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Add support for converting CQL Tuples to FHIR Parameters (#1422)
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* Adding Tuple conversion and tests

* Conversion for CQL tuples to FHIR Parameters

* Fix types

* Fix some mistakes on the tests. Whoops

* Use data-absent extension

* Tuple updates

* Address SonarCloud warnings

* Added nested tuple and empty tuple handling

* Nested and empty tuple tests

* Updated formatting

---------

Co-authored-by: Bryn Rhodes <[email protected]>
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@JPercival @brynrhodes
JPercival and brynrhodes authored Oct 10, 2024
1 parent 4e3be26 commit b50ea52
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Showing 10 changed files with 700 additions and 32 deletions.
2 changes: 1 addition & 1 deletion ...e-fhir/src/main/java/org/opencds/cqf/cql/engine/fhir/converter/BaseFhirTypeConverter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,7 @@ public boolean isFhirType(Object value) {
}

@Override
public Iterable<Object> toFhirTypes(Iterable<?> values) {
public List<Object> toFhirTypes(Iterable<?> values) {
List<Object> converted = new ArrayList<>();
for (Object value : values) {
if (value == null) {
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75 changes: 74 additions & 1 deletion ...-fhir/src/main/java/org/opencds/cqf/cql/engine/fhir/converter/Dstu2FhirTypeConverter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -221,13 +221,86 @@ public ICompositeType toFhirRange(Interval value) {
return range;
}

private static BooleanType emptyBooleanWithExtension(String url, Type value) {
var result = new BooleanType((String) null);
result.addExtension().setUrl(url).setValue(value);
return result;
}

private static void addPartWithNameAndValue(
Parameters.ParametersParameterComponent param, String key, Object value) {
if (value instanceof Parameters.ParametersParameterComponent) {
var part = (Parameters.ParametersParameterComponent) value;
part.setName(key);
param.addPart(part);
} else {
var part = param.addPart().setName(key);
if (value instanceof Resource) {
part.setResource((Resource) value);
} else if (value instanceof Type) {
part.setValue((Type) value);
} else {
throw new IllegalArgumentException(
"Unsupported FHIR type: " + value.getClass().getName());
}
}
}

private static Iterable<?> asIterable(Object value) {
if (value instanceof Iterable) {
return (Iterable<?>) value;
} else {
return null;
}
}

private void addElementToParameter(Parameters.ParametersParameterComponent param, String key, Object value) {
if (value == null) {
// Null value, add a single empty value with an extension indicating the reason
var dataAbsentValue = emptyBooleanWithExtension(
DATA_ABSENT_REASON_EXT_URL, new CodeType(DATA_ABSENT_REASON_UNKNOWN_CODE));
addPartWithNameAndValue(param, key, dataAbsentValue);
return;
}

var iterable = asIterable(value);
if (iterable == null) {
// Single, non-null value
addPartWithNameAndValue(param, key, toFhirType(value));
return;
}

if (!iterable.iterator().hasNext()) {
// Empty list
var emptyListValue = emptyBooleanWithExtension(EMPTY_LIST_EXT_URL, new BooleanType(true));
addPartWithNameAndValue(param, key, emptyListValue);
} else {
// Non-empty list, one part per value
var fhirTypes = this.toFhirTypes(iterable);
for (var fhirType : fhirTypes) {
addPartWithNameAndValue(param, key, fhirType);
}
}
}

@Override
public IBase toFhirTuple(Tuple value) {
if (value == null) {
return null;
}

throw new NotImplementedException("can't convert Tuples");
var parameters = new Parameters();
var param = parameters.addParameter();

if (value.getElements().isEmpty()) {
param.setValue(emptyBooleanWithExtension(EMPTY_TUPLE_EXT_URL, new BooleanType(true)));
}

for (String key : value.getElements().keySet()) {
addElementToParameter(param, key, value.getElements().get(key));
}

return param;
}

@Override
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75 changes: 74 additions & 1 deletion ...-fhir/src/main/java/org/opencds/cqf/cql/engine/fhir/converter/Dstu3FhirTypeConverter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -220,13 +220,86 @@ public ICompositeType toFhirRange(Interval value) {
return range;
}

private static BooleanType emptyBooleanWithExtension(String url, Type value) {
var result = new BooleanType((String) null);
result.addExtension().setUrl(url).setValue(value);
return result;
}

private static void addPartWithNameAndValue(
Parameters.ParametersParameterComponent param, String key, Object value) {
if (value instanceof Parameters.ParametersParameterComponent) {
var part = (Parameters.ParametersParameterComponent) value;
part.setName(key);
param.addPart(part);
} else {
var part = param.addPart().setName(key);
if (value instanceof Resource) {
part.setResource((Resource) value);
} else if (value instanceof Type) {
part.setValue((Type) value);
} else {
throw new IllegalArgumentException(
"Unsupported FHIR type: " + value.getClass().getName());
}
}
}

private static Iterable<?> asIterable(Object value) {
if (value instanceof Iterable) {
return (Iterable<?>) value;
} else {
return null;
}
}

private void addElementToParameter(Parameters.ParametersParameterComponent param, String key, Object value) {
if (value == null) {
// Null value, add a single empty value with an extension indicating the reason
var dataAbsentValue = emptyBooleanWithExtension(
DATA_ABSENT_REASON_EXT_URL, new CodeType(DATA_ABSENT_REASON_UNKNOWN_CODE));
addPartWithNameAndValue(param, key, dataAbsentValue);
return;
}

var iterable = asIterable(value);
if (iterable == null) {
// Single, non-null value
addPartWithNameAndValue(param, key, toFhirType(value));
return;
}

if (!iterable.iterator().hasNext()) {
// Empty list
var emptyListValue = emptyBooleanWithExtension(EMPTY_LIST_EXT_URL, new BooleanType(true));
addPartWithNameAndValue(param, key, emptyListValue);
} else {
// Non-empty list, one part per value
var fhirTypes = this.toFhirTypes(iterable);
for (var fhirType : fhirTypes) {
addPartWithNameAndValue(param, key, fhirType);
}
}
}

@Override
public IBase toFhirTuple(Tuple value) {
if (value == null) {
return null;
}

throw new NotImplementedException("can't convert Tuples");
var parameters = new Parameters();
var param = parameters.addParameter();

if (value.getElements().isEmpty()) {
param.setValue(emptyBooleanWithExtension(EMPTY_TUPLE_EXT_URL, new BooleanType(true)));
}

for (String key : value.getElements().keySet()) {
addElementToParameter(param, key, value.getElements().get(key));
}

return param;
}

@Override
Expand Down
11 changes: 9 additions & 2 deletions ...ngine-fhir/src/main/java/org/opencds/cqf/cql/engine/fhir/converter/FhirTypeConverter.java
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
package org.opencds.cqf.cql.engine.fhir.converter;

import java.math.BigDecimal;
import java.util.List;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseCoding;
import org.hl7.fhir.instance.model.api.ICompositeType;
Expand Down Expand Up @@ -28,6 +29,12 @@
*/
public interface FhirTypeConverter {

static final String EMPTY_LIST_EXT_URL = "http://hl7.org/fhir/StructureDefinition/cqf-isEmptyList";
static final String EMPTY_TUPLE_EXT_URL = "http://hl7.org/fhir/StructureDefinition/cqf-isEmptyTuple";
static final String DATA_ABSENT_REASON_EXT_URL = "http://hl7.org/fhir/StructureDefinition/data-absent-reason";
static final String DATA_ABSENT_REASON_UNKNOWN_CODE = "unknown";
static final String CQL_TYPE_EXT_URL = "http://hl7.org/fhir/StructureDefinition/cqf-cqlType";

// CQL-to-FHIR conversions

/**
Expand All @@ -53,9 +60,9 @@ public interface FhirTypeConverter {
* nulls, and sublist hierarchy
*
* @param values an Iterable containing CQL structures, nulls, or sublists
* @return an Iterable containing FHIR types, nulls, and sublists
* @return an List containing FHIR types, nulls, and sublists
*/
public Iterable<Object> toFhirTypes(Iterable<?> values);
public List<Object> toFhirTypes(Iterable<?> values);

/**
* Converts a String to a FHIR Id
Expand Down
78 changes: 76 additions & 2 deletions ...ine-fhir/src/main/java/org/opencds/cqf/cql/engine/fhir/converter/R4FhirTypeConverter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -179,7 +179,8 @@ public ICompositeType toFhirPeriod(Interval value) {

return period;
} else if (getSimpleName(value.getPointType().getTypeName()).equals("Date")) {
// TODO: This will construct DateTimeType values in FHIR with the system timezone id, not the
// TODO: This will construct DateTimeType values in FHIR with the system
// timezone id, not the
// timezoneoffset of the evaluation request..... this is a bug waiting to happen
if (value.getStart() != null) {
period.setStart(toFhirDate((Date) value.getStart()).getValue());
Expand Down Expand Up @@ -212,13 +213,86 @@ public ICompositeType toFhirRange(Interval value) {
return range;
}

private static BooleanType emptyBooleanWithExtension(String url, Type value) {
var result = new BooleanType((String) null);
result.addExtension().setUrl(url).setValue(value);
return result;
}

private static void addPartWithNameAndValue(
Parameters.ParametersParameterComponent param, String key, Object value) {
if (value instanceof Parameters.ParametersParameterComponent) {
var part = (Parameters.ParametersParameterComponent) value;
part.setName(key);
param.addPart(part);
} else {
var part = param.addPart().setName(key);
if (value instanceof Resource) {
part.setResource((Resource) value);
} else if (value instanceof Type) {
part.setValue((Type) value);
} else {
throw new IllegalArgumentException(
"Unsupported FHIR type: " + value.getClass().getName());
}
}
}

private static Iterable<?> asIterable(Object value) {
if (value instanceof Iterable) {
return (Iterable<?>) value;
} else {
return null;
}
}

private void addElementToParameter(Parameters.ParametersParameterComponent param, String key, Object value) {
if (value == null) {
// Null value, add a single empty value with an extension indicating the reason
var dataAbsentValue = emptyBooleanWithExtension(
DATA_ABSENT_REASON_EXT_URL, new CodeType(DATA_ABSENT_REASON_UNKNOWN_CODE));
addPartWithNameAndValue(param, key, dataAbsentValue);
return;
}

var iterable = asIterable(value);
if (iterable == null) {
// Single, non-null value
addPartWithNameAndValue(param, key, toFhirType(value));
return;
}

if (!iterable.iterator().hasNext()) {
// Empty list
var emptyListValue = emptyBooleanWithExtension(EMPTY_LIST_EXT_URL, new BooleanType(true));
addPartWithNameAndValue(param, key, emptyListValue);
} else {
// Non-empty list, one part per value
var fhirTypes = this.toFhirTypes(iterable);
for (var fhirType : fhirTypes) {
addPartWithNameAndValue(param, key, fhirType);
}
}
}

@Override
public IBase toFhirTuple(Tuple value) {
if (value == null) {
return null;
}

throw new NotImplementedException("can't convert Tuples");
var parameters = new Parameters();
var param = parameters.addParameter();

if (value.getElements().isEmpty()) {
param.setValue(emptyBooleanWithExtension(EMPTY_TUPLE_EXT_URL, new BooleanType(true)));
}

for (String key : value.getElements().keySet()) {
addElementToParameter(param, key, value.getElements().get(key));
}

return param;
}

@Override
Expand Down
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