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Several fixes

This commit is contained in:
James Agnew 2018-06-20 05:53:32 -04:00
parent a46b4a4637
commit 218937e425
10 changed files with 194 additions and 23 deletions
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2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConcept.java
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@ -78,7 +78,7 @@ public class TermConcept implements Serializable {
private String myDisplay;
@OneToMany(mappedBy = "myConcept", orphanRemoval = true)
@Field
@Field(name = "PROPmyProperties", analyzer = @Analyzer(definition = "termConceptPropertyAnalyzer"))
@FieldBridge(impl = TermConceptPropertyFieldBridge.class)
private Collection<TermConceptProperty> myProperties;

22
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptPropertyFieldBridge.java
View File

@ -21,12 +21,16 @@ package ca.uhn.fhir.jpa.entity;
*/
import org.apache.lucene.document.Document;
import org.apache.lucene.document.Field;
import org.apache.lucene.document.StringField;
import org.hibernate.search.bridge.FieldBridge;
import org.hibernate.search.bridge.LuceneOptions;
import org.hibernate.search.bridge.StringBridge;
import java.util.Collection;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
/**
* Allows hibernate search to index individual concepts' properties
*/
@ -51,13 +55,23 @@ public class TermConceptPropertyFieldBridge implements FieldBridge, StringBridge
Collection<TermConceptProperty> properties = (Collection<TermConceptProperty>) theValue;
if (properties != null) {
for (TermConceptProperty next : properties) {
String propValue = next.getKey() + "=" + next.getValue();
theLuceneOptions.addFieldToDocument(theName, propValue, theDocument);
// String propValue = next.getKey() + "=" + next.getValue();
// theLuceneOptions.addFieldToDocument(theName, propValue, theDocument);
//
// if (next.getType() == TermConceptPropertyTypeEnum.CODING) {
// propValue = next.getKey() + "=" + next.getDisplay();
// theLuceneOptions.addFieldToDocument(theName, propValue, theDocument);
// }
theDocument.add(new StringField("PROP"+next.getKey(), next.getValue(), Field.Store.YES));
if (next.getType() == TermConceptPropertyTypeEnum.CODING) {
propValue = next.getKey() + "=" + next.getDisplay();
theLuceneOptions.addFieldToDocument(theName, propValue, theDocument);
if (isNotBlank(next.getDisplay())) {
theDocument.add(new StringField("PROP" + next.getKey(), next.getDisplay(), Field.Store.YES));
}
// theLuceneOptions.addFieldToDocument("PROPmyProperties", next.getKey() + "=" + next.getDisplay(), theDocument);
}
}
}
}

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/LuceneSearchMappingFactory.java
View File

@ -66,7 +66,8 @@ public class LuceneSearchMappingFactory {
.analyzerDef("standardAnalyzer", StandardTokenizerFactory.class)
.filter(LowerCaseFilterFactory.class)
.analyzerDef("exactAnalyzer", StandardTokenizerFactory.class)
.analyzerDef("conceptParentPidsAnalyzer", WhitespaceTokenizerFactory.class);
.analyzerDef("conceptParentPidsAnalyzer", WhitespaceTokenizerFactory.class)
.analyzerDef("termConceptPropertyAnalyzer", WhitespaceTokenizerFactory.class);
return mapping;
}

37
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseHapiTerminologySvcImpl.java
View File

@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.term;
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
*
* http://www.apache.org/licenses/LICENSE-2.0
*
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@ -42,7 +42,9 @@ import com.google.common.base.Stopwatch;
import com.google.common.collect.ArrayListMultimap;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.time.DateUtils;
import org.apache.lucene.index.Term;
import org.apache.lucene.search.Query;
import org.apache.lucene.search.RegexpQuery;
import org.hibernate.ScrollMode;
import org.hibernate.ScrollableResults;
import org.hibernate.search.jpa.FullTextEntityManager;
@ -79,6 +81,7 @@ import java.util.*;
import java.util.concurrent.TimeUnit;
import java.util.stream.Collectors;
import static com.google.common.base.Ascii.toLowerCase;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
@ -352,19 +355,39 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
} else {
addDisplayFilterInexact(qb, bool, nextFilter);
}
} else if ((nextFilter.getProperty().equals("concept") || nextFilter.getProperty().equals("code")) && nextFilter.getOp() == ValueSet.FilterOperator.ISA) {
} else if (nextFilter.getProperty().equals("concept") || nextFilter.getProperty().equals("code")) {
TermConcept code = findCode(system, nextFilter.getValue());
if (code == null) {
throw new InvalidRequestException("Invalid filter criteria - code does not exist: {" + system + "}" + nextFilter.getValue());
}
ourLog.info(" * Filtering on codes with a parent of {}/{}/{}", code.getId(), code.getCode(), code.getDisplay());
bool.must(qb.keyword().onField("myParentPids").matching("" + code.getId()).createQuery());
if (nextFilter.getOp() == ValueSet.FilterOperator.ISA) {
ourLog.info(" * Filtering on codes with a parent of {}/{}/{}", code.getId(), code.getCode(), code.getDisplay());
bool.must(qb.keyword().onField("myParentPids").matching("" + code.getId()).createQuery());
} else {
throw new InvalidRequestException("Don't know how to handle op=" + nextFilter.getOp() + " on property " + nextFilter.getProperty());
}
} else {
bool.must(qb.phrase().onField("myProperties").sentence(nextFilter.getProperty() + "=" + nextFilter.getValue()).createQuery());
if (nextFilter.getOp() == ValueSet.FilterOperator.REGEX) {
String value = nextFilter.getValue();
if (value.endsWith("$")) {
value = value.substring(0,value.length() - 1);
}
Term term = new Term("PROP"+nextFilter.getProperty(), value);
RegexpQuery query = new RegexpQuery(term);
bool.must(query);
} else {
bool.must(qb.phrase().onField("PROP" + nextFilter.getProperty()).sentence(nextFilter.getValue()).createQuery());
// bool.must(qb.phrase().onField("myProperties").sentence(nextFilter.getProperty() + "=" + nextFilter.getValue()).createQuery());
}
}
}
@ -905,7 +928,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
codeSystem.setCurrentVersion(theCodeSystemVersion);
codeSystem = myCodeSystemDao.saveAndFlush(codeSystem);
ourLog.info("Setting codesystemversion on {} concepts...", totalCodeCount);
ourLog.info("Setting CodeSystemVersion[{}] on {} concepts...", codeSystem.getPid(), totalCodeCount);
for (TermConcept next : theCodeSystemVersion.getConcepts()) {
populateVersion(next, codeSystemVersion);

92
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplDstu3Test.java
View File

@ -144,6 +144,98 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
}
@Test
public void testExpandValueSetPropertySearchWithRegexInclude() {
runInTransaction(()->{
CodeSystem codeSystem = new CodeSystem();
codeSystem.setUrl(CS_URL);
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
ResourceTable table = myResourceTableDao.findById(id.getIdPartAsLong()).orElseThrow(IllegalArgumentException::new);
TermCodeSystemVersion cs = new TermCodeSystemVersion();
cs.setResource(table);
TermConcept code;
code = new TermConcept(cs, "50015-7");
code.addPropertyString("SYSTEM", "Bld/Bone mar^Donor");
cs.getConcepts().add(code);
code = new TermConcept(cs, "43343-3");
code.addPropertyString("SYSTEM", "Ser");
cs.getConcepts().add(code);
myTermSvc.storeNewCodeSystemVersion(table.getId(), CS_URL, "SYSTEM NAME", cs);
});
List<String> codes;
ValueSet vs;
ValueSet outcome;
ValueSet.ConceptSetComponent include;
// Include
vs = new ValueSet();
include = vs.getCompose().addInclude();
include.setSystem(CS_URL);
include
.addFilter()
.setProperty("SYSTEM")
.setOp(ValueSet.FilterOperator.REGEX)
.setValue(".*\\^Donor$");
// .setValue("\\\\^Donor$");
outcome = myTermSvc.expandValueSet(vs);
codes = toCodesContains(outcome.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("50015-7"));
}
@Test
public void testExpandValueSetPropertySearchWithRegexExclude() {
CodeSystem codeSystem = new CodeSystem();
codeSystem.setUrl(CS_URL);
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
ResourceTable table = myResourceTableDao.findById(id.getIdPartAsLong()).orElseThrow(IllegalArgumentException::new);
TermCodeSystemVersion cs = new TermCodeSystemVersion();
cs.setResource(table);
TermConcept code;
code = new TermConcept(cs, "50015-7");
code.addPropertyString("SYSTEM", "Bld/Bone mar^Donor");
cs.getConcepts().add(code);
code = new TermConcept(cs, "43343-3");
code.addPropertyString("SYSTEM", "Ser");
cs.getConcepts().add(code);
myTermSvc.storeNewCodeSystemVersion(table.getId(), CS_URL, "SYSTEM NAME", cs);
List<String> codes;
ValueSet vs;
ValueSet outcome;
ValueSet.ConceptSetComponent exclude;
// Include
vs = new ValueSet();
vs.getCompose()
.addInclude()
.setSystem(CS_URL);
exclude = vs.getCompose().addExclude();
exclude.setSystem(CS_URL);
exclude
.addFilter()
.setProperty("SYSTEM")
.setOp(ValueSet.FilterOperator.REGEX)
.setValue("\\\\^Donor$");
outcome = myTermSvc.expandValueSet(vs);
codes = toCodesContains(outcome.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("43343-3"));
}
@Test
public void testExpandValueSetPropertySearch() {
createCodeSystem();
createCodeSystem2();

21
hapi-fhir-jpaserver-base/src/test/resources/loinc/PartRelatedCodeMapping_Beta_1.csv
View File

@ -1,10 +1,11 @@
"PartNumber","PartName","PartTypeName","ExtCodeId","ExtCodeDisplayName","ExtCodeSystem","MapType","ContentOrigin","ExtCodeSystemVersion","ExtCodeSystemCopyrightNotice"
"LP18172-4","Interferon.beta","COMPONENT"," 420710006","Interferon beta (substance)","http://snomed.info/sct","Exact","Both","http://snomed.info/sct/900000000000207008/version/20170731","This material includes SNOMED Clinical Terms® (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO) under license. All rights reserved. SNOMED CT® was originally created by The College of American Pathologists. “SNOMED” and “SNOMED CT” are registered trademarks of the IHTSDO.This material includes content from the US Edition to SNOMED CT, which is developed and maintained by the U.S. National Library of Medicine and is available to authorized UMLS Metathesaurus Licensees from the UTS Downloads site at https://uts.nlm.nih.gov.Use of SNOMED CT content is subject to the terms and conditions set forth in the SNOMED CT Affiliate License Agreement. It is the responsibility of those implementing this product to ensure they are appropriately licensed and for more information on the license, including how to register as an Affiliate Licensee, please refer to http://www.snomed.org/snomed-ct/get-snomed-ct or info@snomed.org<mailto:info@snomed.org>. This may incur a fee in SNOMED International non-Member countries."
"LP31706-2","Nornicotine","COMPONENT","1018001","Nornicotine (substance)","http://snomed.info/sct","Exact","Both","http://snomed.info/sct/900000000000207008/version/20170731","This material includes SNOMED Clinical Terms® (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO) under license. All rights reserved. SNOMED CT® was originally created by The College of American Pathologists. “SNOMED” and “SNOMED CT” are registered trademarks of the IHTSDO.This material includes content from the US Edition to SNOMED CT, which is developed and maintained by the U.S. National Library of Medicine and is available to authorized UMLS Metathesaurus Licensees from the UTS Downloads site at https://uts.nlm.nih.gov.Use of SNOMED CT content is subject to the terms and conditions set forth in the SNOMED CT Affiliate License Agreement. It is the responsibility of those implementing this product to ensure they are appropriately licensed and for more information on the license, including how to register as an Affiliate Licensee, please refer to http://www.snomed.org/snomed-ct/get-snomed-ct or info@snomed.org<mailto:info@snomed.org>. This may incur a fee in SNOMED International non-Member countries."
"LP15826-8","Prostaglandin F2","COMPONENT","10192006","Prostaglandin PGF2 (substance)","http://snomed.info/sct","Exact","Both","http://snomed.info/sct/900000000000207008/version/20170731","This material includes SNOMED Clinical Terms® (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO) under license. All rights reserved. SNOMED CT® was originally created by The College of American Pathologists. “SNOMED” and “SNOMED CT” are registered trademarks of the IHTSDO.This material includes content from the US Edition to SNOMED CT, which is developed and maintained by the U.S. National Library of Medicine and is available to authorized UMLS Metathesaurus Licensees from the UTS Downloads site at https://uts.nlm.nih.gov.Use of SNOMED CT content is subject to the terms and conditions set forth in the SNOMED CT Affiliate License Agreement. It is the responsibility of those implementing this product to ensure they are appropriately licensed and for more information on the license, including how to register as an Affiliate Licensee, please refer to http://www.snomed.org/snomed-ct/get-snomed-ct or info@snomed.org<mailto:info@snomed.org>. This may incur a fee in SNOMED International non-Member countries."
"LP7400-7","Liver","SYSTEM","10200004","Liver structure (body structure)","http://snomed.info/sct","LOINC broader","Both","http://snomed.info/sct/900000000000207008/version/20170731","This material includes SNOMED Clinical Terms® (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO) under license. All rights reserved. SNOMED CT® was originally created by The College of American Pathologists. “SNOMED” and “SNOMED CT” are registered trademarks of the IHTSDO.This material includes content from the US Edition to SNOMED CT, which is developed and maintained by the U.S. National Library of Medicine and is available to authorized UMLS Metathesaurus Licensees from the UTS Downloads site at https://uts.nlm.nih.gov.Use of SNOMED CT content is subject to the terms and conditions set forth in the SNOMED CT Affiliate License Agreement. It is the responsibility of those implementing this product to ensure they are appropriately licensed and for more information on the license, including how to register as an Affiliate Licensee, please refer to http://www.snomed.org/snomed-ct/get-snomed-ct or info@snomed.org<mailto:info@snomed.org>. This may incur a fee in SNOMED International non-Member countries."
"LP29165-5","Liver.FNA","SYSTEM","10200004","Liver structure (body structure)","http://snomed.info/sct","LOINC broader","Both","http://snomed.info/sct/900000000000207008/version/20170731","This material includes SNOMED Clinical Terms® (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO) under license. All rights reserved. SNOMED CT® was originally created by The College of American Pathologists. “SNOMED” and “SNOMED CT” are registered trademarks of the IHTSDO.This material includes content from the US Edition to SNOMED CT, which is developed and maintained by the U.S. National Library of Medicine and is available to authorized UMLS Metathesaurus Licensees from the UTS Downloads site at https://uts.nlm.nih.gov.Use of SNOMED CT content is subject to the terms and conditions set forth in the SNOMED CT Affiliate License Agreement. It is the responsibility of those implementing this product to ensure they are appropriately licensed and for more information on the license, including how to register as an Affiliate Licensee, please refer to http://www.snomed.org/snomed-ct/get-snomed-ct or info@snomed.org<mailto:info@snomed.org>. This may incur a fee in SNOMED International non-Member countries."
"LP15666-8","Inosine","COMPONENT","102640000","Inosine (substance)","http://snomed.info/sct","Exact","Both","http://snomed.info/sct/900000000000207008/version/20170731","This material includes SNOMED Clinical Terms® (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO) under license. All rights reserved. SNOMED CT® was originally created by The College of American Pathologists. “SNOMED” and “SNOMED CT” are registered trademarks of the IHTSDO.This material includes content from the US Edition to SNOMED CT, which is developed and maintained by the U.S. National Library of Medicine and is available to authorized UMLS Metathesaurus Licensees from the UTS Downloads site at https://uts.nlm.nih.gov.Use of SNOMED CT content is subject to the terms and conditions set forth in the SNOMED CT Affiliate License Agreement. It is the responsibility of those implementing this product to ensure they are appropriately licensed and for more information on the license, including how to register as an Affiliate Licensee, please refer to http://www.snomed.org/snomed-ct/get-snomed-ct or info@snomed.org<mailto:info@snomed.org>. This may incur a fee in SNOMED International non-Member countries."
"LP15943-1","Uronate","COMPONENT","102641001","Uronic acid (substance)","http://snomed.info/sct","Exact","Both","http://snomed.info/sct/900000000000207008/version/20170731","This material includes SNOMED Clinical Terms® (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO) under license. All rights reserved. SNOMED CT® was originally created by The College of American Pathologists. “SNOMED” and “SNOMED CT” are registered trademarks of the IHTSDO.This material includes content from the US Edition to SNOMED CT, which is developed and maintained by the U.S. National Library of Medicine and is available to authorized UMLS Metathesaurus Licensees from the UTS Downloads site at https://uts.nlm.nih.gov.Use of SNOMED CT content is subject to the terms and conditions set forth in the SNOMED CT Affiliate License Agreement. It is the responsibility of those implementing this product to ensure they are appropriately licensed and for more information on the license, including how to register as an Affiliate Licensee, please refer to http://www.snomed.org/snomed-ct/get-snomed-ct or info@snomed.org<mailto:info@snomed.org>. This may incur a fee in SNOMED International non-Member countries."
"LP15791-4","Phenylketones","COMPONENT","102642008","Phenylketones (substance)","http://snomed.info/sct","Exact","Both","http://snomed.info/sct/900000000000207008/version/20170731","This material includes SNOMED Clinical Terms® (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO) under license. All rights reserved. SNOMED CT® was originally created by The College of American Pathologists. “SNOMED” and “SNOMED CT” are registered trademarks of the IHTSDO.This material includes content from the US Edition to SNOMED CT, which is developed and maintained by the U.S. National Library of Medicine and is available to authorized UMLS Metathesaurus Licensees from the UTS Downloads site at https://uts.nlm.nih.gov.Use of SNOMED CT content is subject to the terms and conditions set forth in the SNOMED CT Affiliate License Agreement. It is the responsibility of those implementing this product to ensure they are appropriately licensed and for more information on the license, including how to register as an Affiliate Licensee, please refer to http://www.snomed.org/snomed-ct/get-snomed-ct or info@snomed.org<mailto:info@snomed.org>. This may incur a fee in SNOMED International non-Member countries."
"LP15721-1","Malonate","COMPONENT","102648007","Malonic acid (substance)","http://snomed.info/sct","Exact","Both","http://snomed.info/sct/900000000000207008/version/20170731","This material includes SNOMED Clinical Terms® (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO) under license. All rights reserved. SNOMED CT® was originally created by The College of American Pathologists. “SNOMED” and “SNOMED CT” are registered trademarks of the IHTSDO.This material includes content from the US Edition to SNOMED CT, which is developed and maintained by the U.S. National Library of Medicine and is available to authorized UMLS Metathesaurus Licensees from the UTS Downloads site at https://uts.nlm.nih.gov.Use of SNOMED CT content is subject to the terms and conditions set forth in the SNOMED CT Affiliate License Agreement. It is the responsibility of those implementing this product to ensure they are appropriately licensed and for more information on the license, including how to register as an Affiliate Licensee, please refer to http://www.snomed.org/snomed-ct/get-snomed-ct or info@snomed.org<mailto:info@snomed.org>. This may incur a fee in SNOMED International non-Member countries."
"PartNumber","PartName","PartTypeName","ExtCodeId","ExtCodeDisplayName","ExtCodeSystem","MapType","ContentOrigin","ExtCodeSystemVersion","ExtCodeSystemCopyrightNotice"
"LP18172-4","Interferon.beta","COMPONENT"," 420710006","Interferon beta (substance)","http://snomed.info/sct","Exact","Both","http://snomed.info/sct/900000000000207008/version/20170731","This material includes SNOMED Clinical Terms® (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO) under license. All rights reserved. SNOMED CT® was originally created by The College of American Pathologists. “SNOMED” and “SNOMED CT” are registered trademarks of the IHTSDO.This material includes content from the US Edition to SNOMED CT, which is developed and maintained by the U.S. National Library of Medicine and is available to authorized UMLS Metathesaurus Licensees from the UTS Downloads site at https://uts.nlm.nih.gov.Use of SNOMED CT content is subject to the terms and conditions set forth in the SNOMED CT Affiliate License Agreement. It is the responsibility of those implementing this product to ensure they are appropriately licensed and for more information on the license, including how to register as an Affiliate Licensee, please refer to http://www.snomed.org/snomed-ct/get-snomed-ct or info@snomed.org<mailto:info@snomed.org>. This may incur a fee in SNOMED International non-Member countries."
"LP31706-2","Nornicotine","COMPONENT","1018001","Nornicotine (substance)","http://snomed.info/sct","Exact","Both","http://snomed.info/sct/900000000000207008/version/20170731","This material includes SNOMED Clinical Terms® (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO) under license. All rights reserved. SNOMED CT® was originally created by The College of American Pathologists. “SNOMED” and “SNOMED CT” are registered trademarks of the IHTSDO.This material includes content from the US Edition to SNOMED CT, which is developed and maintained by the U.S. National Library of Medicine and is available to authorized UMLS Metathesaurus Licensees from the UTS Downloads site at https://uts.nlm.nih.gov.Use of SNOMED CT content is subject to the terms and conditions set forth in the SNOMED CT Affiliate License Agreement. It is the responsibility of those implementing this product to ensure they are appropriately licensed and for more information on the license, including how to register as an Affiliate Licensee, please refer to http://www.snomed.org/snomed-ct/get-snomed-ct or info@snomed.org<mailto:info@snomed.org>. This may incur a fee in SNOMED International non-Member countries."
"LP15826-8","Prostaglandin F2","COMPONENT","10192006","Prostaglandin PGF2 (substance)","http://snomed.info/sct","Exact","Both","http://snomed.info/sct/900000000000207008/version/20170731","This material includes SNOMED Clinical Terms® (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO) under license. All rights reserved. SNOMED CT® was originally created by The College of American Pathologists. “SNOMED” and “SNOMED CT” are registered trademarks of the IHTSDO.This material includes content from the US Edition to SNOMED CT, which is developed and maintained by the U.S. National Library of Medicine and is available to authorized UMLS Metathesaurus Licensees from the UTS Downloads site at https://uts.nlm.nih.gov.Use of SNOMED CT content is subject to the terms and conditions set forth in the SNOMED CT Affiliate License Agreement. It is the responsibility of those implementing this product to ensure they are appropriately licensed and for more information on the license, including how to register as an Affiliate Licensee, please refer to http://www.snomed.org/snomed-ct/get-snomed-ct or info@snomed.org<mailto:info@snomed.org>. This may incur a fee in SNOMED International non-Member countries."
"LP7400-7","Liver","SYSTEM","10200004","Liver structure (body structure)","http://snomed.info/sct","LOINC broader","Both","http://snomed.info/sct/900000000000207008/version/20170731","This material includes SNOMED Clinical Terms® (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO) under license. All rights reserved. SNOMED CT® was originally created by The College of American Pathologists. “SNOMED” and “SNOMED CT” are registered trademarks of the IHTSDO.This material includes content from the US Edition to SNOMED CT, which is developed and maintained by the U.S. National Library of Medicine and is available to authorized UMLS Metathesaurus Licensees from the UTS Downloads site at https://uts.nlm.nih.gov.Use of SNOMED CT content is subject to the terms and conditions set forth in the SNOMED CT Affiliate License Agreement. It is the responsibility of those implementing this product to ensure they are appropriately licensed and for more information on the license, including how to register as an Affiliate Licensee, please refer to http://www.snomed.org/snomed-ct/get-snomed-ct or info@snomed.org<mailto:info@snomed.org>. This may incur a fee in SNOMED International non-Member countries."
"LP29165-5","Liver.FNA","SYSTEM","10200004","Liver structure (body structure)","http://snomed.info/sct","LOINC broader","Both","http://snomed.info/sct/900000000000207008/version/20170731","This material includes SNOMED Clinical Terms® (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO) under license. All rights reserved. SNOMED CT® was originally created by The College of American Pathologists. “SNOMED” and “SNOMED CT” are registered trademarks of the IHTSDO.This material includes content from the US Edition to SNOMED CT, which is developed and maintained by the U.S. National Library of Medicine and is available to authorized UMLS Metathesaurus Licensees from the UTS Downloads site at https://uts.nlm.nih.gov.Use of SNOMED CT content is subject to the terms and conditions set forth in the SNOMED CT Affiliate License Agreement. It is the responsibility of those implementing this product to ensure they are appropriately licensed and for more information on the license, including how to register as an Affiliate Licensee, please refer to http://www.snomed.org/snomed-ct/get-snomed-ct or info@snomed.org<mailto:info@snomed.org>. This may incur a fee in SNOMED International non-Member countries."
"LP15666-8","Inosine","COMPONENT","102640000","Inosine (substance)","http://snomed.info/sct","Exact","Both","http://snomed.info/sct/900000000000207008/version/20170731","This material includes SNOMED Clinical Terms® (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO) under license. All rights reserved. SNOMED CT® was originally created by The College of American Pathologists. “SNOMED” and “SNOMED CT” are registered trademarks of the IHTSDO.This material includes content from the US Edition to SNOMED CT, which is developed and maintained by the U.S. National Library of Medicine and is available to authorized UMLS Metathesaurus Licensees from the UTS Downloads site at https://uts.nlm.nih.gov.Use of SNOMED CT content is subject to the terms and conditions set forth in the SNOMED CT Affiliate License Agreement. It is the responsibility of those implementing this product to ensure they are appropriately licensed and for more information on the license, including how to register as an Affiliate Licensee, please refer to http://www.snomed.org/snomed-ct/get-snomed-ct or info@snomed.org<mailto:info@snomed.org>. This may incur a fee in SNOMED International non-Member countries."
"LP15943-1","Uronate","COMPONENT","102641001","Uronic acid (substance)","http://snomed.info/sct","Exact","Both","http://snomed.info/sct/900000000000207008/version/20170731","This material includes SNOMED Clinical Terms® (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO) under license. All rights reserved. SNOMED CT® was originally created by The College of American Pathologists. “SNOMED” and “SNOMED CT” are registered trademarks of the IHTSDO.This material includes content from the US Edition to SNOMED CT, which is developed and maintained by the U.S. National Library of Medicine and is available to authorized UMLS Metathesaurus Licensees from the UTS Downloads site at https://uts.nlm.nih.gov.Use of SNOMED CT content is subject to the terms and conditions set forth in the SNOMED CT Affiliate License Agreement. It is the responsibility of those implementing this product to ensure they are appropriately licensed and for more information on the license, including how to register as an Affiliate Licensee, please refer to http://www.snomed.org/snomed-ct/get-snomed-ct or info@snomed.org<mailto:info@snomed.org>. This may incur a fee in SNOMED International non-Member countries."
"LP15791-4","Phenylketones","COMPONENT","102642008","Phenylketones (substance)","http://snomed.info/sct","Exact","Both","http://snomed.info/sct/900000000000207008/version/20170731","This material includes SNOMED Clinical Terms® (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO) under license. All rights reserved. SNOMED CT® was originally created by The College of American Pathologists. “SNOMED” and “SNOMED CT” are registered trademarks of the IHTSDO.This material includes content from the US Edition to SNOMED CT, which is developed and maintained by the U.S. National Library of Medicine and is available to authorized UMLS Metathesaurus Licensees from the UTS Downloads site at https://uts.nlm.nih.gov.Use of SNOMED CT content is subject to the terms and conditions set forth in the SNOMED CT Affiliate License Agreement. It is the responsibility of those implementing this product to ensure they are appropriately licensed and for more information on the license, including how to register as an Affiliate Licensee, please refer to http://www.snomed.org/snomed-ct/get-snomed-ct or info@snomed.org<mailto:info@snomed.org>. This may incur a fee in SNOMED International non-Member countries."
"LP15721-1","Malonate","COMPONENT","102648007","Malonic acid (substance)","http://snomed.info/sct","Exact","Both","http://snomed.info/sct/900000000000207008/version/20170731","This material includes SNOMED Clinical Terms® (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO) under license. All rights reserved. SNOMED CT® was originally created by The College of American Pathologists. “SNOMED” and “SNOMED CT” are registered trademarks of the IHTSDO.This material includes content from the US Edition to SNOMED CT, which is developed and maintained by the U.S. National Library of Medicine and is available to authorized UMLS Metathesaurus Licensees from the UTS Downloads site at https://uts.nlm.nih.gov.Use of SNOMED CT content is subject to the terms and conditions set forth in the SNOMED CT Affiliate License Agreement. It is the responsibility of those implementing this product to ensure they are appropriately licensed and for more information on the license, including how to register as an Affiliate Licensee, please refer to http://www.snomed.org/snomed-ct/get-snomed-ct or info@snomed.org<mailto:info@snomed.org>. This may incur a fee in SNOMED International non-Member countries."
"LP15842-5","Pyridoxine","COMPONENT","1054","Pyridoxine","http://pubchem.ncbi.nlm.nih.gov","Exact",,,

1 PartNumber PartName PartTypeName ExtCodeId ExtCodeDisplayName ExtCodeSystem MapType ContentOrigin ExtCodeSystemVersion ExtCodeSystemCopyrightNotice
2 LP18172-4 Interferon.beta COMPONENT  420710006 Interferon beta (substance) http://snomed.info/sct Exact Both http://snomed.info/sct/900000000000207008/version/20170731 This material includes SNOMED Clinical Terms® (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO) under license. All rights reserved. SNOMED CT® was originally created by The College of American Pathologists. “SNOMED” and “SNOMED CT” are registered trademarks of the IHTSDO.This material includes content from the US Edition to SNOMED CT, which is developed and maintained by the U.S. National Library of Medicine and is available to authorized UMLS Metathesaurus Licensees from the UTS Downloads site at https://uts.nlm.nih.gov.Use of SNOMED CT content is subject to the terms and conditions set forth in the SNOMED CT Affiliate License Agreement. It is the responsibility of those implementing this product to ensure they are appropriately licensed and for more information on the license, including how to register as an Affiliate Licensee, please refer to http://www.snomed.org/snomed-ct/get-snomed-ct or info@snomed.org<mailto:info@snomed.org>. This may incur a fee in SNOMED International non-Member countries.
3 LP31706-2 Nornicotine COMPONENT 1018001 Nornicotine (substance) http://snomed.info/sct Exact Both http://snomed.info/sct/900000000000207008/version/20170731 This material includes SNOMED Clinical Terms® (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO) under license. All rights reserved. SNOMED CT® was originally created by The College of American Pathologists. “SNOMED” and “SNOMED CT” are registered trademarks of the IHTSDO.This material includes content from the US Edition to SNOMED CT, which is developed and maintained by the U.S. National Library of Medicine and is available to authorized UMLS Metathesaurus Licensees from the UTS Downloads site at https://uts.nlm.nih.gov.Use of SNOMED CT content is subject to the terms and conditions set forth in the SNOMED CT Affiliate License Agreement. It is the responsibility of those implementing this product to ensure they are appropriately licensed and for more information on the license, including how to register as an Affiliate Licensee, please refer to http://www.snomed.org/snomed-ct/get-snomed-ct or info@snomed.org<mailto:info@snomed.org>. This may incur a fee in SNOMED International non-Member countries.
4 LP15826-8 Prostaglandin F2 COMPONENT 10192006 Prostaglandin PGF2 (substance) http://snomed.info/sct Exact Both http://snomed.info/sct/900000000000207008/version/20170731 This material includes SNOMED Clinical Terms® (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO) under license. All rights reserved. SNOMED CT® was originally created by The College of American Pathologists. “SNOMED” and “SNOMED CT” are registered trademarks of the IHTSDO.This material includes content from the US Edition to SNOMED CT, which is developed and maintained by the U.S. National Library of Medicine and is available to authorized UMLS Metathesaurus Licensees from the UTS Downloads site at https://uts.nlm.nih.gov.Use of SNOMED CT content is subject to the terms and conditions set forth in the SNOMED CT Affiliate License Agreement. It is the responsibility of those implementing this product to ensure they are appropriately licensed and for more information on the license, including how to register as an Affiliate Licensee, please refer to http://www.snomed.org/snomed-ct/get-snomed-ct or info@snomed.org<mailto:info@snomed.org>. This may incur a fee in SNOMED International non-Member countries.
5 LP7400-7 Liver SYSTEM 10200004 Liver structure (body structure) http://snomed.info/sct LOINC broader Both http://snomed.info/sct/900000000000207008/version/20170731 This material includes SNOMED Clinical Terms® (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO) under license. All rights reserved. SNOMED CT® was originally created by The College of American Pathologists. “SNOMED” and “SNOMED CT” are registered trademarks of the IHTSDO.This material includes content from the US Edition to SNOMED CT, which is developed and maintained by the U.S. National Library of Medicine and is available to authorized UMLS Metathesaurus Licensees from the UTS Downloads site at https://uts.nlm.nih.gov.Use of SNOMED CT content is subject to the terms and conditions set forth in the SNOMED CT Affiliate License Agreement. It is the responsibility of those implementing this product to ensure they are appropriately licensed and for more information on the license, including how to register as an Affiliate Licensee, please refer to http://www.snomed.org/snomed-ct/get-snomed-ct or info@snomed.org<mailto:info@snomed.org>. This may incur a fee in SNOMED International non-Member countries.
6 LP29165-5 Liver.FNA SYSTEM 10200004 Liver structure (body structure) http://snomed.info/sct LOINC broader Both http://snomed.info/sct/900000000000207008/version/20170731 This material includes SNOMED Clinical Terms® (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO) under license. All rights reserved. SNOMED CT® was originally created by The College of American Pathologists. “SNOMED” and “SNOMED CT” are registered trademarks of the IHTSDO.This material includes content from the US Edition to SNOMED CT, which is developed and maintained by the U.S. National Library of Medicine and is available to authorized UMLS Metathesaurus Licensees from the UTS Downloads site at https://uts.nlm.nih.gov.Use of SNOMED CT content is subject to the terms and conditions set forth in the SNOMED CT Affiliate License Agreement. It is the responsibility of those implementing this product to ensure they are appropriately licensed and for more information on the license, including how to register as an Affiliate Licensee, please refer to http://www.snomed.org/snomed-ct/get-snomed-ct or info@snomed.org<mailto:info@snomed.org>. This may incur a fee in SNOMED International non-Member countries.
7 LP15666-8 Inosine COMPONENT 102640000 Inosine (substance) http://snomed.info/sct Exact Both http://snomed.info/sct/900000000000207008/version/20170731 This material includes SNOMED Clinical Terms® (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO) under license. All rights reserved. SNOMED CT® was originally created by The College of American Pathologists. “SNOMED” and “SNOMED CT” are registered trademarks of the IHTSDO.This material includes content from the US Edition to SNOMED CT, which is developed and maintained by the U.S. National Library of Medicine and is available to authorized UMLS Metathesaurus Licensees from the UTS Downloads site at https://uts.nlm.nih.gov.Use of SNOMED CT content is subject to the terms and conditions set forth in the SNOMED CT Affiliate License Agreement. It is the responsibility of those implementing this product to ensure they are appropriately licensed and for more information on the license, including how to register as an Affiliate Licensee, please refer to http://www.snomed.org/snomed-ct/get-snomed-ct or info@snomed.org<mailto:info@snomed.org>. This may incur a fee in SNOMED International non-Member countries.
8 LP15943-1 Uronate COMPONENT 102641001 Uronic acid (substance) http://snomed.info/sct Exact Both http://snomed.info/sct/900000000000207008/version/20170731 This material includes SNOMED Clinical Terms® (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO) under license. All rights reserved. SNOMED CT® was originally created by The College of American Pathologists. “SNOMED” and “SNOMED CT” are registered trademarks of the IHTSDO.This material includes content from the US Edition to SNOMED CT, which is developed and maintained by the U.S. National Library of Medicine and is available to authorized UMLS Metathesaurus Licensees from the UTS Downloads site at https://uts.nlm.nih.gov.Use of SNOMED CT content is subject to the terms and conditions set forth in the SNOMED CT Affiliate License Agreement. It is the responsibility of those implementing this product to ensure they are appropriately licensed and for more information on the license, including how to register as an Affiliate Licensee, please refer to http://www.snomed.org/snomed-ct/get-snomed-ct or info@snomed.org<mailto:info@snomed.org>. This may incur a fee in SNOMED International non-Member countries.
9 LP15791-4 Phenylketones COMPONENT 102642008 Phenylketones (substance) http://snomed.info/sct Exact Both http://snomed.info/sct/900000000000207008/version/20170731 This material includes SNOMED Clinical Terms® (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO) under license. All rights reserved. SNOMED CT® was originally created by The College of American Pathologists. “SNOMED” and “SNOMED CT” are registered trademarks of the IHTSDO.This material includes content from the US Edition to SNOMED CT, which is developed and maintained by the U.S. National Library of Medicine and is available to authorized UMLS Metathesaurus Licensees from the UTS Downloads site at https://uts.nlm.nih.gov.Use of SNOMED CT content is subject to the terms and conditions set forth in the SNOMED CT Affiliate License Agreement. It is the responsibility of those implementing this product to ensure they are appropriately licensed and for more information on the license, including how to register as an Affiliate Licensee, please refer to http://www.snomed.org/snomed-ct/get-snomed-ct or info@snomed.org<mailto:info@snomed.org>. This may incur a fee in SNOMED International non-Member countries.
10 LP15721-1 Malonate COMPONENT 102648007 Malonic acid (substance) http://snomed.info/sct Exact Both http://snomed.info/sct/900000000000207008/version/20170731 This material includes SNOMED Clinical Terms® (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO) under license. All rights reserved. SNOMED CT® was originally created by The College of American Pathologists. “SNOMED” and “SNOMED CT” are registered trademarks of the IHTSDO.This material includes content from the US Edition to SNOMED CT, which is developed and maintained by the U.S. National Library of Medicine and is available to authorized UMLS Metathesaurus Licensees from the UTS Downloads site at https://uts.nlm.nih.gov.Use of SNOMED CT content is subject to the terms and conditions set forth in the SNOMED CT Affiliate License Agreement. It is the responsibility of those implementing this product to ensure they are appropriately licensed and for more information on the license, including how to register as an Affiliate Licensee, please refer to http://www.snomed.org/snomed-ct/get-snomed-ct or info@snomed.org<mailto:info@snomed.org>. This may incur a fee in SNOMED International non-Member countries.
11 LP15842-5 Pyridoxine COMPONENT 1054 Pyridoxine http://pubchem.ncbi.nlm.nih.gov Exact

1
hapi-fhir-jpaserver-base/src/test/resources/loinc/Part_Beta_1.csv
View File

@ -38,3 +38,4 @@
"LP7057-5","SYSTEM","Bld","Blood","ACTIVE"
"LP6838-9","PROPERTY","NFr","Number Fraction","ACTIVE"
"LP6141-8","METHOD","Automated count","Automated count","ACTIVE"
"LP15842-5","COMPONENT","Pyridoxine","Pyridoxine","ACTIVE"

1 PartNumber PartTypeName PartName PartDisplayName Status
38 LP7057-5 SYSTEM Bld Blood ACTIVE
39 LP6838-9 PROPERTY NFr Number Fraction ACTIVE
40 LP6141-8 METHOD Automated count Automated count ACTIVE
41 LP15842-5 COMPONENT Pyridoxine Pyridoxine ACTIVE

4
hapi-fhir-jpaserver-elasticsearch/src/main/java/ca/uhn/fhir/jpa/search/ElasticsearchMappingProvider.java
View File

@ -20,6 +20,7 @@ package ca.uhn.fhir.jpa.search;
* #L%
*/
import org.apache.lucene.analysis.core.WhitespaceTokenizerFactory;
import org.hibernate.search.elasticsearch.analyzer.definition.ElasticsearchAnalysisDefinitionRegistryBuilder;
import org.hibernate.search.elasticsearch.analyzer.definition.ElasticsearchAnalysisDefinitionProvider;
@ -57,5 +58,8 @@ public class ElasticsearchMappingProvider implements ElasticsearchAnalysisDefini
builder.analyzer("exactAnalyzer").withTokenizer("standard");
builder.analyzer("conceptParentPidsAnalyzer").withTokenizer("whitespace");
builder.analyzer("termConceptPropertyAnalyzer").withTokenizer("whitespace");
}
}

30
hapi-fhir-validation/src/test/java/fluentpath/Example20_ValidateResource.java Normal file
View File

@ -0,0 +1,30 @@
package fluentpath;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.validation.FhirValidator;
import ca.uhn.fhir.validation.ValidationResult;
import org.hl7.fhir.dstu3.model.Encounter;
import org.hl7.fhir.dstu3.model.OperationOutcome;
public class Example20_ValidateResource {
public static void main(String[] args) {
// Create an incomplete encounter (status is required)
Encounter enc = new Encounter();
enc.addIdentifier().setSystem("http://acme.org/encNums").setValue("12345");
// Create a new validator
FhirContext ctx = FhirContext.forDstu3();
FhirValidator validator = ctx.newValidator();
// Did we succeed?
ValidationResult result = validator.validateWithResult(enc);
System.out.println("Success: " + result.isSuccessful());
// What was the result
OperationOutcome outcome = (OperationOutcome) result.toOperationOutcome();
IParser parser = ctx.newXmlParser().setPrettyPrint(true);
System.out.println(parser.encodeResourceToString(outcome));
}
}

5
src/changes/changes.xml
View File

@ -66,6 +66,11 @@
<![CDATA[<code>setFlags(flags)</code>]]>
can be used to maintain the previous behaviour.
</action>
<action type="974">
JPA server loading logic has been improved to enhance performance when
loading a large number of results in a page, or when loading multiple
search results with tags. Thanks to Frank Tao for the pull request!
</action>
</release>
<release version="3.4.0" date="2018-05-28">
<action type="add">