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

Correctly index Observation.applies[x] in JPA server

This commit is contained in:
jamesagnew 2015-03-08 16:55:42 -04:00
parent 32ad3ab22c
commit da1d49a108
7 changed files with 84 additions and 58 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/FhirTerser.java
View File

@ -149,12 +149,16 @@ public class FhirTerser {
if (nextDef instanceof RuntimeChildChoiceDefinition) {
for (IBase next : values) {
if (next != null) {
if (name.endsWith("[x]")) {
retVal.add(next);
} else {
String childName = nextDef.getChildNameByDatatype(next.getClass());
if (theSubList.get(0).equals(childName)) {
retVal.add(next);
}
}
}
}
} else {
retVal.addAll(values);
}

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseFhirDao.java
View File

@ -180,8 +180,8 @@ public abstract class BaseFhirDao implements IDao {
if (nextValue.isEmpty()) {
continue;
}
if (nextValue.getReference().getValue().startsWith("#")) {
// This is a contained resource reference
if (nextValue.getReference().isEmpty() || nextValue.getReference().getValue().startsWith("#")) {
// This is a blank or contained resource reference
continue;
}

40
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseSearchParamExtractor.java Normal file
View File

@ -0,0 +1,40 @@
package ca.uhn.fhir.jpa.dao;
import java.util.ArrayList;
import java.util.List;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.util.FhirTerser;
public class BaseSearchParamExtractor {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseSearchParamExtractor.class);
private FhirContext myContext;
public BaseSearchParamExtractor(FhirContext theContext) {
myContext = theContext;
}
protected FhirContext getContext() {
return myContext;
}
protected List<Object> extractValues(String thePaths, IResource theResource) {
List<Object> values = new ArrayList<Object>();
String[] nextPathsSplit = thePaths.split("\\|");
FhirTerser t = myContext.newTerser();
for (String nextPath : nextPathsSplit) {
String nextPathTrimmed = nextPath.trim();
try {
values.addAll(t.getValues(theResource, nextPathTrimmed));
} catch (Exception e) {
RuntimeResourceDefinition def = myContext.getResourceDefinition(theResource);
ourLog.warn("Failed to index values from path[{}] in resource type[{}]: ", nextPathTrimmed, def.getName(), e.toString());
}
}
return values;
}
}

33
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/SearchParamExtractorDstu1.java
View File

@ -63,21 +63,18 @@ import ca.uhn.fhir.model.primitive.BaseDateTimeDt;
import ca.uhn.fhir.model.primitive.IntegerDt;
import ca.uhn.fhir.model.primitive.StringDt;
import ca.uhn.fhir.model.primitive.UriDt;
import ca.uhn.fhir.util.FhirTerser;
class SearchParamExtractorDstu1 implements ISearchParamExtractor {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SearchParamExtractorDstu1.class);
private FhirContext myContext;
class SearchParamExtractorDstu1 extends BaseSearchParamExtractor implements ISearchParamExtractor {
public SearchParamExtractorDstu1(FhirContext theContext) {
myContext = theContext;
super(theContext);
}
@Override
public List<ResourceIndexedSearchParamDate> extractSearchParamDates(ResourceTable theEntity, IResource theResource) {
ArrayList<ResourceIndexedSearchParamDate> retVal = new ArrayList<ResourceIndexedSearchParamDate>();
RuntimeResourceDefinition def = myContext.getResourceDefinition(theResource);
RuntimeResourceDefinition def = getContext().getResourceDefinition(theResource);
for (RuntimeSearchParam nextSpDef : def.getSearchParams()) {
if (nextSpDef.getParamType() != SearchParamTypeEnum.DATE) {
continue;
@ -134,7 +131,7 @@ class SearchParamExtractorDstu1 implements ISearchParamExtractor {
public ArrayList<ResourceIndexedSearchParamNumber> extractSearchParamNumber(ResourceTable theEntity, IResource theResource) {
ArrayList<ResourceIndexedSearchParamNumber> retVal = new ArrayList<ResourceIndexedSearchParamNumber>();
RuntimeResourceDefinition def = myContext.getResourceDefinition(theResource);
RuntimeResourceDefinition def = getContext().getResourceDefinition(theResource);
for (RuntimeSearchParam nextSpDef : def.getSearchParams()) {
if (nextSpDef.getParamType() != SearchParamTypeEnum.NUMBER) {
continue;
@ -231,7 +228,7 @@ class SearchParamExtractorDstu1 implements ISearchParamExtractor {
public List<ResourceIndexedSearchParamQuantity> extractSearchParamQuantity(ResourceTable theEntity, IResource theResource) {
ArrayList<ResourceIndexedSearchParamQuantity> retVal = new ArrayList<ResourceIndexedSearchParamQuantity>();
RuntimeResourceDefinition def = myContext.getResourceDefinition(theResource);
RuntimeResourceDefinition def = getContext().getResourceDefinition(theResource);
for (RuntimeSearchParam nextSpDef : def.getSearchParams()) {
if (nextSpDef.getParamType() != SearchParamTypeEnum.QUANTITY) {
continue;
@ -281,7 +278,7 @@ class SearchParamExtractorDstu1 implements ISearchParamExtractor {
public List<ResourceIndexedSearchParamString> extractSearchParamStrings(ResourceTable theEntity, IResource theResource) {
ArrayList<ResourceIndexedSearchParamString> retVal = new ArrayList<ResourceIndexedSearchParamString>();
RuntimeResourceDefinition def = myContext.getResourceDefinition(theResource);
RuntimeResourceDefinition def = getContext().getResourceDefinition(theResource);
for (RuntimeSearchParam nextSpDef : def.getSearchParams()) {
if (nextSpDef.getParamType() != SearchParamTypeEnum.STRING) {
continue;
@ -369,7 +366,7 @@ class SearchParamExtractorDstu1 implements ISearchParamExtractor {
public List<BaseResourceIndexedSearchParam> extractSearchParamTokens(ResourceTable theEntity, IResource theResource) {
ArrayList<BaseResourceIndexedSearchParam> retVal = new ArrayList<BaseResourceIndexedSearchParam>();
RuntimeResourceDefinition def = myContext.getResourceDefinition(theResource);
RuntimeResourceDefinition def = getContext().getResourceDefinition(theResource);
for (RuntimeSearchParam nextSpDef : def.getSearchParams()) {
if (nextSpDef.getParamType() != SearchParamTypeEnum.TOKEN) {
continue;
@ -475,20 +472,4 @@ class SearchParamExtractorDstu1 implements ISearchParamExtractor {
return retVal;
}
private List<Object> extractValues(String thePaths, IResource theResource) {
List<Object> values = new ArrayList<Object>();
String[] nextPathsSplit = thePaths.split("\\|");
FhirTerser t = myContext.newTerser();
for (String nextPath : nextPathsSplit) {
String nextPathTrimmed = nextPath.trim();
try {
values.addAll(t.getValues(theResource, nextPathTrimmed));
} catch (Exception e) {
RuntimeResourceDefinition def = myContext.getResourceDefinition(theResource);
ourLog.warn("Failed to index values from path[{}] in resource type[{}]: ", nextPathTrimmed, def.getName(), e.toString());
}
}
return values;
}
}

36
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/SearchParamExtractorDstu2.java
View File

@ -20,8 +20,7 @@ package ca.uhn.fhir.jpa.dao;
* #L%
*/
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.*;
import java.math.BigDecimal;
import java.util.ArrayList;
@ -64,14 +63,11 @@ import ca.uhn.fhir.model.primitive.BaseDateTimeDt;
import ca.uhn.fhir.model.primitive.IntegerDt;
import ca.uhn.fhir.model.primitive.StringDt;
import ca.uhn.fhir.model.primitive.UriDt;
import ca.uhn.fhir.util.FhirTerser;
class SearchParamExtractorDstu2 implements ISearchParamExtractor {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SearchParamExtractorDstu2.class);
private FhirContext myContext;
class SearchParamExtractorDstu2 extends BaseSearchParamExtractor implements ISearchParamExtractor {
public SearchParamExtractorDstu2(FhirContext theContext) {
myContext = theContext;
super(theContext);
}
/*
@ -84,7 +80,7 @@ class SearchParamExtractorDstu2 implements ISearchParamExtractor {
public List<ResourceIndexedSearchParamDate> extractSearchParamDates(ResourceTable theEntity, IResource theResource) {
ArrayList<ResourceIndexedSearchParamDate> retVal = new ArrayList<ResourceIndexedSearchParamDate>();
RuntimeResourceDefinition def = myContext.getResourceDefinition(theResource);
RuntimeResourceDefinition def = getContext().getResourceDefinition(theResource);
for (RuntimeSearchParam nextSpDef : def.getSearchParams()) {
if (nextSpDef.getParamType() != SearchParamTypeEnum.DATE) {
continue;
@ -147,7 +143,7 @@ class SearchParamExtractorDstu2 implements ISearchParamExtractor {
public ArrayList<ResourceIndexedSearchParamNumber> extractSearchParamNumber(ResourceTable theEntity, IResource theResource) {
ArrayList<ResourceIndexedSearchParamNumber> retVal = new ArrayList<ResourceIndexedSearchParamNumber>();
RuntimeResourceDefinition def = myContext.getResourceDefinition(theResource);
RuntimeResourceDefinition def = getContext().getResourceDefinition(theResource);
for (RuntimeSearchParam nextSpDef : def.getSearchParams()) {
if (nextSpDef.getParamType() != SearchParamTypeEnum.NUMBER) {
continue;
@ -250,7 +246,7 @@ class SearchParamExtractorDstu2 implements ISearchParamExtractor {
public List<ResourceIndexedSearchParamQuantity> extractSearchParamQuantity(ResourceTable theEntity, IResource theResource) {
ArrayList<ResourceIndexedSearchParamQuantity> retVal = new ArrayList<ResourceIndexedSearchParamQuantity>();
RuntimeResourceDefinition def = myContext.getResourceDefinition(theResource);
RuntimeResourceDefinition def = getContext().getResourceDefinition(theResource);
for (RuntimeSearchParam nextSpDef : def.getSearchParams()) {
if (nextSpDef.getParamType() != SearchParamTypeEnum.QUANTITY) {
continue;
@ -306,7 +302,7 @@ class SearchParamExtractorDstu2 implements ISearchParamExtractor {
public List<ResourceIndexedSearchParamString> extractSearchParamStrings(ResourceTable theEntity, IResource theResource) {
ArrayList<ResourceIndexedSearchParamString> retVal = new ArrayList<ResourceIndexedSearchParamString>();
RuntimeResourceDefinition def = myContext.getResourceDefinition(theResource);
RuntimeResourceDefinition def = getContext().getResourceDefinition(theResource);
for (RuntimeSearchParam nextSpDef : def.getSearchParams()) {
if (nextSpDef.getParamType() != SearchParamTypeEnum.STRING) {
continue;
@ -400,7 +396,7 @@ class SearchParamExtractorDstu2 implements ISearchParamExtractor {
public List<BaseResourceIndexedSearchParam> extractSearchParamTokens(ResourceTable theEntity, IResource theResource) {
ArrayList<BaseResourceIndexedSearchParam> retVal = new ArrayList<BaseResourceIndexedSearchParam>();
RuntimeResourceDefinition def = myContext.getResourceDefinition(theResource);
RuntimeResourceDefinition def = getContext().getResourceDefinition(theResource);
for (RuntimeSearchParam nextSpDef : def.getSearchParams()) {
if (nextSpDef.getParamType() != SearchParamTypeEnum.TOKEN) {
continue;
@ -506,20 +502,4 @@ class SearchParamExtractorDstu2 implements ISearchParamExtractor {
return retVal;
}
private List<Object> extractValues(String thePaths, IResource theResource) {
List<Object> values = new ArrayList<Object>();
String[] nextPathsSplit = thePaths.split("\\|");
FhirTerser t = myContext.newTerser();
for (String nextPath : nextPathsSplit) {
String nextPathTrimmed = nextPath.trim();
try {
values.addAll(t.getValues(theResource, nextPathTrimmed));
} catch (Exception e) {
RuntimeResourceDefinition def = myContext.getResourceDefinition(theResource);
ourLog.warn("Failed to index values from path[{}] in resource type[{}]: ", nextPathTrimmed, def.getName(), e.toString());
}
}
return values;
}
}

17
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoTest.java
View File

@ -294,6 +294,23 @@ public class FhirResourceDaoTest {
}
}
@Test
public void testChoiceParamDateAlt() {
Observation o2 = new Observation();
o2.getCode().addCoding().setSystem("foo").setCode("testChoiceParamDateAlt02");
o2.setApplies(new DateTimeDt("2015-03-08T11:11:11"));
IdDt id2 = ourObservationDao.create(o2).getId();
{
Set<Long> found = ourObservationDao.searchForIds(Observation.SP_DATE, new DateParam(">2001-01-02"));
assertThat(found, contains(id2.getIdPartAsLong()));
}
{
Set<Long> found = ourObservationDao.searchForIds(Observation.SP_DATE, new DateParam(">2016-01-02"));
assertThat(found, not(contains(id2.getIdPartAsLong())));
}
}
@Test
public void testChoiceParamQuantity() {
Observation o3 = new Observation();

4
src/changes/changes.xml
View File

@ -135,6 +135,10 @@
specification, for the Generic Client, Annotation Client, and
Server.
</action>
<action type="fix">
Observation.applies[x] and other similar search fields with multiple allowable
value types were not being correctly indexed in the JPA server.
</action>
</release>
<release version="0.8" date="2014-Dec-17">
<action type="add">