update

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

@@ -20,9 +20,7 @@
 
 import java.time.LocalDate;
 import java.time.format.DateTimeParseException;
-import java.util.Arrays;
-import java.util.List;
-import java.util.Objects;
+import java.util.*;
 import java.util.function.Predicate;
 import java.util.stream.Collectors;
 import org.apache.commons.lang3.builder.EqualsBuilder;
@@ -31,6 +29,12 @@
 
 public class Comparisons {
 
+    private static final Map<String, Integer> TIME_UNIT_CONVERSION = new HashMap<>();
+    static {
+        TIME_UNIT_CONVERSION.put(IntervalUnit.HOUR.getName(), 60 * 60);
+        TIME_UNIT_CONVERSION.put(IntervalUnit.MINUTE.getName(), 60);
+    }
+
     public static Boolean startIsGreaterThanEnd(NumericRange r) {
 
         return Objects.nonNull(r.value) && Objects.nonNull(r.extent) && r.value.intValue() > r.extent.intValue();
@@ -101,31 +105,26 @@ public static Predicate<Concept> compare(Concept source) {
                 .append(concept.vocabularyId, source.vocabularyId)
                 .build();
     }
-
     public static int compareTo(ObservationFilter filter, Window window) {
-        int range1 = (filter.postDays + filter.priorDays) * 24 * 60 * 60;
-        int range2Start = getTimeInSeconds(window.start);
-        int range2End = getTimeInSeconds(window.end);
+        int range1 , range2Start , range2End;
+        if(Objects.nonNull(window.start) && Objects.nonNull(window.start.days)){
+                range1 = filter.postDays + filter.priorDays;
+                range2Start = window.start.coeff * window.start.days;
+                range2End = Objects.nonNull(window.end) && Objects.nonNull(window.end.days) ? window.end.coeff * window.end.days : 0;
+        }else {
+                range1 = (filter.postDays + filter.priorDays) * 24 * 60 * 60;
+                range2Start = getTimeInSeconds(window.start);
+                range2End = getTimeInSeconds(window.end);
+        }
         return range1 - (range2End - range2Start);
     }
-
     private static int getTimeInSeconds(Window.Endpoint endpoint) {
-        if (Objects.isNull(endpoint)) {
-            return 0;
+        return Optional.ofNullable(endpoint)
+                .map(ep -> {
+                    int convertRate = TIME_UNIT_CONVERSION.getOrDefault(ep.timeUnit, 1);
+                    return Objects.nonNull(ep.timeUnitValue) ? ep.coeff * ep.timeUnitValue * convertRate : 0;
+                }).orElse(0);
         }
-        int convertRate;
-        if (endpoint.timeUnit.equals(IntervalUnit.DAY.getName())) {
-            convertRate = 24 * 60 * 60;
-        } else if (endpoint.timeUnit.equals(IntervalUnit.HOUR.getName())) {
-            convertRate = 60 * 60;
-        } else if (endpoint.timeUnit.equals(IntervalUnit.MINUTE.getName())) {
-            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

@@ -18,14 +18,17 @@
 
 package org.ohdsi.circe.check.checkers;
 
-import static org.ohdsi.circe.check.operations.Operations.match;
-import static org.ohdsi.circe.cohortdefinition.DateOffsetStrategy.DateField.StartDate;
-
-import java.util.Objects;
 import org.ohdsi.circe.check.WarningSeverity;
 import org.ohdsi.circe.cohortdefinition.CohortExpression;
 import org.ohdsi.circe.cohortdefinition.DateOffsetStrategy;
 
+import java.util.Arrays;
+import java.util.List;
+import java.util.Objects;
+
+import static org.ohdsi.circe.check.operations.Operations.match;
+import static org.ohdsi.circe.cohortdefinition.DateOffsetStrategy.DateField.StartDate;
+
 public class ExitCriteriaDaysOffsetCheck extends BaseCheck {
 
     private static final String DAYS_OFFSET_WARNING = "Cohort Exit criteria: %ss offset from start date should be greater than 0";
@@ -40,9 +43,15 @@ 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.offsetUnitValue)
-                        .then(dateOffsetStrategy -> reporter.add(String.format(DAYS_OFFSET_WARNING, dateOffsetStrategy.offsetUnit))));
+            .isA(DateOffsetStrategy.class)
+            .then(s -> match((DateOffsetStrategy)s)
+                .when(dateOffsetStrategy -> Objects.equals(StartDate, dateOffsetStrategy.dateField) && (0 == dateOffsetStrategy.offset || 0 == dateOffsetStrategy.offsetUnitValue))
+                .then(dateOffsetStrategy -> {
+                    if(0 == dateOffsetStrategy.offset){
+                        reporter.add(String.format(DAYS_OFFSET_WARNING), "Days");
+                    }else {
+                        reporter.add(String.format(DAYS_OFFSET_WARNING, dateOffsetStrategy.offsetUnit));
+                    }
+                }));
     }
 }

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

@@ -43,8 +43,11 @@ protected void checkCriteria(CorelatedCriteria criteria, String groupName, Warni
         Execution addWarning = () -> reporter.add(WARNING, name);
         match(criteria)
                 .when(c -> c.startWindow != null && ((c.startWindow.start != null
-                        && c.startWindow.start.timeUnitValue != null) || (c.startWindow.end != null
-                        && c.startWindow.end.timeUnitValue != null)))
+                        && c.startWindow.start.days  != null) || (c.startWindow.end != null
+                        && c.startWindow.end.days  != 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

@@ -25,6 +25,7 @@
 import org.ohdsi.circe.cohortdefinition.Window;
 
 import java.util.Objects;
+import java.util.Optional;
 
 public class RangeCheck extends BaseValueCheck {
     private static final String NEGATIVE_VALUE_ERROR = "Time window in criteria \"%s\" has negative value %d at %s";
@@ -52,15 +53,24 @@ protected void checkInclusionRules(final CohortExpression expression, WarningRep
     }
 
     private void checkWindow(Window window, WarningReporter reporter, String name) {
+        Optional.ofNullable(window)
+            .map(w -> checkEndpoint(w, name, "start"))
+            .ifPresent(reporter::add);
 
-        if (Objects.nonNull(window)) {
-            if (Objects.nonNull(window.start) && Objects.nonNull(window.start.timeUnitValue) && window.start.timeUnitValue < 0) {
-                reporter.add(NEGATIVE_VALUE_ERROR, name, window.start.timeUnitValue, "start");
-            }
-            if (Objects.nonNull(window.end) && Objects.nonNull(window.end.timeUnitValue) && window.end.timeUnitValue < 0) {
-                reporter.add(NEGATIVE_VALUE_ERROR, name, window.end.timeUnitValue, "end");
-            }
-        }
+        Optional.ofNullable(window)
+            .map(w -> checkEndpoint(w, name, "end"))
+            .ifPresent(reporter::add);
+    }
+
+    private String checkEndpoint(Window window, String name, String endpointType) {
+        boolean hasValid = Objects.nonNull(window.start) && Objects.nonNull(window.start.days < 0 ? window.start.days : window.start.timeUnitValue) && window.start.days < 0 ? window.start.days < 0 : window.start.timeUnitValue < 0;
+        return Optional.of(window)
+            .filter(w -> hasValid)
+            .map(w -> String.format(NEGATIVE_VALUE_ERROR, name, getEndpointValue(w.start), endpointType))
+            .orElse(null);
+    }
+    private Object getEndpointValue(Window.Endpoint endpoint) {
+        return Objects.nonNull(endpoint.days) ? endpoint.days : endpoint.timeUnitValue;
     }
 
     private void checkObservationFilter(ObservationFilter filter, WarningReporter reporter, String name) {

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

@@ -18,10 +18,7 @@
 
 package org.ohdsi.circe.check.checkers;
 
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
-import java.util.Objects;
+import java.util.*;
 import java.util.function.Function;
 import java.util.stream.Collectors;
 import org.ohdsi.circe.check.WarningSeverity;
@@ -83,17 +80,29 @@ private String formatTimeWindow(TimeWindowInfo ti) {
     }
 
     private String formatDays(Window.Endpoint endpoint) {
-        return Objects.nonNull(endpoint.timeUnitValue) ? String.valueOf(endpoint.timeUnitValue) : "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.timeUnitValue) ? window.start.timeUnitValue : 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 {
         private String name;

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

@@ -20,9 +20,8 @@
 
 import com.fasterxml.jackson.annotation.JsonProperty;
 import com.fasterxml.jackson.databind.ObjectMapper;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
+
+import java.util.*;
 import java.util.stream.Collectors;
 import java.util.stream.IntStream;
 import org.apache.commons.lang3.StringUtils;
@@ -351,10 +350,12 @@ 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));
-    resultSql = StringUtils.replace(resultSql, "@era_pad_unit", expression.collapseSettings.eraPadUnit);
-    resultSql = StringUtils.replace(resultSql, "@era_pad", Integer.toString(expression.collapseSettings.eraPadUnitValue));
-
+    if(!StringUtils.isEmpty(Integer.toString(expression.collapseSettings.eraPad)) && expression.collapseSettings.eraPad != 0){
+        resultSql = StringUtils.replace(resultSql, "@eraconstructorpad", Integer.toString(expression.collapseSettings.eraPad));
+    }else{
+        resultSql = StringUtils.replace(resultSql, "@era_pad_unit", expression.collapseSettings.eraPadUnit);
+        resultSql = StringUtils.replace(resultSql, "@era_pad", Integer.toString(expression.collapseSettings.eraPadUnitValue));
+    }
     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));
@@ -548,20 +549,25 @@ 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.timeUnitValue != null) {
-      startExpression = String.format("DATEADD(%s,%d,%s)", startWindow.start.timeUnit, startWindow.start.coeff * startWindow.start.timeUnitValue, startIndexDateExpression);
+    if (startWindow.start.days != null) {
+          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;
+          startExpression = checkObservationPeriod ? (startWindow.start.coeff == -1 ? "P.OP_START_DATE" : "P.OP_END_DATE") : null;
     }
 
     if (startExpression != null) {
       clauses.add(String.format("%s >= %s", startEventDateExpression, startExpression));
     }
 
-    if (startWindow.end.timeUnitValue != null) {
-      endExpression = String.format("DATEADD(%s,%d,%s)", startWindow.start.timeUnit, startWindow.end.coeff * startWindow.end.timeUnitValue, startIndexDateExpression);
+    if (startWindow.end.days != null) {
+          endExpression = String.format("DATEADD(day,%d,%s)", startWindow.end.coeff * startWindow.end.days, startIndexDateExpression);
+    }
+    else if (startWindow.end.timeUnitValue != null) {
+          endExpression = String.format("DATEADD(%s,%d,%s)", startWindow.start.timeUnit, startWindow.end.coeff * startWindow.end.timeUnitValue, startIndexDateExpression);
     } else {
-      endExpression = checkObservationPeriod ? (startWindow.end.coeff == -1 ? "P.OP_START_DATE" : "P.OP_END_DATE") : null;
+          endExpression = checkObservationPeriod ? (startWindow.end.coeff == -1 ? "P.OP_START_DATE" : "P.OP_END_DATE") : null;
     }
 
     if (endExpression != null) {
@@ -575,20 +581,24 @@ 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.timeUnitValue != null) {
-        startExpression = String.format("DATEADD(%s,%d,%s)", endWindow.start.timeUnit, endWindow.start.coeff * endWindow.start.timeUnitValue, endIndexDateExpression);
+      if (endWindow.start.days != null) {
+          startExpression = String.format("DATEADD(day,%d,%s)", endWindow.start.coeff * endWindow.start.days, endIndexDateExpression);
+      } 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;
+          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.timeUnitValue != null) {
-        endExpression = String.format("DATEADD(%s,%d,%s)", endWindow.start.timeUnit, endWindow.end.coeff * endWindow.end.timeUnitValue, endIndexDateExpression);
+      if (endWindow.end.days != null) {
+            endExpression = String.format("DATEADD(day,%d,%s)", endWindow.end.coeff * endWindow.end.days, endIndexDateExpression);
+      } else if (endWindow.end.timeUnitValue != null) {
+            endExpression = String.format("DATEADD(%s,%d,%s)", endWindow.start.timeUnit, endWindow.end.coeff * endWindow.end.timeUnitValue, endIndexDateExpression);
       } else {
-        endExpression = checkObservationPeriod ? (endWindow.end.coeff == -1 ? "P.OP_START_DATE" : "P.OP_END_DATE") : null;
+            endExpression = checkObservationPeriod ? (endWindow.end.coeff == -1 ? "P.OP_START_DATE" : "P.OP_END_DATE") : null;
       }
 
       if (endExpression != null) {
@@ -765,10 +775,13 @@ 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, "@offsetUnitValue", Integer.toString(strat.offsetUnitValue));
-    strategySql = StringUtils.replace(strategySql, "@offsetUnit", strat.offsetUnit);
+    if(strat.offset  != 0){
+        strategySql = StringUtils.replace(strategySql, "@offset", Integer.toString(strat.offset));
+    }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;
   }
 
@@ -793,4 +806,5 @@ public String getStrategySql(CustomEraStrategy strat, String eventTable) {
   }
 
 // </editor-fold>
+
 }

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

@@ -24,8 +24,10 @@ public class CollapseSettings {
 
     @JsonProperty("CollapseType")
     public CollapseType collapseType = CollapseType.ERA;
+    @JsonProperty("EraPad")
+    public int eraPad  = 0;
     @JsonProperty("EraPadUnit")
-    public String eraPadUnit = IntervalUnit.DAY.getName();
+    public String eraPadUnit;
     @JsonProperty("EraPadUnitValue")
     public int eraPadUnitValue = 0;
 

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

@@ -30,14 +30,15 @@ public enum DateField {
     StartDate,
     EndDate
   }
-
+  @JsonProperty("Offset")
+  public int offset = 0;
   @JsonProperty("DateField")
   public DateField dateField = DateField.StartDate;
 
   @JsonProperty("OffsetUnitValue")
   public int offsetUnitValue = 0;
   @JsonProperty("OffsetUnit")
-  public String offsetUnit = IntervalUnit.DAY.getName();
+  public String offsetUnit;
 
   @Override
   public String accept(IGetEndStrategySqlDispatcher dispatcher, String eventTable) {

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

@@ -3,7 +3,6 @@
 import jdk.nashorn.internal.objects.annotations.Getter;
 
 public enum IntervalUnit {
-    DAY("day"),
     HOUR("hour"),
     MINUTE("minute"),
     SECOND("second");

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

@@ -4,12 +4,9 @@
 import org.ohdsi.circe.cohortdefinition.ConditionOccurrence;
 import org.ohdsi.circe.helper.ResourceHelper;
 
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Optional;
-import java.util.Set;
+import java.text.SimpleDateFormat;
+import java.util.*;
+
 import org.ohdsi.circe.cohortdefinition.DateAdjustment;
 
 import static org.ohdsi.circe.cohortdefinition.builders.BuilderUtils.buildDateRangeClause;
@@ -65,7 +62,6 @@ protected String embedCodesetClause(String query, T criteria) {
 
   @Override
   protected String embedOrdinalExpression(String query, T criteria, List<String> whereClauses) {
-
     // first
     if (criteria.first != null && criteria.first == true) {
       whereClauses.add("C.ordinal = 1");