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Change role chain (PPI) from property set to sequence (ikmdev#54)
* Add tinkar test data unpack for snomed intl 20241001 * Add ITs for snomed intl 20241001 * Change role chain (PPI) from property set to sequence * Add data property type. Fix parse issue with dadaHasValue. --------- Co-authored-by: stenkarl <[email protected]>
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149
...t/java/dev/ikm/tinkar/reasoner/elksnomed/SnomedINTL20241001ElkSnomedClassifierTestIT.java
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| /* | ||
| * Copyright © 2015 Integrated Knowledge Management ([email protected]) | ||
| * | ||
| * 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. | ||
| */ | ||
| package dev.ikm.tinkar.reasoner.elksnomed; | ||
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| import static org.junit.jupiter.api.Assertions.assertEquals; | ||
| import static org.junit.jupiter.api.Assertions.assertNotNull; | ||
| import static org.junit.jupiter.api.Assertions.assertTrue; | ||
|
|
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| import java.util.ArrayList; | ||
| import java.util.HashMap; | ||
| import java.util.HashSet; | ||
| import java.util.List; | ||
| import java.util.Set; | ||
| import java.util.TreeSet; | ||
| import java.util.UUID; | ||
| import java.util.stream.Collectors; | ||
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|
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| import org.junit.jupiter.api.Test; | ||
| import org.slf4j.Logger; | ||
| import org.slf4j.LoggerFactory; | ||
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| import dev.ikm.elk.snomed.SnomedIds; | ||
| import dev.ikm.elk.snomed.SnomedIsa; | ||
| import dev.ikm.elk.snomed.SnomedOntology; | ||
| import dev.ikm.elk.snomed.SnomedOntologyReasoner; | ||
| import dev.ikm.elk.snomed.model.Concept; | ||
| import dev.ikm.tinkar.common.service.PrimitiveData; | ||
| import dev.ikm.tinkar.common.util.uuid.UuidUtil; | ||
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| public class SnomedINTL20241001ElkSnomedClassifierTestIT extends SnomedINTL20241001ElkSnomedTestBase { | ||
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| private static final Logger LOG = LoggerFactory.getLogger(SnomedINTL20241001ElkSnomedClassifierTestIT.class); | ||
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| @Test | ||
| public void supercs() throws Exception { | ||
| ArrayList<String> lines = runSnomedReasoner(); | ||
| assertEquals(634059, lines.size()); | ||
| } | ||
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| @Test | ||
| public void supercsService() throws Exception { | ||
| ArrayList<String> lines = runSnomedReasonerService(); | ||
| assertEquals(634059, lines.size()); | ||
| } | ||
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| private HashMap<Integer, Long> nid_sctid_map; | ||
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| private Set<Long> toSctids(Set<Long> nids) { | ||
| return nids.stream().map(x -> nid_sctid_map.get(x.intValue())).collect(Collectors.toSet()); | ||
| } | ||
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| @Test | ||
| public void isas() throws Exception { | ||
| LOG.info("runSnomedReasoner"); | ||
| ElkSnomedData data = buildSnomedData(); | ||
| LOG.info("Create ontology"); | ||
| SnomedOntology ontology = new SnomedOntology(data.getConcepts(), data.getRoleTypes(), List.of()); | ||
| LOG.info("Create reasoner"); | ||
| SnomedOntologyReasoner reasoner = SnomedOntologyReasoner.create(ontology); | ||
| TreeSet<Long> misses = new TreeSet<>(); | ||
| TreeSet<Long> other_misses = new TreeSet<>(); | ||
| int non_snomed_cnt = 0; | ||
| int miss_cnt = 0; | ||
| int pharma_miss_cnt = 0; | ||
| int other_miss_cnt = 0; | ||
| SnomedIsa isas = SnomedIsa.init(rels_file); | ||
| nid_sctid_map = new HashMap<>(); | ||
| for (long sctid : isas.getOrderedConcepts()) { | ||
| int nid = ElkSnomedData.getNid(sctid); | ||
| nid_sctid_map.put(nid, sctid); | ||
| } | ||
| for (Concept con : ontology.getConcepts()) { | ||
| long nid = con.getId(); | ||
| Set<Long> sups = toSctids(reasoner.getSuperConcepts(nid)); | ||
| Long sctid = nid_sctid_map.get((int) nid); | ||
| if (sctid == null) { | ||
| non_snomed_cnt++; | ||
| continue; | ||
| } | ||
| Set<Long> parents = isas.getParents(sctid); | ||
| if (sctid == SnomedIds.root) { | ||
| assertTrue(parents.isEmpty()); | ||
| } else { | ||
| assertNotNull(parents); | ||
| } | ||
| if (!parents.equals(sups)) { | ||
| misses.add(sctid); | ||
| miss_cnt++; | ||
| if (isas.hasAncestor(sctid, 373873005)) { | ||
| // 373873005 |Pharmaceutical / biologic product (product)| | ||
| pharma_miss_cnt++; | ||
| } else if (isas.hasAncestor(sctid, 127785005)) { | ||
| // 127785005 |Administration of substance to produce immunity, either active or | ||
| // passive (procedure)| | ||
| } else if (isas.hasAncestor(sctid, 713404003)) { | ||
| // 713404003 |Vaccination given (situation)| | ||
| } else if (isas.hasAncestor(sctid, 591000119102l)) { | ||
| // 591000119102 |Vaccine declined by patient (situation)| | ||
| } else if (isas.hasAncestor(sctid, 90351000119108l)) { | ||
| // 90351000119108 |Vaccination not done (situation)| | ||
| } else if (isas.hasAncestor(sctid, 293104008)) { | ||
| // 293104008 |Adverse reaction to component of vaccine product (disorder)| | ||
| } else if (isas.hasAncestor(sctid, 266758009)) { | ||
| // 266758009 |Immunization contraindicated (situation)| | ||
| } else { | ||
| other_misses.add(sctid); | ||
| other_miss_cnt++; | ||
| } | ||
| } | ||
| } | ||
| isas.getOrderedConcepts().stream().filter(other_misses::contains) // | ||
| .limit(10) // | ||
| .forEach((sctid) -> { | ||
| UUID uuid = UuidUtil.fromSNOMED("" + sctid); | ||
| int nid = PrimitiveData.nid(uuid); | ||
| LOG.error("Miss: " + sctid + " " + PrimitiveData.text(nid)); | ||
| Set<Long> sups = toSctids(reasoner.getSuperConcepts(nid)); | ||
| Set<Long> parents = isas.getParents(sctid); | ||
| HashSet<Long> par = new HashSet<>(parents); | ||
| par.removeAll(sups); | ||
| HashSet<Long> sup = new HashSet<>(sups); | ||
| sup.removeAll(parents); | ||
| LOG.error("Sno: " + par); | ||
| LOG.error("Elk: " + sup); | ||
| }); | ||
| LOG.error("Miss cnt: " + miss_cnt); | ||
| LOG.error("Pharma cnt: " + pharma_miss_cnt); | ||
| LOG.error("Other cnt: " + other_miss_cnt); | ||
| assertEquals(282, non_snomed_cnt); | ||
| // TODO this should be 0 after all the data issues are fixed | ||
| assertEquals(21065, miss_cnt); | ||
| assertEquals(20815, pharma_miss_cnt); | ||
| assertEquals(194, other_miss_cnt); | ||
| } | ||
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|
||
| } |
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