Added support for counting distinct target concepts to each additiona…

…l filter item.

Added dependency to sqljdbc4 for POM. Only impacts mssql profile.

.gitignore

@@ -4,4 +4,5 @@
 .project
 /nb-configuration.xml
 /nbactions.xml
-/nbactions-webapi-local.xml
+/nbactions-webapi-local.xml
+/nbactions-webapi-mssql.xml

nb-licenseheader.txt

@@ -0,0 +1,19 @@
+<#if licenseFirst??>
+${licenseFirst}
+</#if>
+${licensePrefix}Copyright ${date?date?string("yyyy")} ${organization!user}.
+${licensePrefix?replace(" +$", "", "r")}
+${licensePrefix}Licensed under the Apache License, Version 2.0 (the "License");
+${licensePrefix}you may not use this file except in compliance with the License.
+${licensePrefix}You may obtain a copy of the License at
+${licensePrefix?replace(" +$", "", "r")}
+${licensePrefix}     http://www.apache.org/licenses/LICENSE-2.0
+${licensePrefix?replace(" +$", "", "r")}
+${licensePrefix}Unless required by applicable law or agreed to in writing, software
+${licensePrefix}distributed under the License is distributed on an "AS IS" BASIS,
+${licensePrefix}WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+${licensePrefix}See the License for the specific language governing permissions and
+${licensePrefix}limitations under the License.
+<#if licenseLast??>
+${licenseLast}
+</#if>

pom.xml

@@ -362,6 +362,14 @@
               <flyway.datasource.password>FLYWAY_PASS</flyway.datasource.password>
               <flyway.locations>classpath:db/migration/sqlserver</flyway.locations>
             </properties>
+            <dependencies>
+              <dependency>
+                <groupId>com.microsoft.sqlserver</groupId>
+                <artifactId>sqljdbc4</artifactId>
+                <version>4.0</version>
+                <type>jar</type>
+              </dependency>
+            </dependencies>	            
           </profile>                  
 	</profiles>
 </project>

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

@@ -187,7 +187,7 @@ private String getCodesetQuery(ConceptSet[] conceptSets) {
       codesetQuery = StringUtils.replace(codesetQuery, "@codesetQueries", StringUtils.join(codesetQueries, "\nUNION\n"));
     }
     else {
-      codesetQuery = StringUtils.replace(codesetQuery, "@codesetQueries", "SELECT concept_id FROM @CDM_schema.CONCEPT where 0 = 1"); // by default, return an empty resultset
+      codesetQuery = StringUtils.replace(codesetQuery, "@codesetQueries", "SELECT -1 as codeset_id, concept_id FROM @CDM_schema.CONCEPT where 0 = 1"); // by default, return an empty resultset
     }
     return codesetQuery;
   }
@@ -287,7 +287,8 @@ public String visit(AdditionalCriteria additionalCriteria)
     query = StringUtils.replace(query,"@windowCriteria",windowCriteria);
 
     String occurrenceCriteria = String.format(
-      "HAVING COUNT(A.PERSON_ID) %s %d", 
+      "HAVING COUNT(%sA.TARGET_CONCEPT_ID) %s %d",
+      additionalCriteria.occurrence.isDistinct ? "DISTINCT " : "",
       getOccurrenceOperator(additionalCriteria.occurrence.type), 
       additionalCriteria.occurrence.count
     );

src/main/java/org/ohdsi/webapi/cohortdefinition/Occurrence.java

@@ -17,4 +17,7 @@ public class Occurrence {
 
   @JsonProperty("Count")
   public int count;
+
+  @JsonProperty("IsDistinct")
+  public boolean isDistinct;  
 }

src/main/resources/resources/cohortdefinition/sql/conditionEra.sql

@@ -1,4 +1,4 @@
-select C.person_id, C.condition_era_start_date as start_date, C.condition_era_end_date as end_date
+select C.person_id, C.condition_era_start_date as start_date, C.condition_era_end_date as end_date, C.CONDITION_CONCEPT_ID as TARGET_CONCEPT_ID
 from 
 (
   select ce.*, ROW_NUMBER() over (PARTITION BY ce.person_id ORDER BY ce.condition_era_start_date) as ordinal

src/main/resources/resources/cohortdefinition/sql/conditionOccurrence.sql

@@ -1,4 +1,4 @@
-select C.person_id, C.condition_start_date as start_date, C.condition_end_date as end_date
+select C.person_id, C.condition_start_date as start_date, C.condition_end_date as end_date, C.CONDITION_CONCEPT_ID as TARGET_CONCEPT_ID
 from 
 (
         select co.*, ROW_NUMBER() over (PARTITION BY co.person_id ORDER BY co.condition_start_date) as ordinal

src/main/resources/resources/cohortdefinition/sql/death.sql

@@ -1,4 +1,4 @@
-select C.person_id, C.death_date as start_date, DATEADD(d,1,C.death_date) as end_date
+select C.person_id, C.death_date as start_date, DATEADD(d,1,C.death_date) as end_date, C.cause_concept_id as TARGET_CONCEPT_ID
 from 
 (
   select d.*

src/main/resources/resources/cohortdefinition/sql/deviceExposure.sql

@@ -1,4 +1,4 @@
-select C.person_id, C.device_exposure_start_date as start_date, C.device_exposure_end_date as end_date
+select C.person_id, C.device_exposure_start_date as start_date, C.device_exposure_end_date as end_date, C.device_concept_id as TARGET_CONCEPT_ID
 from 
 (
   select de.*, ROW_NUMBER() over (PARTITION BY de.person_id ORDER BY de.device_exposure_start_date) as ordinal

src/main/resources/resources/cohortdefinition/sql/doseEra.sql

@@ -1,4 +1,4 @@
-select C.person_id, C.dose_era_start_date as start_date, C.dose_era_end_date as end_date
+select C.person_id, C.dose_era_start_date as start_date, C.dose_era_end_date as end_date, C.drug_concept_id as TARGET_CONCEPT_ID
 from 
 (
   select de.*, ROW_NUMBER() over (PARTITION BY de.person_id ORDER BY de.dose_era_start_date) as ordinal

src/main/resources/resources/cohortdefinition/sql/drugEra.sql

@@ -1,4 +1,4 @@
-select C.person_id, C.drug_era_start_date as start_date, C.drug_era_end_date as end_date
+select C.person_id, C.drug_era_start_date as start_date, C.drug_era_end_date as end_date, C.drug_concept_id as TARGET_CONCEPT_ID
 from 
 (
   select de.*, ROW_NUMBER() over (PARTITION BY de.person_id ORDER BY de.drug_era_start_date) as ordinal

src/main/resources/resources/cohortdefinition/sql/drugExposure.sql

@@ -1,4 +1,4 @@
-select C.person_id, C.drug_exposure_start_date as start_date, C.drug_exposure_end_date as end_date
+select C.person_id, C.drug_exposure_start_date as start_date, C.drug_exposure_end_date as end_date, C.drug_concept_id as TARGET_CONCEPT_ID
 from 
 (
   select de.*, ROW_NUMBER() over (PARTITION BY de.person_id ORDER BY de.drug_exposure_start_date) as ordinal

src/main/resources/resources/cohortdefinition/sql/measurement.sql

@@ -1,4 +1,4 @@
-select C.person_id, C.measurement_date as start_date, DATEADD(d,1,C.measurement_date) as END_DATE
+select C.person_id, C.measurement_date as start_date, DATEADD(d,1,C.measurement_date) as END_DATE, C.measurement_concept_id as TARGET_CONCEPT_ID
 from 
 (
   select m.*, ROW_NUMBER() over (PARTITION BY m.person_id ORDER BY m.measurement_date) as ordinal

src/main/resources/resources/cohortdefinition/sql/observation.sql

@@ -1,4 +1,4 @@
-select C.person_id, C.observation_date as start_date, DATEADD(d,1,C.observation_date) as END_DATE
+select C.person_id, C.observation_date as start_date, DATEADD(d,1,C.observation_date) as END_DATE, C.observation_concept_id as TARGET_CONCEPT_ID
 from 
 (
   select o.*, ROW_NUMBER() over (PARTITION BY o.person_id ORDER BY o.observation_date) as ordinal

src/main/resources/resources/cohortdefinition/sql/observationPeriod.sql

@@ -1,4 +1,4 @@
-select C.person_id, C.observation_period_start_date as start_date, C.observation_period_end_date as end_date
+select C.person_id, C.observation_period_start_date as start_date, C.observation_period_end_date as end_date, C.period_type_concept_id as TARGET_CONCEPT_ID
 from 
 (
         select op.*, ROW_NUMBER() over (PARTITION BY op.person_id ORDER BY op.observation_period_start_date) as ordinal

src/main/resources/resources/cohortdefinition/sql/specimen.sql

@@ -1,4 +1,4 @@
-select C.person_id, C.specimen_date as start_date, DATEADD(d,1,C.specimen_date) as end_date
+select C.person_id, C.specimen_date as start_date, DATEADD(d,1,C.specimen_date) as end_date, C.specimen_concept_id as TARGET_CONCEPT_ID
 from 
 (
   select s.*, ROW_NUMBER() over (PARTITION BY s.person_id ORDER BY s.specimen_date) as ordinal

src/main/resources/resources/cohortdefinition/sql/visitOccurrence.sql

@@ -1,4 +1,4 @@
-select C.person_id, C.visit_start_date as start_date, C.visit_end_date as end_date
+select C.person_id, C.visit_start_date as start_date, C.visit_end_date as end_date, C.visit_concept_id as TARGET_CONCEPT_ID
 from 
 (
   select vo.*, ROW_NUMBER() over (PARTITION BY vo.person_id ORDER BY vo.visit_start_date) as ordinal