finished a lot of refactoring

still has to tidy up a lot
at least most test cases except the cypher transformations work again

QueryMapper/src/main/java/de/uniwue/query/CQL/CQL_2_Graph_Mapper.java

@@ -82,7 +82,6 @@ import org.cqframework.cql.gen.cqlParser.WhereClauseContext;
 import org.cqframework.cql.gen.cqlParser.WithClauseContext;
 
 import de.uniwue.misc.util.RegexUtil;
-import de.uniwue.query.Expression;
 import de.uniwue.query.OperatorType;
 import de.uniwue.query.Primitive;
 import de.uniwue.query.Primitive.PrimitiveDataType;
@@ -216,11 +215,12 @@ public class CQL_2_Graph_Mapper extends System_2_Graph_Mapper {
 
   private void parseReturnClauseContext(ReturnClauseContext returnClause) {
     String prettyPrint = prettyPrint(returnClause);
+    currentOp = query;
+    addOp(OperatorType.RETURN);
     parsingReturnRoot = true;
     TermExpressionContext te = (TermExpressionContext) returnClause.expression();
     TermExpressionTermContext tet = (TermExpressionTermContext) te.expressionTerm();
     TermContext term = tet.term();
-    List<Expression> formerReturns = new ArrayList<Expression>(query.getParameters());
     if (term instanceof TupleSelectorTermContext) {
       TupleSelectorTermContext tst = (TupleSelectorTermContext) term;
       TupleSelectorContext tupleSelector = tst.tupleSelector();
@@ -236,21 +236,16 @@ public class CQL_2_Graph_Mapper extends System_2_Graph_Mapper {
     } else {
       throw new RuntimeException("unexpected");
     }
-    for (Expression anExp : formerReturns) {
-      query.removeParameter(anExp);
-    }
   }
 
   private void parseTupleElementSelectorContext(TupleElementSelectorContext anElem) {
     String prettyPrint = prettyPrint(anElem);
-    currentOp = null;
     String text = anElem.identifier().getText();
     ExpressionContext expression = anElem.expression();
     QueryOperator lastCreatedOp = parseExpression(expression);
     if (lastCreatedOp != null) {
       lastCreatedOp.outputName = text;
     } else if (lastPathElem != null) {
-      query.addParameter(lastPathElem);
       lastPathElem.outputName = text;
     } else {
       throw new RuntimeException("unexpected");
@@ -530,7 +525,12 @@ public class CQL_2_Graph_Mapper extends System_2_Graph_Mapper {
     String prettyPrint = prettyPrint(ae);
     QueryOperator lastOp = currentOp;
     QueryOperator thisOp;
-    thisOp = addOp(OperatorType.AND);
+    // let nested ANDs be put into the same AND with unlimited parameter clauses
+    if (currentOp.type != OperatorType.AND) {
+      thisOp = addOp(OperatorType.AND);
+    } else {
+      thisOp = currentOp;
+    }
     List<ExpressionContext> expression = ae.expression();
     for (ExpressionContext ec : expression) {
       parseExpression(ec);
@@ -841,7 +841,7 @@ public class CQL_2_Graph_Mapper extends System_2_Graph_Mapper {
     String prettyPrint = prettyPrint(mi);
     String text = mi.identifier().getText();
     if (lastPathElem == null) {
-      if (currentOp.type == OperatorType.FIELD) {
+      if ((currentOp != null) && (currentOp.type == OperatorType.FIELD)) {
         currentOp.addParameter(text);
         return currentOp;
       } else {

QueryMapper/src/main/java/de/uniwue/query/Expression.java

@@ -26,7 +26,8 @@ public abstract class Expression {
     if (isOperator()) {
       QueryOperator thisAsOp = asOperator();
       if ((thisAsOp.type == OperatorType.ITERATE) || (thisAsOp.type == OperatorType.FIELD)
-              || (thisAsOp.type == OperatorType.FIELD_WITH_TYPE)) {
+              || (thisAsOp.type == OperatorType.FIELD_WITH_TYPE)
+              || (thisAsOp.type == OperatorType.ALIAS_REF)) {
         return true;
       }
     }
@@ -45,4 +46,6 @@ public abstract class Expression {
     return (QueryOperator) this;
   }
 
+  public abstract Expression clone();
+  
 }

QueryMapper/src/main/java/de/uniwue/query/Primitive.java

@@ -34,4 +34,9 @@ public class Primitive extends Expression {
     return result;
   }
 
+  public Primitive clone() {
+    Primitive result = new Primitive(value);
+    result.dataType = dataType;
+    return result;
+  }
 }

QueryMapper/src/main/java/de/uniwue/query/QueryOperator.java

@@ -20,6 +20,16 @@ public class QueryOperator extends Expression {
     }
   }
 
+  public QueryOperator(QueryOperator aContainerOp, OperatorType opType, boolean insertInChainForContainer) {
+    this.type = opType;
+    if (aContainerOp != null) {
+      parent = aContainerOp.parent;
+      QueryOperator tmp = aContainerOp.parent;
+      tmp.removeParameter(aContainerOp);
+      tmp.addParameter(this);
+    }
+  }
+
   public QueryOperator(QueryOperator aContainerOp, String conceptCode) {
     this(aContainerOp, OperatorType.ITERATE);
     Primitive primitive = new Primitive(conceptCode);
@@ -65,6 +75,14 @@ public class QueryOperator extends Expression {
     this(null, opType);
   }
 
+  public QueryOperator clone() {
+    QueryOperator result = new QueryOperator(type);
+    for (Expression anExp : getParameters()) {
+      result.addParameter(anExp.clone());
+    }
+    return result;
+  }
+  
   public void clear() {
     parameters.clear();
   }
@@ -97,9 +115,15 @@ public class QueryOperator extends Expression {
   }
 
   public void checkConsistency() {
-    if ((parent != null) && !parent.getParameters().contains(this)) {
-      throw new RuntimeException("parent does not contain me");
+    checkDuplicateAliases();
+    checkParentChildSynchonicity();
+    checkAliasExistenceForAliasRefs();
+    for (QueryOperator anOp : getOperators()) {
+      anOp.checkConsistency();
     }
+  }
+
+  private void checkAliasExistenceForAliasRefs() {
     if (type == OperatorType.ALIAS_REF) {
       String alias = getParameters().get(0).asPrimitive().value;
       boolean aliasExists = false;
@@ -112,11 +136,32 @@ public class QueryOperator extends Expression {
         throw new RuntimeException("ALIAS_REF has no matching alias");
       }
     }
-    for (QueryOperator anOp : getOperators()) {
-      anOp.checkConsistency();
+  }
+
+  private void checkParentChildSynchonicity() {
+    if ((parent != null) && !parent.getParameters().contains(this)) {
+      throw new RuntimeException("parent does not contain me");
     }
   }
-  
+
+  private void checkDuplicateAliases() {
+    if (isRoot()) {
+      for (QueryOperator anOp : getRoot().getOpsRecursive()) {
+        if (anOp.alias != null) {
+          for (QueryOperator anOp2 : getRoot().getOpsRecursive()) {
+            if ((anOp.alias != null) && (anOp != anOp2) && anOp.alias.equals(alias)) {
+              throw new RuntimeException("alias '" + anOp.alias + "' appear multiple times");
+            }
+          }
+        }
+      }
+    }
+  }
+
+  public boolean isRoot() {
+    return parent == null;
+  }
+
   public List<Expression> getParameters() {
     return new ArrayList<Expression>(parameters);
   }
@@ -173,6 +218,11 @@ public class QueryOperator extends Expression {
     aParameter.parent = this;
   }
 
+  public void addParameter(Expression aParameter, int index) {
+    this.parameters.add(index, aParameter);
+    aParameter.parent = this;
+  }
+
   public void removeParameter(Expression aParameter) {
     parameters.remove(aParameter);
     aParameter.parent = null;
@@ -250,17 +300,45 @@ public class QueryOperator extends Expression {
   }
 
   public QueryOperator getParentConcept() {
-    if (!isIterator()) {
-      return null;
+    if (!isConcept()) {
+      throw new RuntimeException("no concept");
     }
-    if (type == OperatorType.ITERATE) {
+    if (type == OperatorType.ALIAS_REF) {
+      QueryOperator opReferencedWithAlias = resolveAlias();
+      return opReferencedWithAlias.getParentConcept();
+    } else if (type == OperatorType.ITERATE) {
       // I have no parent because I am a root concept
       return null;
     }
     String aliasRefValue = getParameters().get(0).asOperator().getParameters().get(0)
             .asPrimitive().value;
-    for (QueryOperator anOp : getRoot().getOpsRecursive()) {
-      if ((anOp.alias != null) && anOp.alias.equals(aliasRefValue)) {
+    QueryOperator aliasedOp = getRoot().getOpWithAlias(aliasRefValue);
+    return aliasedOp;
+  }
+
+  public QueryOperator resolveAlias() {
+    if (type != OperatorType.ALIAS_REF) {
+      return this;
+    }
+    String alias = getParameters().get(0).asPrimitive().value;
+    QueryOperator opWithAlias = getOpWithAlias(alias);
+    return opWithAlias;
+  }
+
+  public List<QueryOperator> getAliasRefsWithAlias(String anAlias) {
+    List<QueryOperator> result = new ArrayList<QueryOperator>();
+    for (QueryOperator anAliasRef : getOpsRecursiveWithType(OperatorType.ALIAS_REF)) {
+      if (anAliasRef.getParameters().get(0).asPrimitive().value.equals(anAlias)) {
+        result.add(anAliasRef);
+      }
+    }    
+    return result;
+  }
+  
+  public QueryOperator getOpWithAlias(String anAlias) {
+    List<QueryOperator> ops = getRoot().getOpsRecursive();
+    for (QueryOperator anOp : ops) {
+      if ((anOp.alias != null) && anOp.alias.equals(anAlias)) {
         return anOp;
       }
     }
@@ -310,4 +388,12 @@ public class QueryOperator extends Expression {
     }
   }
 
+  public void removeUnnecessaryANDs() {
+    for (QueryOperator anAnd : getRoot().getOpsRecursiveWithType(OperatorType.AND)) {
+      if (anAnd.getParameters().size() == 1) {
+        anAnd.parent.addParameter(anAnd.getParameters().get(0));
+        anAnd.parent.removeParameter(anAnd);
+      }
+    }
+  }
 }

QueryMapper/src/main/java/de/uniwue/query/openEHR/AQL_2_Graph_Mapper.java

@@ -103,7 +103,7 @@ public class AQL_2_Graph_Mapper extends System_2_Graph_Mapper {
     currentOp = query;
     visitQueryExpr(parseTree);
     moveClausesToOutmostEncapsulatingClauses();
-    removeUnnecessaryANDs();
+    query.removeUnnecessaryANDs();
     return query;
   }
 
@@ -165,7 +165,7 @@ public class AQL_2_Graph_Mapper extends System_2_Graph_Mapper {
     if (nearestFilter != targetClause) {
       aFilter.parent.removeParameter(aFilter);
       if (targetClause.getParameters().size() > 1) {
-        currentOp = targetClause.getParameters().get(1).asOperator();          
+        currentOp = targetClause.getParameters().get(1).asOperator();
         if (currentOp.type != OperatorType.AND) {
           targetClause = insertOp(OperatorType.AND);
         }
@@ -182,15 +182,6 @@ public class AQL_2_Graph_Mapper extends System_2_Graph_Mapper {
     return currentOp;
   }
 
-  private void removeUnnecessaryANDs() {
-    for (QueryOperator anAnd : query.getOpsRecursiveWithType(OperatorType.AND)) {
-      if (anAnd.getParameters().size() == 1) {
-        anAnd.parent.addParameter(anAnd.getParameters().get(0));
-        anAnd.parent.removeParameter(anAnd);
-      }
-    }
-  }
-
   private void visitPredicateOperandContexts(List<PredicateOperandContext> predicateOperand,
           TerminalNode comparableoperator) {
     QueryOperator lastOp = currentOp;

QueryMapper/src/main/java/de/uniwue/query/transform/CodeMapper.java

@@ -6,6 +6,7 @@ import java.util.List;
 import org.springframework.core.io.Resource;
 
 import de.uniwue.misc.util.ResourceUtil;
+import de.uniwue.query.OperatorType;
 import de.uniwue.query.QueryOperator;
 
 public class CodeMapper extends GraphTransformation {
@@ -14,6 +15,8 @@ public class CodeMapper extends GraphTransformation {
 
   public String targetCode;
 
+  public String targetAccessOverride;
+
   public CodeMapper(String sourceCode, String targetCode) {
     this.sourceCode = sourceCode;
     this.targetCode = targetCode;
@@ -24,6 +27,9 @@ public class CodeMapper extends GraphTransformation {
     for (QueryOperator aConcept : query.getIteratorsRecursive()) {
       if (sourceCode.equals(aConcept.getIteratorSelector())) {
         aConcept.setIteratorSelector(targetCode);
+        if (targetAccessOverride != null) {
+          aConcept.type  = OperatorType.valueOf(targetAccessOverride);
+        }
       }
     }
   }
@@ -49,6 +55,10 @@ public class CodeMapper extends GraphTransformation {
       String sourceCode = tokens[0];
       String targetCode = tokens[1];
       CodeMapper mapper = new CodeMapper(sourceCode, targetCode);
+      if (tokens.length > 2) {
+        String targetAccessOverride = tokens[2];
+        mapper.targetAccessOverride = targetAccessOverride;
+      }
       transformations.add(mapper);
     }
   }

QueryMapper/src/main/java/de/uniwue/query/transform/Equality_2_Meronym_Transformation.java

@@ -9,32 +9,27 @@ public class Equality_2_Meronym_Transformation extends GraphTransformation {
 
   @Override
   public void transform(QueryOperator query) {
-    for (QueryOperator anOp : query.getOpsRecursive()) {
-      if (anOp.type == OperatorType.EQUALS) {
-        List<QueryOperator> conceptParam = anOp.getChildConcepts();
-        if (conceptParam.size() != 2) {
-          continue;
-        }
-        QueryOperator newHolonymConc = null, newMeronymConc = null, oldEqualityMember = null;
-        if (conceptParam.get(0).parent != null) {
-          newHolonymConc = conceptParam.get(0);
-          oldEqualityMember = conceptParam.get(1);
-          newMeronymConc = oldEqualityMember.parent;
-        } else if (conceptParam.get(1).parent != null) {
-          newHolonymConc = conceptParam.get(1);
-          oldEqualityMember = conceptParam.get(0);
-          newMeronymConc = oldEqualityMember.parent;
-        }
-        if (newHolonymConc != null) {
-          newHolonymConc.addParameter(newMeronymConc);
-          newMeronymConc.removeParameter(oldEqualityMember);
-          throw new RuntimeException("TODO");
-//          if (newMeronymConc.includeInResult) {
-//            query.rootClause.addParameter(newMeronymConc);
-//          }
-//          anOp.source.removeParameter(anOp);
-//          query.rootConcepts.remove(newMeronymConc);
-        }
+    for (QueryOperator anEquals : query.getOpsRecursiveWithType(OperatorType.EQUALS)) {
+      List<QueryOperator> conceptParam = anEquals.getChildConcepts();
+      if (conceptParam.size() != 2) {
+        continue;
+      }
+      QueryOperator newHolonymConc = null, oldEqualityMember = null;
+      if (conceptParam.get(0).getParentConcept() != null) {
+        newHolonymConc = conceptParam.get(0);
+        oldEqualityMember = conceptParam.get(1).resolveAlias();
+      } else if (conceptParam.get(1).getParentConcept() != null) {
+        newHolonymConc = conceptParam.get(1);
+        oldEqualityMember = conceptParam.get(0).resolveAlias();
+      }
+      if (newHolonymConc != null) {
+        QueryOperator parentConc = newHolonymConc.getParameters().get(0).asOperator()
+                .resolveAlias();
+        parentConc.type = OperatorType.FIELD_WITH_TYPE;
+        QueryOperator aliasRef = new QueryOperator(OperatorType.ALIAS_REF);
+        aliasRef.addParameter(oldEqualityMember.alias);
+        parentConc.addParameter(aliasRef, 0);
+        anEquals.parent.removeParameter(anEquals);
       }
     }
   }

QueryMapper/src/main/java/de/uniwue/query/transform/Meronym_2_Equality_Transformation.java

@@ -15,10 +15,15 @@ public class Meronym_2_Equality_Transformation extends GraphTransformation {
 
   @Override
   public void transform(QueryOperator query) {
-    for (QueryOperator aConc : query.getIteratorsRecursive()) {
-      for (QueryOperator aChild : aConc.getChildConcepts()) {
-        if (parentCode.equals(aConc.getIteratorSelector()) && childCode.equals(aChild.getIteratorSelector())) {
-          transformMeronym_2_Equality(query, aConc, aChild);
+    List<QueryOperator> parents = query.getIteratorsWithSelector(parentCode);
+    for (QueryOperator aParent : parents) {
+      List<QueryOperator> children = query.getIteratorsWithSelector(childCode);
+      for (QueryOperator aChild : children) {
+        if (aChild.type == OperatorType.FIELD) {
+          QueryOperator aliasRef = aChild.getParameters().get(0).asOperator();
+          if (aParent == aliasRef.resolveAlias()) {
+            transformMeronym_2_Equality(query, aParent, aChild);
+          }
         }
       }
     }
@@ -26,17 +31,28 @@ public class Meronym_2_Equality_Transformation extends GraphTransformation {
 
   protected void transformMeronym_2_Equality(QueryOperator query, QueryOperator parent,
           QueryOperator child) {
-    parent.removeParameter(child);
-    query.getRootConcepts().add(child);
-    String newChildSelectorMemberName = null;
-    QueryOperator newMember = null;
-    if (parentCode.equals(parent.getIteratorSelector()) && childCode.equals(child.getIteratorSelector())) {
-      newMember = new QueryOperator(child.parent, child, child2parent_member);
+    child.type = OperatorType.ITERATE;
+    child.removeParameter(child.getParameters().get(0));
+    QueryOperator targetClauseContainer;
+    if (child.parent.getParameters().size() == 1) {
+      targetClauseContainer = child.parent;
+    } else {
+      QueryOperator existingClause = child.parent.getParameters().get(1).asOperator();
+      if (existingClause.type == OperatorType.AND) {
+        targetClauseContainer = existingClause;
+      } else {
+        QueryOperator newAnd = new QueryOperator(child.parent, OperatorType.AND);
+        child.parent.removeParameter(existingClause);
+        newAnd.addParameter(existingClause);
+        targetClauseContainer = newAnd;
+      }
     }
-    QueryOperator equals = new QueryOperator(OperatorType.EQUALS);
-    query.addParameter(equals);
-    equals.addParameter(newMember);
-    equals.addParameter(parent);
+    QueryOperator equals = new QueryOperator(targetClauseContainer, OperatorType.EQUALS);
+    QueryOperator aliasRefToChild = new QueryOperator(equals, OperatorType.ALIAS_REF);
+    aliasRefToChild.addParameter(child.alias);
+    QueryOperator newMember = new QueryOperator(equals, aliasRefToChild, child2parent_member);
+    QueryOperator aliasRefToParent = new QueryOperator(equals, OperatorType.ALIAS_REF);
+    aliasRefToParent.addParameter(parent.alias);
   }
 
   public static void loadMeronym_2_Equality_Transformation(

QueryMapper/src/main/java/de/uniwue/query/transform/PathTransformator.java

@@ -3,9 +3,8 @@ package de.uniwue.query.transform;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;
-import java.util.HashSet;
 import java.util.List;
-import java.util.Set;
+
 import org.springframework.core.io.Resource;
 
 import de.uniwue.misc.util.ResourceUtil;
@@ -14,9 +13,11 @@ import de.uniwue.query.QueryOperator;
 
 public class PathTransformator extends GraphTransformation {
 
-  public String sourceCode, targetCode;
+  public String sourceCode, targetCode, intermediateCode;
+
+  boolean targetIsArray, intermediateIsArray;
 
-  public List<String> pathElems = new ArrayList<String>();
+  public String operation;
 
   private List<String> aliasNames;
 
@@ -33,6 +34,64 @@ public class PathTransformator extends GraphTransformation {
     aliasIndex = 0;
   }
 
+  private void removeIntermediateNonArrayField(QueryOperator query, QueryOperator aSourceConcept,
+          QueryOperator aTargetConcept) {
+    if (aTargetConcept.type == OperatorType.FIELD) {
+      QueryOperator innerAccess = aTargetConcept.getParameters().get(0).asOperator();
+      if ((innerAccess.type == OperatorType.FIELD)
+              && (innerAccess.getParameters().get(1).asPrimitive().value
+                      .equals(intermediateCode))) {
+        // remove the intermediate link
+        aTargetConcept.removeParameter(innerAccess);
+        // add the access to the ALIAS_REF
+        aTargetConcept.addParameter(innerAccess.getParameters().get(0), 0);
+      }
+    }
+  }
+
+  private void removeIntermediateArrayField(QueryOperator query, QueryOperator aSourceConcept,
+          QueryOperator aTargetConcept) {
+    QueryOperator targetFilter = aTargetConcept.parent;
+    QueryOperator firstFilterClause = aSourceConcept.parent.getParameters().get(1).asOperator();
+    QueryOperator pathPartToReplace = firstFilterClause;
+    if (firstFilterClause.type == OperatorType.AND) {
+      for (QueryOperator anAndChild : firstFilterClause.getOperators()) {
+        if (anAndChild.getIteratorsWithSelector(targetCode).contains(aTargetConcept)) {
+          pathPartToReplace = anAndChild;
+        }
+      }
+    }
+    QueryOperator parent = pathPartToReplace.parent;
+    // the aliases have to be kept synchronized
+    String alias = pathPartToReplace.getParameters().get(0).alias;
+    parent.removeParameter(pathPartToReplace);
+    QueryOperator currentFilter = parent;
+    QueryOperator currentConcept = currentFilter.getParameters().get(0).asOperator();
+    for (QueryOperator aliasRef : aSourceConcept.getRoot()
+            .getOpsRecursiveWithType(OperatorType.ALIAS_REF)) {
+      if (aliasRef.getParameters().get(0).asPrimitive().value.equals(alias)) {
+        aliasRef.getParameters().get(0).asPrimitive().value = aSourceConcept.alias;
+      }
+    }
+  }
+
+  private void addIntermediateNonArrayField(QueryOperator query, QueryOperator aSourceConcept,
+          QueryOperator aTargetConcept) {
+
+  }
+
+  private void addIntermediateArrayField(QueryOperator query, QueryOperator aSourceConcept,
+          QueryOperator aTargetConcept) {
+    QueryOperator sourceFilter = aSourceConcept.parent;
+    QueryOperator newFilter = new QueryOperator(sourceFilter, OperatorType.EXISTS);
+    QueryOperator currentConcept = new QueryOperator(newFilter, aSourceConcept, intermediateCode,
+            true);
+    String newAlias = aliasNames.get(aliasIndex++);
+    currentConcept.alias = newAlias;
+    aTargetConcept.parent.getParameters().get(0).asOperator().getParameters().get(0).asOperator()
+            .getParameters().get(0).asPrimitive().value = newAlias;
+  }
+
   @Override
   public void transform(QueryOperator query) {
     initializeNewAliasNames(query);
@@ -41,36 +100,17 @@ public class PathTransformator extends GraphTransformation {
       QueryOperator sourceFilter = aSourceConcept.parent;
       List<QueryOperator> targetConcepts = sourceFilter.getIteratorsWithSelector(targetCode);
       for (QueryOperator aTargetConcept : targetConcepts) {
-        QueryOperator targetFilter = aTargetConcept.parent;
-        QueryOperator firstFilterClause = sourceFilter.getParameters().get(1).asOperator();
-        QueryOperator pathPartToReplace = firstFilterClause;
-        if (firstFilterClause.type == OperatorType.AND) {
-          for (QueryOperator anAndChild : firstFilterClause.getOperators()) {
-            if (anAndChild.getIteratorsWithSelector(targetCode).contains(aTargetConcept)) {
-              pathPartToReplace = anAndChild;
-            }
+        if (intermediateIsArray) {
+          if (operation.equals("remove")) {
+            removeIntermediateArrayField(query, aSourceConcept, aTargetConcept);
+          } else {
+            addIntermediateArrayField(query, aSourceConcept, aTargetConcept);
           }
-        }
-        QueryOperator parent = pathPartToReplace.parent;
-        // the aliases have to be kept synchronized
-        String alias = pathPartToReplace.getParameters().get(0).alias;
-        parent.removeParameter(pathPartToReplace);
-        QueryOperator currentFilter = parent;
-        QueryOperator currentConcept = currentFilter.getParameters().get(0).asOperator();
-        for (String aPathElem : pathElems) {
-          currentFilter = new QueryOperator(currentFilter, OperatorType.EXISTS);
-          currentConcept = new QueryOperator(currentFilter, currentConcept, aPathElem, true);
-          String newAlias = aliasNames.get(aliasIndex++);
-          currentConcept.alias = newAlias;
-          targetFilter.getParameters().get(0).asOperator().getParameters().get(0).asOperator()
-                  .getParameters().get(0).asPrimitive().value = newAlias;
-        }
-        currentFilter.addParameter(targetFilter);
-        if (pathElems.size() == 0) {
-          for (QueryOperator aliasRef : query.getOpsRecursiveWithType(OperatorType.ALIAS_REF)) {
-            if (aliasRef.getParameters().get(0).asPrimitive().value.equals(alias)) {
-              aliasRef.getParameters().get(0).asPrimitive().value = aSourceConcept.alias;
-            }
+        } else {
+          if (operation.equals("remove")) {