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Code Issues Packages Projects Releases Wiki Activity

Issue 3563 mdm nickname support (#3565) 

* added NicknameMap

* added NicknameSvc

* create NicknameInterceptor

* test interceptor integration

* add nickname matcher

* test nickname matcher

* unit test

* documentation

* unit test

* cleanup

* cleanup

* Msg.code()

* Msg.code() in test

* Msg.code()

* review feedback
This commit is contained in:
Ken Stevens 2022-04-28 18:02:56 -04:00 committed by GitHub
parent e0f1b913b7
commit 10ebb082d0
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32 changed files with 2031 additions and 97 deletions
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8
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/api/Constants.java
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@ -22,12 +22,7 @@ package ca.uhn.fhir.rest.api;
import java.nio.charset.Charset;
import java.nio.charset.StandardCharsets;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
import java.util.*;
import static org.apache.commons.lang3.StringUtils.defaultIfBlank;
@ -217,6 +212,7 @@ public class Constants {
public static final String PARAMQUALIFIER_STRING_EXACT = ":exact";
public static final String PARAMQUALIFIER_TOKEN_TEXT = ":text";
public static final String PARAMQUALIFIER_MDM = ":mdm";
public static final String PARAMQUALIFIER_NICKNAME = ":nickname";
public static final String PARAMQUALIFIER_TOKEN_OF_TYPE = ":of-type";
public static final String PARAMQUALIFIER_TOKEN_NOT = ":not";
public static final int STATUS_HTTP_200_OK = 200;

22
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/StringParam.java
View File

@ -21,9 +21,11 @@ package ca.uhn.fhir.rest.param;
*/
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.model.primitive.StringDt;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.HashCodeBuilder;
@ -38,7 +40,8 @@ public class StringParam extends BaseParam implements IQueryParameterType {
private boolean myExact;
private String myValue;
private Boolean myMdmExpand;
private Boolean myNicknameExpand;
/**
* Constructor
@ -77,12 +80,12 @@ public class StringParam extends BaseParam implements IQueryParameterType {
return ParameterUtil.escape(myValue);
}
public boolean isMdmExpand() {
return myMdmExpand != null && myMdmExpand;
public boolean isNicknameExpand() {
return myNicknameExpand != null && myNicknameExpand;
}
public StringParam setMdmExpand(boolean theMdmExpand) {
myMdmExpand = theMdmExpand;
public StringParam setNicknameExpand(boolean theNicknameExpand) {
myNicknameExpand = theNicknameExpand;
return this;
}
@ -98,6 +101,15 @@ public class StringParam extends BaseParam implements IQueryParameterType {
@Override
void doSetValueAsQueryToken(FhirContext theContext, String theParamName, String theQualifier, String theValue) {
if (Constants.PARAMQUALIFIER_NICKNAME.equals(theQualifier)) {
if ("name".equals(theParamName) || "given".equals(theParamName)) {
myNicknameExpand = true;
theQualifier = "";
} else {
throw new InvalidRequestException(Msg.code(2077) + "Modifier " + Constants.PARAMQUALIFIER_NICKNAME + " may only be used with 'name' and 'given' search parameters");
}
}
if (Constants.PARAMQUALIFIER_STRING_EXACT.equals(theQualifier)) {
setExact(true);
} else {

17
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/SearchParameterUtil.java
View File

@ -58,8 +58,8 @@ public class SearchParameterUtil {
* 1. Attempt to find one called 'patient'
* 2. If that fails, find one called 'subject'
* 3. If that fails, find find by Patient Compartment.
* 3.1 If that returns >1 result, throw an error
* 3.2 If that returns 1 result, return it
* 3.1 If that returns >1 result, throw an error
* 3.2 If that returns 1 result, return it
*/
public static Optional<RuntimeSearchParam> getOnlyPatientSearchParamForResourceType(FhirContext theFhirContext, String theResourceType) {
RuntimeSearchParam myPatientSearchParam = null;
@ -115,7 +115,7 @@ public class SearchParameterUtil {
*/
public static boolean isResourceTypeInPatientCompartment(FhirContext theFhirContext, String theResourceType) {
RuntimeResourceDefinition runtimeResourceDefinition = theFhirContext.getResourceDefinition(theResourceType);
return getAllPatientCompartmentRuntimeSearchParams(runtimeResourceDefinition).size() > 0;
return getAllPatientCompartmentRuntimeSearchParams(runtimeResourceDefinition).size() > 0;
}
@ -147,4 +147,15 @@ public class SearchParameterUtil {
.map(t -> t.getValueAsString())
.orElse(null);
}
public static String stripModifier(String theSearchParam) {
String retval;
int colonIndex = theSearchParam.indexOf(":");
if (colonIndex == -1) {
retval = theSearchParam;
} else {
retval = theSearchParam.substring(0, colonIndex);
}
return retval;
}
}

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/3563-nickname-matching.yaml Normal file
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@ -0,0 +1,5 @@
type: add
issue: 3563
title: "Added search parameter modifier :nickname that can be used with 'name' or 'given' search parameters.
E.g. ?Patient?given:nickname=Kenny will match a patient with the given name Kenneth. Also added MDM matching
algorithm named NICKNAME that matches based this."

2
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/search.md
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@ -1,5 +1,7 @@
# JPA Server Search
## Limitations
The HAPI FHIR JPA Server fully implements most [FHIR search](https://www.hl7.org/fhir/search.html) operations for most versions of FHIR. However, there are some known limitations of the current implementation. Here is a partial list of search functionality that is not currently supported in HAPI FHIR:
### Chains within _has

8
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_mdm/mdm_rules.md
View File

@ -406,6 +406,14 @@ The following algorithms are currently supported:
Match names as strings in any order
</td>
<td>John Henry = John HENRY when exact=false, John Henry != Henry John</td>
</tr>
<tr>
<td>NICKNAME</td>
<td>matcher</td>
<td>
True if one name is a nickname of the other
</td>
<td>Ken = Kenneth, Kenny = Ken. Allen != Allan.</td>
</tr>
<tr>
<td>IDENTIFIER</td>

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/JpaConfig.java
View File

@ -128,6 +128,7 @@ import ca.uhn.fhir.jpa.search.warm.CacheWarmingSvcImpl;
import ca.uhn.fhir.jpa.search.warm.ICacheWarmingSvc;
import ca.uhn.fhir.jpa.searchparam.config.SearchParamConfig;
import ca.uhn.fhir.jpa.searchparam.extractor.IResourceLinkResolver;
import ca.uhn.fhir.jpa.searchparam.nickname.NicknameInterceptor;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamProvider;
import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc;
import ca.uhn.fhir.jpa.sp.SearchParamPresenceSvcImpl;
@ -164,6 +165,7 @@ import org.springframework.scheduling.concurrent.ConcurrentTaskScheduler;
import org.springframework.scheduling.concurrent.ScheduledExecutorFactoryBean;
import javax.annotation.Nullable;
import java.io.IOException;
import java.util.Date;
/*
@ -827,4 +829,10 @@ public class JpaConfig {
public MemberMatcherR4Helper memberMatcherR4Helper(FhirContext theFhirContext) {
return new MemberMatcherR4Helper(theFhirContext);
}
@Lazy
@Bean
public NicknameInterceptor nicknameInterceptor() throws IOException {
return new NicknameInterceptor();
}
}

1
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/search/ExtendedLuceneSearchBuilder.java
View File

@ -102,6 +102,7 @@ public class ExtendedLuceneSearchBuilder {
case EMPTY_MODIFIER:
return true;
case Constants.PARAMQUALIFIER_MDM:
case Constants.PARAMQUALIFIER_NICKNAME:
default:
return false;
}

24
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/interceptor/MdmSearchExpandingInterceptor.java
View File

@ -30,13 +30,11 @@ import ca.uhn.fhir.mdm.log.Logs;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.param.ReferenceParam;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.param.TokenParam;
import org.hl7.fhir.instance.model.api.IIdType;
import org.slf4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import java.lang.reflect.Constructor;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
@ -92,7 +90,7 @@ public class MdmSearchExpandingInterceptor {
// If we failed, attempt to expand as a golden resource
if (expandedResourceIds.isEmpty()) {
expandedResourceIds = myMdmLinkExpandSvc.expandMdmByGoldenResourceId(new IdDt(refParam.getValue()));
expandedResourceIds = myMdmLinkExpandSvc.expandMdmByGoldenResourceId(new IdDt(refParam.getValue()));
}
//Rebuild the search param list.
@ -104,8 +102,7 @@ public class MdmSearchExpandingInterceptor {
.forEach(toAdd::add);
}
}
}
else if (theParamName.equalsIgnoreCase("_id")) {
} else if (theParamName.equalsIgnoreCase("_id")) {
expandIdParameter(iQueryParameterType, toAdd, toRemove);
}
}
@ -117,6 +114,7 @@ public class MdmSearchExpandingInterceptor {
/**
* Expands out the provided _id parameter into all the various
* ids of linked resources.
*
* @param theIdParameter
* @param theAddList
* @param theRemoveList
@ -130,29 +128,21 @@ public class MdmSearchExpandingInterceptor {
IIdType id;
Creator<? extends IQueryParameterType> creator;
boolean mdmExpand = false;
if (theIdParameter instanceof StringParam) {
StringParam param = (StringParam) theIdParameter;
mdmExpand = param.isMdmExpand();
id = new IdDt(param.getValue());
creator = StringParam::new;
}
else if (theIdParameter instanceof TokenParam) {
if (theIdParameter instanceof TokenParam) {
TokenParam param = (TokenParam) theIdParameter;
mdmExpand = param.isMdmExpand();
id = new IdDt(param.getValue());
creator = TokenParam::new;
}
else {
} else {
creator = null;
id = null;
}
if (id == null || creator == null) {
if (id == null) {
// in case the _id paramter type is different from the above
ourLog.warn("_id parameter of incorrect type. Expected StringParam or TokenParam, but got {}. No expansion will be done!",
theIdParameter.getClass().getSimpleName());
}
else if (mdmExpand) {
} else if (mdmExpand) {
ourLog.debug("_id parameter must be expanded out from: {}", id.getValue());
Set<String> expandedResourceIds = myMdmLinkExpandSvc.expandMdmBySourceResourceId(id);

4
hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmSearchParamSvc.java
View File

@ -31,6 +31,7 @@ import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.searchparam.extractor.SearchParamExtractorService;
import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
import ca.uhn.fhir.util.SearchParameterUtil;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.springframework.beans.factory.annotation.Autowired;
@ -61,7 +62,8 @@ public class MdmSearchParamSvc {
public List<String> getValueFromResourceForSearchParam(IBaseResource theResource, String theSearchParam) {
String resourceType = myFhirContext.getResourceType(theResource);
RuntimeSearchParam activeSearchParam = mySearchParamRegistry.getActiveSearchParam(resourceType, theSearchParam);
String searchParam = SearchParameterUtil.stripModifier(theSearchParam);
RuntimeSearchParam activeSearchParam = mySearchParamRegistry.getActiveSearchParam(resourceType, searchParam);
return mySearchParamExtractorService.extractParamValuesAsStrings(activeSearchParam, theResource);
}

179
hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/provider/MdmProviderMatchR4Test.java
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@ -15,6 +15,7 @@ import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.IOException;
import java.util.List;
import java.util.stream.Collectors;
@ -161,68 +162,134 @@ public class MdmProviderMatchR4Test extends BaseProviderR4Test {
public void testMatchWithCoarseDateGranularity() throws Exception {
setMdmRuleJson("mdm/coarse-birthdate-mdm-rules.json");
String granularPatient = "{\n" +
" \"resourceType\": \"Patient\",\n" +
" \"active\": true,\n" +
" \"name\": [\n" +
" {\n" +
" \"family\": \"PETERSON\",\n" +
" \"given\": [\n" +
" \"GARY\",\n" +
" \"D\"\n" +
" ]\n" +
" }\n" +
" ],\n" +
" \"telecom\": [\n" +
" {\n" +
" \"system\": \"phone\",\n" +
" \"value\": \"100100100\",\n" +
" \"use\": \"home\"\n" +
" }\n" +
" ],\n" +
" \"gender\": \"male\",\n" +
" \"birthDate\": \"1991-10-10\",\n" +
" \"address\": [\n" +
" {\n" +
" \"state\": \"NY\",\n" +
" \"postalCode\": \"12313\"\n" +
" }\n" +
" ]\n" +
"}";
String granularPatient = """
{
"resourceType": "Patient",
"active": true,
"name": [
{
"family": "PETERSON",
"given": [
"GARY",
"D"
]
}
],
"telecom": [
{
"system": "phone",
"value": "100100100",
"use": "home"
}
],
"gender": "male",
"birthDate": "1991-10-10",
"address": [
{
"state": "NY",
"postalCode": "12313"
}
]
}""";
IBaseResource iBaseResource = myFhirContext.newJsonParser().parseResource(granularPatient);
createPatient((Patient) iBaseResource);
String coarsePatient = "{\n" +
" \"resourceType\": \"Patient\",\n" +
" \"active\": true,\n" +
" \"name\": [\n" +
" {\n" +
" \"family\": \"PETERSON\",\n" +
" \"given\": [\n" +
" \"GARY\",\n" +
" \"D\"\n" +
" ]\n" +
" }\n" +
" ],\n" +
" \"telecom\": [\n" +
" {\n" +
" \"system\": \"phone\",\n" +
" \"value\": \"100100100\",\n" +
" \"use\": \"home\"\n" +
" }\n" +
" ],\n" +
" \"gender\": \"male\",\n" +
" \"birthDate\": \"1991-10\",\n" +
" \"address\": [\n" +
" {\n" +
" \"state\": \"NY\",\n" +
" \"postalCode\": \"12313\"\n" +
" }\n" +
" ]\n" +
"}";
String coarsePatient = """
{
"resourceType": "Patient",
"active": true,
"name": [
{
"family": "PETERSON",
"given": [
"GARY",
"D"
]
}
],
"telecom": [
{
"system": "phone",
"value": "100100100",
"use": "home"
}
],
"gender": "male",
"birthDate": "1991-10",
"address": [
{
"state": "NY",
"postalCode": "12313"
}
]
}""";
IBaseResource coarseResource = myFhirContext.newJsonParser().parseResource(coarsePatient);
Bundle result = (Bundle) myMdmProvider.match((Patient) coarseResource, new SystemRequestDetails());
assertEquals(1, result.getEntry().size());
}
@Test
public void testNicknameMatch() throws IOException {
setMdmRuleJson("mdm/nickname-mdm-rules.json");
String formalPatientJson = """
{
"resourceType": "Patient",
"active": true,
"name": [
{
"family": "PETERSON",
"given": [
"Gregory"
]
}
],
"gender": "male"
}""";
Patient formalPatient = (Patient) myFhirContext.newJsonParser().parseResource(formalPatientJson);
createPatient(formalPatient);
String noMatchPatientJson = """
{
"resourceType": "Patient",
"active": true,
"name": [
{
"family": "PETERSON",
"given": [
"Bob"
]
}
],
"gender": "male"
}""";
Patient noMatchPatient = (Patient) myFhirContext.newJsonParser().parseResource(noMatchPatientJson);
createPatient(noMatchPatient);
{
Bundle result = (Bundle) myMdmProvider.match(noMatchPatient, new SystemRequestDetails());
assertEquals(0, result.getEntry().size());
}
String nickPatientJson = """
{
"resourceType": "Patient",
"active": true,
"name": [
{
"family": "PETERSON",
"given": [
"Greg"
]
}
],
"gender": "male"
}""";
{
Patient nickPatient = (Patient) myFhirContext.newJsonParser().parseResource(nickPatientJson);
Bundle result = (Bundle) myMdmProvider.match(nickPatient, new SystemRequestDetails());
assertEquals(1, result.getEntry().size());
}
}
}

2
hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmCandidateSearchCriteriaBuilderSvcTest.java
View File

@ -1,8 +1,8 @@
package ca.uhn.fhir.jpa.mdm.svc;
import ca.uhn.fhir.mdm.rules.json.MdmResourceSearchParamJson;
import ca.uhn.fhir.jpa.mdm.BaseMdmR4Test;
import ca.uhn.fhir.jpa.mdm.svc.candidate.MdmCandidateSearchCriteriaBuilderSvc;
import ca.uhn.fhir.mdm.rules.json.MdmResourceSearchParamJson;
import org.hl7.fhir.r4.model.HumanName;
import org.hl7.fhir.r4.model.Patient;
import org.junit.jupiter.api.Test;

57
hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmCandidateSearchSvcIT.java
View File

@ -4,15 +4,21 @@ import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.mdm.BaseMdmR4Test;
import ca.uhn.fhir.jpa.mdm.svc.candidate.MdmCandidateSearchSvc;
import ca.uhn.fhir.jpa.mdm.svc.candidate.TooManyCandidatesException;
import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.searchparam.nickname.NicknameInterceptor;
import ca.uhn.fhir.mdm.rules.config.MdmSettings;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Practitioner;
import org.hl7.fhir.r4.model.Reference;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.springframework.beans.factory.annotation.Autowired;
import java.io.IOException;
import java.util.Collection;
import java.util.Collections;
import java.util.Date;
@ -28,10 +34,21 @@ public class MdmCandidateSearchSvcIT extends BaseMdmR4Test {
MdmCandidateSearchSvc myMdmCandidateSearchSvc;
@Autowired
MdmSettings myMdmSettings;
@Autowired
MatchUrlService myMatchUrlService;
private NicknameInterceptor myNicknameInterceptor;
@BeforeEach
public void before() throws IOException {
myNicknameInterceptor = new NicknameInterceptor();
myInterceptorRegistry.registerInterceptor(myNicknameInterceptor);
}
@AfterEach
public void resetMdmSettings() {
myMdmSettings.setCandidateSearchLimit(MdmSettings.DEFAULT_CANDIDATE_SEARCH_LIMIT);
myInterceptorRegistry.unregisterInterceptor(myNicknameInterceptor);
}
@Test
@ -43,6 +60,42 @@ public class MdmCandidateSearchSvcIT extends BaseMdmR4Test {
assertEquals(1, result.size());
}
@Test
public void testNickname() {
Practitioner formal = new Practitioner();
formal.getNameFirstRep().addGiven("William");
formal.getNameFirstRep().setFamily("Shatner");
formal.setActive(true);
myPractitionerDao.create(formal);
{
// First confirm we can search for this practitioner using a nickname search
SearchParameterMap map = myMatchUrlService.getResourceSearch("Practitioner?given:nickname=Bill&family=Shatner").getSearchParameterMap();
map.setLoadSynchronous(true);
IBundleProvider result = myPractitionerDao.search(map);
assertEquals(1, result.size());
Practitioner first = (Practitioner) result.getResources(0, 1).get(0);
assertEquals("William", first.getNameFirstRep().getGivenAsSingleString());
}
{
// Now achieve the same match via mdm
Practitioner nick = new Practitioner();
nick.getNameFirstRep().addGiven("Bill");
nick.getNameFirstRep().setFamily("Shatner");
Collection<IAnyResource> result = myMdmCandidateSearchSvc.findCandidates("Practitioner", nick, RequestPartitionId.allPartitions());
assertEquals(1, result.size());
}
{
// Should not match Bob
Practitioner noMatch = new Practitioner();
noMatch.getNameFirstRep().addGiven("Bob");
noMatch.getNameFirstRep().setFamily("Shatner");
Collection<IAnyResource> result = myMdmCandidateSearchSvc.findCandidates("Practitioner", noMatch, RequestPartitionId.allPartitions());
assertEquals(0, result.size());
}
}
@Test
public void findCandidatesMultipleMatchesDoNotCauseDuplicates() {
@ -83,9 +136,9 @@ public class MdmCandidateSearchSvcIT extends BaseMdmR4Test {
Patient newJane = buildJanePatient();
createActivePatient();
assertEquals(1, runInTransaction(()->myMdmCandidateSearchSvc.findCandidates("Patient", newJane, RequestPartitionId.allPartitions()).size()));
assertEquals(1, runInTransaction(() -> myMdmCandidateSearchSvc.findCandidates("Patient", newJane, RequestPartitionId.allPartitions()).size()));
createActivePatient();
assertEquals(2, runInTransaction(()->myMdmCandidateSearchSvc.findCandidates("Patient", newJane, RequestPartitionId.allPartitions()).size()));
assertEquals(2, runInTransaction(() -> myMdmCandidateSearchSvc.findCandidates("Patient", newJane, RequestPartitionId.allPartitions()).size()));
try {
createActivePatient();

7
hapi-fhir-jpaserver-mdm/src/test/resources/mdm/mdm-rules.json
View File

@ -25,6 +25,13 @@
"searchParams": [
"general-practitioner"
]
},
{
"resourceType": "Practitioner",
"searchParams": [
"given:nickname",
"family"
]
}
],
"candidateFilterSearchParams": [

44
hapi-fhir-jpaserver-mdm/src/test/resources/mdm/nickname-mdm-rules.json Normal file
View File

@ -0,0 +1,44 @@
{
"version":"1",
"mdmTypes": ["Patient", "Practitioner"],
"candidateSearchParams":[
{
"resourceType": "*",
"searchParams": [
"given:nickname",
"family"
]
}
],
"candidateFilterSearchParams":[],
"matchFields":[
{
"name":"gender",
"resourceType":"Patient",
"resourcePath":"gender",
"matcher":{
"algorithm":"STRING"
}
},
{
"name":"nickname",
"resourceType":"*",
"resourcePath":"name.given",
"matcher":{
"algorithm":"NICKNAME"
}
},
{
"name":"lastname",
"resourceType":"*",
"resourcePath":"name.family",
"matcher":{
"algorithm":"STRING",
"exact": true
}
}
],
"matchResultMap":{
"nickname,lastname": "MATCH"
}
}

67
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/nickname/NicknameInterceptor.java Normal file
View File

@ -0,0 +1,67 @@
package ca.uhn.fhir.jpa.searchparam.nickname;
import ca.uhn.fhir.interceptor.api.Hook;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.rest.param.StringParam;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.Locale;
import java.util.Map;
public class NicknameInterceptor {
private static final Logger ourLog = LoggerFactory.getLogger(NicknameInterceptor.class);
private final NicknameSvc myNicknameSvc;
public NicknameInterceptor() throws IOException {
myNicknameSvc = new NicknameSvc();
}
@Hook(Pointcut.STORAGE_PRESEARCH_REGISTERED)
public void expandNicknames(SearchParameterMap theSearchParameterMap) {
for (Map.Entry<String, List<List<IQueryParameterType>>> set : theSearchParameterMap.entrySet()) {
String paramName = set.getKey();
List<List<IQueryParameterType>> andList = set.getValue();
for (List<IQueryParameterType> orList : andList) {
// here we will know if it's an _id param or not
// from theSearchParameterMap.keySet()
expandAnyNicknameParameters(paramName, orList);
}
}
}
/**
* If a Parameter is a string parameter, and it has been set to expand Nicknames, perform the expansion.
*/
private void expandAnyNicknameParameters(String theParamName, List<IQueryParameterType> orList) {
List<IQueryParameterType> toAdd = new ArrayList<>();
List<IQueryParameterType> toRemove = new ArrayList<>();
for (IQueryParameterType iQueryParameterType : orList) {
if (iQueryParameterType instanceof StringParam) {
StringParam stringParam = (StringParam) iQueryParameterType;
if (stringParam.isNicknameExpand()) {
ourLog.debug("Found a nickname parameter to expand: {} {}", theParamName, stringParam);
toRemove.add(stringParam);
//First, attempt to expand as a formal name
String name = stringParam.getValue().toLowerCase(Locale.ROOT);
List<String> expansions = myNicknameSvc.getEquivalentNames(name);
if (expansions == null) {
continue;
}
ourLog.debug("Parameter has been expanded to: {} {}", theParamName, String.join(", ", expansions));
expansions.stream()
.map(StringParam::new)
.forEach(toAdd::add);
}
}
}
orList.removeAll(toRemove);
orList.addAll(toAdd);
}
}

47
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/nickname/NicknameMap.java Normal file
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@ -0,0 +1,47 @@
package ca.uhn.fhir.jpa.searchparam.nickname;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.Reader;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
class NicknameMap {
private final Map<String, List<String>> myFormalToNick = new HashMap<>();
private final Map<String, List<String>> myNicknameToFormal = new HashMap<>();
void load(Reader theReader) throws IOException {
try (BufferedReader reader = new BufferedReader(theReader)) {
String line;
while ((line = reader.readLine()) != null) {
String[] parts = line.split(",");
String key = parts[0];
List<String> values = new ArrayList<>(Arrays.asList(parts).subList(1, parts.length));
add(key, values);
}
}
}
private void add(String theKey, List<String> theValues) {
myFormalToNick.put(theKey, theValues);
for (String value : theValues) {
myNicknameToFormal.putIfAbsent(value, new ArrayList<>());
myNicknameToFormal.get(value).add(theKey);
}
}
int size() {
return myFormalToNick.size();
}
List<String> getNicknamesFromFormalNameOrNull(String theName) {
return myFormalToNick.get(theName);
}
List<String> getFormalNamesFromNicknameOrNull(String theNickname) {
return myNicknameToFormal.get(theNickname);
}
}

53
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/nickname/NicknameSvc.java Normal file
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@ -0,0 +1,53 @@
package ca.uhn.fhir.jpa.searchparam.nickname;
import org.springframework.core.io.ClassPathResource;
import org.springframework.core.io.Resource;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.Reader;
import java.util.ArrayList;
import java.util.List;
public class NicknameSvc {
private final NicknameMap myNicknameMap = new NicknameMap();
public NicknameSvc() throws IOException {
Resource nicknameCsvResource = new ClassPathResource("/nickname/names.csv");
try (InputStream inputStream = nicknameCsvResource.getInputStream()) {
try (Reader reader = new InputStreamReader(inputStream)) {
myNicknameMap.load(reader);
}
}
}
public int size() {
return myNicknameMap.size();
}
public List<String> getEquivalentNames(String theName) {
List<String> retval = new ArrayList<>();
retval.add(theName);
List<String> expansions;
expansions = getNicknamesFromFormalNameOrNull(theName);
if (expansions != null) {
retval.addAll(expansions);
} else {
expansions = getFormalNamesFromNicknameOrNull(theName);
if (expansions != null) {
retval.addAll(expansions);
}
}
return retval;
}
List<String> getNicknamesFromFormalNameOrNull(String theName) {
return myNicknameMap.getNicknamesFromFormalNameOrNull(theName);
}
List<String> getFormalNamesFromNicknameOrNull(String theNickname) {
return myNicknameMap.getFormalNamesFromNicknameOrNull(theNickname);
}
}

201
hapi-fhir-jpaserver-searchparam/src/main/resources/nickname/License.txt Normal file
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@ -0,0 +1,201 @@
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12
hapi-fhir-jpaserver-searchparam/src/main/resources/nickname/README.md Normal file
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@ -0,0 +1,12 @@
# nickname-and-diminutive-names-lookup
A simple CSV file containing US given names (first name) and their associated nicknames or diminutive names.
This lookup file was initially created by mining this
<a href="http://www.caagri.org/nicknames.html">genealogy page</a>. Because the lookup originates from a dataset used for genealogy purposes there are old names that aren't commonly used these days, but there are recent ones as well. Examples are "gregory", "greg", or "geoffrey", "geoff". There was also a significant effort to make it machine readable, i.e. separate it with commas, remove human conventions, like "rickie(y)" would need to be made into two different names "rickie", and "ricky".
There are Java, Perl, Python, and R parsers provided for convenience.
This is a relatively large list with roughly 1600 names. Any help from people to clean this list up and add to it is greatly appreciated.
This project was created by <a href="http://www.odu.edu/">Old Dominion University</a> - <a href="http://ws-dl.blogspot.com/">Web Science and Digital Libraries Research Group</a>. More information about the creation of this lookup can be found <a href="https://ws-dl.blogspot.com/2010/08/lookup-for-nicknames-and-diminutive.html">here</a>.

2
hapi-fhir-jpaserver-searchparam/src/main/resources/nickname/README.txt Normal file
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@ -0,0 +1,2 @@
The files in this folder were cloned from https://github.com/carltonnorthern/nickname-and-diminutive-names-lookup

1084
hapi-fhir-jpaserver-searchparam/src/main/resources/nickname/names.csv Normal file
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File diff suppressed because it is too large Load Diff

59
hapi-fhir-jpaserver-searchparam/src/test/java/ca/uhn/fhir/jpa/searchparam/nickname/NicknameInterceptorTest.java Normal file
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@ -0,0 +1,59 @@
package ca.uhn.fhir.jpa.searchparam.nickname;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.rest.param.StringParam;
import org.junit.jupiter.api.Test;
import java.io.IOException;
import static org.junit.jupiter.api.Assertions.assertEquals;
class NicknameInterceptorTest {
@Test
public void testExpandForward() throws IOException {
// setup
String formalName = "kenneth";
SearchParameterMap sp = new SearchParameterMap();
sp.add("name", new StringParam(formalName).setNicknameExpand(true));
NicknameInterceptor svc = new NicknameInterceptor();
// execute
svc.expandNicknames(sp);
// verify
String newSearch = sp.toNormalizedQueryString(null);
assertEquals("?name=ken,kendrick,kenneth,kenny", newSearch);
}
@Test
public void testExpandBackward() throws IOException {
// setup
String nickname = "ken";
SearchParameterMap sp = new SearchParameterMap();
sp.add("name", new StringParam(nickname).setNicknameExpand(true));
NicknameInterceptor svc = new NicknameInterceptor();
// execute
svc.expandNicknames(sp);
// verify
String newSearch = sp.toNormalizedQueryString(null);
assertEquals("?name=ken,kendall,kendrick,kendrik,kenneth,kenny,kent,mckenna", newSearch);
}
@Test
public void testNothingToExpand() throws IOException {
// setup
String unusualName = "X Æ A-12";
SearchParameterMap sp = new SearchParameterMap();
sp.add("name", new StringParam(unusualName).setNicknameExpand(true));
NicknameInterceptor svc = new NicknameInterceptor();
// execute
svc.expandNicknames(sp);
// verify
String newSearch = sp.toNormalizedQueryString(null);
assertEquals("?name=x%20%C3%A6%20a-12", newSearch);
}
}

30
hapi-fhir-jpaserver-searchparam/src/test/java/ca/uhn/fhir/jpa/searchparam/nickname/NicknameMapTest.java Normal file
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@ -0,0 +1,30 @@
package ca.uhn.fhir.jpa.searchparam.nickname;
import org.junit.jupiter.api.Test;
import java.io.IOException;
import java.io.StringReader;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.junit.jupiter.api.Assertions.assertEquals;
class NicknameMapTest {
@Test
public void testLoad() throws IOException {
String testData = """
kendall,ken,kenny
kendra,kenj,kenji,kay,kenny
kendrick,ken,kenny
kendrik,ken,kenny
kenneth,ken,kenny,kendrick
kenny,ken,kenneth
kent,ken,kenny,kendrick
""";
NicknameMap map = new NicknameMap();
map.load(new StringReader(testData));
assertEquals(7, map.size());
assertThat(map.getNicknamesFromFormalNameOrNull("kenneth"), containsInAnyOrder("ken", "kenny", "kendrick"));
assertThat(map.getFormalNamesFromNicknameOrNull("ken"), containsInAnyOrder("kendall", "kendrick", "kendrik", "kenneth", "kenny", "kent"));
}
}

15
hapi-fhir-jpaserver-searchparam/src/test/java/ca/uhn/fhir/jpa/searchparam/nickname/NicknameSvcTest.java Normal file
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@ -0,0 +1,15 @@
package ca.uhn.fhir.jpa.searchparam.nickname;
import org.junit.jupiter.api.Test;
import java.io.IOException;
import static org.junit.jupiter.api.Assertions.assertEquals;
class NicknameSvcTest {
@Test
public void testReadfile() throws IOException {
NicknameSvc nicknameSvc = new NicknameSvc();
assertEquals(1082, nicknameSvc.size());
}
}

57
hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/provider/r4/NicknameSearchR4Test.java Normal file
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@ -0,0 +1,57 @@
package ca.uhn.fhir.jpa.provider.r4;
import ca.uhn.fhir.jpa.searchparam.nickname.NicknameInterceptor;
import ca.uhn.fhir.util.BundleUtil;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.Patient;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.springframework.beans.factory.annotation.Autowired;
import java.util.List;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.hasSize;
import static org.junit.jupiter.api.Assertions.assertEquals;
public class NicknameSearchR4Test extends BaseResourceProviderR4Test {
@Autowired
NicknameInterceptor myNicknameInterceptor;
@Override
@AfterEach
public void after() throws Exception {
super.after();
myInterceptorRegistry.unregisterInterceptor(myNicknameInterceptor);
}
@BeforeEach
@Override
public void before() throws Exception {
super.before();
myInterceptorRegistry.registerInterceptor(myNicknameInterceptor);
}
@Test
public void testExpandNickname() {
Patient patient1 = new Patient();
patient1.getNameFirstRep().addGiven("ken");
myClient.create().resource(patient1).execute();
Patient patient2 = new Patient();
patient2.getNameFirstRep().addGiven("bob");
myClient.create().resource(patient2).execute();
Bundle result = myClient
.loadPage()
.byUrl(ourServerBase + "/Patient?name:nickname=kenneth")
.andReturnBundle(Bundle.class)
.execute();
List<Patient> resources = BundleUtil.toListOfResourcesOfType(myFhirContext,result, Patient.class);
assertThat(resources, hasSize(1));
assertEquals("ken", resources.get(0).getNameFirstRep().getGivenAsSingleString());
}
}

8
hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/rules/config/MdmRuleValidator.java
View File

@ -20,14 +20,14 @@ package ca.uhn.fhir.mdm.rules.config;
* #L%
*/
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.fhirpath.IFhirPath;
import ca.uhn.fhir.mdm.api.MdmConstants;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.mdm.api.IMdmRuleValidator;
import ca.uhn.fhir.mdm.api.MdmConstants;
import ca.uhn.fhir.mdm.rules.json.MdmFieldMatchJson;
import ca.uhn.fhir.mdm.rules.json.MdmFilterSearchParamJson;
import ca.uhn.fhir.mdm.rules.json.MdmResourceSearchParamJson;
@ -36,6 +36,7 @@ import ca.uhn.fhir.mdm.rules.json.MdmSimilarityJson;
import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
import ca.uhn.fhir.util.FhirTerser;
import ca.uhn.fhir.util.SearchParameterUtil;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@ -150,7 +151,8 @@ public class MdmRuleValidator implements IMdmRuleValidator {
}
private void validateResourceSearchParam(String theFieldName, String theResourceType, String theSearchParam) {
if (mySearchParamRetriever.getActiveSearchParam(theResourceType, theSearchParam) == null) {
String searchParam = SearchParameterUtil.stripModifier(theSearchParam);
if (mySearchParamRetriever.getActiveSearchParam(theResourceType, searchParam) == null) {
throw new ConfigurationException(Msg.code(1511) + "Error in " + theFieldName + ": " + theResourceType + " does not have a search parameter called '" + theSearchParam + "'");
}
}

1
hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/rules/matcher/MdmMatcherEnum.java
View File

@ -40,6 +40,7 @@ public enum MdmMatcherEnum {
NYSIIS(new HapiStringMatcher(new PhoneticEncoderMatcher(PhoneticEncoderEnum.NYSIIS))),
REFINED_SOUNDEX(new HapiStringMatcher(new PhoneticEncoderMatcher(PhoneticEncoderEnum.REFINED_SOUNDEX))),
SOUNDEX(new HapiStringMatcher(new PhoneticEncoderMatcher(PhoneticEncoderEnum.SOUNDEX))),
NICKNAME(new HapiStringMatcher(new NicknameMatcher())),
STRING(new HapiStringMatcher()),
SUBSTRING(new HapiStringMatcher(new SubstringStringMatcher())),

30
hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/rules/matcher/NicknameMatcher.java Normal file
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@ -0,0 +1,30 @@
package ca.uhn.fhir.mdm.rules.matcher;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.jpa.searchparam.nickname.NicknameSvc;
import java.io.IOException;
import java.util.List;
import java.util.Locale;
public class NicknameMatcher implements IMdmStringMatcher {
private final NicknameSvc myNicknameSvc;
public NicknameMatcher() {
try {
myNicknameSvc = new NicknameSvc();
} catch (IOException e) {
throw new ConfigurationException(Msg.code(2078) + "Unable to load nicknames", e);
}
}
@Override
public boolean matches(String theLeftString, String theRightString) {
String leftString = theLeftString.toLowerCase(Locale.ROOT);
String rightString = theRightString.toLowerCase(Locale.ROOT);
List<String> leftNames = myNicknameSvc.getEquivalentNames(leftString);
return leftNames.contains(rightString);
}
}

25
hapi-fhir-server-mdm/src/test/java/ca/uhn/fhir/mdm/rules/matcher/NicknameMatcherTest.java Normal file
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@ -0,0 +1,25 @@
package ca.uhn.fhir.mdm.rules.matcher;
import org.junit.jupiter.api.Test;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertTrue;
class NicknameMatcherTest {
IMdmStringMatcher matcher = new NicknameMatcher();
@Test
public void testMatches() {
assertTrue(matcher.matches("Ken", "ken"));
assertTrue(matcher.matches("ken", "Ken"));
assertTrue(matcher.matches("Ken", "Ken"));
assertTrue(matcher.matches("Kenneth", "Ken"));
assertTrue(matcher.matches("Kenneth", "Kenny"));
assertTrue(matcher.matches("Ken", "Kenneth"));
assertTrue(matcher.matches("Kenny", "Kenneth"));
assertFalse(matcher.matches("Ken", "Bob"));
// These aren't nickname matches. If you want matches like these use a phonetic matcher
assertFalse(matcher.matches("Allen", "Allan"));
}
}

19
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/interceptor/auth/RuleTarget.java
View File

@ -48,11 +48,24 @@ public class RuleTarget {
for (Map.Entry<String, String[]> entry : theParameters.entrySet()) {
String key = entry.getKey();
String[] value = entry.getValue();
if (key.endsWith(Constants.PARAMQUALIFIER_MDM)) {
key = key.split(Constants.PARAMQUALIFIER_MDM)[0];
}
key = stripMdmQualifier(key);
key = stripNicknameQualifier(key);
retval.put(key, value);
}
return retval;
}
private String stripMdmQualifier(String theKey) {
if (theKey.endsWith(Constants.PARAMQUALIFIER_MDM)) {
theKey = theKey.split(Constants.PARAMQUALIFIER_MDM)[0];
}
return theKey;
}
private String stripNicknameQualifier(String theKey) {
if (theKey.endsWith(Constants.PARAMQUALIFIER_NICKNAME)) {
theKey = theKey.split(Constants.PARAMQUALIFIER_NICKNAME)[0];
}
return theKey;
}
}

30
hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/param/TokenParamTest.java
View File

@ -2,12 +2,14 @@ package ca.uhn.fhir.rest.param;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import org.junit.jupiter.api.Test;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertNotEquals;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.junit.jupiter.api.Assertions.fail;
public class TokenParamTest {
private static final FhirContext ourCtx = FhirContext.forR4Cached();
@ -48,4 +50,32 @@ public class TokenParamTest {
assertEquals("type-value|identifier-value", param.getValue());
}
@Test
public void testNameNickname() {
StringParam param = new StringParam();
assertFalse(param.isNicknameExpand());
param.setValueAsQueryToken(ourCtx, "name", Constants.PARAMQUALIFIER_NICKNAME, "kenny");
assertTrue(param.isNicknameExpand());
}
@Test
public void testGivenNickname() {
StringParam param = new StringParam();
assertFalse(param.isNicknameExpand());
param.setValueAsQueryToken(ourCtx, "given", Constants.PARAMQUALIFIER_NICKNAME, "kenny");
assertTrue(param.isNicknameExpand());
}
@Test
public void testInvalidNickname() {
StringParam param = new StringParam();
assertFalse(param.isNicknameExpand());
try {
param.setValueAsQueryToken(ourCtx, "family", Constants.PARAMQUALIFIER_NICKNAME, "kenny");
fail();
} catch (InvalidRequestException e) {
assertEquals("HAPI-2077: Modifier :nickname may only be used with 'name' and 'given' search parameters", e.getMessage());
}
}
}