree(Set<Map.Entry<String, Object>> xmlSet, int depth,
 
                 try {
                     RelationConvert res = CxxMdrConvert.convert(Settings.getCxxmdr(), conv);
+
+                    res.getValues().entrySet().forEach(e -> {
+                        queryFhirTs(m, e);
+                    });
+
                     System.out.println(res);
                 } catch (JsonProcessingException e) {
                     // TODO Auto-generated catch block
@@ -92,4 +120,16 @@ public static void walkXmlTree(Set<Map.Entry<String, Object>> xmlSet, int depth,
         }
     }
 
+    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()));
+            } else if (fa.getConceptMap() != null) {
+                e.setValue(FhirResolver.conceptMap(fa.getConceptMap(), fa.getId(), fa.getSource(),
+                        fa.getTarget(), (String) e.getValue()).getCode());
+            }
+        }
+    }
+
 }

src/main/java/de/uksh/medic/etl/jobs/FhirResolver.java

@@ -68,9 +68,9 @@ public static Coding conceptMap(URI conceptMapUri, String conceptMapId, URI sour
         return new Coding();
     }
 
-    public static String lookUp(URI source, String version, String code) {
+    public static String lookUp(URI system, String version, String code) {
         Parameters params = new Parameters();
-        params.addParameter("system", new UriType(source));
+        params.addParameter("system", new UriType(system));
         params.addParameter("code", code);
         params.addParameter("version", version);
         try {

src/main/java/de/uksh/medic/etl/jobs/mdr/centraxx/CxxMdrAttributes.java

@@ -0,0 +1,87 @@
+package de.uksh.medic.etl.jobs.mdr.centraxx;
+
+import de.uksh.medic.etl.model.FhirAttributes;
+import de.uksh.medic.etl.model.mdr.centraxx.CxxAttributeValue;
+import de.uksh.medic.etl.model.mdr.centraxx.CxxList;
+import de.uksh.medic.etl.settings.CxxMdrSettings;
+import java.net.URI;
+import java.net.URISyntaxException;
+import org.springframework.http.HttpEntity;
+import org.springframework.http.HttpHeaders;
+import org.springframework.http.HttpMethod;
+import org.springframework.http.MediaType;
+import org.springframework.http.ResponseEntity;
+import org.springframework.util.LinkedMultiValueMap;
+import org.springframework.util.MultiValueMap;
+import org.springframework.web.client.HttpClientErrorException;
+import org.springframework.web.client.RestTemplate;
+import org.springframework.web.util.UriComponentsBuilder;
+import org.tinylog.Logger;
+
+/**
+ * Class to fetch attributes from a Kairos CentraXX MDR.
+ */
+public final class CxxMdrAttributes {
+
+    private CxxMdrAttributes() {
+    }
+
+    /**
+     * Retrieves a FhirAttributes object for a specified MDR attribute.
+     *
+     * @param mdr        Configuration for MDR.
+     * @param mdrProfile profile / form / ItemSet where the item is defined
+     * @param key        key of the requested attribute
+     * @return FhirAttributes object
+     * @throws URISyntaxException
+     */
+    public static FhirAttributes getAttributes(CxxMdrSettings mdr, String mdrProfile, String key)
+            throws URISyntaxException {
+
+        if (mdr.isTokenExpired()) {
+            CxxMdrLogin.login(mdr);
+        }
+
+        MultiValueMap<String, String> form = new LinkedMultiValueMap<>();
+        form.set("code", mdrProfile);
+        form.set("domainCode", "fhir");
+        form.set("itemCode", key);
+
+        RestTemplate rt = new RestTemplate();
+        HttpHeaders headers = new HttpHeaders();
+        UriComponentsBuilder builder = UriComponentsBuilder
+                .fromHttpUrl(mdr.getUrl() + "/rest/v1/itemsets/attributes/item");
+        builder.queryParams(form);
+        headers.add(HttpHeaders.CONTENT_TYPE, MediaType.APPLICATION_JSON.toString());
+        headers.add(HttpHeaders.ACCEPT, MediaType.APPLICATION_JSON.toString());
+        headers.add("Authorization", "Bearer " + mdr.getToken());
+        try {
+            ResponseEntity<CxxList> response = rt.exchange(builder.build().encode().toUri(), HttpMethod.GET,
+                    new HttpEntity<>(headers), CxxList.class);
+            CxxList l = response.getBody();
+            if (l != null && l.getContent() != null) {
+                FhirAttributes ch = new FhirAttributes();
+                for (CxxAttributeValue av : l.getContent()) {
+                    switch (av.getAttribute()) {
+                        case SYSTEM -> ch.setSystem(new URI(av.getValue()));
+                        case SOURCE -> ch.setSource(new URI(av.getValue()));
+                        case TARGET -> ch.setTarget(new URI(av.getValue()));
+                        case ID -> ch.setId(av.getValue());
+                        case CONCEPTMAP -> ch.setConceptMap(new URI(av.getValue()));
+                        case CODE -> ch.setCode(av.getValue());
+                        case VERSION -> ch.setVersion(av.getValue());
+                        default -> {
+                        }
+                    }
+                }
+                return ch;
+            }
+            return null;
+
+        } catch (final HttpClientErrorException e) {
+            Logger.error("Object " + form.get("itemCode") + " not found in MDR!");
+            return null;
+        }
+    }
+
+}

src/main/java/de/uksh/medic/etl/model/FhirAttributes.java

@@ -0,0 +1,74 @@
+package de.uksh.medic.etl.model;
+
+import java.net.URI;
+
+public class FhirAttributes {
+
+    private URI system;
+    private URI source;
+    private URI target;
+    private URI conceptMap;
+    private String id;
+    private String code;
+    private String version;
+
+    public FhirAttributes() {
+    }
+
+    public URI getSystem() {
+        return system;
+    }
+
+    public void setSystem(URI system) {
+        this.system = system;
+    }
+
+    public URI getSource() {
+        return source;
+    }
+
+    public void setSource(URI source) {
+        this.source = source;
+    }
+
+    public URI getTarget() {
+        return target;
+    }
+
+    public void setTarget(URI target) {
+        this.target = target;
+    }
+
+    public String getId() {
+        return id;
+    }
+
+    public void setId(String id) {
+        this.id = id;
+    }
+
+    public URI getConceptMap() {
+        return conceptMap;
+    }
+
+    public void setConceptMap(URI conceptMap) {
+        this.conceptMap = conceptMap;
+    }
+
+    public String getCode() {
+        return code;
+    }
+
+    public void setCode(String code) {
+        this.code = code;
+    }
+
+    public String getVersion() {
+        return version;
+    }
+
+    public void setVersion(String version) {
+        this.version = version;
+    }
+
+}

src/main/java/de/uksh/medic/etl/model/mdr/MdrAttributes.java

@@ -0,0 +1,66 @@
+package de.uksh.medic.etl.model.mdr;
+
+import com.fasterxml.jackson.annotation.JsonCreator;
+import com.fasterxml.jackson.annotation.JsonValue;
+
+/**
+ * Enum for Attributes queried from MDR.
+ */
+public enum MdrAttributes {
+    /**
+     * system attribute in MDR.
+     */
+    SYSTEM("system"),
+    /**
+     * source attribute in MDR.
+     */
+    SOURCE("source"),
+    /**
+     * target attribute in MDR.
+     */
+    TARGET("target"),
+    /**
+     * ID attribute in MDR.
+     */
+    ID("id"),
+    /**
+     * conceptMap attribute in MDR.
+     */
+    CONCEPTMAP("conceptMap"),
+    /**
+     * code attribute in MDR.
+     */
+    CODE("code"),
+    /**
+     * version attribute in MDR.
+     */
+    VERSION("version");
+
+    private final String label;
+
+    MdrAttributes(String label) {
+        this.label = label;
+    }
+
+    @Override
+    @JsonValue
+    public String toString() {
+        return this.label;
+    }
+
+    /**
+     * Look Enum up from String.
+     * @param s string to be looked up
+     * @return corresponding Enum
+     */
+    @JsonCreator
+    public static MdrAttributes fromString(String s) {
+        for (MdrAttributes a : MdrAttributes.values()) {
+            if (a.label.equalsIgnoreCase(s)) {
+                return a;
+            }
+        }
+        return null;
+    }
+
+}

src/main/java/de/uksh/medic/etl/model/mdr/centraxx/CxxAttributeValue.java

@@ -0,0 +1,32 @@
+package de.uksh.medic.etl.model.mdr.centraxx;
+
+import de.uksh.medic.etl.model.mdr.MdrAttributes;
+import java.util.List;
+
+/**
+ * Model for AttributeValue in Kairos CentraXX MDR.
+ */
+public class CxxAttributeValue {
+
+    private String domain;
+    private MdrAttributes attribute;
+    private String value;
+    private List<CxxLinks> links;
+
+    public String getDomain() {
+        return domain;
+    }
+
+    public MdrAttributes getAttribute() {
+        return attribute;
+    }
+
+    public String getValue() {
+        return value;
+    }
+
+    public List<CxxLinks> getLinks() {
+        return links;
+    }
+
+}

src/main/java/de/uksh/medic/etl/model/mdr/centraxx/CxxList.java

@@ -0,0 +1,21 @@
+package de.uksh.medic.etl.model.mdr.centraxx;
+
+import java.util.List;
+
+/**
+ * Model for List in Kairos CentraXX MDR.
+ */
+public class CxxList {
+
+    private List<CxxAttributeValue> content;
+    private List<CxxLinks> links;
+
+    public List<CxxAttributeValue> getContent() {
+        return content;
+    }
+
+    public List<CxxLinks> getLinks() {
+        return links;
+    }
+
+}