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Merge pull request #1501 from jamesagnew/1483-need-consistent-assignment-of-fullurl-id-and-url-for-loinc 

Fixed inconsistent IDs and URLs for LOINC.
This commit is contained in:
Diederik Muylwyk 2019-09-23 15:59:21 -04:00 committed by GitHub
parent 6f44d7c360 25798ee3e2
commit 2a2e8e0ab8
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GPG Key ID: 4AEE18F83AFDEB23
5 changed files with 20 additions and 11 deletions
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2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseHapiTerminologySvcImpl.java
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@ -1630,7 +1630,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
jobDefinition.setJobClass(SaveDeferredJob.class); jobDefinition.setJobClass(SaveDeferredJob.class);
mySchedulerService.scheduleFixedDelay(5000, false, jobDefinition); mySchedulerService.scheduleFixedDelay(5000, false, jobDefinition);
// Register scheduled job to save deferred concepts // Register scheduled job to pre-expand ValueSets
// In the future it would be great to make this a cluster-aware task somehow // In the future it would be great to make this a cluster-aware task somehow
ScheduledJobDefinition vsJobDefinition = new ScheduledJobDefinition(); ScheduledJobDefinition vsJobDefinition = new ScheduledJobDefinition();
vsJobDefinition.setId(BaseHapiTerminologySvcImpl.class.getName() + "_preExpandValueSets"); vsJobDefinition.setId(BaseHapiTerminologySvcImpl.class.getName() + "_preExpandValueSets");

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincIeeeMedicalDeviceCodeHandler.java
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@ -36,7 +36,7 @@ import static org.apache.commons.lang3.StringUtils.trim;
public class LoincIeeeMedicalDeviceCodeHandler extends BaseLoincHandler implements IRecordHandler { public class LoincIeeeMedicalDeviceCodeHandler extends BaseLoincHandler implements IRecordHandler {
public static final String LOINC_IEEE_CM_ID = "LOINC-IEEE-MEDICAL-DEVICE-CM"; public static final String LOINC_IEEE_CM_ID = "loinc-to-ieee-device-codes";
public static final String LOINC_IEEE_CM_URI = "http://loinc.org/cm/loinc-to-ieee-device-codes"; public static final String LOINC_IEEE_CM_URI = "http://loinc.org/cm/loinc-to-ieee-device-codes";
public static final String LOINC_IEEE_CM_NAME = "LOINC/IEEE Device Code Mappings"; public static final String LOINC_IEEE_CM_NAME = "LOINC/IEEE Device Code Mappings";
private static final String CM_COPYRIGHT = "This content from LOINC® is copyright © 1995 Regenstrief Institute, Inc. and the LOINC Committee, and available at no cost under the license at https://loinc.org/license/. The LOINC/IEEE Medical Device Code Mapping Table contains content from IEEE (http://ieee.org), copyright © 2017 IEEE."; private static final String CM_COPYRIGHT = "This content from LOINC® is copyright © 1995 Regenstrief Institute, Inc. and the LOINC Committee, and available at no cost under the license at https://loinc.org/license/. The LOINC/IEEE Medical Device Code Mapping Table contains content from IEEE (http://ieee.org), copyright © 2017 IEEE.";

21
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincPartRelatedCodeMappingHandler.java
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@ -40,21 +40,26 @@ public class LoincPartRelatedCodeMappingHandler extends BaseLoincHandler impleme
public static final String LOINC_SCT_PART_MAP_ID = "loinc-parts-to-snomed-ct"; public static final String LOINC_SCT_PART_MAP_ID = "loinc-parts-to-snomed-ct";
public static final String LOINC_SCT_PART_MAP_URI = "http://loinc.org/cm/loinc-parts-to-snomed-ct"; public static final String LOINC_SCT_PART_MAP_URI = "http://loinc.org/cm/loinc-parts-to-snomed-ct";
public static final String LOINC_TERM_TO_RPID_PART_MAP_ID = "loinc-term-to-rpids";
public static final String LOINC_TERM_TO_RPID_PART_MAP_URI = "http://loinc.org/cm/loinc-to-rpids";
public static final String LOINC_TERM_TO_RPID_PART_MAP_NAME = "LOINC Terms to RadLex RPIDs";
public static final String LOINC_PART_TO_RID_PART_MAP_ID = "loinc-part-to-rids";
public static final String LOINC_PART_TO_RID_PART_MAP_URI = "http://loinc.org/cm/loinc-to-rids";
public static final String LOINC_PART_TO_RID_PART_MAP_NAME = "LOINC Parts to RadLex RIDs";
private static final String LOINC_SCT_PART_MAP_NAME = "LOINC Part Map to SNOMED CT"; private static final String LOINC_SCT_PART_MAP_NAME = "LOINC Part Map to SNOMED CT";
public static final String LOINC_TERM_TO_RPID_PART_MAP_ID = "loinc-term-to-rpids";
public static final String LOINC_TERM_TO_RPID_PART_MAP_URI = "http://loinc.org/cm/loinc-term-to-rpids";
public static final String LOINC_TERM_TO_RPID_PART_MAP_NAME = "LOINC Terms to RadLex RPIDs";
public static final String LOINC_PART_TO_RID_PART_MAP_ID = "loinc-part-to-rids";
public static final String LOINC_PART_TO_RID_PART_MAP_URI = "http://loinc.org/cm/loinc-part-to-rids";
public static final String LOINC_PART_TO_RID_PART_MAP_NAME = "LOINC Parts to RadLex RIDs";
private static final String LOINC_RXNORM_PART_MAP_ID = "loinc-parts-to-rxnorm"; private static final String LOINC_RXNORM_PART_MAP_ID = "loinc-parts-to-rxnorm";
private static final String LOINC_RXNORM_PART_MAP_URI = "http://loinc.org/cm/loinc-parts-to-rxnorm"; private static final String LOINC_RXNORM_PART_MAP_URI = "http://loinc.org/cm/loinc-parts-to-rxnorm";
private static final String LOINC_RXNORM_PART_MAP_NAME = "LOINC Part Map to RxNORM"; private static final String LOINC_RXNORM_PART_MAP_NAME = "LOINC Part Map to RxNORM";
private static final String CM_COPYRIGHT = "This content from LOINC® is copyright © 1995 Regenstrief Institute, Inc. and the LOINC Committee, and available at no cost under the license at https://loinc.org/license/. The LOINC Part File, LOINC/SNOMED CT Expression Association and Map Sets File, RELMA database and associated search index files include SNOMED Clinical Terms (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO) under license. All rights are reserved. SNOMED CT® was originally created by The College of American Pathologists. “SNOMED” and “SNOMED CT” are registered trademarks of the IHTSDO. 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. Under the terms of the Affiliate License, use of SNOMED CT in countries that are not IHTSDO Members is subject to reporting and fee payment obligations. However, IHTSDO agrees to waive the requirements to report and pay fees for use of SNOMED CT content included in the LOINC Part Mapping and LOINC Term Associations for purposes that support or enable more effective use of LOINC. 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.";
private static final String LOINC_PUBCHEM_PART_MAP_URI = "http://loinc.org/cm/loinc-parts-to-pubchem";
private static final String LOINC_PUBCHEM_PART_MAP_ID = "loinc-parts-to-pubchem"; private static final String LOINC_PUBCHEM_PART_MAP_ID = "loinc-parts-to-pubchem";
private static final String LOINC_PUBCHEM_PART_MAP_URI = "http://loinc.org/cm/loinc-parts-to-pubchem";
private static final String LOINC_PUBCHEM_PART_MAP_NAME = "LOINC Part Map to PubChem"; private static final String LOINC_PUBCHEM_PART_MAP_NAME = "LOINC Part Map to PubChem";
private static final String CM_COPYRIGHT = "This content from LOINC® is copyright © 1995 Regenstrief Institute, Inc. and the LOINC Committee, and available at no cost under the license at https://loinc.org/license/. The LOINC Part File, LOINC/SNOMED CT Expression Association and Map Sets File, RELMA database and associated search index files include SNOMED Clinical Terms (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO) under license. All rights are reserved. SNOMED CT® was originally created by The College of American Pathologists. “SNOMED” and “SNOMED CT” are registered trademarks of the IHTSDO. 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. Under the terms of the Affiliate License, use of SNOMED CT in countries that are not IHTSDO Members is subject to reporting and fee payment obligations. However, IHTSDO agrees to waive the requirements to report and pay fees for use of SNOMED CT content included in the LOINC Part Mapping and LOINC Term Associations for purposes that support or enable more effective use of LOINC. 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.";
public LoincPartRelatedCodeMappingHandler(Map<String, TermConcept> theCode2concept, List<ValueSet> theValueSets, List<ConceptMap> theConceptMaps, Properties theUploadProperties) { public LoincPartRelatedCodeMappingHandler(Map<String, TermConcept> theCode2concept, List<ValueSet> theValueSets, List<ConceptMap> theConceptMaps, Properties theUploadProperties) {
super(theCode2concept, theValueSets, theConceptMaps, theUploadProperties); super(theCode2concept, theValueSets, theConceptMaps, theUploadProperties);
} }

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincUniversalOrderSetHandler.java
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@ -33,7 +33,7 @@ import static org.apache.commons.lang3.StringUtils.trim;
public class LoincUniversalOrderSetHandler extends BaseLoincHandler implements IRecordHandler { public class LoincUniversalOrderSetHandler extends BaseLoincHandler implements IRecordHandler {
public static final String VS_ID = "loinc-universal-order-set-vs"; public static final String VS_ID = "loinc-universal-order-set";
public static final String VS_URI = "http://loinc.org/vs/loinc-universal-order-set"; public static final String VS_URI = "http://loinc.org/vs/loinc-universal-order-set";
public static final String VS_NAME = "LOINC Universal Order Set"; public static final String VS_NAME = "LOINC Universal Order Set";

4
src/changes/changes.xml
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@ -193,6 +193,10 @@
resulted in some ValueSets with duplicate codes. This has been corrected by specifying a path with each resulted in some ValueSets with duplicate codes. This has been corrected by specifying a path with each
filename. filename.
</action> </action>
<action type="fix" issue="1483">
Some resource IDs and URLs for LOINC ValueSets and ConceptMaps were inconsistently populated by the
terminology uploader. This has been corrected.
</action>
</release> </release>
<release version="4.0.3" date="2019-09-03" description="Igloo (Point Release)"> <release version="4.0.3" date="2019-09-03" description="Igloo (Point Release)">
<action type="fix"> <action type="fix">