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Co-authored-by: Pavel Grafkin <pavgra@gmail.com> Co-authored-by: Vitaly Koulakov <vitaly.koulakov@gmail.com> Co-authored-by: Chris Knoll <cknoll@ohdsi.org>
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49 changes: 49 additions & 0 deletions
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src/main/java/org/ohdsi/circe/check/checkers/ConceptSetSelectionCheck.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,49 @@ | ||
| /* | ||
| * Copyright 2017 Observational Health Data Sciences and Informatics | ||
| * 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. | ||
| * | ||
| * Authors: Vitaly Koulakov | ||
| * | ||
| */ | ||
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| package org.ohdsi.circe.check.checkers; | ||
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| import org.ohdsi.circe.check.WarningSeverity; | ||
| import org.ohdsi.circe.check.operations.Execution; | ||
| import org.ohdsi.circe.check.utils.CriteriaNameHelper; | ||
| import org.ohdsi.circe.cohortdefinition.ConditionEra; | ||
| import org.ohdsi.circe.cohortdefinition.ConditionOccurrence; | ||
| import org.ohdsi.circe.cohortdefinition.Criteria; | ||
| import org.ohdsi.circe.cohortdefinition.Death; | ||
| import org.ohdsi.circe.cohortdefinition.DeviceExposure; | ||
| import org.ohdsi.circe.cohortdefinition.DoseEra; | ||
| import org.ohdsi.circe.cohortdefinition.DrugEra; | ||
| import org.ohdsi.circe.cohortdefinition.DrugExposure; | ||
| import org.ohdsi.circe.cohortdefinition.Measurement; | ||
| import org.ohdsi.circe.cohortdefinition.Observation; | ||
| import org.ohdsi.circe.cohortdefinition.ProcedureOccurrence; | ||
| import org.ohdsi.circe.cohortdefinition.Specimen; | ||
| import org.ohdsi.circe.cohortdefinition.VisitDetail; | ||
| import org.ohdsi.circe.cohortdefinition.VisitOccurrence; | ||
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| import java.util.Objects; | ||
| import java.util.function.Function; | ||
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| import static org.ohdsi.circe.check.operations.Operations.match; | ||
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| public class ConceptSetSelectionCheck extends BaseValueCheck { | ||
| @Override | ||
| protected BaseCheckerFactory getFactory(WarningReporter reporter, String name) { | ||
| return ConceptSetSelectionCheckerFactory.getFactory(reporter, name); | ||
| } | ||
| } |
85 changes: 85 additions & 0 deletions
85
src/main/java/org/ohdsi/circe/check/checkers/ConceptSetSelectionCheckerFactory.java
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,85 @@ | ||
| /* | ||
| * Copyright 2017 Observational Health Data Sciences and Informatics | ||
| * 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. | ||
| * | ||
| * Authors: Sergey Suvorov | ||
| * | ||
| */ | ||
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| package org.ohdsi.circe.check.checkers; | ||
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| import org.ohdsi.circe.check.Constants; | ||
| import org.ohdsi.circe.cohortdefinition.ConceptSetSelection; | ||
| import org.ohdsi.circe.cohortdefinition.ConditionEra; | ||
| import org.ohdsi.circe.cohortdefinition.ConditionOccurrence; | ||
| import org.ohdsi.circe.cohortdefinition.Criteria; | ||
| import org.ohdsi.circe.cohortdefinition.Death; | ||
| import org.ohdsi.circe.cohortdefinition.DemographicCriteria; | ||
| import org.ohdsi.circe.cohortdefinition.DeviceExposure; | ||
| import org.ohdsi.circe.cohortdefinition.DoseEra; | ||
| import org.ohdsi.circe.cohortdefinition.DrugEra; | ||
| import org.ohdsi.circe.cohortdefinition.DrugExposure; | ||
| import org.ohdsi.circe.cohortdefinition.Measurement; | ||
| import org.ohdsi.circe.cohortdefinition.Observation; | ||
| import org.ohdsi.circe.cohortdefinition.ObservationPeriod; | ||
| import org.ohdsi.circe.cohortdefinition.PayerPlanPeriod; | ||
| import org.ohdsi.circe.cohortdefinition.ProcedureOccurrence; | ||
| import org.ohdsi.circe.cohortdefinition.Specimen; | ||
| import org.ohdsi.circe.cohortdefinition.VisitDetail; | ||
| import org.ohdsi.circe.cohortdefinition.VisitOccurrence; | ||
| import org.ohdsi.circe.vocabulary.Concept; | ||
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| import java.util.Objects; | ||
| import java.util.function.Consumer; | ||
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| import static org.ohdsi.circe.check.Constants.Attributes.UNIT_ATTR; | ||
| import static org.ohdsi.circe.check.operations.Operations.match; | ||
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| public class ConceptSetSelectionCheckerFactory extends BaseCheckerFactory{ | ||
| private static final String WARNING_EMPTY_VALUE = "%s in the %s has empty %s value"; | ||
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| private ConceptSetSelectionCheckerFactory(WarningReporter reporter, String groupName) { | ||
| super(reporter, groupName); | ||
| } | ||
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| public static ConceptSetSelectionCheckerFactory getFactory(WarningReporter reporter, String groupName) { | ||
| return new ConceptSetSelectionCheckerFactory(reporter, groupName); | ||
| } | ||
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| @Override | ||
| protected Consumer<Criteria> getCheck(Criteria criteria) { | ||
| Consumer<Criteria> result = c -> { }; | ||
| if (criteria instanceof VisitDetail) { | ||
| result = c -> { | ||
| VisitDetail vd = (VisitDetail) c; | ||
| checkConcept(vd.visitDetailTypeCS, Constants.Criteria.VISIT_DETAIL, Constants.Attributes.VISIT_DETAIL_TYPE_ATTR); | ||
| checkConcept(vd.genderCS, Constants.Criteria.VISIT_DETAIL, Constants.Attributes.GENDER_ATTR); | ||
| checkConcept(vd.providerSpecialtyCS, Constants.Criteria.VISIT_DETAIL, Constants.Attributes.PROVIDER_SPECIALITY_ATTR); | ||
| checkConcept(vd.placeOfServiceCS, Constants.Criteria.VISIT_DETAIL, Constants.Attributes.PLACE_OF_SERVICE_ATTR); | ||
| }; | ||
| } | ||
| return result; | ||
| } | ||
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| @Override | ||
| protected Consumer<DemographicCriteria> getCheck(DemographicCriteria criteria) { | ||
| return c -> {}; | ||
| } | ||
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| private void checkConcept(ConceptSetSelection conceptSetSelection, String criteriaName, String attribute) { | ||
| Consumer<String> warning = (t) -> reporter.add(t, groupName, criteriaName, attribute); | ||
| match(conceptSetSelection) | ||
| .when(r -> Objects.nonNull(r) && Objects.isNull(r.codesetId)) | ||
| .then(() -> warning.accept(WARNING_EMPTY_VALUE)); | ||
| } | ||
| } |
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