mirror of
https://github.com/hapifhir/hapi-fhir.git
synced 2025-02-16 18:05:19 +00:00
Issue 4052 addition of properties to the loinc terminology uploading process (#4135)
* Allow for easier override of DataSource and dialect * Add debug logging * Load AskAtOrderEntry and AssociatedObservations properties from loinc.cvs. Add changelog. * Add disabled sandbox test used to develop loinc upload modifications * Add flags to easily select running mode * Add validation counters and use gziped csv input to save space in repo * Implement revision suggestions. As test is a sandbox remove large files and add readme and test notes to locate them before running the test. * Add new CODING property handler to run after all TermConcepts are created, to have them accessible for extracting display value * Add small test file to ease setup Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
This commit is contained in:
jmarchionatto
GitHub
parent
422ef87a5d
commit
f00f65aae4
@ -14,6 +14,7 @@ import ca.uhn.fhir.jpa.term.icd10.Icd10Loader;
|
||||
import ca.uhn.fhir.jpa.term.icd10cm.Icd10CmLoader;
|
||||
import ca.uhn.fhir.jpa.term.loinc.LoincAnswerListHandler;
|
||||
import ca.uhn.fhir.jpa.term.loinc.LoincAnswerListLinkHandler;
|
||||
import ca.uhn.fhir.jpa.term.loinc.LoincCodingPropertiesHandler;
|
||||
import ca.uhn.fhir.jpa.term.loinc.LoincConsumerNameHandler;
|
||||
import ca.uhn.fhir.jpa.term.loinc.LoincDocumentOntologyHandler;
|
||||
import ca.uhn.fhir.jpa.term.loinc.LoincGroupFileHandler;
|
||||
@ -634,7 +635,7 @@ public class TermLoaderSvcImpl implements ITermLoaderSvc {
|
||||
iterateOverZipFileCsv(theDescriptors, theUploadProperties.getProperty(LOINC_PART_FILE.getCode(), LOINC_PART_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
|
||||
Map<PartTypeAndPartName, String> partTypeAndPartNameToPartNumber = ((LoincPartHandler) handler).getPartTypeAndPartNameToPartNumber();
|
||||
|
||||
// LOINC codes
|
||||
// LOINC string properties
|
||||
handler = new LoincHandler(codeSystemVersion, code2concept, propertyNamesToTypes, partTypeAndPartNameToPartNumber);
|
||||
iterateOverZipFileCsv(theDescriptors, theUploadProperties.getProperty(LOINC_FILE.getCode(), LOINC_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
|
||||
|
||||
@ -707,6 +708,10 @@ public class TermLoaderSvcImpl implements ITermLoaderSvc {
|
||||
handler = new LoincConsumerNameHandler(code2concept);
|
||||
iterateOverZipFileCsvOptional(theDescriptors, theUploadProperties.getProperty(LOINC_CONSUMER_NAME_FILE.getCode(), LOINC_CONSUMER_NAME_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
|
||||
|
||||
// LOINC coding properties (must run after all TermConcepts were created)
|
||||
handler = new LoincCodingPropertiesHandler(code2concept, propertyNamesToTypes);
|
||||
iterateOverZipFileCsv(theDescriptors, theUploadProperties.getProperty(LOINC_FILE.getCode(), LOINC_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
|
||||
|
||||
// Linguistic Variants
|
||||
handler = new LoincLinguisticVariantsHandler(linguisticVariants);
|
||||
iterateOverZipFileCsvOptional(theDescriptors, theUploadProperties.getProperty(LOINC_LINGUISTIC_VARIANTS_FILE.getCode(), LOINC_LINGUISTIC_VARIANTS_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
|
||||
|
||||
@ -0,0 +1,126 @@
|
||||
package ca.uhn.fhir.jpa.term.loinc;
|
||||
|
||||
/*-
|
||||
* #%L
|
||||
* HAPI FHIR JPA Server
|
||||
* %%
|
||||
* Copyright (C) 2014 - 2022 Smile CDR, Inc.
|
||||
* %%
|
||||
* 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.
|
||||
* See the License for the specific language governing permissions and
|
||||
* limitations under the License.
|
||||
* #L%
|
||||
*/
|
||||
|
||||
import ca.uhn.fhir.jpa.entity.TermConcept;
|
||||
import ca.uhn.fhir.jpa.term.IZipContentsHandlerCsv;
|
||||
import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
|
||||
import org.apache.commons.csv.CSVRecord;
|
||||
import org.hl7.fhir.r4.model.CodeSystem;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import java.util.Arrays;
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import static org.apache.commons.lang3.StringUtils.isBlank;
|
||||
import static org.apache.commons.lang3.StringUtils.isNotBlank;
|
||||
import static org.apache.commons.lang3.StringUtils.trim;
|
||||
|
||||
/**
|
||||
* Handler to process coding type properties 'AskAtOrderEntry' and 'AssociatedObservations'.
|
||||
*
|
||||
* These properties are added in a specific handler which is involved after all TermConcepts
|
||||
* are created, because they require a 'display' value associated to other TermConcept (pointed by the 'code'
|
||||
* property value), which require that concept to have been created.
|
||||
*/
|
||||
public class LoincCodingPropertiesHandler implements IZipContentsHandlerCsv {
|
||||
private static final Logger ourLog = LoggerFactory.getLogger(LoincCodingPropertiesHandler.class);
|
||||
|
||||
public static final String ASK_AT_ORDER_ENTRY_PROP_NAME = "AskAtOrderEntry";
|
||||
public static final String ASSOCIATED_OBSERVATIONS_PROP_NAME = "AssociatedObservations";
|
||||
public static final String LOINC_NUM = "LOINC_NUM";
|
||||
|
||||
|
||||
private final Map<String, TermConcept> myCode2Concept;
|
||||
private final Map<String, CodeSystem.PropertyType> myPropertyNameTypeMap;
|
||||
|
||||
|
||||
public LoincCodingPropertiesHandler(Map<String, TermConcept> theCode2concept,
|
||||
Map<String, CodeSystem.PropertyType> thePropertyNameTypeMap) {
|
||||
myCode2Concept = theCode2concept;
|
||||
myPropertyNameTypeMap = thePropertyNameTypeMap;
|
||||
}
|
||||
|
||||
|
||||
@Override
|
||||
public void accept(CSVRecord theRecord) {
|
||||
if ( ! anyValidProperty()) { return; }
|
||||
|
||||
String code = trim(theRecord.get(LOINC_NUM));
|
||||
if (isBlank(code)) { return; }
|
||||
|
||||
|
||||
String askAtOrderEntryValue = trim(theRecord.get(ASK_AT_ORDER_ENTRY_PROP_NAME));
|
||||
String associatedObservationsValue = trim(theRecord.get(ASSOCIATED_OBSERVATIONS_PROP_NAME));
|
||||
|
||||
// any of the record properties have a valid value?
|
||||
if (isBlank(askAtOrderEntryValue) && isBlank(associatedObservationsValue)) {
|
||||
return;
|
||||
}
|
||||
|
||||
TermConcept srcTermConcept = myCode2Concept.get(code);
|
||||
|
||||
if (isNotBlank(askAtOrderEntryValue)) {
|
||||
addCodingProperties(srcTermConcept, ASK_AT_ORDER_ENTRY_PROP_NAME, askAtOrderEntryValue);
|
||||
}
|
||||
|
||||
if (isNotBlank(associatedObservationsValue)) {
|
||||
addCodingProperties(srcTermConcept, ASSOCIATED_OBSERVATIONS_PROP_NAME, associatedObservationsValue);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* Validates that at least one ot target properties is defined in loinc.xml file and is of type "CODING"
|
||||
*/
|
||||
private boolean anyValidProperty() {
|
||||
CodeSystem.PropertyType askAtOrderEntryPropType = myPropertyNameTypeMap.get(ASK_AT_ORDER_ENTRY_PROP_NAME);
|
||||
CodeSystem.PropertyType associatedObservationsPropType = myPropertyNameTypeMap.get(ASSOCIATED_OBSERVATIONS_PROP_NAME);
|
||||
|
||||
return askAtOrderEntryPropType == CodeSystem.PropertyType.CODING
|
||||
|| associatedObservationsPropType == CodeSystem.PropertyType.CODING;
|
||||
}
|
||||
|
||||
|
||||
private void addCodingProperties(TermConcept theSrcTermConcept, String thePropertyName, String thePropertyValue) {
|
||||
List<String> propertyCodeValues = parsePropertyCodeValues(thePropertyValue);
|
||||
for (String propertyCodeValue : propertyCodeValues) {
|
||||
TermConcept targetTermConcept = myCode2Concept.get(propertyCodeValue);
|
||||
if (targetTermConcept == null) {
|
||||
ourLog.error("Couldn't find TermConcept for code: '{}'. Display property set to blank for property: '{}'",
|
||||
propertyCodeValue, thePropertyName);
|
||||
continue;
|
||||
}
|
||||
theSrcTermConcept.addPropertyCoding(thePropertyName, ITermLoaderSvc.LOINC_URI, propertyCodeValue, targetTermConcept.getDisplay());
|
||||
ourLog.trace("Adding coding property: {} to concept.code {}", thePropertyName, theSrcTermConcept.getCode());
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
private List<String> parsePropertyCodeValues(String theValue) {
|
||||
return Arrays.stream( theValue.split(";") )
|
||||
.map(String::trim)
|
||||
.collect(Collectors.toList());
|
||||
}
|
||||
}
|
||||
@ -25,7 +25,6 @@ import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
|
||||
import ca.uhn.fhir.jpa.entity.TermConcept;
|
||||
import ca.uhn.fhir.jpa.term.IZipContentsHandlerCsv;
|
||||
import ca.uhn.fhir.jpa.term.TermLoaderSvcImpl;
|
||||
import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
|
||||
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
|
||||
import org.apache.commons.csv.CSVRecord;
|
||||
import org.apache.commons.lang3.Validate;
|
||||
@ -33,10 +32,7 @@ import org.hl7.fhir.r4.model.CodeSystem;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import java.util.Arrays;
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import static org.apache.commons.lang3.StringUtils.isNotBlank;
|
||||
import static org.apache.commons.lang3.StringUtils.trim;
|
||||
@ -44,10 +40,6 @@ import static org.apache.commons.lang3.StringUtils.trim;
|
||||
public class LoincHandler implements IZipContentsHandlerCsv {
|
||||
|
||||
private static final Logger ourLog = LoggerFactory.getLogger(LoincHandler.class);
|
||||
|
||||
// most coding properties are not loaded by this handler, except these
|
||||
private static final List<String> myCodingPropertiesToLoad = List.of("AskAtOrderEntry", "AssociatedObservations");
|
||||
|
||||
private final Map<String, TermConcept> myCode2Concept;
|
||||
private final TermCodeSystemVersion myCodeSystemVersion;
|
||||
private final Map<String, CodeSystem.PropertyType> myPropertyNames;
|
||||
@ -97,14 +89,7 @@ public class LoincHandler implements IZipContentsHandlerCsv {
|
||||
break;
|
||||
|
||||
case CODING:
|
||||
if (myCodingPropertiesToLoad.contains(nextPropertyName)) {
|
||||
List<String> propertyCodeValues = parsePropertyCodeValues(nextPropertyValue);
|
||||
for (String propertyCodeValue : propertyCodeValues) {
|
||||
concept.addPropertyCoding(nextPropertyName, ITermLoaderSvc.LOINC_URI, propertyCodeValue, display);
|
||||
ourLog.trace("Adding coding property: {} to concept.code {}", nextPropertyName, concept.getCode());
|
||||
}
|
||||
}
|
||||
// rest of "Coding" property types are handled by partlink, hierarchy, RsnaPlaybook or DocumentOntology handlers
|
||||
// "Coding" property types are handled by loincCodingProperties, partlink, hierarchy, RsnaPlaybook or DocumentOntology handlers
|
||||
break;
|
||||
|
||||
case DECIMAL:
|
||||
@ -123,10 +108,4 @@ public class LoincHandler implements IZipContentsHandlerCsv {
|
||||
myCode2Concept.put(code, concept);
|
||||
}
|
||||
}
|
||||
|
||||
private List<String> parsePropertyCodeValues(String theValue) {
|
||||
return Arrays.stream( theValue.split(";") )
|
||||
.map(String::trim)
|
||||
.collect(Collectors.toList());
|
||||
}
|
||||
}
|
||||
|
||||
@ -0,0 +1,155 @@
|
||||
package ca.uhn.fhir.jpa.term.loinc;
|
||||
|
||||
import ca.uhn.fhir.jpa.entity.TermConcept;
|
||||
import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
|
||||
import ch.qos.logback.classic.Level;
|
||||
import ch.qos.logback.classic.Logger;
|
||||
import ch.qos.logback.classic.spi.ILoggingEvent;
|
||||
import ch.qos.logback.core.read.ListAppender;
|
||||
import org.apache.commons.csv.CSVRecord;
|
||||
import org.hl7.fhir.r4.model.CodeSystem;
|
||||
import org.junit.jupiter.api.BeforeEach;
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.junit.jupiter.api.extension.ExtendWith;
|
||||
import org.junit.jupiter.params.ParameterizedTest;
|
||||
import org.junit.jupiter.params.provider.ValueSource;
|
||||
import org.mockito.Mock;
|
||||
import org.mockito.junit.jupiter.MockitoExtension;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import java.util.HashMap;
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
|
||||
import static ca.uhn.fhir.jpa.term.loinc.LoincCodingPropertiesHandler.ASK_AT_ORDER_ENTRY_PROP_NAME;
|
||||
import static ca.uhn.fhir.jpa.term.loinc.LoincCodingPropertiesHandler.ASSOCIATED_OBSERVATIONS_PROP_NAME;
|
||||
import static ca.uhn.fhir.jpa.term.loinc.LoincCodingPropertiesHandler.LOINC_NUM;
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
import static org.junit.jupiter.api.Assertions.assertTrue;
|
||||
import static org.mockito.ArgumentMatchers.anyString;
|
||||
import static org.mockito.Mockito.lenient;
|
||||
import static org.mockito.Mockito.never;
|
||||
import static org.mockito.Mockito.times;
|
||||
import static org.mockito.Mockito.verify;
|
||||
import static org.mockito.Mockito.when;
|
||||
|
||||
@ExtendWith(MockitoExtension.class)
|
||||
class LoincCodingPropertiesHandlerTest {
|
||||
|
||||
private static final String CODE_A = "code-A";
|
||||
|
||||
private static LoincCodingPropertiesHandler testedHandler;
|
||||
|
||||
@Mock private CSVRecord myCsvRecord;
|
||||
@Mock private TermConcept myTargetTermConcept;
|
||||
@Mock private TermConcept myRefTermConcept1;
|
||||
@Mock private TermConcept myRefTermConcept2;
|
||||
|
||||
private final Map<String, TermConcept> myCode2concept = new HashMap<>();
|
||||
private final Map<String, CodeSystem.PropertyType> myPropertyNameTypeMap = new HashMap<>();
|
||||
|
||||
|
||||
@BeforeEach
|
||||
void setUp() {
|
||||
myCode2concept.put(CODE_A, myTargetTermConcept);
|
||||
testedHandler = new LoincCodingPropertiesHandler(myCode2concept, myPropertyNameTypeMap);
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
void not_any_property_valid_does_nothing() {
|
||||
myPropertyNameTypeMap.put("prop_1", CodeSystem.PropertyType.CODING); // uninteresting property name
|
||||
myPropertyNameTypeMap.put(ASK_AT_ORDER_ENTRY_PROP_NAME, CodeSystem.PropertyType.STRING); // wrong property type
|
||||
|
||||
testedHandler.accept(myCsvRecord);
|
||||
|
||||
verify(myTargetTermConcept, never()).addPropertyCoding(anyString(), anyString(), anyString(), anyString());
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
void record_no_loinc_num_property_does_nothing() {
|
||||
myPropertyNameTypeMap.put(ASK_AT_ORDER_ENTRY_PROP_NAME, CodeSystem.PropertyType.CODING); // wrong property type
|
||||
when(myCsvRecord.get(LOINC_NUM)).thenReturn(null);
|
||||
|
||||
testedHandler.accept(myCsvRecord);
|
||||
|
||||
verify(myTargetTermConcept, never()).addPropertyCoding(anyString(), anyString(), anyString(), anyString());
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
void no_property_valid_value_does_nothing() {
|
||||
myPropertyNameTypeMap.put(ASK_AT_ORDER_ENTRY_PROP_NAME, CodeSystem.PropertyType.CODING); // wrong property type
|
||||
when(myCsvRecord.get(LOINC_NUM)).thenReturn(CODE_A);
|
||||
|
||||
testedHandler.accept(myCsvRecord);
|
||||
|
||||
verify(myTargetTermConcept, never()).addPropertyCoding(anyString(), anyString(), anyString(), anyString());
|
||||
}
|
||||
|
||||
|
||||
@ParameterizedTest
|
||||
@ValueSource(strings = {ASK_AT_ORDER_ENTRY_PROP_NAME, ASSOCIATED_OBSERVATIONS_PROP_NAME})
|
||||
void each_tested_record_prop_creates_term_concept_prop(String thePropName) {
|
||||
myPropertyNameTypeMap.put(thePropName, CodeSystem.PropertyType.CODING);
|
||||
when(myCsvRecord.get(LOINC_NUM)).thenReturn(CODE_A);
|
||||
myCode2concept.put(CODE_A, myTargetTermConcept);
|
||||
myCode2concept.put("ref-code-01", myRefTermConcept1);
|
||||
myCode2concept.put("ref-code-02", myRefTermConcept2);
|
||||
lenient().when(myCsvRecord.get(thePropName)).thenReturn("ref-code-01; ref-code-02");
|
||||
when(myRefTermConcept1.getDisplay()).thenReturn("display-value-01");
|
||||
when(myRefTermConcept2.getDisplay()).thenReturn("display-value-02");
|
||||
|
||||
testedHandler.accept(myCsvRecord);
|
||||
|
||||
verify(myTargetTermConcept, times(1)).addPropertyCoding(
|
||||
thePropName, ITermLoaderSvc.LOINC_URI, "ref-code-01", "display-value-01");
|
||||
|
||||
verify(myTargetTermConcept, times(1)).addPropertyCoding(
|
||||
thePropName, ITermLoaderSvc.LOINC_URI, "ref-code-02", "display-value-02");
|
||||
}
|
||||
|
||||
|
||||
@ParameterizedTest
|
||||
@ValueSource(strings = {ASK_AT_ORDER_ENTRY_PROP_NAME, ASSOCIATED_OBSERVATIONS_PROP_NAME})
|
||||
void each_tested_record_prop_not_existing_target_is_logged(String thePropName) {
|
||||
myPropertyNameTypeMap.put(thePropName, CodeSystem.PropertyType.CODING);
|
||||
when(myCsvRecord.get(LOINC_NUM)).thenReturn(CODE_A);
|
||||
myCode2concept.put(CODE_A, myTargetTermConcept);
|
||||
myCode2concept.put("ref-code-01", myRefTermConcept1);
|
||||
lenient().when(myCsvRecord.get(thePropName)).thenReturn("ref-code-01; ref-code-02");
|
||||
when(myRefTermConcept1.getDisplay()).thenReturn("display-value-01");
|
||||
|
||||
Logger testLogger = (Logger) LoggerFactory.getLogger(LoincCodingPropertiesHandler.class);
|
||||
ListAppender<ILoggingEvent> testListAppender = addTestLogAppenderForClass(testLogger);
|
||||
|
||||
try {
|
||||
// call method under test
|
||||
testedHandler.accept(myCsvRecord);
|
||||
|
||||
// JUnit assertions
|
||||
List<ILoggingEvent> logsList = testListAppender.list;
|
||||
assertEquals(1, logsList.size());
|
||||
assertEquals(Level.ERROR, logsList.get(0).getLevel());
|
||||
assertTrue(logsList.get(0).getFormattedMessage().startsWith("Couldn't find TermConcept for code: 'ref-code-02'"));
|
||||
assertTrue(logsList.get(0).getFormattedMessage().contains(thePropName));
|
||||
|
||||
} finally {
|
||||
testLogger.detachAppender(testListAppender);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
private ListAppender<ILoggingEvent> addTestLogAppenderForClass(Logger theLogger) {
|
||||
// create and start a ListAppender
|
||||
ListAppender<ILoggingEvent> testListAppender = new ListAppender<>();
|
||||
testListAppender.start();
|
||||
|
||||
// add the appender to the logger
|
||||
theLogger.addAppender(testListAppender);
|
||||
|
||||
return testListAppender;
|
||||
}
|
||||
|
||||
}
|
||||
@ -0,0 +1 @@
|
||||
mock-maker-inline
|
||||
@ -20,6 +20,8 @@ import ca.uhn.fhir.jpa.test.BaseJpaTest;
|
||||
import ca.uhn.fhir.jpa.test.config.TestHSearchAddInConfig;
|
||||
import ca.uhn.fhir.jpa.test.config.TestR4Config;
|
||||
import ca.uhn.fhir.util.StopWatch;
|
||||
import com.google.common.collect.ArrayListMultimap;
|
||||
import com.google.common.collect.Multimap;
|
||||
import net.ttddyy.dsproxy.support.ProxyDataSourceBuilder;
|
||||
import org.apache.commons.csv.CSVFormat;
|
||||
import org.apache.commons.csv.CSVParser;
|
||||
@ -28,6 +30,7 @@ import org.apache.commons.csv.QuoteMode;
|
||||
import org.apache.commons.dbcp2.BasicDataSource;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.commons.lang3.StringUtils;
|
||||
import org.apache.commons.lang3.tuple.Pair;
|
||||
import org.hibernate.dialect.PostgreSQL10Dialect;
|
||||
import org.hl7.fhir.r4.model.CodeableConcept;
|
||||
import org.hl7.fhir.r4.model.Coding;
|
||||
@ -35,6 +38,7 @@ import org.hl7.fhir.r4.model.ValueSet;
|
||||
import org.junit.jupiter.api.Disabled;
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.junit.jupiter.api.extension.ExtendWith;
|
||||
import org.junit.jupiter.api.function.Executable;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
@ -51,27 +55,32 @@ import javax.annotation.Nonnull;
|
||||
import javax.persistence.EntityManager;
|
||||
import javax.persistence.Query;
|
||||
import java.io.File;
|
||||
import java.io.FileInputStream;
|
||||
import java.io.FileNotFoundException;
|
||||
import java.io.InputStream;
|
||||
import java.io.IOException;
|
||||
import java.io.Reader;
|
||||
import java.io.StringReader;
|
||||
import java.nio.charset.StandardCharsets;
|
||||
import java.text.DecimalFormat;
|
||||
import java.util.ArrayList;
|
||||
import java.util.Arrays;
|
||||
import java.util.Collection;
|
||||
import java.util.Comparator;
|
||||
import java.util.HashMap;
|
||||
import java.util.HashSet;
|
||||
import java.util.Iterator;
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
import java.util.Optional;
|
||||
import java.util.Set;
|
||||
import java.util.stream.Collectors;
|
||||
import java.util.zip.GZIPInputStream;
|
||||
import java.util.zip.ZipEntry;
|
||||
import java.util.zip.ZipFile;
|
||||
|
||||
import static ca.uhn.fhir.jpa.term.loinc.LoincCodingPropertiesHandler.ASK_AT_ORDER_ENTRY_PROP_NAME;
|
||||
import static ca.uhn.fhir.jpa.term.loinc.LoincCodingPropertiesHandler.ASSOCIATED_OBSERVATIONS_PROP_NAME;
|
||||
import static java.util.stream.Collectors.mapping;
|
||||
import static java.util.stream.Collectors.toSet;
|
||||
import static org.junit.jupiter.api.Assertions.assertAll;
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
import static org.junit.jupiter.api.Assertions.assertFalse;
|
||||
import static org.junit.jupiter.api.Assertions.assertNotNull;
|
||||
@ -81,59 +90,54 @@ import static org.junit.jupiter.api.Assertions.fail;
|
||||
/**
|
||||
* Sandbox test (not intended to run on CI build) so must be kept disabled
|
||||
*
|
||||
* Requires the loinc-full resource directory to contain the following three files:
|
||||
* _ Loinc.csv.gz
|
||||
* _ Loinc_1.11.zip and
|
||||
* Requires the loinc-full resource directory to contain the following files:
|
||||
* _ Loinc_1.11.zip
|
||||
* _ v1.11_loincupload.properties
|
||||
*
|
||||
* but they are too large for the repo, so before running this test, copy them from:
|
||||
* but last one is too large for the repo, so before running this test, copy it from:
|
||||
* https://drive.google.com/drive/folders/18be2R5IurlWnugkl18nDG7wrwPsOtfR-?usp=sharing
|
||||
* (SmileCDR has access)
|
||||
*
|
||||
* Can be executed with Lucene or Elastic configuration
|
||||
*
|
||||
* Requires 4Gb mem to run, so pom needs to be changed to run from IDE:
|
||||
* <surefire_jvm_args>-Dfile.encoding=UTF-8 -Xmx5g</surefire_jvm_args>
|
||||
* or to run from maven use:
|
||||
* mvn test -pl :hapi-fhir-jpaserver-test-utilities -Dtest=LoincFullLoadR4SandboxIT#uploadLoincCodeSystem -Dsurefire_jvm_args="-Xmx5g"
|
||||
*
|
||||
*/
|
||||
@Disabled("Sandbox test which requires 5Gb memory")
|
||||
@Disabled("Sandbox test")
|
||||
@ExtendWith(SpringExtension.class)
|
||||
@ContextConfiguration(classes = {
|
||||
LoincFullLoadR4SandboxIT.NoopMandatoryTransactionListener.class
|
||||
|
||||
// one of the following needs to be present
|
||||
// TestR4Config.class // uses in-memory DB
|
||||
,LoincFullLoadR4SandboxIT.OverriddenR4Config.class // your configured persistent DB
|
||||
|
||||
// pick up elastic or lucene engine:
|
||||
// pick up elastic, lucene or no-full-text engine:
|
||||
,TestHSearchAddInConfig.NoFT.class
|
||||
})
|
||||
public class LoincFullLoadR4SandboxIT extends BaseJpaTest {
|
||||
private static final Logger ourLog = LoggerFactory.getLogger(LoincFullLoadR4SandboxIT.class);
|
||||
|
||||
private static final DecimalFormat ourDecimalFormat = new DecimalFormat("#,###");
|
||||
|
||||
|
||||
public static final boolean USE_REAL_DB = true;
|
||||
public static final boolean LOAD_DB = false;
|
||||
public static final String DB_NAME = "testDB_new";
|
||||
public static final String DB_NAME = "cdr_loinc_display";
|
||||
|
||||
|
||||
|
||||
private static final DecimalFormat ourDecimalFormat = new DecimalFormat("#,###");
|
||||
public static final String LOINC_URL = "http://loinc.org";
|
||||
public static final String TEST_FILES_CLASSPATH = "loinc-full/";
|
||||
|
||||
public static final boolean CLEANUP_DATA = true;
|
||||
|
||||
static {
|
||||
System.setProperty("unlimited_db_connection", "true");
|
||||
}
|
||||
|
||||
private final Collection<Executable> mapToAsserts = new ArrayList<>();
|
||||
|
||||
|
||||
// -----------------------------------------------------------------------------------------
|
||||
// full LOINC file 1.11 (initially cloned from 2.73 for tests, with custom lonc.xml file with added 24 new properties)
|
||||
// full LOINC file 1.11 Initially cloned from 2.73 for tests, with custom lonc.xml file with added 24 new properties
|
||||
// Note that internal defined version is 2.78
|
||||
|
||||
public static final String CS_VERSION = "1.11";
|
||||
// public static final String CS_VERSION = "1.11";
|
||||
public static final String CS_VERSION = "2.78";
|
||||
public static final int CS_CONCEPTS_COUNT = 234_390;
|
||||
public static final int ASSOCIATED_OBSERVATIONS_COUNT = 8_058;
|
||||
public static final int ASK_AT_ORDER_ENTRY_COUNT = 65;
|
||||
@ -141,11 +145,12 @@ public class LoincFullLoadR4SandboxIT extends BaseJpaTest {
|
||||
public static final String LOINC_PROPERTIES_CLASSPATH =
|
||||
ResourceUtils.CLASSPATH_URL_PREFIX + TEST_FILES_CLASSPATH + "v1.11_loincupload.properties";
|
||||
|
||||
public static final String LOINC_ZIP_CLASSPATH =
|
||||
ResourceUtils.CLASSPATH_URL_PREFIX + TEST_FILES_CLASSPATH + "Loinc_1.11.zip";
|
||||
public static final String BASE_LOINC_FILE_NAME = "Loinc_1.11";
|
||||
|
||||
public static final String LOINC_CSV_ZIP_CLASSPATH =
|
||||
ResourceUtils.CLASSPATH_URL_PREFIX + TEST_FILES_CLASSPATH + "Loinc.csv.gz";
|
||||
public static final String LOINC_ZIP_CLASSPATH =
|
||||
ResourceUtils.CLASSPATH_URL_PREFIX + TEST_FILES_CLASSPATH + BASE_LOINC_FILE_NAME + ".zip";
|
||||
public static final String LOINC_CSV_ZIP_ENTRY_PATH = BASE_LOINC_FILE_NAME + "/LoincTable/Loinc.csv";
|
||||
public static final String LOINC_MAP_TO_ZIP_ENTRY_PATH = BASE_LOINC_FILE_NAME + "/LoincTable/MapTo.csv";
|
||||
// -----------------------------------------------------------------------------------------
|
||||
|
||||
@Autowired private FhirContext myFhirCtx;
|
||||
@ -158,14 +163,11 @@ public class LoincFullLoadR4SandboxIT extends BaseJpaTest {
|
||||
@Autowired private ITermCodeSystemDao myTermCodeSystemDao;
|
||||
@Autowired private ITermCodeSystemVersionDao myTermCodeSystemVersionDao;
|
||||
|
||||
|
||||
@Autowired
|
||||
@Qualifier("myValueSetDaoR4")
|
||||
protected IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> myValueSetDao;
|
||||
private IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> myValueSetDao;
|
||||
|
||||
|
||||
|
||||
private long termCodeSystemVersionWithVersionId;
|
||||
private TermCodeSystemVersion termCodeSystemVersion;
|
||||
|
||||
private int associatedObservationsCount = 0;
|
||||
private int askAtOrderEntryCount = 0;
|
||||
@ -202,7 +204,7 @@ public class LoincFullLoadR4SandboxIT extends BaseJpaTest {
|
||||
@Test()
|
||||
public void uploadLoincCodeSystem() throws Exception {
|
||||
|
||||
if (USE_REAL_DB && LOAD_DB) {
|
||||
if (LOAD_DB) {
|
||||
List<ITermLoaderSvc.FileDescriptor> myFileDescriptors = buildFileDescriptors();
|
||||
|
||||
// upload terminology
|
||||
@ -212,24 +214,29 @@ public class LoincFullLoadR4SandboxIT extends BaseJpaTest {
|
||||
|
||||
// save all deferred concepts, properties, links, etc
|
||||
sw.restart();
|
||||
myTerminologyDeferredStorageSvc.saveAllDeferred();
|
||||
saveAllDeferredNoTimeout();
|
||||
|
||||
ourLog.info("=================> Saving all terminology deferred entities took {}", sw);
|
||||
validateSavedConceptsCount();
|
||||
|
||||
sw.restart();
|
||||
myTermReadSvc.preExpandDeferredValueSetsToTerminologyTables();
|
||||
ourLog.info("=================> Pre-expanding ValueSets took {}", sw);
|
||||
|
||||
// tested properties have no special relation with ValueSet(s), however we mey want
|
||||
// ValueSets to be expanded in same cases so don't remove the following commented code
|
||||
// sw.restart();
|
||||
// myTermReadSvc.preExpandDeferredValueSetsToTerminologyTables();
|
||||
// ourLog.info("=================> Pre-expanding ValueSets took {}", sw);
|
||||
|
||||
return;
|
||||
}
|
||||
|
||||
// validation:
|
||||
// create from loinc.csv file map of code | set of not-blank-properties
|
||||
// query each code and validate that all properties in map are set (can we check type also)
|
||||
// create from mapto.csv file map of code | Pair<mapToCode, display>
|
||||
// query each code and validate that all properties in both maps are set
|
||||
|
||||
List<Map<String, String>> conceptPropertyRecords = readCsvRecordsAsMap();
|
||||
List<Map<String, String>> conceptPropertyCvsMap = readLoincCsvRecordsAsMap();
|
||||
Multimap<String, Pair<String, String>> conceptMapToCvsMap = ArrayListMultimap.create();
|
||||
|
||||
validateCreatedConceptsHaveAllProperties( conceptPropertyRecords );
|
||||
validateCreatedConceptsHaveAllProperties( conceptPropertyCvsMap, conceptMapToCvsMap );
|
||||
|
||||
ourLog.info("Processed properties : {}", processedPropertiesCounter);
|
||||
ourLog.info("associatedObservationsCount : {}", associatedObservationsCount);
|
||||
@ -239,7 +246,17 @@ public class LoincFullLoadR4SandboxIT extends BaseJpaTest {
|
||||
assertEquals(ASK_AT_ORDER_ENTRY_COUNT, askAtOrderEntryCount);
|
||||
assertEquals(ASSOCIATED_OBSERVATIONS_COUNT, associatedObservationsCount);
|
||||
|
||||
}
|
||||
// ass asserts are used for some validation, but we want all problems to be displayed,
|
||||
// we just collect assertions and execute them all et the end (here).
|
||||
assertAll(mapToAsserts);
|
||||
}
|
||||
|
||||
|
||||
private void saveAllDeferredNoTimeout() {
|
||||
while( ! myTerminologyDeferredStorageSvc.isStorageQueueEmpty() ) {
|
||||
myTerminologyDeferredStorageSvc.saveDeferred();
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Used occasionally for some manual validation - don't delete
|
||||
@ -249,7 +266,7 @@ public class LoincFullLoadR4SandboxIT extends BaseJpaTest {
|
||||
Query q = myEntityManager.createQuery("from ForcedId where myForcedId like 'LG8749-6%'");
|
||||
@SuppressWarnings("unchecked")
|
||||
List<ForcedId> fIds = (List<ForcedId>) q.getResultList();
|
||||
long res_id = fIds.stream().map(ForcedId::getId).sorted().findFirst().get();
|
||||
long res_id = fIds.stream().map(ForcedId::getId).sorted().findFirst().orElse(fail("ForcedId not found"));
|
||||
|
||||
Query q1 = myEntityManager.createQuery("from ResourceTable where id = " + res_id);
|
||||
@SuppressWarnings("unchecked")
|
||||
@ -269,7 +286,9 @@ public class LoincFullLoadR4SandboxIT extends BaseJpaTest {
|
||||
}
|
||||
|
||||
|
||||
private void validateCreatedConceptsHaveAllProperties(List<Map<String, String>> theConceptPropertyInputMap) {
|
||||
private void validateCreatedConceptsHaveAllProperties(List<Map<String, String>> theConceptPropertyInputMap,
|
||||
Multimap<String, Pair<String, String>> theConceptMapToCvsMap) {
|
||||
|
||||
TermCodeSystemVersion tcsVersion = getTermCodeSystemVersion();
|
||||
|
||||
ourLog.info("Properties to process: {}", ourDecimalFormat.format(theConceptPropertyInputMap.size()));
|
||||
@ -281,7 +300,7 @@ public class LoincFullLoadR4SandboxIT extends BaseJpaTest {
|
||||
runInTransaction(() -> {
|
||||
Optional<TermConcept> tcFomDbOpt = myTermConceptDao.findByCodeSystemAndCode(tcsVersion, recordCode);
|
||||
tcFomDbOpt.ifPresentOrElse(
|
||||
tc -> validateTermConceptEntry(tc, tcRecordMap),
|
||||
tc -> validateTermConceptEntry(tc, tcRecordMap, theConceptMapToCvsMap),
|
||||
() -> ourLog.error("Couldn't find TermConcept with code: {} in DB", recordCode));
|
||||
});
|
||||
|
||||
@ -301,23 +320,33 @@ public class LoincFullLoadR4SandboxIT extends BaseJpaTest {
|
||||
}
|
||||
|
||||
|
||||
private void validateTermConceptEntry(TermConcept theTermConcept, Map<String, String> theRecordMap) {
|
||||
private void validateTermConceptEntry(TermConcept theTermConcept,
|
||||
Map<String, String> theRecordMap, Multimap<String, Pair<String, String>> theConceptMapToCvsMap) {
|
||||
|
||||
String recordCode = getRecordCode(theRecordMap);
|
||||
if ( ! theTermConcept.getCode().equals(recordCode) ) {
|
||||
fail("Received non matching inputs code from file: " + recordCode + ", code from DB: " + theTermConcept.getCode());
|
||||
}
|
||||
|
||||
ourLog.trace("Validating TC with code: {}", theTermConcept.getCode());
|
||||
Map<String, Set<String>> tcConceptPropertyMap = theTermConcept.getProperties().stream()
|
||||
.collect(Collectors.groupingBy(TermConceptProperty::getKey, HashMap::new, mapping(TermConceptProperty::getValue, toSet())));
|
||||
ourLog.trace("Validating new properties for TC with code: {}", theTermConcept.getCode());
|
||||
// map of TC property name | set of property values
|
||||
HashMap<String, Set<String>> tcConceptPropertyMap = theTermConcept.getProperties().stream()
|
||||
.collect(Collectors.groupingBy(TermConceptProperty::getKey,
|
||||
HashMap::new,
|
||||
mapping(TermConceptProperty::getValue, toSet())));
|
||||
|
||||
validateNewProperties(recordCode, theRecordMap, tcConceptPropertyMap);
|
||||
validateNewProperties(theTermConcept, theRecordMap, tcConceptPropertyMap);
|
||||
|
||||
Collection<Pair<String, String>> toMapRecordForTermConcept = theConceptMapToCvsMap.get(recordCode);
|
||||
// validateMapToProperties(recordCode, tcConceptPropertyMap, toMapRecordForTermConcept);
|
||||
}
|
||||
|
||||
|
||||
private void validateNewProperties(String theTcCode, Map<String, String> theRecordPropsMap, Map<String, Set<String>> theTcConceptPropertyMap) {
|
||||
private void validateNewProperties(TermConcept theTermConcept, Map<String, String> theRecordPropsMap,
|
||||
HashMap<String, Set<String>> theTcConceptPropertyMap) {
|
||||
|
||||
// make sure we are good so far and both entries to compare are for same TermConcept code
|
||||
assertEquals(theTcCode, theRecordPropsMap.get("LOINC_NUM"), "theTcCode and record key (LOINC_NUM) must match");
|
||||
assertEquals(theTermConcept.getCode(), theRecordPropsMap.get("LOINC_NUM"), "theTcCode and record key (LOINC_NUM) must match");
|
||||
|
||||
for (Map.Entry<String, String> recordEntry : theRecordPropsMap.entrySet()) {
|
||||
|
||||
@ -327,41 +356,76 @@ public class LoincFullLoadR4SandboxIT extends BaseJpaTest {
|
||||
// bypass old properties
|
||||
if ( ! newRecordPropertyNames.contains(recordEntry.getKey()) ) { continue; }
|
||||
|
||||
Set<String> tcConceptPropValues = theTcConceptPropertyMap.get(recordEntry.getKey());
|
||||
if (CollectionUtils.isEmpty(tcConceptPropValues)) {
|
||||
ourLog.error("TCConcept with code: {} does not have property: {} which in csv file has value: {}",
|
||||
theTcCode, recordEntry.getKey(), recordEntry.getValue());
|
||||
continue;
|
||||
}
|
||||
Set<String> tcConceptValues = theTcConceptPropertyMap.get(recordEntry.getKey());
|
||||
|
||||
// special case because we need to parse ';' separated codes from file property value
|
||||
if ( "AssociatedObservations".equals(recordEntry.getKey()) ) {
|
||||
if ( ASSOCIATED_OBSERVATIONS_PROP_NAME.equals(recordEntry.getKey()) ) {
|
||||
associatedObservationsCount++;
|
||||
validateAssociatedObservations(theTcCode, recordEntry, tcConceptPropValues);
|
||||
validateCodingProperties(theTermConcept, ASSOCIATED_OBSERVATIONS_PROP_NAME, recordEntry, tcConceptValues);
|
||||
continue;
|
||||
}
|
||||
|
||||
if ( "AskAtOrderEntry".equals(recordEntry.getKey()) ) { askAtOrderEntryCount++; }
|
||||
if ( ASK_AT_ORDER_ENTRY_PROP_NAME.equals(recordEntry.getKey()) ) {
|
||||
askAtOrderEntryCount++;
|
||||
validateCodingProperties(theTermConcept, ASK_AT_ORDER_ENTRY_PROP_NAME, recordEntry, tcConceptValues);
|
||||
continue;
|
||||
}
|
||||
|
||||
if ( ! tcConceptPropValues.contains(recordEntry.getValue()) ) {
|
||||
ourLog.error("For TC code: {}, prop: {}, values don't match. Record value: {} TC prop value: {}",
|
||||
theTcCode, recordEntry.getKey(), recordEntry.getValue(), String.join(" - ", tcConceptPropValues));
|
||||
if (CollectionUtils.isEmpty(tcConceptValues)) {
|
||||
ourLog.error("TermConcept with code: {} does not have property: {} which in csv file has value: {}",
|
||||
theTermConcept.getCode(), recordEntry.getKey(), recordEntry.getValue());
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* Validate that all file property codes become a "Coding" property on the TermConcept
|
||||
* and display properties are the display of the target TermConcept
|
||||
*/
|
||||
private void validateAssociatedObservations(String theTcCode, Map.Entry<String, String> recordEntry, Set<String> tcConceptPropValues) {
|
||||
private void validateCodingProperties(TermConcept theSourceTermConcept, String thePropName,
|
||||
Map.Entry<String, String> recordEntry, Set<String> theTCPropValues) {
|
||||
|
||||
List<String> recordPropertyCodes = parsePropertyCodeValues(recordEntry.getValue());
|
||||
|
||||
// validate each property in the records was uploaded to the corresponding TermConcept
|
||||
for (String recordPropertyCode : recordPropertyCodes) {
|
||||
if ( ! tcConceptPropValues.contains(recordPropertyCode) ) {
|
||||
ourLog.error("For TC code: {}, prop: {}, record code: {} not found among properties: {}",
|
||||
theTcCode, recordEntry.getKey(), recordPropertyCode, String.join(" - ", tcConceptPropValues));
|
||||
if ( ! theTCPropValues.contains(recordPropertyCode) ) {
|
||||
ourLog.error("For TC code: {}, prop: {}, record code: {} not found among uploaded TC properties: {}",
|
||||
theSourceTermConcept.getCode(), recordEntry.getKey(), recordPropertyCode, String.join(" - ", theTCPropValues));
|
||||
}
|
||||
|
||||
// validate that the display value for each uploaded TC property of name thePropertyName is the display of the TC pointed by the TC code
|
||||
validatePropertiesDisplay(theSourceTermConcept, thePropName, recordPropertyCode);
|
||||
}
|
||||
|
||||
// also check that uploaded TC only has properties is has to have
|
||||
for (String tcPropValue : theTCPropValues) {
|
||||
if ( ! recordEntry.getValue().contains(tcPropValue)) {
|
||||
ourLog.error("TC with code: {}, has a property with code: {}, which is not in defined property list: {}",
|
||||
theSourceTermConcept.getCode(), tcPropValue, recordEntry.getValue());
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
private void validatePropertiesDisplay(TermConcept theSourceTermConcept, String thePropName, String recordPropertyCode) {
|
||||
// from source TermConcept obtain the map of thePropName properties: property code - display
|
||||
Map<String, String> srcTcCodeDisplayMap = theSourceTermConcept.getProperties().stream()
|
||||
.filter(p -> p.getKey().equals(thePropName))
|
||||
.collect(Collectors.toMap(TermConceptProperty::getValue, TermConceptProperty::getDisplay));
|
||||
|
||||
for (Map.Entry<String, String> tcCodeDisplayEntry : srcTcCodeDisplayMap.entrySet()) {
|
||||
Optional<TermConcept> targetTermConceptOpt =
|
||||
myTermConceptDao.findByCodeSystemAndCode(termCodeSystemVersion, tcCodeDisplayEntry.getKey());
|
||||
if (targetTermConceptOpt.isEmpty()) {
|
||||
ourLog.error("For TC code: {}, target TC with code: {} is not present in DB", theSourceTermConcept.getCode(), recordPropertyCode);
|
||||
}
|
||||
|
||||
TermConcept targetTermConcept = targetTermConceptOpt.get();
|
||||
if ( ! tcCodeDisplayEntry.getValue().equals(targetTermConcept.getDisplay()) ) {
|
||||
ourLog.error("For TC with code: {}, display is: {}, while target TC display is: {}",
|
||||
theSourceTermConcept.getCode(), tcCodeDisplayEntry.getValue(), targetTermConcept.getDisplay());
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
@ -373,8 +437,8 @@ public class LoincFullLoadR4SandboxIT extends BaseJpaTest {
|
||||
}
|
||||
|
||||
|
||||
private List<Map<String, String>> readCsvRecordsAsMap() throws Exception {
|
||||
CSVParser parser = getCsvRecords();
|
||||
private List<Map<String, String>> readLoincCsvRecordsAsMap() throws Exception {
|
||||
CSVParser parser = getParserForZipFile(LOINC_ZIP_CLASSPATH, LOINC_CSV_ZIP_ENTRY_PATH);
|
||||
Iterator<CSVRecord> iter = parser.iterator();
|
||||
|
||||
Map<String, Integer> headerMap = parser.getHeaderMap();
|
||||
@ -402,17 +466,9 @@ public class LoincFullLoadR4SandboxIT extends BaseJpaTest {
|
||||
}
|
||||
|
||||
|
||||
public String getCvsStringFromZip(String theFilePath) throws Exception {
|
||||
InputStream stream = new FileInputStream(ResourceUtils.getFile(theFilePath));
|
||||
assertNotNull(stream);
|
||||
stream = new GZIPInputStream(stream);
|
||||
return IOUtils.toString(stream, StandardCharsets.UTF_8);
|
||||
}
|
||||
|
||||
|
||||
@Nonnull
|
||||
private CSVParser getCsvRecords() throws Exception {
|
||||
Reader reader = new StringReader(getCvsStringFromZip(LOINC_CSV_ZIP_CLASSPATH));
|
||||
private CSVParser getParserForZipFile(String theZipFileClassPath, String theFileEntryPath) throws Exception {
|
||||
Reader reader = new StringReader(getCvsStringFromZip(theZipFileClassPath, theFileEntryPath));
|
||||
|
||||
CSVFormat format = CSVFormat
|
||||
.newFormat(',')
|
||||
@ -424,20 +480,41 @@ public class LoincFullLoadR4SandboxIT extends BaseJpaTest {
|
||||
}
|
||||
|
||||
|
||||
public String getCvsStringFromZip(String theFilePath, String theZipFileEntryPath) {
|
||||
try (ZipFile zipFile = new ZipFile(ResourceUtils.getFile(theFilePath))) {
|
||||
|
||||
ZipEntry zipEntry = zipFile.getEntry(theZipFileEntryPath);
|
||||
assertNotNull(zipEntry, "Couldn't find file: " + theZipFileEntryPath + " inside zip file: " + theFilePath);
|
||||
return IOUtils.toString(zipFile.getInputStream(zipEntry), StandardCharsets.UTF_8);
|
||||
|
||||
} catch (IOException e) {
|
||||
fail(e.getMessage());
|
||||
}
|
||||
|
||||
fail("Couldn't find " + theFilePath + "/" + theZipFileEntryPath);
|
||||
return null;
|
||||
}
|
||||
|
||||
|
||||
private void validateSavedConceptsCount() {
|
||||
termCodeSystemVersionWithVersionId = getTermCodeSystemVersion().getPid();
|
||||
Long tcsvId = getTermCodeSystemVersion().getPid();
|
||||
int dbVersionedTermConceptCount = runInTransaction(() ->
|
||||
myTermConceptDao.countByCodeSystemVersion(termCodeSystemVersionWithVersionId) );
|
||||
ourLog.info("=================> Number of stored concepts for version {}: {}", CS_VERSION, dbVersionedTermConceptCount);
|
||||
myTermConceptDao.countByCodeSystemVersion(tcsvId) );
|
||||
ourLog.info("=================> Number of stored concepts for version {}: {}",
|
||||
CS_VERSION, ourDecimalFormat.format(dbVersionedTermConceptCount));
|
||||
assertEquals(CS_CONCEPTS_COUNT, dbVersionedTermConceptCount);
|
||||
}
|
||||
|
||||
|
||||
private TermCodeSystemVersion getTermCodeSystemVersion() {
|
||||
if (termCodeSystemVersion != null) {
|
||||
return termCodeSystemVersion;
|
||||
}
|
||||
|
||||
return runInTransaction(() -> {
|
||||
TermCodeSystem myTermCodeSystem = myTermCodeSystemDao.findByCodeSystemUri(LOINC_URL);
|
||||
TermCodeSystemVersion termCodeSystemVersion = myTermCodeSystemVersionDao
|
||||
.findByCodeSystemPidAndVersion(myTermCodeSystem.getPid(), CS_VERSION);
|
||||
assertNotNull(myTermCodeSystem);
|
||||
termCodeSystemVersion = myTermCodeSystemVersionDao.findByCodeSystemPidAndVersion(myTermCodeSystem.getPid(), CS_VERSION);
|
||||
assertNotNull(termCodeSystemVersion);
|
||||
return termCodeSystemVersion;
|
||||
});
|
||||
|
||||
@ -0,0 +1,89 @@
|
||||
#################
|
||||
### MANDATORY ###
|
||||
#################
|
||||
|
||||
# Answer lists (ValueSets of potential answers/values for LOINC "questions")
|
||||
## File must be present
|
||||
loinc.answerlist.file=AccessoryFiles/AnswerFile/AnswerList.csv
|
||||
# Answer list links (connects LOINC observation codes to answer list codes)
|
||||
## File must be present
|
||||
loinc.answerlist.link.file=AccessoryFiles/AnswerFile/LoincAnswerListLink.csv
|
||||
|
||||
# Document ontology
|
||||
## File must be present
|
||||
loinc.document.ontology.file=AccessoryFiles/DocumentOntology/DocumentOntology.csv
|
||||
|
||||
# LOINC codes
|
||||
## File must be present
|
||||
loinc.file=LoincTable/Loinc.csv
|
||||
|
||||
# LOINC hierarchy
|
||||
## File must be present
|
||||
loinc.hierarchy.file=AccessoryFiles/ComponentHierarchyBySystem/ComponentHierarchyBySystem.csv
|
||||
|
||||
# IEEE medical device codes
|
||||
## File must be present
|
||||
loinc.ieee.medical.device.code.mapping.table.file=AccessoryFiles/LoincIeeeMedicalDeviceCodeMappingTable/LoincIeeeMedicalDeviceCodeMappingTable.csv
|
||||
|
||||
# Imaging document codes
|
||||
## File must be present
|
||||
loinc.imaging.document.codes.file=AccessoryFiles/ImagingDocuments/ImagingDocumentCodes.csv
|
||||
|
||||
# Part
|
||||
## File must be present
|
||||
loinc.part.file=AccessoryFiles/PartFile/Part.csv
|
||||
|
||||
# Part link
|
||||
## File must be present
|
||||
loinc.part.link.primary.file=AccessoryFiles/PartFile/LoincPartLink_Primary.csv
|
||||
loinc.part.link.supplementary.file=AccessoryFiles/PartFile/LoincPartLink_Supplementary.csv
|
||||
|
||||
# Part related code mapping
|
||||
## File must be present
|
||||
loinc.part.related.code.mapping.file=AccessoryFiles/PartFile/PartRelatedCodeMapping.csv
|
||||
|
||||
# RSNA playbook
|
||||
## File must be present
|
||||
loinc.rsna.playbook.file=AccessoryFiles/LoincRsnaRadiologyPlaybook/LoincRsnaRadiologyPlaybook.csv
|
||||
|
||||
# Top 2000 codes - SI
|
||||
## File must be present
|
||||
loinc.top2000.common.lab.results.si.file=AccessoryFiles/Top2000Results/SI/Top2000CommonLabResultsSi.csv
|
||||
# Top 2000 codes - US
|
||||
## File must be present
|
||||
loinc.top2000.common.lab.results.us.file=AccessoryFiles/Top2000Results/US/Top2000CommonLabResultsUs.csv
|
||||
|
||||
# Universal lab order ValueSet
|
||||
## File must be present
|
||||
loinc.universal.lab.order.valueset.file=AccessoryFiles/LoincUniversalLabOrdersValueSet/LoincUniversalLabOrdersValueSet.csv
|
||||
|
||||
################
|
||||
### OPTIONAL ###
|
||||
################
|
||||
|
||||
# This is the version identifier for the LOINC code system
|
||||
## Key may be omitted if only a single version of LOINC is being kept.
|
||||
loinc.codesystem.version=1.11
|
||||
|
||||
loinc.codesystem.make.current=false
|
||||
|
||||
# This is the version identifier for the answer list file
|
||||
## Key may be omitted
|
||||
loinc.answerlist.version=Beta.1
|
||||
|
||||
# This is the version identifier for uploaded ConceptMap resources
|
||||
## Key may be omitted
|
||||
loinc.conceptmap.version=Beta.1
|
||||
|
||||
# Group
|
||||
## Default value if key not provided: AccessoryFiles/GroupFile/Group.csv
|
||||
## File may be omitted
|
||||
loinc.group.file=AccessoryFiles/GroupFile/Group.csv
|
||||
# Group terms
|
||||
## Default value if key not provided: AccessoryFiles/GroupFile/GroupLoincTerms.csv
|
||||
## File may be omitted
|
||||
loinc.group.terms.file=AccessoryFiles/GroupFile/GroupLoincTerms.csv
|
||||
# Parent group
|
||||
## Default value if key not provided: AccessoryFiles/GroupFile/ParentGroup.csv
|
||||
## File may be omitted
|
||||
loinc.parent.group.file=AccessoryFiles/GroupFile/ParentGroup.csv
|
||||
Loading…
x
Reference in New Issue
Block a user