Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Add support for converting CQL Tuples to FHIR Parameters #1422

Merged
merged 10 commits into from
Oct 10, 2024
Merged

Add support for converting CQL Tuples to FHIR Parameters #1422

Show file tree
Hide file tree
Changes from 5 commits
Commits
Show all changes
10 commits
Select commit Hold shift + click to select a range
eaad9e7
Adding Tuple conversion and tests
JPercival Oct 7, 2024
e8fbd41
Conversion for CQL tuples to FHIR Parameters
JPercival Oct 7, 2024
372d306
Fix types
JPercival Oct 7, 2024
2eb8c4b
Fix some mistakes on the tests. Whoops
JPercival Oct 7, 2024
f8c0cbb
Use data-absent extension
JPercival Oct 8, 2024
0951dfb
Tuple updates
JPercival Oct 10, 2024
6262d0d
Address SonarCloud warnings
JPercival Oct 10, 2024
3a07036
Added nested tuple and empty tuple handling
brynrhodes Oct 10, 2024
e5e6fd6
Nested and empty tuple tests
brynrhodes Oct 10, 2024
8f790d3
Updated formatting
JPercival Oct 10, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
31 changes: 30 additions & 1 deletion ...-fhir/src/main/java/org/opencds/cqf/cql/engine/fhir/converter/Dstu2FhirTypeConverter.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@

import java.math.BigDecimal;
import java.util.Calendar;
import java.util.Collection;
import java.util.GregorianCalendar;
import java.util.stream.Collectors;
import org.apache.commons.lang3.NotImplementedException;
Expand Down Expand Up @@ -227,7 +228,35 @@ public IBase toFhirTuple(Tuple value) {
return null;
}

throw new NotImplementedException("can't convert Tuples");
var parameters = new Parameters();
if (value.getElements().isEmpty()) {
return parameters;
}

var param = parameters.addParameter();
for (String key : value.getElements().keySet()) {
var part = param.addPart();
part.setName(key);
var element = value.getElements().get(key);
if (element == null) {
part.addExtension()
JPercival marked this conversation as resolved.
Show resolved Hide resolved
.setUrl(DATA_ABSENT_REASON_EXT_URL)
.setValue(new CodeType(DATA_ABSENT_REASON_UNKNOWN_CODE));
} else if (element instanceof Collection && ((Collection<?>) element).isEmpty()) {
part.addExtension().setUrl(EMPTY_LIST_EXT_URL).setValue(new BooleanType(true));
JPercival marked this conversation as resolved.
Show resolved Hide resolved
} else {
var result = toFhirType(element);
JPercival marked this conversation as resolved.
Show resolved Hide resolved
if (result instanceof Resource) {
part.setResource((Resource) result);
} else if (result instanceof Type) {
part.setValue((Type) result);
} else {
throw new IllegalArgumentException("Tuple contains unsupported type");
}
}
}

return parameters;
}

@Override
Expand Down
31 changes: 30 additions & 1 deletion ...-fhir/src/main/java/org/opencds/cqf/cql/engine/fhir/converter/Dstu3FhirTypeConverter.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@

import java.math.BigDecimal;
import java.time.format.DateTimeFormatter;
import java.util.Collection;
import java.util.stream.Collectors;
import org.apache.commons.lang3.NotImplementedException;
import org.hl7.fhir.dstu3.model.*;
Expand Down Expand Up @@ -226,7 +227,35 @@ public IBase toFhirTuple(Tuple value) {
return null;
}

throw new NotImplementedException("can't convert Tuples");
var parameters = new Parameters();
if (value.getElements().isEmpty()) {
return parameters;
}

var param = parameters.addParameter();
for (String key : value.getElements().keySet()) {
var part = param.addPart();
part.setName(key);
var element = value.getElements().get(key);
if (element == null) {
part.addExtension()
.setUrl(DATA_ABSENT_REASON_EXT_URL)
.setValue(new CodeType(DATA_ABSENT_REASON_UNKNOWN_CODE));
} else if (element instanceof Collection && ((Collection<?>) element).isEmpty()) {
part.addExtension().setUrl(EMPTY_LIST_EXT_URL).setValue(new BooleanType(true));
} else {
var result = toFhirType(element);
if (result instanceof Resource) {
part.setResource((Resource) result);
} else if (result instanceof Type) {
part.setValue((Type) result);
} else {
throw new IllegalArgumentException("Tuple contains unsupported type");
}
}
}

return parameters;
}

@Override
Expand Down
4 changes: 4 additions & 0 deletions ...ngine-fhir/src/main/java/org/opencds/cqf/cql/engine/fhir/converter/FhirTypeConverter.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,10 @@
*/
public interface FhirTypeConverter {

static final String EMPTY_LIST_EXT_URL = "http://hl7.org/fhir/StructureDefinition/cqf-isEmptyList";
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";

// CQL-to-FHIR conversions

/**
Expand Down
31 changes: 30 additions & 1 deletion ...ine-fhir/src/main/java/org/opencds/cqf/cql/engine/fhir/converter/R4FhirTypeConverter.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@

import java.math.BigDecimal;
import java.time.format.DateTimeFormatter;
import java.util.Collection;
import java.util.stream.Collectors;
import org.apache.commons.lang3.NotImplementedException;
import org.hl7.fhir.instance.model.api.IBase;
Expand Down Expand Up @@ -218,7 +219,35 @@ public IBase toFhirTuple(Tuple value) {
return null;
}

throw new NotImplementedException("can't convert Tuples");
var parameters = new Parameters();
if (value.getElements().isEmpty()) {
return parameters;
}

var param = parameters.addParameter();
for (String key : value.getElements().keySet()) {
var part = param.addPart();
part.setName(key);
var element = value.getElements().get(key);
if (element == null) {
part.addExtension()
.setUrl(DATA_ABSENT_REASON_EXT_URL)
.setValue(new CodeType(DATA_ABSENT_REASON_UNKNOWN_CODE));
} else if (element instanceof Collection && ((Collection<?>) element).isEmpty()) {
part.addExtension().setUrl(EMPTY_LIST_EXT_URL).setValue(new BooleanType(true));
} else {
var result = toFhirType(element);
if (result instanceof Resource) {
part.setResource((Resource) result);
} else if (result instanceof Type) {
part.setValue((Type) result);
} else {
throw new IllegalArgumentException("Tuple contains unsupported type");
}
}
}

return parameters;
}

@Override
Expand Down
31 changes: 30 additions & 1 deletion ...ine-fhir/src/main/java/org/opencds/cqf/cql/engine/fhir/converter/R5FhirTypeConverter.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@

import java.math.BigDecimal;
import java.time.format.DateTimeFormatter;
import java.util.Collection;
import java.util.stream.Collectors;
import org.apache.commons.lang3.NotImplementedException;
import org.hl7.fhir.instance.model.api.IBase;
Expand Down Expand Up @@ -218,7 +219,35 @@ public IBase toFhirTuple(Tuple value) {
return null;
}

throw new NotImplementedException("can't convert Tuples");
var parameters = new Parameters();
if (value.getElements().isEmpty()) {
return parameters;
}

var param = parameters.addParameter();
for (String key : value.getElements().keySet()) {
var part = param.addPart();
part.setName(key);
var element = value.getElements().get(key);
if (element == null) {
part.addExtension()
.setUrl(DATA_ABSENT_REASON_EXT_URL)
.setValue(new CodeType(DATA_ABSENT_REASON_UNKNOWN_CODE));
} else if (element instanceof Collection && ((Collection<?>) element).isEmpty()) {
part.addExtension().setUrl(EMPTY_LIST_EXT_URL).setValue(new BooleanType(true));
} else {
var result = toFhirType(element);
if (result instanceof Resource) {
part.setResource((Resource) result);
} else if (result instanceof DataType) {
part.setValue((DataType) result);
} else {
throw new IllegalArgumentException("Tuple contains unsupported type");
}
}
}

return parameters;
}

@Override
Expand Down
50 changes: 44 additions & 6 deletions ...fhir/src/test/java/org/opencds/cqf/cql/engine/fhir/converter/Dstu2TypeConverterTests.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@

import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.instanceOf;
import static org.junit.Assert.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertNull;
Expand All @@ -27,9 +28,12 @@
import org.hl7.fhir.dstu2.model.DateTimeType;
import org.hl7.fhir.dstu2.model.DateType;
import org.hl7.fhir.dstu2.model.DecimalType;
import org.hl7.fhir.dstu2.model.Encounter;
import org.hl7.fhir.dstu2.model.IdType;
import org.hl7.fhir.dstu2.model.InstantType;
import org.hl7.fhir.dstu2.model.IntegerType;
import org.hl7.fhir.dstu2.model.Parameters;
import org.hl7.fhir.dstu2.model.Parameters.ParametersParameterComponent;
import org.hl7.fhir.dstu2.model.Patient;
import org.hl7.fhir.dstu2.model.Period;
import org.hl7.fhir.dstu2.model.Range;
Expand Down Expand Up @@ -67,7 +71,7 @@ protected Boolean compareIterables(Iterable<Object> left, Iterable<Object> right
return !leftIterator.hasNext() && !rightIterator.hasNext();
}

@SuppressWarnings("unchecked")
@SuppressWarnings({"unchecked", "null"})
protected Boolean compareObjects(Object left, Object right) {
if (left == null ^ right == null) {
return false;
Expand Down Expand Up @@ -522,15 +526,49 @@ void invalidIntervalToFhirInterval() {
});
}

private static ParametersParameterComponent getPartByName(ParametersParameterComponent ppc, String name) {
return ppc.getPart().stream()
.filter(p -> p.getName().equals(name))
.findFirst()
.get();
}

@Test
void tupleToFhirTuple() {
IBase expected = typeConverter.toFhirTuple(null);
assertNull(expected);
Parameters actual = (Parameters) typeConverter.toFhirTuple(null);
assertNull(actual);

var tuple = new Tuple();
assertThrows(NotImplementedException.class, () -> {
typeConverter.toFhirTuple(tuple);
});
actual = (Parameters) typeConverter.toFhirTuple(tuple);
assertNotNull(actual);
assertTrue(actual.isEmpty());

tuple.getElements().put("W", null);
tuple.getElements().put("X", 5);
tuple.getElements().put("Y", new Encounter().setId("123"));
tuple.getElements().put("Z", new ArrayList<>());

actual = (Parameters) typeConverter.toFhirTuple(tuple);
assertNotNull(actual);
assertEquals(1, actual.getParameter().size());

var first = actual.getParameter().get(0);
assertEquals(4, first.getPart().size());

var w = getPartByName(first, "W");
assertEquals(
FhirTypeConverter.DATA_ABSENT_REASON_EXT_URL,
w.getExtension().get(0).getUrl());

var x = getPartByName(first, "X");
assertEquals(5, ((IntegerType) x.getValue()).getValue());

var y = getPartByName(first, "Y");
assertEquals("123", y.getResource().getId());

var z = getPartByName(first, "Z");
assertEquals(
FhirTypeConverter.EMPTY_LIST_EXT_URL, z.getExtension().get(0).getUrl());
}

// FHIR-to-CQL
Expand Down
50 changes: 44 additions & 6 deletions ...fhir/src/test/java/org/opencds/cqf/cql/engine/fhir/converter/Dstu3TypeConverterTests.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@
import static org.hamcrest.Matchers.instanceOf;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertNull;
import static org.junit.jupiter.api.Assertions.assertThrows;
import static org.junit.jupiter.api.Assertions.assertTrue;
Expand All @@ -27,9 +28,12 @@
import org.hl7.fhir.dstu3.model.DateTimeType;
import org.hl7.fhir.dstu3.model.DateType;
import org.hl7.fhir.dstu3.model.DecimalType;
import org.hl7.fhir.dstu3.model.Encounter;
import org.hl7.fhir.dstu3.model.IdType;
import org.hl7.fhir.dstu3.model.InstantType;
import org.hl7.fhir.dstu3.model.IntegerType;
import org.hl7.fhir.dstu3.model.Parameters;
import org.hl7.fhir.dstu3.model.Parameters.ParametersParameterComponent;
import org.hl7.fhir.dstu3.model.Patient;
import org.hl7.fhir.dstu3.model.Period;
import org.hl7.fhir.dstu3.model.Range;
Expand Down Expand Up @@ -67,7 +71,7 @@ protected Boolean compareIterables(Iterable<Object> left, Iterable<Object> right
return !leftIterator.hasNext() && !rightIterator.hasNext();
}

@SuppressWarnings("unchecked")
@SuppressWarnings({"unchecked", "null"})
protected Boolean compareObjects(Object left, Object right) {
if (left == null ^ right == null) {
return false;
Expand Down Expand Up @@ -526,15 +530,49 @@ void invalidIntervalToFhirInterval() {
});
}

private static ParametersParameterComponent getPartByName(ParametersParameterComponent ppc, String name) {
return ppc.getPart().stream()
.filter(p -> p.getName().equals(name))
.findFirst()
.get();
}

@Test
void tupleToFhirTuple() {
IBase expected = typeConverter.toFhirTuple(null);
assertNull(expected);
Parameters actual = (Parameters) typeConverter.toFhirTuple(null);
assertNull(actual);

var tuple = new Tuple();
assertThrows(NotImplementedException.class, () -> {
typeConverter.toFhirTuple(tuple);
});
actual = (Parameters) typeConverter.toFhirTuple(tuple);
assertNotNull(actual);
assertTrue(actual.isEmpty());

tuple.getElements().put("W", null);
tuple.getElements().put("X", 5);
tuple.getElements().put("Y", new Encounter().setId("123"));
tuple.getElements().put("Z", new ArrayList<>());

actual = (Parameters) typeConverter.toFhirTuple(tuple);
assertNotNull(actual);
assertEquals(1, actual.getParameter().size());

var first = actual.getParameterFirstRep();
assertEquals(4, first.getPart().size());

var w = getPartByName(first, "W");
assertEquals(
FhirTypeConverter.DATA_ABSENT_REASON_EXT_URL,
w.getExtension().get(0).getUrl());

var x = getPartByName(first, "X");
assertEquals(5, ((IntegerType) x.getValue()).getValue());

var y = getPartByName(first, "Y");
assertEquals("123", y.getResource().getId());

var z = getPartByName(first, "Z");
assertEquals(
FhirTypeConverter.EMPTY_LIST_EXT_URL, z.getExtension().get(0).getUrl());
}

// FHIR-to-CQL
Expand Down
Loading
Loading