Opt 1.4 parser and converter

README.md

@@ -453,7 +453,8 @@ The following features are experimental. This means its working or API will like
 Starting from version 0.7, Archie can import ADL 1.4 files, and convert them to ADL 2. To do so, do the following:
 
 ```java
-ADL14ConversionConfiguration conversionConfiguration = new ADL14ConversionConfiguration();
+//this is the default configuration. You can implement your own if you want to
+ADL14ConversionConfiguration conversionConfiguration = OpenEHRADL14ConversionConfiguration.getConfig();
 ADL14Converter converter = new ADL14Converter(BuiltinReferenceModels.getMetaModels(), conversionConfiguration);
 
 List<Archetype> archetypes = new ArrayList<>();
@@ -498,7 +499,7 @@ The conversion log can be serialized to a file for storage using Jackson, so it
 
 ### Conversion Configuration
 
-You may have noticed an instance of `ADL14ConversionConfiguration` in the previous example. In this configuration the mapping from term codes as used in ADL 1.4 to term URIs as used in ADL 2 can be specified. See the `ConversionConfigForTest.java` file for an example on how this works, and how this can be serialized to a file, and the file `/tools/src/test/java/com/nedap/archie/adl14/configuration.json` for an example of a simple serialized configuration that contains sane defaults for snomed, loinc and openehr URIs.
+You may have noticed an instance of `ADL14ConversionConfiguration` in the previous example. In this configuration the mapping from term codes as used in ADL 1.4 to term URIs as used in ADL 2 can be specified. The archie-utils package provides a default configuration in the class `OpenEHRADL14ConversionConfiguration`. It is possible to supply your own, see the default implementation on how this works, and how this can be serialized to a file, and the file `/archie-utils/src/main/resources/adl14conversionconfiguration.json` for an example of a simple serialized configuration that contains sane defaults for snomed, loinc and openehr URIs.
 
 If you leave the configuration empty, the converter will fall back to a default URI conversion.
 

aom/src/main/java/com/nedap/archie/adl14/ADL14ConversionConfiguration.java

@@ -21,6 +21,9 @@
      */
     private boolean applyDiff = true;
 
+    /** If true, allow empty node ids where specialisations occur. for OPT conversion */
+    private boolean allowEmptyNodeIdsForSpecializations = false;
+
 
     /**
      * ADL 1.4 contains no rm release version, 2 does. So one needs to be added. Set to the desired rm_release. Defaults to 1.1.0
@@ -64,6 +67,14 @@
         this.applyDiff = applyDiff;
     }
 
+    public boolean isAllowEmptyNodeIdsForSpecializations() {
+        return allowEmptyNodeIdsForSpecializations;
+    }
+
+    public void setAllowEmptyNodeIdsForSpecializations(boolean allowEmptyNodeIdsForSpecializations) {
+        this.allowEmptyNodeIdsForSpecializations = allowEmptyNodeIdsForSpecializations;
+    }
+
     public String getRmRelease() {
         return rmRelease;
     }

aom/src/main/java/com/nedap/archie/adl14/ADL14DescriptionConverter.java

@@ -10,6 +10,9 @@ public class ADL14DescriptionConverter {
 
     public void convert(Archetype archetype) {
         ResourceDescription description = archetype.getDescription();
+        if(description == null) {
+            return;
+        }
         description.setLicence(description.getOtherDetails().remove("licence"));
         description.setOriginalNamespace(description.getOtherDetails().remove("original_namespace"));
         description.setOriginalPublisher(description.getOtherDetails().remove("original_publisher"));

aom/src/main/java/com/nedap/archie/adl14/ADL14NodeIDConverter.java

@@ -5,16 +5,9 @@
 import com.nedap.archie.adl14.log.ConvertedCodeResult;
 import com.nedap.archie.adl14.log.CreatedCode;
 import com.nedap.archie.adl14.log.ReasonForCodeCreation;
-import com.nedap.archie.aom.Archetype;
-import com.nedap.archie.aom.ArchetypeHRID;
-import com.nedap.archie.aom.ArchetypeSlot;
-import com.nedap.archie.aom.CArchetypeRoot;
-import com.nedap.archie.aom.CAttribute;
-import com.nedap.archie.aom.CComplexObject;
-import com.nedap.archie.aom.CComplexObjectProxy;
-import com.nedap.archie.aom.CObject;
-import com.nedap.archie.aom.CPrimitiveObject;
+import com.nedap.archie.aom.*;
 import com.nedap.archie.aom.primitives.CString;
+import com.nedap.archie.aom.rmoverlay.RmOverlay;
 import com.nedap.archie.aom.terminology.ArchetypeTerm;
 import com.nedap.archie.aom.terminology.ValueSet;
 import com.nedap.archie.aom.utils.AOMUtils;
@@ -102,10 +95,40 @@
         generateMissingNodeIds(archetype.getDefinition());
 
         convertTermDefinitions(archetype, convertedCodes);
+        convertAnnotations(archetype);
+        convertRmOverlay(archetype);
         previousConversionApplier.removeCreatedUnusedTermCodesAndValueSets();
         return new ADL2ConversionLog(/*convertedCodes*/ null, createdCodes, createdValueSets);
     }
 
+    private void convertAnnotations(Archetype archetype) {
+        ResourceAnnotations converted = new ResourceAnnotations();
+        converted.setDocumentation(new LinkedHashMap<>());
+        if(archetype.getAnnotations() != null && archetype.getAnnotations().getDocumentation() != null) {
+            for(String language:archetype.getAnnotations().getDocumentation().keySet()) {
+                Map<String, Map<String, String>> convertedLanguageMap = new LinkedHashMap<>();
+                converted.getDocumentation().put(language, convertedLanguageMap);
+                Map<String, Map<String, String>> documentationMap = archetype.getAnnotations().getDocumentation().get(language);
+                for(String path:documentationMap.keySet()) {
+                    convertedLanguageMap.put(convertPath(path), documentationMap.get(path));
+                }
+            }
+        }
+        archetype.setAnnotations(converted);
+    }
+
+    private void convertRmOverlay(Archetype archetype) {
+        RmOverlay convertedOverlay = new RmOverlay();
+        convertedOverlay.setRmVisibility(new LinkedHashMap<>());
+        if(archetype.getRmOverlay() != null && archetype.getRmOverlay().getRmVisibility() != null) {
+            for(String path:archetype.getRmOverlay().getRmVisibility().keySet()) {
+                convertedOverlay.getRmVisibility().put(convertPath(path), archetype.getRmOverlay().getRmVisibility().get(path));
+            }
+        }
+        archetype.setRmOverlay(convertedOverlay);
+    }
+
+
     private void correctItemsCardinality(CObject cObject) {
         for(CAttribute attribute:cObject.getAttributes()) {
             if(attribute.getRmAttributeName().equalsIgnoreCase("items") && cObject.getRmTypeName().equalsIgnoreCase("CLUSTER") && attribute.getCardinality() != null) {
@@ -203,7 +226,6 @@
     }
 
     private void generateMissingNodeIds(CObject cObject) {
-
         if(!(cObject instanceof CPrimitiveObject) && cObject.getNodeId() == null) {
             String path = cObject.getPath();
             if(archetype.getParentArchetypeId() != null && flatParentArchetype != null) {

aom/src/main/java/com/nedap/archie/adl14/ADL14TermConstraintConverter.java

@@ -136,6 +136,21 @@
                         URI uri = new ADL14ConversionUtil(converter.getConversionConfiguration()).convertToUri(termCode);
                         Map<String, URI> termBindingsMap = findOrCreateTermBindings(termCode);
 
+                        //TODO: check if this is a converted or old term binding - old is unusual, but could be possible!
+                        String termBinding = findOrAddTermBindingAndCode(termCode, uri, termBindingsMap);
+                        cTerminologyCode.setConstraint(Lists.newArrayList(termBinding));
+                    } catch (URISyntaxException e) {
+                        //TODO
+                        logger.error("error converting term", e);
+                    }
+                } else if (cTerminologyCode.getConstraint().size() == 2) {
+                    //still one code.
+                    try {
+                        termCode = TerminologyCode.createFromString(cTerminologyCode.getConstraint().get(0), null, cTerminologyCode.getConstraint().get(1));
+                        //do not create a value set, create a code plus binding to the old non-local code
+                        URI uri = new ADL14ConversionUtil(converter.getConversionConfiguration()).convertToUri(termCode);
+                        Map<String, URI> termBindingsMap = findOrCreateTermBindings(termCode);
+
                         //TODO: check if this is a converted or old term binding - old is unusual, but could be possible!
                         String termBinding = findOrAddTermBindingAndCode(termCode, uri, termBindingsMap);
                         cTerminologyCode.setConstraint(Lists.newArrayList(termBinding));
@@ -197,6 +212,9 @@
     }
 
     private Map<String, URI> findOrCreateTermBindings(TerminologyCode termCode) {
+        if(termCode.getTerminologyId() == null) {
+            throw new IllegalArgumentException("terminology id cannot be null!");
+        }
         Map<String, URI> termBindings =  archetype.getTerminology().getTermBindings().get(termCode.getTerminologyId());
 
         if(termBindings == null) {