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Add EXTERNAL_COPYRIGHT_NOTICE property for LOINC uploader.

This commit is contained in:
Diederik Muylwyk 2019-09-13 11:49:01 -04:00
parent 0831feb2c3
commit 75ddba7f2d
4 changed files with 33 additions and 19 deletions
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1
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptProperty.java
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@ -62,6 +62,7 @@ public class TermConceptProperty implements Serializable {
@Column(name = "PROP_KEY", nullable = false, length = MAX_LENGTH)
@NotBlank
private String myKey;
// FIXME: DM 2019-09-13 - We presently truncate down to 500. The longest value for EXTERNAL_COPYRIGHT_NOTICE is 2,597 so we should use a LOB instead of a String.
@Column(name = "PROP_VAL", nullable = true, length = MAX_LENGTH)
private String myValue;
@Column(name = "PROP_TYPE", nullable = false, length = MAX_PROPTYPE_ENUM_LENGTH)

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcImpl.java
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@ -480,6 +480,11 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
}
}
// FIXME: DM 2019-09-13 - Manually add EXTERNAL_COPYRIGHT_NOTICE property until Regenstrief adds this to loinc.xml
String externalCopyRightNoticeCode = "EXTERNAL_COPYRIGHT_NOTICE";
CodeSystem.PropertyType externalCopyRightNoticeType = CodeSystem.PropertyType.STRING;
propertyNamesToTypes.put(externalCopyRightNoticeCode, externalCopyRightNoticeType);
IRecordHandler handler;
// Part

15
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcLoincTest.java
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@ -68,7 +68,7 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
ValueSet vs;
ConceptMap.ConceptMapGroupComponent group;
// Normal loinc code
// Normal LOINC code
code = concepts.get("10013-1");
assertEquals("10013-1", code.getCode());
assertEquals(IHapiTerminologyLoaderSvc.LOINC_URI, code.getCodingProperties("PROPERTY").get(0).getSystem());
@ -84,10 +84,17 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
assertEquals("http://loinc.org", code.getCodingProperties("COMPONENT").get(0).getSystem());
assertEquals("LP19258-0", code.getCodingProperties("COMPONENT").get(0).getCode());
// Loinc code with answer
// LOINC code with answer
code = concepts.get("61438-8");
assertThat(code.getStringProperties("answer-list"), contains("LL1000-0"));
// LOINC code with 3rd party copyright
code = concepts.get("47239-9");
// FIXME: DM 2019-09-13 - We presently truncate down to 500. The longest value for EXTERNAL_COPYRIGHT_NOTICE is 2,597 so we should use a LOB instead of a String.
// String expectedExternalCopyrightNotice = "Copyright © 2006 World Health Organization. Used with permission. Publications of the World Health Organization can be obtained from WHO Press, World Health Organization, 20 Avenue Appia, 1211 Geneva 27, Switzerland (tel: +41 22 791 2476; fax: +41 22 791 4857; email: bookorders@who.int). Requests for permission to reproduce or translate WHO publications – whether for sale or for noncommercial distribution – should be addressed to WHO Press, at the above address (fax: +41 22 791 4806; email: permissions@who.int). The designations employed and the presentation of the material in this publication do not imply the expression of any opinion whatsoever on the part of the World Health Organization concerning the legal status of any country, territory, city or area or of its authorities, or concerning the delimitation of its frontiers or boundaries. Dotted lines on maps represent approximate border lines for which there may not yet be full agreement. The mention of specific companies or of certain manufacturers’ products does not imply that they are endorsed or recommended by the World Health Organization in preference to others of a similar nature that are not mentioned. Errors and omissions excepted, the names of proprietary products are distinguished by initial capital letters. All reasonable precautions have been taken by WHO to verify the information contained in this publication. However, the published material is being distributed without warranty of any kind, either express or implied. The responsibility for the interpretation and use of the material lies with the reader. In no event shall the World Health Organization be liable for damages arising from its use.";
String expectedExternalCopyrightNotice = "Copyright © 2006 World Health Organization. Used with permission. Publications of the World Health Organization can be obtained from WHO Press, World Health Organization, 20 Avenue Appia, 1211 Geneva 27, Switzerland (tel: +41 22 791 2476; fax: +41 22 791 4857; email: bookorders@who.int). Requests for permission to reproduce or translate WHO publications – whether for sale or for noncommercial distribution – should be addressed to WHO Press, at the above address (fax: +41 22 791 4806; email: perm";
assertEquals(expectedExternalCopyrightNotice, code.getStringProperty("EXTERNAL_COPYRIGHT_NOTICE"));
// Answer list
code = concepts.get("LL1001-8");
assertEquals("LL1001-8", code.getCode());
@ -330,7 +337,7 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
Map<String, ValueSet> valueSets = extractValueSets();
Map<String, ConceptMap> conceptMaps = extractConceptMaps();
// Normal loinc code
// Normal LOINC code
TermConcept code = concepts.get("10013-1");
assertEquals("10013-1", code.getCode());
@ -394,7 +401,7 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
ValueSet vs;
ConceptMap.ConceptMapGroupComponent group;
// Normal loinc code
// Normal LOINC code
code = concepts.get("10013-1");
assertEquals("10013-1", code.getCode());
assertEquals(IHapiTerminologyLoaderSvc.LOINC_URI, code.getCodingProperties("PROPERTY").get(0).getSystem());

1
hapi-fhir-jpaserver-base/src/test/resources/loinc/LoincTable/Loinc.csv
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@ -13,3 +13,4 @@
"17787-3" ,"Study report" ,"Find" ,"Pt" ,"Neck>Thyroid gland","Doc" ,"NM" ,"RAD" ,"2.61" ,"MIN" , ,"ACTIVE", ,2 , , , , , , , ,"Document; Finding; Findings; Imaging; Point in time; Radiology; Random; Study report; Thy" ,"NM Thyroid Study report" ,"Both" , , , , ,"NM Thyroid gland Study report" , , , , , , ,"Changed System from ""Thyroid"" for conformance with the LOINC/RadLex unified model.; Method of ""Radnuc"" was changed to ""NM"". The LOINC/RadLex Committee agreed to use a subset of the two-letter DICOM modality codes as the primary modality identifier." ,0 ,0 ,0 ,"IG exists" , , , ,"81220-6;72230-6" ,"1.0l" ,
"17788-1" ,"Large unstained cells/100 leukocytes" ,"NFr" ,"Pt" ,"Bld" ,"Qn" ,"Automated count","HEM/BC" ,"2.50" ,"MIN" ,"Part of auto diff output of Bayer H*3S; peroxidase negative cells too large to be classified as lymph or basophil" ,"ACTIVE", ,1 , , , , , ,"Y" ,"%" ,"100WBC; Auto; Automated detection; Blood; Cell; Cellularity; Elec; Elect; Electr; HEMATOLOGY/CELL COUNTS; Leuc; Leuk; Leukocyte; Lkcs; LUC; Number Fraction; Percent; Point in time; QNT; Quan; Quant; Quantitative; Random; WB; WBC; WBCs; White blood cell; White blood cells; Whole blood" ,"LUC/leuk NFr Bld Auto" ,"Observation", , , ,"%" ,"Large unstained cells/100 leukocytes in Blood by Automated count" , , ,"%" , , , , ,1894 ,0 ,1894 , , , , , ,"1.0l" ,
"11488-4" ,"Consultation note" ,"Find" ,"Pt" ,"{Setting}" ,"Doc" ,"{Role}" ,"DOC.ONTOLOGY","2.63" ,"MIN" , ,"ACTIVE", ,2 , , , , , , , ,"Consult note; DOC.ONT; Document; Encounter; Evaluation and management; Evaluation and management note; Finding; Findings; notes; Point in time; Random; Visit note" ,"Consult note" ,"Both" , , , , ,"Consult note" , , , , , , ,"Edit made because this term is conformant to the Document Ontology axis values and therefore are being placed in this class.; Based on Clinical LOINC Committee decision during the September 2014 meeting, {Provider} was changed to {Author Type} to emphasize a greater breadth of potential document authors. At the September 2015 Clinical LOINC Committee meeting, the Committee decided to change {Author Type} to {Role} to align with the 'Role' axis name in the LOINC Document Ontology.; Because it is too difficult to maintain and because the distinction between documents and sections is not clear-cut nor necessary in most cases, the DOCUMENT_SECTION field has been deemed to have little value. The field has been set to null in the December 2017 release in preparation for removal in the December 2018 release. These changes were approved by the Clinical LOINC Committee.",0 ,0 ,0 ,"IG exists" , , , ,"81222-2;72231-4;81243-8","1.0j-a" ,"Y"
"47239-9" ,"Reason for stopping HIV Rx" ,"Type" ,"Pt" ,"^Patient" ,"Nom" ,"Reported" ,"ART" ,"2.50" ,"MIN" ,"Reason for stopping antiretroviral therapy" ,"ACTIVE", ,2 , , , , , ,"N" , ,"AIDS; Anti-retroviral therapy; ART; Human immunodeficiency virus; Nominal; Point in time; Random; Treatment; Typ" ,"Reason for stopping HIV Rx" ,"Observation", , ,"Copyright © 2006 World Health Organization. Used with permission. Publications of the World Health Organization can be obtained from WHO Press, World Health Organization, 20 Avenue Appia, 1211 Geneva 27, Switzerland (tel: +41 22 791 2476; fax: +41 22 791 4857; email: bookorders@who.int). Requests for permission to reproduce or translate WHO publications – whether for sale or for noncommercial distribution – should be addressed to WHO Press, at the above address (fax: +41 22 791 4806; email: permissions@who.int). The designations employed and the presentation of the material in this publication do not imply the expression of any opinion whatsoever on the part of the World Health Organization concerning the legal status of any country, territory, city or area or of its authorities, or concerning the delimitation of its frontiers or boundaries. Dotted lines on maps represent approximate border lines for which there may not yet be full agreement. The mention of specific companies or of certain manufacturers’ products does not imply that they are endorsed or recommended by the World Health Organization in preference to others of a similar nature that are not mentioned. Errors and omissions excepted, the names of proprietary products are distinguished by initial capital letters. All reasonable precautions have been taken by WHO to verify the information contained in this publication. However, the published material is being distributed without warranty of any kind, either express or implied. The responsibility for the interpretation and use of the material lies with the reader. In no event shall the World Health Organization be liable for damages arising from its use.", ,"Reason for stopping HIV treatment" , , , , , , , ,0 ,0 ,0 , ,"WHO_HIV" , , , ,"2.22" ,

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