Query: Add EXPLINEAGEOF sql

experiment/src/org/labkey/experiment/ExperimentUpgradeCode.java

@@ -63,14 +63,12 @@
 import org.labkey.api.security.roles.SiteAdminRole;
 import org.labkey.api.settings.AppProps;
 import org.labkey.api.util.logging.LogHelper;
-import org.labkey.experiment.api.ClosureQueryHelper;
 import org.labkey.experiment.api.ExpSampleTypeImpl;
 import org.labkey.experiment.api.ExperimentServiceImpl;
 import org.labkey.experiment.api.MaterialSource;
 import org.labkey.experiment.api.property.DomainImpl;
 import org.labkey.experiment.api.property.DomainPropertyImpl;
 import org.labkey.experiment.api.property.StorageProvisionerImpl;
-import org.labkey.experiment.samples.SampleTimelineAuditProvider;
 
 import java.sql.Connection;
 import java.sql.SQLException;

query/src/org/labkey/query/sql/QInLineage.java

@@ -28,42 +28,71 @@
 import org.labkey.api.query.column.BuiltInColumnTypes;
 import org.labkey.query.QueryServiceImpl;
 
+import java.util.Objects;
+
+import static org.labkey.query.sql.antlr.SqlBaseParser.EXPANCESTORSOF;
+import static org.labkey.query.sql.antlr.SqlBaseParser.EXPDESCENDANTSOF;
+import static org.labkey.query.sql.antlr.SqlBaseParser.EXPLINEAGEOF;
 
 final public class QInLineage extends QExpr
 {
     final boolean _in;
+    final boolean _children;
     final boolean _parents;
+    final String _method;
 
-    public QInLineage(boolean in, boolean parents)
+    public QInLineage(boolean in, int methodTokenType)
     {
-        this._in = in;
-        this._parents = parents;
+        super(QNode.class);
+
+        _in = in;
+        _method = switch (methodTokenType)
+        {
+            case EXPANCESTORSOF -> {
+                _children = false;
+                _parents = true;
+                yield "EXPANCESTORSOF";
+            }
+            case EXPDESCENDANTSOF -> {
+                _children = true;
+                _parents = false;
+                yield "EXPDESCENDANTSOF";
+            }
+            case EXPLINEAGEOF -> {
+                _children = true;
+                _parents = true;
+                yield "EXPLINEAGEOF";
+            }
+            default -> throw new IllegalArgumentException("Invalid QInLineage method token type: " + methodTokenType);
+        };
     }
 
     String operator()
     {
-        return (_in ? " IN " : " NOT IN ") + (_parents ? "EXPANCESTORSOF " : "EXPDESCENDANTSOF " );
+        return (_in ? " IN " : " NOT IN ") + _method + " ";
     }
 
     @Override
     public void appendSql(SqlBuilder builder, Query query)
     {
-        SQLTableInfo sqlti = new SQLTableInfo(query.getSchema().getDbSchema(), "_");
         var children = childList();
-        var LHS = ((QExpr) getFirstChild());
-        var RHS = ((QQuery) getLastChild());
+        var LHS = (QExpr) firstOrThrow(children);
+        var RHS = (QQuery) secondOrThrow(children);
 
-        // LHS should be a 'lineage object', e.g. the result of calling {ExtTable}.expObject()
+        // LHS should be a 'lineage object', e.g., the result of calling {ExtTable}.expObject()
         ColumnInfo lhsCol = null;
         if (LHS instanceof QueryServiceImpl.QColumnInfo || LHS instanceof QMethodCall)
+        {
+            SQLTableInfo sqlti = new SQLTableInfo(query.getSchema().getDbSchema(), "_");
             lhsCol = LHS.createColumnInfo(sqlti, "_", query);
+        }
         if (lhsCol == null || !Strings.CS.equals(lhsCol.getConceptURI(), BuiltInColumnTypes.EXPOBJECTID_CONCEPT_URI))
         {
-            query.getParseErrors().add(new QueryParseException(operator() + " requires argument to be a lineage object", null, getLine(), getColumn()));
+            query.getParseErrors().add(new QueryParseException(_method + " requires argument to be a lineage object", null, getLine(), getColumn()));
             return;
         }
 
-        // RHS should be SELECT with one column of 'lineage object', e.g. the result of calling {ExtTable}.expObject()
+        // RHS should be SELECT with one column of 'lineage object', e.g., the result of calling {ExtTable}.expObject()
         QueryRelation r = RHS._select;
         var map = r.getAllColumns();
         var col = map.size() != 1 ? null : map.values().iterator().next();
@@ -72,15 +101,31 @@ public void appendSql(SqlBuilder builder, Query query)
             col.copyColumnAttributesTo(rhsCol);
         if (!Strings.CS.equals(rhsCol.getConceptURI(), BuiltInColumnTypes.EXPOBJECTID_CONCEPT_URI))
         {
-            query.getParseErrors().add(new QueryParseException(operator() + " requires argument to be a lineage object", null, getLine(), getColumn()));
+            query.getParseErrors().add(new QueryParseException(_method + " requires argument to be a lineage object", null, getLine(), getColumn()));
             return;
         }
 
         SqlBuilder subquery = new SqlBuilder(builder.getDialect());
         RHS.appendSql(subquery, query);
         // subquery will have surrounding parens, but the double parens don't cause a problem
 
-        ExpLineageOptions options = new ExpLineageOptions(_parents, !_parents, 1000);
+        // Parse depth argument
+        int depth = 1_000;
+        {
+            QNode depthExpr = child(children, 2);
+            if (depthExpr != null)
+            {
+                if (!(depthExpr instanceof QNumber n))
+                {
+                    query.getParseErrors().add(new QueryParseException(_method + " requires second argument to be an integer", null, getLine(), getColumn()));
+                    return;
+                }
+
+                depth = n.getValue().intValue();
+            }
+        }
+
+        ExpLineageOptions options = new ExpLineageOptions(_parents, _children, depth);
         options.setUseObjectIds(true);          // expObject() returns objectid not lsid
         options.setOnlySelectObjectId(true);    // generate one column SELECT, also don't join to material/data/protocolapplication
         SQLFragment lineage = ExperimentService.get().generateExperimentTreeSQL(subquery, options);
@@ -93,7 +138,6 @@ public void appendSql(SqlBuilder builder, Query query)
         builder.append("))");
     }
 
-
     @Override
     public void appendSource(SourceBuilder builder)
     {
@@ -109,18 +153,16 @@ public void appendSource(SourceBuilder builder)
         builder.popPrefix(")");
     }
 
-
     @Override @NotNull
     public JdbcType getJdbcType()
     {
         return JdbcType.BOOLEAN;
     }
 
-
     @Override
     public boolean equalsNode(QNode other)
     {
-        return (other instanceof QInLineage o) && _in == o._in && _parents == o._parents;
+        return other instanceof QInLineage o && _in == o._in && Objects.equals(_method, o._method);
     }
 
     @Override

query/src/org/labkey/query/sql/QNode.java

@@ -18,6 +18,7 @@
 
 import org.antlr.runtime.CommonToken;
 import org.antlr.runtime.tree.CommonTree;
+import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 import org.junit.Assert;
 import org.junit.Test;
@@ -34,6 +35,7 @@
 import java.util.LinkedList;
 import java.util.List;
 import java.util.Map;
+import java.util.Objects;
 
 import static org.labkey.query.sql.antlr.SqlBaseParser.FALSE;
 import static org.labkey.query.sql.antlr.SqlBaseParser.IDENT;
@@ -109,7 +111,7 @@ public Iterable<QNode> children()
 		return _children;
     }
 
-    public List<QNode> childList()
+    public LinkedList<QNode> childList()
     {
 		return _children;
     }
@@ -373,15 +375,12 @@ protected void dump(PrintWriter out, String nl, IdentityHashMap<Object,Object> d
             	c.dump(out, nl + "    |", dumped);
     }
 
-
-
     public void addFieldRefs(Object referant)
     {
         for (QNode child : childList())
             child.addFieldRefs(referant);
     }
 
-
     public void releaseFieldRefs(Object referant)
     {
         for (QNode child : childList())
@@ -398,6 +397,35 @@ public void setHasTransformableAggregate(boolean hasTransformableAggregate)
         _hasTransformableAggregate = hasTransformableAggregate;
     }
 
+    static @Nullable QNode child(LinkedList<QNode> children, int index)
+    {
+        return children.size() > index ? children.get(index) : null;
+    }
+
+    static @NotNull QNode childOrThrow(LinkedList<QNode> children, int index)
+    {
+        return Objects.requireNonNull(child(children, index));
+    }
+
+    static QNode first(LinkedList<QNode> children)
+    {
+        return child(children, 0);
+    }
+
+    static @NotNull QNode firstOrThrow(LinkedList<QNode> children)
+    {
+        return childOrThrow(children, 0);
+    }
+
+    static QNode second(LinkedList<QNode> children)
+    {
+        return child(children, 1);
+    }
+
+    static @NotNull QNode secondOrThrow(LinkedList<QNode> children)
+    {
+        return childOrThrow(children, 1);
+    }
 
     public static class TestCase extends Assert
     {

query/src/org/labkey/query/sql/SqlBase.g

@@ -191,6 +191,7 @@ EXCEPT : 'except';
 EXISTS : 'exists';
 EXPDESCENDANTSOF : 'expdescendantsof';
 EXPANCESTORSOF : 'expancestorsof';
+EXPLINEAGEOF : 'explineageof';
 FALSE : 'false';
 FROM : 'from';
 FULL : 'full';
@@ -423,7 +424,7 @@ fromRange
 
 
 tableMethod
-    : (EXPANCESTORSOF | EXPDESCENDANTSOF) op=OPEN^ {$op.setType(METHOD_CALL);} subQuery CLOSE!
+    : (EXPANCESTORSOF | EXPDESCENDANTSOF | EXPLINEAGEOF) op=OPEN^ {$op.setType(METHOD_CALL);} subQuery (COMMA! expression)? CLOSE!
     ;
 
 
@@ -679,7 +680,7 @@ likeEscape
 
 
 inList
-	: (EXPANCESTORSOF | EXPDESCENDANTSOF) op=OPEN^ {$op.setType(METHOD_CALL);} subQuery CLOSE!
+	: (EXPANCESTORSOF | EXPDESCENDANTSOF | EXPLINEAGEOF) op=OPEN^ {$op.setType(METHOD_CALL);} subQuery (COMMA! expression)? CLOSE!
 	| compoundExpr -> ^(IN_LIST compoundExpr)
 	;