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Cleanup ADL14Converter code (#648)
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* Remove unused setExistingRepository method

* Add documentation to DescriptionConverter

* remove commented code and add to documentation of DefaultMultiplicitiesSetter

* Cleanup ConversionResult

* cleanup DefaultRmStructureRemover

* Rename ArchetypeParsePostProcessor and formatting

* Cleanup ADL14NodeIDConverter

* Update faulty comment about default occurrences

* Set back javadoc comment

* revert removing setExistingRepository method and add comment about it being part of the public API

* change javadoc comment formatting
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@VeraPrinsen
VeraPrinsen authored Jan 16, 2025
1 parent b7fbc56 commit 2e07d73
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Showing 12 changed files with 273 additions and 300 deletions.
21 changes: 5 additions & 16 deletions aom/src/main/java/com/nedap/archie/adl14/ADL14DefaultMultiplicitiesSetter.java
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Expand Up @@ -9,10 +9,10 @@
import com.nedap.archie.rminfo.MetaModels;

/**
* Sets the default occurrences with ADL 1.4 rules, if not explicitly set in a given Archetype.
* Sets the default occurrences with ADL 1.4 rules ({1..1}), if not explicitly set in a given Archetype.
* Useful for conversion to ADL 2, where the default values are different, and it is good to start
* with the correct values already present.
*
* <p>
* Cardinality and existence are also specified to have a default value. However, this is not used
* in practice (source, several openEHR community members). Adding that to the conversion would
* lead to problems. So these are left out.
Expand All @@ -31,20 +31,9 @@ public void setDefaults(Archetype archetype) {
}

private void correctItemsMultiplicities(CObject cObject) {
for(CAttribute attribute:cObject.getAttributes()) {
// according to the specification, the following lines must be added.
// however, in practice this is not followed, and adding it would
// lead to more problems
/*
if(attribute.getCardinality() == null) {
attribute.setCardinality(new Cardinality(0, 1));
}
if(attribute.getExistence() == null) {
attribute.setExistence(new MultiplicityInterval(1, 1));
}*/
for(CObject child:attribute.getChildren()) {
if(child.getOccurrences() == null &&
metaModels.isMultiple(cObject.getRmTypeName(), attribute.getRmAttributeName())) {
for (CAttribute attribute : cObject.getAttributes()) {
for (CObject child : attribute.getChildren()) {
if (child.getOccurrences() == null && metaModels.isMultiple(cObject.getRmTypeName(), attribute.getRmAttributeName())) {
child.setOccurrences(new MultiplicityInterval(1, 1));
}
correctItemsMultiplicities(child);
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7 changes: 5 additions & 2 deletions aom/src/main/java/com/nedap/archie/adl14/ADL14DescriptionConverter.java
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Expand Up @@ -6,6 +6,11 @@
import java.util.LinkedHashMap;
import java.util.Map;

/**
* Converts the Description section from ADL1.4 to ADL2
* <a href="https://specifications.openehr.org/releases/AM/latest/ADL1.4.html#_description_section">Specifications ADL1.4</a>
* <a href="https://specifications.openehr.org/releases/AM/Release-2.3.0/ADL2.html#_description_section">Specifications ADL2</a>
*/
public class ADL14DescriptionConverter {

public void convert(Archetype archetype) {
Expand Down Expand Up @@ -44,12 +49,10 @@ public void convert(Archetype archetype) {
}
description.setIpAcknowledgements(acknowledgements);
}

String revision = description.getOtherDetails().remove("revision");
if(revision != null) {
archetype.getArchetypeId().setReleaseVersion(revision);
}

archetype.setGenerated(true);
}
}
271 changes: 140 additions & 131 deletions aom/src/main/java/com/nedap/archie/adl14/ADL14NodeIDConverter.java
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4 changes: 2 additions & 2 deletions aom/src/main/java/com/nedap/archie/adl14/ADL14Parser.java
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Expand Up @@ -10,7 +10,7 @@
import com.nedap.archie.antlr.errors.ANTLRParserErrors;
import com.nedap.archie.antlr.errors.ArchieErrorListener;
import com.nedap.archie.aom.Archetype;
import com.nedap.archie.aom.utils.ArchetypeParsePostProcesser;
import com.nedap.archie.aom.utils.ArchetypeParsePostProcessor;
import com.nedap.archie.rminfo.MetaModels;
import org.antlr.v4.runtime.CharStream;
import org.antlr.v4.runtime.CharStreams;
Expand Down Expand Up @@ -74,7 +74,7 @@ public Archetype parse(CharStream stream, ADL14ConversionConfiguration conversio
walker = new ParseTreeWalker();
walker.walk(listener, tree);
result = listener.getArchetype();
ArchetypeParsePostProcesser.fixArchetype(result);
ArchetypeParsePostProcessor.fixArchetype(result);
if (metaModels != null) {
metaModels.selectModel(result);
if (metaModels.getSelectedBmmModel() != null) {
Expand Down
38 changes: 10 additions & 28 deletions aom/src/main/java/com/nedap/archie/adl14/ADL2ConversionResult.java
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Expand Up @@ -7,7 +7,7 @@

/**
* ADL 2 conversion result. Always has the archetypeId field set.
* Either has archetype and conversionLog non-null in case of a succesful conversion, or
* Either has archetype and conversionLog non-null in case of a successful conversion, or
* exception non-null in case of an unexpected Exception
*/
public class ADL2ConversionResult {
Expand All @@ -18,24 +18,14 @@ public class ADL2ConversionResult {
private MessageLogger log;
private Exception exception;

/**
* empty constructor for JSON parsing. Do not use
*/
/** Empty construction for Jackson parsing, do not use */
public ADL2ConversionResult() {

}

public ADL2ConversionResult(Archetype archetype) {
this.archetypeId = archetype.getArchetypeId().getFullId();
this(archetype.getArchetypeId().getFullId(), null);
this.archetype = archetype;
log = new MessageLogger();
}

public ADL2ConversionResult(Archetype archetype, ADL2ConversionLog conversionLog) {
this.archetypeId = archetype.getArchetypeId().getFullId();
this.archetype = archetype;
this.conversionLog = conversionLog;
log = new MessageLogger();
}

public ADL2ConversionResult(String archetypeId, Exception exception) {
Expand All @@ -44,14 +34,11 @@ public ADL2ConversionResult(String archetypeId, Exception exception) {
log = new MessageLogger();
}

/* GETTERS **/
public String getArchetypeId() {
return archetypeId;
}

public void setArchetypeId(String archetypeId) {
this.archetypeId = archetypeId;
}

public Archetype getArchetype() {
return archetype;
}
Expand All @@ -60,14 +47,6 @@ public ADL2ConversionLog getConversionLog() {
return conversionLog;
}

public void setConversionLog(ADL2ConversionLog conversionLog) {
this.conversionLog = conversionLog;
}

public void setArchetype(Archetype archetype) {
this.archetype = archetype;
}

public MessageLogger getLog() {
return log;
}
Expand All @@ -76,9 +55,12 @@ public Exception getException() {
return exception;
}

public void setException(Exception exception) {
this.exception = exception;
/* SETTERS **/
public void setArchetype(Archetype archetype) {
this.archetype = archetype;
}


public void setConversionLog(ADL2ConversionLog conversionLog) {
this.conversionLog = conversionLog;
}
}
4 changes: 2 additions & 2 deletions aom/src/main/java/com/nedap/archie/adlparser/ADLParser.java
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Expand Up @@ -8,7 +8,7 @@
import com.nedap.archie.antlr.errors.ArchieErrorListener;
import com.nedap.archie.antlr.errors.ANTLRParserErrors;
import com.nedap.archie.aom.Archetype;
import com.nedap.archie.aom.utils.ArchetypeParsePostProcesser;
import com.nedap.archie.aom.utils.ArchetypeParsePostProcessor;
import com.nedap.archie.rminfo.MetaModels;
import org.antlr.v4.runtime.CharStream;
import org.antlr.v4.runtime.*;
Expand Down Expand Up @@ -97,7 +97,7 @@ public Archetype parse(CharStream stream) throws ADLParseException {
walker.walk(listener, tree);
result = listener.getArchetype();
//set some values that are not directly in ODIN or ADL
ArchetypeParsePostProcesser.fixArchetype(result);
ArchetypeParsePostProcessor.fixArchetype(result);

if (modelConstraintImposer != null && result.getDefinition() != null) {
modelConstraintImposer.imposeConstraints(result.getDefinition());
Expand Down
4 changes: 2 additions & 2 deletions aom/src/main/java/com/nedap/archie/aom/Archetype.java
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Expand Up @@ -9,7 +9,7 @@
import com.nedap.archie.aom.terminology.ArchetypeTerminology;
import com.nedap.archie.aom.terminology.ValueSet;
import com.nedap.archie.aom.utils.AOMUtils;
import com.nedap.archie.aom.utils.ArchetypeParsePostProcesser;
import com.nedap.archie.aom.utils.ArchetypeParsePostProcessor;
import com.nedap.archie.definitions.AdlCodeDefinitions;
import com.nedap.archie.query.AOMPathQuery;
import com.nedap.archie.rminfo.RMProperty;
Expand Down Expand Up @@ -236,7 +236,7 @@ public Archetype clone() {

Archetype result = (Archetype) super.clone();
//fix some things that are not handled automatically
ArchetypeParsePostProcesser.fixArchetype(result);
ArchetypeParsePostProcessor.fixArchetype(result);
return result;

}
Expand Down
30 changes: 15 additions & 15 deletions ...om/utils/ArchetypeParsePostProcesser.java → ...om/utils/ArchetypeParsePostProcessor.java
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Expand Up @@ -16,10 +16,10 @@
/**
* Sets some values that are not directly in ADL or ODIN, such as original language in terminology, etc.
*/
public class ArchetypeParsePostProcesser {
public class ArchetypeParsePostProcessor {

public static void fixArchetype(Archetype archetype) {
if(archetype.getTerminology() != null) {
if (archetype.getTerminology() != null) {
ArchetypeTerminology terminology = archetype.getTerminology();
//codes are in model, but do not appear in odin. Set them here
fillArchetypeTermCodes(terminology.getTermDefinitions());
Expand All @@ -37,33 +37,33 @@ public static void fixArchetype(Archetype archetype) {
private static void setParents(Archetype archetype) {
Stack<CObject> workList = new Stack<>();
workList.add(archetype.getDefinition());
while(!workList.empty()) {
while (!workList.empty()) {
CObject cObject = workList.pop();
if(cObject instanceof CPrimitiveObject) {
if (cObject instanceof CPrimitiveObject) {
cObject.setNodeId("id9999");//also in the implementation, but check to be sure
}
for(CAttribute attribute:cObject.getAttributes()) {
for (CAttribute attribute : cObject.getAttributes()) {

attribute.setParent(cObject);
for(CObject child:attribute.getChildren()) {
for (CObject child : attribute.getChildren()) {
child.setParent(attribute);
}
workList.addAll(attribute.getChildren());
}
if(cObject instanceof CComplexObject) {
if (cObject instanceof CComplexObject) {
//TODO: fix tuple so it has proper multiple references to the separate structures, instead of a complete duplication of data in json
CComplexObject cComplexObject = (CComplexObject) cObject;
for(CAttributeTuple tuple: cComplexObject.getAttributeTuples()) {
for(CAttribute attribute:tuple.getMembers()) {
for (CAttributeTuple tuple : cComplexObject.getAttributeTuples()) {
for (CAttribute attribute : tuple.getMembers()) {
attribute.setSocParent(tuple);
attribute.setParent(cObject);
workList.addAll(attribute.getChildren());
cComplexObject.replaceAttribute(attribute);
}
for(CPrimitiveTuple primitiveTuple:tuple.getTuples()) {
for (CPrimitiveTuple primitiveTuple : tuple.getTuples()) {
int index = 0;
for(CPrimitiveObject<?, ?> object:primitiveTuple.getMembers()) {
if(index < tuple.getMembers().size()) {
for (CPrimitiveObject<?, ?> object : primitiveTuple.getMembers()) {
if (index < tuple.getMembers().size()) {
CAttribute attribute = tuple.getMember(index);
object.setSocParent(primitiveTuple);
object.setParent(attribute);
Expand All @@ -79,9 +79,9 @@ private static void setParents(Archetype archetype) {
}

private static void fillArchetypeTermCodes(Map<String, Map<String, ArchetypeTerm>> termSet) {
if(termSet != null) {
for(Map<String, ArchetypeTerm> language:termSet.values()) {
for(String term:language.keySet()) {
if (termSet != null) {
for (Map<String, ArchetypeTerm> language : termSet.values()) {
for (String term : language.keySet()) {
language.get(term).setCode(term);
}
}
Expand Down
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