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Use TIB terminology service for instrument lookup (#983)
Uses the external TIB terminology service to look up ontologies for instruments.
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project-management/src/main/java/life/qbic/projectmanagement/application/measurement/MeasurementService.java

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@@ -23,6 +23,7 @@
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import life.qbic.projectmanagement.application.OrganisationLookupService;
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import life.qbic.projectmanagement.application.ProjectInformationService;
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import life.qbic.projectmanagement.application.ontology.SpeciesLookupService;
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import life.qbic.projectmanagement.application.ontology.TerminologyService;
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import life.qbic.projectmanagement.application.sample.SampleIdCodeEntry;
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import life.qbic.projectmanagement.application.sample.SampleInformationService;
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import life.qbic.projectmanagement.domain.model.OntologyTerm;
@@ -65,28 +66,29 @@ public class MeasurementService {
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private final MeasurementDomainService measurementDomainService;
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private final MeasurementLookupService measurementLookupService;
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private final SampleInformationService sampleInformationService;
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private final SpeciesLookupService speciesLookupService;
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private final OrganisationLookupService organisationLookupService;
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private final ProjectInformationService projectInformationService;
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private final MeasurementRepository measurementRepository;
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private final TerminologyService terminologyService;
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@Autowired
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public MeasurementService(MeasurementDomainService measurementDomainService,
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SampleInformationService sampleInformationService,
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SpeciesLookupService speciesLookupService,
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OrganisationLookupService organisationLookupService,
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MeasurementLookupService measurementLookupService,
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ProjectInformationService projectInformationService,
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MeasurementRepository measurementRepository,
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TerminologyService terminologyService,
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ApplicationContext context) {
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this.measurementDomainService = Objects.requireNonNull(measurementDomainService);
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this.sampleInformationService = Objects.requireNonNull(sampleInformationService);
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this.speciesLookupService = Objects.requireNonNull(speciesLookupService);
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this.organisationLookupService = Objects.requireNonNull(organisationLookupService);
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this.measurementLookupService = Objects.requireNonNull(measurementLookupService);
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this.projectInformationService = Objects.requireNonNull(projectInformationService);
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this.measurementRepository = Objects.requireNonNull(measurementRepository);
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this.context = Objects.requireNonNull(context);
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this.terminologyService = Objects.requireNonNull(terminologyService);
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}
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/**
@@ -778,7 +780,7 @@ private boolean allMeasurementCodesExist(List<String> measurementCode) {
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}
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private Optional<OntologyTerm> resolveOntologyCURI(String ontologyCURI) {
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return speciesLookupService.findByCURI(ontologyCURI).map(OntologyTerm::from);
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return terminologyService.findByCurie(ontologyCURI);
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}
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private Optional<SampleIdCodeEntry> queryIdCodePair(SampleCode sampleCode) {

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