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

Merge branch 'master' into windows-fixes-2

This commit is contained in:
Ken Stevens 2019-01-30 18:01:17 -05:00
parent adb037e805 5f29e4fbf3
commit 6b601708dd
8 changed files with 288 additions and 71 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

10
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/DateParam.java
View File

@ -255,7 +255,15 @@ public class DateParam extends BaseParamWithPrefix<DateParam> implements /*IQuer
return b.build();
}
public class DateParamDateTimeHolder extends BaseDateTimeDt {
public static class DateParamDateTimeHolder extends BaseDateTimeDt {
/**
* Constructor
*/
public DateParamDateTimeHolder() {
super();
}
@Override
protected TemporalPrecisionEnum getDefaultPrecisionForDatatype() {
return TemporalPrecisionEnum.SECOND;

86
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/SearchBuilder.java
View File

@ -80,7 +80,6 @@ import org.hl7.fhir.instance.model.api.IIdType;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Scope;
import org.springframework.stereotype.Component;
import org.thymeleaf.util.ListUtils;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
@ -385,7 +384,8 @@ public class SearchBuilder implements ISearchBuilder {
List<Predicate> codePredicates = new ArrayList<>();
for (IQueryParameterType nextOr : theList) {
for (int orIdx = 0; orIdx < theList.size(); orIdx++) {
IQueryParameterType nextOr = theList.get(orIdx);
if (nextOr instanceof ReferenceParam) {
ReferenceParam ref = (ReferenceParam) nextOr;
@ -496,6 +496,8 @@ public class SearchBuilder implements ISearchBuilder {
boolean foundChainMatch = false;
for (Class<? extends IBaseResource> nextType : resourceTypes) {
String chain = ref.getChain();
String remainingChain = null;
int chainDotIndex = chain.indexOf('.');
@ -504,7 +506,6 @@ public class SearchBuilder implements ISearchBuilder {
chain = chain.substring(0, chainDotIndex);
}
for (Class<? extends IBaseResource> nextType : resourceTypes) {
RuntimeResourceDefinition typeDef = myContext.getResourceDefinition(nextType);
String subResourceName = typeDef.getName();
@ -531,37 +532,29 @@ public class SearchBuilder implements ISearchBuilder {
}
}
IQueryParameterType chainValue;
if (remainingChain != null) {
if (param == null || param.getParamType() != RestSearchParameterTypeEnum.REFERENCE) {
ourLog.debug("Type {} parameter {} is not a reference, can not chain {}", nextType.getSimpleName(), chain, remainingChain);
ArrayList<IQueryParameterType> orValues = Lists.newArrayList();
for (IQueryParameterType next : theList) {
String nextValue = next.getValueAsQueryToken(myContext);
IQueryParameterType chainValue = mapReferenceChainToRawParamType(remainingChain, param, theParamName, qualifier, nextType, chain, isMeta, nextValue);
if (chainValue == null) {
continue;
}
chainValue = new ReferenceParam();
chainValue.setValueAsQueryToken(myContext, theParamName, qualifier, resourceId);
((ReferenceParam) chainValue).setChain(remainingChain);
} else if (isMeta) {
IQueryParameterType type = myMatchUrlService.newInstanceType(chain);
type.setValueAsQueryToken(myContext, theParamName, qualifier, resourceId);
chainValue = type;
} else {
chainValue = toParameterType(param, qualifier, resourceId);
}
foundChainMatch = true;
orValues.add(chainValue);
}
Subquery<Long> subQ = myResourceTableQuery.subquery(Long.class);
Root<ResourceTable> subQfrom = subQ.from(ResourceTable.class);
subQ.select(subQfrom.get("myId").as(Long.class));
List<List<? extends IQueryParameterType>> andOrParams = new ArrayList<>();
andOrParams.add(Collections.singletonList(chainValue));
andOrParams.add(orValues);
/*
* We're doing a chain call, so push the current query root
* and predicate list down and put new ones at the top of the
* stack and run a subuery
* stack and run a subquery
*/
Root<ResourceTable> stackRoot = myResourceTableRoot;
ArrayList<Predicate> stackPredicates = myPredicates;
@ -573,9 +566,11 @@ public class SearchBuilder implements ISearchBuilder {
// Create the subquery predicates
myPredicates.add(myBuilder.equal(myResourceTableRoot.get("myResourceType"), subResourceName));
myPredicates.add(myBuilder.isNull(myResourceTableRoot.get("myDeleted")));
searchForIdsWithAndOr(subResourceName, chain, andOrParams);
if (foundChainMatch) {
searchForIdsWithAndOr(subResourceName, chain, andOrParams);
subQ.where(toArray(myPredicates));
}
/*
* Pop the old query root and predicate list back
@ -593,6 +588,10 @@ public class SearchBuilder implements ISearchBuilder {
if (!foundChainMatch) {
throw new InvalidRequestException(myContext.getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "invalidParameterChain", theParamName + '.' + ref.getChain()));
}
myPredicates.add(myBuilder.or(toArray(codePredicates)));
return;
}
} else {
@ -604,6 +603,28 @@ public class SearchBuilder implements ISearchBuilder {
myPredicates.add(myBuilder.or(toArray(codePredicates)));
}
private IQueryParameterType mapReferenceChainToRawParamType(String remainingChain, RuntimeSearchParam param, String theParamName, String qualifier, Class<? extends IBaseResource> nextType, String chain, boolean isMeta, String resourceId) {
IQueryParameterType chainValue;
if (remainingChain != null) {
if (param == null || param.getParamType() != RestSearchParameterTypeEnum.REFERENCE) {
ourLog.debug("Type {} parameter {} is not a reference, can not chain {}", nextType.getSimpleName(), chain, remainingChain);
return null;
}
chainValue = new ReferenceParam();
chainValue.setValueAsQueryToken(myContext, theParamName, qualifier, resourceId);
((ReferenceParam) chainValue).setChain(remainingChain);
} else if (isMeta) {
IQueryParameterType type = myMatchUrlService.newInstanceType(chain);
type.setValueAsQueryToken(myContext, theParamName, qualifier, resourceId);
chainValue = type;
} else {
chainValue = toParameterType(param, qualifier, resourceId);
}
return chainValue;
}
private void addPredicateResourceId(List<List<? extends IQueryParameterType>> theValues) {
for (List<? extends IQueryParameterType> nextValue : theValues) {
Set<Long> orPids = new HashSet<>();
@ -794,24 +815,27 @@ public class SearchBuilder implements ISearchBuilder {
private void addPredicateToken(String theResourceName, String theParamName, List<? extends IQueryParameterType> theList) {
Join<ResourceTable, ResourceIndexedSearchParamToken> join = createOrReuseJoin(JoinEnum.TOKEN, theParamName);
if (theList.get(0).getMissing() != null) {
Join<ResourceTable, ResourceIndexedSearchParamToken> join = createOrReuseJoin(JoinEnum.TOKEN, theParamName);
addPredicateParamMissing(theResourceName, theParamName, theList.get(0).getMissing(), join);
return;
}
List<Predicate> codePredicates = new ArrayList<>();
Join<ResourceTable, ResourceIndexedSearchParamToken> join = null;
for (IQueryParameterType nextOr : theList) {
if (nextOr instanceof TokenParam) {
TokenParam id = (TokenParam) nextOr;
if (id.isText()) {
addPredicateString(theResourceName, theParamName, theList);
continue;
break;
}
}
if (join == null) {
join = createOrReuseJoin(JoinEnum.TOKEN, theParamName);
}
Predicate singleCode = createPredicateToken(nextOr, theResourceName, theParamName, myBuilder, join);
codePredicates.add(singleCode);
}
@ -972,8 +996,9 @@ public class SearchBuilder implements ISearchBuilder {
@SuppressWarnings("unchecked")
private <T> Join<ResourceTable, T> createOrReuseJoin(JoinEnum theType, String theSearchParameterName) {
JoinKey key = new JoinKey(theSearchParameterName, theType);
return (Join<ResourceTable, T>) myIndexJoins.computeIfAbsent(key, k -> {
Join<ResourceTable, ResourceIndexedSearchParamDate> join = null;
switch (theType) {
case DATE:
join = myResourceTableRoot.join("myParamsDate", JoinType.LEFT);
@ -997,13 +1022,8 @@ public class SearchBuilder implements ISearchBuilder {
join = myResourceTableRoot.join("myParamsToken", JoinType.LEFT);
break;
}
JoinKey key = new JoinKey(theSearchParameterName, theType);
if (!myIndexJoins.containsKey(key)) {
myIndexJoins.put(key, join);
}
return (Join<ResourceTable, T>) join;
return join;
});
}
private Predicate createPredicateDate(IQueryParameterType theParam, String theResourceName, String theParamName, CriteriaBuilder theBuilder, From<?, ResourceIndexedSearchParamDate> theFrom) {

92
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/CaptureQueriesListener.java Normal file
View File

@ -0,0 +1,92 @@
package ca.uhn.fhir.jpa.config;
import net.ttddyy.dsproxy.ExecutionInfo;
import net.ttddyy.dsproxy.QueryInfo;
import net.ttddyy.dsproxy.proxy.ParameterSetOperation;
import net.ttddyy.dsproxy.support.ProxyDataSourceBuilder;
import org.hibernate.engine.jdbc.internal.BasicFormatterImpl;
import java.util.ArrayList;
import java.util.Collections;
import java.util.LinkedList;
import java.util.List;
import java.util.stream.Collectors;
public class CaptureQueriesListener implements ProxyDataSourceBuilder.SingleQueryExecution {
private static final LinkedList<Query> LAST_N_QUERIES = new LinkedList<>();
@Override
public void execute(ExecutionInfo execInfo, List<QueryInfo> queryInfoList) {
synchronized (LAST_N_QUERIES) {
for (QueryInfo next : queryInfoList) {
String sql = next.getQuery();
List<String> params;
if (next.getParametersList().size() > 0 && next.getParametersList().get(0).size() > 0) {
List<ParameterSetOperation> values = next
.getParametersList()
.get(0);
params = values.stream()
.map(t -> t.getArgs()[1])
.map(t -> t != null ? t.toString() : "NULL")
.collect(Collectors.toList());
} else {
params = new ArrayList<>();
}
LAST_N_QUERIES.add(0, new Query(sql, params));
}
while (LAST_N_QUERIES.size() > 100) {
LAST_N_QUERIES.removeLast();
}
}
}
public static class Query {
private final String myThreadName = Thread.currentThread().getName();
private final String mySql;
private final List<String> myParams;
Query(String theSql, List<String> theParams) {
mySql = theSql;
myParams = Collections.unmodifiableList(theParams);
}
public String getThreadName() {
return myThreadName;
}
public String getSql(boolean theInlineParams, boolean theFormat) {
String retVal = mySql;
if (theFormat) {
retVal = new BasicFormatterImpl().format(retVal);
}
if (theInlineParams) {
List<String> nextParams = new ArrayList<>(myParams);
while (retVal.contains("?") && nextParams.size() > 0) {
int idx = retVal.indexOf("?");
retVal = retVal.substring(0, idx) + nextParams.remove(0) + retVal.substring(idx + 1);
}
}
return retVal;
}
}
public static void clear() {
synchronized (LAST_N_QUERIES) {
LAST_N_QUERIES.clear();
}
}
/**
* Index 0 is newest!
*/
public static ArrayList<Query> getLastNQueries() {
synchronized (LAST_N_QUERIES) {
return new ArrayList<>(LAST_N_QUERIES);
}
}
}

1
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestR4Config.java
View File

@ -100,6 +100,7 @@ public class TestR4Config extends BaseJavaConfigR4 {
// .logSlowQueryBySlf4j(10, TimeUnit.SECONDS)
// .countQuery(new ThreadQueryCountHolder())
.beforeQuery(new BlockLargeNumbersOfParamsListener())
.afterQuery(new CaptureQueriesListener())
.countQuery(singleQueryCountHolder())
.build();

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/BaseJpaTest.java
View File

@ -1,6 +1,7 @@
package ca.uhn.fhir.jpa.dao;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.config.CaptureQueriesListener;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.model.interceptor.api.IInterceptorRegistry;
import ca.uhn.fhir.jpa.model.interceptor.api.Pointcut;
@ -94,6 +95,7 @@ public abstract class BaseJpaTest {
@After
public void afterPerformCleanup() {
BaseHapiFhirResourceDao.setDisableIncrementOnUpdateForUnitTest(false);
CaptureQueriesListener.clear();
}
@After

91
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchNoFtTest.java
View File

@ -1,9 +1,10 @@
package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.jpa.config.CaptureQueriesListener;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.model.entity.*;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap.EverythingModeEnum;
import ca.uhn.fhir.jpa.model.entity.*;
import ca.uhn.fhir.jpa.util.TestUtil;
import ca.uhn.fhir.model.api.Include;
import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
@ -13,6 +14,7 @@ import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.param.*;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.MethodNotAllowedException;
import com.google.common.collect.Lists;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.instance.model.api.IAnyResource;
@ -39,6 +41,7 @@ import java.io.IOException;
import java.math.BigDecimal;
import java.nio.charset.StandardCharsets;
import java.util.*;
import java.util.stream.Collectors;
import static org.hamcrest.Matchers.*;
import static org.junit.Assert.*;
@ -53,6 +56,7 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
myDaoConfig.setReuseCachedSearchResultsForMillis(new DaoConfig().getReuseCachedSearchResultsForMillis());
myDaoConfig.setFetchSizeDefaultMaximum(new DaoConfig().getFetchSizeDefaultMaximum());
myDaoConfig.setAllowContainsSearches(new DaoConfig().isAllowContainsSearches());
myDaoConfig.setSearchPreFetchThresholds(new DaoConfig().getSearchPreFetchThresholds());
}
@Before
@ -614,7 +618,7 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
expect1.setResource(resource);
expect1.calculateHashes();
assertThat("Got: \"" + results.toString()+"\"", results, containsInAnyOrder(expect0, expect1));
assertThat("Got: \"" + results.toString() + "\"", results, containsInAnyOrder(expect0, expect1));
}
});
}
@ -1060,7 +1064,7 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
QuantityParam v1 = new QuantityParam(ParamPrefixEnum.GREATERTHAN_OR_EQUALS, 150, "http://bar", "code1");
SearchParameterMap map = new SearchParameterMap().setLoadSynchronous(true).add(param, v1);
IBundleProvider result = myObservationDao.search(map);
assertThat("Got: "+ toUnqualifiedVersionlessIdValues(result), toUnqualifiedVersionlessIdValues(result), containsInAnyOrder(id1.getValue()));
assertThat("Got: " + toUnqualifiedVersionlessIdValues(result), toUnqualifiedVersionlessIdValues(result), containsInAnyOrder(id1.getValue()));
}
}
@ -1092,7 +1096,7 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
CompositeParam<TokenParam, QuantityParam> val = new CompositeParam<>(v0, v1);
SearchParameterMap map = new SearchParameterMap().setLoadSynchronous(true).add(param, val);
IBundleProvider result = myObservationDao.search(map);
assertThat("Got: "+ toUnqualifiedVersionlessIdValues(result), toUnqualifiedVersionlessIdValues(result), containsInAnyOrder(id2.getValue()));
assertThat("Got: " + toUnqualifiedVersionlessIdValues(result), toUnqualifiedVersionlessIdValues(result), containsInAnyOrder(id2.getValue()));
}
{
TokenParam v0 = new TokenParam("http://foo", "code1");
@ -1140,6 +1144,40 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
}
/**
* See #1174
*/
@Test
public void testSearchDateInSavedSearch() {
for (int i = 1; i <= 9; i++) {
Patient p1 = new Patient();
p1.getBirthDateElement().setValueAsString("1980-01-0" + i);
String id1 = myPatientDao.create(p1).getId().toUnqualifiedVersionless().getValue();
}
myDaoConfig.setSearchPreFetchThresholds(Lists.newArrayList(3, 6, 10));
{
// Don't load synchronous
SearchParameterMap map = new SearchParameterMap();
map.setLastUpdated(new DateRangeParam().setUpperBound(new DateParam(ParamPrefixEnum.LESSTHAN, "2022-01-01")));
IBundleProvider found = myPatientDao.search(map);
Set<String> dates = new HashSet<>();
for (int i = 0; i < 9; i++) {
Patient nextResource = (Patient) found.getResources(i, i + 1).get(0);
dates.add(nextResource.getBirthDateElement().getValueAsString());
}
assertThat(dates, hasItems(
"1980-01-01",
"1980-01-09"
));
assertFalse(map.isLoadSynchronous());
assertNull(map.getLoadSynchronousUpTo());
}
}
/**
* #222
*/
@ -2160,6 +2198,51 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
}
@Test
public void testSearchLinkToken() {
// /fhirapi/MedicationRequest?category=community&identifier=urn:oid:2.16.840.1.113883.3.7418.12.3%7C&intent=order&medication.code:text=calcitriol,hectorol,Zemplar,rocaltrol,vectical,vitamin%20D,doxercalciferol,paricalcitol&status=active,completed
Medication m = new Medication();
m.getCode().setText("valueb");
myMedicationDao.create(m);
MedicationRequest mr = new MedicationRequest();
mr.addCategory().addCoding().setCode("community");
mr.addIdentifier().setSystem("urn:oid:2.16.840.1.113883.3.7418.12.3").setValue("1");
mr.setIntent(MedicationRequest.MedicationRequestIntent.ORDER);
mr.setMedication(new Reference(m.getId()));
myMedicationRequestDao.create(mr);
SearchParameterMap sp = new SearchParameterMap();
sp.setLoadSynchronous(true);
sp.add("category", new TokenParam("community"));
sp.add("identifier", new TokenParam("urn:oid:2.16.840.1.113883.3.7418.12.3", "1"));
sp.add("intent", new TokenParam("order"));
ReferenceParam param1 = new ReferenceParam("valuea").setChain("code:text");
ReferenceParam param2 = new ReferenceParam("valueb").setChain("code:text");
ReferenceParam param3 = new ReferenceParam("valuec").setChain("code:text");
sp.add("medication", new ReferenceOrListParam().addOr(param1).addOr(param2).addOr(param3));
IBundleProvider retrieved = myMedicationRequestDao.search(sp);
assertEquals(1, retrieved.size().intValue());
List<String> queries = CaptureQueriesListener
.getLastNQueries()
.stream()
.filter(t -> t.getThreadName().equals("main"))
.filter(t -> t.getSql(false, false).toLowerCase().contains("select"))
.filter(t -> t.getSql(false, false).toLowerCase().contains("token"))
.map(t -> t.getSql(true, true))
.collect(Collectors.toList());
ourLog.info("Queries:\n {}", queries.stream().findFirst());
String searchQuery = queries.get(0);
assertEquals(searchQuery, 3, StringUtils.countMatches(searchQuery.toUpperCase(), "HFJ_SPIDX_TOKEN"));
assertEquals(searchQuery, 5, StringUtils.countMatches(searchQuery.toUpperCase(), "LEFT OUTER JOIN"));
}
@Test
public void testSearchTokenParam() {
Patient patient = new Patient();

2
pom.xml
View File

@ -534,7 +534,7 @@
<jetty_version>9.4.14.v20181114</jetty_version>
<jsr305_version>3.0.2</jsr305_version>
<!--<hibernate_version>5.2.10.Final</hibernate_version>-->
<hibernate_version>5.4.0.Final</hibernate_version>
<hibernate_version>5.4.1.Final</hibernate_version>
<!-- Update lucene version when you update hibernate-search version -->
<hibernate_search_version>5.11.0.Final</hibernate_search_version>
<lucene_version>5.5.5</lucene_version>

11
src/changes/changes.xml
View File

@ -333,6 +333,17 @@
whether a call out to the database may be required. I say "may" because subscription matches fail fast
so a negative match may be performed in-memory, but a positive match will require a database call.
</action>
<action type="fix">
When performing a JPA search with a chained :text modifier
(e.g. MedicationStatement?medication.code:text=aspirin,tylenol) a series
of unneccesary joins were introduced to the generated SQL query, harming
performance. This has been fixed.
</action>
<action type="fix">
A serialization error when performing some searches in the JPA server
using data parameters has been fixed. Thanks to GitHub user
@PickOneFish for reporting!
</action>
</release>
<release version="3.6.0" date="2018-11-12" description="Food">
<action type="add">