Support for datetime calculations in cohort definitions

src/main/java/org/ohdsi/circe/check/checkers/Comparisons.java

@@ -102,18 +102,48 @@ public static Predicate<Concept> compare(Concept source) {
                 .build();
     }
 
-    public static int compareTo(ObservationFilter filter, Window window) {
-
-        int range1 = filter.postDays + filter.priorDays;
-        int range2Start = 0, range2End = 0;
-        if (Objects.nonNull(window.start) && Objects.nonNull(window.start.days)) {
-            range2Start = window.start.coeff * window.start.days;
-        }
-        if (Objects.nonNull(window.end) && Objects.nonNull(window.end.days)) {
-            range2End = window.end.coeff * window.end.days;
-        }
-        return range1 - (range2End - range2Start);
+  /**
+   * If timeUnit is equal to values such as Hours, Minutes, Seconds, the values will be converted to seconds
+   * Otherwise it will return to the previous logic.
+   * @param filter
+   * @param window
+   * @return
+   */
+  public static int compareTo(ObservationFilter filter, Window window) {
+    int range1, range2Start = 0, range2End = 0;
+    if (Objects.nonNull(window.start) && Objects.nonNull(window.start.timeUnit) && !IntervalUnit.DAY.getName().equals(window.start.timeUnit)) {
+      range1 = (filter.postDays + filter.priorDays) * 24 * 60 * 60;
+      range2Start = getTimeInSeconds(window.start);
+      range2End = getTimeInSeconds(window.end);
+    } else {
+      range1 = filter.postDays + filter.priorDays;
+      if (Objects.nonNull(window.start) && Objects.nonNull(window.start.days)) {
+        range2Start = window.start.coeff * window.start.days;
+      }
+      if (Objects.nonNull(window.end) && Objects.nonNull(window.end.days)) {
+        range2End = window.end.coeff * window.end.days;
+      }
+    }
+    return range1 - (range2End - range2Start);
+  }
+
+  /**
+   * @return Convert values to seconds.
+   */
+  private static int getTimeInSeconds(Window.Endpoint endpoint) {
+    if (Objects.isNull(endpoint)) {
+      return 0;
     }
+    int convertRate;
+    if (IntervalUnit.HOUR.getName().equals(endpoint.timeUnit)) {
+      convertRate = 60 * 60;
+    } else if (IntervalUnit.MINUTE.getName().equals(endpoint.timeUnit)) {
+      convertRate = 60;
+    } else convertRate = 1;
+    return Objects.nonNull(endpoint.timeUnitValue)
+      ? endpoint.coeff * endpoint.timeUnitValue * convertRate
+      : 0;
+  }
 
     public static boolean compare(Criteria c1, Criteria c2) {
 

src/main/java/org/ohdsi/circe/check/checkers/ExitCriteriaDaysOffsetCheck.java

@@ -28,7 +28,7 @@
 
 public class ExitCriteriaDaysOffsetCheck extends BaseCheck {
 
-    private static final String DAYS_OFFSET_WARNING = "Cohort Exit criteria: Days offset from start date should be greater than 0";
+    private static final String DAYS_OFFSET_WARNING = "Cohort Exit criteria: %ss offset from start date should be greater than 0";
 
     @Override
     protected WarningSeverity defineSeverity() {
@@ -40,9 +40,9 @@ protected WarningSeverity defineSeverity() {
     protected void check(CohortExpression expression, WarningReporter reporter) {
 
         match(expression.endStrategy)
-                .isA(DateOffsetStrategy.class)
-                .then(s -> match((DateOffsetStrategy)s)
-                        .when(dateOffsetStrategy -> Objects.equals(StartDate, dateOffsetStrategy.dateField) && 0 == dateOffsetStrategy.offset)
-                        .then(() -> reporter.add(DAYS_OFFSET_WARNING)));
+            .isA(DateOffsetStrategy.class)
+            .then(s -> match((DateOffsetStrategy)s)
+                .when(dateOffsetStrategy -> Objects.equals(StartDate, dateOffsetStrategy.dateField) &&  0 == dateOffsetStrategy.offsetUnitValue)
+                .then(dateOffsetStrategy -> reporter.add(String.format(DAYS_OFFSET_WARNING, dateOffsetStrategy.offsetUnit))));
     }
 }

src/main/java/org/ohdsi/circe/check/checkers/FirstTimeInHistoryCheck.java

@@ -42,9 +42,10 @@ protected void checkCriteria(CorelatedCriteria criteria, String groupName, Warni
         String name = CriteriaNameHelper.getCriteriaName(criteria.criteria) + " at " + groupName;
         Execution addWarning = () -> reporter.add(WARNING, name);
         match(criteria)
-                .when(c -> c.startWindow != null && ((c.startWindow.start != null
-                        && c.startWindow.start.days != null) || (c.startWindow.end != null
-                        && c.startWindow.end.days != null)))
+            .when(c -> c.startWindow != null && ((c.startWindow.start != null && c.startWindow.start.days  != null)
+                || (c.startWindow.end != null && c.startWindow.end.days  != null))
+                || c.startWindow != null && (( c.startWindow.start != null && c.startWindow.start.timeUnitValue != null)
+                || (c.startWindow.end != null) && c.startWindow.end.timeUnitValue != null))
                 .then(cc -> match(cc.criteria)
                         .isA(ConditionEra.class)
                         .then(c -> match((ConditionEra)c)

src/main/java/org/ohdsi/circe/check/checkers/RangeCheck.java

@@ -52,17 +52,23 @@ protected void checkInclusionRules(final CohortExpression expression, WarningRep
     }
 
     private void checkWindow(Window window, WarningReporter reporter, String name) {
+        if (Objects.isNull(window)) {
+            return;
+        }
+        checkAndReportIfNegative(window.start, reporter, name, "start");
+        checkAndReportIfNegative(window.end, reporter, name, "end");
 
-        if (Objects.nonNull(window)) {
-            if (Objects.nonNull(window.start) && Objects.nonNull(window.start.days) && window.start.days < 0) {
-                reporter.add(NEGATIVE_VALUE_ERROR, name, window.start.days, "start");
-            }
-            if (Objects.nonNull(window.end) && Objects.nonNull(window.end.days) && window.end.days < 0) {
-                reporter.add(NEGATIVE_VALUE_ERROR, name, window.end.days, "end");
-            }
+    }
+
+    private void checkAndReportIfNegative(Window.Endpoint windowDetails, WarningReporter reporter, String name, String type) {
+        if (Objects.nonNull(windowDetails) && Objects.nonNull(windowDetails.days) && windowDetails.days < 0) {
+            reporter.add(NEGATIVE_VALUE_ERROR, name, windowDetails.days, type);
+        } else if (Objects.nonNull(windowDetails) && Objects.nonNull(windowDetails.timeUnitValue) && windowDetails.timeUnitValue < 0) {
+            reporter.add(NEGATIVE_VALUE_ERROR, name, windowDetails.timeUnitValue, type);
         }
     }
 
+
     private void checkObservationFilter(ObservationFilter filter, WarningReporter reporter, String name) {
 
         if (Objects.nonNull(filter)) {

src/main/java/org/ohdsi/circe/check/checkers/TimePatternCheck.java

@@ -22,6 +22,7 @@
 import java.util.List;
 import java.util.Map;
 import java.util.Objects;
+import java.util.Optional;
 import java.util.function.Function;
 import java.util.stream.Collectors;
 import org.ohdsi.circe.check.WarningSeverity;
@@ -83,16 +84,28 @@ private String formatTimeWindow(TimeWindowInfo ti) {
     }
 
     private String formatDays(Window.Endpoint endpoint) {
-        return Objects.nonNull(endpoint.days) ? String.valueOf(endpoint.days) : "all";
+        return Objects.nonNull(endpoint.days) ? String.valueOf(endpoint.days) :
+                Objects.nonNull(endpoint.timeUnitValue) ? String.valueOf(endpoint.timeUnitValue) : "all";
+
     }
 
     private String formatCoeff(Window.Endpoint endpoint) {
         return endpoint.coeff < 0 ? "before " : "after ";
     }
 
+
     private Integer startDays(Window window) {
-        return Objects.nonNull(window) && Objects.nonNull(window.start) ?
-                (Objects.nonNull(window.start.days) ? window.start.days : 0) * window.start.coeff : 0;
+        return Optional.ofNullable(window)
+            .map(w -> w.start)
+            .map(start -> {
+                int coefficient = Optional.ofNullable(start.coeff).orElse(0);
+                return Optional.ofNullable(start.days)
+                    .map(days -> days * coefficient)
+                    .orElseGet(() -> Optional.ofNullable(start.timeUnitValue)
+                        .map(timeUnitValue -> timeUnitValue * coefficient)
+                        .orElse(0));
+            })
+            .orElse(0);
     }
 
     class TimeWindowInfo {

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

@@ -351,8 +351,13 @@ public String buildExpressionQuery(CohortExpression expression, BuildExpressionQ
 
     resultSql = StringUtils.replace(resultSql, "@cohort_end_unions", StringUtils.join(endDateSelects, "\nUNION ALL\n"));
 
-    resultSql = StringUtils.replace(resultSql, "@eraconstructorpad", Integer.toString(expression.collapseSettings.eraPad));
-
+    if (!StringUtils.isEmpty(Integer.toString(expression.collapseSettings.eraPad)) && (expression.collapseSettings.eraPadUnit == null || IntervalUnit.DAY.getName().equals(expression.collapseSettings.eraPadUnit))) {
+      resultSql = StringUtils.replace(resultSql, "@eraconstructorpad", Integer.toString(expression.collapseSettings.eraPad));
+      resultSql = StringUtils.replace(resultSql, "@era_pad_unit", expression.collapseSettings.eraPadUnit);
+    } else {
+      resultSql = StringUtils.replace(resultSql, "@eraconstructorpad", Integer.toString(expression.collapseSettings.eraPadUnitValue));
+      resultSql = StringUtils.replace(resultSql, "@era_pad_unit", expression.collapseSettings.eraPadUnit);
+    }
     resultSql = StringUtils.replace(resultSql, "@inclusionRuleTable", getInclusionRuleTableSql(expression));
     resultSql = StringUtils.replace(resultSql, "@inclusionImpactAnalysisByEventQuery", getInclusionAnalysisQuery("#qualified_events", 0));
     resultSql = StringUtils.replace(resultSql, "@inclusionImpactAnalysisByPersonQuery", getInclusionAnalysisQuery("#best_events", 1));
@@ -546,8 +551,10 @@ public String getWindowedCriteriaQuery(String sqlTemplate, WindowedCriteria crit
     Window startWindow = criteria.startWindow;
     String startIndexDateExpression = (startWindow.useIndexEnd != null && startWindow.useIndexEnd) ? "P.END_DATE" : "P.START_DATE";
     String startEventDateExpression = (startWindow.useEventEnd != null && startWindow.useEventEnd) ? "A.END_DATE" : "A.START_DATE";
-    if (startWindow.start.days != null) {
+    if (startWindow.start.days != null && (startWindow.start.timeUnit == null || startWindow.start.timeUnit.equals(IntervalUnit.DAY.getName()))) {
       startExpression = String.format("DATEADD(day,%d,%s)", startWindow.start.coeff * startWindow.start.days, startIndexDateExpression);
+    } else if (startWindow.start.timeUnitValue != null) {
+      startExpression = String.format("DATEADD(%s,%d,%s)", startWindow.start.timeUnit, startWindow.start.coeff * startWindow.start.timeUnitValue, startIndexDateExpression);
     } else {
       startExpression = checkObservationPeriod ? (startWindow.start.coeff == -1 ? "P.OP_START_DATE" : "P.OP_END_DATE") : null;
     }
@@ -556,9 +563,12 @@ public String getWindowedCriteriaQuery(String sqlTemplate, WindowedCriteria crit
       clauses.add(String.format("%s >= %s", startEventDateExpression, startExpression));
     }
 
-    if (startWindow.end.days != null) {
+    if (startWindow.end.days != null && (startWindow.end.timeUnit == null || IntervalUnit.DAY.getName().equals(startWindow.end.timeUnit))) {
       endExpression = String.format("DATEADD(day,%d,%s)", startWindow.end.coeff * startWindow.end.days, startIndexDateExpression);
-    } else {
+    }else if(startWindow.end.timeUnitValue != null){
+      endExpression = String.format("DATEADD(%s,%d,%s)", startWindow.end.timeUnit, startWindow.end.coeff * startWindow.end.timeUnitValue, startIndexDateExpression);
+    }
+    else {
       endExpression = checkObservationPeriod ? (startWindow.end.coeff == -1 ? "P.OP_START_DATE" : "P.OP_END_DATE") : null;
     }
 
@@ -573,19 +583,26 @@ public String getWindowedCriteriaQuery(String sqlTemplate, WindowedCriteria crit
       String endIndexDateExpression = (endWindow.useIndexEnd != null && endWindow.useIndexEnd) ? "P.END_DATE" : "P.START_DATE";
       // for backwards compatability, having a null endWindow.useIndexEnd means they SHOULD use the index end date.
       String endEventDateExpression = (endWindow.useEventEnd == null || endWindow.useEventEnd) ? "A.END_DATE" : "A.START_DATE";
-      if (endWindow.start.days != null) {
+      if (endWindow.start.days != null && (endWindow.start.timeUnit == null || IntervalUnit.DAY.getName().equals(endWindow.start.timeUnit))) {
         startExpression = String.format("DATEADD(day,%d,%s)", endWindow.start.coeff * endWindow.start.days, endIndexDateExpression);
-      } else {
+      }else if(endWindow.start.timeUnitValue != null){
+        startExpression = String.format("DATEADD(%s,%d,%s)", endWindow.start.timeUnit, endWindow.start.coeff * endWindow.start.timeUnitValue, endIndexDateExpression);
+      }
+      else {
         startExpression = checkObservationPeriod ? (endWindow.start.coeff == -1 ? "P.OP_START_DATE" : "P.OP_END_DATE") : null;
       }
 
       if (startExpression != null) {
         clauses.add(String.format("%s >= %s", endEventDateExpression, startExpression));
       }
 
-      if (endWindow.end.days != null) {
+      if (endWindow.end.days != null && (endWindow.end.timeUnit == null || IntervalUnit.DAY.getName().equals(endWindow.end.timeUnit))) {
         endExpression = String.format("DATEADD(day,%d,%s)", endWindow.end.coeff * endWindow.end.days, endIndexDateExpression);
-      } else {
+      }
+      else if(endWindow.end.timeUnitValue != null){
+        endExpression = String.format("DATEADD(%s,%d,%s)", endWindow.end.timeUnit, endWindow.end.coeff * endWindow.end.timeUnitValue, endIndexDateExpression);
+      }
+      else {
         endExpression = checkObservationPeriod ? (endWindow.end.coeff == -1 ? "P.OP_START_DATE" : "P.OP_END_DATE") : null;
       }
 
@@ -763,7 +780,13 @@ private String getDateFieldForOffsetStrategy(DateOffsetStrategy.DateField dateFi
   @Override
   public String getStrategySql(DateOffsetStrategy strat, String eventTable) {
     String strategySql = StringUtils.replace(DATE_OFFSET_STRATEGY_TEMPLATE, "@eventTable", eventTable);
-    strategySql = StringUtils.replace(strategySql, "@offset", Integer.toString(strat.offset));
+    if (strat.offsetUnit == null || IntervalUnit.DAY.getName().equals(strat.offsetUnit)) {
+      strategySql = StringUtils.replace(strategySql, "@offsetUnitValue", Integer.toString(strat.offset));
+      strategySql = StringUtils.replace(strategySql, "@offsetUnit", "day");
+    } else {
+      strategySql = StringUtils.replace(strategySql, "@offsetUnitValue", Integer.toString(strat.offsetUnitValue));
+      strategySql = StringUtils.replace(strategySql, "@offsetUnit", strat.offsetUnit);
+    }
     strategySql = StringUtils.replace(strategySql, "@dateField", getDateFieldForOffsetStrategy(strat.dateField));
 
     return strategySql;
@@ -777,13 +800,33 @@ public String getStrategySql(CustomEraStrategy strat, String eventTable) {
     }
 
     String drugExposureEndDateExpression = DEFAULT_DRUG_EXPOSURE_END_DATE_EXPRESSION;
-    if (strat.daysSupplyOverride != null) {
+    if (strat.daysSupplyOverride != null && IntervalUnit.DAY.getName().equals(strat.gapUnit)) {
       drugExposureEndDateExpression = String.format("DATEADD(day,%d,DRUG_EXPOSURE_START_DATE)", strat.daysSupplyOverride);
+    }else if(strat.daysSupplyOverride != null && IntervalUnit.HOUR.getName().equals(strat.gapUnit)){
+      drugExposureEndDateExpression = String.format("DATEADD(hour,%d,DRUG_EXPOSURE_START_DATE)", strat.daysSupplyOverride);
+    }else if(strat.daysSupplyOverride != null && IntervalUnit.MINUTE.getName().equals(strat.gapUnit)){
+      drugExposureEndDateExpression = String.format("DATEADD(minute,%d,DRUG_EXPOSURE_START_DATE)", strat.daysSupplyOverride);
+    }else if(strat.daysSupplyOverride != null && IntervalUnit.SECOND.getName().equals(strat.gapUnit)){
+      drugExposureEndDateExpression = String.format("DATEADD(second,%d,DRUG_EXPOSURE_START_DATE)", strat.daysSupplyOverride);
     }
     String strategySql = StringUtils.replace(CUSTOM_ERA_STRATEGY_TEMPLATE, "@eventTable", eventTable);
     strategySql = StringUtils.replace(strategySql, "@drugCodesetId", strat.drugCodesetId.toString());
-    strategySql = StringUtils.replace(strategySql, "@gapDays", Integer.toString(strat.gapDays));
-    strategySql = StringUtils.replace(strategySql, "@offset", Integer.toString(strat.offset));
+    if (IntervalUnit.DAY.getName().equals(strat.gapUnit)) {
+      strategySql = StringUtils.replace(strategySql, "@gapUnitValue", Integer.toString(strat.gapDays));
+      strategySql = StringUtils.replace(strategySql, "@gapUnit", "day");
+    }else {
+      strategySql = StringUtils.replace(strategySql, "@gapUnitValue", Integer.toString(strat.gapUnitValue));
+      strategySql = StringUtils.replace(strategySql, "@gapUnit", strat.gapUnit);
+
+    }
+    if(IntervalUnit.DAY.getName().equals(strat.offsetUnit) || strat.offsetUnit == null){
+      strategySql = StringUtils.replace(strategySql, "@offsetUnitValue", Integer.toString(strat.offset));
+      strategySql = StringUtils.replace(strategySql, "@offsetUnit", "day");
+    }else {
+      strategySql = StringUtils.replace(strategySql, "@offsetUnitValue", Integer.toString(strat.offsetUnitValue));
+      strategySql = StringUtils.replace(strategySql, "@offsetUnit", strat.offsetUnit);
+    }
+
     strategySql = StringUtils.replace(strategySql, "@drugExposureEndDateExpression", drugExposureEndDateExpression);
 
     return strategySql;

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

@@ -18,14 +18,22 @@
  */
 package org.ohdsi.circe.cohortdefinition;
 
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import com.fasterxml.jackson.annotation.JsonProperty;
 
+@JsonIgnoreProperties(ignoreUnknown = true)
 public class CollapseSettings {
 
 	@JsonProperty("CollapseType")
 	public CollapseType collapseType = CollapseType.ERA;
 
 	@JsonProperty("EraPad")
 	public int eraPad = 0;
-
+
+  @JsonProperty("EraPadUnit")
+  public String eraPadUnit = IntervalUnit.DAY.getName();
+
+  @JsonProperty("EraPadUnitValue")
+  public int eraPadUnitValue = 0;
+
 }

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

@@ -22,6 +22,7 @@
 import com.fasterxml.jackson.annotation.JsonSubTypes;
 import com.fasterxml.jackson.annotation.JsonTypeInfo;
 import com.fasterxml.jackson.annotation.JsonTypeInfo.As;
+
 import org.ohdsi.circe.cohortdefinition.builders.BuilderOptions;
 
 /**
@@ -60,5 +61,14 @@ public String accept(IGetCriteriaSqlDispatcher dispatcher) {
 
   @JsonProperty("DateAdjustment")
   public DateAdjustment dateAdjustment;
+
+  /**
+   * This is a marker for the proper table columns definition while constructing the SELECT part of the result SQL
+   * in the corresponding SQL builder to reflect the values being defined in the associated WindowCriteria
+   * 
+   * The DAY value should be set only if all the WindowCriteria's Window.Endpoint values are DAY
+   */
+  @JsonProperty("IntervalUnit")
+  public String intervalUnit;
 
 }

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

@@ -31,9 +31,17 @@ public class CustomEraStrategy  extends EndStrategy {
 
   @JsonProperty("GapDays")
   public int gapDays = 0;
+  @JsonProperty("GapUnit")
+  public String gapUnit = "day";
+  @JsonProperty("GapUnitValue")
+  public int gapUnitValue = 0;
 
   @JsonProperty("Offset")
   public int offset = 0;
+  @JsonProperty("OffsetUnit")
+  public String offsetUnit = "day";
+  @JsonProperty("OffsetUnitValue")
+  public int offsetUnitValue = 0;
 
   @JsonProperty("DaysSupplyOverride")
   public Integer daysSupplyOverride = null;

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

@@ -18,25 +18,32 @@
  */
 package org.ohdsi.circe.cohortdefinition;
 
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import com.fasterxml.jackson.annotation.JsonProperty;
 
 /**
  *
  * @author Chris Knoll <[email protected]>
  */
+@JsonIgnoreProperties(ignoreUnknown = true)
 public class DateOffsetStrategy extends EndStrategy {
 
   public enum DateField {
     StartDate,
     EndDate
   }
-  
+
   @JsonProperty("DateField")
   public DateField dateField = DateField.StartDate;
 
   @JsonProperty("Offset")
   public int offset = 0;
-
+
+  @JsonProperty("OffsetUnitValue")
+  public int offsetUnitValue = 0;
+  @JsonProperty("OffsetUnit")
+  public String offsetUnit = "day";
+
   @Override
   public String accept(IGetEndStrategySqlDispatcher dispatcher, String eventTable) {
     return dispatcher.getStrategySql(this, eventTable);