Enabling calculations in between two related Measurements by adding a new criteria attribute

pom.xml

@@ -5,7 +5,7 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>org.ohdsi</groupId>
   <artifactId>circe</artifactId>
-  <version>1.11.3-SNAPSHOT</version>
+  <version>1.11.4-SNAPSHOT</version>
   <properties>
     <maven.compiler.source>1.8</maven.compiler.source>
     <maven.compiler.target>1.8</maven.compiler.target>

src/main/java/org/ohdsi/circe/cohortdefinition/Measurement.java

@@ -85,6 +85,9 @@ public class Measurement extends Criteria {
   @JsonProperty("VisitType")
   public Concept[] visitType;
 
+  @JsonProperty("MeasurementOperand")
+  public MeasurementOperand measurementOperand;
+
   @Override
   public String accept(IGetCriteriaSqlDispatcher dispatcher, BuilderOptions options)
   {

src/main/java/org/ohdsi/circe/cohortdefinition/MeasurementOperand.java

@@ -0,0 +1,16 @@
+package org.ohdsi.circe.cohortdefinition;
+
+import com.fasterxml.jackson.annotation.JsonProperty;
+
+public class MeasurementOperand {
+  @JsonProperty("Measurement")
+  public Measurement measurement;
+  @JsonProperty("Operator")
+  public String operator;
+  @JsonProperty("Limit")
+  public String limit = "First";
+  @JsonProperty("ValueAsNumber")
+  public NumericRange valueAsNumber;
+  @JsonProperty("SameVisit")
+  public Boolean sameVisit = true;
+}

src/main/java/org/ohdsi/circe/cohortdefinition/builders/CriteriaSqlBuilder.java

@@ -30,25 +30,29 @@ public String getCriteriaSql(T criteria, BuilderOptions options) {
     query = embedJoinClauses(query, joinClauses);
     query = embedWhereClauses(query, whereClauses);
 
+    query = embedAdditionalColumns(query, criteria, options);
+
+    return query;
+  }
+
+  protected String embedAdditionalColumns(String query, T criteria, BuilderOptions options) {
     if (options != null) {
       List<CriteriaColumn> filteredColumns = options.additionalColumns.stream()
-              .filter((column) -> !this.getDefaultColumns().contains(column))
-              .collect(Collectors.toList());
+        .filter((column) -> !this.getDefaultColumns().contains(column))
+        .collect(Collectors.toList());
       if (filteredColumns.size() > 0) {
-        query = StringUtils.replace(query, "@additionalColumns", ", " + this.getAdditionalColumns(filteredColumns));
+        return StringUtils.replace(query, "@additionalColumns", ", " + this.getAdditionalColumns(criteria, filteredColumns));
       } else {
-        query = StringUtils.replace(query, "@additionalColumns", "");
+        return StringUtils.replace(query, "@additionalColumns", "");
       }
     } else {
-      query = StringUtils.replace(query, "@additionalColumns", "");
+      return StringUtils.replace(query, "@additionalColumns", "");
     }
-
-    return query;
   }
 
   protected abstract String getTableColumnForCriteriaColumn(CriteriaColumn column);
 
-  protected String getAdditionalColumns(List<CriteriaColumn> columns) {
+  protected String getAdditionalColumns(T criteria, List<CriteriaColumn> columns) {
     String cols = String.join(", ", columns.stream()
             .map((column) -> {
               return String.format("%s as %s", getTableColumnForCriteriaColumn(column), column.columnName());

src/main/java/org/ohdsi/circe/cohortdefinition/builders/MeasurementSqlBuilder.java

@@ -4,11 +4,18 @@
 import org.ohdsi.circe.cohortdefinition.Measurement;
 import org.ohdsi.circe.helper.ResourceHelper;
 
+import java.text.MessageFormat;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.HashSet;
 import java.util.List;
+import java.util.Objects;
+import java.util.Optional;
 import java.util.Set;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
+
 import org.ohdsi.circe.cohortdefinition.DateAdjustment;
 
 import static org.ohdsi.circe.cohortdefinition.builders.BuilderUtils.buildDateRangeClause;
@@ -25,7 +32,7 @@ public class MeasurementSqlBuilder<T extends Measurement> extends CriteriaSqlBui
 
   // default select columns are the columns that will always be returned from the subquery, but are added to based on the specific criteria
   private final List<String> DEFAULT_SELECT_COLUMNS = new ArrayList<>(Arrays.asList("m.person_id", "m.measurement_id", "m.measurement_concept_id", "m.visit_occurrence_id",
-          "m.value_as_number", "m.range_high", "m.range_low"));
+    "m.value_as_number", "m.range_high", "m.range_low"));
 
   @Override
   protected Set<CriteriaColumn> getDefaultColumns() {
@@ -38,6 +45,34 @@ protected String getQueryTemplate() {
     return MEASUREMENT_TEMPLATE;
   }
 
+/*
+  @Override
+  protected String embedAdditionalColumns(String query, T criteria, BuilderOptions options) {
+    if (criteria.measurementOperand != null) {
+      String additionalColumns = getAdditionalColumns(criteria, Optional.ofNullable(options).map(o -> o.additionalColumns).orElse(new ArrayList<>()));
+      return StringUtils.replace(query, "@additionalColumns", additionalColumns);
+    } else {
+      return super.embedAdditionalColumns(query, criteria, options);
+    }
+  }
+*/
+
+/*
+  @Override
+  protected String getAdditionalColumns(T criteria, List<CriteriaColumn> columns) {
+    return Stream.concat(
+        Stream.of(super.getAdditionalColumns(criteria, columns)),
+        Optional.ofNullable(criteria.measurementOperand).map(measurementOperand ->
+          Stream.of(
+            MessageFormat.format("row_number() over (PARTITION BY C.person_id ORDER BY SC.start_date, SC.event_id {0}) as ordinal",
+              Optional.ofNullable(measurementOperand.limit).map(limit -> limit.equals("Last") ? "DESC" : "").orElse(""))
+          )
+        ).orElse(Stream.empty())
+      )
+      .collect(Collectors.joining(","));
+  }
+*/
+
   @Override
   protected String getTableColumnForCriteriaColumn(CriteriaColumn column) {
     switch (column) {
@@ -60,10 +95,10 @@ protected String getTableColumnForCriteriaColumn(CriteriaColumn column) {
   protected String embedCodesetClause(String query, T criteria) {
 
     return StringUtils.replace(query, "@codesetClause",
-            getCodesetJoinExpression(criteria.codesetId,
-                    "m.measurement_concept_id",
-                    criteria.measurementSourceConcept,
-                    "m.measurement_source_concept_id")
+      getCodesetJoinExpression(criteria.codesetId,
+        "m.measurement_concept_id",
+        criteria.measurementSourceConcept,
+        "m.measurement_source_concept_id")
     );
   }
 
@@ -115,11 +150,12 @@ protected List<String> resolveSelectClauses(T criteria) {
     // dateAdjustment or default start/end dates
     if (criteria.dateAdjustment != null) {
       selectCols.add(BuilderUtils.getDateAdjustmentExpression(criteria.dateAdjustment,
-              criteria.dateAdjustment.startWith == DateAdjustment.DateType.START_DATE ? "m.measurement_date" : "DATEADD(day,1,m.measurement_date)",
-              criteria.dateAdjustment.endWith == DateAdjustment.DateType.START_DATE ? "m.measurement_date" : "DATEADD(day,1,m.measurement_date)"));
+        criteria.dateAdjustment.startWith == DateAdjustment.DateType.START_DATE ? "m.measurement_date" : "DATEADD(day,1,m.measurement_date)",
+        criteria.dateAdjustment.endWith == DateAdjustment.DateType.START_DATE ? "m.measurement_date" : "DATEADD(day,1,m.measurement_date)"));
     } else {
       selectCols.add("m.measurement_date as start_date, DATEADD(day,1,m.measurement_date) as end_date");
     }
+
     return selectCols;
   }
 
@@ -138,6 +174,15 @@ protected List<String> resolveJoinClauses(T criteria) {
     if (criteria.providerSpecialty != null && criteria.providerSpecialty.length > 0) {
       joinClauses.add("LEFT JOIN @cdm_database_schema.PROVIDER PR on C.provider_id = PR.provider_id");
     }
+    if (criteria.measurementOperand != null && criteria.measurementOperand.measurement != null) {
+      BuilderOptions options = new BuilderOptions();
+      options.additionalColumns = Collections.singletonList(CriteriaColumn.VALUE_AS_NUMBER);
+      String subquery = getCriteriaSql((T) criteria.measurementOperand.measurement, options);
+      joinClauses.add(MessageFormat.format("JOIN (SELECT E.person_id, E.event_id, E.visit_occurrence_id, E.value_as_number, row_number() over (PARTITION BY E.person_id ORDER BY E.start_date, E.event_id {1}) as ordinal FROM (\n{0}\n) E) SC on C.person_id = SC.person_id",
+        subquery,
+        Optional.ofNullable(criteria.measurementOperand.limit).map(limit -> limit.equals("Last") ? "DESC" : "").orElse("")
+      ));
+    }
 
     return joinClauses;
   }
@@ -226,6 +271,18 @@ protected List<String> resolveWhereClauses(T criteria) {
       whereClauses.add(String.format("V.visit_concept_id in (%s)", StringUtils.join(getConceptIdsFromConcepts(criteria.visitType), ",")));
     }
 
+    //Calculation
+    if (criteria.measurementOperand != null) {
+      whereClauses.add(buildNumericRangeClause(
+        MessageFormat.format("(C.value_as_number {0} SC.value_as_number)", criteria.measurementOperand.operator),
+        criteria.measurementOperand.valueAsNumber, ".4f")
+      );
+      if (Optional.ofNullable(criteria.measurementOperand.sameVisit).orElse(false)) {
+        whereClauses.add("SC.visit_occurrence_id = C.visit_occurrence_id");
+      }
+      whereClauses.add("SC.ordinal = 1");
+    }
+
     return whereClauses;
   }
 }

src/main/resources/resources/cohortdefinition/printfriendly/criteriaTypes.ftl

@@ -151,7 +151,9 @@ c.visitType??><#local temp>a visit occurrence that is: <@inputTypes.ConceptList
 measurement<#if isPlural && !(c.first!false)>s</#if> of ${utils.codesetName(c.codesetId!"", "any measurement")}<#if 
 c.measurementSourceConcept??> (including ${utils.codesetName(c.measurementSourceConcept, "any measurement")} source concepts)</#if><#if 
 c.first!false> for the first time in the person's history</#if><#if attrs?size gt 0>, ${attrs?join("; ")}</#if><#if 
-c.CorrelatedCriteria??>; <@Group group=c.CorrelatedCriteria level=level indexLabel=utils.codesetName(c.codesetId!"", "any measurement") /><#else>.</#if></#macro>
+c.CorrelatedCriteria??>; <@Group group=c.CorrelatedCriteria level=level indexLabel=utils.codesetName(c.codesetId!"", "any measurement") /><#else>.</#if>
+<#if c.measurementOperand??>numeric value calculated as <@MeasurementOperand c=c.measurementOperand level=level+1 /></#if><#nested />
+</#macro>
 
 <#macro Observation c level isPlural=true countCriteria={} indexLabel="cohort entry"><#local attrs = []><#local attrs = []><#if countCriteria?has_content>
 <#local temp><@WindowCriteria countCriteria=countCriteria indexLabel=indexLabel/></#local><#if temp?has_content><#local attrs+=[temp]></#if></#if>
@@ -308,3 +310,14 @@ temp><@EventDateCriteria c.occurrenceStartDate!{} c.occurrenceEndDate!{} /></#lo
 c.race??><#local temp>race is: <@inputTypes.ConceptList list=c.race/></#local><#local attrs+=[temp]></#if><#if
 c.ethnicity??><#local temp>ethnicity is: <@inputTypes.ConceptList list=c.ethnicity/></#local><#local attrs+=[temp]></#if><#if 
 attrs?size gt 0>with the following event criteria: ${attrs?join("; ")}.<#else>any event (no demographic criteria specified).</#if></#macro>
+
+<#-- Calculation Criteria -->
+<#macro MeasurementOperand c level>primary measurement ${c.operator} <#local temp><@MeasurementLimit limit = c.limit /></#local> <#local temp><@Measurement c=c.measurement level=level+1> <#if c.sameVisit>in the same visit</#if> <#if c.valueAsNumber??>which are <@inputTypes.NumericRange range=c.valueAsNumber /></#if> </@Measurement></#local> ${temp}</#macro>
+
+<#-- Limits -->
+<#assign measurementLimitOptions = [
+{"id": "First", "name": "earliest event"},
+{"id": "Last", "name": "latest event"}
+]/>
+
+<#macro MeasurementLimit limit>${utils.optionName(measurementLimitOptions, limit)}</#macro>