honeymoose
/
hapi-fhir
mirror of https://github.com/hapifhir/hapi-fhir.git
1
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity

3242 search content param removed not readded (#3244) 

* 3242 initial changes and nonsense tests

* 3242 added changelog

* 3242 cleanup

* cleanup

* 3242 updated for review

* cleanup

* 3242 review fixes

* review fixes

* fix changelog file

* review fixes

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
This commit is contained in:
TipzCM 2022-01-04 14:38:52 -05:00 committed by GitHub
parent aafc42fdd8
commit b148121ab3
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
7 changed files with 226 additions and 11 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_0/3242-fix-bug-that-mutates-searchparam-map.yaml Normal file
View File

@ -0,0 +1,5 @@
---
issue: 3242
type: fix
title: "Fixed bug that caused queries that checked Elasticsearch when setting `_total=accurate` searches to return all
values when using _content or _text parameters"

14
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FulltextSearchSvcImpl.java
View File

@ -100,15 +100,12 @@ public class FulltextSearchSvcImpl implements IFulltextSearchSvc {
return requiresHibernateSearchAccess;
}
private List<ResourcePersistentId> doSearch(String theResourceType, SearchParameterMap theParams, ResourcePersistentId theReferencingPid) {
// keep this in sync with supportsSomeOf();
SearchSession session = Search.session(myEntityManager);
List<Long> longPids = session.search(ResourceTable.class)
//Selects are replacements for projection and convert more cleanly than the old implementation.
// Selects are replacements for projection and convert more cleanly than the old implementation.
.select(
f -> f.field("myId", Long.class)
)
@ -118,11 +115,20 @@ public class FulltextSearchSvcImpl implements IFulltextSearchSvc {
/*
* Handle _content parameter (resource body content)
*
* Posterity:
* We do not want the HAPI-FHIR dao's to process the
* _content parameter, so we remove it from the map here
*/
List<List<IQueryParameterType>> contentAndTerms = theParams.remove(Constants.PARAM_CONTENT);
builder.addStringTextSearch(Constants.PARAM_CONTENT, contentAndTerms);
/*
* Handle _text parameter (resource narrative content)
*
* Positerity:
* We do not want the HAPI-FHIR dao's to process the
* _text parameter, so we remove it from the map here
*/
List<List<IQueryParameterType>> textAndTerms = theParams.remove(Constants.PARAM_TEXT);
builder.addStringTextSearch(Constants.PARAM_TEXT, textAndTerms);

26
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImpl.java
View File

@ -89,14 +89,12 @@ import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.annotation.Propagation;
import org.springframework.transaction.annotation.Transactional;
import org.springframework.transaction.support.TransactionCallbackWithoutResult;
import org.springframework.transaction.support.TransactionSynchronizationManager;
import org.springframework.transaction.support.TransactionTemplate;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import javax.annotation.PostConstruct;
import javax.persistence.EntityManager;
import javax.validation.constraints.NotNull;
import java.io.IOException;
import java.time.Instant;
import java.time.temporal.ChronoUnit;
@ -1059,7 +1057,6 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
* search, and starts it.
*/
private void doSearch() {
/*
* If the user has explicitly requested a _count, perform a
*
@ -1072,7 +1069,17 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
if (wantCount) {
ourLog.trace("Performing count");
ISearchBuilder sb = newSearchBuilder();
Iterator<Long> countIterator = sb.createCountQuery(myParams, mySearch.getUuid(), myRequest, myRequestPartitionId);
/*
* createCountQuery
* NB: (see createQuery below)
* Because FulltextSearchSvcImpl will (internally)
* mutate the myParams (searchmap),
* (specifically removing the _content and _text filters)
* we will have to clone those parameters here so that
* the "correct" params are used in createQuery below
*/
Iterator<Long> countIterator = sb.createCountQuery(myParams.clone(), mySearch.getUuid(), myRequest, myRequestPartitionId);
Long count = countIterator.hasNext() ? countIterator.next() : 0L;
ourLog.trace("Got count {}", count);
@ -1146,7 +1153,18 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
}
/*
* createQuery
* Construct the SQL query we'll be sending to the database
*
* NB: (See createCountQuery above)
* We will pass the original myParams here (not a copy)
* because we actually _want_ the mutation of the myParams to happen.
* Specifically because SearchBuilder itself will _expect_
* not to have these parameters when dumping back
* to our DB.
*
* This is an odd implementation behaviour, but the change
* for this will require a lot more handling at higher levels
*/
try (IResultIterator resultIterator = sb.createQuery(myParams, mySearchRuntimeDetails, myRequest, myRequestPartitionId)) {
assert (resultIterator != null);

74
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirSearchDaoR4Test.java
View File

@ -3,12 +3,15 @@ package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.SearchTotalModeEnum;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.param.StringAndListParam;
import ca.uhn.fhir.rest.param.StringOrListParam;
import ca.uhn.fhir.rest.param.StringParam;
import org.hl7.fhir.r4.model.Organization;
import org.hl7.fhir.r4.model.Patient;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.dao.InvalidDataAccessApiUsageException;
@ -37,6 +40,62 @@ public class FhirSearchDaoR4Test extends BaseJpaR4Test {
assert !TransactionSynchronizationManager.isActualTransactionActive();
}
@Test
public void testSearchReturnsExpectedPatientsWhenContentTypeUsed() {
// setup
String content = "yui";
Long id1;
{
Patient patient = new Patient();
patient.addName().addGiven(content).setFamily("hirasawa");
id1 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless().getIdPartAsLong();
}
Long id2;
{
Patient patient = new Patient();
patient.addName().addGiven("mio").setFamily("akiyama");
id2 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless().getIdPartAsLong();
}
SearchParameterMap params = new SearchParameterMap();
params.add("_content", new StringParam(content));
// test
List<ResourcePersistentId> ids = mySearchDao.search("Patient",
params);
// verify results
Assertions.assertEquals(1, ids.size());
Assertions.assertEquals(id1, ids.get(0).getIdAsLong());
}
@Test
public void testSearchesWithAccurateCountReturnOnlyExpectedResults() {
// create 2 patients
Patient patient = new Patient();
patient.addName().setFamily("hirasawa");
myPatientDao.create(patient);
Patient patient2 = new Patient();
patient2.addName().setFamily("akiyama");
myPatientDao.create(patient2);
// construct searchmap with Accurate search mode
SearchParameterMap map = new SearchParameterMap();
map.add(Constants.PARAM_CONTENT, new StringParam("hirasawa"));
map.setSearchTotalMode(SearchTotalModeEnum.ACCURATE);
// test
IBundleProvider ret = myPatientDao.search(map);
// only one should be returned
Assertions.assertEquals(1, ret.size());
Patient retPatient = (Patient) ret.getAllResources().get(0);
Assertions.assertEquals(patient.getName().get(0).getFamily(),
retPatient.getName().get(0).getFamily());
}
@Test
public void testContentSearch() {
Long id1;
@ -64,7 +123,7 @@ public class FhirSearchDaoR4Test extends BaseJpaR4Test {
id3 = myOrganizationDao.create(org, mySrd).getId().toUnqualifiedVersionless().getIdPartAsLong();
}
SearchParameterMap map = new SearchParameterMap();
SearchParameterMap map;
String resourceName = "Patient";
// One term
@ -72,6 +131,7 @@ public class FhirSearchDaoR4Test extends BaseJpaR4Test {
StringAndListParam content = new StringAndListParam();
content.addAnd(new StringOrListParam().addOr(new StringParam("AAAS")));
map = new SearchParameterMap();
map.add(Constants.PARAM_CONTENT, content);
List<ResourcePersistentId> found = mySearchDao.search(resourceName, map);
assertThat(ResourcePersistentId.toLongList(found), containsInAnyOrder(id1));
@ -81,6 +141,8 @@ public class FhirSearchDaoR4Test extends BaseJpaR4Test {
StringAndListParam content = new StringAndListParam();
content.addAnd(new StringOrListParam().addOr(new StringParam("AAAS")).addOr(new StringParam("AAAB")));
map = new SearchParameterMap();
map.add(Constants.PARAM_CONTENT, content);
map.add(Constants.PARAM_CONTENT, content);
List<ResourcePersistentId> found = mySearchDao.search(resourceName, map);
assertThat(ResourcePersistentId.toLongList(found), containsInAnyOrder(id1, id2));
@ -91,6 +153,7 @@ public class FhirSearchDaoR4Test extends BaseJpaR4Test {
content.addAnd(new StringOrListParam().addOr(new StringParam("AAAS")));
content.addAnd(new StringOrListParam().addOr(new StringParam("CCC")));
map = new SearchParameterMap();
map.add(Constants.PARAM_CONTENT, content);
List<ResourcePersistentId> found = mySearchDao.search(resourceName, map);
assertThat(ResourcePersistentId.toLongList(found), containsInAnyOrder(id1));
@ -101,6 +164,7 @@ public class FhirSearchDaoR4Test extends BaseJpaR4Test {
content.addAnd(new StringOrListParam().addOr(new StringParam("AAAB")).addOr(new StringParam("AAAS")));
content.addAnd(new StringOrListParam().addOr(new StringParam("CCC")));
map = new SearchParameterMap();
map.add(Constants.PARAM_CONTENT, content);
List<ResourcePersistentId> found = mySearchDao.search(resourceName, map);
assertThat(ResourcePersistentId.toLongList(found), containsInAnyOrder(id1, id2));
@ -110,6 +174,7 @@ public class FhirSearchDaoR4Test extends BaseJpaR4Test {
StringAndListParam content = new StringAndListParam();
content.addAnd(new StringOrListParam().addOr(new StringParam("CCC")).addOr(new StringParam("DDD")));
map = new SearchParameterMap();
map.add(Constants.PARAM_CONTENT, content);
List<ResourcePersistentId> found = mySearchDao.search(null, map);
assertThat(ResourcePersistentId.toLongList(found), containsInAnyOrder(id1, id2, id3));
@ -137,7 +202,7 @@ public class FhirSearchDaoR4Test extends BaseJpaR4Test {
myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless().getIdPartAsLong();
}
SearchParameterMap map = new SearchParameterMap();
SearchParameterMap map;
String resourceName = "Patient";
// One term
@ -145,6 +210,7 @@ public class FhirSearchDaoR4Test extends BaseJpaR4Test {
StringAndListParam content = new StringAndListParam();
content.addAnd(new StringOrListParam().addOr(new StringParam("AAAS")));
map = new SearchParameterMap();
map.add(Constants.PARAM_TEXT, content);
List<ResourcePersistentId> found = mySearchDao.search(resourceName, map);
assertThat(ResourcePersistentId.toLongList(found), containsInAnyOrder(id1));
@ -154,6 +220,7 @@ public class FhirSearchDaoR4Test extends BaseJpaR4Test {
StringAndListParam content = new StringAndListParam();
content.addAnd(new StringOrListParam().addOr(new StringParam("AAAS")).addOr(new StringParam("AAAB")));
map = new SearchParameterMap();
map.add(Constants.PARAM_TEXT, content);
List<ResourcePersistentId> found = mySearchDao.search(resourceName, map);
assertThat(ResourcePersistentId.toLongList(found), containsInAnyOrder(id1, id2));
@ -164,6 +231,7 @@ public class FhirSearchDaoR4Test extends BaseJpaR4Test {
content.addAnd(new StringOrListParam().addOr(new StringParam("AAAS")));
content.addAnd(new StringOrListParam().addOr(new StringParam("CCC")));
map = new SearchParameterMap();
map.add(Constants.PARAM_TEXT, content);
List<ResourcePersistentId> found = mySearchDao.search(resourceName, map);
assertThat(ResourcePersistentId.toLongList(found), containsInAnyOrder(id1));
@ -174,6 +242,7 @@ public class FhirSearchDaoR4Test extends BaseJpaR4Test {
content.addAnd(new StringOrListParam().addOr(new StringParam("AAAB")).addOr(new StringParam("AAAS")));
content.addAnd(new StringOrListParam().addOr(new StringParam("CCC")));
map = new SearchParameterMap();
map.add(Constants.PARAM_TEXT, content);
List<ResourcePersistentId> found = mySearchDao.search(resourceName, map);
assertThat(ResourcePersistentId.toLongList(found), containsInAnyOrder(id1, id2));
@ -183,6 +252,7 @@ public class FhirSearchDaoR4Test extends BaseJpaR4Test {
StringAndListParam content = new StringAndListParam();
content.addAnd(new StringOrListParam().addOr(new StringParam("div")));
map = new SearchParameterMap();
map.add(Constants.PARAM_TEXT, content);
List<ResourcePersistentId> found = mySearchDao.search(resourceName, map);
assertThat(ResourcePersistentId.toLongList(found), empty());

1
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImplTest.java
View File

@ -621,7 +621,6 @@ public class SearchCoordinatorSvcImplTest {
*/
@Test
public void testFetchAllResultsReturnsNull() {
when(myDaoRegistry.getResourceDao(anyString())).thenReturn(myCallingDao);
when(myCallingDao.getContext()).thenReturn(ourCtx);

37
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/SearchParameterMap.java
View File

@ -18,6 +18,7 @@ import ca.uhn.fhir.rest.param.QuantityParam;
import ca.uhn.fhir.rest.param.TokenParamModifier;
import ca.uhn.fhir.util.ObjectUtil;
import ca.uhn.fhir.util.UrlUtil;
import com.fasterxml.jackson.annotation.JsonIgnore;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.builder.ToStringBuilder;
@ -89,6 +90,42 @@ public class SearchParameterMap implements Serializable {
super();
}
/**
* Creates and returns a copy of this map
*/
@JsonIgnore
@Override
public SearchParameterMap clone() {
SearchParameterMap map = new SearchParameterMap();
map.setSummaryMode(getSummaryMode());
map.setSort(getSort());
map.setSearchTotalMode(getSearchTotalMode());
map.setRevIncludes(getRevIncludes());
map.setIncludes(getIncludes());
map.setEverythingMode(getEverythingMode());
map.setCount(getCount());
map.setDeleteExpunge(isDeleteExpunge());
map.setLastN(isLastN());
map.setLastNMax(getLastNMax());
map.setLastUpdated(getLastUpdated());
map.setLoadSynchronous(isLoadSynchronous());
map.setNearDistanceParam(getNearDistanceParam());
map.setLoadSynchronousUpTo(getLoadSynchronousUpTo());
map.setOffset(getOffset());
map.setSearchContainedMode(getSearchContainedMode());
for (Map.Entry<String, List<List<IQueryParameterType>>> entry : mySearchParameterMap.entrySet()) {
List<List<IQueryParameterType>> params = entry.getValue();
for (List<IQueryParameterType> p : params) {
for (IQueryParameterType t : p) {
map.add(entry.getKey(), t);
}
}
}
return map;
}
/**
* Constructor
*/

80
hapi-fhir-jpaserver-searchparam/src/test/java/ca/uhn/fhir/jpa/searchparam/SearchParameterMapTest.java
View File

@ -2,11 +2,21 @@ package ca.uhn.fhir.jpa.searchparam;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.model.api.Include;
import ca.uhn.fhir.rest.api.SearchContainedModeEnum;
import ca.uhn.fhir.rest.api.SearchTotalModeEnum;
import ca.uhn.fhir.rest.api.SortSpec;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.QuantityParam;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.param.TokenOrListParam;
import ca.uhn.fhir.rest.param.TokenParam;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
import java.sql.Date;
import java.time.Instant;
import java.util.HashSet;
import java.util.List;
import static ca.uhn.fhir.rest.param.TokenParamModifier.TEXT;
@ -97,7 +107,77 @@ class SearchParameterMapTest {
List<List<IQueryParameterType>> unqualifiedAnds = map.remove("code");
assertThat(unqualifiedAnds, is(nullValue()));
}
@Test
public void clone_searchParams_copiesAllFields() {
HashSet<Include> includes = new HashSet<>();
Include i = new Include("test", true);
includes.add(i);
SearchParameterMap orig = new SearchParameterMap();
orig.setOffset(1);
orig.setLoadSynchronousUpTo(2);
orig.setLoadSynchronous(true);
orig.setNearDistanceParam(new QuantityParam());
orig.setCount(3);
orig.setLastNMax(4);
orig.setLastN(true);
orig.setDeleteExpunge(true);
orig.setIncludes(includes);
orig.setSearchTotalMode(SearchTotalModeEnum.ACCURATE);
orig.setLastUpdated(new DateRangeParam());
orig.setSearchContainedMode(SearchContainedModeEnum.BOTH);
orig.setEverythingMode(SearchParameterMap.EverythingModeEnum.ENCOUNTER_INSTANCE);
orig.setSort(new SortSpec());
orig.add("something", new StringParam("value"));
// test
SearchParameterMap copy = orig.clone();
// verify that they are not the same
Assertions.assertNotEquals(orig, copy);
// ... but that they are equal
Assertions.assertEquals(orig.toNormalizedQueryString(null),
copy.toNormalizedQueryString(null));
Assertions.assertEquals(orig.getOffset(), copy.getOffset());
Assertions.assertEquals(orig.getLoadSynchronousUpTo(), copy.getLoadSynchronousUpTo());
Assertions.assertEquals(orig.isLoadSynchronous(), copy.isLoadSynchronous());
Assertions.assertEquals(orig.getNearDistanceParam(), copy.getNearDistanceParam());
Assertions.assertEquals(orig.getCount(), copy.getCount());
Assertions.assertEquals(orig.getLastNMax(), copy.getLastNMax());
Assertions.assertEquals(orig.isLastN(), copy.isLastN());
Assertions.assertEquals(orig.isDeleteExpunge(), copy.isDeleteExpunge());
Assertions.assertEquals(orig.getIncludes(), copy.getIncludes());
Assertions.assertEquals(orig.getSearchTotalMode(), copy.getSearchTotalMode());
Assertions.assertEquals(orig.getLastUpdated(), copy.getLastUpdated());
Assertions.assertEquals(orig.getSearchContainedMode(), copy.getSearchContainedMode());
Assertions.assertEquals(orig.getEverythingMode(), copy.getEverythingMode());
Assertions.assertEquals(orig.getSort(), copy.getSort());
Assertions.assertEquals(orig.get("something"), copy.get("something"));
// verify changing one does not change the other
orig.setOffset(100);
Assertions.assertNotEquals(orig.toNormalizedQueryString(null),
copy.toNormalizedQueryString(null));
}
@Test
public void clone_searchParams_haveSameSearchParamsMap() {
SearchParameterMap orig = new SearchParameterMap();
orig.add("string", new StringParam("stringvalue"));
orig.add("datetime", new DateRangeParam(Date.from(Instant.now()),
new Date(2000, 11, 11)));
orig.add("int", new QuantityParam(1));
// test
SearchParameterMap clone = orig.clone();
// verify
Assertions.assertEquals(orig.size(), clone.size());
Assertions.assertEquals(orig.get("string"), clone.get("string"));
Assertions.assertEquals(orig.get("datetime"), clone.get("datetime"));
Assertions.assertEquals(orig.get("int"), clone.get("int"));
}
}