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SO-3740: Filter for unpublished members in snomed_common_rule_4 #394

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Sep 23, 2019
Merged

SO-3740: Filter for unpublished members in snomed_common_rule_4 #394

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3d29295
SO-3740: Filter for unpublished members in snomed_common_rule_4
AAAlinaaa Sep 5, 2019
341547b
SO-3740: Limit size of description search, rename variable
AAAlinaaa Sep 19, 2019
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36 changes: 33 additions & 3 deletions ...ternational.snowowl.validation.snomed/src/main/resources/scripts/ruleSnomedCommon4.groovy
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Original file line number Diff line number Diff line change
@@ -1,20 +1,26 @@
package scripts

import com.b2international.snowowl.core.ApplicationContext
import com.b2international.snowowl.core.ComponentIdentifier
import com.b2international.snowowl.core.date.EffectiveTimes
import com.b2international.snowowl.core.request.SearchResourceRequestIterator
import com.b2international.snowowl.eventbus.IEventBus
import com.b2international.snowowl.snomed.SnomedConstants.Concepts
import com.b2international.snowowl.snomed.common.SnomedTerminologyComponentConstants
import com.b2international.snowowl.snomed.core.domain.Acceptability
import com.b2international.snowowl.snomed.core.domain.SnomedConcept
import com.b2international.snowowl.snomed.core.domain.SnomedConcepts
import com.b2international.snowowl.snomed.core.domain.SnomedDescription
import com.b2international.snowowl.snomed.core.domain.refset.SnomedReferenceSetMembers
import com.b2international.snowowl.snomed.datastore.SnomedDatastoreActivator
import com.b2international.snowowl.snomed.datastore.index.entry.SnomedDescriptionIndexEntry
import com.b2international.snowowl.snomed.datastore.request.SnomedConceptSearchRequestBuilder
import com.b2international.snowowl.snomed.datastore.request.SnomedRequests
import com.b2international.snowowl.snomed.snomedrefset.SnomedRefSetType
import com.google.common.collect.HashMultiset
import com.google.common.collect.Lists
import com.google.common.collect.Sets
import com.google.common.collect.Multiset
import com.google.common.collect.Sets

final List<ComponentIdentifier> issues = Lists.newArrayList()

Expand All @@ -35,9 +41,33 @@ SnomedConceptSearchRequestBuilder conceptsRequestBuilder = SnomedRequests.prepar
.setExpand("preferredDescriptions()")

if (params.isUnpublishedOnly) {
conceptsRequestBuilder.filterByEffectiveTime(EffectiveTimes.UNSET_EFFECTIVE_TIME)

def descriptionsIdsWithUnpublishedLanguageMembers = SnomedRequests.prepareSearchMember()
.filterByReferencedComponentType(SnomedTerminologyComponentConstants.DESCRIPTION_NUMBER)
.filterByRefSetType(SnomedRefSetType.LANGUAGE)
.filterByEffectiveTime(EffectiveTimes.UNSET_EFFECTIVE_TIME)
.filterByActive(true)
.all()
.build()
.execute(ctx)
.collect({ it.referencedComponent.id})

def conceptsWithUnpublishedLanguageMembers = SnomedRequests.prepareSearchDescription()
.filterByIds(descriptionsIdsWithUnpublishedLanguageMembers)
.setLimit(descriptionsIdsWithUnpublishedLanguageMembers.size())
.setFields(SnomedDescriptionIndexEntry.Fields.CONCEPT_ID)
.build()
.execute(ctx)
.collect({SnomedDescription d -> d.getConceptId()})

if (!conceptsWithUnpublishedLanguageMembers.isEmpty()) {
conceptsRequestBuilder.filterByIds(conceptsWithUnpublishedLanguageMembers)
} else {
return issues
}

}

final SearchResourceRequestIterator<SnomedConceptSearchRequestBuilder, SnomedConcepts> iterator = new SearchResourceRequestIterator<>(conceptsRequestBuilder, {scrolledBuilder ->
return scrolledBuilder.build().execute(ctx)
});
Expand Down
110 changes: 86 additions & 24 deletions ...c/tests/java/com/b2international/snowowl/validation/snomed/GenericValidationRuleTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -18,28 +18,37 @@

import static com.b2international.snowowl.test.commons.snomed.RandomSnomedIdentiferGenerator.generateConceptId;
import static com.b2international.snowowl.test.commons.snomed.RandomSnomedIdentiferGenerator.generateDescriptionId;
import static com.b2international.snowowl.snomed.common.SnomedTerminologyComponentConstants.DESCRIPTION_NUMBER;

import java.util.UUID;

import org.eclipse.emf.cdo.common.id.CDOIDUtil;
import org.eclipse.emf.spi.cdo.InternalCDOObject;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.junit.runners.Parameterized;

import com.b2international.collections.PrimitiveSets;
import com.b2international.snowowl.core.ComponentIdentifier;
import com.b2international.snowowl.core.validation.issue.ValidationIssues;
import com.b2international.snowowl.snomed.SnomedConstants;
import com.b2international.snowowl.snomed.SnomedConstants.Concepts;
import com.b2international.snowowl.snomed.common.SnomedTerminologyComponentConstants;
import com.b2international.snowowl.snomed.core.domain.Acceptability;
import com.b2international.snowowl.snomed.core.domain.refset.SnomedReferenceSet;
import com.b2international.snowowl.snomed.datastore.index.constraint.SnomedConstraintDocument;
import com.b2international.snowowl.snomed.datastore.index.entry.SnomedConceptDocument;
import com.b2international.snowowl.snomed.datastore.index.entry.SnomedDescriptionFragment;
import com.b2international.snowowl.snomed.datastore.index.entry.SnomedDescriptionIndexEntry;
import com.b2international.snowowl.snomed.datastore.index.entry.SnomedRefSetMemberIndexEntry;
import com.b2international.snowowl.snomed.datastore.index.entry.SnomedRelationshipIndexEntry;
import com.b2international.snowowl.snomed.mrcm.AttributeConstraint;
import com.b2international.snowowl.snomed.mrcm.HierarchyConceptSetDefinition;
import com.b2international.snowowl.snomed.mrcm.HierarchyInclusionType;
import com.b2international.snowowl.snomed.mrcm.RelationshipPredicate;
import com.b2international.snowowl.snomed.snomedrefset.SnomedRefSetType;
import com.google.common.collect.ImmutableList;
import com.google.common.collect.ImmutableSet;

/**
*
Expand Down Expand Up @@ -172,65 +181,118 @@ public void ruleSnomedCommon3() throws Exception {
public void ruleSnomedCommon4() throws Exception {
final String ruleId = "snomed-common-4";
indexRule(ruleId);


SnomedReferenceSet refset = new SnomedReferenceSet();
refset.setActive(true);
refset.setStorageKey(nextStorageKey());
refset.setType(SnomedRefSetType.LANGUAGE);
refset.setReferencedComponentType(SnomedTerminologyComponentConstants.DESCRIPTION);

SnomedConceptDocument languageRefset = concept(generateConceptId()).refSet(refset)
.parents(PrimitiveSets.newLongOpenHashSet(Long.parseLong(SnomedConstants.Concepts.REFSET_ROOT_CONCEPT)))
.build();

// index concept with two FSNs in the same language refset
String concept1Id = generateConceptId();
SnomedDescriptionIndexEntry fsn1 = description(generateDescriptionId(), Concepts.FULLY_SPECIFIED_NAME, "Fully specified name 1 (tag)")
.conceptId(concept1Id)
.acceptability(Concepts.REFSET_LANGUAGE_TYPE_ES, Acceptability.PREFERRED)
.activeMemberOf(ImmutableSet.of(languageRefset.getId()))
.acceptability(languageRefset.getId(), Acceptability.PREFERRED)
.build();
indexRevision(MAIN, nextStorageKey(), fsn1);
SnomedRefSetMemberIndexEntry fsn1Member = member(UUID.randomUUID().toString(), fsn1.getId(), DESCRIPTION_NUMBER, languageRefset.getId())
.active(true)
.referenceSetType(SnomedRefSetType.LANGUAGE)
.build();
SnomedDescriptionIndexEntry fsn2 = description(generateDescriptionId(), Concepts.FULLY_SPECIFIED_NAME, "Fully specified name 2 (tag)")
.conceptId(concept1Id)
.acceptability(Concepts.REFSET_LANGUAGE_TYPE_ES, Acceptability.PREFERRED)
.activeMemberOf(ImmutableSet.of(languageRefset.getId()))
.acceptability(languageRefset.getId(), Acceptability.PREFERRED)
.build();
SnomedRefSetMemberIndexEntry fsn2Member = member(UUID.randomUUID().toString(), fsn2.getId(), DESCRIPTION_NUMBER, languageRefset.getId())
.active(true)
.referenceSetType(SnomedRefSetType.LANGUAGE)
.build();
indexRevision(MAIN, nextStorageKey(), fsn2);
SnomedConceptDocument c1 = concept(concept1Id)
.preferredDescriptions(ImmutableList.of(
new SnomedDescriptionFragment(fsn1.getId(), fsn1.getStorageKey(), fsn1.getTypeId(), fsn1.getTerm(), Concepts.REFSET_LANGUAGE_TYPE_ES),
new SnomedDescriptionFragment(fsn2.getId(), fsn2.getStorageKey(), fsn2.getTypeId(), fsn2.getTerm(), Concepts.REFSET_LANGUAGE_TYPE_ES)))
new SnomedDescriptionFragment(fsn1.getId(), fsn1.getStorageKey(), fsn1.getTypeId(), fsn1.getTerm(), languageRefset.getId()),
new SnomedDescriptionFragment(fsn2.getId(), fsn2.getStorageKey(), fsn2.getTypeId(), fsn2.getTerm(), languageRefset.getId())))
.build();
indexRevision(MAIN, nextStorageKey(), c1);


// index concept with two PTs in the same language refset
String concept2Id = generateConceptId();
SnomedDescriptionIndexEntry pt1 = description(generateDescriptionId(), Concepts.SYNONYM, "Preferred term 1")
.acceptability(Concepts.REFSET_LANGUAGE_TYPE_ES, Acceptability.PREFERRED)
.activeMemberOf(ImmutableSet.of(languageRefset.getId()))
.acceptability(languageRefset.getId(), Acceptability.PREFERRED)
.conceptId(concept2Id)
.build();
indexRevision(MAIN, nextStorageKey(), pt1);
SnomedRefSetMemberIndexEntry pt1Member = member(UUID.randomUUID().toString(), pt1.getId(), DESCRIPTION_NUMBER, languageRefset.getId())
.active(true)
.referenceSetType(SnomedRefSetType.LANGUAGE)
.build();
SnomedDescriptionIndexEntry pt2 = description(generateDescriptionId(), Concepts.SYNONYM, "Preferred term 2")
.acceptability(Concepts.REFSET_LANGUAGE_TYPE_ES, Acceptability.PREFERRED)
.activeMemberOf(ImmutableSet.of(languageRefset.getId()))
.acceptability(languageRefset.getId(), Acceptability.PREFERRED)
.conceptId(concept2Id)
.build();
indexRevision(MAIN, nextStorageKey(), pt2);
SnomedRefSetMemberIndexEntry pt2Member = member(UUID.randomUUID().toString(), pt2.getId(), DESCRIPTION_NUMBER, languageRefset.getId())
.active(true)
.referenceSetType(SnomedRefSetType.LANGUAGE)
.build();
SnomedConceptDocument c2 = concept(concept2Id)
.preferredDescriptions(
ImmutableList.of(
new SnomedDescriptionFragment(pt1.getId(), pt1.getStorageKey(), pt1.getTypeId(), pt1.getTerm(), Concepts.REFSET_LANGUAGE_TYPE_ES),
new SnomedDescriptionFragment(pt2.getId(), pt2.getStorageKey(), pt2.getTypeId(), pt2.getTerm(), Concepts.REFSET_LANGUAGE_TYPE_ES)))
new SnomedDescriptionFragment(pt1.getId(), pt1.getStorageKey(), pt1.getTypeId(), pt1.getTerm(), languageRefset.getId()),
new SnomedDescriptionFragment(pt2.getId(), pt2.getStorageKey(), pt2.getTypeId(), pt2.getTerm(), languageRefset.getId())))
.build();
indexRevision(MAIN, nextStorageKey(), c2);


// index concept with only one PT and one FSN in a given language refset
String concept3Id = generateConceptId();
SnomedDescriptionIndexEntry fsn3 = description(generateDescriptionId(), Concepts.FULLY_SPECIFIED_NAME, "Fully specified name 3 (tag)")
.conceptId(concept3Id)
.acceptability(Concepts.REFSET_LANGUAGE_TYPE_ES, Acceptability.PREFERRED)
.activeMemberOf(ImmutableSet.of(languageRefset.getId()))
.acceptability(languageRefset.getId(), Acceptability.PREFERRED)
.build();
SnomedRefSetMemberIndexEntry fsn3Member = member(UUID.randomUUID().toString(), fsn3.getId(), DESCRIPTION_NUMBER, languageRefset.getId())
.active(true)
.referenceSetType(SnomedRefSetType.LANGUAGE)
.build();
indexRevision(MAIN, nextStorageKey(), fsn3);
SnomedDescriptionIndexEntry pt3 = description(generateDescriptionId(), Concepts.SYNONYM, "Preferred term 3")
.acceptability(Concepts.REFSET_LANGUAGE_TYPE_ES, Acceptability.PREFERRED)
.activeMemberOf(ImmutableSet.of(languageRefset.getId()))
.acceptability(languageRefset.getId(), Acceptability.PREFERRED)
.conceptId(concept3Id)
.build();
indexRevision(MAIN, nextStorageKey(), pt3);
SnomedRefSetMemberIndexEntry pt3Member = member(UUID.randomUUID().toString(), pt3.getId(), DESCRIPTION_NUMBER, languageRefset.getId())
.active(true)
.referenceSetType(SnomedRefSetType.LANGUAGE)
.build();
SnomedConceptDocument c3 = concept(concept3Id)
.preferredDescriptions(ImmutableList.of(
new SnomedDescriptionFragment(fsn3.getId(), fsn3.getStorageKey(), fsn3.getTypeId(), fsn3.getTerm(), Concepts.REFSET_LANGUAGE_TYPE_ES),
new SnomedDescriptionFragment(pt3.getId(), pt3.getStorageKey(), pt3.getTypeId(), pt3.getTerm(), Concepts.REFSET_LANGUAGE_TYPE_ES)
new SnomedDescriptionFragment(fsn3.getId(), fsn3.getStorageKey(), fsn3.getTypeId(), fsn3.getTerm(), languageRefset.getId()),
new SnomedDescriptionFragment(pt3.getId(), pt3.getStorageKey(), pt3.getTypeId(), pt3.getTerm(), languageRefset.getId())
))
.build();
indexRevision(MAIN, nextStorageKey(), c3);

index().write(MAIN, currentTime(), writer -> {
writer.put(nextStorageKey(), languageRefset);
writer.put(nextStorageKey(), fsn1);
writer.put(nextStorageKey(), fsn2);
writer.put(nextStorageKey(), c1);
writer.put(nextStorageKey(), pt1);
writer.put(nextStorageKey(), pt2);
writer.put(nextStorageKey(), c2);
writer.put(nextStorageKey(), fsn3);
writer.put(nextStorageKey(), pt3);
writer.put(nextStorageKey(), c3);
writer.put(nextStorageKey(), fsn1Member);
writer.put(nextStorageKey(), fsn2Member);
writer.put(nextStorageKey(), fsn3Member);
writer.put(nextStorageKey(), pt1Member);
writer.put(nextStorageKey(), pt2Member);
writer.put(nextStorageKey(), pt3Member);

writer.commit();
return null;
});

ValidationIssues issues = validate(ruleId);
assertAffectedComponents(issues, ComponentIdentifier.of(SnomedTerminologyComponentConstants.CONCEPT_NUMBER, c1.getId()),
Expand Down