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Changes recommended during code review.

This commit is contained in:
ianmarshall 2020-06-09 09:59:03 -04:00
parent 3c600e06d4
commit 122bd97344
3 changed files with 57 additions and 26 deletions
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4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/lastn.md
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@ -16,6 +16,8 @@ As described in the [FHIR specification](http://hl7.org/fhir/observation-operati
# Limitations
Currently only Elasticsearch versions up to 6.5.4 are supported.
Search parameters other than those listed above are currently not supported.
The grouping of Observation resources by `Observation.code` means that the `$lastn` operation will not work in cases where `Observation.code` has more than one coding.
@ -38,4 +40,6 @@ In addition, the Elasticsearch client service, `ElasticsearchSvcImpl` will need
}
```
The Elasticsearch client service requires that security be enabled in the Elasticsearch clusters, and that an Elasticsearch user be available with permissions to create an index and to index, update and delete documents as needed.
See the [JavaDoc](/hapi-fhir/apidocs/hapi-fhir-jpaserver-base/ca/uhn/fhir/jpa/search/lastn/IElasticsearchSvc.html) for more information regarding the Elasticsearch client service.

71
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/lastn/ElasticsearchSvcImpl.java
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@ -81,6 +81,7 @@ import static org.apache.commons.lang3.StringUtils.isBlank;
public class ElasticsearchSvcImpl implements IElasticsearchSvc {
// Index Constants
public static final String OBSERVATION_INDEX = "observation_index";
public static final String OBSERVATION_CODE_INDEX = "code_index";
public static final String OBSERVATION_DOCUMENT_TYPE = "ca.uhn.fhir.jpa.model.entity.ObservationIndexedSearchParamLastNEntity";
@ -88,14 +89,34 @@ public class ElasticsearchSvcImpl implements IElasticsearchSvc {
public static final String OBSERVATION_INDEX_SCHEMA_FILE = "ObservationIndexSchema.json";
public static final String OBSERVATION_CODE_INDEX_SCHEMA_FILE = "ObservationCodeIndexSchema.json";
private final RestHighLevelClient myRestHighLevelClient;
private final ObjectMapper objectMapper = new ObjectMapper();
// Aggregation Constants
private final String GROUP_BY_SUBJECT = "group_by_subject";
private final String GROUP_BY_SYSTEM = "group_by_system";
private final String GROUP_BY_CODE = "group_by_code";
private final String MOST_RECENT_EFFECTIVE = "most_recent_effective";
// Observation index document element names
private final String OBSERVATION_IDENTIFIER_FIELD_NAME = "identifier";
private final String OBSERVATION_SUBJECT_FIELD_NAME = "subject";
private final String OBSERVATION_CODEVALUE_FIELD_NAME = "codeconceptcodingcode";
private final String OBSERVATION_CODESYSTEM_FIELD_NAME = "codeconceptcodingsystem";
private final String OBSERVATION_CODEHASH_FIELD_NAME = "codeconceptcodingcode_system_hash";
private final String OBSERVATION_CODEDISPLAY_FIELD_NAME = "codeconceptcodingdisplay";
private final String OBSERVATION_CODE_TEXT_FIELD_NAME = "codeconcepttext";
private final String OBSERVATION_EFFECTIVEDTM_FIELD_NAME = "effectivedtm";
private final String OBSERVATION_CATEGORYHASH_FIELD_NAME = "categoryconceptcodingcode_system_hash";
private final String OBSERVATION_CATEGORYVALUE_FIELD_NAME = "categoryconceptcodingcode";
private final String OBSERVATION_CATEGORYSYSTEM_FIELD_NAME = "categoryconceptcodingsystem";
private final String OBSERVATION_CATEGORYDISPLAY_FIELD_NAME = "categoryconceptcodingdisplay";
private final String OBSERVATION_CATEGORYTEXT_FIELD_NAME = "categoryconcepttext";
// Code index document element names
private final String CODE_HASH = "codingcode_system_hash";
private final String CODE_TEXT = "text";
private final RestHighLevelClient myRestHighLevelClient;
private final ObjectMapper objectMapper = new ObjectMapper();
public ElasticsearchSvcImpl(String theHostname, int thePort, String theUsername, String thePassword) {
myRestHighLevelClient = ElasticsearchRestClientFactory.createElasticsearchHighLevelRestClient(theHostname, thePort, theUsername, thePassword);
@ -239,7 +260,7 @@ public class ElasticsearchSvcImpl implements IElasticsearchSvc {
}
private CompositeAggregationBuilder createObservationSubjectAggregationBuilder(Integer theMaxNumberObservationsPerCode, String[] theTopHitsInclude) {
CompositeValuesSourceBuilder<?> subjectValuesBuilder = new TermsValuesSourceBuilder("subject").field("subject");
CompositeValuesSourceBuilder<?> subjectValuesBuilder = new TermsValuesSourceBuilder(OBSERVATION_SUBJECT_FIELD_NAME).field(OBSERVATION_SUBJECT_FIELD_NAME);
List<CompositeValuesSourceBuilder<?>> compositeAggSubjectSources = new ArrayList<>();
compositeAggSubjectSources.add(subjectValuesBuilder);
CompositeAggregationBuilder compositeAggregationSubjectBuilder = new CompositeAggregationBuilder(GROUP_BY_SUBJECT, compositeAggSubjectSources);
@ -250,14 +271,14 @@ public class ElasticsearchSvcImpl implements IElasticsearchSvc {
}
private TermsAggregationBuilder createObservationCodeAggregationBuilder(int theMaxNumberObservationsPerCode, String[] theTopHitsInclude) {
TermsAggregationBuilder observationCodeCodeAggregationBuilder = new TermsAggregationBuilder(GROUP_BY_CODE, ValueType.STRING).field("codeconceptcodingcode");
TermsAggregationBuilder observationCodeCodeAggregationBuilder = new TermsAggregationBuilder(GROUP_BY_CODE, ValueType.STRING).field(OBSERVATION_CODEVALUE_FIELD_NAME);
observationCodeCodeAggregationBuilder.order(BucketOrder.key(true));
// Top Hits Aggregation
observationCodeCodeAggregationBuilder.subAggregation(AggregationBuilders.topHits("most_recent_effective")
.sort("effectivedtm", SortOrder.DESC)
observationCodeCodeAggregationBuilder.subAggregation(AggregationBuilders.topHits(MOST_RECENT_EFFECTIVE)
.sort(OBSERVATION_EFFECTIVEDTM_FIELD_NAME, SortOrder.DESC)
.fetchSource(theTopHitsInclude, null).size(theMaxNumberObservationsPerCode));
observationCodeCodeAggregationBuilder.size(10000);
TermsAggregationBuilder observationCodeSystemAggregationBuilder = new TermsAggregationBuilder(GROUP_BY_SYSTEM, ValueType.STRING).field("codeconceptcodingsystem");
TermsAggregationBuilder observationCodeSystemAggregationBuilder = new TermsAggregationBuilder(GROUP_BY_SYSTEM, ValueType.STRING).field(OBSERVATION_CODESYSTEM_FIELD_NAME);
observationCodeSystemAggregationBuilder.order(BucketOrder.key(true));
observationCodeSystemAggregationBuilder.subAggregation(observationCodeCodeAggregationBuilder);
return observationCodeSystemAggregationBuilder;
@ -339,7 +360,7 @@ public class ElasticsearchSvcImpl implements IElasticsearchSvc {
private SearchHit[] getLastNMatches(Terms.Bucket theObservationCodeBucket) {
Aggregations topHitObservationCodes = theObservationCodeBucket.getAggregations();
ParsedTopHits parsedTopHits = topHitObservationCodes.get("most_recent_effective");
ParsedTopHits parsedTopHits = topHitObservationCodes.get(MOST_RECENT_EFFECTIVE);
return parsedTopHits.getHits().getHits();
}
@ -371,7 +392,7 @@ public class ElasticsearchSvcImpl implements IElasticsearchSvc {
SearchSourceBuilder searchSourceBuilder = new SearchSourceBuilder();
// Query
BoolQueryBuilder boolQueryBuilder = QueryBuilders.boolQuery();
boolQueryBuilder.must(QueryBuilders.termQuery("subject", theSubjectParam));
boolQueryBuilder.must(QueryBuilders.termQuery(OBSERVATION_SUBJECT_FIELD_NAME, theSubjectParam));
addCategoriesCriteria(boolQueryBuilder, theSearchParameterMap, theFhirContext);
addObservationCodeCriteria(boolQueryBuilder, theSearchParameterMap, theFhirContext);
addDateCriteria(boolQueryBuilder, theSearchParameterMap, theFhirContext);
@ -408,19 +429,19 @@ public class ElasticsearchSvcImpl implements IElasticsearchSvc {
textOnlyList.addAll(getCodingTextOnlyValues(nextAnd));
}
if (codeSystemHashList.size() > 0) {
theBoolQueryBuilder.must(QueryBuilders.termsQuery("categoryconceptcodingcode_system_hash", codeSystemHashList));
theBoolQueryBuilder.must(QueryBuilders.termsQuery(OBSERVATION_CATEGORYHASH_FIELD_NAME, codeSystemHashList));
}
if (codeOnlyList.size() > 0) {
theBoolQueryBuilder.must(QueryBuilders.termsQuery("categoryconceptcodingcode", codeOnlyList));
theBoolQueryBuilder.must(QueryBuilders.termsQuery(OBSERVATION_CATEGORYVALUE_FIELD_NAME, codeOnlyList));
}
if (systemOnlyList.size() > 0) {
theBoolQueryBuilder.must(QueryBuilders.termsQuery("categoryconceptcodingsystem", systemOnlyList));
theBoolQueryBuilder.must(QueryBuilders.termsQuery(OBSERVATION_CATEGORYSYSTEM_FIELD_NAME, systemOnlyList));
}
if (textOnlyList.size() > 0) {
BoolQueryBuilder myTextBoolQueryBuilder = QueryBuilders.boolQuery();
for (String textOnlyParam : textOnlyList) {
myTextBoolQueryBuilder.should(QueryBuilders.matchPhrasePrefixQuery("categoryconceptcodingdisplay", textOnlyParam));
myTextBoolQueryBuilder.should(QueryBuilders.matchPhrasePrefixQuery("categoryconcepttext", textOnlyParam));
myTextBoolQueryBuilder.should(QueryBuilders.matchPhrasePrefixQuery(OBSERVATION_CATEGORYDISPLAY_FIELD_NAME, textOnlyParam));
myTextBoolQueryBuilder.should(QueryBuilders.matchPhrasePrefixQuery(OBSERVATION_CATEGORYTEXT_FIELD_NAME, textOnlyParam));
}
theBoolQueryBuilder.must(myTextBoolQueryBuilder);
}
@ -506,19 +527,19 @@ public class ElasticsearchSvcImpl implements IElasticsearchSvc {
textOnlyList.addAll(getCodingTextOnlyValues(nextAnd));
}
if (codeSystemHashList.size() > 0) {
theBoolQueryBuilder.must(QueryBuilders.termsQuery("codeconceptcodingcode_system_hash", codeSystemHashList));
theBoolQueryBuilder.must(QueryBuilders.termsQuery(OBSERVATION_CODEHASH_FIELD_NAME, codeSystemHashList));
}
if (codeOnlyList.size() > 0) {
theBoolQueryBuilder.must(QueryBuilders.termsQuery("codeconceptcodingcode", codeOnlyList));
theBoolQueryBuilder.must(QueryBuilders.termsQuery(OBSERVATION_CODEVALUE_FIELD_NAME, codeOnlyList));
}
if (systemOnlyList.size() > 0) {
theBoolQueryBuilder.must(QueryBuilders.termsQuery("codeconceptcodingsystem", systemOnlyList));
theBoolQueryBuilder.must(QueryBuilders.termsQuery(OBSERVATION_CODESYSTEM_FIELD_NAME, systemOnlyList));
}
if (textOnlyList.size() > 0) {
BoolQueryBuilder myTextBoolQueryBuilder = QueryBuilders.boolQuery();
for (String textOnlyParam : textOnlyList) {
myTextBoolQueryBuilder.should(QueryBuilders.matchPhrasePrefixQuery("codeconceptcodingdisplay", textOnlyParam));
myTextBoolQueryBuilder.should(QueryBuilders.matchPhrasePrefixQuery("codeconcepttext", textOnlyParam));
myTextBoolQueryBuilder.should(QueryBuilders.matchPhrasePrefixQuery(OBSERVATION_CODEDISPLAY_FIELD_NAME, textOnlyParam));
myTextBoolQueryBuilder.should(QueryBuilders.matchPhrasePrefixQuery(OBSERVATION_CODE_TEXT_FIELD_NAME, textOnlyParam));
}
theBoolQueryBuilder.must(myTextBoolQueryBuilder);
}
@ -545,7 +566,7 @@ public class ElasticsearchSvcImpl implements IElasticsearchSvc {
private void createDateCriteria(DateParam theDate, BoolQueryBuilder theBoolQueryBuilder) {
Long dateInstant = theDate.getValue().getTime();
RangeQueryBuilder myRangeQueryBuilder = new RangeQueryBuilder("effectivedtm");
RangeQueryBuilder myRangeQueryBuilder = new RangeQueryBuilder(OBSERVATION_EFFECTIVEDTM_FIELD_NAME);
ParamPrefixEnum prefix = theDate.getPrefix();
if (prefix == ParamPrefixEnum.GREATERTHAN || prefix == ParamPrefixEnum.STARTS_AFTER) {
@ -557,7 +578,7 @@ public class ElasticsearchSvcImpl implements IElasticsearchSvc {
} else if (prefix == ParamPrefixEnum.GREATERTHAN_OR_EQUALS) {
theBoolQueryBuilder.should(myRangeQueryBuilder.gte(dateInstant));
} else {
theBoolQueryBuilder.should(new MatchQueryBuilder("effectivedtm", dateInstant));
theBoolQueryBuilder.should(new MatchQueryBuilder(OBSERVATION_EFFECTIVEDTM_FIELD_NAME, dateInstant));
}
}
@ -652,9 +673,9 @@ public class ElasticsearchSvcImpl implements IElasticsearchSvc {
SearchSourceBuilder searchSourceBuilder = new SearchSourceBuilder();
BoolQueryBuilder boolQueryBuilder = QueryBuilders.boolQuery();
if (theCodeSystemHash != null) {
boolQueryBuilder.must(QueryBuilders.termQuery("codingcode_system_hash", theCodeSystemHash));
boolQueryBuilder.must(QueryBuilders.termQuery(CODE_HASH, theCodeSystemHash));
} else {
boolQueryBuilder.must(QueryBuilders.matchPhraseQuery("text", theText));
boolQueryBuilder.must(QueryBuilders.matchPhraseQuery(CODE_TEXT, theText));
}
searchSourceBuilder.query(boolQueryBuilder);

8
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseR4SearchLastN.java
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@ -166,7 +166,7 @@ public class BaseR4SearchLastN extends BaseJpaTest {
obs.getSubject().setReferenceElement(thePatientId);
obs.getCode().addCoding().setCode(theObservationCode).setSystem(codeSystem);
obs.setValue(new StringType(theObservationCode + "_0"));
Date effectiveDtm = new Date(observationDate.getTimeInMillis() - (3600*1000*(theTimeOffset+idx)));
Date effectiveDtm = calculateObservationDateFromOffset(theTimeOffset, idx);
obs.setEffective(new DateTimeType(effectiveDtm));
obs.getCategoryFirstRep().addCoding().setCode(theCategoryCode).setSystem(categorySystem);
String observationId = myObservationDao.create(obs, mockSrd()).getId().toUnqualifiedVersionless().getValue();
@ -177,6 +177,12 @@ public class BaseR4SearchLastN extends BaseJpaTest {
}
}
private Date calculateObservationDateFromOffset(Integer theTimeOffset, Integer theObservationIndex) {
int milliSecondsPerHour = 3600*1000;
// Generate a Date by subtracting a calculated number of hours from the static observationDate property.
return new Date(observationDate.getTimeInMillis() - (milliSecondsPerHour*(theTimeOffset+theObservationIndex)));
}
protected ServletRequestDetails mockSrd() {
return mySrd;
}