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Fix for path parsing in STU3 SPs (#3503)

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Tadgh 2022-03-30 08:40:17 -07:00 committed by GitHub
parent f88d2d63bd
commit 05bc208192
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8 changed files with 104 additions and 7 deletions
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4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/3469-stu3-fhirpath-validation-failure.yaml Normal file
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@ -0,0 +1,4 @@
---
type: fix
issue: 3469
title: "Previously, `or` expressions were not being properly validated in FHIRPath in STU3 due to a bug with expression path splitting. This has been corrected."

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoSearchParameterDstu3.java
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@ -64,8 +64,10 @@ public class FhirResourceDaoSearchParameterDstu3 extends BaseHapiFhirResourceDao
protected void validateResourceForStorage(SearchParameter theResource, ResourceTable theEntityToSave) {
super.validateResourceForStorage(theResource, theEntityToSave);
org.hl7.fhir.r4.model.SearchParameter resource = (org.hl7.fhir.r4.model.SearchParameter) VersionConvertorFactory_30_40.convertResource(theResource, new BaseAdvisor_30_40(false));
FhirResourceDaoSearchParameterR4.validateSearchParam(
(org.hl7.fhir.r4.model.SearchParameter) VersionConvertorFactory_30_40.convertResource(theResource, new BaseAdvisor_30_40(false)),
resource,
getContext(), getConfig(), mySearchParamRegistry, mySearchParamExtractor);
}

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoSearchParameterR4.java
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@ -174,9 +174,7 @@ public class FhirResourceDaoSearchParameterR4 extends BaseHapiFhirResourceDao<Se
}
}
}
} else {
if (!isUnique && theResource.getType() != Enumerations.SearchParamType.COMPOSITE && theResource.getType() != Enumerations.SearchParamType.SPECIAL && !REGEX_SP_EXPRESSION_HAS_PATH.matcher(expression).matches()) {
throw new UnprocessableEntityException(Msg.code(1120) + "SearchParameter.expression value \"" + expression + "\" is invalid");
}

31
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3SearchCustomSearchParamTest.java
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@ -2,6 +2,7 @@ package ca.uhn.fhir.jpa.dao.dstu3;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamToken;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.model.api.Include;
@ -53,6 +54,8 @@ import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.contains;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.hamcrest.Matchers.empty;
import static org.hamcrest.Matchers.is;
import static org.hamcrest.Matchers.notNullValue;
import static org.hamcrest.Matchers.startsWith;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.fail;
@ -87,6 +90,34 @@ public class FhirResourceDaoDstu3SearchCustomSearchParamTest extends BaseJpaDstu
}
}
@Test
public void testCreateSpWithMultiplePaths(){
SearchParameter sp = new SearchParameter();
sp.setCode("telephone-unformatted");
sp.setStatus(Enumerations.PublicationStatus.ACTIVE);
sp.setExpression("Patient.telecom.where(system='phone' or system='email')");
sp.getBase().add(new CodeType("Patient"));
sp.setType(Enumerations.SearchParamType.TOKEN);
DaoMethodOutcome daoMethodOutcome = mySearchParameterDao.create(sp);
assertThat(daoMethodOutcome.getId(), is(notNullValue()));
sp.setExpression("Patient.telecom.where(system='phone') or Patient.telecome.where(system='email')");
sp.setCode("telephone-unformatted-2");
daoMethodOutcome = mySearchParameterDao.create(sp);
assertThat(daoMethodOutcome.getId(), is(notNullValue()));
sp.setExpression("Patient.telecom.where(system='phone' or system='email') | Patient.telecome.where(system='email')");
sp.setCode("telephone-unformatted-3");
daoMethodOutcome = mySearchParameterDao.create(sp);
assertThat(daoMethodOutcome.getId(), is(notNullValue()));
sp.setExpression("Patient.telecom.where(system='phone' or system='email') | Patient.telecom.where(system='email') or Patient.telecom.where(system='mail' | system='phone')");
sp.setCode("telephone-unformatted-3");
daoMethodOutcome = mySearchParameterDao.create(sp);
assertThat(daoMethodOutcome.getId(), is(notNullValue()));
}
@Test
public void testCreateInvalidParamInvalidResourceName() {
SearchParameter fooSp = new SearchParameter();

1
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3Test.java
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@ -96,7 +96,6 @@ import java.util.Collections;
import java.util.Comparator;
import java.util.Date;
import java.util.List;
import java.util.Set;
import static org.apache.commons.lang3.StringUtils.defaultString;
import static org.hamcrest.MatcherAssert.assertThat;

47
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/BaseSearchParamExtractor.java
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@ -85,7 +85,6 @@ import java.util.Objects;
import java.util.Optional;
import java.util.Set;
import java.util.TreeSet;
import java.util.regex.Pattern;
import java.util.stream.Collectors;
import static org.apache.commons.lang3.StringUtils.isBlank;
@ -95,7 +94,6 @@ import static org.apache.commons.lang3.StringUtils.trim;
public abstract class BaseSearchParamExtractor implements ISearchParamExtractor {
public static final Set<String> COORDS_INDEX_PATHS;
private static final Pattern SPLIT = Pattern.compile("\\||( or )");
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseSearchParamExtractor.class);
static {
@ -1119,10 +1117,53 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
if (!thePaths.contains("|") && !thePaths.contains(" or ")) {
return new String[]{thePaths};
}
return SPLIT.split(thePaths);
return splitOutOfParensOrs(thePaths);
}
}
/**
* Iteratively splits a string on any ` or ` or | that is ** not** contained inside a set of parentheses. e.g.
*
* "Patient.select(a or b)" --> ["Patient.select(a or b)"]
* "Patient.select(a or b) or Patient.select(c or d )" --> ["Patient.select(a or b)", "Patient.select(c or d)"]
* "Patient.select(a|b) or Patient.select(c or d )" --> ["Patient.select(a|b)", "Patient.select(c or d)"]
* "Patient.select(b) | Patient.select(c)" --> ["Patient.select(b)", "Patient.select(c)"]
*
* @param thePaths The string to split
* @return The split string
*/
private String[] splitOutOfParensOrs(String thePaths) {
List<String> topLevelOrExpressions = splitOutOfParensToken(thePaths, " or ");
List<String> retVal = topLevelOrExpressions.stream()
.flatMap(s -> splitOutOfParensToken(s, "|").stream())
.collect(Collectors.toList());
return retVal.toArray(new String[retVal.size()]);
}
private List<String> splitOutOfParensToken(String thePath, String theToken) {
int tokenLength = theToken.length();
int index = thePath.indexOf(theToken);
int rightIndex = 0;
List<String> retVal = new ArrayList<>();
while (index > -1 ) {
String left = thePath.substring(rightIndex, index);
if (allParensHaveBeenClosed(left)) {
retVal.add(left);
rightIndex = index + tokenLength;
}
index = thePath.indexOf(theToken, index + tokenLength);
}
retVal.add(thePath.substring(rightIndex));
return retVal;
}
private boolean allParensHaveBeenClosed(String thePaths) {
int open = StringUtils.countMatches(thePaths, "(");
int close = StringUtils.countMatches(thePaths, ")");
return open == close;
}
private BigDecimal normalizeQuantityContainingTimeUnitsIntoDaysForNumberParam(String theSystem, String theCode, BigDecimal theValue) {
if (SearchParamConstants.UCUM_NS.equals(theSystem)) {
if (isNotBlank(theCode)) {

21
hapi-fhir-jpaserver-searchparam/src/test/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorDstu3Test.java
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@ -43,6 +43,9 @@ import java.util.stream.Collectors;
import java.util.stream.IntStream;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.equalTo;
import static org.hamcrest.Matchers.is;
import static org.junit.jupiter.api.Assertions.assertEquals;
public class SearchParamExtractorDstu3Test {
@ -105,6 +108,24 @@ public class SearchParamExtractorDstu3Test {
assertEquals("2", params.iterator().next().getValue().toPlainString());
}
@Test
public void testPathSplitOnSpsWorks() {
ISearchParamRegistry searchParamRegistry = new MySearchParamRegistry();
SearchParamExtractorDstu3 extractor = new SearchParamExtractorDstu3(new ModelConfig(), new PartitionSettings(), ourCtx, searchParamRegistry);
String threeSegmentPath = "Patient.telecom.where(system='phone' or system='email') | Patient.telecom.where(system='email') or Patient.telecom.where(system='mail' | system='phone')";
String[] expressions = extractor.split(threeSegmentPath);
assertThat(expressions.length, is(equalTo(3)));
assertThat(expressions[0], containsString("Patient.telecom.where(system='phone' or system='email')"));
assertThat(expressions[1], containsString("Patient.telecom.where(system='email')"));
assertThat(expressions[2], containsString("Patient.telecom.where(system='mail' | system='phone')"));
String zeroPathSplit = "Patient.telecom.where(system='phone' or system='email')";
String[] singularExpression = extractor.split(zeroPathSplit);
assertThat(singularExpression.length, is(equalTo(1)));
assertThat(singularExpression[0], containsString("Patient.telecom.where(system='phone' or system='email')"));
}
@Test
public void testEncounterDuration_NotNormalized() {

1
hapi-fhir-validation/src/test/java/org/hl7/fhir/dstu3/utils/FhirPathEngineTest.java
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@ -6,6 +6,7 @@ import ca.uhn.fhir.util.TestUtil;
import org.hl7.fhir.dstu3.hapi.ctx.HapiWorkerContext;
import org.hl7.fhir.dstu3.model.Base;
import org.hl7.fhir.dstu3.model.BooleanType;
import org.hl7.fhir.dstu3.model.ContactPoint;
import org.hl7.fhir.dstu3.model.DateTimeType;
import org.hl7.fhir.dstu3.model.Observation;
import org.hl7.fhir.dstu3.model.Patient;