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🦍 Big refactor to get the HF phenotype running.
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83 changes: 83 additions & 0 deletions
83
src/main/java/edu/phema/elm_to_omop/translate/CorelatedCriteriaTranslator.java
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,83 @@ | ||
| package edu.phema.elm_to_omop.translate; | ||
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| import edu.phema.elm_to_omop.helper.CirceUtil; | ||
| import edu.phema.elm_to_omop.translate.criteria.CriteriaTranslator; | ||
| import edu.phema.elm_to_omop.translate.criteria.comparison.ComparisonExpressionTranslator; | ||
| import edu.phema.elm_to_omop.translate.criteria.correlation.CorrelatedQueryTranslator; | ||
| import edu.phema.elm_to_omop.translate.exception.PhemaNotImplementedException; | ||
| import org.hl7.elm.r1.*; | ||
| import org.ohdsi.circe.cohortdefinition.CorelatedCriteria; | ||
| import org.ohdsi.circe.cohortdefinition.Occurrence; | ||
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| import java.util.List; | ||
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| /** | ||
| * Class responsible for generating CorelatedCriteria [sic]. CorelatedCriteria criteria are used for applying | ||
| * restrictions to Circe domain Criteria (e.g. ConditionOccurrence). | ||
| * <p> | ||
| * These restrictions include: | ||
| * <p> | ||
| * - start and end window restrictions relative to the index event (the containing Criteria, or the cohort entry event) | ||
| * - occurrence count (e.g. EXACTLY 3 procedures, AT_LEAST 1 condition) | ||
| * - visit restriction relative to the index event (the containing Criteria, or the cohort entry event) | ||
| * <p> | ||
| * Confusingly, a Criteria has field called CorelatedCriteria, which is of type CriteriaGroup. | ||
| */ | ||
| public class CorelatedCriteriaTranslator { | ||
| private static CorelatedCriteria generateCorelatedCriteriaForRetrieve(Retrieve retrieve, PhemaElmaToOmopTranslatorContext context) throws Exception { | ||
| Occurrence occurrence = CirceUtil.defaultOccurrence(); | ||
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| CorelatedCriteria corelatedCriteria = CirceUtil.defaultCorelatedCriteria(); | ||
| corelatedCriteria.occurrence = occurrence; | ||
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| corelatedCriteria.criteria = CriteriaTranslator.generateCriteriaForExpression(retrieve, context); | ||
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| return corelatedCriteria; | ||
| } | ||
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| private static CorelatedCriteria generateCorelatedCriteriaForQuery(Query query, PhemaElmaToOmopTranslatorContext context) throws Exception { | ||
| List<RelationshipClause> relationships = query.getRelationship(); | ||
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| if (relationships == null || relationships.size() == 0) { | ||
| // We are dealing with an uncorrelated query | ||
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| // We don't currently support where clause filtering | ||
| if (query.getWhere() != null) { | ||
| throw new PhemaNotImplementedException("Query filtering which Where clause is currently unsupported"); | ||
| } | ||
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| // Right now we basic just support a simple aliased query like [Condition: "valueset"] C, which is exactly | ||
| // the same a simple retrieve, so we evaluate it as such. If there are no relationships, there should only | ||
| // be one AliasedSource | ||
| return generateCorelatedCriteriaForExpression(query.getSource().get(0).getExpression(), context); | ||
| } else if (relationships.size() == 1) { | ||
| // We are dealing with a correlated query | ||
| return CorrelatedQueryTranslator.generateCorelatedCriteriaForCorrelatedQuery(query, context); | ||
| } else { | ||
| throw new PhemaNotImplementedException("The translator is currently only able to handle a single relationship for a data element"); | ||
| } | ||
| } | ||
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| /** | ||
| * Given an Expression from CQL/ELM, convert it into an OHDSI CorelatedCriteria. | ||
| * | ||
| * @param expression The ELM expression | ||
| * @param context The ELM translation context | ||
| * @return The CorelatedCriteria for the expression | ||
| * @throws Exception | ||
| */ | ||
| public static CorelatedCriteria generateCorelatedCriteriaForExpression(Expression expression, PhemaElmaToOmopTranslatorContext context) throws Exception { | ||
| if (expression instanceof Retrieve) { | ||
| return generateCorelatedCriteriaForRetrieve((Retrieve) expression, context); | ||
| } else if (expression instanceof Exists) { | ||
| return generateCorelatedCriteriaForExpression(((Exists) expression).getOperand(), context); | ||
| } else if (expression instanceof Query) { | ||
| return generateCorelatedCriteriaForQuery((Query) expression, context); | ||
| } else if (ComparisonExpressionTranslator.isNumericComparison(expression)) { | ||
| return ComparisonExpressionTranslator.generateCorelatedCriteriaForComparison(expression, context); | ||
| } else { | ||
| // TODO - Need to handle more than simple query types | ||
| throw new PhemaNotImplementedException(String.format("Unable to generate CorelatedCriteria for type: %s", expression.getClass().getName())); | ||
| } | ||
| } | ||
| } |
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src/main/java/edu/phema/elm_to_omop/translate/CriteriaGroupTranslator.java
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,95 @@ | ||
| package edu.phema.elm_to_omop.translate; | ||
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| import edu.phema.elm_to_omop.helper.CirceUtil; | ||
| import edu.phema.elm_to_omop.translate.criteria.demographic.DemographicExpressionTranslator; | ||
| import edu.phema.elm_to_omop.translate.exception.PhemaNotImplementedException; | ||
| import org.hl7.elm.r1.And; | ||
| import org.hl7.elm.r1.BinaryExpression; | ||
| import org.hl7.elm.r1.Expression; | ||
| import org.hl7.elm.r1.Or; | ||
| import org.ohdsi.circe.cohortdefinition.CorelatedCriteria; | ||
| import org.ohdsi.circe.cohortdefinition.CriteriaGroup; | ||
| import org.ohdsi.circe.cohortdefinition.DemographicCriteria; | ||
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| /** | ||
| * Class responsible for building CriteriaGroups. CriteriaGroups are used to group a potentially heterogeneous | ||
| * collection of CorelatedCriteria, DemographicCriteria, and/or other CriteriaGroups together when you want all or some | ||
| * of them to apply. | ||
| * <p> | ||
| * CriteriaGroups can represent the following types of relationships: | ||
| * <p> | ||
| * - ALL | ||
| * - ANY | ||
| * - AT_LEAST x | ||
| * - AT_MOST x | ||
| * <p> | ||
| * where x is some integer. | ||
| * <p> | ||
| * In CQL, these ideas can be represented using AND and OR statements, or by using the Count aggregate expression. | ||
| */ | ||
| public class CriteriaGroupTranslator { | ||
| /** | ||
| * Generates a Circe CriteriaGroup from a ELM BinaryExpression. Creating "ANY" (OR) and "ALL" (AND) CriteriaGroups | ||
| * is how nested boolean logic is implemented. Only these two boolean expressions generated CriteriaGroups. Every | ||
| * other type of ELM expression generates a CorelatedCriteria | ||
| * | ||
| * @param expression The ELM BinaryExpression (must be And or Or) | ||
| * @param context The translation context | ||
| * @return The created "ANY" or "ALL" CriteriaGroup | ||
| * @throws Exception | ||
| */ | ||
| private static CriteriaGroup generateCriteriaGroupForBinaryExpression(BinaryExpression expression, PhemaElmaToOmopTranslatorContext context) throws Exception { | ||
| CriteriaGroup criteriaGroup = new CriteriaGroup(); | ||
| criteriaGroup.type = PhemaElmToOmopTranslator.getInclusionExpressionType(expression).toString(); | ||
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| for (Expression operand : expression.getOperand()) { | ||
| Expression operandExp = operand; | ||
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| if (DemographicExpressionTranslator.isDemographicExpression(operandExp)) { | ||
| DemographicCriteria demographicCriteria = DemographicExpressionTranslator.generateDemographicCriteriaForExpression(operandExp); | ||
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| criteriaGroup.demographicCriteriaList = CirceUtil.addDemographicCriteria(criteriaGroup.demographicCriteriaList, demographicCriteria); | ||
| } else { | ||
| // Are we nesting even further? | ||
| if (PhemaElmToOmopTranslator.isBooleanExpression(operandExp)) { | ||
| criteriaGroup.groups = CirceUtil.addCriteriaGroup(criteriaGroup.groups, generateCriteriaGroupForBinaryExpression((BinaryExpression) operandExp, context)); | ||
| } else { | ||
| CorelatedCriteria corelatedCriteria = CorelatedCriteriaTranslator.generateCorelatedCriteriaForExpression(operandExp, context); | ||
| if (corelatedCriteria == null) { | ||
| throw new PhemaNotImplementedException("The translator was unable to process this type of expression"); | ||
| } | ||
| criteriaGroup.criteriaList = CirceUtil.addCorelatedCriteria(criteriaGroup.criteriaList, corelatedCriteria); | ||
| } | ||
| } | ||
| } | ||
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| return criteriaGroup; | ||
| } | ||
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| /** | ||
| * This is the entry point for CriteriaGroup generation. This method will delegate CriteriaGroup generation | ||
| * based on the type of expression. An exception will be thrown if we do not support translating the expression | ||
| * | ||
| * @param expression The ELM expression | ||
| * @param context The translation context | ||
| * @return The created CriteriaGroup | ||
| * @throws Exception | ||
| */ | ||
| public static CriteriaGroup generateCriteriaGroupForExpression(Expression expression, PhemaElmaToOmopTranslatorContext context) throws Exception { | ||
| Expression expr = PhemaElmToOmopTranslator.invertNot(expression); | ||
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| CriteriaGroup criteriaGroup = new CriteriaGroup(); | ||
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| if (DemographicExpressionTranslator.isDemographicExpression(expr)) { | ||
| DemographicCriteria demographicCriteria = DemographicExpressionTranslator.generateDemographicCriteriaForExpression(expr); | ||
| criteriaGroup.demographicCriteriaList = CirceUtil.addDemographicCriteria(criteriaGroup.demographicCriteriaList, demographicCriteria); | ||
| } else if (expr instanceof And || expr instanceof Or) { | ||
| return generateCriteriaGroupForBinaryExpression((BinaryExpression) expr, context); | ||
| } else { | ||
| CorelatedCriteria corelatedCriteria = CorelatedCriteriaTranslator.generateCorelatedCriteriaForExpression(expr, context); | ||
| criteriaGroup.criteriaList = CirceUtil.addCorelatedCriteria(criteriaGroup.criteriaList, corelatedCriteria); | ||
| } | ||
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| return criteriaGroup; | ||
| } | ||
| } |
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