Fix xml namespace

aom/src/main/java/com/nedap/archie/aom/Archetype.java

@@ -10,12 +10,18 @@
 import com.nedap.archie.definitions.AdlCodeDefinitions;
 import com.nedap.archie.query.AOMPathQuery;
 import com.nedap.archie.xml.adapters.ArchetypeTerminologyAdapter;
+import com.nedap.archie.xml.adapters.StringDictionaryMapAdapter;
+import com.nedap.archie.xml.adapters.StringDictionaryUtil;
+import com.nedap.archie.xml.types.StringDictionaryItem;
 
+import javax.xml.bind.Marshaller;
+import javax.xml.bind.Unmarshaller;
 import javax.xml.bind.annotation.XmlAccessType;
 import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;
+import javax.xml.bind.annotation.XmlTransient;
 import javax.xml.bind.annotation.XmlType;
 import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
 import java.util.LinkedHashMap;
@@ -46,7 +52,7 @@
         "buildUid",
         "rmRelease",
         "generated",
-        "otherMetaData"
+        "xmlOtherMetaData"
 })
 public class Archetype extends AuthoredResource {
 
@@ -70,10 +76,31 @@ public class Archetype extends AuthoredResource {
     private String rmRelease;
     @XmlAttribute(name="is_generated")
     private Boolean generated = false;
+    //this is a specific map type to make a JAXB-adapter work. ugly jaxb
+    //alternative: define an extra field, use hooks to fill it just in time instead
+    @XmlTransient
+    private LinkedHashMap<String, String> otherMetaData = new LinkedHashMap<>();
 
     @XmlElement(name="other_meta_data")
-    //TODO: this probably requires a custom XmlAdapter
-    private Map<String, String> otherMetaData = new LinkedHashMap<>();
+    @JsonIgnore
+    private List<StringDictionaryItem> xmlOtherMetaData;
+
+    // Invoked by Jaxb Marshaller after unmarshalling
+    public void afterUnmarshal(Unmarshaller unmarshaller, Object parent) {
+        if(xmlOtherMetaData != null) {
+            otherMetaData = StringDictionaryUtil.convertStringDictionaryListToStringMap(xmlOtherMetaData);
+        }
+    }
+
+    // Invoked by Jaxb Marshaller before marshalling
+    public boolean beforeMarshal(Marshaller marshaller) {
+        if(otherMetaData == null) {
+            xmlOtherMetaData = null;
+        } else {
+            xmlOtherMetaData = StringDictionaryUtil.convertStringMapIntoStringDictionaryList(otherMetaData);
+        }
+        return true;
+    }
 
     public String getParentArchetypeId() {
         return parentArchetypeId;
@@ -162,7 +189,7 @@ public Map<String, String> getOtherMetaData() {
     }
 
     public void setOtherMetaData(Map<String, String> otherMetaData) {
-        this.otherMetaData = otherMetaData;
+        this.otherMetaData = new LinkedHashMap<>(otherMetaData);
     }
 
     public void addOtherMetadata(String text, String value) {

aom/src/main/java/com/nedap/archie/aom/LanguageSection.java

@@ -4,6 +4,7 @@
 import com.nedap.archie.base.OpenEHRBase;
 import com.nedap.archie.base.terminology.TerminologyCode;
 
+import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
 import java.util.Map;
 import java.util.concurrent.ConcurrentHashMap;
 

aom/src/main/java/com/nedap/archie/aom/OperationalTemplate.java

@@ -1,16 +1,26 @@
 package com.nedap.archie.aom;
 
+import javax.xml.bind.Marshaller;
+import javax.xml.bind.Unmarshaller;
 import javax.xml.bind.annotation.XmlAccessType;
 import javax.xml.bind.annotation.XmlAccessorType;
 import com.nedap.archie.aom.terminology.ArchetypeTerm;
 import com.nedap.archie.aom.terminology.ArchetypeTerminology;
 import com.nedap.archie.aom.utils.AOMUtils;
 import com.nedap.archie.paths.PathSegment;
+import com.nedap.archie.xml.adapters.ArchetypeTerminologyAdapter;
+import com.nedap.archie.xml.adapters.StringDictionaryUtil;
+import com.nedap.archie.xml.types.StringDictionaryItem;
+import com.nedap.archie.xml.types.XmlArchetypeTerminology;
 
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;
+import javax.xml.bind.annotation.XmlTransient;
 import javax.xml.bind.annotation.XmlType;
+import java.net.URISyntaxException;
+import java.util.ArrayList;
 import java.util.Collections;
+import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.concurrent.ConcurrentHashMap;
@@ -26,11 +36,72 @@ public class OperationalTemplate extends AuthoredArchetype {
     /**
      * terminology extracts from subarchetypes, for example snomed codes, multiple choice thingies, etc
      */
-    @XmlElement(name="terminology_extracts") //TODO: requires an adapter for JAXB to work
+    @XmlTransient
     private Map<String, ArchetypeTerminology> terminologyExtracts = new ConcurrentHashMap<>();//TODO: is this correct?
-    @XmlElement(name="component_terminologies") //TODO: requires an adapter for JAXB to work
+    @XmlTransient
     private Map<String, ArchetypeTerminology> componentTerminologies = new ConcurrentHashMap<>();
 
+    @XmlElement(name="terminology_extracts")
+    private List<XmlArchetypeTerminology> xmlTerminologyExtracts;
+    @XmlElement(name="component_terminologies")
+    private List<XmlArchetypeTerminology> xmlComponentTerminologies;
+
+    @Override
+    public void afterUnmarshal(Unmarshaller unmarshaller, Object parent) {
+        super.afterUnmarshal(unmarshaller, parent);
+        if(xmlTerminologyExtracts != null) {
+            ArchetypeTerminologyAdapter archetypeTerminologyAdapter = new ArchetypeTerminologyAdapter();
+            for(XmlArchetypeTerminology terminology:xmlTerminologyExtracts) {
+                try {
+                    ArchetypeTerminology converted = archetypeTerminologyAdapter.unmarshal(terminology);
+                    terminologyExtracts.put(terminology.getArchetypeId(), converted);
+                } catch (URISyntaxException e) {
+                    throw new RuntimeException(e);
+                }
+            }
+        }
+        if(xmlComponentTerminologies != null) {
+            ArchetypeTerminologyAdapter archetypeTerminologyAdapter = new ArchetypeTerminologyAdapter();
+            for(XmlArchetypeTerminology terminology:xmlComponentTerminologies) {
+                try {
+                    ArchetypeTerminology converted = archetypeTerminologyAdapter.unmarshal(terminology);
+                    componentTerminologies.put(terminology.getArchetypeId(), converted);
+                } catch (URISyntaxException e) {
+                    throw new RuntimeException(e);
+                }
+            }
+        }
+    }
+
+    // Invoked by Marshaller after it has created an instance of this object.
+    @Override
+    public boolean beforeMarshal(Marshaller marshaller) {
+        super.beforeMarshal(marshaller);
+        if(terminologyExtracts != null && !terminologyExtracts.isEmpty()) {
+            ArchetypeTerminologyAdapter archetypeTerminologyAdapter = new ArchetypeTerminologyAdapter();
+            xmlTerminologyExtracts = new ArrayList<>();
+            for(Map.Entry<String, ArchetypeTerminology> terminology:terminologyExtracts.entrySet()) {
+                XmlArchetypeTerminology converted = archetypeTerminologyAdapter.marshal(terminology.getValue());
+                converted.setArchetypeId(terminology.getKey());
+                xmlTerminologyExtracts.add(converted);
+            }
+        } else {
+            xmlTerminologyExtracts = null;
+        }
+        if(componentTerminologies != null && !componentTerminologies.isEmpty()) {
+            ArchetypeTerminologyAdapter archetypeTerminologyAdapter = new ArchetypeTerminologyAdapter();
+            xmlComponentTerminologies = new ArrayList<>();
+            for(Map.Entry<String, ArchetypeTerminology> terminology:componentTerminologies.entrySet()) {
+                XmlArchetypeTerminology converted = archetypeTerminologyAdapter.marshal(terminology.getValue());
+                converted.setArchetypeId(terminology.getKey());
+                xmlComponentTerminologies.add(converted);
+            }
+        } else {
+            xmlComponentTerminologies = null;
+        }
+        return true;
+    }
+
 
     public Map<String, ArchetypeTerminology> getTerminologyExtracts() {
         return terminologyExtracts;

aom/src/main/java/com/nedap/archie/aom/package-info.java

@@ -0,0 +1,5 @@
+@javax.xml.bind.annotation.XmlSchema(namespace = "http://schemas.openehr.org/v1",  elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED, attributeFormDefault = javax.xml.bind.annotation.XmlNsForm.UNQUALIFIED)
+
+package com.nedap.archie.aom;
+
+import javax.xml.bind.annotation.XmlNs;

aom/src/main/java/com/nedap/archie/aom/primitives/package-info.java

@@ -0,0 +1,5 @@
+@javax.xml.bind.annotation.XmlSchema(namespace = "http://schemas.openehr.org/v1",  elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED, attributeFormDefault = javax.xml.bind.annotation.XmlNsForm.UNQUALIFIED)
+
+package com.nedap.archie.aom.primitives;
+
+import javax.xml.bind.annotation.XmlNs;

aom/src/main/java/com/nedap/archie/aom/terminology/ArchetypeTerminology.java

@@ -30,14 +30,11 @@ public class ArchetypeTerminology extends ArchetypeModelObject {
     private String originalLanguage;
     @XmlElement(name="concept_code")
     private String conceptCode;
-    @XmlTransient//TODO!
-    //@XmlElement(name="term_definitions")
+    @XmlTransient //converted to XmlArchetypeTerminology, so not used in jaxb
     private Map<String, Map<String, ArchetypeTerm>> termDefinitions = new ConcurrentHashMap<>();
-    //@XmlElement(name="term_bindings")
-    @XmlTransient//TODO!
+    @XmlTransient //converted to XmlArchetypeTerminology, so not used in jaxb
     private Map<String, Map<String, URI>> termBindings = new ConcurrentHashMap<>();
-    //@XmlElement(name="terminology_extracts")
-    @XmlTransient//TODO!
+    @XmlTransient //converted to XmlArchetypeTerminology, so not used in jaxb
     private Map<String, Map<String, ArchetypeTerm>> terminologyExtracts = new ConcurrentHashMap<>();
     @XmlElement(name="value_sets")
     private Map<String, ValueSet> valueSets = new ConcurrentHashMap<>();

aom/src/main/java/com/nedap/archie/aom/terminology/package-info.java

@@ -0,0 +1,5 @@
+@javax.xml.bind.annotation.XmlSchema(namespace = "http://schemas.openehr.org/v1",  elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED, attributeFormDefault = javax.xml.bind.annotation.XmlNsForm.UNQUALIFIED)
+
+package com.nedap.archie.aom.terminology;
+
+import javax.xml.bind.annotation.XmlNs;

aom/src/main/java/com/nedap/archie/rules/package-info.java

@@ -0,0 +1,5 @@
+@javax.xml.bind.annotation.XmlSchema(namespace = "http://schemas.openehr.org/v1",  elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED, attributeFormDefault = javax.xml.bind.annotation.XmlNsForm.UNQUALIFIED)
+
+package com.nedap.archie.rules;
+
+import javax.xml.bind.annotation.XmlNs;

aom/src/main/java/com/nedap/archie/xml/adapters/ArchetypeTerminologyAdapter.java

@@ -10,6 +10,7 @@
 
 import javax.xml.bind.annotation.adapters.XmlAdapter;
 import java.net.URI;
+import java.net.URISyntaxException;
 import java.util.ArrayList;
 import java.util.LinkedHashMap;
 import java.util.List;
@@ -23,7 +24,7 @@
 public class ArchetypeTerminologyAdapter extends XmlAdapter<XmlArchetypeTerminology, ArchetypeTerminology> {
 
     @Override
-    public XmlArchetypeTerminology marshal(ArchetypeTerminology terminology) throws Exception {
+    public XmlArchetypeTerminology marshal(ArchetypeTerminology terminology) {
         if(terminology == null) {
             return null;
         }
@@ -71,7 +72,7 @@ private List<CodeDefinitionSet> convertIntoCodeDefinitionSetList(Map<String, Map
     }
 
     @Override
-    public ArchetypeTerminology unmarshal(XmlArchetypeTerminology xmlTerminology) throws Exception {
+    public ArchetypeTerminology unmarshal(XmlArchetypeTerminology xmlTerminology) throws URISyntaxException {
         if(xmlTerminology == null) {
             return null;
         }
@@ -97,7 +98,7 @@ private Map<String, ValueSet> convertIntoValueSetMap(List<ValueSet> valueSets) {
         return result;
     }
 
-    private Map<String, Map<String, URI>> convertIntoTermBindingsMap(List<TermBindingSet> termBindings) throws Exception{
+    private Map<String, Map<String, URI>> convertIntoTermBindingsMap(List<TermBindingSet> termBindings) throws URISyntaxException {
         Map<String, Map<String, URI>> result = new LinkedHashMap<>();
         for(TermBindingSet set:termBindings) {
             Map<String, URI> termMap = StringDictionaryUtil.convertStringDictionaryListToUriMap(set.getItems());

aom/src/main/java/com/nedap/archie/xml/adapters/StringDictionaryMapAdapter.java

@@ -0,0 +1,21 @@
+package com.nedap.archie.xml.adapters;
+
+import com.nedap.archie.aom.TranslationDetails;
+import com.nedap.archie.xml.types.StringDictionaryItem;
+import com.nedap.archie.xml.types.XmlTranslationDetails;
+
+import javax.xml.bind.annotation.adapters.XmlAdapter;
+import java.util.ArrayList;
+import java.util.LinkedHashMap;
+
+public class StringDictionaryMapAdapter extends XmlAdapter<ArrayList<StringDictionaryItem>, LinkedHashMap<String, String>> {
+    @Override
+    public LinkedHashMap<String, String> unmarshal(ArrayList<StringDictionaryItem> v) throws Exception {
+        return StringDictionaryUtil.convertStringDictionaryListToStringMap(v);
+    }
+
+    @Override
+    public ArrayList<StringDictionaryItem> marshal(LinkedHashMap<String, String> v) throws Exception {
+        return StringDictionaryUtil.convertStringMapIntoStringDictionaryList(v);
+    }
+}

aom/src/main/java/com/nedap/archie/xml/adapters/StringDictionaryUtil.java

@@ -53,11 +53,11 @@ public static Map<String, URI> convertStringDictionaryListToUriMap(List<StringDi
         return termMap;
     }
 
-    public static Map<String, String> convertStringDictionaryListToStringMap(List<StringDictionaryItem> items) {
+    public static LinkedHashMap<String, String> convertStringDictionaryListToStringMap(List<StringDictionaryItem> items) {
         if(items == null) {
             return null;
         }
-        Map<String, String> termMap = new LinkedHashMap<>();
+        LinkedHashMap<String, String> termMap = new LinkedHashMap<>();
         for(StringDictionaryItem term:items) {
             termMap.put(term.getId(),term.getValue());
         }

aom/src/main/java/com/nedap/archie/xml/types/XmlArchetypeTerminology.java

@@ -18,6 +18,8 @@
 @XmlAccessorType(XmlAccessType.FIELD)
 public class XmlArchetypeTerminology {
 
+    @XmlAttribute(name="archetype_id")
+    private String archetypeId;
     @XmlAttribute(name="is_differential")
     private Boolean differential;
     @XmlAttribute(name="original_language")
@@ -34,6 +36,14 @@ public class XmlArchetypeTerminology {
     @XmlElement(name="value_sets")
     private List<ValueSet> valueSets = new ArrayList<>();
 
+    public String getArchetypeId() {
+        return archetypeId;
+    }
+
+    public void setArchetypeId(String archetypeId) {
+        this.archetypeId = archetypeId;
+    }
+
     public List<CodeDefinitionSet> getTermDefinitions() {
         return termDefinitions;
     }

aom/src/main/java/com/nedap/archie/xml/types/XmlResourceDescription.java

@@ -42,7 +42,7 @@ public class XmlResourceDescription {
     private List<StringDictionaryItem> conversionDetails;
     @XmlElement(name = "other_details")
     private List<StringDictionaryItem> otherDetails;
-    @XmlElement(required = true, type = ResourceDescriptionItem.class)
+    @XmlElement(required = true, type = XmlResourceDescriptionItem.class)
     private List<XmlResourceDescriptionItem> details;
 
     public List<StringDictionaryItem> getOriginalAuthor() {

aom/src/main/java/com/nedap/archie/xml/types/package-info.java

@@ -0,0 +1,5 @@
+@javax.xml.bind.annotation.XmlSchema(namespace = "http://schemas.openehr.org/v1",  elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED, attributeFormDefault = javax.xml.bind.annotation.XmlNsForm.UNQUALIFIED)
+
+package com.nedap.archie.xml.types;
+
+import javax.xml.bind.annotation.XmlNs;

archie-utils/src/main/java/com/nedap/archie/xml/JAXBUtil.java

@@ -1,6 +1,12 @@
 package com.nedap.archie.xml;
 
 import com.google.common.collect.Lists;
+import com.nedap.archie.aom.AuthoredResource;
+import com.nedap.archie.aom.LanguageSection;
+import com.nedap.archie.aom.ResourceDescription;
+import com.nedap.archie.aom.ResourceDescriptionItem;
+import com.nedap.archie.aom.TranslationDetails;
+import com.nedap.archie.aom.terminology.ArchetypeTerminology;
 import com.nedap.archie.rminfo.ArchieAOMInfoLookup;
 import com.nedap.archie.rminfo.ArchieRMInfoLookup;
 import com.nedap.archie.xml.types.XmlResourceDescriptionItem;
@@ -39,6 +45,7 @@ private static synchronized void initArchieJaxbContext() {
                 classes.addAll(ArchieRMInfoLookup.getInstance().getRmTypeNameToClassMap().values());
                 //extra classes from the adapters package that are not directly referenced.\
                 classes.add(XmlResourceDescriptionItem.class);
+                removeClasses(classes);
                 archieJaxbContext = JAXBContext.newInstance(classes.toArray(new Class[0]));
             } catch (JAXBException e) {
                 throw new RuntimeException(e);//programmer error, tests will fail
@@ -51,6 +58,7 @@ public static synchronized JAXBContext createAOMContext() {
             List<Class<?>> classes = Lists.newArrayList(ArchieAOMInfoLookup.getInstance().getRmTypeNameToClassMap().values());
             //extra classes from the adapters package that are not directly referenced.\
             classes.add(XmlResourceDescriptionItem.class);
+            removeClasses(classes);
             return JAXBContext.newInstance(classes.toArray(new Class[0]));
         } catch (JAXBException e) {
             throw new RuntimeException(e);//programmer error, tests will fail
@@ -60,10 +68,28 @@ public static synchronized JAXBContext createAOMContext() {
     public static synchronized JAXBContext createRMContext() {
         try {
             List<Class<?>> classes = Lists.newArrayList(ArchieRMInfoLookup.getInstance().getRmTypeNameToClassMap().values());
+            removeClasses(classes);
             return JAXBContext.newInstance(classes.toArray(new Class[0]));
         } catch (JAXBException e) {
             throw new RuntimeException(e);//programmer error, tests will fail
         }
     }
 
+    private static void removeClasses(List<Class<?>> classes) {
+        //remove classes that are adapted to other classes anyway, particularly those using maps
+        removeAllInstances(classes, ResourceDescription.class);
+        removeAllInstances(classes, ResourceDescriptionItem.class);
+        removeAllInstances(classes, LanguageSection.class);
+        removeAllInstances(classes, ArchetypeTerminology.class);
+        removeAllInstances(classes, TranslationDetails.class);
+        removeAllInstances(classes, AuthoredResource.class);
+    }
+
+    private static <T> void removeAllInstances(List<T> something, T instance) {
+        boolean found;
+        do {
+             found = something.remove(instance);
+        } while(found);
+    }
+
 }