Parse domain specific types, add conversion config to archie-utils

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.
 

archie-utils/build.gradle

@@ -1,4 +1,4 @@
-description = "Utils for the Archie OpenEHR library"
+description = "OpenEHR-RM specific utils for the Archie OpenEHR library"
 
 dependencies {
 	compile project(':base')

tools/src/test/java/com/nedap/archie/adl14/ConversionConfigForTest.java → archie-utils/src/main/java/com/nedap/archie/adl14/OpenEHRADL14ConversionConfiguration.java

@@ -1,18 +1,17 @@
 package com.nedap.archie.adl14;
 
+
 import com.nedap.archie.json.JacksonUtil;
 
 import java.io.IOException;
 import java.io.InputStream;
 
-public class ConversionConfigForTest {
-
+public class OpenEHRADL14ConversionConfiguration {
 
     public static ADL14ConversionConfiguration getConfig() throws IOException {
-
-        try(InputStream stream = ConversionConfigForTest.class.getResourceAsStream("configuration.json")) {
+        try(InputStream stream = OpenEHRADL14ConversionConfiguration.class.getResourceAsStream("/adl14conversionconfiguration.json")) {
             return JacksonUtil.getObjectMapper().readValue(stream, ADL14ConversionConfiguration.class);
         }
-
     }
+
 }

archie-utils/src/main/resources/adl14conversionconfiguration.json

@@ -0,0 +1,25 @@
+{
+  "terminology_conversion_templates": [
+    {
+      "terminology_id": "snomedct",
+      "template": "http://snomed.info/id/$code_string"
+    },
+    {
+      "terminology_id": "snomed-ct",
+      "template": "http://snomed.info/id/$code_string"
+    },
+    {
+      "terminology_id": "snomed",
+      "template": "http://snomed.info/id/$code_string"
+    },
+    {
+      "terminology_id": "openehr",
+      "template": "http://openehr.org/id/$code_string"
+    },
+    {
+      "terminology_id": "loinc",
+      "template": "http://loinc.org/id/$code_string"
+    }
+
+  ]
+}

opt14/src/main/java/com/nedap/archie/opt14/IntervalConverter.java → opt14/src/main/java/com/nedap/archie/opt14/BaseTypesConverter.java

@@ -3,8 +3,9 @@
 import com.nedap.archie.base.Cardinality;
 import com.nedap.archie.base.Interval;
 import com.nedap.archie.base.MultiplicityInterval;
+import com.nedap.archie.base.terminology.TerminologyCode;
 
-public class IntervalConverter {
+public class BaseTypesConverter {
 
     public static Cardinality convertCardinality(CARDINALITY cardinality14) {
         if(cardinality14 == null) {
@@ -52,4 +53,11 @@ public static com.nedap.archie.base.Interval<Double> convertInterval(IntervalOfR
                 range.isUpperIncluded() == null ? true : range.isUpperIncluded());
     }
 
+    public static TerminologyCode convert(CODEPHRASE definingCode) {
+        if(definingCode == null) {
+            return null;
+        }
+        return TerminologyCode.createFromString(definingCode.getTerminologyId().getValue(), null, definingCode.getCodeString());
+    }
+
 }

opt14/src/main/java/com/nedap/archie/opt14/DefinitionConverter.java

@@ -9,8 +9,8 @@
 import com.nedap.archie.aom.Template;
 import com.nedap.archie.aom.TemplateOverlay;
 
-import static com.nedap.archie.opt14.IntervalConverter.convertCardinality;
-import static com.nedap.archie.opt14.IntervalConverter.convertMultiplicity;
+import static com.nedap.archie.opt14.BaseTypesConverter.convertCardinality;
+import static com.nedap.archie.opt14.BaseTypesConverter.convertMultiplicity;
 import static com.nedap.archie.opt14.PrimitiveConverter.convertPrimitive;
 
 public class DefinitionConverter {
@@ -30,7 +30,7 @@ private CComplexObject convert(CCOMPLEXOBJECT cComplexObject14) {
         CComplexObject cComplexObject = new CComplexObject();
         cComplexObject.setNodeId(cComplexObject14.getNodeId());
         cComplexObject.setRmTypeName(cComplexObject14.getRmTypeName());
-        cComplexObject.setOccurrences(IntervalConverter.convertMultiplicity(cComplexObject14.getOccurrences()));
+        cComplexObject.setOccurrences(BaseTypesConverter.convertMultiplicity(cComplexObject14.getOccurrences()));
 
         for (CATTRIBUTE attribute14 : cComplexObject14.getAttributes()) {
             cComplexObject.addAttribute(convert(attribute14));
@@ -81,7 +81,7 @@ private CObject convertSlot(ARCHETYPESLOT cobject14) {
         archetypeSlot.setNodeId(cobject14.getNodeId());
         archetypeSlot.setRmTypeName(cobject14.getRmTypeName());
 
-        archetypeSlot.setOccurrences(IntervalConverter.convertMultiplicity(cobject14.getOccurrences()));
+        archetypeSlot.setOccurrences(BaseTypesConverter.convertMultiplicity(cobject14.getOccurrences()));
         //TODO: assertions for include/exclude, should be straightforward
         return archetypeSlot;
     }
@@ -99,7 +99,7 @@ private CObject convertRoot(CARCHETYPEROOT cRoot14) {
         CArchetypeRoot root = new CArchetypeRoot();
         root.setArchetypeRef(overlay.getArchetypeId().getFullId());
         root.setNodeId(cRoot14.getNodeId());
-        root.setOccurrences(IntervalConverter.convertMultiplicity(cRoot14.getOccurrences()));
+        root.setOccurrences(BaseTypesConverter.convertMultiplicity(cRoot14.getOccurrences()));
         root.setRmTypeName(cRoot14.getRmTypeName());
         return root;
     }

opt14/src/main/java/com/nedap/archie/opt14/DescriptionConverter.java

@@ -19,14 +19,18 @@ public static void convert(Template template, OPERATIONALTEMPLATE opt14) {
                 author.put(item.getId(), item.getValue());
             }
         }
+        if(description14.getOtherDetails() != null) {
+            for(StringDictionaryItem item:description14.getOtherDetails()) {
+                description.getOtherDetails().put(item.getId(), item.getValue());
+            }
+        }
+
+        description.setOtherContributors(description14.getOtherContributors());
+
         description.setOriginalAuthor(author);
         template.setDescription(description);
 
-        template.setOriginalLanguage(
-                TerminologyCode.createFromString(
-                        opt14.getLanguage().getTerminologyId().getValue(),
-                        null,
-                        opt14.getLanguage().getCodeString()));
+        template.setOriginalLanguage(BaseTypesConverter.convert(opt14.getLanguage()));
         //TODO: implement me further
     }
 }

opt14/src/main/java/com/nedap/archie/opt14/DomainTypeConverter.java

@@ -1,9 +1,82 @@
 package com.nedap.archie.opt14;
 
+import com.nedap.archie.adl14.aom14.CDVOrdinal;
+import com.nedap.archie.adl14.aom14.CDVOrdinalItem;
+import com.nedap.archie.adl14.aom14.CDVQuantity;
+
+import com.nedap.archie.adl14.aom14.CDVQuantityAssumedValue;
+import com.nedap.archie.adl14.aom14.CDVQuantityItem;
+import com.nedap.archie.adl14.treewalkers.Adl14CComplexObjectParser;
 import com.nedap.archie.aom.CObject;
+import com.nedap.archie.base.terminology.TerminologyCode;
+
+import java.util.LinkedHashMap;
+import java.util.Map;
+
+import static com.nedap.archie.opt14.BaseTypesConverter.convert;
 
 public class DomainTypeConverter {
     public static CObject convertDomainType(CDOMAINTYPE cobject14) {
+        if(cobject14 instanceof CDVORDINAL) {
+            return convertCDVOrdinal((CDVORDINAL) cobject14);
+        } else if (cobject14 instanceof CDVQUANTITY) {
+            return convertCDVQuantity((CDVQUANTITY) cobject14);
+        } else if (cobject14 instanceof CDVSTATE) {
+
+        } else if (cobject14 instanceof CCODEPHRASE) {
+
+        }
         return null;
     }
+
+    private static CObject convertCDVOrdinal(CDVORDINAL ordinal14) {
+        CDVOrdinal ordinal = new CDVOrdinal();
+        Map<String, CDVOrdinalItem> items = new LinkedHashMap<>();
+        if(ordinal14.getList() != null) {
+            Integer i = 0;
+            for(DVORDINAL dvordinal14:ordinal14.getList()) {
+                CDVOrdinalItem item = new CDVOrdinalItem();
+                item.setValue(dvordinal14.getValue());
+                if(dvordinal14.getSymbol() != null) {
+                    item.setSymbol(convert(dvordinal14.getSymbol().getDefiningCode()));
+                }
+                items.put(i.toString(), item);
+                i++;
+            }
+        }
+        //TODO: no assumed value in our own model, but there is in the OPT form.
+
+        return Adl14CComplexObjectParser.convertCDVOrdinal(ordinal);
+    }
+
+    private static CObject convertCDVQuantity(CDVQUANTITY cobject14) {
+        CDVQUANTITY quantity14 = cobject14;
+        CDVQuantity quantity = new CDVQuantity();
+        Map<String, CDVQuantityItem> items = new LinkedHashMap<>();
+
+        if(quantity14.getList() != null) {
+            Integer i = 0;
+            for(CQUANTITYITEM item14:quantity14.getList()) {
+                CDVQuantityItem item = new CDVQuantityItem();
+                item.setMagnitude(BaseTypesConverter.convertInterval(item14.getMagnitude()));
+                item.setPrecision(BaseTypesConverter.convertInterval(item14.getPrecision()));
+                item.setUnits(item14.getUnits());
+                items.put(i.toString(), item);
+                i++;
+            }
+        }
+        quantity.setList(items);
+
+        quantity.setProperty(convert(quantity14.getProperty()));
+
+        DVQUANTITY assumedValue14 = quantity14.getAssumedValue();
+        if(assumedValue14 != null) {
+            CDVQuantityAssumedValue assumedValue = new CDVQuantityAssumedValue();
+            assumedValue.setMagnitude(assumedValue14.getMagnitude());
+            assumedValue.setPrecision(assumedValue14.getPrecision() == null ? null : assumedValue14.getPrecision().longValue());
+            assumedValue.setUnits(assumedValue14.getUnits());
+            quantity.setAssumedValue(assumedValue);
+        }
+        return Adl14CComplexObjectParser.convertCDvQuantity(quantity);
+    }
 }

opt14/src/main/java/com/nedap/archie/opt14/Opt14Converter.java

@@ -9,6 +9,9 @@ public Template convert(OPERATIONALTEMPLATE opt14) {
         Template template = new Template();
         template.setArchetypeId(new ArchetypeHRID("openEHR-EHR-" + opt14.getDefinition().getRmTypeName() + "." + opt14.getTemplateId().getValue() + "v1.0.0"));
         template.setParentArchetypeId(opt14.getDefinition().getArchetypeId().getValue());
+        if(opt14.getUid() != null) {
+            template.setUid(opt14.getUid().getValue());
+        }
         DescriptionConverter.convert(template, opt14);
 
         new DefinitionConverter().convert(template, opt14);

opt14/src/main/java/com/nedap/archie/opt14/PrimitiveConverter.java

@@ -6,7 +6,7 @@
 import com.nedap.archie.aom.primitives.CReal;
 import com.nedap.archie.aom.primitives.CString;
 
-import static com.nedap.archie.opt14.IntervalConverter.convertInterval;
+import static com.nedap.archie.opt14.BaseTypesConverter.convertInterval;
 
 public class PrimitiveConverter {
 

opt14/src/main/java/com/nedap/archie/opt14/TerminologyConverter.java

@@ -17,7 +17,7 @@ public static ArchetypeTerminology createTerminology(OPERATIONALTEMPLATE opt14,
             ArchetypeTerm term = new ArchetypeTerm();
             term.setCode(term14.getCode());
             for(StringDictionaryItem item:term14.getItems()) {
-                term.put(item.getId(), item.getId());
+                term.put(item.getId(), item.getValue());
             }
             terms.put(term14.getCode(), term);
         }

tools/src/test/java/com/nedap/archie/adl14/ADL14TerminologySupportTest.java

@@ -15,7 +15,7 @@ public class ADL14TerminologySupportTest {
 
     @Test
     public void terminologyBindingsConverted() throws IOException {
-        ADL14ConversionConfiguration conversionConfiguration = ConversionConfigForTest.getConfig();
+        ADL14ConversionConfiguration conversionConfiguration = OpenEHRADL14ConversionConfiguration.getConfig();
         ADL14Converter converter = new ADL14Converter(BuiltinReferenceModels.getMetaModels(), conversionConfiguration);
         String createdAtCode = null;
         //apply the first conversion and store the log. It has created an at code to bind to [openehr::124], used in a DV_QUANTITY.property

tools/src/test/java/com/nedap/archie/adl14/ArchetypeSlotConversionTest.java

@@ -20,7 +20,7 @@ public class ArchetypeSlotConversionTest {
 
     @Test
     public void testSlotConversion() throws Exception {
-        ADL14ConversionConfiguration conversionConfiguration = ConversionConfigForTest.getConfig();
+        ADL14ConversionConfiguration conversionConfiguration = OpenEHRADL14ConversionConfiguration.getConfig();
         ADL14Converter converter = new ADL14Converter(BuiltinReferenceModels.getMetaModels(), conversionConfiguration);
         ADL2ConversionRunLog log = null;
 

tools/src/test/java/com/nedap/archie/adl14/LargeSetOfADL14sTest.java

@@ -41,7 +41,7 @@ public class LargeSetOfADL14sTest {
 
     @Before
     public void setup() throws Exception {
-        conversionConfiguration = ConversionConfigForTest.getConfig();
+        conversionConfiguration = OpenEHRADL14ConversionConfiguration.getConfig();
     }
 
     @Test

tools/src/test/java/com/nedap/archie/adl14/PreviousLogConversionTest.java

@@ -21,7 +21,7 @@ public class PreviousLogConversionTest {
     @Test
     public void applyConsistentConversion() throws Exception {
 
-        ADL14ConversionConfiguration conversionConfiguration = ConversionConfigForTest.getConfig();
+        ADL14ConversionConfiguration conversionConfiguration = OpenEHRADL14ConversionConfiguration.getConfig();
         ADL14Converter converter = new ADL14Converter(BuiltinReferenceModels.getMetaModels(), conversionConfiguration);
         ADL2ConversionRunLog log = null;
 
@@ -51,7 +51,7 @@ public void applyConsistentConversion() throws Exception {
 
     @Test
     public void testValueSet() throws Exception {
-        ADL14ConversionConfiguration conversionConfiguration = ConversionConfigForTest.getConfig();
+        ADL14ConversionConfiguration conversionConfiguration = OpenEHRADL14ConversionConfiguration.getConfig();
         ADL14Converter converter = new ADL14Converter(BuiltinReferenceModels.getMetaModels(), conversionConfiguration);
         ADL2ConversionRunLog log = null;
 
@@ -88,7 +88,7 @@ public void testValueSet() throws Exception {
 
     @Test
     public void unusedValuesAreRemoved() throws Exception {
-        ADL14ConversionConfiguration conversionConfiguration = ConversionConfigForTest.getConfig();
+        ADL14ConversionConfiguration conversionConfiguration = OpenEHRADL14ConversionConfiguration.getConfig();
         ADL14Converter converter = new ADL14Converter(BuiltinReferenceModels.getMetaModels(), conversionConfiguration);
         ADL2ConversionRunLog log = null;
         String createdAtCode = null;