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Add term binding validation for IANA_media-type terminology #625

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merged 7 commits into from
Sep 12, 2024
Merged

Add term binding validation for IANA_media-type terminology #625

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1ad0b42
initial setup
mathijshudepohl Aug 22, 2024
16b859c
Use same TerminologyAccess class
mathijshudepohl Aug 22, 2024
cb8e885
WIP tests
mathijshudepohl Aug 23, 2024
84e7ee8
Add id to path for reaching media_type, use code_string for check
mathijshudepohl Aug 23, 2024
1311705
Always add /code_string to path when CTerminologyCode
mathijshudepohl Aug 26, 2024
3d8ff21
Fix test
mathijshudepohl Aug 26, 2024
c52183c
Allow all characters in media type, except newlines
mathijshudepohl Sep 10, 2024
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15 changes: 12 additions & 3 deletions openehr-terminology/src/main/java/com/nedap/archie/terminology/OpenEHRTerminologyAccess.java
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Expand Up @@ -19,8 +19,10 @@

public class OpenEHRTerminologyAccess implements TerminologyAccess {

static volatile OpenEHRTerminologyAccess instance;
private static final Pattern openEHRTermIdPattern = Pattern.compile("http://openehr.org/id/(?<id>[0-9]+)");
private static final Pattern IANATermIdPattern = Pattern.compile("https://www.w3.org/ns/iana/media-types/(?<type>.+)/(?<subtype>.+)#Resource");

static volatile OpenEHRTerminologyAccess instance;
static boolean READ_FROM_JSON = true;

@JsonProperty
Expand Down Expand Up @@ -130,7 +132,15 @@
return Collections.emptyList();
}

private static final Pattern openEHRTermIdPattern = Pattern.compile("http://openehr.org/id/(?<id>[0-9]+)");
public String parseIANATerminologyURI(String uri) {
Matcher matcher = IANATermIdPattern.matcher(uri);
if(matcher.matches()) {
String type = matcher.group("type");
String subType = matcher.group("subtype");
return type + "/" + subType;
}
return null;

Check warning on line 142 in openehr-terminology/src/main/java/com/nedap/archie/terminology/OpenEHRTerminologyAccess.java

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openehr-terminology/src/main/java/com/nedap/archie/terminology/OpenEHRTerminologyAccess.java#L142 

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}

public String parseTerminologyURI(String uri) {
Matcher matcher = openEHRTermIdPattern.matcher(uri);
Expand Down Expand Up @@ -191,7 +201,6 @@
.collect(Collectors.toList());
return codes.stream().filter(c -> c.getCodeString().equalsIgnoreCase(code)).findFirst().orElse(null);
}

}


25 changes: 25 additions & 0 deletions tools/src/main/java/com/nedap/archie/rmobjectvalidator/PrimitiveObjectConstraintHelper.java
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Expand Up @@ -128,6 +128,8 @@
values = terminologyCode.getValueSetExpanded();
} else if (terminologyId.equalsIgnoreCase("openehr")) {
values = getOpenEHRValueSetExpanded(terminologyCode);
} else if (terminologyId.equalsIgnoreCase("IANA_media-types")) {
values = getIANAMediaTypesValueSetExpanded(terminologyCode);
} else {
// This is not a local nor an openehr terminology.
// If a term binding is there, we may be able to validate, if external, we wil not be able to.
Expand Down Expand Up @@ -169,6 +171,29 @@
return result;
}

private List<String> getIANAMediaTypesValueSetExpanded(CTerminologyCode terminologyCode) {
List<String> atCodes = terminologyCode.getValueSetExpanded();
ArchetypeTerminology terminology = getTerminology(terminologyCode);
OpenEHRTerminologyAccess terminologyAccess = OpenEHRTerminologyAccess.getInstance();
List<String> result = new ArrayList<>();

if(terminology == null) {
return result;

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}

for (String atCode : atCodes) {
URI termBinding = terminology.getTermBinding("IANA_media-types", atCode);
if (termBinding != null) {
String value = terminologyAccess.parseIANATerminologyURI(termBinding.toString());
if (value != null) {
result.add(value);
}
}
}

return result;
}

private ArchetypeTerminology getTerminology(CTerminologyCode cTerminologyCode) {
Archetype archetype = cTerminologyCode.getArchetype();
if(archetype != null) {
Expand Down
2 changes: 1 addition & 1 deletion tools/src/main/java/com/nedap/archie/rules/evaluation/FixableAssertionsChecker.java
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Expand Up @@ -150,7 +150,7 @@ private void handleMatches(AssertionResult assertionResult, int index, BinaryOpe
/// it would be better to check the actual type, but hasn't been done now
//this limits this to the OpenEHR RM
path = path + "/defining_code/code_string";
} else if (path.endsWith("defining_code")) {
} else {
path = path + "/code_string";
}
setPathsToValues(assertionResult, path, valueList);
Expand Down
24 changes: 24 additions & 0 deletions tools/src/test/java/com/nedap/archie/rmobjectvalidator/TerminologyCodeConstraintsTest.java
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Expand Up @@ -48,6 +48,10 @@ public void setupArchetype() {
put("openehr", new HashMap<String, URI>() {{
put("at9000", URI.create("http://openehr.org/id/532"));
}});

put("IANA_media-types", new HashMap<String, URI>() {{
put("at9001", URI.create("https://www.w3.org/ns/iana/media-types/text/plain#Resource"));
}});
}});
archetype.setTerminology(terminology);

Expand Down Expand Up @@ -115,6 +119,26 @@ public void openEHRTerminology() {
assertFalse(validationHelper.isValidValue(code, null));
}

@Test
public void IANATerminology() {
CTerminologyCode code = new CTerminologyCode();
code.setParent(new DummyRulesPrimitiveObjectParent(archetype));
code.addConstraint("at9001");
code.setConstraintStatus(ConstraintStatus.REQUIRED);

DvCodedText text = new DvCodedText();
text.setValue("does not matter for this validation");
text.setDefiningCode(new CodePhrase("[IANA_media-types::text/plain]"));
assertTrue(validationHelper.isValidValue(code, text));
text.setDefiningCode(new CodePhrase("[IANA_media-types::abc/def]"));
assertFalse(validationHelper.isValidValue(code, text));
text.setDefiningCode(new CodePhrase());
assertFalse(validationHelper.isValidValue(code, text));
text.setDefiningCode(null);
assertFalse(validationHelper.isValidValue(code, text));
assertFalse(validationHelper.isValidValue(code, null));
}

@Test
public void terminologyCodeConstraint() {
CTerminologyCode code = new CTerminologyCode();
Expand Down
25 changes: 19 additions & 6 deletions tools/src/test/java/com/nedap/archie/rules/evaluation/ParsedRulesEvaluationTest.java
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Expand Up @@ -15,6 +15,7 @@
import com.nedap.archie.rm.datastructures.Element;
import com.nedap.archie.rm.datatypes.CodePhrase;
import com.nedap.archie.rm.datavalues.DvCodedText;
import com.nedap.archie.rm.datavalues.encapsulated.DvMultimedia;
import com.nedap.archie.rm.datavalues.quantity.DvQuantity;
import com.nedap.archie.rm.support.identification.TerminologyId;
import com.nedap.archie.rminfo.ArchieRMInfoLookup;
Expand Down Expand Up @@ -818,25 +819,37 @@ public void termBindingConstraint() throws IOException, ADLParseException {
DvCodedText codedText = (DvCodedText) root.itemAtPath("items[id2]/value[id3]");
codedText.setDefiningCode(new CodePhrase(new TerminologyId("openehr"), "526"));
EvaluationResult evaluationResult = ruleEvaluation.evaluate(root, archetype.getRules().getRules());
assertEquals(2, evaluationResult.getAssertionResults().size());
assertEquals(3, evaluationResult.getAssertionResults().size());
assertTrue(evaluationResult.getAssertionResults().get(0).getResult());

codedText.setDefiningCode(new CodePhrase(new TerminologyId("openehr"), "527"));
evaluationResult = ruleEvaluation.evaluate(root, archetype.getRules().getRules());
assertEquals(2, evaluationResult.getAssertionResults().size());
assertEquals(3, evaluationResult.getAssertionResults().size());
assertFalse(evaluationResult.getAssertionResults().get(0).getResult());

// Rule with value set
DvCodedText codedText2 = (DvCodedText) root.itemAtPath("items[id4]/value[id5]");
codedText2.setDefiningCode(new CodePhrase(new TerminologyId("openehr"), "526"));
EvaluationResult evaluationResult2 = ruleEvaluation.evaluate(root, archetype.getRules().getRules());
assertEquals(2, evaluationResult2.getAssertionResults().size());
assertTrue(evaluationResult2.getAssertionResults().get(1).getResult());
evaluationResult = ruleEvaluation.evaluate(root, archetype.getRules().getRules());
assertEquals(3, evaluationResult.getAssertionResults().size());
assertTrue(evaluationResult.getAssertionResults().get(1).getResult());

codedText2.setDefiningCode(new CodePhrase(new TerminologyId("openehr"), "528"));
evaluationResult = ruleEvaluation.evaluate(root, archetype.getRules().getRules());
assertEquals(2, evaluationResult.getAssertionResults().size());
assertEquals(3, evaluationResult.getAssertionResults().size());
assertFalse(evaluationResult.getAssertionResults().get(1).getResult());

// Rule with external terminology term binding
DvMultimedia dvMultimedia = (DvMultimedia) root.itemAtPath("items[id6]/value[id7]");
dvMultimedia.setMediaType(new CodePhrase(new TerminologyId("IANA_media-types"), "image/jpeg"));
evaluationResult = ruleEvaluation.evaluate(root, archetype.getRules().getRules());
assertEquals(3, evaluationResult.getAssertionResults().size());
assertTrue(evaluationResult.getAssertionResults().get(2).getResult());

dvMultimedia.setMediaType(new CodePhrase(new TerminologyId("IANA_media-types"), "text/plain"));
evaluationResult = ruleEvaluation.evaluate(root, archetype.getRules().getRules());
assertEquals(3, evaluationResult.getAssertionResults().size());
assertFalse(evaluationResult.getAssertionResults().get(2).getResult());
}

}
10 changes: 10 additions & 0 deletions tools/src/test/resources/com/nedap/archie/rules/evaluation/matches_term_binding.adls
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Expand Up @@ -34,12 +34,18 @@ definition
DV_CODED_TEXT[id5]
}
}
ELEMENT[id6] occurrences matches {1} matches {
value matches {
DV_MULTIMEDIA[id7]
}
}
}
}

rules
/items[id2]/value/defining_code matches {[at9000]}
/items[id4]/value/defining_code matches {[ac3]}
/items[id6]/value/media_type matches {[at9008]}

terminology
term_bindings = <
Expand All @@ -53,6 +59,10 @@ terminology
["at9006"] = <http://openehr.org/id/531>
["at9007"] = <http://openehr.org/id/532>
>
["IANA_media-types"] = <
["at9008"] = <https://www.w3.org/ns/iana/media-types/image/jpeg#Resource>
["at9009"] = <https://www.w3.org/ns/iana/media-types/text/plain#Resource>
>
>
value_sets = <
["ac3"] = <
Expand Down