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Test fixes

This commit is contained in:
James Agnew 2018-07-05 19:17:06 -04:00
parent c9d7b88cab
commit c8f0e0047f
5 changed files with 13 additions and 6 deletions
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3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcImpl.java
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@ -162,6 +162,9 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
int nextLoggedCount = 0; int nextLoggedCount = 0;
while (iter.hasNext()) { while (iter.hasNext()) {
CSVRecord nextRecord = iter.next(); CSVRecord nextRecord = iter.next();
if (nextRecord.isConsistent()==false) {
continue;
}
theHandler.accept(nextRecord); theHandler.accept(nextRecord);
count++; count++;
if (count >= nextLoggedCount) { if (count >= nextLoggedCount) {

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincPartRelatedCodeMappingHandler.java
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@ -43,7 +43,7 @@ public class LoincPartRelatedCodeMappingHandler extends BaseLoincHandler impleme
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_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_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_TERM_TO_RPID_PART_MAP_NAME = "LOINC Terms to RadLex RPIDs";
public static final String LOINC_PART_TO_RID_PART_MAP_ID = "loinc-term-to-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-rpids"; public static final String LOINC_PART_TO_RID_PART_MAP_URI = "http://loinc.org/cm/loinc-to-rpids";
public static final String LOINC_PART_TO_RID_PART_MAP_NAME = "LOINC Parts to RadLex 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";

8
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcLoincTest.java
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@ -246,11 +246,11 @@ public class TerminologyLoaderSvcLoincTest {
// all entries have the same source and target so these should be null // all entries have the same source and target so these should be null
assertEquals(IHapiTerminologyLoaderSvc.LOINC_URI, group.getSource()); assertEquals(IHapiTerminologyLoaderSvc.LOINC_URI, group.getSource());
assertEquals(LoincRsnaPlaybookHandler.RPID_CS_URI, group.getTarget()); assertEquals(LoincRsnaPlaybookHandler.RPID_CS_URI, group.getTarget());
assertEquals("LP199995-4", group.getElement().get(0).getCode()); assertEquals("24531-6", group.getElement().get(0).getCode());
assertEquals("Neck", group.getElement().get(0).getDisplay()); assertEquals("US Retroperitoneum", group.getElement().get(0).getDisplay());
assertEquals(1, group.getElement().get(0).getTarget().size()); assertEquals(1, group.getElement().get(0).getTarget().size());
assertEquals("RID7488", group.getElement().get(0).getTarget().get(0).getCode()); assertEquals("RPID2142", group.getElement().get(0).getTarget().get(0).getCode());
assertEquals("neck", group.getElement().get(0).getTarget().get(0).getDisplay()); assertEquals("US Retroperitoneum", group.getElement().get(0).getTarget().get(0).getDisplay());
assertEquals(Enumerations.ConceptMapEquivalence.EQUAL, group.getElement().get(0).getTarget().get(0).getEquivalence()); assertEquals(Enumerations.ConceptMapEquivalence.EQUAL, group.getElement().get(0).getTarget().get(0).getEquivalence());
// TOP 2000 - US // TOP 2000 - US

1
hapi-fhir-jpaserver-base/src/test/resources/logback-test.xml
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@ -1,5 +1,4 @@
<configuration> <configuration>
<appender name="STDOUT" class="ch.qos.logback.core.ConsoleAppender"> <appender name="STDOUT" class="ch.qos.logback.core.ConsoleAppender">
<filter class="ch.qos.logback.classic.filter.ThresholdFilter"> <filter class="ch.qos.logback.classic.filter.ThresholdFilter">
<level>INFO</level> <level>INFO</level>

5
hapi-fhir-jpaserver-base/src/test/resources/loinc/Part.csv
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@ -39,3 +39,8 @@
"LP6838-9","PROPERTY","NFr","Number Fraction","ACTIVE" "LP6838-9","PROPERTY","NFr","Number Fraction","ACTIVE"
"LP6141-8","METHOD","Automated count","Automated count","ACTIVE" "LP6141-8","METHOD","Automated count","Automated count","ACTIVE"
"LP15842-5","COMPONENT","Pyridoxine","Pyridoxine","ACTIVE" "LP15842-5","COMPONENT","Pyridoxine","Pyridoxine","ACTIVE"
"LP19258-0","COMPONENT","Large unstained cells","Large unstained cells","ACTIVE"
"LP32887-9","SYSTEM","{Setting}","{Setting}","ACTIVE"
"LP187178-1","METHOD","{Role}","Role-unspecified","ACTIVE"
"LP72311-1","COMPONENT","Consultation note","Consultation note","ACTIVE"

1 PartNumber PartTypeName PartName PartDisplayName Status
39 LP6838-9 PROPERTY NFr Number Fraction ACTIVE
40 LP6141-8 METHOD Automated count Automated count ACTIVE
41 LP15842-5 COMPONENT Pyridoxine Pyridoxine ACTIVE
42 LP19258-0 COMPONENT Large unstained cells Large unstained cells ACTIVE
43 LP32887-9 SYSTEM {Setting} {Setting} ACTIVE
44 LP187178-1 METHOD {Role} Role-unspecified ACTIVE
45 LP72311-1 COMPONENT Consultation note Consultation note ACTIVE
46