Handle standard and non-standard concept sets in criteria.

Fixes #160

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

@@ -10,26 +10,26 @@
 
 public abstract class BuilderUtils {
 
-    private final static String CODESET_JOIN_TEMPLATE = "JOIN #Codesets codesets on (@codesetClauses)";
-
+    private final static String CODESET_JOIN_TEMPLATE = "JOIN #Codesets %s on (%s = %s.concept_id and %s.codeset_id = %d)";
+    private final static String STANARD_ALIAS = "cs";
+    private final static String NON_STANARD_ALIAS = "cns";
+
     public static String getCodesetJoinExpression(Integer standardCodesetId, String standardConceptColumn, Integer sourceCodesetId, String sourceConceptColumn) {
 
-        final String codsetJoinClause = "(%s = codesets.concept_id and codesets.codeset_id = %d)";
         String joinExpression = "";
-
         ArrayList<String> codesetClauses = new ArrayList<>();
 
         if (standardCodesetId != null) {
-            codesetClauses.add(String.format(codsetJoinClause, standardConceptColumn, standardCodesetId));
+            codesetClauses.add(String.format(CODESET_JOIN_TEMPLATE, STANARD_ALIAS, standardConceptColumn, STANARD_ALIAS, STANARD_ALIAS, standardCodesetId));
         }
 
         // conditionSourceConcept
         if (sourceCodesetId != null) {
-            codesetClauses.add(String.format(codsetJoinClause, sourceConceptColumn, sourceCodesetId));
+            codesetClauses.add(String.format(CODESET_JOIN_TEMPLATE, NON_STANARD_ALIAS, sourceConceptColumn, NON_STANARD_ALIAS, NON_STANARD_ALIAS, sourceCodesetId));
         }
 
         if (codesetClauses.size() > 0) {
-            joinExpression = StringUtils.replace(CODESET_JOIN_TEMPLATE, "@codesetClauses", StringUtils.join(codesetClauses, " AND "));
+            joinExpression = StringUtils.join(codesetClauses, "\n");
         }
 
 

src/test/java/org/ohdsi/circe/cohortdefinition/CohortGeneration_5_0_0_Test.java

@@ -771,4 +771,50 @@ public void testCensorWindow() throws Exception {
     Assertion.assertEquals(expectedDataSet, actualDataSet);     
   }
 
+  /**
+   * Other Tests
+   */
+  @Test
+  public void testMixedConceptsets() throws Exception {
+    final String RESULTS_SCHEMA = "mixedConceptsets";
+    final String[] testDataSetsPrep = new String[] { 
+      "/datasets/vocabulary.json",
+      "/cohortgeneration/mixedConceptsets/mixedConceptsets_PREP.json" 
+    };
+    final IDatabaseConnection dbUnitCon = getConnection();
+
+    // prepare results schema for the specified options.resultSchema
+    prepareSchema(RESULTS_SCHEMA, RESULTS_DDL_PATH);
+
+    // load test data into DB.
+    final IDataSet dsPrep = DataSetFactory.createDataSet(testDataSetsPrep);
+    DatabaseOperation.CLEAN_INSERT.execute(dbUnitCon, dsPrep); // clean load of the DB. Careful, clean means "delete the old stuff"
+
+    CohortExpressionQueryBuilder.BuildExpressionQueryOptions options;
+    CohortExpression expression;   
+    String cohortSql;
+
+    // load the default expression: 
+    // all drug exposure events, fixed offset of endDate + 31 days.
+
+    // cohort 1 will use the default expression from JSON.
+    expression = CohortExpression.fromJson(ResourceHelper.GetResourceAsString("/cohortgeneration/mixedConceptsets/mixedConceptsetsExpression.json"));
+    options = buildExpressionQueryOptions(1, RESULTS_SCHEMA);
+    cohortSql = buildExpressionSql(expression, options);
+    // execute on database, expect no errors
+    jdbcTemplate.batchUpdate(SqlSplit.splitSql(cohortSql));
+
+    // Validate results
+    // Load actual records from cohort table
+    final ITable actualTable = dbUnitCon.createQueryTable(RESULTS_SCHEMA + ".cohort", String.format("SELECT * from %s ORDER BY cohort_definition_id, subject_id, cohort_start_date", RESULTS_SCHEMA + ".cohort"));
+    // Load expected data from an XML dataset
+    final String[] testDataSetsVerify = new String[] {"/cohortgeneration/mixedConceptsets/mixedConceptsets_VERIFY.json"};
+    final IDataSet expectedDataSet = DataSetFactory.createDataSet(testDataSetsVerify);
+    final ITable expectedTable = expectedDataSet.getTable(RESULTS_SCHEMA + ".cohort");
+
+    // Assert actual database table match expected table
+    Assertion.assertEquals(expectedTable, actualTable);
+
+  }
+
 }

src/test/resources/cohortgeneration/mixedConceptsets/mixedConceptsetsExpression.json

@@ -0,0 +1,77 @@
+{
+  "ConceptSets": [
+    {
+      "id": 0,
+      "name": "Standard Conceptset",
+      "expression": {
+        "items": [
+          {
+            "concept": {
+              "CONCEPT_CLASS_ID": "Clinical Finding",
+              "CONCEPT_CODE": "C1P1",
+              "CONCEPT_ID": 2,
+              "CONCEPT_NAME": "Child 1 [Parent: 1]",
+              "DOMAIN_ID": "CONDITION",
+              "INVALID_REASON": "V",
+              "INVALID_REASON_CAPTION": "Valid",
+              "STANDARD_CONCEPT": "S",
+              "STANDARD_CONCEPT_CAPTION": "Standard",
+              "VOCABULARY_ID": "TestVocab"
+            },
+            "includeDescendants": true
+          }
+        ]
+      }
+    },{
+      "id": 1,
+      "name": "Non-Standard Conceptset",
+      "expression": {
+        "items": [
+          {
+            "concept": {
+              "CONCEPT_CLASS_ID": "Clinical Finding",
+              "CONCEPT_CODE": "C2P1",
+              "CONCEPT_ID": 3,
+              "CONCEPT_NAME": "Child 2 [Parent 1]",
+              "DOMAIN_ID": "CONDITION",
+              "INVALID_REASON": "V",
+              "INVALID_REASON_CAPTION": "Valid",
+              "STANDARD_CONCEPT": "S",
+              "STANDARD_CONCEPT_CAPTION": "Standard",
+              "VOCABULARY_ID": "TestVocab"
+            },
+            "includeDescendants": true
+          }
+        ]
+      }
+    }
+  ],
+  "PrimaryCriteria": {
+    "CriteriaList": [{
+        "ConditionOccurrence": {
+          "CodesetId": 0,
+          "ConditionSourceConcept": 1
+        }
+    }],
+    "ObservationWindow": {
+      "PriorDays": 0,
+      "PostDays": 0
+    },
+    "PrimaryCriteriaLimit": {
+      "Type": "First"
+    }
+  },
+  "QualifiedLimit": {
+    "Type": "First"
+  },
+  "ExpressionLimit": {
+    "Type": "First"
+  },
+  "InclusionRules": [],
+  "CensoringCriteria": [],
+  "CollapseSettings": {
+    "CollapseType": "ERA",
+    "EraPad": 0
+  },
+  "CensorWindow": {}
+}

src/test/resources/cohortgeneration/mixedConceptsets/mixedConceptsets_PREP.json

@@ -0,0 +1,37 @@
+{
+  "cdm.person": [
+    {
+      "person_id":1,
+      "gender_concept_id":0,
+      "year_of_birth":0,
+      "race_concept_id":0,
+      "ethnicity_concept_id":0
+    }
+  ],
+  "cdm.condition_occurrence": [
+    {
+      "condition_occurrence_id": 1,
+      "person_id":1,
+      "condition_concept_id":2,
+      "condition_start_date":"2000-02-01",
+      "condition_type_concept_id":0
+    },
+    {
+      "condition_occurrence_id": 2,
+      "person_id":1,
+      "condition_concept_id":2,
+      "condition_source_concept_id":3,
+      "condition_start_date":"2000-07-01",
+      "condition_type_concept_id":0
+    }
+  ],
+  "cdm.observation_period" : [
+    {
+      "observation_period_id": 1,
+      "person_id":1,
+      "observation_period_start_date":"2000-01-01",
+      "observation_period_end_date":"2001-01-01",
+      "period_type_concept_id": 0
+    }
+  ]
+}

src/test/resources/cohortgeneration/mixedConceptsets/mixedConceptsets_VERIFY.json

@@ -0,0 +1,10 @@
+{
+  "mixedConceptsets.cohort": [
+    {
+      "cohort_definition_id":1,
+      "subject_id":1,
+      "cohort_start_date":"2000-07-01",
+      "cohort_end_date":"2001-01-01"
+    }
+  ]
+}