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Migrated SnomedLoincStartData to Composer (#61)
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@stenkarl
stenkarl authored Nov 11, 2024
1 parent c0d9a72 commit a0693da
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2 changes: 1 addition & 1 deletion src/main/java/dev/ikm/tinkar/sandbox/SnomedLoincLidrStarterData.java
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Expand Up @@ -50,7 +50,7 @@ public static void main(String args[]){
}

private static void configureConceptsAndPatterns(StarterData starterData, UUIDUtility uuidUtility){
SnomedLoincStarterData.configureConceptsAndPatterns(starterData, uuidUtility);
//SnomedLoincStarterData.configureConceptsAndPatterns(starterData, uuidUtility);

//LOINC Long Common Name
PublicId publicId = PublicIds.of(UUID.nameUUIDFromBytes("LOINC Long Name".getBytes()));
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174 changes: 126 additions & 48 deletions src/main/java/dev/ikm/tinkar/sandbox/SnomedLoincStarterData.java
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@@ -1,75 +1,153 @@
package dev.ikm.tinkar.sandbox;

import dev.ikm.tinkar.common.service.CachingService;
import dev.ikm.tinkar.common.service.PrimitiveData;
import dev.ikm.tinkar.common.service.ServiceKeys;
import dev.ikm.tinkar.common.service.ServiceProperties;
import dev.ikm.tinkar.common.util.uuid.UuidUtil;
import dev.ikm.tinkar.composer.Composer;
import dev.ikm.tinkar.composer.Session;
import dev.ikm.tinkar.composer.assembler.ConceptAssembler;
import dev.ikm.tinkar.composer.template.Definition;
import dev.ikm.tinkar.composer.template.FullyQualifiedName;
import dev.ikm.tinkar.composer.template.Identifier;
import dev.ikm.tinkar.composer.template.StatedAxiom;
import dev.ikm.tinkar.composer.template.StatedNavigation;
import dev.ikm.tinkar.composer.template.Synonym;
import dev.ikm.tinkar.composer.template.TinkarBaseModel;
import dev.ikm.tinkar.composer.template.USDialect;
import dev.ikm.tinkar.entity.EntityService;
import dev.ikm.tinkar.entity.export.ExportEntitiesController;
import dev.ikm.tinkar.starterdata.StarterData;
import dev.ikm.tinkar.starterdata.UUIDUtility;
import dev.ikm.tinkar.terms.EntityProxy;
import dev.ikm.tinkar.terms.TinkarTerm;
import dev.ikm.tinkar.terms.State;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.io.File;
import java.util.List;
import java.util.concurrent.ExecutionException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import static dev.ikm.tinkar.terms.TinkarTerm.DESCRIPTION_NOT_CASE_SENSITIVE;
import static dev.ikm.tinkar.terms.TinkarTerm.ENGLISH_LANGUAGE;
import static dev.ikm.tinkar.terms.TinkarTerm.IDENTIFIER_SOURCE;
import static dev.ikm.tinkar.terms.TinkarTerm.PREFERRED;
import static dev.ikm.tinkar.terms.TinkarTerm.PRIMORDIAL_MODULE;
import static dev.ikm.tinkar.terms.TinkarTerm.PRIMORDIAL_PATH;
import static dev.ikm.tinkar.terms.TinkarTerm.UNIVERSALLY_UNIQUE_IDENTIFIER;
import static dev.ikm.tinkar.terms.TinkarTerm.USER;

public class SnomedLoincStarterData {

private static final Logger LOG = LoggerFactory.getLogger(SnomedLoincStarterData.class.getSimpleName());

private static File exportDataStore;
private static File exportFile;
public static void main(String args[]){
private final File datastore;
private final File exportFile;

exportDataStore = new File(args[0]);
public SnomedLoincStarterData(String[] args) {
datastore = new File(args[0]);
exportFile = new File(args[1]);

UUIDUtility uuidUtility = new UUIDUtility();

StarterData starterData = new StarterData(exportDataStore, uuidUtility)
.init()
.authoringSTAMP(
TinkarTerm.ACTIVE_STATE,
System.currentTimeMillis(),
TinkarTerm.USER,
TinkarTerm.PRIMORDIAL_MODULE,
TinkarTerm.PRIMORDIAL_PATH);

configureConceptsAndPatterns(starterData, uuidUtility);
starterData.build(); //Natively writing data to spined array
exportStarterData(); //exports starter data to pb.zip
starterData.shutdown();
}

protected static void configureConceptsAndPatterns(StarterData starterData, UUIDUtility uuidUtility){
SnomedStarterData.configureConceptsAndPatterns(starterData, uuidUtility);
private void transform() {
EntityService.get().beginLoadPhase();
try {
Composer composer = new Composer("SnomedCT Loinc Starter Data");
Session session = composer.open(
State.ACTIVE,
System.currentTimeMillis(),
USER,
PRIMORDIAL_MODULE,
PRIMORDIAL_PATH);
createConcepts(session);
composer.commitSession(session);
} finally {
EntityService.get().endLoadPhase();
}
}

private void createConcepts(Session session) {
EntityProxy.Concept snomedLoincAuthor = EntityProxy.Concept.make("SNOMED CT LOINC Collaboration Author", new UUIDUtility().createUUID("SNOMED CT LOINC Collaboration Author"));
starterData.concept(snomedLoincAuthor)
.fullyQualifiedName("IHTSDO SNOMED CT LOINC Collaboration Author", TinkarTerm.PREFERRED)
.synonym("SNOMED CT LOINC Collaboration Author", TinkarTerm.PREFERRED)
.definition("International Health Terminology Standards Development Organisation (IHTSDO) SNOMED CT LOINC Collaboration Author", TinkarTerm.PREFERRED)
.identifier(TinkarTerm.UNIVERSALLY_UNIQUE_IDENTIFIER, snomedLoincAuthor.asUuidArray()[0].toString())
.statedDefinition(List.of(TinkarTerm.USER))
.build();

/* UUID from SNOMED Browser - This is the ECL query : '705114005 |LOINC Code System (qualifier value)|' */

session.compose((ConceptAssembler conceptAssembler) -> conceptAssembler.concept(snomedLoincAuthor))
.attach((FullyQualifiedName fqn) -> fqn
.text("IHTSDO SNOMED CT LOINC Collaboration Author")
.language(ENGLISH_LANGUAGE)
.caseSignificance(DESCRIPTION_NOT_CASE_SENSITIVE)
.attach(usDialect()))
.attach((Synonym synonym) -> synonym
.text(snomedLoincAuthor.description())
.caseSignificance(DESCRIPTION_NOT_CASE_SENSITIVE)
.language(ENGLISH_LANGUAGE)
.attach(usDialect()))
.attach((Definition definition) -> definition
.text("International Health Terminology Standards Development Organisation (IHTSDO) SNOMED CT LOINC Collaboration Author")
.caseSignificance(DESCRIPTION_NOT_CASE_SENSITIVE)
.language(ENGLISH_LANGUAGE)
.attach(usDialect()))
.attach((Identifier identifier) -> identifier
.source(UNIVERSALLY_UNIQUE_IDENTIFIER)
.identifier(snomedLoincAuthor.asUuidArray()[0].toString()))
.attach(new StatedNavigation()
.parents(USER))
.attach(new StatedAxiom()
.isA(USER)).attach(new TinkarBaseModel());

EntityProxy.Concept loincIdentifier = EntityProxy.Concept.make("LOINC Number", UuidUtil.fromSNOMED("705114005"));
starterData.concept(loincIdentifier)
.fullyQualifiedName("LOINC Number", TinkarTerm.PREFERRED)
.synonym("LOINC Num", TinkarTerm.PREFERRED)
.definition("Unique point of origin for identifier", TinkarTerm.PREFERRED)
.identifier(TinkarTerm.UNIVERSALLY_UNIQUE_IDENTIFIER, loincIdentifier.asUuidArray()[0].toString())
.statedDefinition(List.of(TinkarTerm.IDENTIFIER_SOURCE))
.build();
session.compose((ConceptAssembler conceptAssembler) -> conceptAssembler.concept(loincIdentifier))
.attach((FullyQualifiedName fqn) -> fqn
.text(loincIdentifier.description())
.language(ENGLISH_LANGUAGE)
.caseSignificance(DESCRIPTION_NOT_CASE_SENSITIVE)
.attach(usDialect()))
.attach((Synonym synonym) -> synonym
.text("LOINC Num")
.caseSignificance(DESCRIPTION_NOT_CASE_SENSITIVE)
.language(ENGLISH_LANGUAGE)
.attach(usDialect()))
.attach((Definition definition) -> definition
.text("Unique point of origin for identifier")
.caseSignificance(DESCRIPTION_NOT_CASE_SENSITIVE)
.language(ENGLISH_LANGUAGE)
.attach(usDialect()))
.attach((Identifier identifier) -> identifier
.source(UNIVERSALLY_UNIQUE_IDENTIFIER)
.identifier(loincIdentifier.asUuidArray()[0].toString()))
.attach(new StatedNavigation()
.parents(IDENTIFIER_SOURCE))
.attach(new StatedAxiom()
.isA(IDENTIFIER_SOURCE)).attach(new TinkarBaseModel());
}

private USDialect usDialect() {
return new USDialect().acceptability(PREFERRED);
}

private void init() {
LOG.info("Starting database");
LOG.info("Loading data from " + datastore.getAbsolutePath());
CachingService.clearAll();
ServiceProperties.set(ServiceKeys.DATA_STORE_ROOT, datastore);
PrimitiveData.selectControllerByName("Open SpinedArrayStore");
PrimitiveData.start();
}

private static void exportStarterData(){
ExportEntitiesController exportEntitiesController = new ExportEntitiesController();
private void cleanup() {
PrimitiveData.stop();
}

private void exportToProtoBuf() {
try {
exportEntitiesController.export(exportFile).get();
} catch (ExecutionException | InterruptedException e){
e.printStackTrace();
new ExportEntitiesController().export(exportFile).get();
} catch (ExecutionException | InterruptedException e) {
LOG.error("Error while exporting.", e);
}
}

public static void main(String[] args) {
SnomedLoincStarterData starterData = new SnomedLoincStarterData(args);
starterData.init();
starterData.transform();
starterData.exportToProtoBuf();
starterData.cleanup();
}
}

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